From deeef6cb15f1e47d6259cd6508db3f7debb95102 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 13:05:21 +0200 Subject: [PATCH 01/44] more files --- .../add/experimental/morphology/page.tsx | 20 + .../explore/interactive/add/layout.tsx | 7 + .../interactive-navigation-menu.tsx | 44 +- .../ContributeLayout/index.tsx | 47 + .../contribute/_components/atoms/index.ts | 170 +++ .../circuit-details/circuit-details.tsx | 22 + .../_components/circuit-details/index.ts | 1 + .../circuit-name/circuit-name.module.css | 50 + .../circuit-preview.module.css | 14 + .../circuit-preview/circuit-preview.tsx | 25 + .../_components/circuit-preview/index.ts | 1 + .../contribute/_components/components.tsx | 964 ++++++++++++++++++ .../_components/file-viewer/index.tsx | 81 ++ .../contribute/_components/hooks/circuit.ts | 88 ++ .../_components/hooks/config-atom.ts | 30 + .../contribute/_components/hooks/schema.ts | 157 +++ .../contribute/_components/section.tsx | 221 ++++ .../_components/simulation-files/index.tsx | 198 ++++ .../_components/simulation-status/index.tsx | 50 + .../_components/tabs-selector/index.ts | 1 + .../tabs-selector/tabs-selector.tsx | 43 + .../contribute/_components/tooltip/index.ts | 1 + .../_components/tooltip/tooltip.module.css | 39 + .../_components/tooltip/tooltip.tsx | 20 + src/features/contribute/_components/utils.ts | 73 ++ src/features/contribute/error-registry.ts | 7 + src/features/contribute/index.tsx | 616 +++++++++++ .../contribute/small-microcircuit.module.css | 32 + src/features/contribute/types.ts | 35 + 29 files changed, 3047 insertions(+), 10 deletions(-) create mode 100755 src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx create mode 100755 src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx create mode 100755 src/components/explore-section/ContributeLayout/index.tsx create mode 100644 src/features/contribute/_components/atoms/index.ts create mode 100644 src/features/contribute/_components/circuit-details/circuit-details.tsx create mode 100644 src/features/contribute/_components/circuit-details/index.ts create mode 100644 src/features/contribute/_components/circuit-name/circuit-name.module.css create mode 100644 src/features/contribute/_components/circuit-preview/circuit-preview.module.css create mode 100644 src/features/contribute/_components/circuit-preview/circuit-preview.tsx create mode 100644 src/features/contribute/_components/circuit-preview/index.ts create mode 100644 src/features/contribute/_components/components.tsx create mode 100644 src/features/contribute/_components/file-viewer/index.tsx create mode 100644 src/features/contribute/_components/hooks/circuit.ts create mode 100644 src/features/contribute/_components/hooks/config-atom.ts create mode 100644 src/features/contribute/_components/hooks/schema.ts create mode 100644 src/features/contribute/_components/section.tsx create mode 100644 src/features/contribute/_components/simulation-files/index.tsx create mode 100644 src/features/contribute/_components/simulation-status/index.tsx create mode 100644 src/features/contribute/_components/tabs-selector/index.ts create mode 100644 src/features/contribute/_components/tabs-selector/tabs-selector.tsx create mode 100644 src/features/contribute/_components/tooltip/index.ts create mode 100644 src/features/contribute/_components/tooltip/tooltip.module.css create mode 100644 src/features/contribute/_components/tooltip/tooltip.tsx create mode 100644 src/features/contribute/_components/utils.ts create mode 100755 src/features/contribute/error-registry.ts create mode 100755 src/features/contribute/index.tsx create mode 100755 src/features/contribute/small-microcircuit.module.css create mode 100755 src/features/contribute/types.ts diff --git a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx new file mode 100755 index 000000000..318ca8323 --- /dev/null +++ b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx @@ -0,0 +1,20 @@ +'use client'; + +import { useParams } from 'next/navigation'; + +import ContributeConfig from '@/features/contribute'; +import { WorkspaceContext } from '@/types/common'; + +type Params = WorkspaceContext & { circuit_id: string }; + +export default function ContributeConfiguration() { + const { virtualLabId, projectId } = useParams(); + console.log('ContributeConfiguration function entered'); + return ( + + ); +} diff --git a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx new file mode 100755 index 000000000..8e7fe075a --- /dev/null +++ b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx @@ -0,0 +1,7 @@ +import { ReactNode } from 'react'; +import ContributeLayout from '@/components/explore-section/ContributeLayout'; + +export default function ContributeDataLayout({ children }: { children: ReactNode }) { + console.log('ContributeDataLayout function entered'); + return {children}; +} diff --git a/src/components/entities-type-stats/interactive-navigation-menu.tsx b/src/components/entities-type-stats/interactive-navigation-menu.tsx index 9346c16fc..f9c919b83 100644 --- a/src/components/entities-type-stats/interactive-navigation-menu.tsx +++ b/src/components/entities-type-stats/interactive-navigation-menu.tsx @@ -60,8 +60,10 @@ function EntityTypeStats(props: StatsPanelProps) { return match(selectedTab) .with('experimental-data', () => ( <> - {Object.entries(ExperimentalEntitiesTileTypes).map(([key, value]) => { + {Object.entries(ExperimentalEntitiesTileTypes).map(([key, value], index) => { const href = `${pathName}/${value?.explore.basePrefix}/${value.slug}`; + + const baseHref = `${pathName}/${value?.explore.basePrefix}/${value.slug}`; let records = ''; let isError = false; @@ -74,16 +76,38 @@ function EntityTypeStats(props: StatsPanelProps) { isError = !!error || typeof tmpResult === 'string'; } + // Find the last occurrence of '/interactive/' and insert '/add/' after it + const lastInteractiveIndex = pathName.lastIndexOf('/interactive'); + let addHref = baseHref; + if (lastInteractiveIndex !== -1) { + const pathBeforeInteractive = pathName.substring( + 0, + lastInteractiveIndex + '/interactive'.length + ); + const pathAfterInteractive = baseHref.substring(baseHref.indexOf('/experimental')); // Assuming /experimental is always after /interactive + addHref = `${pathBeforeInteractive}/add${pathAfterInteractive}`; + } + return ( - +
+ + {index === 0 && ( + + add + + )} +
); })} diff --git a/src/components/explore-section/ContributeLayout/index.tsx b/src/components/explore-section/ContributeLayout/index.tsx new file mode 100755 index 000000000..5a175d01d --- /dev/null +++ b/src/components/explore-section/ContributeLayout/index.tsx @@ -0,0 +1,47 @@ +// File: app/virtual-lab/explore/interactive/add/layout.tsx (or wherever your 'add' route lives) + +'use client'; + +import { ReactNode } from 'react'; +import { usePathname } from 'next/navigation'; +import { ErrorBoundary } from 'react-error-boundary'; +import SimpleErrorComponent from '@/components/GenericErrorFallback'; +import BackToInteractiveExplorationBtn from '@/components/explore-section/BackToInteractiveExplorationBtn'; + +export default function ContributeLayout({ children }: { children: ReactNode }) { + const pathname = usePathname(); + console.log('ContributeLayout function entered'); + // Determine the href for the back button. + // Goal: If current is /virtual-lab/explore/interactive/add/experimental/morphology + // It should go back to /virtual-lab/explore/interactive + const splittedPathname = pathname.split('/'); + let interactivePageHref = '/'; // Default fallback + + const addIndex = splittedPathname.indexOf('add'); + + if (addIndex > -1) { + // If 'add' is found, take all segments up to (but not including) 'add' + interactivePageHref = splittedPathname.slice(0, addIndex).join('/'); + } else { + // Fallback: If 'add' is not in the path (unexpected for this layout), + // go back one level from the current path. + interactivePageHref = splittedPathname.slice(0, splittedPathname.length - 1).join('/'); + } + + // Ensure the path starts with a '/' if it's not empty (e.g., if it's just 'virtual-lab/explore/interactive') + if (interactivePageHref === '') { + interactivePageHref = '/'; + } else if (!interactivePageHref.startsWith('/')) { + interactivePageHref = '/' + interactivePageHref; + } + + return ( +
+ + + +
{children}
+ +
+ ); +} diff --git a/src/features/contribute/_components/atoms/index.ts b/src/features/contribute/_components/atoms/index.ts new file mode 100644 index 000000000..25ceed256 --- /dev/null +++ b/src/features/contribute/_components/atoms/index.ts @@ -0,0 +1,170 @@ +import { atom } from 'jotai'; +import { atomWithRefresh } from 'jotai/utils'; +import isEqual from 'lodash/isEqual'; + +import { downloadAsset } from '@/api/entitycore/queries/assets'; +import { getCircuit } from '@/api/entitycore/queries/model/circuit'; +import { getCircuitSimulations } from '@/api/entitycore/queries/simulation/circuit-simulation'; +import { getCircuitSimulationExecutions } from '@/api/entitycore/queries/simulation/circuit-simulation-execution'; +import { getCircuitSimulationResult } from '@/api/entitycore/queries/simulation/circuit-simulation-result'; +import { EntityTypeValue } from '@/api/entitycore/types'; +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; +import { ICircuitSimulation } from '@/api/entitycore/types/entities/circuit-simulation'; +import { ICircuitSimulationExecution } from '@/api/entitycore/types/entities/circuit-simulation-execution'; +import { ICircuitSimulationResult } from '@/api/entitycore/types/entities/circuit-simulation-result'; +import { getLatestSimExecStatus } from '@/features/small-microcircuit/_components/utils'; +import { SimExecStatusMap } from '@/features/small-microcircuit/types'; +import { WorkspaceContext } from '@/types/common'; +import { atomFamilyWithExpiration, readAtomFamilyWithExpiration } from '@/util/atoms'; + +const simExecBySimIdAtomFamily = readAtomFamilyWithExpiration( + ({ simulationId, context }: { simulationId: string; context: WorkspaceContext }) => + atom>(async () => { + const simulationExecutionFilters = { used__id: simulationId }; + const res = await getCircuitSimulationExecutions({ + filters: simulationExecutionFilters, + context, + }); + + return res.data[0]; + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +export const simExecRemoteStatusMapAtomFamily = atomFamilyWithExpiration( + ({ simulationIds, context }: { simulationIds: string[]; context: WorkspaceContext }) => + atomWithRefresh>(async () => { + const simulationExecutionFilters = { used__id__in: simulationIds.join(',') }; + const res = await getCircuitSimulationExecutions({ + filters: simulationExecutionFilters, + context, + }); + + return res.data.reduce( + (map, simExec) => map.set(simExec.used[0].id, simExec.status), + new Map() + ); + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +type SimExecStatusMapAtomFamilyArg = { simulationIds: string[]; context: WorkspaceContext }; + +export const simExecStatusMapAtomFamily = atomFamilyWithExpiration( + ({ simulationIds, context }: SimExecStatusMapAtomFamilyArg) => { + const simExecRemoteStatusMapAtom = simExecRemoteStatusMapAtomFamily({ + simulationIds, + context, + }); + + const localStatusMapAtom = atom(new Map()); + + return atom, [SimExecStatusMap], void>( + async (get) => { + const remoteStatusMap = await get(simExecRemoteStatusMapAtom); + const localStatusMap = get(localStatusMapAtom); + + const simIds = Array.from(new Set([...remoteStatusMap.keys(), ...localStatusMap.keys()])); + const statusMap = simIds.reduce((map, simId) => { + const remoteStatus = remoteStatusMap.get(simId); + const localStatus = localStatusMap.get(simId); + // If both are set we take the latest possible one, + // because the status change in a particular sequence. + // See definition of getLatestSimExecStatus + const status = + remoteStatus && localStatus + ? getLatestSimExecStatus(remoteStatus, localStatus) + : (localStatus ?? remoteStatus); + return map.set(simId, status); + }, new Map()); + + return statusMap; + }, + (get, set, newStatusMap) => set(localStatusMapAtom, new Map(newStatusMap)) + ); + }, + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +export const simResultBySimIdAtomFamily = readAtomFamilyWithExpiration( + ({ simulationId, context }: { simulationId: string; context: WorkspaceContext }) => + atom>(async (get) => { + const execution = await get(simExecBySimIdAtomFamily({ simulationId, context })); + + if (!execution?.generated?.[0]) { + throw new Error('Simulation Result not found'); + } + + return getCircuitSimulationResult({ id: execution.generated[0].id, context }); + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +export const simulationsByCampaignIdAtomFamily = readAtomFamilyWithExpiration( + ({ campaignId, context }: { campaignId: string; context: WorkspaceContext }) => + atom>(async () => { + const filters = { simulation_campaign_id: campaignId }; + const res = await getCircuitSimulations({ filters, context }); + + return res.data; + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +export const circuitAtomFamily = readAtomFamilyWithExpiration( + ({ circuitId, context }: { circuitId: string; context: WorkspaceContext }) => + atom>(async () => { + return getCircuit({ id: circuitId, context }); + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); + +export const fileAtomFamily = readAtomFamilyWithExpiration( + ({ + id, + entityId, + entityType, + assetPath, + context, + }: { + id: string; + entityId: string; + entityType: EntityTypeValue; + assetPath?: string; + context: WorkspaceContext; + }) => + atom>(async () => { + const res = await downloadAsset({ + ctx: context, + entityId, + id, + entityType, + assetPath, + asRawResponse: true, + }); + + return res.json(); + }), + { + ttl: 120000, // 2 minutes + areEqual: isEqual, + } +); diff --git a/src/features/contribute/_components/circuit-details/circuit-details.tsx b/src/features/contribute/_components/circuit-details/circuit-details.tsx new file mode 100644 index 000000000..f8f856fd3 --- /dev/null +++ b/src/features/contribute/_components/circuit-details/circuit-details.tsx @@ -0,0 +1,22 @@ +import React from 'react'; +import { Input } from 'antd'; + +import Tooltip from '../tooltip'; + +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; + +interface CircuitDetailsProps { + className?: string; + circuit: ICircuit; +} + +export default function CircuitDetails({ className, circuit }: CircuitDetailsProps) { + return ( +
+ + + + +
+ ); +} diff --git a/src/features/contribute/_components/circuit-details/index.ts b/src/features/contribute/_components/circuit-details/index.ts new file mode 100644 index 000000000..42451142f --- /dev/null +++ b/src/features/contribute/_components/circuit-details/index.ts @@ -0,0 +1 @@ +export { default } from './circuit-details'; diff --git a/src/features/contribute/_components/circuit-name/circuit-name.module.css b/src/features/contribute/_components/circuit-name/circuit-name.module.css new file mode 100644 index 000000000..61b1f9711 --- /dev/null +++ b/src/features/contribute/_components/circuit-name/circuit-name.module.css @@ -0,0 +1,50 @@ +.circuitName { + position: relative; + text-align: end; +} + +.circuitName > .name svg { + margin-left: 1em; + color: #005; +} + +.name { + font-weight: bold; + font-variant: small-caps; +} + +.description { + margin-top: 16px; + white-space: pre-wrap; + position: absolute; + background: #0050b3ee; + color: #fff; + padding: 0.5em 1em; + border-radius: 0.25em; + position: absolute; + left: 0; + right: 0; + width: 100%; + pointer-events: none; + z-index: 9; + text-align: start; + transition: all 0.3s; + opacity: 0; +} + +.circuitName:hover .description { + opacity: 1; +} + +.description::after { + content: ''; + border: 16px solid transparent; + border-bottom: 16px solid #0050b3ee; + position: absolute; + top: -16px; + left: 50%; + width: 0; + height: 0; + margin: -16px; + transform: scale(0.5, 1); +} diff --git a/src/features/contribute/_components/circuit-preview/circuit-preview.module.css b/src/features/contribute/_components/circuit-preview/circuit-preview.module.css new file mode 100644 index 000000000..2e4f7d702 --- /dev/null +++ b/src/features/contribute/_components/circuit-preview/circuit-preview.module.css @@ -0,0 +1,14 @@ +div.circuitPreview { + width: 100%; + height: 100%; + min-height: 0; + overflow: visible; +} + +.circuitPreview > .image { + background: #fff; + border-radius: 1em; + box-shadow: 0 2px 8px #0002; + width: 100%; + height: 100%; +} diff --git a/src/features/contribute/_components/circuit-preview/circuit-preview.tsx b/src/features/contribute/_components/circuit-preview/circuit-preview.tsx new file mode 100644 index 000000000..8862833f2 --- /dev/null +++ b/src/features/contribute/_components/circuit-preview/circuit-preview.tsx @@ -0,0 +1,25 @@ +/* eslint-disable @next/next/no-img-element */ +import React from 'react'; + +import { useCircuitImageURL } from '../hooks/circuit'; +import { classNames } from '@/util/utils'; +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; +import ZoomableImage from '@/components/zoomable-image'; + +import styles from './circuit-preview.module.css'; + +interface CircuitPreviewProps { + className?: string; + circuit: ICircuit | undefined | null; +} + +export default function CircuitPreview({ className, circuit }: CircuitPreviewProps) { + const url = useCircuitImageURL(circuit?.id); + + return ( +
+ {/* Circuit preview */} + +
+ ); +} diff --git a/src/features/contribute/_components/circuit-preview/index.ts b/src/features/contribute/_components/circuit-preview/index.ts new file mode 100644 index 000000000..677278f17 --- /dev/null +++ b/src/features/contribute/_components/circuit-preview/index.ts @@ -0,0 +1 @@ +export { default } from './circuit-preview'; diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx new file mode 100644 index 000000000..ee93f0735 --- /dev/null +++ b/src/features/contribute/_components/components.tsx @@ -0,0 +1,964 @@ +// components.tsx +import { useEffect, useState, useRef } from 'react'; +import { atom, useAtom } from 'jotai'; +import { InputNumber, Input, Select, Button } from 'antd'; +import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; + +import { JSONSchema } from '../types'; +import { isPlainObject } from './utils'; +import CircuitDetails from './circuit-details'; +import Tooltip from './tooltip'; + +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; +import { classNames } from '@/util/utils'; + +type Primitive = null | boolean | number | string; +interface Object { + [key: string]: Primitive | Primitive[] | Object; +} + +export type ConfigValue = Primitive | Primitive[] | Object; + +export type Config = Record; + +// Updated structure for MTYPE classification +const MTYPE_CLASSES = [ + { mtype_pref_label: 'L23_NBC', mtype_id: '6605787b-ba14-43fd-a954-de9cff4b15a0' }, + { mtype_pref_label: 'L23_NGC', mtype_id: 'dd16dca0-e567-416b-b8b7-f8fbcaa05af0' }, + { mtype_pref_label: 'L23_PC', mtype_id: '0791edc9-7ad4-4a94-a4a5-feab9b690d7e' }, + { mtype_pref_label: 'L23_PTPC', mtype_id: '52ea242f-6591-425a-8eae-962fa0b4dfe0' }, + { mtype_pref_label: 'L23_SBC', mtype_id: 'fbb8b577-92f4-4c93-b355-0982ef5a3c7c' }, + { mtype_pref_label: 'L23_STPC', mtype_id: '93be8237-9861-4870-9977-ff1cf9e7462c' }, + { mtype_pref_label: 'L2_ChC', mtype_id: '91ba3deb-1139-4bc6-a12f-6a64a0ed0e92' }, + { mtype_pref_label: 'L2_IPC', mtype_id: 'e55f12e1-807c-42f6-ba98-91d6d30c57d7' }, + { mtype_pref_label: 'L2_MC', mtype_id: 'ea51f2c8-95fc-4940-a400-c37a3ff2d9eb' }, + { mtype_pref_label: 'L2_PC', mtype_id: 'dd73956b-423e-42c5-87d9-9e2cc84356b9' }, + { mtype_pref_label: 'L2_TPC', mtype_id: '7abf03d5-30b0-41ae-a02b-1f4e26c243a8' }, + { mtype_pref_label: 'L2_TPC:A', mtype_id: '9b04acb1-4737-4088-8d22-0658414bdda1' }, + { mtype_pref_label: 'L2_TPC:B', mtype_id: '4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda' }, + { mtype_pref_label: 'L3_MC', mtype_id: '52578494-b41c-499b-9717-5d11f4b2f068' }, + { mtype_pref_label: 'L3_PC', mtype_id: '87fec7dd-7a2f-400a-aee0-94d1946cf1ab' }, + { mtype_pref_label: 'L3_TPC', mtype_id: '229c31f1-a6ec-4d8c-85d3-d8175ffde109' }, + { mtype_pref_label: 'L3_TPC:A', mtype_id: 'dd346e90-7bca-4976-bf9a-303b6a94b339' }, + { mtype_pref_label: 'L3_TPC:B', mtype_id: 'a71d226c-2c56-40ee-a4be-9726fc430932' }, + { mtype_pref_label: 'L3_TPC:C', mtype_id: 'd9b7bd4d-cec9-4fec-a448-79320de89f2a' }, + { mtype_pref_label: 'L4_BP', mtype_id: 'a55f6ce7-068a-4c5e-a883-de5f4304612e' }, + { mtype_pref_label: 'L4_BTC', mtype_id: '8315d249-6678-4d55-b581-3b6f9eb48e86' }, + { mtype_pref_label: 'L4_ChC', mtype_id: '0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6' }, + { mtype_pref_label: 'L4_DBC', mtype_id: '8de61c06-31e8-4483-bd98-608bc874b369' }, + { mtype_pref_label: 'L4_LBC', mtype_id: 'bb875a91-4ae5-4f6f-b050-5ad952e9cd6c' }, + { mtype_pref_label: 'L4_MC', mtype_id: '0bdf029e-a55a-444c-a7c9-9d0ff51239a5' }, + { mtype_pref_label: 'L4_NBC', mtype_id: '72673af9-2f2b-4a9a-95dc-552777ab63b9' }, + { mtype_pref_label: 'L4_NGC', mtype_id: '41f41550-5e0e-4de7-b52d-62110c338a27' }, + { mtype_pref_label: 'L4_PC', mtype_id: 'ad5769c6-7e86-4433-8f34-9efcb4f0d182' }, + { mtype_pref_label: 'L4_SBC', mtype_id: '43a7d86b-71c5-4a10-be62-ef6cf95ca694' }, + { mtype_pref_label: 'L4_SSC', mtype_id: '400a55f7-e162-4fd1-80a0-4f2facea7cec' }, + { mtype_pref_label: 'L4_TPC', mtype_id: '02e13718-5227-4c28-b838-04dd0c2c67f2' }, + { mtype_pref_label: 'L4_UPC', mtype_id: '2ef7e0b5-39e4-441b-a72a-c7186afa7f5c' }, + { mtype_pref_label: 'L56_PC', mtype_id: '629d6d6f-93f9-43d8-8a99-277740fd8f22' }, + { mtype_pref_label: 'L5_BP', mtype_id: '7b16c860-ae76-4ddf-b093-4e28620b3712' }, +]; + +// Helper function to check if a field value is considered "empty" or invalid +const isEmptyValue = (value: ConfigValue): boolean => { + if (value === null || value === undefined || value === '') return true; + if (Array.isArray(value) && value.length === 0) return true; + if (typeof value === 'object' && value !== null && Object.keys(value).length === 0) return true; + return false; +}; + +// Helper function to validate required fields +const getRequiredFieldErrors = ( + state: Record, + schema: JSONSchema +): string[] => { + const errors: string[] = []; + const requiredFields = schema.required || []; + + requiredFields.forEach((fieldName) => { + const value = state[fieldName]; + if (isEmptyValue(value)) { + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + errors.push(`${fieldTitle} is required`); + } + }); + + return errors; +}; + +export function JSONSchemaForm({ + disabled, + schema, + stateAtom, + config, + circuit, + onAddReferenceClick, + nodeId, + currentCategory, + onValidationChange, // New prop to communicate validation state to parent +}: { + disabled: boolean; + config: Config; + schema: JSONSchema; + circuit: ICircuit | undefined | null; + stateAtom: ReturnType>; + onAddReferenceClick: (reference: string) => void; + nodeId?: string; + currentCategory?: string; + onValidationChange?: (isValid: boolean, errors: string[]) => void; +}) { + const skip = ['type']; + + const [state, setState] = useAtom(stateAtom); + const [addingElement, setAddingElement] = useState<{ [key: string]: boolean }>({ + legacy_id: true, + }); + const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}); + const [validationErrors, setValidationErrors] = useState([]); + const [touchedFields, setTouchedFields] = useState>(new Set()); + + const referenceTypesToConfigKeys: Record = { + NeuronSetReference: 'neuron_sets', + TimestampsReference: 'timestamps', + }; + + const referenceTypesToTitles: Record = { + NeuronSetReference: 'Neuron Set', + TimestampsReference: 'Timestamps', + }; + + // Callback ref to avoid dependency issues + const onValidationChangeRef = useRef(onValidationChange); + useEffect(() => { + onValidationChangeRef.current = onValidationChange; + }); + + // Validate form whenever state changes + useEffect(() => { + const errors = getRequiredFieldErrors(state, schema); + + // Only update if errors actually changed + setValidationErrors((prevErrors) => { + const errorsChanged = + prevErrors.length !== errors.length || + prevErrors.some((error, index) => error !== errors[index]); + + if (errorsChanged && onValidationChangeRef.current) { + onValidationChangeRef.current(errors.length === 0, errors); + } + + return errorsChanged ? errors : prevErrors; + }); + }, [state, schema]); + + useEffect(() => { + if (!schema.properties) return; + + const initial: Record = {}; + + Object.entries(schema.properties).forEach(([key, value]) => { + if (key === 'type') initial[key] = value.const ?? null; + else if (key === 'legacy_id') initial[key] = []; + else if (key === 'strain_id') initial[key] = null; + else if (key === 'license_id') + initial[key] = 'c268a20e-b78a-4332-a5e1-38e26c4454b9'; // Default to undefined UUID + else initial[key] = value.default ?? null; + }); + + // Auto-populate brain region id if we're in morphology category + if (currentCategory === 'morphology' && nodeId) { + const brainRegionIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion' + ); + }); + + if (brainRegionIdKey) { + initial[brainRegionIdKey] = nodeId; + } + } + + // Auto-populate species id (hardcoded mouse species ID) + const speciesIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species' + ); + }); + + if (speciesIdKey) { + initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + } + + // Auto-populate atlas id + const atlasIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' + ); + }); + + if (atlasIdKey) { + initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd'; + } + + console.log('Initial state for morphology:', initial); + setState((prev) => { + const newState = { ...initial, ...prev }; + console.log('Updated state for morphology:', newState); + return newState; + }); + }, [stateAtom, setState, schema.properties, nodeId, currentCategory]); + + // Helper function to mark field as touched + const markFieldTouched = (fieldName: string) => { + setTouchedFields((prev) => new Set(prev).add(fieldName)); + }; + + // Helper function to check if a field has an error + const hasFieldError = (fieldName: string): boolean => { + const isRequired = schema.required?.includes(fieldName); + const isTouched = touchedFields.has(fieldName); + const isEmpty = isEmptyValue(state[fieldName]); + return isRequired && isTouched && isEmpty; + }; + + // Helper function to get field error message + const getFieldErrorMessage = (fieldName: string): string | null => { + if (!hasFieldError(fieldName)) return null; + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + return `${fieldTitle} is required`; + }; + + function renderInput(k: string, v: JSONSchema) { + const obj = { + ...v, + ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), + }; + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); + const isRequired = schema.required?.includes(k); + const fieldError = getFieldErrorMessage(k); + const hasError = hasFieldError(k); + + const isBrainRegionIdField = + currentCategory === 'morphology' && + (normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion'); + const isSpeciesIdField = + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species'; + const isAtlasIdField = + normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas'; + const isExperimentDateField = + normalizedKey === 'experimentdate' || + normalizedKey === 'experiment_date' || + normalizedKey === 'date' || + v.title?.toLowerCase().includes('date'); + const isStrainIdField = + normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain'; + const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; + const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id'; + const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; + const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; + + // Common input props for consistency + const commonInputProps = { + disabled, + className: `w-full ${hasError ? 'border-red-500' : ''}`, + onBlur: () => markFieldTouched(k), + }; + + if (isBrainRegionIdField && nodeId) { + return ( +
+ +
+ ); + } + + if (isSpeciesIdField) { + return ( +
+ +
+ ); + } + + if (isAtlasIdField) { + return ( +
+ +
+ ); + } + + if (isExperimentDateField) { + const formatDate = (value: string) => { + const cleaned = value.replace(/[^\d\s-]/g, ''); + const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0); + if (parts.length === 0) return ''; + if (parts.length === 1) return parts[0]; + if (parts.length === 2) return `${parts[0]} ${parts[1]}`; + return parts.slice(0, 3).join(' '); + }; + + const validateDateFormat = (value: string) => { + if (!value) return true; + const parts = value.split(' '); + if (parts.length !== 3) return false; + const [day, month, year] = parts; + const dayNum = parseInt(day); + const monthNum = parseInt(month); + const yearNum = parseInt(year); + return ( + dayNum >= 1 && + dayNum <= 31 && + monthNum >= 1 && + monthNum <= 12 && + yearNum >= 1900 && + yearNum <= new Date().getFullYear() + ); + }; + + const currentValue = typeof state[k] === 'string' ? state[k] : ''; + const isValid = validateDateFormat(currentValue); + const showDateError = !isValid && currentValue; + + return ( +
+ { + const formatted = formatDate(e.currentTarget.value); + setState({ ...state, [k]: formatted }); + }} + placeholder="DD MM YYYY (e.g., 15 03 2024)" + /> + {showDateError && ( +
+ Please use format: DD MM YYYY (day month year) +
+ )} + {fieldError &&
{fieldError}
} +
+ ); + } + + if (isStrainIdField) { + const allSpeciesStrains = [ + { + species_id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', + species_name: 'Mouse', + strains: { + 'C57BL/6': '123e4567-e89b-12d3-a456-426614174000', + 'BALB/c': '456e7890-e29b-41d4-a716-446655440001', + }, + }, + { + species_id: '789e0123-e29b-41d4-a716-446655440002', + species_name: 'Rat', + strains: { + 'Sprague Dawley': '890e1234-e29b-41d4-a716-446655440003', + }, + }, + ]; + + const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + const selectedSpecies = allSpeciesStrains.find((s) => s.species_id === speciesId); + + if (!selectedSpecies) { + return ( +
+ + {fieldError &&
{fieldError}
} +
+ ); + } + + const strainOptions = Object.entries(selectedSpecies.strains).map(([name, id]) => ({ + label: name, + value: id, + })); + + return ( +
+ { + setState({ ...state, [k]: newV }); + markFieldTouched(k); + }} + value={state[k]} + options={obj.enum.map((subv: string) => ({ + label: subv, + value: subv, + }))} + placeholder="Select age period" + /> + {fieldError &&
{fieldError}
} +
+ ); + } + console.warn('No enum found for age_period:', obj); + return ( +
+ { + setState({ ...state, [k]: e.currentTarget.value }); + }} + placeholder="Enter age period" + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (isLegacyIdField) { + return ( +
+
+
+ {Array.isArray(state[k]) && + state[k].map((e, i) => ( +
+ {e}{' '} + {!disabled && ( + { + const newElements = [...state[k]]; + newElements.splice(i, 1); + setState({ ...state, [k]: newElements }); + markFieldTouched(k); + }} + /> + )} +
+ ))} +
+ {!addingElement[k] && !disabled && ( + setAddingElement({ ...addingElement, [k]: true })} + className="text-primary-8" + /> + )} + {addingElement[k] && !disabled && ( +
+ setNewElement({ ...newElement, [k]: e.currentTarget.value })} + placeholder="Enter legacy ID" + /> + {newElement[k] && ( + { + setState({ + ...state, + [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], + }); + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + markFieldTouched(k); + }} + /> + )} + { + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + }} + className="text-primary-8" + /> +
+ )} +
+ {fieldError &&
{fieldError}
} +
+ ); + } + + // New condition for 'license id' field + if (isLicenseIdField) { + const licenseOptions = { + undefined: 'c268a20e-b78a-4332-a5e1-38e26c4454b9', + 'CC BY-NC-SA 4.0 Deed': '9e766299-b873-4162-9207-30fcd583d933', + 'CC BY-NC 2.0 Deed': 'fafcd04d-a967-4eec-b2e1-3afb2d63a41a', + 'CC BY-NC 4.0 Deed': '1283454d-b5ad-488f-acb7-d00b9f02873d', + 'CC BY 2.0 Deed': '211ac318-504d-44b9-b250-3cae8980d2e9', + 'CC BY 4.0 Deed': 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', + 'CC0 1.0 Deed': '74b8c953-67f5-4e95-ac58-095274901328', + 'NGV_Data Licence_v1.0': '0c39107e-3b68-4f1f-904a-5c7f1b4f89c5', + }; + + const options = Object.entries(licenseOptions).map(([name, id]) => ({ + label: name, + value: id, + })); + + // Find the key corresponding to the current state value to set the label + const currentLicenseLabel = Object.keys(licenseOptions).find( + (key) => licenseOptions[key] === state[k] + ); + + return ( +
+ { + setState({ ...state, [k]: newV }); + markFieldTouched(k); + }} + value={currentMtypeLabel || state[k]} + options={options} + placeholder="Select an MTYPE CLASS" + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (k === 'circuit' && circuit) return ; + + if (v.is_block_reference && v.properties && typeof v.properties.type.const === 'string') { + const referenceKey = referenceTypesToConfigKeys[v.properties.type.const]; + const referenceTitle = referenceTypesToTitles[v.properties.type.const]; + if (!referenceKey) return null; + const referenceConfig = config[referenceKey]; + if (!isPlainObject(referenceConfig)) return null; + + const referees = Object.entries(referenceConfig).filter(([_, val]) => { + return isPlainObject(val); + }); + + if (referees.length === 0) { + return ( +
+ + {fieldError &&
{fieldError}
} +
+ ); + } + + const defaultV = + isPlainObject(state[k]) && typeof state[k].block_name === 'string' + ? state[k].block_name + : null; + + return ( +
+ { + setState({ ...state, [k]: newV }); + markFieldTouched(k); + }} + value={state[k]} + options={obj.enum.map((subv: string) => ({ + label: subv, + value: subv, + }))} + placeholder={`Select ${v.title || k}`} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (obj.type === 'number' || obj.type === 'integer') { + return ( +
+ { + setState({ ...state, [k]: value }); + }} + onBlur={() => markFieldTouched(k)} + className={`w-full ${hasError ? 'border-red-500' : ''}`} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (obj.type === 'string') { + return ( +
+ { + setState({ ...state, [k]: e.currentTarget.value }); + }} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + console.warn(`Unhandled schema type for key: ${k}`, obj); + return ( +
+ { + setState({ ...state, [k]: e.currentTarget.value }); + }} + placeholder={`Enter value for ${v.title || k}`} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + console.log('Rendering JSONSchemaForm with config:', config); + console.log('Current state:', state); + console.log('Validation errors:', validationErrors); + + return ( +
+
{schema.title}
+
{schema.description}
+ + {/* Show overall validation errors summary if there are any */} + {validationErrors.length > 0 && ( +
+
+ Please fix the following required fields: +
+
    + {validationErrors.map((error, index) => ( +
  • {error}
    • + ))} +
+
+ )} + +
+ {schema.properties && + Object.entries(schema.properties) + .filter(([k]) => { + return !skip.includes(k); + }) + .map(([k, v]) => { + const isRequired = schema.required?.includes(k); + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); + const isStrainIdField = + normalizedKey === 'strainid' || + normalizedKey === 'strain_id' || + normalizedKey === 'strain'; + const isAgePeriodField = + normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; + const isLicenseIdField = + normalizedKey === 'licenseid' || normalizedKey === 'license_id'; + const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; + + if (currentCategory === 'subject' && normalizedKey === 'ageperiod') { + console.log('Age period field:', { + key: k, + schema: v, + title: v.title, + resolved: { + ...v, + ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), + }, + }); + } + + return ( +
+
+
+ {isStrainIdField + ? 'STRAIN' + : isAgePeriodField + ? 'AGE PERIOD' + : isLicenseIdField + ? 'LICENSE' // New condition for license title + : isMtypeClassIdField + ? 'MTYPE CLASS' + : v.title || k} + {isRequired && *} +
+ {v.units &&
{v.units}
} +
+ {renderInput(k, v)} +
+ ); + })} +
+
+ ); +} + +export function Tab({ + tab, + selectedTab, + children, + onClick, + rounded = 'rounded-full', + extraClass, + disabled, +}: { + tab: string; + selectedTab: string; + onClick?: () => void; + rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full'; + children?: React.ReactNode; + extraClass?: string; + disabled?: boolean; +}) { + return ( + + ); +} + +export function Chevron({ rotate }: { rotate?: number }) { + return ( + + + + ); +} diff --git a/src/features/contribute/_components/file-viewer/index.tsx b/src/features/contribute/_components/file-viewer/index.tsx new file mode 100644 index 000000000..e8d736a3a --- /dev/null +++ b/src/features/contribute/_components/file-viewer/index.tsx @@ -0,0 +1,81 @@ +import { Suspense } from 'react'; +import { match } from 'ts-pattern'; +import { useAtomValue } from 'jotai'; + +import { File } from '../simulation-files'; +import { fileAtomFamily } from '../atoms'; + +import EphysViewer from '@/features/ephys-viewer'; +import { classNames } from '@/util/utils'; +import { WorkspaceContext } from '@/types/common'; +import { ICircuitSimulationResult } from '@/api/entitycore/types/entities/circuit-simulation-result'; + +type FileViewerProps = { + file?: File; + context: WorkspaceContext; + className?: string; +}; + +export function FileViewer({ file, context, className = '' }: FileViewerProps) { + const fileName = file?.assetPath?.split('/').at(-1) ?? file?.asset.path.split('/').at(-1); + const fileExt = fileName?.split('.').at(-1)?.toLowerCase(); + + const viewerContent = match(fileExt) + .with(undefined, () =>

Select a file for preview

) + .with('json', () => ) + .with('nwb', () => ) + .otherwise(() => ); + + return ( +
+
+ Loading...
}>{viewerContent} +
+ + ); +} + +type JsonFileViewerProps = { + file: File; + context: WorkspaceContext; +}; + +function JsonFileViewer({ file, context }: JsonFileViewerProps) { + const parsedJson = useAtomValue( + fileAtomFamily({ + id: file.asset.id, + entityId: file.entity.id, + entityType: file.entity.type, + assetPath: file.assetPath, + context, + }) + ); + + return 
{JSON.stringify(parsedJson, null, 2)}
; +} + +type NwbFileViewerProps = { + file: File; + context: WorkspaceContext; +}; + +function NwbFileViewer({ file, context }: NwbFileViewerProps) { + return ; +} + +type PlaceholderFileViewerProps = { + file: File; +}; + +function PlaceholderFileViewer({ file }: PlaceholderFileViewerProps) { + const fileName = file?.assetPath?.split('/').at(-1) ?? file?.asset.path.split('/').at(-1); + const fileExt = fileName?.split('.').at(-1)?.toLowerCase(); + + return ( +
+ + Preview for {fileExt} files is not supported yet + +
+ ); +} diff --git a/src/features/contribute/_components/hooks/circuit.ts b/src/features/contribute/_components/hooks/circuit.ts new file mode 100644 index 000000000..4d3ae3c9b --- /dev/null +++ b/src/features/contribute/_components/hooks/circuit.ts @@ -0,0 +1,88 @@ +import React from 'react'; + +import { getCircuit } from '@/api/entitycore/queries/model/circuit'; +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; +import { useAppNotification } from '@/components/notification'; +import { AssetLabel } from '@/api/entitycore/types/shared/global'; +import { downloadAsset } from '@/api/entitycore/queries/assets'; +import { EntityTypeEnum } from '@/api/entitycore/types'; + +const pendingQueries = new Map>(); + +/** + * Retrieve a circuit from EntityCore. + * @param circuitId + * @returns `undefined` if the query is pending, `null` if an error occured and the circuit in case of success. + */ +export function useCircuit(circuitId: string | undefined): ICircuit | undefined | null { + const { error } = useAppNotification(); + const [circuit, setCircuit] = React.useState(undefined); + + React.useEffect(() => { + if (!circuitId) { + setCircuit(undefined); + return; + } + + getQuery(circuitId) + .then(setCircuit) + .catch((ex) => { + error({ + message: `Unable to retrieve circuit "${circuitId}"!\n${ex}`, + }); + setCircuit(null); + }); + }, [circuitId, error]); + + return circuit; +} + +export function useCircuitImageURL(circuitId: string | undefined) { + const { error } = useAppNotification(); + const [url, setUrl] = React.useState(undefined); + const circuit = useCircuit(circuitId); + + React.useEffect(() => { + const action = async () => { + if (!circuit) return; + + const asset = circuit.assets.find( + (item) => item.label === AssetLabel.simulation_designer_image + ); + if (!asset) { + error({ message: `No image found for circuit "${circuit.name}" (${circuitId})!` }); + return; + } + try { + const resp = await downloadAsset({ + entityType: EntityTypeEnum.Circuit, + entityId: circuit.id, + id: asset.id, + asRawResponse: false, + }); + if (!(resp instanceof ArrayBuffer)) { + throw new Error('Wrong image format: expected ArrayBuffer!'); + } + const blob = new Blob([resp], { type: asset.content_type }); + const newUrl = URL.createObjectURL(blob); + setUrl(newUrl); + } catch (ex) { + error({ + message: `Unable to download image for circuit "${circuit.name}"!\n${ex}`, + }); + } + }; + action(); + }, [circuit, circuitId, error]); + + return url; +} + +function getQuery(circuitId: string): Promise { + const query = pendingQueries.get(circuitId); + if (query) return query; + + const newQuery = getCircuit({ id: circuitId }); + pendingQueries.set(circuitId, newQuery); + return newQuery; +} diff --git a/src/features/contribute/_components/hooks/config-atom.ts b/src/features/contribute/_components/hooks/config-atom.ts new file mode 100644 index 000000000..9fbb48e61 --- /dev/null +++ b/src/features/contribute/_components/hooks/config-atom.ts @@ -0,0 +1,30 @@ +import React from 'react'; +import { atom, useAtom } from 'jotai'; + +import { JSONSchema, AtomsMap } from '../../types'; +import { Config } from '../components'; +import { isAtom } from '../utils'; + +export function useConfigAtom(schema: JSONSchema | null, atomsMap: AtomsMap) { + const configAtom = React.useMemo(() => { + return atom((get) => { + const result: Config = {}; + Object.keys(atomsMap).forEach((key) => { + if (isAtom(atomsMap[key])) result[key] = get(atomsMap[key]); + else { + result[key] = {}; + Object.entries(atomsMap[key]).forEach(([subkey, v]) => { + if (typeof result[key] === 'string') return; + result[key][subkey] = get(v); + }); + } + }); + + result.type = schema?.properties?.type.const ?? ''; + + return result; + }); + }, [atomsMap, schema]); + const [config] = useAtom(configAtom); + return config; +} diff --git a/src/features/contribute/_components/hooks/schema.ts b/src/features/contribute/_components/hooks/schema.ts new file mode 100644 index 000000000..6beb8c33f --- /dev/null +++ b/src/features/contribute/_components/hooks/schema.ts @@ -0,0 +1,157 @@ +import React from 'react'; +import { atom } from 'jotai'; +import { NotificationInstance } from 'antd/es/notification/interface'; + +import $RefParser from '@apidevtools/json-schema-ref-parser'; + +import { AtomsMap, JSONSchema } from '../../types'; +import { ConfigValue, Config } from '../components'; +import { isPlainObject, isAtom } from '../utils'; +import { assertErrorMessage } from '@/util/utils'; + +export function useObioneJsonSchema( + circuitId: string, + notification: NotificationInstance, + setSchema: React.Dispatch>, + setAtomsMap: (atomsMap: AtomsMap) => void, + initialConfig?: Config +) { + React.useEffect(() => { + async function fetchSpec() { + try { + const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); + const json = await res.json(); + const dereferenced = await $RefParser.dereference(json); + // @ts-ignore + const theSchema = dereferenced.components.schemas.SimulationsForm as JSONSchema; + if (!theSchema.properties) return; + + setSchema(theSchema); + + const map: { + [key: string]: + | ReturnType>> + | Record>>>; + } = {}; + + if (initialConfig) { + Object.entries(initialConfig) + .filter(([k]) => { + return isRootCategory(theSchema, k); + }) + .forEach(([k, v]) => { + if (isPlainObject(v)) map[k] = atom>(v); + }); + + Object.entries(initialConfig) + .filter(([k]) => { + return !isRootCategory(theSchema, k); + }) + .forEach(([k, v]) => { + map[k] = {}; + + Object.entries(v).forEach(([subK, subV]) => { + if (!isPlainObject(subV) || isAtom(map[k])) return; + map[k][subK] = atom>(subV); + }); + }); + } else { + // Setting up initial values and constants. + Object.entries(theSchema.properties).forEach(([k, v]) => { + if (!v.additionalProperties) { + const initial: Record = {}; + + if (v.properties) + Object.entries(v.properties).forEach(([subkey, subValue]) => { + if (subkey === 'type') initial[subkey] = subValue.const ?? null; + else initial[subkey] = subValue.default ?? null; + }); + + if (k === 'initialize') { + initial.circuit = { + type: 'CircuitFromID', + id_str: circuitId, + }; + } + + map[k] = atom>(initial); + } else map[k] = {}; + }); + } + + setAtomsMap(map); + } catch (e) { + // eslint-disable-next-line no-console + console.error(assertErrorMessage(e)); + notification.error({ message: assertErrorMessage(e) }); + } + } + + fetchSpec(); + }, [notification, setAtomsMap, setSchema, initialConfig]); +} + +export function isRootCategory(schema: JSONSchema, key: string) { + return schema.properties?.[key] && !schema.properties[key].additionalProperties; +} + +export function resolveKey(schema: JSONSchema, tabKey: string, itemIdx: number | null) { + if (typeof itemIdx === null) throw new Error('Invalid itemIdx'); + if (!schema.properties?.[tabKey]?.singular_name) throw new Error(`Invalid schema for ${tabKey}`); + if (isRootCategory(schema, tabKey)) throw new Error("Shouldn't be a root category"); + + return `${schema.properties[tabKey].singular_name.replaceAll(' ', '')}_${itemIdx}`; +} + +export function useObioneJsonConfigurationSchema( + circuitId: string, + notification: NotificationInstance, + setSchema: React.Dispatch>, + setAtomsMap: (atomsMap: AtomsMap) => void +) { + React.useEffect(() => { + async function fetchSpec() { + try { + const res = await fetch(`http://0.0.0.0:8100/openapi.json`); + // const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); + console.log('Fetching schema'); + const json = await res.json(); + const dereferenced = await $RefParser.dereference(json); + // @ts-ignore + const theSchema = dereferenced.components.schemas.ContributeMorphologyForm as JSONSchema; + if (!theSchema.properties) return; + + setSchema(theSchema); + + const map: { + [key: string]: + | ReturnType>> + | Record>>>; + } = {}; + + // Setting up initial values and constants. + Object.entries(theSchema.properties).forEach(([k, v]) => { + if (!v.additionalProperties) { + const initial: Record = {}; + + if (v.properties) + Object.entries(v.properties).forEach(([subkey, subValue]) => { + if (subkey === 'type') initial[subkey] = subValue.const ?? null; + else initial[subkey] = subValue.default ?? null; + }); + + map[k] = atom>(initial); + } else map[k] = {}; + }); + + setAtomsMap(map); + } catch (e) { + // eslint-disable-next-line no-console + console.error(assertErrorMessage(e)); + notification.error({ message: assertErrorMessage(e) }); + } + } + + fetchSpec(); + }, [notification, setAtomsMap, setSchema]); +} diff --git a/src/features/contribute/_components/section.tsx b/src/features/contribute/_components/section.tsx new file mode 100644 index 000000000..b8dc739c7 --- /dev/null +++ b/src/features/contribute/_components/section.tsx @@ -0,0 +1,221 @@ +/* eslint-disable no-param-reassign */ +import React, { Fragment } from 'react'; +import { atom } from 'jotai'; +import { + CheckCircleFilled, + DeleteOutlined, + PlusCircleOutlined, + WarningFilled, +} from '@ant-design/icons'; +import { ErrorObject } from 'ajv'; + +import { AtomsMap, JSONSchema } from '../types'; +import { Chevron, Config, ConfigValue, Tab } from './components'; +import { isAtom, isPlainObject } from './utils'; +import { isRootCategory, resolveKey } from './hooks/schema'; + +import { classNames } from '@/util/utils'; + +export function Section({ + schema, + k, + sectionSchema, + atomsMap, + setAtomsMap, + configTab, + setConfigTab, + config, + campaignId, + loading, + errors, + selectedItemIdx, + setSelectedItemIdx, + setEditing, + setSelectedCategory, + readOnly, +}: { + schema: JSONSchema | null; // The global schema + k: string; // secition key + sectionSchema: JSONSchema; // The schema for this section + atomsMap: AtomsMap; + setAtomsMap: React.Dispatch>; + configTab: string; // Key for selected section + setConfigTab: (configTab: string) => void; + config: Config; + campaignId: string; + loading: boolean; + errors: ErrorObject, unknown>[] | null | undefined; + selectedItemIdx: number | null; + setSelectedItemIdx: (selectedItemIdx: number | null) => void; + setEditing: React.Dispatch>; + setSelectedCategory: React.Dispatch>; + readOnly?: boolean; +}) { + if (!schema || !schema?.properties) return; + + const handleHeaderClick = (subkey: string, subValue: unknown) => { + if (isPlainObject(subValue)) { + setSelectedCategory(typeof subValue.type === 'string' ? subValue.type : ''); + setSelectedItemIdx(parseInt(subkey.split('_')[1], 10)); + } + setEditing(true); + }; + + return ( + <> + { + if (configTab === k && !isRootCategory(schema, k)) { + setEditing(false); + setSelectedCategory(''); + setSelectedItemIdx(null); + setConfigTab(''); + return; + } + + setConfigTab(k); + setSelectedItemIdx(null); + if (!sectionSchema.additionalProperties) setEditing(true); + else setEditing(false); + }} + extraClass="w-full flex justify-between h-[50px] min-h-[50px] items-center drop-shadow" + > + {schema.properties?.[k]?.title} +
+ {errors?.find((error) => error.instancePath.startsWith('/' + k)) ? ( + + ) : ( + + )} + +
+ + {sectionSchema.additionalProperties && configTab === k && config[k] && ( + <> + {Object.entries(config[k]).map(([subkey, subValue]) => { + const idx = parseInt(subkey.split('_')[1], 10); + + const isSelected = configTab === k && idx === selectedItemIdx; + + return ( + +
handleHeaderClick(subkey, subValue)} + onKeyDown={(evt) => { + if (evt.key === ' ' || evt.key === 'Enter') { + handleHeaderClick(subkey, subValue); + } + }} + > + {subkey} +
+ {errors?.find((error) => error.instancePath.startsWith(`/${k}/${subkey}`)) ? ( + + ) : ( + + )} + + {!campaignId && !loading && !readOnly && ( + { + e.stopPropagation(); + + setSelectedCategory(''); + setEditing(false); + + const selectedTabAtoms = atomsMap[configTab]; + if (!isAtom(selectedTabAtoms)) { + const refereeKey = resolveKey(schema, configTab, idx); + + delete selectedTabAtoms[refereeKey]; + + // Initialize case + const configInitialize = config.initialize; + if ( + isPlainObject(configInitialize) && + isPlainObject(configInitialize.node_set) && + typeof configInitialize.node_set.block_name === 'string' && + configInitialize.node_set.block_name === refereeKey + ) { + atomsMap.initialize = atom>({ + ...configInitialize, + node_set: null, + }); + } + + // Check all keys in the config + Object.entries(config) + .filter(([configK]) => configK !== 'initialize') + .forEach(([configK, configV]) => { + if (typeof configV !== 'object') return; + + // Check all keys in a section (e.g stimuli, recordings) + Object.entries(configV).forEach(([entryKey, entryV]) => { + if (!isPlainObject(entryV)) return; + + // Check all values in a particular object (a single stimuli, a single timestamp, etc) + Object.entries(entryV).forEach(([fieldK, field]) => { + if ( + !isPlainObject(entryV) || + !isPlainObject(field) || + typeof field.block_name !== 'string' || + isAtom(atomsMap[configK]) || // skip top level atoms (e.g initialize) + field.block_name !== refereeKey + ) + return; + + // Deleting the reference to current object + + delete entryV[fieldK]; //eslint-disable-line + + // The atom that has a reference to current object + atomsMap[configK][entryKey] = + atom>(entryV); + }); + }); + }); + + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...selectedTabAtoms, + }, + }); + } + + setSelectedItemIdx(null); + }} + /> + )} +
+
+ + ); + })} + {!campaignId && !loading && !readOnly && ( + + )} + + )} + + ); +} diff --git a/src/features/contribute/_components/simulation-files/index.tsx b/src/features/contribute/_components/simulation-files/index.tsx new file mode 100644 index 000000000..0d2a8ca2c --- /dev/null +++ b/src/features/contribute/_components/simulation-files/index.tsx @@ -0,0 +1,198 @@ +import { useAtomValue } from 'jotai'; +import { Suspense, useMemo } from 'react'; +import { ErrorBoundary } from 'react-error-boundary'; + +import { ICircuitSimulation } from '@/api/entitycore/types/entities/circuit-simulation'; +import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; +import { IEntity } from '@/api/entitycore/types/entities/entity'; +import { IAsset } from '@/api/entitycore/types/shared/global'; +import { + circuitAtomFamily, + simResultBySimIdAtomFamily, +} from '@/features/small-microcircuit/_components/atoms'; +import { WorkspaceContext } from '@/types/common'; +import { classNames } from '@/util/utils'; + +export type File = { + asset: IAsset; + entity: IEntity; + assetPath?: string; +}; + +type SimulationFilesProps = { + simulation: ICircuitSimulation; + execStatus?: CircuitSimulationExecutionStatus | null; + selectedFile?: File; + onSelect: (file: File) => void; + context: WorkspaceContext; +}; + +export function SimulationFiles({ + simulation, + execStatus, + selectedFile, + onSelect, + context, +}: SimulationFilesProps) { + const outputAvailable = + execStatus && + [CircuitSimulationExecutionStatus.ERROR, CircuitSimulationExecutionStatus.DONE].includes( + execStatus + ); + + return ( + <> +

Input files

+ +

Output files

+ Loading...}> + {outputAvailable && ( + There was an issue loading output files + } + resetKeys={[simulation]} + > + + + )} + + + ); +} + +type SimulationInputFilesProps = { + simulation: ICircuitSimulation; + context: WorkspaceContext; + selectedFile?: File; + onSelect: (file: File) => void; + className?: string; +}; + +function SimulationInputFiles({ + simulation, + context, + selectedFile, + onSelect, + className = '', +}: SimulationInputFilesProps) { + const circuit = useAtomValue(circuitAtomFamily({ circuitId: simulation.entity_id, context })); + // TODO: fetch circuitConfig + const sonataCircuitAsset = circuit.assets.find((asset) => asset.label === 'sonata_circuit'); + const circuitConfigFile: File = useMemo( + () => ({ + entity: circuit, + asset: sonataCircuitAsset!, + assetPath: 'circuit_config.json', + }), + [circuit, sonataCircuitAsset] + ); + + const files: File[] = useMemo( + () => [circuitConfigFile, ...simulation.assets.map((asset) => ({ asset, entity: simulation }))], + [simulation, circuitConfigFile] + ); + + return ( +
+ {files.map((file) => ( + + ))} +
+ ); +} + +type SimulationOutputFilesProps = { + simulation: ICircuitSimulation; + context: WorkspaceContext; + selectedFile?: File; + onSelect: (file: File) => void; + className?: string; +}; + +function SimulationOutputFiles({ + simulation, + onSelect, + selectedFile, + context, + className = '', +}: SimulationOutputFilesProps) { + const simResult = useAtomValue( + simResultBySimIdAtomFamily({ simulationId: simulation.id, context }) + ); + + const files: File[] = useMemo( + () => simResult.assets.map((asset) => ({ asset, entity: simResult })), + [simResult] + ); + + return ( +
+ {files.map((file) => ( + + ))} +
+ ); +} + +type SimulationFileProps = { + file: File; + selected?: boolean; + onSelect: (file: File) => void; +}; + +function SimulationFile({ file, selected, onSelect }: SimulationFileProps) { + const fileName = file.assetPath?.split('/').at(-1) ?? file.asset.path.split('/').at(-1); + const fileExt = fileName?.split('.').at(-1); + + return ( + + ); +} diff --git a/src/features/contribute/_components/simulation-status/index.tsx b/src/features/contribute/_components/simulation-status/index.tsx new file mode 100644 index 000000000..499d77215 --- /dev/null +++ b/src/features/contribute/_components/simulation-status/index.tsx @@ -0,0 +1,50 @@ +import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; + +export function SimulationStatusBadge({ status }: { status?: CircuitSimulationExecutionStatus }) { + const color = status ? statusColorMap[status] : '#fafafa'; + const showSpinner = status && ['pending', 'running'].includes(status); + + // TODO: move spinner outside of the module. + + return ( +
+ {showSpinner && ( + + + + + )} + + + {status ?? ''} + +
+ ); +} +const statusColorMap: Record = { + created: '#434343', + pending: '#fa8c16', + running: '#1890ff', + done: '#389e0d', + error: '#f5222d', +}; diff --git a/src/features/contribute/_components/tabs-selector/index.ts b/src/features/contribute/_components/tabs-selector/index.ts new file mode 100644 index 000000000..e516b026d --- /dev/null +++ b/src/features/contribute/_components/tabs-selector/index.ts @@ -0,0 +1 @@ +export { default } from './tabs-selector'; diff --git a/src/features/contribute/_components/tabs-selector/tabs-selector.tsx b/src/features/contribute/_components/tabs-selector/tabs-selector.tsx new file mode 100644 index 000000000..3b2b02a17 --- /dev/null +++ b/src/features/contribute/_components/tabs-selector/tabs-selector.tsx @@ -0,0 +1,43 @@ +import React from 'react'; + +import { Tab } from '../components'; +import { TabType } from '../../types'; +import { classNames } from '@/util/utils'; + +interface TabsSelectorProps { + className?: string; + tab: TabType; + setTab(tab: TabType): void; + disableSimulationTab: boolean; +} + +export default function TabsSelector({ + className, + tab, + setTab, + disableSimulationTab, +}: TabsSelectorProps) { + return ( +
+
+ setTab('configuration')} + > + Configuration + + setTab('simulations')} + disabled={disableSimulationTab} + > + Simulations + +
+
+ ); +} diff --git a/src/features/contribute/_components/tooltip/index.ts b/src/features/contribute/_components/tooltip/index.ts new file mode 100644 index 000000000..bb106e207 --- /dev/null +++ b/src/features/contribute/_components/tooltip/index.ts @@ -0,0 +1 @@ +export { default } from './tooltip'; diff --git a/src/features/contribute/_components/tooltip/tooltip.module.css b/src/features/contribute/_components/tooltip/tooltip.module.css new file mode 100644 index 000000000..a4e563aa8 --- /dev/null +++ b/src/features/contribute/_components/tooltip/tooltip.module.css @@ -0,0 +1,39 @@ +.tooltipContainer { + position: relative; + overflow: visible; +} + +.tooltip { + position: relative; + background: #0050b3ee; + color: #fff; + padding: 0.5em 1em; + border-radius: 0.25em; + position: absolute; + left: 0; + right: 0; + bottom: 0; + width: 100%; + pointer-events: none; + z-index: 9; + transform: translateY(calc(100% + 16px)); + transition: all 0.2s; + opacity: 0; +} + +.tooltipContainer:hover .tooltip { + opacity: 1; +} + +.tooltip::after { + content: ''; + border: 16px solid transparent; + border-bottom: 16px solid #0050b3ee; + position: absolute; + top: -16px; + left: 50%; + width: 0; + height: 0; + margin: -16px; + transform: scale(0.5, 1); +} diff --git a/src/features/contribute/_components/tooltip/tooltip.tsx b/src/features/contribute/_components/tooltip/tooltip.tsx new file mode 100644 index 000000000..45a1501f4 --- /dev/null +++ b/src/features/contribute/_components/tooltip/tooltip.tsx @@ -0,0 +1,20 @@ +import React from 'react'; + +import { classNames } from '@/util/utils'; + +import styles from './tooltip.module.css'; + +interface TooltipProps { + className?: string; + value?: React.ReactNode; + children: React.ReactNode; +} + +export default function Tooltip({ className, value, children }: TooltipProps) { + return ( +
+ {children} + {value &&
{value}
} +
+ ); +} diff --git a/src/features/contribute/_components/utils.ts b/src/features/contribute/_components/utils.ts new file mode 100644 index 000000000..f4f3c34a2 --- /dev/null +++ b/src/features/contribute/_components/utils.ts @@ -0,0 +1,73 @@ +import { Atom } from 'jotai'; +import uniq from 'lodash/uniq'; +import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; + +export type Primitive = null | boolean | number | string; +export interface ConfigObject { + [key: string]: Primitive | Primitive[] | ConfigObject; +} + +export function isPlainObject(value: unknown): value is Record { + return typeof value === 'object' && !Array.isArray(value) && value !== null; +} + +export function isAtom(val: unknown): val is Atom { + return typeof val === 'object' && val !== null && 'read' in val; +} + +export const ORDERING: Record = { + assets: { + order: 0, + category: 'Assets', + }, + morphology: { + order: 1, + category: 'Setup', + }, + contribution: { + order: 2, + category: 'Contribution', + }, + subject: { + order: 4, + category: 'Subject', + }, + license: { + order: 5, + category: 'License', + }, + mtype: { + order: 6, + category: 'Mtype', + }, + // publication: { + // order: 7, + // category: 'Publication', + // }, + // scientificartifact: { + // order: 8, + // category: 'Scientific Artifact', + // }, +}; + +export const CATEGORIES: string[] = uniq(Object.values(ORDERING).map((o) => o.category)); + +const simExecStatusListordered = [ + CircuitSimulationExecutionStatus.CREATED, + CircuitSimulationExecutionStatus.PENDING, + CircuitSimulationExecutionStatus.RUNNING, + CircuitSimulationExecutionStatus.DONE, + CircuitSimulationExecutionStatus.ERROR, +]; + +export function getLatestSimExecStatus( + remoteStatus: CircuitSimulationExecutionStatus, + localStatus: CircuitSimulationExecutionStatus +) { + const remoteStatusIdx = simExecStatusListordered.indexOf(remoteStatus); + const localStatusIdx = simExecStatusListordered.indexOf(localStatus); + + const latestStatus = Math.max(remoteStatusIdx, localStatusIdx); + + return simExecStatusListordered[latestStatus]; +} diff --git a/src/features/contribute/error-registry.ts b/src/features/contribute/error-registry.ts new file mode 100755 index 000000000..afc71adf6 --- /dev/null +++ b/src/features/contribute/error-registry.ts @@ -0,0 +1,7 @@ +import { messages } from '@/i18n/en/simulation'; + +const errorCodeToTranslationKey: Record = { + ACCOUNTING_INSUFFICIENT_FUNDS_ERROR: messages.LowFundsError, +}; + +export default errorCodeToTranslationKey; diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx new file mode 100755 index 000000000..66c406951 --- /dev/null +++ b/src/features/contribute/index.tsx @@ -0,0 +1,616 @@ +// index.tsx + +'use client'; + +import { + LoadingOutlined, + RightOutlined, + UploadOutlined, + CheckCircleFilled, +} from '@ant-design/icons'; +import Ajv, { AnySchema } from 'ajv'; +import { atom, useAtomValue, useSetAtom } from 'jotai'; +import { Fragment, Suspense, useEffect, useMemo, useRef, useState } from 'react'; +import { useParams } from 'next/navigation'; +import { Progress } from 'antd'; +import { match } from 'ts-pattern'; +import { + simExecRemoteStatusMapAtomFamily, + simExecStatusMapAtomFamily, + simulationsByCampaignIdAtomFamily, +} from './_components/atoms'; +import CircuitPreview from './_components/circuit-preview'; +import { Config, ConfigValue, JSONSchemaForm } from './_components/components'; +import { FileViewer } from './_components/file-viewer'; +import { useCircuit } from './_components/hooks/circuit'; +import { useConfigAtom } from './_components/hooks/config-atom'; +import { + isRootCategory, + resolveKey, + useObioneJsonConfigurationSchema, +} from './_components/hooks/schema'; +import { Section } from './_components/section'; +import TabsSelector from './_components/tabs-selector'; +import { CATEGORIES, isAtom, ORDERING } from './_components/utils'; +import { AtomsMap, JSONSchema, TabType } from './types'; +import { resolveDataKey } from '@/utils/key-builder'; +import { useBrainRegionHierarchy } from '@/features/brain-region-hierarchy/context'; +import { ICircuitSimulation } from '@/api/entitycore/types/entities/circuit-simulation'; +import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; +import ApiError from '@/api/error'; +import authFetch from '@/authFetch'; +import { useAppNotification } from '@/components/notification'; +import { ButtonCopyId } from '@/features/details-view/button-copy-id'; +import { useLastTruthyValue } from '@/hooks/hooks'; +import { messages } from '@/i18n/en/simulation'; +import { runSimulation } from '@/services/small-scale-simulator/circuit'; +import { MessageType } from '@/services/small-scale-simulator/types'; +import { assertErrorMessage, classNames } from '@/util/utils'; +import { getErrorMessage } from '@/utils/error'; +import styles from './small-microcircuit.module.css'; + +export default function ContributeMorphologyConfiguration({ + circuitId, + virtualLabId, + projectId, + initialCampaignId, + initialConfig, +}: { + circuitId: string; + virtualLabId: string; + projectId: string; + initialCampaignId?: string; + initialConfig?: Config; +}) { + if (!!initialCampaignId !== !!initialConfig) + throw new Error('Both or none of initialCampaignId, initialConfigId should be passed'); + + const params = useParams(); + const { node } = useBrainRegionHierarchy({ + dataKey: resolveDataKey({ section: 'explore', projectId }), + }); + + const [configTab, setConfigTab] = useState('info'); + const [editing, setEditing] = useState(true); + const [schema, setSchema] = useState(null); + const [selectedCategory, setSelectedCategory] = useState(''); + const [selectedItemIdx, setSelectedItemIdx] = useState(null); + const [loading, setLoading] = useState(false); + const [showConfig, setShowConfig] = useState(false); + const [selectedFile, setSelectedFile] = useState(null); + const [fileStatus, setFileStatus] = useState<{ + message?: string; + }>({}); + const [newJsonPayload, setNewJsonPayload] = useState(null); + const notification = useAppNotification(); + const [campaignId, setCampaignId] = useState(initialCampaignId ?? ''); + const initialConfigValidated = useRef(false); + + // Add success state + const [isSuccess, setIsSuccess] = useState(false); + + // Add validation state + const [formValidation, setFormValidation] = useState<{ + isValid: boolean; + errors: string[]; + }>({ + isValid: true, + errors: [], + }); + + const selectedCatSchema = schema?.properties?.[configTab]?.additionalProperties?.anyOf?.find( + (s) => s.properties?.type.const === selectedCategory + ); + + const handleAddReferenceClick = (referenceTab: string) => { + setConfigTab(referenceTab); + setEditing(true); + setSelectedCategory(''); + }; + + // Handle validation changes from the form + const handleValidationChange = (isValid: boolean, errors: string[]) => { + setFormValidation({ isValid, errors }); + }; + + const readOnly = initialConfig !== undefined; + + const validate = useMemo(() => { + const ajv = new Ajv({ strictSchema: false, allErrors: true }); + if (!schema) return; + return ajv.compile(schema as AnySchema); + }, [schema]); + + const [atomsMap, setAtomsMap] = useState({}); + + const config = useConfigAtom(schema, atomsMap, node.id, configTab); + + if (validate && initialConfig && !initialConfigValidated.current) { + initialConfigValidated.current = true; + validate(initialConfig); + if (validate.errors) throw new Error('Invalid Simulation Campaign Configuration'); + } + + const errors = useMemo(() => { + if (validate) validate(config); + return validate?.errors; + }, [validate, config]); + + useObioneJsonConfigurationSchema(circuitId, notification, setSchema, setAtomsMap); + + const hasSuccessfulUpload = Object.values(fileStatus).some( + (status) => status?.status === 'success' + ); + + // Update the submit button condition + const canSubmit = + !errors?.length && !loading && !readOnly && selectedFile && formValidation.isValid; + + // Show success page if upload was successful + if (isSuccess) { + return ( +
+
+
+ ✓ Morphology created successfully +
+ +
+
+ ); + } + + if (!schema) { + return ( +
+ +
+ ); + } + + return ( +
+
+
+
+
+ {/* Show overall form validation status */} + {!formValidation.isValid && formValidation.errors.length > 0 && ( +
+
Required fields missing:
+
{formValidation.errors.join(', ')}
+
+ )} + +
Assets
+
{ + setConfigTab('assets'); + setEditing(true); + setSelectedCategory(''); + setSelectedItemIdx(null); + }} + > + Assets +
+ {selectedFile ? ( + + ) : ( +
// Placeholder to maintain spacing + )} + +
+
+ {CATEGORIES.filter((c) => c !== 'Assets').map((c) => { + return ( + +
{c}
+ {schema.properties && + Object.entries(schema.properties) + .filter(([k]) => k !== 'type' && ORDERING[k]?.category === c) + .sort((a, b) => { + const order = (k: string) => ORDERING[k]?.order ?? 999; + return order(a[0]) - order(b[0]); + }) + .map(([k, v]) => { + return ( +
+ ); + })} + + ); + })} +
+ {!readOnly && ( + + )} +
+
+ {configTab === 'assets' && editing && ( +
+
+ UPLOAD MORPHOLOGY FILE +
+
+ One reference file should be loaded. +
+
+
+ + {fileStatus?.message && ( + {fileStatus.message} + )} +
+
+
+ )} + {schema.properties && + schema.properties?.[configTab]?.additionalProperties?.anyOf && + !selectedCategory && + editing && + configTab !== 'assets' && ( +
+ {schema.properties[configTab].additionalProperties.anyOf.map((o) => { + return ( + +
{ + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) + Object.entries(o.properties).forEach(([subkey, subValue]) => { + if (subkey === 'type') initial[subkey] = subValue.const ?? null; + else initial[subkey] = subValue.default ?? null; + }); + const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...atomsMap[configTab], + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + }); + }} + > +
{o.title}
+
{o.description}
+
+ + ); + })} +
+ )} + {schema.properties && + schema.properties?.[configTab] && + editing && + (isRootCategory(schema, configTab) || selectedCatSchema) && + configTab !== 'assets' && ( + + )} +
+
+ {showConfig && ( +
+
+
+

New Record JSON

+ +
+ + 
+              {JSON.stringify(newJsonPayload, null, 2)}
+
+ +
+ +
+
+
+ )} +
+ ); +} diff --git a/src/features/contribute/small-microcircuit.module.css b/src/features/contribute/small-microcircuit.module.css new file mode 100755 index 000000000..0a4777633 --- /dev/null +++ b/src/features/contribute/small-microcircuit.module.css @@ -0,0 +1,32 @@ +div.threeColumns { + display: grid; + grid-template-columns: minmax(0, 1fr) minmax(0, 1fr) minmax(0, 2fr); + gap: 5px; + height: calc(100% - 100px); +} + +div.threeColumns > div { + min-height: 0; + height: 100%; +} + +div.threeColumns > div.scrollable { + overflow-y: auto; + overflow-x: visible; +} + +div.threeColumns > div:first-child { + display: grid; + grid-template-rows: 1fr auto; + gap: 1em; + overflow: unset; +} + +header.header { + display: flex; + flex-wrap: nowrap; + flex-direction: row; + justify-content: space-between; + align-items: center; + gap: 1em; +} diff --git a/src/features/contribute/types.ts b/src/features/contribute/types.ts new file mode 100755 index 000000000..2217e8e2b --- /dev/null +++ b/src/features/contribute/types.ts @@ -0,0 +1,35 @@ +import { atom } from 'jotai'; + +import { ConfigValue } from './_components/components'; +import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; + +export type JSONSchema = { + type?: 'string' | 'number' | 'integer' | 'object' | 'array' | 'boolean' | 'null'; + properties?: { [key: string]: JSONSchema }; + items?: JSONSchema | JSONSchema[]; + required?: string[]; + enum?: any[]; + const?: string; + additionalProperties?: JSONSchema; + oneOf?: JSONSchema[]; + anyOf?: JSONSchema[]; + allOf?: JSONSchema[]; + not?: JSONSchema; + format?: string; + title?: string; + description?: string; + default?: any; + examples?: any[]; + [key: string]: any; + singular_name?: string; +}; + +export interface AtomsMap { + [key: string]: + | ReturnType>> + | Record>>>; +} + +export type TabType = 'configuration' | 'simulations'; + +export type SimExecStatusMap = Map; From 8d79750fde788e0359011da76d13d8a96f824a53 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 14:03:59 +0200 Subject: [PATCH 02/44] fixed linting --- .../contribute/_components/components.tsx | 80 +++++++++---------- src/features/contribute/index.tsx | 42 ++-------- 2 files changed, 48 insertions(+), 74 deletions(-) diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx index ee93f0735..e7677510f 100644 --- a/src/features/contribute/_components/components.tsx +++ b/src/features/contribute/_components/components.tsx @@ -23,40 +23,40 @@ export type Config = Record; // Updated structure for MTYPE classification const MTYPE_CLASSES = [ - { mtype_pref_label: 'L23_NBC', mtype_id: '6605787b-ba14-43fd-a954-de9cff4b15a0' }, - { mtype_pref_label: 'L23_NGC', mtype_id: 'dd16dca0-e567-416b-b8b7-f8fbcaa05af0' }, - { mtype_pref_label: 'L23_PC', mtype_id: '0791edc9-7ad4-4a94-a4a5-feab9b690d7e' }, - { mtype_pref_label: 'L23_PTPC', mtype_id: '52ea242f-6591-425a-8eae-962fa0b4dfe0' }, - { mtype_pref_label: 'L23_SBC', mtype_id: 'fbb8b577-92f4-4c93-b355-0982ef5a3c7c' }, - { mtype_pref_label: 'L23_STPC', mtype_id: '93be8237-9861-4870-9977-ff1cf9e7462c' }, - { mtype_pref_label: 'L2_ChC', mtype_id: '91ba3deb-1139-4bc6-a12f-6a64a0ed0e92' }, - { mtype_pref_label: 'L2_IPC', mtype_id: 'e55f12e1-807c-42f6-ba98-91d6d30c57d7' }, - { mtype_pref_label: 'L2_MC', mtype_id: 'ea51f2c8-95fc-4940-a400-c37a3ff2d9eb' }, - { mtype_pref_label: 'L2_PC', mtype_id: 'dd73956b-423e-42c5-87d9-9e2cc84356b9' }, - { mtype_pref_label: 'L2_TPC', mtype_id: '7abf03d5-30b0-41ae-a02b-1f4e26c243a8' }, - { mtype_pref_label: 'L2_TPC:A', mtype_id: '9b04acb1-4737-4088-8d22-0658414bdda1' }, - { mtype_pref_label: 'L2_TPC:B', mtype_id: '4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda' }, - { mtype_pref_label: 'L3_MC', mtype_id: '52578494-b41c-499b-9717-5d11f4b2f068' }, - { mtype_pref_label: 'L3_PC', mtype_id: '87fec7dd-7a2f-400a-aee0-94d1946cf1ab' }, - { mtype_pref_label: 'L3_TPC', mtype_id: '229c31f1-a6ec-4d8c-85d3-d8175ffde109' }, - { mtype_pref_label: 'L3_TPC:A', mtype_id: 'dd346e90-7bca-4976-bf9a-303b6a94b339' }, - { mtype_pref_label: 'L3_TPC:B', mtype_id: 'a71d226c-2c56-40ee-a4be-9726fc430932' }, - { mtype_pref_label: 'L3_TPC:C', mtype_id: 'd9b7bd4d-cec9-4fec-a448-79320de89f2a' }, - { mtype_pref_label: 'L4_BP', mtype_id: 'a55f6ce7-068a-4c5e-a883-de5f4304612e' }, - { mtype_pref_label: 'L4_BTC', mtype_id: '8315d249-6678-4d55-b581-3b6f9eb48e86' }, - { mtype_pref_label: 'L4_ChC', mtype_id: '0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6' }, - { mtype_pref_label: 'L4_DBC', mtype_id: '8de61c06-31e8-4483-bd98-608bc874b369' }, - { mtype_pref_label: 'L4_LBC', mtype_id: 'bb875a91-4ae5-4f6f-b050-5ad952e9cd6c' }, - { mtype_pref_label: 'L4_MC', mtype_id: '0bdf029e-a55a-444c-a7c9-9d0ff51239a5' }, - { mtype_pref_label: 'L4_NBC', mtype_id: '72673af9-2f2b-4a9a-95dc-552777ab63b9' }, - { mtype_pref_label: 'L4_NGC', mtype_id: '41f41550-5e0e-4de7-b52d-62110c338a27' }, - { mtype_pref_label: 'L4_PC', mtype_id: 'ad5769c6-7e86-4433-8f34-9efcb4f0d182' }, - { mtype_pref_label: 'L4_SBC', mtype_id: '43a7d86b-71c5-4a10-be62-ef6cf95ca694' }, - { mtype_pref_label: 'L4_SSC', mtype_id: '400a55f7-e162-4fd1-80a0-4f2facea7cec' }, - { mtype_pref_label: 'L4_TPC', mtype_id: '02e13718-5227-4c28-b838-04dd0c2c67f2' }, - { mtype_pref_label: 'L4_UPC', mtype_id: '2ef7e0b5-39e4-441b-a72a-c7186afa7f5c' }, - { mtype_pref_label: 'L56_PC', mtype_id: '629d6d6f-93f9-43d8-8a99-277740fd8f22' }, - { mtype_pref_label: 'L5_BP', mtype_id: '7b16c860-ae76-4ddf-b093-4e28620b3712' }, + {"mtype_pref_label":"L23_NBC","mtype_id":"6605787b-ba14-43fd-a954-de9cff4b15a0"}, + {"mtype_pref_label":"L23_NGC","mtype_id":"dd16dca0-e567-416b-b8b7-f8fbcaa05af0"}, + {"mtype_pref_label":"L23_PC","mtype_id":"0791edc9-7ad4-4a94-a4a5-feab9b690d7e"}, + {"mtype_pref_label":"L23_PTPC","mtype_id":"52ea242f-6591-425a-8eae-962fa0b4dfe0"}, + {"mtype_pref_label":"L23_SBC","mtype_id":"fbb8b577-92f4-4c93-b355-0982ef5a3c7c"}, + {"mtype_pref_label":"L23_STPC","mtype_id":"93be8237-9861-4870-9977-ff1cf9e7462c"}, + {"mtype_pref_label":"L2_ChC","mtype_id":"91ba3deb-1139-4bc6-a12f-6a64a0ed0e92"}, + {"mtype_pref_label":"L2_IPC","mtype_id":"e55f12e1-807c-42f6-ba98-91d6d30c57d7"}, + {"mtype_pref_label":"L2_MC","mtype_id":"ea51f2c8-95fc-4940-a400-c37a3ff2d9eb"}, + {"mtype_pref_label":"L2_PC","mtype_id":"dd73956b-423e-42c5-87d9-9e2cc84356b9"}, + {"mtype_pref_label":"L2_TPC","mtype_id":"7abf03d5-30b0-41ae-a02b-1f4e26c243a8"}, + {"mtype_pref_label":"L2_TPC:A","mtype_id":"9b04acb1-4737-4088-8d22-0658414bdda1"}, + {"mtype_pref_label":"L2_TPC:B","mtype_id":"4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda"}, + {"mtype_pref_label":"L3_MC","mtype_id":"52578494-b41c-499b-9717-5d11f4b2f068"}, + {"mtype_pref_label":"L3_PC","mtype_id":"87fec7dd-7a2f-400a-aee0-94d1946cf1ab"}, + {"mtype_pref_label":"L3_TPC","mtype_id":"229c31f1-a6ec-4d8c-85d3-d8175ffde109"}, + {"mtype_pref_label":"L3_TPC:A","mtype_id":"dd346e90-7bca-4976-bf9a-303b6a94b339"}, + {"mtype_pref_label":"L3_TPC:B","mtype_id":"a71d226c-2c56-40ee-a4be-9726fc430932"}, + {"mtype_pref_label":"L3_TPC:C","mtype_id":"d9b7bd4d-cec9-4fec-a448-79320de89f2a"}, + {"mtype_pref_label":"L4_BP","mtype_id":"a55f6ce7-068a-4c5e-a883-de5f4304612e"}, + {"mtype_pref_label":"L4_BTC","mtype_id":"8315d249-6678-4d55-b581-3b6f9eb48e86"}, + {"mtype_pref_label":"L4_ChC","mtype_id":"0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6"}, + {"mtype_pref_label":"L4_DBC","mtype_id":"8de61c06-31e8-4483-bd98-608bc874b369"}, + {"mtype_pref_label":"L4_LBC","mtype_id":"bb875a91-4ae5-4f6f-b050-5ad952e9cd6c"}, + {"mtype_pref_label":"L4_MC","mtype_id":"0bdf029e-a55a-444c-a7c9-9d0ff51239a5"}, + {"mtype_pref_label":"L4_NBC","mtype_id":"72673af9-2f2b-4a9a-95dc-552777ab63b9"}, + {"mtype_pref_label":"L4_NGC","mtype_id":"41f41550-5e0e-4de7-b52d-62110c338a27"}, + {"mtype_pref_label":"L4_PC","mtype_id":"ad5769c6-7e86-4433-8f34-9efcb4f0d182"}, + {"mtype_pref_label":"L4_SBC","mtype_id":"43a7d86b-71c5-4a10-be62-ef6cf95ca694"}, + {"mtype_pref_label":"L4_SSC","mtype_id":"400a55f7-e162-4fd1-80a0-4f2facea7cec"}, + {"mtype_pref_label":"L4_TPC","mtype_id":"02e13718-5227-4c28-b838-04dd0c2c67f2"}, + {"mtype_pref_label":"L4_UPC","mtype_id":"2ef7e0b5-39e4-441b-a72a-c7186afa7f5c"}, + {"mtype_pref_label":"L56_PC","mtype_id":"629d6d6f-93f9-43d8-8a99-277740fd8f22"}, + {"mtype_pref_label":"L5_BP","mtype_id":"7b16c860-ae76-4ddf-b093-4e28620b3712"} ]; // Helper function to check if a field value is considered "empty" or invalid @@ -243,7 +243,7 @@ export function JSONSchemaForm({ ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), }; const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - const isRequired = schema.required?.includes(k); + const fieldError = getFieldErrorMessage(k); const hasError = hasFieldError(k); @@ -564,18 +564,18 @@ export function JSONSchemaForm({
); } - + // New condition for 'mtype class id' if (isMtypeClassIdField) { const options = MTYPE_CLASSES.map((mtype) => ({ label: mtype.mtype_pref_label, value: mtype.mtype_id, })); - + const currentMtypeLabel = MTYPE_CLASSES.find( (mtype) => mtype.mtype_id === state[k] )?.mtype_pref_label; - + return (
{ - console.log(`Updating strain_id to: ${newV}`); - setState((prev) => { - const newState = { ...prev, [k]: newV }; - console.log('New state after strain_id update:', newState); - return newState; - }); + setState((prev) => ({ ...prev, [k]: newV })); markFieldTouched(k); }} value={state[k]} @@ -424,7 +415,6 @@ export function JSONSchemaForm({ } if (isAgePeriodField) { - console.log('Rendering age_period field:', { key: k, schema: v, resolved: obj }); if (obj.enum) { return (
@@ -445,7 +435,6 @@ export function JSONSchemaForm({
); } - console.warn('No enum found for age_period:', obj); return (
{Array.isArray(state[k]) && state[k].map((e, i) => ( -
+
{e}{' '} {!disabled && ( { - const newElements = [...state[k]]; + const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; newElements.splice(i, 1); setState({ ...state, [k]: newElements }); markFieldTouched(k); @@ -659,7 +648,7 @@ export function JSONSchemaForm({ {isPlainObject(state[k]) && Array.isArray(state[k].elements) && state[k].elements.map((e, i) => ( -
+
{e}{' '} {!disabled && ( - {newElement[k] !== null && ( + {!isNil(newElement[k]) && ( { @@ -803,7 +793,6 @@ export function JSONSchemaForm({ ); } - console.warn(`Unhandled schema type for key: ${k}`, obj); return (
{schema.title}
@@ -836,7 +821,7 @@ export function JSONSchemaForm({
    {validationErrors.map((error, index) => ( -
  • {error}
    • +
  • {error}
    • ))}
@@ -861,18 +846,6 @@ export function JSONSchemaForm({ normalizedKey === 'licenseid' || normalizedKey === 'license_id'; const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; - if (currentCategory === 'subject' && normalizedKey === 'ageperiod') { - console.log('Age period field:', { - key: k, - schema: v, - title: v.title, - resolved: { - ...v, - ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), - }, - }); - } - return (
@@ -888,7 +861,7 @@ export function JSONSchemaForm({ : isAgePeriodField ? 'AGE PERIOD' : isLicenseIdField - ? 'LICENSE' // New condition for license title + ? 'LICENSE' : isMtypeClassIdField ? 'MTYPE CLASS' : v.title || k} diff --git a/src/features/contribute/_components/hooks/schema.ts b/src/features/contribute/_components/hooks/schema.ts index 6beb8c33f..41016d5eb 100644 --- a/src/features/contribute/_components/hooks/schema.ts +++ b/src/features/contribute/_components/hooks/schema.ts @@ -10,7 +10,7 @@ import { isPlainObject, isAtom } from '../utils'; import { assertErrorMessage } from '@/util/utils'; export function useObioneJsonSchema( - circuitId: string, + notification: NotificationInstance, setSchema: React.Dispatch>, setAtomsMap: (atomsMap: AtomsMap) => void, @@ -67,13 +67,6 @@ export function useObioneJsonSchema( else initial[subkey] = subValue.default ?? null; }); - if (k === 'initialize') { - initial.circuit = { - type: 'CircuitFromID', - id_str: circuitId, - }; - } - map[k] = atom>(initial); } else map[k] = {}; }); From e2169e1f8e09a8b8c7283f767f89a1c1c0414466 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 14:26:05 +0200 Subject: [PATCH 04/44] more linting --- src/features/contribute/index.tsx | 59 ++++++++++++++++++++++++++----- 1 file changed, 50 insertions(+), 9 deletions(-) diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx index 88705b9cb..69d91ed3a 100755 --- a/src/features/contribute/index.tsx +++ b/src/features/contribute/index.tsx @@ -1,4 +1,3 @@ -// index.tsx 'use client'; import { @@ -9,7 +8,7 @@ import { } from '@ant-design/icons'; import Ajv, { AnySchema } from 'ajv'; import { atom } from 'jotai'; -import { Fragment, useMemo, useRef, useState } from 'react'; +import { Fragment, useMemo, useRef, useState, KeyboardEvent } from 'react'; import { Config, ConfigValue, JSONSchemaForm } from './_components/components'; import { useConfigAtom } from './_components/hooks/config-atom'; import { @@ -121,14 +120,15 @@ export default function ContributeMorphologyConfiguration({ !errors?.length && !loading && !readOnly && selectedFile && formValidation.isValid; // Show success page if upload was successful -if (isSuccess) { + if (isSuccess) { return (
-
+
✓ Morphology created successfully
- {CATEGORIES.filter((c) => c !== 'Assets').map((c) => { - return ( - -
{c}
- {schema.properties && - Object.entries(schema.properties) - .filter(([k]) => k !== 'type' && ORDERING[k]?.category === c) - .sort((a, b) => { - const order = (k: string) => ORDERING[k]?.order ?? 999; - return order(a[0]) - order(b[0]); - }) - .map(([k, v]) => { - return ( -
- ); - })} - - ); - })} + {CATEGORIES.filter((c) => c !== 'Assets').map((c) => ( + +
{c}
+ {schema.properties && + Object.entries(schema.properties) + .filter(([k]) => k !== 'type' && ORDERING[k]?.category === c) + .sort((a, b) => { + const order = (k: string) => ORDERING[k]?.order ?? 999; + return order(a[0]) - order(b[0]); + }) + .map(([k, v]) => ( +
+ ))} + + ))}
{!readOnly && ( @@ -464,10 +482,9 @@ export default function ContributeMorphologyConfiguration({ htmlFor="file-upload" className={classNames( 'flex cursor-pointer items-center justify-center rounded-full px-4 py-2 text-sm', - loading - ? 'bg-gray-300 text-gray-500' - : 'bg-primary-8 hover:bg-primary-9 text-white', - readOnly && 'cursor-not-allowed opacity-50' + loading || readOnly + ? 'bg-gray-300 text-gray-500 cursor-not-allowed opacity-50' + : 'bg-primary-8 hover:bg-primary-9 text-white' )} > @@ -503,70 +520,67 @@ export default function ContributeMorphologyConfiguration({ editing && configTab !== 'assets' && (
- {schema.properties[configTab].additionalProperties.anyOf.map((o) => { - return ( - -
{ - if (isRootCategory(schema, configTab)) return; - setSelectedCategory(o.properties?.type.const ?? ''); - const initial: Record = {}; - if (o.properties) - Object.entries(o.properties).forEach(([subkey, subValue]) => { - if (subkey === 'type') initial[subkey] = subValue.const ?? null; - else initial[subkey] = subValue.default ?? null; - }); - const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => - parseInt(subkey.split('_')[1], 10) - ); - itemIndexes.sort((a, b) => a - b); - const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; - setSelectedItemIdx(itemIdx); - setAtomsMap({ - ...atomsMap, - [configTab]: { - ...atomsMap[configTab], - [resolveKey(schema, configTab, itemIdx)]: - atom>(initial), - }, + {schema.properties[configTab].additionalProperties.anyOf.map((o) => ( +
{ + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) { + Object.entries(o.properties).forEach(([subkey, subValue]) => { + initial[subkey] = subkey === 'type' ? subValue.const ?? null : subValue.default ?? null; + }); + } + const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...atomsMap[configTab], + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + }); + }} + onKeyDown={(e: KeyboardEvent) => { + if (e.key === 'Enter' || e.key === ' ') { + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) { + Object.entries(o.properties).forEach(([subkey, subValue]) => { + initial[subkey] = subkey === 'type' ? subValue.const ?? null : subValue.default ?? null; }); - }} - onKeyDown={(e: KeyboardEvent) => { - if (e.key === 'Enter' || e.key === ' ') { - if (isRootCategory(schema, configTab)) return; - setSelectedCategory(o.properties?.type.const ?? ''); - const initial: Record = {}; - if (o.properties) - Object.entries(o.properties).forEach(([subkey, subValue]) => { - if (subkey === 'type') initial[subkey] = subValue.const ?? null; - else initial[subkey] = subValue.default ?? null; - }); - const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => - parseInt(subkey.split('_')[1], 10) - ); - itemIndexes.sort((a, b) => a - b); - const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; - setSelectedItemIdx(itemIdx); - setAtomsMap({ - ...atomsMap, - [configTab]: { - ...atomsMap[configTab], - [resolveKey(schema, configTab, itemIdx)]: - atom>(initial), - }, - }); - } - }} - > -
{o.title}
-
{o.description}
-
- - ); - })} + } + const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...atomsMap[configTab], + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + }); + } + }} + > +
{o.title}
+
{o.description}
+
+ ))}
)} {schema.properties && From fe55d22ea44b5a26b2d80f586cca02421713b940 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 14:50:03 +0200 Subject: [PATCH 06/44] more linting --- .../contribute/_components/components.tsx | 116 ++++++++++-------- 1 file changed, 67 insertions(+), 49 deletions(-) diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx index 793b4b2da..62e7f5802 100644 --- a/src/features/contribute/_components/components.tsx +++ b/src/features/contribute/_components/components.tsx @@ -1,4 +1,3 @@ -// components.tsx import { useEffect, useState, useRef } from 'react'; import { atom, useAtom } from 'jotai'; import { InputNumber, Input, Select, Button } from 'antd'; @@ -28,7 +27,7 @@ const MTYPE_CLASSES = [ {"mtype_pref_label":"L23_NGC","mtype_id":"dd16dca0-e567-416b-b8b7-f8fbcaa05af0"}, {"mtype_pref_label":"L23_PC","mtype_id":"0791edc9-7ad4-4a94-a4a5-feab9b690d7e"}, {"mtype_pref_label":"L23_PTPC","mtype_id":"52ea242f-6591-425a-8eae-962fa0b4dfe0"}, - {"mtype_pref_label":"L23_SBC","mtype_id":"fbb8b577-92f4-4c93-b355-0982ef5a3c7c"}, + {"mtype_pref_label":"L23_SBC","mtype_id":"fbb8b577-92f4-4c93-b355-0982af5a3c7c"}, {"mtype_pref_label":"L23_STPC","mtype_id":"93be8237-9861-4870-9977-ff1cf9e7462c"}, {"mtype_pref_label":"L2_ChC","mtype_id":"91ba3deb-1139-4bc6-a12f-6a64a0ed0e92"}, {"mtype_pref_label":"L2_IPC","mtype_id":"e55f12e1-807c-42f6-ba98-91d6d30c57d7"}, @@ -266,17 +265,16 @@ export function JSONSchemaForm({ const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; - // Common input props for consistency - const commonInputProps = { - disabled, - className: `w-full ${hasError ? 'border-red-500' : ''}`, - onBlur: () => markFieldTouched(k), - }; - if (isBrainRegionIdField && nodeId) { return (
- + markFieldTouched(k)} + value={nodeId} + readOnly + />
); } @@ -285,9 +283,10 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value="b7ad4cca-4ac2-4095-9781-37fb68fe9ca1" - className="w-full bg-gray-100" readOnly />
@@ -298,9 +297,10 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value="e3e70682-c209-4cac-a29f-6fbed82c07cd" - className="w-full bg-gray-100" readOnly />
@@ -342,7 +342,8 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value={currentValue} className={`w-full ${hasError || showDateError ? 'border-red-500' : ''}`} onChange={(e) => { @@ -400,7 +401,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} onChange={(newV) => { setState({ ...state, [k]: newV }); markFieldTouched(k); @@ -438,7 +443,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { setState({ ...state, [k]: e.currentTarget.value }); @@ -456,14 +463,14 @@ export function JSONSchemaForm({
{Array.isArray(state[k]) && - state[k].map((e, i) => ( -
+ state[k].map((e) => ( +
{e}{' '} {!disabled && ( { const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; - newElements.splice(i, 1); + newElements.splice(newElements.indexOf(e), 1); setState({ ...state, [k]: newElements }); markFieldTouched(k); }} @@ -540,7 +547,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} onChange={(newV) => { setState({ ...state, [k]: newV }); markFieldTouched(k); @@ -614,7 +625,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} onChange={(newV) => { setState({ ...state, [k]: newV }); markFieldTouched(k); @@ -782,7 +797,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { setState({ ...state, [k]: e.currentTarget.value }); @@ -796,7 +813,9 @@ export function JSONSchemaForm({ return (
markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { setState({ ...state, [k]: e.currentTarget.value }); @@ -807,6 +826,21 @@ export function JSONSchemaForm({
); } + + function getFieldTitle(k: string, v: JSONSchema, normalizedKey: string): string { + if (normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain') { + return 'STRAIN'; + } else if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') { + return 'AGE PERIOD'; + } else if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') { + return 'LICENSE'; + } else if (normalizedKey === 'mtypeclassid') { + return 'MTYPE CLASS'; + } else { + return v.title || k; + } + } + return (
@@ -820,7 +854,7 @@ export function JSONSchemaForm({ Please fix the following required fields:
    - {validationErrors.map((error, index) => ( + {validationErrors.map((error) => (
  • {error}
    • ))}
@@ -836,15 +870,7 @@ export function JSONSchemaForm({ .map(([k, v]) => { const isRequired = schema.required?.includes(k); const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - const isStrainIdField = - normalizedKey === 'strainid' || - normalizedKey === 'strain_id' || - normalizedKey === 'strain'; - const isAgePeriodField = - normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; - const isLicenseIdField = - normalizedKey === 'licenseid' || normalizedKey === 'license_id'; - const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; + const fieldTitle = getFieldTitle(k, v, normalizedKey); return (
@@ -856,15 +882,7 @@ export function JSONSchemaForm({ )} title={v.description} > - {isStrainIdField - ? 'STRAIN' - : isAgePeriodField - ? 'AGE PERIOD' - : isLicenseIdField - ? 'LICENSE' - : isMtypeClassIdField - ? 'MTYPE CLASS' - : v.title || k} + {fieldTitle} {isRequired && *}
{v.units &&
{v.units}
} From 1f511e3579d6303d0147ee8b965229c99e7ad582 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 14:54:21 +0200 Subject: [PATCH 07/44] more linting --- src/features/contribute/index.tsx | 53 ++++++++++++++++--------------- 1 file changed, 28 insertions(+), 25 deletions(-) diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx index 10d63382d..60c03a4dd 100755 --- a/src/features/contribute/index.tsx +++ b/src/features/contribute/index.tsx @@ -311,32 +311,35 @@ export default function ContributeMorphologyConfiguration({ const subjectId = subjectResponseData.id; // --- END: New pre-flight API call --- - const newJson = { - authorized_public: false, - license_id: null, - name: morphologyConfig.name || 'test', - description: morphologyConfig.description || 'string', - location: { - x: 0, - y: 0, - z: 0, - }, - legacy_id: Array.isArray(morphologyConfig.legacy_id) - ? morphologyConfig.legacy_id - : typeof morphologyConfig.legacy_id === 'string' - ? [morphologyConfig.legacy_id] - : [], - species_id: - morphologyConfig.species_id || - morphologyConfig.species || - 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', - strain_id: morphologyConfig.strain_id || null, - brain_region_id: - morphologyConfig.brain_region_id || morphologyConfig.brain_region || node.id, - subject_id: subjectId, - }; - setNewJsonPayload(newJson); + const legacyId = Array.isArray(morphologyConfig.legacy_id) + ? morphologyConfig.legacy_id + : typeof morphologyConfig.legacy_id === 'string' + ? [morphologyConfig.legacy_id] + : []; + + const newJson = { + authorized_public: false, + license_id: null, + name: morphologyConfig.name || 'test', + description: morphologyConfig.description || 'string', + location: { + x: 0, + y: 0, + z: 0, + }, + legacy_id: legacyId, + species_id: + morphologyConfig.species_id || + morphologyConfig.species || + 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', + strain_id: morphologyConfig.strain_id || null, + brain_region_id: + morphologyConfig.brain_region_id || morphologyConfig.brain_region || node.id, + subject_id: subjectId, +}; + + setNewJsonPayload(newJson); const headers = { accept: 'application/json', From 68ed8311c61165986a86d654277d894d172df2c1 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 16:20:17 +0200 Subject: [PATCH 08/44] more linting --- src/features/contribute/index.tsx | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx index 60c03a4dd..f29c316c3 100755 --- a/src/features/contribute/index.tsx +++ b/src/features/contribute/index.tsx @@ -312,11 +312,15 @@ export default function ContributeMorphologyConfiguration({ // --- END: New pre-flight API call --- - const legacyId = Array.isArray(morphologyConfig.legacy_id) - ? morphologyConfig.legacy_id - : typeof morphologyConfig.legacy_id === 'string' - ? [morphologyConfig.legacy_id] - : []; + let legacyId; + +if (Array.isArray(morphologyConfig.legacy_id)) { + legacyId = morphologyConfig.legacy_id; +} else if (typeof morphologyConfig.legacy_id === 'string') { + legacyId = [morphologyConfig.legacy_id]; +} else { + legacyId = []; +} const newJson = { authorized_public: false, From df59fa732be27822f86126b33f70b4b69628de69 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 16:45:30 +0200 Subject: [PATCH 09/44] more linting --- .../explore/interactive/add/layout.tsx | 1 - .../interactive-navigation-menu.tsx | 2 - .../ContributeLayout/index.tsx | 2 +- src/features/cell-composition/how-to.md | 4 - .../contribute/_components/components.tsx | 104 +++++++++--------- .../contribute/_components/hooks/schema.ts | 1 - src/features/contribute/index.tsx | 103 ++++++++--------- .../build/me-model/configure.tsx | 8 +- 8 files changed, 107 insertions(+), 118 deletions(-) diff --git a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx index 813531a61..fdbc79a4d 100755 --- a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx +++ b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/layout.tsx @@ -2,6 +2,5 @@ import { ReactNode } from 'react'; import ContributeLayout from '@/components/explore-section/ContributeLayout'; export default function ContributeDataLayout({ children }: { children: ReactNode }) { - return {children}; } diff --git a/src/components/entities-type-stats/interactive-navigation-menu.tsx b/src/components/entities-type-stats/interactive-navigation-menu.tsx index 3e46a88cb..bcbf5438a 100644 --- a/src/components/entities-type-stats/interactive-navigation-menu.tsx +++ b/src/components/entities-type-stats/interactive-navigation-menu.tsx @@ -61,8 +61,6 @@ function EntityTypeStats(props: StatsPanelProps) { .with('experimental-data', () => ( <> {Object.entries(ExperimentalEntitiesTileTypes).map(([key, value], index) => { - - const baseHref = `${pathName}/${value?.explore.basePrefix}/${value.slug}`; let records = ''; let isError = false; diff --git a/src/components/explore-section/ContributeLayout/index.tsx b/src/components/explore-section/ContributeLayout/index.tsx index 054a58896..55bceb0f1 100755 --- a/src/components/explore-section/ContributeLayout/index.tsx +++ b/src/components/explore-section/ContributeLayout/index.tsx @@ -10,7 +10,7 @@ import BackToInteractiveExplorationBtn from '@/components/explore-section/BackTo export default function ContributeLayout({ children }: { children: ReactNode }) { const pathname = usePathname(); - + // Determine the href for the back button. // Goal: If current is /virtual-lab/explore/interactive/add/experimental/morphology // It should go back to /virtual-lab/explore/interactive diff --git a/src/features/cell-composition/how-to.md b/src/features/cell-composition/how-to.md index bcbb3c3a0..e84bf62e4 100644 --- a/src/features/cell-composition/how-to.md +++ b/src/features/cell-composition/how-to.md @@ -26,27 +26,23 @@ flowchart TD ## How to process: 1. **Initialization** - - start with a brain region id (selected by the user) - retrieve all leaf regions under that brain region (use `brainRegionHierarchyAtom`) - create volume maps for each leaf region (using `brainRegionAtlasAtom`) 2. **Node Construction** - - for each leaf region: - process mTypes and their child eTypes - build tree nodes with cell counts and densities - calculate composition data based on volumes 3. **Node Aggregation** - - merge nodes that represent the same mType/eType across different leaf regions - sum cell counts across regions - recalculate densities based on aggregated volumes - create links between parent mTypes and child eTypes 4. **Final Calculations** - - calculate total neuron and glial cell counts - determine total volume (not needed for now) - compute the whole composition densities diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx index 62e7f5802..c731cca78 100644 --- a/src/features/contribute/_components/components.tsx +++ b/src/features/contribute/_components/components.tsx @@ -2,7 +2,7 @@ import { useEffect, useState, useRef } from 'react'; import { atom, useAtom } from 'jotai'; import { InputNumber, Input, Select, Button } from 'antd'; import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; -import { isNil } from 'lodash'; +import isNil from 'lodash/isNil'; import { JSONSchema } from '../types'; import { isPlainObject } from './utils'; @@ -23,40 +23,40 @@ export type Config = Record; // Updated structure for MTYPE classification const MTYPE_CLASSES = [ - {"mtype_pref_label":"L23_NBC","mtype_id":"6605787b-ba14-43fd-a954-de9cff4b15a0"}, - {"mtype_pref_label":"L23_NGC","mtype_id":"dd16dca0-e567-416b-b8b7-f8fbcaa05af0"}, - {"mtype_pref_label":"L23_PC","mtype_id":"0791edc9-7ad4-4a94-a4a5-feab9b690d7e"}, - {"mtype_pref_label":"L23_PTPC","mtype_id":"52ea242f-6591-425a-8eae-962fa0b4dfe0"}, - {"mtype_pref_label":"L23_SBC","mtype_id":"fbb8b577-92f4-4c93-b355-0982af5a3c7c"}, - {"mtype_pref_label":"L23_STPC","mtype_id":"93be8237-9861-4870-9977-ff1cf9e7462c"}, - {"mtype_pref_label":"L2_ChC","mtype_id":"91ba3deb-1139-4bc6-a12f-6a64a0ed0e92"}, - {"mtype_pref_label":"L2_IPC","mtype_id":"e55f12e1-807c-42f6-ba98-91d6d30c57d7"}, - {"mtype_pref_label":"L2_MC","mtype_id":"ea51f2c8-95fc-4940-a400-c37a3ff2d9eb"}, - {"mtype_pref_label":"L2_PC","mtype_id":"dd73956b-423e-42c5-87d9-9e2cc84356b9"}, - {"mtype_pref_label":"L2_TPC","mtype_id":"7abf03d5-30b0-41ae-a02b-1f4e26c243a8"}, - {"mtype_pref_label":"L2_TPC:A","mtype_id":"9b04acb1-4737-4088-8d22-0658414bdda1"}, - {"mtype_pref_label":"L2_TPC:B","mtype_id":"4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda"}, - {"mtype_pref_label":"L3_MC","mtype_id":"52578494-b41c-499b-9717-5d11f4b2f068"}, - {"mtype_pref_label":"L3_PC","mtype_id":"87fec7dd-7a2f-400a-aee0-94d1946cf1ab"}, - {"mtype_pref_label":"L3_TPC","mtype_id":"229c31f1-a6ec-4d8c-85d3-d8175ffde109"}, - {"mtype_pref_label":"L3_TPC:A","mtype_id":"dd346e90-7bca-4976-bf9a-303b6a94b339"}, - {"mtype_pref_label":"L3_TPC:B","mtype_id":"a71d226c-2c56-40ee-a4be-9726fc430932"}, - {"mtype_pref_label":"L3_TPC:C","mtype_id":"d9b7bd4d-cec9-4fec-a448-79320de89f2a"}, - {"mtype_pref_label":"L4_BP","mtype_id":"a55f6ce7-068a-4c5e-a883-de5f4304612e"}, - {"mtype_pref_label":"L4_BTC","mtype_id":"8315d249-6678-4d55-b581-3b6f9eb48e86"}, - {"mtype_pref_label":"L4_ChC","mtype_id":"0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6"}, - {"mtype_pref_label":"L4_DBC","mtype_id":"8de61c06-31e8-4483-bd98-608bc874b369"}, - {"mtype_pref_label":"L4_LBC","mtype_id":"bb875a91-4ae5-4f6f-b050-5ad952e9cd6c"}, - {"mtype_pref_label":"L4_MC","mtype_id":"0bdf029e-a55a-444c-a7c9-9d0ff51239a5"}, - {"mtype_pref_label":"L4_NBC","mtype_id":"72673af9-2f2b-4a9a-95dc-552777ab63b9"}, - {"mtype_pref_label":"L4_NGC","mtype_id":"41f41550-5e0e-4de7-b52d-62110c338a27"}, - {"mtype_pref_label":"L4_PC","mtype_id":"ad5769c6-7e86-4433-8f34-9efcb4f0d182"}, - {"mtype_pref_label":"L4_SBC","mtype_id":"43a7d86b-71c5-4a10-be62-ef6cf95ca694"}, - {"mtype_pref_label":"L4_SSC","mtype_id":"400a55f7-e162-4fd1-80a0-4f2facea7cec"}, - {"mtype_pref_label":"L4_TPC","mtype_id":"02e13718-5227-4c28-b838-04dd0c2c67f2"}, - {"mtype_pref_label":"L4_UPC","mtype_id":"2ef7e0b5-39e4-441b-a72a-c7186afa7f5c"}, - {"mtype_pref_label":"L56_PC","mtype_id":"629d6d6f-93f9-43d8-8a99-277740fd8f22"}, - {"mtype_pref_label":"L5_BP","mtype_id":"7b16c860-ae76-4ddf-b093-4e28620b3712"} + { mtype_pref_label: 'L23_NBC', mtype_id: '6605787b-ba14-43fd-a954-de9cff4b15a0' }, + { mtype_pref_label: 'L23_NGC', mtype_id: 'dd16dca0-e567-416b-b8b7-f8fbcaa05af0' }, + { mtype_pref_label: 'L23_PC', mtype_id: '0791edc9-7ad4-4a94-a4a5-feab9b690d7e' }, + { mtype_pref_label: 'L23_PTPC', mtype_id: '52ea242f-6591-425a-8eae-962fa0b4dfe0' }, + { mtype_pref_label: 'L23_SBC', mtype_id: 'fbb8b577-92f4-4c93-b355-0982af5a3c7c' }, + { mtype_pref_label: 'L23_STPC', mtype_id: '93be8237-9861-4870-9977-ff1cf9e7462c' }, + { mtype_pref_label: 'L2_ChC', mtype_id: '91ba3deb-1139-4bc6-a12f-6a64a0ed0e92' }, + { mtype_pref_label: 'L2_IPC', mtype_id: 'e55f12e1-807c-42f6-ba98-91d6d30c57d7' }, + { mtype_pref_label: 'L2_MC', mtype_id: 'ea51f2c8-95fc-4940-a400-c37a3ff2d9eb' }, + { mtype_pref_label: 'L2_PC', mtype_id: 'dd73956b-423e-42c5-87d9-9e2cc84356b9' }, + { mtype_pref_label: 'L2_TPC', mtype_id: '7abf03d5-30b0-41ae-a02b-1f4e26c243a8' }, + { mtype_pref_label: 'L2_TPC:A', mtype_id: '9b04acb1-4737-4088-8d22-0658414bdda1' }, + { mtype_pref_label: 'L2_TPC:B', mtype_id: '4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda' }, + { mtype_pref_label: 'L3_MC', mtype_id: '52578494-b41c-499b-9717-5d11f4b2f068' }, + { mtype_pref_label: 'L3_PC', mtype_id: '87fec7dd-7a2f-400a-aee0-94d1946cf1ab' }, + { mtype_pref_label: 'L3_TPC', mtype_id: '229c31f1-a6ec-4d8c-85d3-d8175ffde109' }, + { mtype_pref_label: 'L3_TPC:A', mtype_id: 'dd346e90-7bca-4976-bf9a-303b6a94b339' }, + { mtype_pref_label: 'L3_TPC:B', mtype_id: 'a71d226c-2c56-40ee-a4be-9726fc430932' }, + { mtype_pref_label: 'L3_TPC:C', mtype_id: 'd9b7bd4d-cec9-4fec-a448-79320de89f2a' }, + { mtype_pref_label: 'L4_BP', mtype_id: 'a55f6ce7-068a-4c5e-a883-de5f4304612e' }, + { mtype_pref_label: 'L4_BTC', mtype_id: '8315d249-6678-4d55-b581-3b6f9eb48e86' }, + { mtype_pref_label: 'L4_ChC', mtype_id: '0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6' }, + { mtype_pref_label: 'L4_DBC', mtype_id: '8de61c06-31e8-4483-bd98-608bc874b369' }, + { mtype_pref_label: 'L4_LBC', mtype_id: 'bb875a91-4ae5-4f6f-b050-5ad952e9cd6c' }, + { mtype_pref_label: 'L4_MC', mtype_id: '0bdf029e-a55a-444c-a7c9-9d0ff51239a5' }, + { mtype_pref_label: 'L4_NBC', mtype_id: '72673af9-2f2b-4a9a-95dc-552777ab63b9' }, + { mtype_pref_label: 'L4_NGC', mtype_id: '41f41550-5e0e-4de7-b52d-62110c338a27' }, + { mtype_pref_label: 'L4_PC', mtype_id: 'ad5769c6-7e86-4433-8f34-9efcb4f0d182' }, + { mtype_pref_label: 'L4_SBC', mtype_id: '43a7d86b-71c5-4a10-be62-ef6cf95ca694' }, + { mtype_pref_label: 'L4_SSC', mtype_id: '400a55f7-e162-4fd1-80a0-4f2facea7cec' }, + { mtype_pref_label: 'L4_TPC', mtype_id: '02e13718-5227-4c28-b838-04dd0c2c67f2' }, + { mtype_pref_label: 'L4_UPC', mtype_id: '2ef7e0b5-39e4-441b-a72a-c7186afa7f5c' }, + { mtype_pref_label: 'L56_PC', mtype_id: '629d6d6f-93f9-43d8-8a99-277740fd8f22' }, + { mtype_pref_label: 'L5_BP', mtype_id: '7b16c860-ae76-4ddf-b093-4e28620b3712' }, ]; // Helper function to check if a field value is considered "empty" or invalid @@ -562,18 +562,18 @@ export function JSONSchemaForm({
); } - + // New condition for 'mtype class id' if (isMtypeClassIdField) { const options = MTYPE_CLASSES.map((mtype) => ({ label: mtype.mtype_pref_label, value: mtype.mtype_id, })); - + const currentMtypeLabel = MTYPE_CLASSES.find( (mtype) => mtype.mtype_id === state[k] )?.mtype_pref_label; - + return (
{fieldError &&
{fieldError}
}
- ); + ) } const strainOptions = Object.entries(selectedSpecies.strains).map(([name, id]) => ({ label: name, value: id, - })); + })) return (
@@ -405,8 +403,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState((prev) => ({ ...prev, [k]: newV })); - markFieldTouched(k); + setState((prev) => ({ ...prev, [k]: newV })) + markFieldTouched(k) }} value={state[k]} options={strainOptions} @@ -414,7 +412,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } if (isAgePeriodField) { @@ -426,8 +424,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); + setState({ ...state, [k]: newV }) + markFieldTouched(k) }} value={state[k]} options={obj.enum.map((subv: string) => ({ @@ -438,7 +436,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } return (
@@ -448,13 +446,13 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); + setState({ ...state, [k]: e.currentTarget.value }) }} placeholder="Enter age period" /> {fieldError &&
{fieldError}
}
- ); + ) } if (isLegacyIdField) { @@ -469,10 +467,10 @@ export function JSONSchemaForm({ {!disabled && ( { - const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; - newElements.splice(newElements.indexOf(e), 1); - setState({ ...state, [k]: newElements }); - markFieldTouched(k); + const newElements = [...(Array.isArray(state[k]) ? state[k] : [])] + newElements.splice(newElements.indexOf(e), 1) + setState({ ...state, [k]: newElements }) + markFieldTouched(k) }} /> )} @@ -499,17 +497,17 @@ export function JSONSchemaForm({ setState({ ...state, [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], - }); - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - markFieldTouched(k); + }) + setAddingElement({ ...addingElement, [k]: false }) + setNewElement({ ...newElement, [k]: null }) + markFieldTouched(k) }} /> )} { - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); + setAddingElement({ ...addingElement, [k]: false }) + setNewElement({ ...newElement, [k]: null }) }} className="text-primary-8" /> @@ -518,7 +516,7 @@ export function JSONSchemaForm({
{fieldError &&
{fieldError}
}
- ); + ) } // New condition for 'license id' field @@ -532,17 +530,17 @@ export function JSONSchemaForm({ 'CC BY 4.0 Deed': 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', 'CC0 1.0 Deed': '74b8c953-67f5-4e95-ac58-095274901328', 'NGV_Data Licence_v1.0': '0c39107e-3b68-4f1f-904a-5c7f1b4f89c5', - }; + } const options = Object.entries(licenseOptions).map(([name, id]) => ({ label: name, value: id, - })); + })) // Find the key corresponding to the current state value to set the label const currentLicenseLabel = Object.keys(licenseOptions).find( - (key) => licenseOptions[key] === state[k] - ); + (key) => licenseOptions[key] === state[k], + ) return (
@@ -551,8 +549,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); + setState({ ...state, [k]: newV }) + markFieldTouched(k) }} value={currentLicenseLabel || state[k]} // Use the label for display, or the value if not found options={options} @@ -560,7 +558,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } // New condition for 'mtype class id' @@ -568,11 +566,11 @@ export function JSONSchemaForm({ const options = MTYPE_CLASSES.map((mtype) => ({ label: mtype.mtype_pref_label, value: mtype.mtype_id, - })); + })) const currentMtypeLabel = MTYPE_CLASSES.find( - (mtype) => mtype.mtype_id === state[k] - )?.mtype_pref_label; + (mtype) => mtype.mtype_id === state[k], + )?.mtype_pref_label return (
@@ -581,8 +579,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); + setState({ ...state, [k]: newV }) + markFieldTouched(k) }} value={currentMtypeLabel || state[k]} options={options} @@ -590,21 +588,21 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } - if (k === 'circuit' && circuit) return ; + if (k === 'circuit' && circuit) return if (v.is_block_reference && v.properties && typeof v.properties.type.const === 'string') { - const referenceKey = referenceTypesToConfigKeys[v.properties.type.const]; - const referenceTitle = referenceTypesToTitles[v.properties.type.const]; - if (!referenceKey) return null; - const referenceConfig = config[referenceKey]; - if (!isPlainObject(referenceConfig)) return null; + const referenceKey = referenceTypesToConfigKeys[v.properties.type.const] + const referenceTitle = referenceTypesToTitles[v.properties.type.const] + if (!referenceKey) return null + const referenceConfig = config[referenceKey] + if (!isPlainObject(referenceConfig)) return null const referees = Object.entries(referenceConfig).filter(([, val]) => { - return isPlainObject(val); - }); + return isPlainObject(val) + }) if (referees.length === 0) { return ( @@ -614,13 +612,13 @@ export function JSONSchemaForm({ {fieldError &&
{fieldError}
}
- ); + ) } const defaultV = isPlainObject(state[k]) && typeof state[k].block_name === 'string' ? state[k].block_name - : null; + : null return (
@@ -630,7 +628,7 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} onChange={(newV: string) => { if (!v.properties?.type.const || typeof v.properties.type.const !== 'string') - throw new Error('Invalid reference definition'); + throw new Error('Invalid reference definition') setState({ ...state, @@ -639,8 +637,8 @@ export function JSONSchemaForm({ type: v.properties.type.const, block_dict_name: referenceKey, }, - }); - markFieldTouched(k); + }) + markFieldTouched(k) }} value={defaultV} options={referees.map(([subkey]) => ({ @@ -650,7 +648,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } if (k === 'neuron_ids') { @@ -666,16 +664,16 @@ export function JSONSchemaForm({ {!disabled && ( { - if (!isPlainObject(state[k]) || !Array.isArray(state[k].elements)) return; + if (!isPlainObject(state[k]) || !Array.isArray(state[k].elements)) return if (state[k].elements.length === 1) { - setState({ ...state, [k]: null }); - markFieldTouched(k); - return; + setState({ ...state, [k]: null }) + markFieldTouched(k) + return } - const newElements = [...state[k].elements]; - newElements.splice(newElements.indexOf(e), 1); + const newElements = [...state[k].elements] + newElements.splice(newElements.indexOf(e), 1) setState({ ...state, [k]: { @@ -683,8 +681,8 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: newElements, }, - }); - markFieldTouched(k); + }) + markFieldTouched(k) }} /> )} @@ -704,7 +702,7 @@ export function JSONSchemaForm({ step={1} min={0} onChange={(newV) => { - setNewElement({ ...newElement, [k]: newV }); + setNewElement({ ...newElement, [k]: newV }) }} /> {!isNil(newElement[k]) && ( @@ -719,7 +717,7 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: [newElement[k]], }, - }); + }) } else if (isPlainObject(state[k]) && Array.isArray(state[k].elements)) { setState({ ...state, @@ -728,18 +726,18 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: [...state[k].elements, newElement[k]], }, - }); + }) } - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - markFieldTouched(k); + setAddingElement({ ...addingElement, [k]: false }) + setNewElement({ ...newElement, [k]: null }) + markFieldTouched(k) }} /> )} { - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); + setAddingElement({ ...addingElement, [k]: false }) + setNewElement({ ...newElement, [k]: null }) }} className="text-primary-8" /> @@ -748,7 +746,7 @@ export function JSONSchemaForm({
{fieldError &&
{fieldError}
}
- ); + ) } if (obj.enum) { @@ -759,8 +757,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); + setState({ ...state, [k]: newV }) + markFieldTouched(k) }} value={state[k]} options={obj.enum.map((subv: string) => ({ @@ -771,7 +769,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ); + ) } if (obj.type === 'number' || obj.type === 'integer') { @@ -783,14 +781,14 @@ export function JSONSchemaForm({ disabled={disabled} value={typeof state[k] === 'number' ? state[k] : null} onChange={(value) => { - setState({ ...state, [k]: value }); + setState({ ...state, [k]: value }) }} onBlur={() => markFieldTouched(k)} className={`w-full ${hasError ? 'border-red-500' : ''}`} /> {fieldError &&
{fieldError}
}
- ); + ) } if (obj.type === 'string') { @@ -802,12 +800,12 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); + setState({ ...state, [k]: e.currentTarget.value }) }} /> {fieldError &&
{fieldError}
}
- ); + ) } return ( @@ -818,22 +816,22 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); + setState({ ...state, [k]: e.currentTarget.value }) }} placeholder={`Enter value for ${v.title || k}`} /> {fieldError &&
{fieldError}
}
- ); + ) } function getFieldTitle(k: string, v: JSONSchema, normalizedKey: string): string { if (normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain') - return 'STRAIN'; - if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD'; - if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE'; - if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS'; - return v.title || k; + return 'STRAIN' + if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD' + if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE' + if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS' + return v.title || k } return ( @@ -859,12 +857,12 @@ export function JSONSchemaForm({ {schema.properties && Object.entries(schema.properties) .filter(([k]) => { - return !skip.includes(k); + return !skip.includes(k) }) .map(([k, v]) => { - const isRequired = schema.required?.includes(k); - const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - const fieldTitle = getFieldTitle(k, v, normalizedKey); + const isRequired = schema.required?.includes(k) + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, '') + const fieldTitle = getFieldTitle(k, v, normalizedKey) return (
@@ -872,7 +870,7 @@ export function JSONSchemaForm({
@@ -883,11 +881,11 @@ export function JSONSchemaForm({
{renderInput(k, v)}
- ); + ) })}
- ); + ) } export function Tab({ @@ -899,13 +897,13 @@ export function Tab({ extraClass, disabled, }: { - tab: string; - selectedTab: string; - onClick?: () => void; - rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full'; - children?: React.ReactNode; - extraClass?: string; - disabled?: boolean; + tab: string + selectedTab: string + onClick?: () => void + rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full' + children?: React.ReactNode + extraClass?: string + disabled?: boolean }) { return ( - ); + ) } export function Chevron({ rotate }: { rotate?: number }) { @@ -945,5 +943,5 @@ export function Chevron({ rotate }: { rotate?: number }) { strokeLinejoin="round" /> - ); + ) } diff --git a/src/page-wrappers/build/me-model/configure.tsx b/src/page-wrappers/build/me-model/configure.tsx index 12a9631f1..7ffb859cd 100644 --- a/src/page-wrappers/build/me-model/configure.tsx +++ b/src/page-wrappers/build/me-model/configure.tsx @@ -1,56 +1,56 @@ -'use client'; +'use client' -import { App, Button } from 'antd'; -import { useAtomValue, useSetAtom } from 'jotai'; -import get from 'lodash/get'; -import omit from 'lodash/omit'; -import { useRouter } from 'next/navigation'; -import { useTransition } from 'react'; -import z from 'zod'; +import { App, Button } from 'antd' +import { useAtomValue, useSetAtom } from 'jotai' +import get from 'lodash/get' +import omit from 'lodash/omit' +import { useRouter } from 'next/navigation' +import { useTransition } from 'react' +import z from 'zod' -import EModelOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/emodel-overview-card'; -import MorphologyOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/morphology-overview-card'; +import EModelOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/emodel-overview-card' +import MorphologyOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/morphology-overview-card' // import CustomButton from '@/components/buttons/custom-btn'; -import { createMEModel } from '@/api/entitycore/queries'; -import { CreateMEModelSchema, ValidationStatus } from '@/api/entitycore/types/entities/me-model'; -import { tryCatch } from '@/api/utils'; -import { DataType } from '@/constants/explore-section/list-views'; -import { renderArray, renderEmptyOrValue } from '@/entity-configuration/definitions/renderer'; -import { MEmodel } from '@/entity-configuration/domain/model/me-model'; -import { activityAtomFamily } from '@/features/activity-view/context'; -import { useBuildMeModelSessionState } from '@/features/entities/me-model/build/create.state-session'; -import { messages } from '@/i18n/en/me-model'; -import { OneshotSession } from '@/services/accounting'; -import { useEntitiesCountAtom } from '@/services/entitycore/entities-count'; -import { runSingleNeuronAnalysis } from '@/services/small-scale-simulator'; -import { useRefreshDataAtom } from '@/state/explore-section/list-view-atoms'; -import { virtualLabProjectUsersAtomFamily } from '@/state/virtual-lab/projects'; -import { ServiceSubtype } from '@/types/accounting'; -import { WorkspaceContextSchema } from '@/types/common'; -import { classNames } from '@/util/utils'; -import { resolveDataKey } from '@/utils/key-builder'; -import { resolveExploreDetailsPageUrl } from '@/utils/url-builder'; +import { createMEModel } from '@/api/entitycore/queries' +import { CreateMEModelSchema, ValidationStatus } from '@/api/entitycore/types/entities/me-model' +import { tryCatch } from '@/api/utils' +import { DataType } from '@/constants/explore-section/list-views' +import { renderArray, renderEmptyOrValue } from '@/entity-configuration/definitions/renderer' +import { MEmodel } from '@/entity-configuration/domain/model/me-model' +import { activityAtomFamily } from '@/features/activity-view/context' +import { useBuildMeModelSessionState } from '@/features/entities/me-model/build/create.state-session' +import { messages } from '@/i18n/en/me-model' +import { OneshotSession } from '@/services/accounting' +import { useEntitiesCountAtom } from '@/services/entitycore/entities-count' +import { runSingleNeuronAnalysis } from '@/services/small-scale-simulator' +import { useRefreshDataAtom } from '@/state/explore-section/list-view-atoms' +import { virtualLabProjectUsersAtomFamily } from '@/state/virtual-lab/projects' +import { ServiceSubtype } from '@/types/accounting' +import { WorkspaceContextSchema } from '@/types/common' +import { classNames } from '@/util/utils' +import { resolveDataKey } from '@/utils/key-builder' +import { resolveExploreDetailsPageUrl } from '@/utils/url-builder' -import type { IMEModel } from '@/api/entitycore/types/entities/me-model'; -import type { WorkspaceContext } from '@/types/common'; +import type { IMEModel } from '@/api/entitycore/types/entities/me-model' +import type { WorkspaceContext } from '@/types/common' -const LOW_FUNDS_ERROR_CODE = 'INSUFFICIENT_FUNDS'; +const LOW_FUNDS_ERROR_CODE = 'INSUFFICIENT_FUNDS' -const CreateMeModelContextSchema = CreateMEModelSchema.merge(WorkspaceContextSchema); -type TCreateMeModelContext = z.infer; +const CreateMeModelContextSchema = CreateMEModelSchema.merge(WorkspaceContextSchema) +type TCreateMeModelContext = z.infer function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { stateId: string }) { const { sessionValue } = useBuildMeModelSessionState({ stateId, virtualLabId, projectId, - }); + }) const contributors = useAtomValue(virtualLabProjectUsersAtomFamily({ projectId, virtualLabId })) - ?.data?.users; - const { mmodel } = sessionValue; - const { emodel } = sessionValue; + ?.data?.users + const { mmodel } = sessionValue + const { emodel } = sessionValue const fields = [ { className: 'col-span-6', @@ -88,7 +88,7 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state title: 'e-type', value: renderEmptyOrValue(renderArray(emodel?.etypes?.map((m) => m.pref_label) || [])), }, - ]; + ] return (
@@ -99,17 +99,17 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state
))}
- ); + ) } type Props = { - ctx: WorkspaceContext; + ctx: WorkspaceContext searchParams: { - s: string; - m: string; - e: string; - }; -}; + s: string + m: string + e: string + } +} function CustomButton({ loading, @@ -118,11 +118,11 @@ function CustomButton({ onClick, children, }: { - loading: boolean; - disable: boolean; - className?: string; - onClick?: () => void; - children?: React.ReactNode; + loading: boolean + disable: boolean + className?: string + onClick?: () => void + children?: React.ReactNode }) { return ( - ); + ) } export default function Configure({ ctx, searchParams }: Props) { - const { push: navigate } = useRouter(); - const { notification } = App.useApp(); - const [isPending, startTransition] = useTransition(); - const emodelId = get(searchParams, 'e', undefined); - const morphologyId = get(searchParams, 'm', undefined); - const stateId = get(searchParams, 's', undefined); + const { push: navigate } = useRouter() + const { notification } = App.useApp() + const [isPending, startTransition] = useTransition() + const emodelId = get(searchParams, 'e', undefined) + const morphologyId = get(searchParams, 'm', undefined) + const stateId = get(searchParams, 's', undefined) const exploreDataKey = resolveDataKey({ projectId: ctx.projectId, section: 'explore', entity: MEmodel, - }); + }) - const refreshEntityCountsToParent = useEntitiesCountAtom(); - const refreshDataAtom = useRefreshDataAtom(exploreDataKey); + const refreshEntityCountsToParent = useEntitiesCountAtom() + const refreshDataAtom = useRefreshDataAtom(exploreDataKey) const refreshActivityAtom = useSetAtom( activityAtomFamily({ key: resolveDataKey({ @@ -171,33 +171,33 @@ export default function Configure({ ctx, searchParams }: Props) { projectId: ctx.projectId, virtualLabId: ctx.virtualLabId, type: 'memodel', - }) - ); + }), + ) const { sessionValue } = useBuildMeModelSessionState({ stateId: stateId || '', virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, - }); + }) if (!stateId) { - navigate('./'); - return; + navigate('./') + return } const showErrorNotification = (error: any, type: 'validation' | 'http') => { - let message = messages.DefaultErrorMsg; + let message = messages.DefaultErrorMsg if (type === 'http') message = error?.cause?.error_code === LOW_FUNDS_ERROR_CODE ? messages.LowFundsError - : messages.DefaultErrorMsg; - else message = messages.ValidationError; + : messages.DefaultErrorMsg + else message = messages.ValidationError notification.error({ duration: 10, message, - }); - }; + }) + } const buildMeModel = async () => { const body: Partial = { @@ -211,26 +211,26 @@ export default function Configure({ ctx, searchParams }: Props) { brain_region_id: sessionValue.mmodel?.brain_region.id ?? sessionValue.brainRegion?.id, strain_id: sessionValue.mmodel?.strain?.id ?? null, validation_status: ValidationStatus.Initialized, - }; + } const { error: validationError, data: validationData } = - await CreateMeModelContextSchema.safeParseAsync(body); + await CreateMeModelContextSchema.safeParseAsync(body) if (validationError) { - showErrorNotification(validationError, 'validation'); - return { data: null, error: validationError, errorType: 'validation' as const }; + showErrorNotification(validationError, 'validation') + return { data: null, error: validationError, errorType: 'validation' as const } } const accountingSession = new OneshotSession({ subtype: ServiceSubtype.SingleCellBuild, virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, count: 1, - }); + }) const { data, error } = await tryCatch( accountingSession.useWith(() => createMEModel({ body: omit(validationData, ['virtualLabId', 'projectId']), context: ctx, - }) + }), ), undefined, { @@ -240,39 +240,39 @@ export default function Configure({ ctx, searchParams }: Props) { virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, }, - } - ); + }, + ) - return { data, error, errorType: 'http' as const }; - }; + return { data, error, errorType: 'http' as const } + } const onClick = async () => { startTransition(async () => { - const { data, error, errorType } = await buildMeModel(); + const { data, error, errorType } = await buildMeModel() if (error || !data) { - showErrorNotification(error, errorType); - return; + showErrorNotification(error, errorType) + return } try { - await runSingleNeuronAnalysis({ ctx, modelId: data.id }); + await runSingleNeuronAnalysis({ ctx, modelId: data.id }) } catch (runAnalysisError) { - const message = messages.RunAnalysisError; - notification.error({ message, duration: 20 }); + const message = messages.RunAnalysisError + notification.error({ message, duration: 20 }) } - refreshDataAtom(); - refreshActivityAtom(); - refreshEntityCountsToParent(data.brain_region.id); + refreshDataAtom() + refreshActivityAtom() + refreshEntityCountsToParent(data.brain_region.id) navigate( resolveExploreDetailsPageUrl({ ctx, dataType: DataType.CircuitMEModel, entityId: data.id, - }) - ); - }); - }; + }), + ) + }) + } const validateTrigger = sessionValue.emodel && sessionValue.mmodel && (
@@ -280,7 +280,7 @@ export default function Configure({ ctx, searchParams }: Props) { {isPending ? 'Creating ME-model' : 'Save'}
- ); + ) return ( <> @@ -307,5 +307,5 @@ export default function Configure({ ctx, searchParams }: Props) {
{validateTrigger} - ); + ) } From 9437077cc677ba439274714d16d1004fa16ae8bf Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 17:17:31 +0200 Subject: [PATCH 12/44] more linting --- .../contribute/_components/components.tsx | 458 +++++++++--------- .../build/me-model/configure.tsx | 194 ++++---- 2 files changed, 327 insertions(+), 325 deletions(-) diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx index 2413d293b..cbf36e002 100644 --- a/src/features/contribute/_components/components.tsx +++ b/src/features/contribute/_components/components.tsx @@ -1,25 +1,25 @@ -import { useEffect, useState, useRef } from 'react' -import { atom, useAtom } from 'jotai' -import { InputNumber, Input, Select, Button } from 'antd' -import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons' -import isNil from 'lodash/isNil' +import { useEffect, useState, useRef } from 'react'; +import { atom, useAtom } from 'jotai'; +import { InputNumber, Input, Select, Button } from 'antd'; +import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; +import isNil from 'lodash/isNil'; -import { JSONSchema } from '../types' -import { isPlainObject } from './utils' -import CircuitDetails from './circuit-details' -import Tooltip from './tooltip' +import { JSONSchema } from '../types'; +import { isPlainObject } from './utils'; +import CircuitDetails from './circuit-details'; +import Tooltip from './tooltip'; -import { ICircuit } from '@/api/entitycore/types/entities/circuit' -import { classNames } from '@/util/utils' +import { ICircuit } from '@/api/entitycore/types/entities/circuit'; +import { classNames } from '@/util/utils'; -type Primitive = null | boolean | number | string +type Primitive = null | boolean | number | string; interface Object { - [key: string]: Primitive | Primitive[] | Object + [key: string]: Primitive | Primitive[] | Object; } -export type ConfigValue = Primitive | Primitive[] | Object +export type ConfigValue = Primitive | Primitive[] | Object; -export type Config = Record +export type Config = Record; // Updated structure for MTYPE classification const MTYPE_CLASSES = [ @@ -57,35 +57,35 @@ const MTYPE_CLASSES = [ { mtype_pref_label: 'L4_UPC', mtype_id: '2ef7e0b5-39e4-441b-a72a-c7186afa7f5c' }, { mtype_pref_label: 'L56_PC', mtype_id: '629d6d6f-93f9-43d8-8a99-277740fd8f22' }, { mtype_pref_label: 'L5_BP', mtype_id: '7b16c860-ae76-4ddf-b093-4e28620b3712' }, -] +]; // Helper function to check if a field value is considered "empty" or invalid const isEmptyValue = (value: ConfigValue): boolean => { - if (isNil(value) || value === '') return true - if (Array.isArray(value) && value.length === 0) return true - if (typeof value === 'object' && value !== null && Object.keys(value).length === 0) return true - return false -} + if (isNil(value) || value === '') return true; + if (Array.isArray(value) && value.length === 0) return true; + if (typeof value === 'object' && value !== null && Object.keys(value).length === 0) return true; + return false; +}; // Helper function to validate required fields const getRequiredFieldErrors = ( state: Record, - schema: JSONSchema, + schema: JSONSchema ): string[] => { - const errors: string[] = [] - const requiredFields = schema.required || [] + const errors: string[] = []; + const requiredFields = schema.required || []; requiredFields.forEach((fieldName) => { - const value = state[fieldName] + const value = state[fieldName]; if (isEmptyValue(value)) { - const fieldSchema = schema.properties?.[fieldName] - const fieldTitle = fieldSchema?.title || fieldName - errors.push(`${fieldTitle} is required`) + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + errors.push(`${fieldTitle} is required`); } - }) + }); - return errors -} + return errors; +}; export function JSONSchemaForm({ disabled, @@ -98,170 +98,172 @@ export function JSONSchemaForm({ currentCategory, onValidationChange, }: { - disabled: boolean - config: Config - schema: JSONSchema - circuit: ICircuit | undefined | null - stateAtom: ReturnType> - onAddReferenceClick: (reference: string) => void - nodeId?: string - currentCategory?: string - onValidationChange?: (isValid: boolean, errors: string[]) => void + disabled: boolean; + config: Config; + schema: JSONSchema; + circuit: ICircuit | undefined | null; + stateAtom: ReturnType>; + onAddReferenceClick: (reference: string) => void; + nodeId?: string; + currentCategory?: string; + onValidationChange?: (isValid: boolean, errors: string[]) => void; }) { - const skip = ['type'] + const skip = ['type']; - const [state, setState] = useAtom(stateAtom) + const [state, setState] = useAtom(stateAtom); const [addingElement, setAddingElement] = useState<{ [key: string]: boolean }>({ legacy_id: true, - }) - const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}) - const [validationErrors, setValidationErrors] = useState([]) - const [touchedFields, setTouchedFields] = useState>(new Set()) + }); + const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}); + const [validationErrors, setValidationErrors] = useState([]); + const [touchedFields, setTouchedFields] = useState>(new Set()); const referenceTypesToConfigKeys: Record = { NeuronSetReference: 'neuron_sets', TimestampsReference: 'timestamps', - } + }; const referenceTypesToTitles: Record = { NeuronSetReference: 'Neuron Set', TimestampsReference: 'Timestamps', - } + }; // Callback ref to avoid dependency issues - const onValidationChangeRef = useRef(onValidationChange) + const onValidationChangeRef = useRef(onValidationChange); useEffect(() => { - onValidationChangeRef.current = onValidationChange - }) + onValidationChangeRef.current = onValidationChange; + }); // Validate form whenever state changes useEffect(() => { - const errors = getRequiredFieldErrors(state, schema) + const errors = getRequiredFieldErrors(state, schema); // Only update if errors actually changed setValidationErrors((prevErrors) => { const errorsChanged = prevErrors.length !== errors.length || - prevErrors.some((error, index) => error !== errors[index]) + prevErrors.some((error, index) => error !== errors[index]); if (errorsChanged && onValidationChangeRef.current) { - onValidationChangeRef.current(errors.length === 0, errors) + onValidationChangeRef.current(errors.length === 0, errors); } - return errorsChanged ? errors : prevErrors - }) - }, [state, schema]) + return errorsChanged ? errors : prevErrors; + }); + }, [state, schema]); useEffect(() => { - if (!schema.properties) return + if (!schema.properties) return; - const initial: Record = {} + const initial: Record = {}; Object.entries(schema.properties).forEach(([key, value]) => { - if (key === 'type') initial[key] = value.const ?? null - else if (key === 'legacy_id') initial[key] = [] - else if (key === 'strain_id') initial[key] = null + if (key === 'type') initial[key] = value.const ?? null; + else if (key === 'legacy_id') initial[key] = []; + else if (key === 'strain_id') initial[key] = null; else if (key === 'license_id') - initial[key] = 'c268a20e-b78a-4332-a5e1-38e26c4454b9' // Default to undefined UUID - else initial[key] = value.default ?? null - }) + initial[key] = 'c268a20e-b78a-4332-a5e1-38e26c4454b9'; // Default to undefined UUID + else initial[key] = value.default ?? null; + }); // Auto-populate brain region id if we're in morphology category if (currentCategory === 'morphology' && nodeId) { const brainRegionIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, '') + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); return ( normalizedKey === 'brainregionid' || normalizedKey === 'brain_region_id' || normalizedKey === 'brainregion' - ) - }) + ); + }); if (brainRegionIdKey) { - initial[brainRegionIdKey] = nodeId + initial[brainRegionIdKey] = nodeId; } } // Auto-populate species id (hardcoded mouse species ID) const speciesIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, '') + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); return ( normalizedKey === 'speciesid' || normalizedKey === 'species_id' || normalizedKey === 'species' - ) - }) + ); + }); if (speciesIdKey) { - initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1' + initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; } // Auto-populate atlas id const atlasIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, '') + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); return ( normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' - ) - }) + ); + }); if (atlasIdKey) { - initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd' + initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd'; } - setState((prev) => ({ ...initial, ...prev })) - }, [stateAtom, setState, schema.properties, nodeId, currentCategory]) + setState((prev) => ({ ...initial, ...prev })); + }, [stateAtom, setState, schema.properties, nodeId, currentCategory]); // Helper function to mark field as touched const markFieldTouched = (fieldName: string) => { - setTouchedFields((prev) => new Set(prev).add(fieldName)) - } + setTouchedFields((prev) => new Set(prev).add(fieldName)); + }; // Helper function to check if a field has an error const hasFieldError = (fieldName: string): boolean => { - const isRequired = schema.required?.includes(fieldName) - const isTouched = touchedFields.has(fieldName) - const isEmpty = isEmptyValue(state[fieldName]) - return isRequired && isTouched && isEmpty - } + const isRequired = schema.required?.includes(fieldName); + const isTouched = touchedFields.has(fieldName); + const isEmpty = isEmptyValue(state[fieldName]); + return isRequired && isTouched && isEmpty; + }; // Helper function to get field error message const getFieldErrorMessage = (fieldName: string): string | null => { - if (!hasFieldError(fieldName)) return null - const fieldSchema = schema.properties?.[fieldName] - const fieldTitle = fieldSchema?.title || fieldName - return `${fieldTitle} is required` - } + if (!hasFieldError(fieldName)) return null; + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + return `${fieldTitle} is required`; + }; function renderInput(k: string, v: JSONSchema) { const obj = { ...v, ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), - } - const normalizedKey = k.toLowerCase().replace(/[\s_]/g, '') + }; + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - const fieldError = getFieldErrorMessage(k) - const hasError = hasFieldError(k) + const fieldError = getFieldErrorMessage(k); + const hasError = hasFieldError(k); const isBrainRegionIdField = currentCategory === 'morphology' && (normalizedKey === 'brainregionid' || normalizedKey === 'brain_region_id' || - normalizedKey === 'brainregion') + normalizedKey === 'brainregion'); const isSpeciesIdField = - normalizedKey === 'speciesid' || normalizedKey === 'species_id' || normalizedKey === 'species' + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species'; const isAtlasIdField = - normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' + normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas'; const isExperimentDateField = normalizedKey === 'experimentdate' || normalizedKey === 'experiment_date' || normalizedKey === 'date' || - v.title?.toLowerCase().includes('date') + v.title?.toLowerCase().includes('date'); const isStrainIdField = - normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain' - const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period' - const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id' - const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id' - const isMtypeClassIdField = normalizedKey === 'mtypeclassid' + normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain'; + const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; + const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id'; + const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; + const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; if (isBrainRegionIdField && nodeId) { return ( @@ -274,7 +276,7 @@ export function JSONSchemaForm({ readOnly />
- ) + ); } if (isSpeciesIdField) { @@ -288,7 +290,7 @@ export function JSONSchemaForm({ readOnly />
- ) + ); } if (isAtlasIdField) { @@ -302,27 +304,27 @@ export function JSONSchemaForm({ readOnly />
- ) + ); } if (isExperimentDateField) { const formatDate = (value: string) => { - const cleaned = value.replace(/[^\d\s-]/g, '') - const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0) - if (parts.length === 0) return '' - if (parts.length === 1) return parts[0] - if (parts.length === 2) return `${parts[0]} ${parts[1]}` - return parts.slice(0, 3).join(' ') - } + const cleaned = value.replace(/[^\d\s-]/g, ''); + const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0); + if (parts.length === 0) return ''; + if (parts.length === 1) return parts[0]; + if (parts.length === 2) return `${parts[0]} ${parts[1]}`; + return parts.slice(0, 3).join(' '); + }; const validateDateFormat = (value: string) => { - if (!value) return true - const parts = value.split(' ') - if (parts.length !== 3) return false - const [day, month, year] = parts - const dayNum = parseInt(day, 10) - const monthNum = parseInt(month, 10) - const yearNum = parseInt(year, 10) + if (!value) return true; + const parts = value.split(' '); + if (parts.length !== 3) return false; + const [day, month, year] = parts; + const dayNum = parseInt(day, 10); + const monthNum = parseInt(month, 10); + const yearNum = parseInt(year, 10); return ( dayNum >= 1 && dayNum <= 31 && @@ -330,12 +332,12 @@ export function JSONSchemaForm({ monthNum <= 12 && yearNum >= 1900 && yearNum <= new Date().getFullYear() - ) - } + ); + }; - const currentValue = typeof state[k] === 'string' ? state[k] : '' - const isValid = validateDateFormat(currentValue) - const showDateError = !isValid && currentValue + const currentValue = typeof state[k] === 'string' ? state[k] : ''; + const isValid = validateDateFormat(currentValue); + const showDateError = !isValid && currentValue; return (
@@ -345,8 +347,8 @@ export function JSONSchemaForm({ value={currentValue} className={`w-full ${hasError || showDateError ? 'border-red-500' : ''}`} onChange={(e) => { - const formatted = formatDate(e.currentTarget.value) - setState({ ...state, [k]: formatted }) + const formatted = formatDate(e.currentTarget.value); + setState({ ...state, [k]: formatted }); }} placeholder="DD MM YYYY (e.g., 15 03 2024)" /> @@ -357,7 +359,7 @@ export function JSONSchemaForm({ )} {fieldError &&
{fieldError}
}
- ) + ); } if (isStrainIdField) { @@ -377,10 +379,10 @@ export function JSONSchemaForm({ 'Sprague Dawley': '890e1234-e29b-41d4-a716-446655440003', }, }, - ] + ]; - const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1' - const selectedSpecies = allSpeciesStrains.find((s) => s.species_id === speciesId) + const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + const selectedSpecies = allSpeciesStrains.find((s) => s.species_id === speciesId); if (!selectedSpecies) { return ( @@ -388,13 +390,13 @@ export function JSONSchemaForm({ {fieldError &&
{fieldError}
} - ) + ); } const strainOptions = Object.entries(selectedSpecies.strains).map(([name, id]) => ({ label: name, value: id, - })) + })); return (
@@ -403,8 +405,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState((prev) => ({ ...prev, [k]: newV })) - markFieldTouched(k) + setState((prev) => ({ ...prev, [k]: newV })); + markFieldTouched(k); }} value={state[k]} options={strainOptions} @@ -412,7 +414,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ) + ); } if (isAgePeriodField) { @@ -424,8 +426,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }) - markFieldTouched(k) + setState({ ...state, [k]: newV }); + markFieldTouched(k); }} value={state[k]} options={obj.enum.map((subv: string) => ({ @@ -436,7 +438,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
} - ) + ); } return (
@@ -446,13 +448,13 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }) + setState({ ...state, [k]: e.currentTarget.value }); }} placeholder="Enter age period" /> {fieldError &&
{fieldError}
}
- ) + ); } if (isLegacyIdField) { @@ -467,10 +469,10 @@ export function JSONSchemaForm({ {!disabled && ( { - const newElements = [...(Array.isArray(state[k]) ? state[k] : [])] - newElements.splice(newElements.indexOf(e), 1) - setState({ ...state, [k]: newElements }) - markFieldTouched(k) + const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; + newElements.splice(newElements.indexOf(e), 1); + setState({ ...state, [k]: newElements }); + markFieldTouched(k); }} /> )} @@ -497,17 +499,17 @@ export function JSONSchemaForm({ setState({ ...state, [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], - }) - setAddingElement({ ...addingElement, [k]: false }) - setNewElement({ ...newElement, [k]: null }) - markFieldTouched(k) + }); + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + markFieldTouched(k); }} /> )} { - setAddingElement({ ...addingElement, [k]: false }) - setNewElement({ ...newElement, [k]: null }) + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); }} className="text-primary-8" /> @@ -516,7 +518,7 @@ export function JSONSchemaForm({ {fieldError &&
{fieldError}
} - ) + ); } // New condition for 'license id' field @@ -530,17 +532,17 @@ export function JSONSchemaForm({ 'CC BY 4.0 Deed': 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', 'CC0 1.0 Deed': '74b8c953-67f5-4e95-ac58-095274901328', 'NGV_Data Licence_v1.0': '0c39107e-3b68-4f1f-904a-5c7f1b4f89c5', - } + }; const options = Object.entries(licenseOptions).map(([name, id]) => ({ label: name, value: id, - })) + })); // Find the key corresponding to the current state value to set the label const currentLicenseLabel = Object.keys(licenseOptions).find( - (key) => licenseOptions[key] === state[k], - ) + (key) => licenseOptions[key] === state[k] + ); return (
@@ -549,8 +551,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }) - markFieldTouched(k) + setState({ ...state, [k]: newV }); + markFieldTouched(k); }} value={currentLicenseLabel || state[k]} // Use the label for display, or the value if not found options={options} @@ -558,7 +560,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ) + ); } // New condition for 'mtype class id' @@ -566,11 +568,11 @@ export function JSONSchemaForm({ const options = MTYPE_CLASSES.map((mtype) => ({ label: mtype.mtype_pref_label, value: mtype.mtype_id, - })) + })); const currentMtypeLabel = MTYPE_CLASSES.find( - (mtype) => mtype.mtype_id === state[k], - )?.mtype_pref_label + (mtype) => mtype.mtype_id === state[k] + )?.mtype_pref_label; return (
@@ -579,8 +581,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }) - markFieldTouched(k) + setState({ ...state, [k]: newV }); + markFieldTouched(k); }} value={currentMtypeLabel || state[k]} options={options} @@ -588,21 +590,21 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ) + ); } - if (k === 'circuit' && circuit) return + if (k === 'circuit' && circuit) return ; if (v.is_block_reference && v.properties && typeof v.properties.type.const === 'string') { - const referenceKey = referenceTypesToConfigKeys[v.properties.type.const] - const referenceTitle = referenceTypesToTitles[v.properties.type.const] - if (!referenceKey) return null - const referenceConfig = config[referenceKey] - if (!isPlainObject(referenceConfig)) return null + const referenceKey = referenceTypesToConfigKeys[v.properties.type.const]; + const referenceTitle = referenceTypesToTitles[v.properties.type.const]; + if (!referenceKey) return null; + const referenceConfig = config[referenceKey]; + if (!isPlainObject(referenceConfig)) return null; const referees = Object.entries(referenceConfig).filter(([, val]) => { - return isPlainObject(val) - }) + return isPlainObject(val); + }); if (referees.length === 0) { return ( @@ -612,13 +614,13 @@ export function JSONSchemaForm({ {fieldError &&
{fieldError}
} - ) + ); } const defaultV = isPlainObject(state[k]) && typeof state[k].block_name === 'string' ? state[k].block_name - : null + : null; return (
@@ -628,7 +630,7 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} onChange={(newV: string) => { if (!v.properties?.type.const || typeof v.properties.type.const !== 'string') - throw new Error('Invalid reference definition') + throw new Error('Invalid reference definition'); setState({ ...state, @@ -637,8 +639,8 @@ export function JSONSchemaForm({ type: v.properties.type.const, block_dict_name: referenceKey, }, - }) - markFieldTouched(k) + }); + markFieldTouched(k); }} value={defaultV} options={referees.map(([subkey]) => ({ @@ -648,7 +650,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
}
- ) + ); } if (k === 'neuron_ids') { @@ -664,16 +666,16 @@ export function JSONSchemaForm({ {!disabled && ( { - if (!isPlainObject(state[k]) || !Array.isArray(state[k].elements)) return + if (!isPlainObject(state[k]) || !Array.isArray(state[k].elements)) return; if (state[k].elements.length === 1) { - setState({ ...state, [k]: null }) - markFieldTouched(k) - return + setState({ ...state, [k]: null }); + markFieldTouched(k); + return; } - const newElements = [...state[k].elements] - newElements.splice(newElements.indexOf(e), 1) + const newElements = [...state[k].elements]; + newElements.splice(newElements.indexOf(e), 1); setState({ ...state, [k]: { @@ -681,8 +683,8 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: newElements, }, - }) - markFieldTouched(k) + }); + markFieldTouched(k); }} /> )} @@ -702,7 +704,7 @@ export function JSONSchemaForm({ step={1} min={0} onChange={(newV) => { - setNewElement({ ...newElement, [k]: newV }) + setNewElement({ ...newElement, [k]: newV }); }} /> {!isNil(newElement[k]) && ( @@ -717,7 +719,7 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: [newElement[k]], }, - }) + }); } else if (isPlainObject(state[k]) && Array.isArray(state[k].elements)) { setState({ ...state, @@ -726,18 +728,18 @@ export function JSONSchemaForm({ name: 'example_id_neuron_set', elements: [...state[k].elements, newElement[k]], }, - }) + }); } - setAddingElement({ ...addingElement, [k]: false }) - setNewElement({ ...newElement, [k]: null }) - markFieldTouched(k) + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + markFieldTouched(k); }} /> )} { - setAddingElement({ ...addingElement, [k]: false }) - setNewElement({ ...newElement, [k]: null }) + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); }} className="text-primary-8" /> @@ -746,7 +748,7 @@ export function JSONSchemaForm({ {fieldError &&
{fieldError}
} - ) + ); } if (obj.enum) { @@ -757,8 +759,8 @@ export function JSONSchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }) - markFieldTouched(k) + setState({ ...state, [k]: newV }); + markFieldTouched(k); }} value={state[k]} options={obj.enum.map((subv: string) => ({ @@ -769,7 +771,7 @@ export function JSONSchemaForm({ /> {fieldError &&
{fieldError}
} - ) + ); } if (obj.type === 'number' || obj.type === 'integer') { @@ -781,14 +783,14 @@ export function JSONSchemaForm({ disabled={disabled} value={typeof state[k] === 'number' ? state[k] : null} onChange={(value) => { - setState({ ...state, [k]: value }) + setState({ ...state, [k]: value }); }} onBlur={() => markFieldTouched(k)} className={`w-full ${hasError ? 'border-red-500' : ''}`} /> {fieldError &&
{fieldError}
} - ) + ); } if (obj.type === 'string') { @@ -800,12 +802,12 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }) + setState({ ...state, [k]: e.currentTarget.value }); }} /> {fieldError &&
{fieldError}
} - ) + ); } return ( @@ -816,22 +818,22 @@ export function JSONSchemaForm({ onBlur={() => markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }) + setState({ ...state, [k]: e.currentTarget.value }); }} placeholder={`Enter value for ${v.title || k}`} /> {fieldError &&
{fieldError}
} - ) + ); } function getFieldTitle(k: string, v: JSONSchema, normalizedKey: string): string { if (normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain') - return 'STRAIN' - if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD' - if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE' - if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS' - return v.title || k + return 'STRAIN'; + if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD'; + if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE'; + if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS'; + return v.title || k; } return ( @@ -857,12 +859,12 @@ export function JSONSchemaForm({ {schema.properties && Object.entries(schema.properties) .filter(([k]) => { - return !skip.includes(k) + return !skip.includes(k); }) .map(([k, v]) => { - const isRequired = schema.required?.includes(k) - const normalizedKey = k.toLowerCase().replace(/[\s_]/g, '') - const fieldTitle = getFieldTitle(k, v, normalizedKey) + const isRequired = schema.required?.includes(k); + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); + const fieldTitle = getFieldTitle(k, v, normalizedKey); return (
@@ -870,7 +872,7 @@ export function JSONSchemaForm({
@@ -881,11 +883,11 @@ export function JSONSchemaForm({
{renderInput(k, v)}
- ) + ); })} - ) + ); } export function Tab({ @@ -897,13 +899,13 @@ export function Tab({ extraClass, disabled, }: { - tab: string - selectedTab: string - onClick?: () => void - rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full' - children?: React.ReactNode - extraClass?: string - disabled?: boolean + tab: string; + selectedTab: string; + onClick?: () => void; + rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full'; + children?: React.ReactNode; + extraClass?: string; + disabled?: boolean; }) { return ( - ) + ); } export function Chevron({ rotate }: { rotate?: number }) { @@ -943,5 +945,5 @@ export function Chevron({ rotate }: { rotate?: number }) { strokeLinejoin="round" /> - ) + ); } diff --git a/src/page-wrappers/build/me-model/configure.tsx b/src/page-wrappers/build/me-model/configure.tsx index 7ffb859cd..12a9631f1 100644 --- a/src/page-wrappers/build/me-model/configure.tsx +++ b/src/page-wrappers/build/me-model/configure.tsx @@ -1,56 +1,56 @@ -'use client' +'use client'; -import { App, Button } from 'antd' -import { useAtomValue, useSetAtom } from 'jotai' -import get from 'lodash/get' -import omit from 'lodash/omit' -import { useRouter } from 'next/navigation' -import { useTransition } from 'react' -import z from 'zod' +import { App, Button } from 'antd'; +import { useAtomValue, useSetAtom } from 'jotai'; +import get from 'lodash/get'; +import omit from 'lodash/omit'; +import { useRouter } from 'next/navigation'; +import { useTransition } from 'react'; +import z from 'zod'; -import EModelOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/emodel-overview-card' -import MorphologyOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/morphology-overview-card' +import EModelOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/emodel-overview-card'; +import MorphologyOverviewCard from '@/features/entities/me-model/detail-view/card-viewers/morphology-overview-card'; // import CustomButton from '@/components/buttons/custom-btn'; -import { createMEModel } from '@/api/entitycore/queries' -import { CreateMEModelSchema, ValidationStatus } from '@/api/entitycore/types/entities/me-model' -import { tryCatch } from '@/api/utils' -import { DataType } from '@/constants/explore-section/list-views' -import { renderArray, renderEmptyOrValue } from '@/entity-configuration/definitions/renderer' -import { MEmodel } from '@/entity-configuration/domain/model/me-model' -import { activityAtomFamily } from '@/features/activity-view/context' -import { useBuildMeModelSessionState } from '@/features/entities/me-model/build/create.state-session' -import { messages } from '@/i18n/en/me-model' -import { OneshotSession } from '@/services/accounting' -import { useEntitiesCountAtom } from '@/services/entitycore/entities-count' -import { runSingleNeuronAnalysis } from '@/services/small-scale-simulator' -import { useRefreshDataAtom } from '@/state/explore-section/list-view-atoms' -import { virtualLabProjectUsersAtomFamily } from '@/state/virtual-lab/projects' -import { ServiceSubtype } from '@/types/accounting' -import { WorkspaceContextSchema } from '@/types/common' -import { classNames } from '@/util/utils' -import { resolveDataKey } from '@/utils/key-builder' -import { resolveExploreDetailsPageUrl } from '@/utils/url-builder' +import { createMEModel } from '@/api/entitycore/queries'; +import { CreateMEModelSchema, ValidationStatus } from '@/api/entitycore/types/entities/me-model'; +import { tryCatch } from '@/api/utils'; +import { DataType } from '@/constants/explore-section/list-views'; +import { renderArray, renderEmptyOrValue } from '@/entity-configuration/definitions/renderer'; +import { MEmodel } from '@/entity-configuration/domain/model/me-model'; +import { activityAtomFamily } from '@/features/activity-view/context'; +import { useBuildMeModelSessionState } from '@/features/entities/me-model/build/create.state-session'; +import { messages } from '@/i18n/en/me-model'; +import { OneshotSession } from '@/services/accounting'; +import { useEntitiesCountAtom } from '@/services/entitycore/entities-count'; +import { runSingleNeuronAnalysis } from '@/services/small-scale-simulator'; +import { useRefreshDataAtom } from '@/state/explore-section/list-view-atoms'; +import { virtualLabProjectUsersAtomFamily } from '@/state/virtual-lab/projects'; +import { ServiceSubtype } from '@/types/accounting'; +import { WorkspaceContextSchema } from '@/types/common'; +import { classNames } from '@/util/utils'; +import { resolveDataKey } from '@/utils/key-builder'; +import { resolveExploreDetailsPageUrl } from '@/utils/url-builder'; -import type { IMEModel } from '@/api/entitycore/types/entities/me-model' -import type { WorkspaceContext } from '@/types/common' +import type { IMEModel } from '@/api/entitycore/types/entities/me-model'; +import type { WorkspaceContext } from '@/types/common'; -const LOW_FUNDS_ERROR_CODE = 'INSUFFICIENT_FUNDS' +const LOW_FUNDS_ERROR_CODE = 'INSUFFICIENT_FUNDS'; -const CreateMeModelContextSchema = CreateMEModelSchema.merge(WorkspaceContextSchema) -type TCreateMeModelContext = z.infer +const CreateMeModelContextSchema = CreateMEModelSchema.merge(WorkspaceContextSchema); +type TCreateMeModelContext = z.infer; function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { stateId: string }) { const { sessionValue } = useBuildMeModelSessionState({ stateId, virtualLabId, projectId, - }) + }); const contributors = useAtomValue(virtualLabProjectUsersAtomFamily({ projectId, virtualLabId })) - ?.data?.users - const { mmodel } = sessionValue - const { emodel } = sessionValue + ?.data?.users; + const { mmodel } = sessionValue; + const { emodel } = sessionValue; const fields = [ { className: 'col-span-6', @@ -88,7 +88,7 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state title: 'e-type', value: renderEmptyOrValue(renderArray(emodel?.etypes?.map((m) => m.pref_label) || [])), }, - ] + ]; return (
@@ -99,17 +99,17 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state
))} - ) + ); } type Props = { - ctx: WorkspaceContext + ctx: WorkspaceContext; searchParams: { - s: string - m: string - e: string - } -} + s: string; + m: string; + e: string; + }; +}; function CustomButton({ loading, @@ -118,11 +118,11 @@ function CustomButton({ onClick, children, }: { - loading: boolean - disable: boolean - className?: string - onClick?: () => void - children?: React.ReactNode + loading: boolean; + disable: boolean; + className?: string; + onClick?: () => void; + children?: React.ReactNode; }) { return ( - ) + ); } export default function Configure({ ctx, searchParams }: Props) { - const { push: navigate } = useRouter() - const { notification } = App.useApp() - const [isPending, startTransition] = useTransition() - const emodelId = get(searchParams, 'e', undefined) - const morphologyId = get(searchParams, 'm', undefined) - const stateId = get(searchParams, 's', undefined) + const { push: navigate } = useRouter(); + const { notification } = App.useApp(); + const [isPending, startTransition] = useTransition(); + const emodelId = get(searchParams, 'e', undefined); + const morphologyId = get(searchParams, 'm', undefined); + const stateId = get(searchParams, 's', undefined); const exploreDataKey = resolveDataKey({ projectId: ctx.projectId, section: 'explore', entity: MEmodel, - }) + }); - const refreshEntityCountsToParent = useEntitiesCountAtom() - const refreshDataAtom = useRefreshDataAtom(exploreDataKey) + const refreshEntityCountsToParent = useEntitiesCountAtom(); + const refreshDataAtom = useRefreshDataAtom(exploreDataKey); const refreshActivityAtom = useSetAtom( activityAtomFamily({ key: resolveDataKey({ @@ -171,33 +171,33 @@ export default function Configure({ ctx, searchParams }: Props) { projectId: ctx.projectId, virtualLabId: ctx.virtualLabId, type: 'memodel', - }), - ) + }) + ); const { sessionValue } = useBuildMeModelSessionState({ stateId: stateId || '', virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, - }) + }); if (!stateId) { - navigate('./') - return + navigate('./'); + return; } const showErrorNotification = (error: any, type: 'validation' | 'http') => { - let message = messages.DefaultErrorMsg + let message = messages.DefaultErrorMsg; if (type === 'http') message = error?.cause?.error_code === LOW_FUNDS_ERROR_CODE ? messages.LowFundsError - : messages.DefaultErrorMsg - else message = messages.ValidationError + : messages.DefaultErrorMsg; + else message = messages.ValidationError; notification.error({ duration: 10, message, - }) - } + }); + }; const buildMeModel = async () => { const body: Partial = { @@ -211,26 +211,26 @@ export default function Configure({ ctx, searchParams }: Props) { brain_region_id: sessionValue.mmodel?.brain_region.id ?? sessionValue.brainRegion?.id, strain_id: sessionValue.mmodel?.strain?.id ?? null, validation_status: ValidationStatus.Initialized, - } + }; const { error: validationError, data: validationData } = - await CreateMeModelContextSchema.safeParseAsync(body) + await CreateMeModelContextSchema.safeParseAsync(body); if (validationError) { - showErrorNotification(validationError, 'validation') - return { data: null, error: validationError, errorType: 'validation' as const } + showErrorNotification(validationError, 'validation'); + return { data: null, error: validationError, errorType: 'validation' as const }; } const accountingSession = new OneshotSession({ subtype: ServiceSubtype.SingleCellBuild, virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, count: 1, - }) + }); const { data, error } = await tryCatch( accountingSession.useWith(() => createMEModel({ body: omit(validationData, ['virtualLabId', 'projectId']), context: ctx, - }), + }) ), undefined, { @@ -240,39 +240,39 @@ export default function Configure({ ctx, searchParams }: Props) { virtualLabId: ctx.virtualLabId, projectId: ctx.projectId, }, - }, - ) + } + ); - return { data, error, errorType: 'http' as const } - } + return { data, error, errorType: 'http' as const }; + }; const onClick = async () => { startTransition(async () => { - const { data, error, errorType } = await buildMeModel() + const { data, error, errorType } = await buildMeModel(); if (error || !data) { - showErrorNotification(error, errorType) - return + showErrorNotification(error, errorType); + return; } try { - await runSingleNeuronAnalysis({ ctx, modelId: data.id }) + await runSingleNeuronAnalysis({ ctx, modelId: data.id }); } catch (runAnalysisError) { - const message = messages.RunAnalysisError - notification.error({ message, duration: 20 }) + const message = messages.RunAnalysisError; + notification.error({ message, duration: 20 }); } - refreshDataAtom() - refreshActivityAtom() - refreshEntityCountsToParent(data.brain_region.id) + refreshDataAtom(); + refreshActivityAtom(); + refreshEntityCountsToParent(data.brain_region.id); navigate( resolveExploreDetailsPageUrl({ ctx, dataType: DataType.CircuitMEModel, entityId: data.id, - }), - ) - }) - } + }) + ); + }); + }; const validateTrigger = sessionValue.emodel && sessionValue.mmodel && (
@@ -280,7 +280,7 @@ export default function Configure({ ctx, searchParams }: Props) { {isPending ? 'Creating ME-model' : 'Save'}
- ) + ); return ( <> @@ -307,5 +307,5 @@ export default function Configure({ ctx, searchParams }: Props) { {validateTrigger} - ) + ); } From 68cc9129be7daabc32fb4a5514a185fd4f55ac20 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 17:32:54 +0200 Subject: [PATCH 13/44] more linting --- src/page-wrappers/build/me-model/configure.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/page-wrappers/build/me-model/configure.tsx b/src/page-wrappers/build/me-model/configure.tsx index 12a9631f1..4cf346531 100644 --- a/src/page-wrappers/build/me-model/configure.tsx +++ b/src/page-wrappers/build/me-model/configure.tsx @@ -184,7 +184,7 @@ export default function Configure({ ctx, searchParams }: Props) { return; } - const showErrorNotification = (error: any, type: 'validation' | 'http') => { + const showErrorNotification = (error: unknown, type: 'validation' | 'http') => { let message = messages.DefaultErrorMsg; if (type === 'http') message = @@ -256,7 +256,7 @@ export default function Configure({ ctx, searchParams }: Props) { try { await runSingleNeuronAnalysis({ ctx, modelId: data.id }); - } catch (runAnalysisError) { + } catch (_runAnalysisError) { const message = messages.RunAnalysisError; notification.error({ message, duration: 20 }); } From 8bca0b12235a25d200ac99886afc2a3f84b906f9 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 17:50:40 +0200 Subject: [PATCH 14/44] more linting --- src/features/cell-composition/how-to.md | 72 +++---------------------- 1 file changed, 7 insertions(+), 65 deletions(-) diff --git a/src/features/cell-composition/how-to.md b/src/features/cell-composition/how-to.md index e84bf62e4..6a0bed7a1 100644 --- a/src/features/cell-composition/how-to.md +++ b/src/features/cell-composition/how-to.md @@ -1,10 +1,15 @@ # HOW-TO: Construct Brain Cell Composition -This short document explains how cell composition has been constructed, which builds a hierarchical representation of brain cell types and their densities across brain regions. +This short document explains how cell composition has been constructed, +which builds a hierarchical representation of brain cell types and their +densities across brain regions. ## Overview -The cell composition feature processes hierarchical brain region data along with cell type information to generate a unified view of neuron and glial cell distributions. It handles relationships between `brain_region`, `mTypes`, `eTypes`. +The cell composition feature processes hierarchical brain region data +along with cell type information to generate a unified view of neuron +and glial cell distributions. It handles relationships between +`brain_region`, `mTypes`, `eTypes`. ## Data Flow @@ -21,66 +26,3 @@ flowchart TD H --> J[calculate total composition] I --> K[return needed data] J --> K -``` - -## How to process: - -1. **Initialization** - - start with a brain region id (selected by the user) - - retrieve all leaf regions under that brain region (use `brainRegionHierarchyAtom`) - - create volume maps for each leaf region (using `brainRegionAtlasAtom`) - -2. **Node Construction** - - for each leaf region: - - process mTypes and their child eTypes - - build tree nodes with cell counts and densities - - calculate composition data based on volumes - -3. **Node Aggregation** - - merge nodes that represent the same mType/eType across different leaf regions - - sum cell counts across regions - - recalculate densities based on aggregated volumes - - create links between parent mTypes and child eTypes - -4. **Final Calculations** - - calculate total neuron and glial cell counts - - determine total volume (not needed for now) - - compute the whole composition densities - -## Implementation Details - -### Composite IDs - -The system uses composite IDs (`mTypeId__eTypeId`) to ensure that when the same eType appears under different mTypes, they are treated as distinct nodes. This preserves the hierarchical relationship. - -```mermaid -graph TD - mType1 --> eType1_1[eType1 under mType1] - mType1 --> eType2_1[eType2 under mType1] - mType2 --> eType1_2[eType1 under mType2] - mType2 --> eType3[eType3] -``` - -### Volume and Density calculations: - -- **cell count** = density × volume -- **aggregated density** = totalCellCount / TotalVolume -- **neuron count scale** = 1e-9 - -### Node merging: - -When the same node (by composite ID) appears in multiple leaf regions: - -1. merge the lists of associated leaf regions -2. sum the cell counts from all regions -3. recalculate densities based on the total volume of all associated regions -4. combine related nodes (for mTypes pointing to eTypes) - -## Output: - -The final output contains: - -- **nodes**: Array of tree nodes representing mTypes and eTypes -- **links**: Connections between parent mTypes and child eTypes -- **totalVolume**: Combined volume of all leaf regions -- **totalComposition**: Overall neuron and glial cell densities and counts From 08b692cef9bb19af0e5d52863f5c31de6d8c6804 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 17:52:52 +0200 Subject: [PATCH 15/44] more linting --- src/page-wrappers/build/me-model/configure.tsx | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/page-wrappers/build/me-model/configure.tsx b/src/page-wrappers/build/me-model/configure.tsx index 4cf346531..92ad7fa7a 100644 --- a/src/page-wrappers/build/me-model/configure.tsx +++ b/src/page-wrappers/build/me-model/configure.tsx @@ -256,9 +256,10 @@ export default function Configure({ ctx, searchParams }: Props) { try { await runSingleNeuronAnalysis({ ctx, modelId: data.id }); - } catch (_runAnalysisError) { + } catch (runAnalysisError) { const message = messages.RunAnalysisError; notification.error({ message, duration: 20 }); + console.error(runAnalysisError); } refreshDataAtom(); From be935d71e08ad672b3bfbdbe549be3d381c294f5 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 18:25:10 +0200 Subject: [PATCH 16/44] more linting --- src/features/cell-composition/how-to.md | 1 + 1 file changed, 1 insertion(+) diff --git a/src/features/cell-composition/how-to.md b/src/features/cell-composition/how-to.md index 6a0bed7a1..0076f4d73 100644 --- a/src/features/cell-composition/how-to.md +++ b/src/features/cell-composition/how-to.md @@ -26,3 +26,4 @@ flowchart TD H --> J[calculate total composition] I --> K[return needed data] J --> K +``` From 21bf9a124a07276c6f6b741f8be479df0d28c7db Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 12 Aug 2025 22:06:09 +0200 Subject: [PATCH 17/44] more linting --- src/page-wrappers/build/me-model/configure.tsx | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/src/page-wrappers/build/me-model/configure.tsx b/src/page-wrappers/build/me-model/configure.tsx index 92ad7fa7a..0b7408feb 100644 --- a/src/page-wrappers/build/me-model/configure.tsx +++ b/src/page-wrappers/build/me-model/configure.tsx @@ -49,8 +49,7 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state const contributors = useAtomValue(virtualLabProjectUsersAtomFamily({ projectId, virtualLabId })) ?.data?.users; - const { mmodel } = sessionValue; - const { emodel } = sessionValue; + const { mmodel, emodel } = sessionValue; const fields = [ { className: 'col-span-6', @@ -68,13 +67,7 @@ function Header({ stateId, virtualLabId, projectId }: WorkspaceContext & { state }, { title: 'created by', - value: ( -
    - {contributors?.map(({ id, name }) => ( -
  • {name}
    • - ))} -
- ), + value:
    {contributors?.map(({ id, name }) =>
  • {name}
    • )}
, }, { title: 'created date', @@ -131,8 +124,7 @@ function CustomButton({ className, 'bg-primary-9 h-14 rounded-none border border-white px-14 text-white', 'hover:border-primary-8! hover:bg-primary-8! hover:border! hover:font-bold hover:text-white! hover:shadow-xs', - 'disabled:border-gray-400 disabled:bg-white! disabled:text-gray-700! disabled:hover:text-gray-700!', - 'disabled:hover:border-gray-400! disabled:hover:bg-white! disabled:hover:text-gray-700!' + 'disabled:border-gray-400 disabled:bg-white! disabled:text-gray-700! disabled:hover:border-gray-400! disabled:hover:bg-white! disabled:hover:text-gray-700!' )} type="default" size="large" @@ -259,7 +251,7 @@ export default function Configure({ ctx, searchParams }: Props) { } catch (runAnalysisError) { const message = messages.RunAnalysisError; notification.error({ message, duration: 20 }); - console.error(runAnalysisError); + console.error(runAnalysisError); } refreshDataAtom(); From b5efac245f8e79f61a64d56893acb9ad1beed4f7 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Wed, 13 Aug 2025 13:03:09 +0200 Subject: [PATCH 18/44] made buttons consistent --- src/features/contribute/index.tsx | 49 +++++++++++++++++++++---------- 1 file changed, 33 insertions(+), 16 deletions(-) diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx index 3d190de4e..dcd8e3971 100755 --- a/src/features/contribute/index.tsx +++ b/src/features/contribute/index.tsx @@ -2,13 +2,14 @@ import { LoadingOutlined, - RightOutlined, UploadOutlined, CheckCircleFilled, + WarningFilled, + RightOutlined, } from '@ant-design/icons'; import Ajv, { AnySchema } from 'ajv'; import { atom } from 'jotai'; -import { Fragment, useMemo, useRef, useState, KeyboardEvent } from 'react'; +import { Fragment, useMemo, useRef, useState, KeyboardEvent, useEffect } from 'react'; import { Config, ConfigValue, JSONSchemaForm } from './_components/components'; import { useConfigAtom } from './_components/hooks/config-atom'; import { @@ -76,6 +77,11 @@ export default function ContributeMorphologyConfiguration({ errors: [], }); + // Debug log to verify selectedFile state + useEffect(() => { + console.log('selectedFile state:', selectedFile); + }, [selectedFile]); + const selectedCatSchema = schema?.properties?.[configTab]?.additionalProperties?.anyOf?.find( (s) => s.properties?.type.const === selectedCategory ); @@ -157,17 +163,10 @@ export default function ContributeMorphologyConfiguration({ return (
-
+
- {/* Show overall form validation status */} - {!formValidation.isValid && formValidation.errors.length > 0 && ( -
-
Required fields missing:
-
{formValidation.errors.join(', ')}
-
- )} - + {/* ... form validation */}
Assets
Assets -
+
{selectedFile ? ( - + <> + + + ) : ( -
+ <> + + + )} -
{CATEGORIES.filter((c) => c !== 'Assets').map((c) => ( @@ -491,6 +507,7 @@ export default function ContributeMorphologyConfiguration({ disabled={loading || readOnly} onChange={(e) => { const file = e.target.files?.[0]; + console.log('File selected:', file); // Debug log if (file) { setSelectedFile(file); setFileStatus({ message: `File selected: ${file.name}` }); @@ -642,4 +659,4 @@ export default function ContributeMorphologyConfiguration({ )}
); -} +} \ No newline at end of file From 2dfa4846487cc364a32ff58a4f79de46ad8ecc59 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Wed, 13 Aug 2025 13:11:46 +0200 Subject: [PATCH 19/44] more linting --- src/features/contribute/index.tsx | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx index dcd8e3971..78aa0b8a4 100755 --- a/src/features/contribute/index.tsx +++ b/src/features/contribute/index.tsx @@ -163,7 +163,7 @@ export default function ContributeMorphologyConfiguration({ return (
-
+
{/* ... form validation */} @@ -198,10 +198,7 @@ export default function ContributeMorphologyConfiguration({ className="text-green-600" style={{ fontSize: '14px', visibility: 'visible' }} /> - + ) : ( <> @@ -209,10 +206,7 @@ export default function ContributeMorphologyConfiguration({ className="assets-warning text-yellow-400" style={{ fontSize: '14px', visibility: 'visible' }} /> - + )}
@@ -659,4 +653,4 @@ export default function ContributeMorphologyConfiguration({ )}
); -} \ No newline at end of file +} From 8d8ef6d96ae791b27b0bf12de651e883e8bd0458 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Tue, 9 Sep 2025 17:13:45 +0200 Subject: [PATCH 20/44] linting --- .../morphology/_components/components.tsx | 1379 +++++++++++++++++ src/features/contribute/morphology/index.tsx | 601 +++++++ 2 files changed, 1980 insertions(+) create mode 100644 src/features/contribute/morphology/_components/components.tsx create mode 100755 src/features/contribute/morphology/index.tsx diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx new file mode 100644 index 000000000..67656a50b --- /dev/null +++ b/src/features/contribute/morphology/_components/components.tsx @@ -0,0 +1,1379 @@ +import { useEffect, useState } from 'react'; +import { atom, useAtom } from 'jotai'; +import { InputNumber, Input, Select, Button } from 'antd'; +import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; +import isNil from 'lodash/isNil'; + +import { JSONMorphologySchema } from '../types'; +import { isPlainObject } from './utils'; +import Tooltip from './tooltip'; + +import { classNames } from '@/util/utils'; +import { getSession } from '@/authFetch'; + +// Define interfaces for API response data +interface SpeciesRecord { + id: string; + name: string; +} + +interface StrainRecord { + id: string; + name: string; + species_id: string; +} + +interface PersonRecord { + id: string; + pref_label?: string; +} + +interface RoleRecord { + id: string; + name?: string; +} + +interface SubjectRecord { + id: string; + name?: string; +} + +interface LicenseRecord { + id: string; + label?: string; +} + +interface MtypeRecord { + id: string; + pref_label?: string; + alt_label?: string; +} + +interface BrainRegionResponse { + name: string; +} + +interface SpeciesData { + data: SpeciesRecord[]; +} + +interface StrainData { + data: StrainRecord[]; +} + +interface PersonData { + data: PersonRecord[]; +} + +interface RoleData { + data: RoleRecord[]; +} + +interface SubjectData { + data: SubjectRecord[]; +} + +interface LicenseData { + data: LicenseRecord[]; +} + +interface MtypeData { + data: MtypeRecord[]; +} + +type Primitive = null | boolean | number | string; +interface Object { + [key: string]: Primitive | Primitive[] | Object; +} + +export type ConfigValue = Primitive | Primitive[] | Object; + +export type Config = Record; + +// Move session fetch to a function to avoid top-level await +const getSessionWithCheck = async () => { + const session = await getSession(); + if (!session) { + throw new Error('Failed to get session'); + } + return session; +}; + +// Export getRequiredFieldErrors so it can be used in index.tsx +export const isEmptyValue = (value: ConfigValue): boolean => { + if (isNil(value) || value === '') return true; + if (Array.isArray(value) && value.length === 0) return true; + if (typeof value === 'object' && value !== null && Object.keys(value).length === 0) return true; + return false; +}; + +// Export getRequiredFieldErrors +export const getRequiredFieldErrors = ( + state: Record, + schema: JSONMorphologySchema +): string[] => { + const errors: string[] = []; + const requiredFields = schema.required || []; + + requiredFields.forEach((fieldName) => { + const value = state[fieldName]; + if (isEmptyValue(value)) { + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + errors.push(`${fieldTitle} is required`); + } + }); + + return errors; +}; + +const processData = async (token: string): Promise => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const urlSpecies = 'https://staging.openbraininstitute.org/api/entitycore/subject'; + const urlStrain = 'https://staging.openbraininstitute.org/api/entitycore/strain'; + + let json_data_species: SpeciesData = { data: [] }; + let json_data_strain: StrainData = { data: [] }; + + try { + const [responseSpecies, responseStrain] = await Promise.all([ + fetch(urlSpecies, { headers }), + fetch(urlStrain, { headers }), + ]); + + if (!responseSpecies.ok) { + throw new Error(`Species request failed with status code: ${responseSpecies.status}`); + } + if (!responseStrain.ok) { + throw new Error(`Strain request failed with status code: ${responseStrain.status}`); + } + + json_data_species = await responseSpecies.json(); + json_data_strain = await responseStrain.json(); + } catch (error) { + console.error((error as Error).message); + return null; + } + + // Add the generic records as in the Python code + json_data_species.data.push({ + id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', + name: 'Generic Mus musculus', + }); + json_data_species.data.push({ + id: '3b1c2a25-b4fb-468d-98d2-d2d431ac8b4a', + name: 'Generic Rattus norvegicus', + }); + + const speclist: Array<{ + species_id: string; + species_name: string; + strains: Record; + }> = []; + + for (const species_record of json_data_species.data) { + if (species_record.name === 'Unknown') { + continue; + } + + const filtered_data = json_data_strain.data.filter( + (item) => item.species_id === species_record.id + ); + + const strains: Record = {}; + for (const strain of filtered_data) { + strains[strain.name] = strain.id; + } + + const species_entry = { + species_id: species_record.id, + species_name: species_record.name, + strains, + }; + + speclist.push(species_entry); + } + + return JSON.stringify(speclist, null, 2); +}; + +const fetchAgents = async (token: string): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/person'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Agent request failed with status code: ${response.status}`); + } + const json_data_person: PersonData = await response.json(); + + const person_dict: Record = {}; + for (const item of json_data_person.data) { + if (item.pref_label) { + person_dict[item.pref_label] = item.id; + } + } + return person_dict; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +const fetchRoles = async (token: string): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/role'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Role request failed with status code: ${response.status}`); + } + const json_data_role: RoleData = await response.json(); + + const role_dict: Record = {}; + for (const item of json_data_role.data) { + if (item.name) { + role_dict[item.name] = item.id; + } + } + return role_dict; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +const fetchSubjects = async ( + token: string +): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/subject'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Subject request failed with status code: ${response.status}`); + } + const json_data_subject: SubjectData = await response.json(); + + const subject_list: Array<{ label: string; value: string }> = []; + for (const item of json_data_subject.data) { + if (item.name) { + const subject_entry = { + label: item.name, + value: item.id, + }; + subject_list.push(subject_entry); + } + } + return subject_list; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +const fetchLicenses = async ( + token: string +): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/license'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`License request failed with status code: ${response.status}`); + } + const json_data_license: LicenseData = await response.json(); + + const license_list: Array<{ label: string; value: string }> = []; + for (const item of json_data_license.data) { + if (item.label && item.label !== 'undefined') { + const license_entry = { + label: item.label, + value: item.id, + }; + license_list.push(license_entry); + } + } + return license_list; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +const fetchMtypes = async ( + token: string +): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/mtype'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`MTYPE request failed with status code: ${response.status}`); + } + const json_data_mtype: MtypeData = await response.json(); + + const mtype_list: Array<{ mtype_pref_label: string; mtype_id: string }> = []; + for (const item of json_data_mtype.data) { + if (item.pref_label) { + const alt_label = item.alt_label ? ` ${item.alt_label}` : ''; + const mtype_entry = { + mtype_pref_label: item.pref_label + alt_label, + mtype_id: item.id, + }; + mtype_list.push(mtype_entry); + } + } + return mtype_list; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +const fetchBrainRegion = async (token: string, brainRegionId: string): Promise => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = `https://staging.openbraininstitute.org/api/entitycore/brain-region/${brainRegionId}`; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Brain region request failed with status code: ${response.status}`); + } + const json_data: BrainRegionResponse = await response.json(); + return json_data.name; + } catch (error) { + console.error((error as Error).message); + return null; + } +}; + +export function JSONMorphologySchemaForm({ + disabled, + schema, + stateAtom, + config, + onAddReferenceClick, + nodeId, + currentCategory, +}: { + disabled: boolean; + config: Config; + schema: JSONMorphologySchema; + stateAtom: ReturnType>; + onAddReferenceClick: (reference: string) => void; + nodeId?: string; + currentCategory?: string; +}) { + const skip = ['type']; + + const [state, setState] = useAtom(stateAtom); + const [addingElement, setAddingElement] = useState<{ [key: string]: boolean }>({ + legacy_id: true, + }); + const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}); + const [validationErrors, setValidationErrors] = useState([]); + const [touchedFields, setTouchedFields] = useState>(new Set()); + + // NEW STATE TO STORE API DATA + const [allSpeciesStrains, setAllSpeciesStrains] = useState; + }> | null>(null); + const [allAgents, setAllAgents] = useState | null>(null); + const [allRoles, setAllRoles] = useState | null>(null); + const [allSubjects, setAllSubjects] = useState | null>( + null + ); + const [allLicenses, setAllLicenses] = useState | null>( + null + ); + const [allMtypes, setAllMtypes] = useState | null>(null); + const [brainRegionName, setBrainRegionName] = useState(null); + + const referenceTypesToConfigKeys: Record = { + NeuronSetReference: 'neuron_sets', + TimestampsReference: 'timestamps', + }; + + const referenceTypesToTitles: Record = { + NeuronSetReference: 'Neuron Set', + TimestampsReference: 'Timestamps', + }; + + // Validate form whenever state changes + useEffect(() => { + const errors = getRequiredFieldErrors(state, schema); + setValidationErrors(errors); + }, [state, schema]); + + // Fetch API data on component mount + useEffect(() => { + const fetchData = async () => { + const session = await getSessionWithCheck(); + if (!session) return; + + try { + const [speciesData, agentsData, rolesData, subjectsData, licensesData, mtypesData] = + await Promise.all([ + processData(session.accessToken), + fetchAgents(session.accessToken), + fetchRoles(session.accessToken), + fetchSubjects(session.accessToken), + fetchLicenses(session.accessToken), + fetchMtypes(session.accessToken), + ]); + + let brainRegionName = null; + if (nodeId) { + brainRegionName = await fetchBrainRegion(session.accessToken, nodeId); + } + + if (speciesData) { + const parsedData = JSON.parse(speciesData); + setAllSpeciesStrains(parsedData); + } + if (agentsData) { + setAllAgents(agentsData); + } + if (rolesData) { + setAllRoles(rolesData); + } + if (subjectsData) { + setAllSubjects(subjectsData); + } + if (licensesData) { + setAllLicenses(licensesData); + setState((prev) => ({ + ...prev, + license_id: prev.license_id || 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', + })); + } + if (mtypesData) { + setAllMtypes(mtypesData); + } + if (brainRegionName) { + setBrainRegionName(brainRegionName); + } + } catch (error) { + console.error((error as Error).message); + } + }; + fetchData(); + }, [nodeId, setState]); + + // Rest of the useEffect hook for initial state population... + useEffect(() => { + if (!schema.properties) return; + + const initial: Record = {}; + + Object.entries(schema.properties).forEach(([key, value]) => { + if (key === 'type') initial[key] = value.const ?? null; + else if (key === 'legacy_id') initial[key] = []; + else if (key === 'strain_id') initial[key] = null; + else if (key === 'subject_id') + initial[key] = '1c71c68c-44a4-4972-955d-7e0f264425e3'; // Default to first subject_id + else if (key === 'license_id') + initial[key] = 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7'; // Default to CC BY 4.0 Deed + else initial[key] = value.default ?? null; + }); + + if (currentCategory === 'morphology' && nodeId) { + const brainRegionIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion' + ); + }); + + if (brainRegionIdKey) { + initial[brainRegionIdKey] = nodeId; + } + } + + const speciesIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species' + ); + }); + + if (speciesIdKey) { + initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + } + + const atlasIdKey = Object.keys(schema.properties || {}).find((key) => { + const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); + return ( + normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' + ); + }); + + if (atlasIdKey) { + initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd'; + } + + setState((prev) => ({ ...initial, ...prev })); + }, [stateAtom, setState, schema.properties, nodeId, currentCategory]); + + const markFieldTouched = (fieldName: string) => { + setTouchedFields((prev) => new Set(prev).add(fieldName)); + }; + + const hasFieldError = (fieldName: string): boolean => { + const isRequired = schema.required?.includes(fieldName) ?? false; + const isTouched = touchedFields.has(fieldName); + const isEmpty = isEmptyValue(state[fieldName]); + return isRequired && isTouched && isEmpty; + }; + + const getFieldErrorMessage = (fieldName: string): string | null => { + if (!hasFieldError(fieldName)) return null; + const fieldSchema = schema.properties?.[fieldName]; + const fieldTitle = fieldSchema?.title || fieldName; + return `${fieldTitle} is required`; + }; + + function renderInput(k: string, v: JSONMorphologySchema) { + const obj = { + ...v, + ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), + }; + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); + + const fieldError = getFieldErrorMessage(k); + const hasError = hasFieldError(k); + + const isBrainRegionIdField = + currentCategory === 'morphology' && + (normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion'); + const isSpeciesIdField = + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species'; + const isAtlasIdField = + normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas'; + const isExperimentDateField = + normalizedKey === 'experimentdate' || + normalizedKey === 'experiment_date' || + normalizedKey === 'date' || + v.title?.toLowerCase().includes('date'); + const isStrainIdField = + normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain'; + const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; + const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id'; + const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; + const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; + const isSubjectIdField = normalizedKey === 'subjectid' || normalizedKey === 'subject_id'; + const isRoleIdField = + normalizedKey === 'roleid' || normalizedKey === 'role_id' || normalizedKey === 'role'; + const isAgentIdField = + normalizedKey === 'agentid' || normalizedKey === 'agent_id' || normalizedKey === 'agent'; + + if (isBrainRegionIdField && nodeId) { + return ( +
+ markFieldTouched(k)} + value={brainRegionName ? brainRegionName : 'Loading...'} + readOnly + /> +
+ ); + } + + if (isSpeciesIdField) { + const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + const selectedSpecies = allSpeciesStrains + ? allSpeciesStrains.find((s) => s.species_id === speciesId) + : null; + const speciesName = selectedSpecies ? selectedSpecies.species_name : 'Loading...'; + + return ( +
+ markFieldTouched(k)} + value={speciesName} + readOnly + /> +
+ ); + } + + if (isAtlasIdField) { + return ( +
+ markFieldTouched(k)} + value="e3e70682-c209-4cac-a29f-6fbed82c07cd" + readOnly + /> +
+ ); + } + + if (isExperimentDateField) { + const formatDate = (value: string) => { + const cleaned = value.replace(/[^\d\s-]/g, ''); + const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0); + if (parts.length === 0) return ''; + if (parts.length === 1) return parts[0]; + if (parts.length === 2) return `${parts[0]} ${parts[1]}`; + return parts.slice(0, 3).join(' '); + }; + + const validateDateFormat = (value: string) => { + if (!value) return true; + const parts = value.split(' '); + if (parts.length !== 3) return false; + const [day, month, year] = parts; + const dayNum = parseInt(day, 10); + const monthNum = parseInt(month, 10); + const yearNum = parseInt(year, 10); + return ( + dayNum >= 1 && + dayNum <= 31 && + monthNum >= 1 && + monthNum <= 12 && + yearNum >= 1900 && + yearNum <= new Date().getFullYear() + ); + }; + + const currentValue = typeof state[k] === 'string' ? state[k] : ''; + const isValid = validateDateFormat(currentValue); + const showDateError = !isValid && currentValue; + + return ( +
+ markFieldTouched(k)} + value={currentValue} + className={`w-full ${hasError || showDateError ? 'border-red-500' : ''}`} + onChange={(e) => { + const formatted = formatDate(e.currentTarget.value); + setState({ ...state, [k]: formatted }); + }} + placeholder="DD MM YYYY (e.g., 15 03 2024)" + /> + {showDateError && ( +
+ Please use format: DD MM YYYY (day month year) +
+ )} + {fieldError &&
{fieldError}
} +
+ ); + } + + if (isStrainIdField) { + if (!allSpeciesStrains) { + return ( +
+ +
+ ); + } + + const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + const selectedSpecies = allSpeciesStrains.find((s) => s.species_id === speciesId); + + if (!selectedSpecies) { + return ( +
+ + {fieldError &&
{fieldError}
} +
+ ); + } + + const strainOptions = Object.entries(selectedSpecies.strains).map(([name, id]) => ({ + label: name, + value: id, + })); + + return ( +
+ markFieldTouched(k)} + onChange={(newV) => { + setState({ ...state, [k]: newV }); + markFieldTouched(k); + }} + value={state[k]} + options={obj.enum.map((subv: string) => ({ + label: subv, + value: subv, + }))} + placeholder="Select age period" + /> + {fieldError &&
{fieldError}
} +
+ ); + } + return ( +
+ markFieldTouched(k)} + value={typeof state[k] === 'string' ? state[k] : ''} + onChange={(e) => { + setState({ ...state, [k]: e.currentTarget.value }); + }} + placeholder="Enter age period" + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (isLegacyIdField) { + return ( +
+
+
+ {Array.isArray(state[k]) && + state[k].map((e) => ( +
+ {e}{' '} + {!disabled && ( + { + const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; + newElements.splice(newElements.indexOf(e), 1); + setState({ ...state, [k]: newElements }); + markFieldTouched(k); + }} + /> + )} +
+ ))} +
+ {!addingElement[k] && !disabled && ( + setAddingElement({ ...addingElement, [k]: true })} + className="text-primary-8" + /> + )} + {addingElement[k] && !disabled && ( +
+ setNewElement({ ...newElement, [k]: e.currentTarget.value })} + placeholder="Enter legacy ID" + /> + {newElement[k] && ( + { + setState({ + ...state, + [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], + }); + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + markFieldTouched(k); + }} + /> + )} + { + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + }} + className="text-primary-8" + /> +
+ )} +
+ {fieldError &&
{fieldError}
} +
+ ); + } + + if (isLicenseIdField) { + if (!allLicenses) { + return ( +
+ +
+ ); + } + + const options = allLicenses.map((license) => ({ + label: license.label, + value: license.value, + })); + + return ( +
+ +
+ ); + } + + const options = allSubjects.map((subject) => ({ + label: subject.label, + value: subject.value, + })); + + return ( +
+ +
+ ); + } + + const options = allMtypes.map((mtype) => ({ + label: mtype.mtype_pref_label, + value: mtype.mtype_id, + })); + + return ( +
+ +
+ ); + } + + const options = Object.entries(allRoles).map(([label, value]) => ({ + label, + value, + })); + + return ( +
+ +
+ ); + } + + const options = Object.entries(allAgents).map(([label, value]) => ({ + label, + value, + })); + + return ( +
+ markFieldTouched(k)} + onChange={(newV: string) => { + if (!v.properties?.type.const || typeof v.properties.type.const !== 'string') + throw new Error('Invalid reference definition'); + + setState({ + ...state, + [k]: { + block_name: newV, + type: v.properties.type.const, + block_dict_name: referenceKey, + }, + }); + markFieldTouched(k); + }} + value={defaultV} + options={referees.map(([subkey]) => ({ + label: subkey, + value: subkey, + }))} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (k === 'neuron_ids') { + return ( +
+
+
+ {isPlainObject(state[k]) && + Array.isArray(state[k].elements) && + state[k].elements.map((e) => ( +
+ {e}{' '} + {!disabled && ( + { + if (!isPlainObject(state[k]) || !Array.isArray(state[k].elements)) return; + + if (state[k].elements.length === 1) { + setState({ ...state, [k]: null }); + markFieldTouched(k); + return; + } + + const newElements = [...state[k].elements]; + newElements.splice(newElements.indexOf(e), 1); + setState({ + ...state, + [k]: { + type: 'NamedTuple', + name: 'example_id_neuron_set', + elements: newElements, + }, + }); + markFieldTouched(k); + }} + /> + )} +
+ ))} +
+ {!addingElement[k] && !disabled && ( + setAddingElement({ ...addingElement, [k]: true })} + className="text-primary-8" + /> + )} + {addingElement[k] && !disabled && ( +
+ { + setNewElement({ ...newElement, [k]: newV }); + }} + /> + {!isNil(newElement[k]) && ( + { + if (!state[k]) { + setState({ + ...state, + [k]: { + type: 'NamedTuple', + name: 'example_id_neuron_set', + elements: [newElement[k]], + }, + }); + } else if (isPlainObject(state[k]) && Array.isArray(state[k].elements)) { + setState({ + ...state, + [k]: { + type: 'NamedTuple', + name: 'example_id_neuron_set', + elements: [...state[k].elements, newElement[k]], + }, + }); + } + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + markFieldTouched(k); + }} + /> + )} + { + setAddingElement({ ...addingElement, [k]: false }); + setNewElement({ ...newElement, [k]: null }); + }} + className="text-primary-8" + /> +
+ )} +
+ {fieldError &&
{fieldError}
} +
+ ); + } + + if (obj.type === 'number' || obj.type === 'integer') { + return ( +
+ { + setState({ ...state, [k]: value }); + }} + onBlur={() => markFieldTouched(k)} + className={`w-full ${hasError ? 'border-red-500' : ''}`} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + if (obj.type === 'string') { + return ( +
+ markFieldTouched(k)} + value={typeof state[k] === 'string' ? state[k] : ''} + onChange={(e) => { + setState({ ...state, [k]: e.currentTarget.value }); + }} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + return ( +
+ markFieldTouched(k)} + value={typeof state[k] === 'string' ? state[k] : ''} + onChange={(e) => { + setState({ ...state, [k]: e.currentTarget.value }); + }} + placeholder={`Enter value for ${v.title || k}`} + /> + {fieldError &&
{fieldError}
} +
+ ); + } + + function getFieldTitle(k: string, v: JSONMorphologySchema, normalizedKey: string): string { + if ( + normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion' + ) + return 'BRAIN REGION'; + if ( + normalizedKey === 'speciesid' || + normalizedKey === 'species_id' || + normalizedKey === 'species' + ) + return 'SPECIES'; + if (normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain') + return 'STRAIN'; + if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD'; + if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE'; + if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS'; + if (normalizedKey === 'subjectid' || normalizedKey === 'subject_id') return 'SUBJECT'; + if (normalizedKey === 'roleid' || normalizedKey === 'role_id' || normalizedKey === 'role') + return 'ROLE'; + if (normalizedKey === 'agentid' || normalizedKey === 'agent_id' || normalizedKey === 'agent') + return 'AGENT'; + + return v.title || k; + } + + return ( +
+
{schema.title}
+
{schema.description}
+ + {validationErrors.length > 0 && ( +
+
+ Please fix the following required fields: +
+
    + {validationErrors.map((error) => ( +
  • {error}
    • + ))} +
+
+ )} + +
+ {schema.properties && + Object.entries(schema.properties) + .filter(([k]) => { + return !skip.includes(k); + }) + .map(([k, v]) => { + const isRequired = schema.required?.includes(k) ?? false; + const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); + const fieldTitle = getFieldTitle(k, v, normalizedKey); + + return ( +
+
+
+ {fieldTitle} + {isRequired && *} +
+ {v.units &&
{v.units}
} +
+ {renderInput(k, v)} +
+ ); + })} +
+
+ ); +} + +export function Tab({ + tab, + selectedTab, + children, + onClick, + rounded = 'rounded-full', + extraClass, + disabled, +}: { + tab: string; + selectedTab: string; + onClick?: () => void; + rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full'; + children?: React.ReactNode; + extraClass?: string; + disabled?: boolean; +}) { + return ( + + ); +} + +export function Chevron({ rotate }: { rotate?: number }) { + return ( + + + + ); +} diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx new file mode 100755 index 000000000..92e13a507 --- /dev/null +++ b/src/features/contribute/morphology/index.tsx @@ -0,0 +1,601 @@ +'use client'; + +import { + LoadingOutlined, + UploadOutlined, + CheckCircleFilled, + WarningFilled, + RightOutlined, +} from '@ant-design/icons'; +import Ajv, { AnySchema } from 'ajv'; +import { atom } from 'jotai'; +import { Fragment, useMemo, useRef, useState, KeyboardEvent, useEffect } from 'react'; +import { Config, ConfigValue, JSONMorphologySchemaForm } from './_components/components'; +import { useConfigAtom } from './_components/hooks/config-atom'; +import { + isRootCategory, + resolveKey, + useObioneJsonConfigurationSchema, +} from './_components/hooks/schema'; +import { Section } from './_components/section'; +import { CATEGORIES, isAtom, ORDERING } from './_components/utils'; +import { AtomsMap, JSONMorphologySchema } from './types'; +import { resolveDataKey } from '@/utils/key-builder'; +import { useBrainRegionHierarchy } from '@/features/brain-region-hierarchy/context'; +import ApiError from '@/api/error'; +import authFetch from '@/authFetch'; +import { useAppNotification } from '@/components/notification'; +import { classNames } from '@/util/utils'; +import styles from './small-microcircuit.module.css'; + +export default function ContributeMorphologyConfiguration({ + circuitId, + virtualLabId, + projectId, + initialCampaignId, + initialConfig, +}: { + circuitId: string; + virtualLabId: string; + projectId: string; + initialCampaignId?: string; + initialConfig?: Config; +}) { + if (!!initialCampaignId !== !!initialConfig) { + throw new Error('Both or none of initialCampaignId, initialConfigId should be passed'); + } + + const { node } = useBrainRegionHierarchy({ + dataKey: resolveDataKey({ section: 'explore', projectId }), + }); + + const [configTab, setConfigTab] = useState('info'); + const [editing, setEditing] = useState(true); + const [schema, setSchema] = useState(null); + const [selectedCategory, setSelectedCategory] = useState(''); + const [selectedItemIdx, setSelectedItemIdx] = useState(null); + const [loading, setLoading] = useState(false); + const [showConfig, setShowConfig] = useState(false); + const [selectedFile, setSelectedFile] = useState(null); + const [fileStatus, setFileStatus] = useState<{ + message?: string; + }>({}); + const [newJsonPayload, setNewJsonPayload] = useState(null); + const notification = useAppNotification(); + const [campaignId, setCampaignId] = useState(initialCampaignId ?? ''); + const initialConfigValidated = useRef(false); + + // Add success state + const [isSuccess, setIsSuccess] = useState(false); + + // Add validation state + const [formValidation] = useState<{ + isValid: boolean; + errors: string[]; + }>({ + isValid: true, + errors: [], + }); + + // Debug log to verify selectedFile state + useEffect(() => { + console.log('selectedFile state:', selectedFile); + }, [selectedFile]); + + const selectedCatSchema = schema?.properties?.[configTab]?.additionalProperties?.anyOf?.find( + (s) => s.properties?.type.const === selectedCategory + ); + + const handleAddReferenceClick = (referenceTab: string) => { + setConfigTab(referenceTab); + setEditing(true); + setSelectedCategory(''); + }; + + const readOnly = initialConfig !== undefined; + + const validate = useMemo(() => { + const ajv = new Ajv({ strictSchema: false, allErrors: true }); + if (!schema) { + return; + } + return ajv.compile(schema as AnySchema); + }, [schema]); + + const [atomsMap, setAtomsMap] = useState({}); + + // Fix TS2554: Adjust useConfigAtom call to pass only schema and atomsMap + const config = useConfigAtom(schema, atomsMap); + + if (validate && initialConfig && !initialConfigValidated.current) { + initialConfigValidated.current = true; + validate(initialConfig); + if (validate.errors) { + throw new Error('Invalid Simulation Campaign Configuration'); + } + } + + const errors = useMemo(() => { + if (validate) { + validate(config); + } + return validate?.errors; + }, [validate, config]); + + useObioneJsonConfigurationSchema(circuitId, notification, setSchema, setAtomsMap); + + // Update the submit button condition + const canSubmit = + !errors?.length && !loading && !readOnly && selectedFile && formValidation.isValid; + + // Show success page if upload was successful + if (isSuccess) { + return ( +
+
+
+ ✓ Morphology created successfully +
+ +
+
+ ); + } + + if (!schema) { + return ( +
+ +
+ ); + } + + return ( +
+
+
+
+
+ {/* ... form validation */} +
Assets
+
{ + setConfigTab('assets'); + setEditing(true); + setSelectedCategory(''); + setSelectedItemIdx(null); + }} + onKeyDown={(e: KeyboardEvent) => { + if (e.key === 'Enter' || e.key === ' ') { + setConfigTab('assets'); + setEditing(true); + setSelectedCategory(''); + setSelectedItemIdx(null); + } + }} + > + Assets +
+ {selectedFile ? ( + <> + + + + ) : ( + <> + + + + )} +
+
+ {CATEGORIES.filter((c) => c !== 'Assets').map((c) => ( + +
{c}
+ {schema.properties && + Object.entries(schema.properties) + .filter(([k]) => k !== 'type' && ORDERING[k]?.category === c) + .sort((a, b) => { + const order = (k: string) => ORDERING[k]?.order ?? 999; + return order(a[0]) - order(b[0]); + }) + .map(([k, v]) => ( +
+ ))} + + ))} + {!readOnly && ( + + )} +
+
+
+ {configTab === 'assets' && editing && ( +
+
+ UPLOAD MORPHOLOGY FILE +
+
+ One reference file should be loaded. +
+
+
+ + {fileStatus?.message && ( + {fileStatus.message} + )} +
+
+
+ )} + {schema.properties && + schema.properties?.[configTab]?.additionalProperties?.anyOf && + !selectedCategory && + editing && + configTab !== 'assets' && ( +
+ {schema.properties[configTab].additionalProperties.anyOf.map((o) => ( +
{ + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) { + Object.entries(o.properties).forEach(([subkey, subValue]) => { + initial[subkey] = + subkey === 'type' + ? (subValue.const ?? null) + : (subValue.default ?? null); + }); + } + const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...atomsMap[configTab], + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + }); + }} + onKeyDown={(e: KeyboardEvent) => { + if (e.key === 'Enter' || e.key === ' ') { + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) { + Object.entries(o.properties).forEach(([subkey, subValue]) => { + initial[subkey] = + subkey === 'type' + ? (subValue.const ?? null) + : (subValue.default ?? null); + }); + } + const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap({ + ...atomsMap, + [configTab]: { + ...atomsMap[configTab], + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + }); + } + }} + > +
{o.title}
+
{o.description}
+
+ ))} +
+ )} + {schema.properties && + schema.properties?.[configTab] && + editing && + (isRootCategory(schema, configTab) || selectedCatSchema) && + configTab !== 'assets' && ( + + )} +
+
+ {showConfig && ( +
+
+
+

New Record JSON

+ +
+ + 
+              {JSON.stringify(newJsonPayload, null, 2)}
+
+ +
+ +
+
+
+ )} +
+ ); +} From 0c93cea546f29451dd8556d8a0c575bf9aeec19c Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Thu, 11 Sep 2025 21:49:27 +0200 Subject: [PATCH 21/44] updated with feedback --- .../morphology/_components/components.tsx | 574 +++--------------- .../_components/hooks/config-atom.ts | 52 ++ .../morphology/_components/hooks/schema.ts | 209 +++++++ src/features/contribute/morphology/index.tsx | 452 ++++++++------ src/features/contribute/morphology/types.ts | 36 ++ 5 files changed, 632 insertions(+), 691 deletions(-) create mode 100644 src/features/contribute/morphology/_components/hooks/config-atom.ts create mode 100644 src/features/contribute/morphology/_components/hooks/schema.ts create mode 100755 src/features/contribute/morphology/types.ts diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index 67656a50b..d3d654541 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -1,17 +1,15 @@ +// src/features/contribute/morphology/_components/components.tsx import { useEffect, useState } from 'react'; -import { atom, useAtom } from 'jotai'; -import { InputNumber, Input, Select, Button } from 'antd'; -import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; +import { useAtom, PrimitiveAtom } from 'jotai'; +import { InputNumber, Input, Select } from 'antd'; import isNil from 'lodash/isNil'; import { JSONMorphologySchema } from '../types'; -import { isPlainObject } from './utils'; import Tooltip from './tooltip'; import { classNames } from '@/util/utils'; import { getSession } from '@/authFetch'; -// Define interfaces for API response data interface SpeciesRecord { id: string; name: string; @@ -81,16 +79,15 @@ interface MtypeData { data: MtypeRecord[]; } -type Primitive = null | boolean | number | string; +type Primitive = null | boolean | number | string | undefined; interface Object { - [key: string]: Primitive | Primitive[] | Object; + [key: string]: ConfigValue; } export type ConfigValue = Primitive | Primitive[] | Object; -export type Config = Record; +export type Config = Record>; -// Move session fetch to a function to avoid top-level await const getSessionWithCheck = async () => { const session = await getSession(); if (!session) { @@ -99,7 +96,6 @@ const getSessionWithCheck = async () => { return session; }; -// Export getRequiredFieldErrors so it can be used in index.tsx export const isEmptyValue = (value: ConfigValue): boolean => { if (isNil(value) || value === '') return true; if (Array.isArray(value) && value.length === 0) return true; @@ -107,7 +103,6 @@ export const isEmptyValue = (value: ConfigValue): boolean => { return false; }; -// Export getRequiredFieldErrors export const getRequiredFieldErrors = ( state: Record, schema: JSONMorphologySchema @@ -159,7 +154,6 @@ const processData = async (token: string): Promise => { return null; } - // Add the generic records as in the Python code json_data_species.data.push({ id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', name: 'Generic Mus musculus', @@ -353,9 +347,10 @@ const fetchMtypes = async ( mtype_list.push(mtype_entry); } } + return mtype_list; } catch (error) { - console.error((error as Error).message); + console.error('fetchMtypes: Error', (error as Error).message); return null; } }; @@ -385,30 +380,20 @@ export function JSONMorphologySchemaForm({ disabled, schema, stateAtom, - config, - onAddReferenceClick, nodeId, - currentCategory, }: { disabled: boolean; - config: Config; schema: JSONMorphologySchema; - stateAtom: ReturnType>; - onAddReferenceClick: (reference: string) => void; + stateAtom: PrimitiveAtom<{ [key: string]: ConfigValue }>; nodeId?: string; currentCategory?: string; }) { const skip = ['type']; const [state, setState] = useAtom(stateAtom); - const [addingElement, setAddingElement] = useState<{ [key: string]: boolean }>({ - legacy_id: true, - }); - const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}); const [validationErrors, setValidationErrors] = useState([]); const [touchedFields, setTouchedFields] = useState>(new Set()); - // NEW STATE TO STORE API DATA const [allSpeciesStrains, setAllSpeciesStrains] = useState | null>(null); const [brainRegionName, setBrainRegionName] = useState(null); - const referenceTypesToConfigKeys: Record = { - NeuronSetReference: 'neuron_sets', - TimestampsReference: 'timestamps', - }; - - const referenceTypesToTitles: Record = { - NeuronSetReference: 'Neuron Set', - TimestampsReference: 'Timestamps', - }; - - // Validate form whenever state changes useEffect(() => { const errors = getRequiredFieldErrors(state, schema); setValidationErrors(errors); }, [state, schema]); - // Fetch API data on component mount useEffect(() => { const fetchData = async () => { const session = await getSessionWithCheck(); @@ -481,237 +454,89 @@ export function JSONMorphologySchemaForm({ } if (licensesData) { setAllLicenses(licensesData); - setState((prev) => ({ - ...prev, - license_id: prev.license_id || 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', - })); } if (mtypesData) { setAllMtypes(mtypesData); } - if (brainRegionName) { - setBrainRegionName(brainRegionName); - } + setBrainRegionName(brainRegionName); } catch (error) { - console.error((error as Error).message); + console.error('Failed to fetch data:', error); } }; - fetchData(); - }, [nodeId, setState]); - - // Rest of the useEffect hook for initial state population... - useEffect(() => { - if (!schema.properties) return; - - const initial: Record = {}; - - Object.entries(schema.properties).forEach(([key, value]) => { - if (key === 'type') initial[key] = value.const ?? null; - else if (key === 'legacy_id') initial[key] = []; - else if (key === 'strain_id') initial[key] = null; - else if (key === 'subject_id') - initial[key] = '1c71c68c-44a4-4972-955d-7e0f264425e3'; // Default to first subject_id - else if (key === 'license_id') - initial[key] = 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7'; // Default to CC BY 4.0 Deed - else initial[key] = value.default ?? null; - }); - - if (currentCategory === 'morphology' && nodeId) { - const brainRegionIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'brainregionid' || - normalizedKey === 'brain_region_id' || - normalizedKey === 'brainregion' - ); - }); - - if (brainRegionIdKey) { - initial[brainRegionIdKey] = nodeId; - } - } - - const speciesIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'speciesid' || - normalizedKey === 'species_id' || - normalizedKey === 'species' - ); - }); - if (speciesIdKey) { - initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; - } - - const atlasIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' - ); - }); - - if (atlasIdKey) { - initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd'; - } - - setState((prev) => ({ ...initial, ...prev })); - }, [stateAtom, setState, schema.properties, nodeId, currentCategory]); - - const markFieldTouched = (fieldName: string) => { - setTouchedFields((prev) => new Set(prev).add(fieldName)); - }; - - const hasFieldError = (fieldName: string): boolean => { - const isRequired = schema.required?.includes(fieldName) ?? false; - const isTouched = touchedFields.has(fieldName); - const isEmpty = isEmptyValue(state[fieldName]); - return isRequired && isTouched && isEmpty; - }; + fetchData(); + }, [nodeId]); - const getFieldErrorMessage = (fieldName: string): string | null => { - if (!hasFieldError(fieldName)) return null; - const fieldSchema = schema.properties?.[fieldName]; - const fieldTitle = fieldSchema?.title || fieldName; - return `${fieldTitle} is required`; + const markFieldTouched = (field: string) => { + setTouchedFields((prev) => new Set([...prev, field])); }; - function renderInput(k: string, v: JSONMorphologySchema) { - const obj = { - ...v, - ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), - }; + function renderInput(k: string, obj: JSONMorphologySchema) { const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - - const fieldError = getFieldErrorMessage(k); - const hasError = hasFieldError(k); - const isBrainRegionIdField = - currentCategory === 'morphology' && - (normalizedKey === 'brainregionid' || - normalizedKey === 'brain_region_id' || - normalizedKey === 'brainregion'); + normalizedKey === 'brainregionid' || + normalizedKey === 'brain_region_id' || + normalizedKey === 'brainregion'; const isSpeciesIdField = normalizedKey === 'speciesid' || normalizedKey === 'species_id' || normalizedKey === 'species'; - const isAtlasIdField = - normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas'; - const isExperimentDateField = - normalizedKey === 'experimentdate' || - normalizedKey === 'experiment_date' || - normalizedKey === 'date' || - v.title?.toLowerCase().includes('date'); const isStrainIdField = normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain'; - const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; - const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id'; const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; - const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; const isSubjectIdField = normalizedKey === 'subjectid' || normalizedKey === 'subject_id'; + const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; const isRoleIdField = normalizedKey === 'roleid' || normalizedKey === 'role_id' || normalizedKey === 'role'; const isAgentIdField = normalizedKey === 'agentid' || normalizedKey === 'agent_id' || normalizedKey === 'agent'; - if (isBrainRegionIdField && nodeId) { - return ( -
- markFieldTouched(k)} - value={brainRegionName ? brainRegionName : 'Loading...'} - readOnly - /> -
- ); - } - - if (isSpeciesIdField) { - const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; - const selectedSpecies = allSpeciesStrains - ? allSpeciesStrains.find((s) => s.species_id === speciesId) + const isRequired = schema.required?.includes(k) ?? false; + const hasBeenTouched = touchedFields.has(k); + const fieldError = + hasBeenTouched && isRequired && isEmptyValue(state[k]) + ? `${obj.title || k} is required` : null; - const speciesName = selectedSpecies ? selectedSpecies.species_name : 'Loading...'; - - return ( -
- markFieldTouched(k)} - value={speciesName} - readOnly - /> -
- ); - } + const hasError = !!fieldError; - if (isAtlasIdField) { + if (isBrainRegionIdField) { return (
- markFieldTouched(k)} - value="e3e70682-c209-4cac-a29f-6fbed82c07cd" - readOnly - /> + + {fieldError &&
{fieldError}
}
); } - if (isExperimentDateField) { - const formatDate = (value: string) => { - const cleaned = value.replace(/[^\d\s-]/g, ''); - const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0); - if (parts.length === 0) return ''; - if (parts.length === 1) return parts[0]; - if (parts.length === 2) return `${parts[0]} ${parts[1]}`; - return parts.slice(0, 3).join(' '); - }; - - const validateDateFormat = (value: string) => { - if (!value) return true; - const parts = value.split(' '); - if (parts.length !== 3) return false; - const [day, month, year] = parts; - const dayNum = parseInt(day, 10); - const monthNum = parseInt(month, 10); - const yearNum = parseInt(year, 10); + if (isSpeciesIdField) { + if (!allSpeciesStrains) { return ( - dayNum >= 1 && - dayNum <= 31 && - monthNum >= 1 && - monthNum <= 12 && - yearNum >= 1900 && - yearNum <= new Date().getFullYear() +
+ +
); - }; + } - const currentValue = typeof state[k] === 'string' ? state[k] : ''; - const isValid = validateDateFormat(currentValue); - const showDateError = !isValid && currentValue; + const options = allSpeciesStrains.map((species) => ({ + label: species.species_name, + value: species.species_id, + })); return (
- markFieldTouched(k)} - value={currentValue} - className={`w-full ${hasError || showDateError ? 'border-red-500' : ''}`} - onChange={(e) => { - const formatted = formatDate(e.currentTarget.value); - setState({ ...state, [k]: formatted }); + onChange={(newV) => { + setState((prev) => ({ ...prev, [k]: newV })); + markFieldTouched(k); }} - placeholder="DD MM YYYY (e.g., 15 03 2024)" + value={state[k]} + options={options} + placeholder="Select a species" + allowClear /> - {showDateError && ( -
- Please use format: DD MM YYYY (day month year) -
- )} {fieldError &&
{fieldError}
}
); @@ -756,116 +581,13 @@ export function JSONMorphologySchemaForm({ value={state[k]} options={strainOptions} placeholder="Select a strain" + allowClear /> {fieldError &&
{fieldError}
}
); } - if (isAgePeriodField) { - if (obj.enum) { - return ( -
- markFieldTouched(k)} - value={typeof state[k] === 'string' ? state[k] : ''} - onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); - }} - placeholder="Enter age period" - /> - {fieldError &&
{fieldError}
} -
- ); - } - - if (isLegacyIdField) { - return ( -
-
-
- {Array.isArray(state[k]) && - state[k].map((e) => ( -
- {e}{' '} - {!disabled && ( - { - const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; - newElements.splice(newElements.indexOf(e), 1); - setState({ ...state, [k]: newElements }); - markFieldTouched(k); - }} - /> - )} -
- ))} -
- {!addingElement[k] && !disabled && ( - setAddingElement({ ...addingElement, [k]: true })} - className="text-primary-8" - /> - )} - {addingElement[k] && !disabled && ( -
- setNewElement({ ...newElement, [k]: e.currentTarget.value })} - placeholder="Enter legacy ID" - /> - {newElement[k] && ( - { - setState({ - ...state, - [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], - }); - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - markFieldTouched(k); - }} - /> - )} - { - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - }} - className="text-primary-8" - /> -
- )} -
- {fieldError &&
{fieldError}
} -
- ); - } - if (isLicenseIdField) { if (!allLicenses) { return ( @@ -887,12 +609,13 @@ export function JSONMorphologySchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); + setState((prev) => ({ ...prev, [k]: newV })); markFieldTouched(k); }} value={state[k]} options={options} placeholder="Select a license" + allowClear /> {fieldError &&
{fieldError}
}
@@ -920,12 +643,13 @@ export function JSONMorphologySchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); + setState((prev) => ({ ...prev, [k]: newV })); markFieldTouched(k); }} value={state[k]} options={options} placeholder="Select a subject" + allowClear /> {fieldError &&
{fieldError}
}
@@ -953,12 +677,16 @@ export function JSONMorphologySchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); + setState((prev) => { + const newState = { ...prev, [k]: newV }; + return newState; + }); markFieldTouched(k); }} value={state[k]} options={options} placeholder="Select an MTYPE CLASS" + allowClear /> {fieldError &&
{fieldError}
}
@@ -986,12 +714,13 @@ export function JSONMorphologySchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); + setState((prev) => ({ ...prev, [k]: newV })); markFieldTouched(k); }} value={state[k]} options={options} placeholder="Select a role" + allowClear /> {fieldError &&
{fieldError}
}
@@ -1019,184 +748,29 @@ export function JSONMorphologySchemaForm({ className={`w-full ${hasError ? 'border-red-500' : ''}`} onBlur={() => markFieldTouched(k)} onChange={(newV) => { - setState({ ...state, [k]: newV }); + setState((prev) => ({ ...prev, [k]: newV })); markFieldTouched(k); }} value={state[k]} options={options} placeholder="Select an agent" + allowClear /> {fieldError &&
{fieldError}
}
); } - if (v.is_block_reference && v.properties && typeof v.properties.type.const === 'string') { - const referenceKey = referenceTypesToConfigKeys[v.properties.type.const]; - const referenceTitle = referenceTypesToTitles[v.properties.type.const]; - if (!referenceKey) return null; - const referenceConfig = config[referenceKey]; - if (!isPlainObject(referenceConfig)) return null; - - const referees = Object.entries(referenceConfig).filter(([, val]) => { - return isPlainObject(val); - }); - - if (referees.length === 0) { - return ( -
- - {fieldError &&
{fieldError}
} -
- ); - } - - const defaultV = - isPlainObject(state[k]) && typeof state[k].block_name === 'string' - ? state[k].block_name - : null; - - return ( -
- onFieldChange(field, { ...value, [key]: e.target.value })} + /> +
+ ))} +
+ ) : ( + onFieldChange(field, e.target.value)} + /> + )} +
+ ); +} + +export default function DetailHeader< + T extends EntityCoreIdentifiableNamed & Partial>, +>({ fields, detail, extraHeaderAction, @@ -44,38 +94,90 @@ export default function DetailHeader({ commonFieldsClassName, fieldsClassName, onDownload, + isEditing = false, + onEditToggle, + onSave, + onFieldChange, }: { fields: Array; detail: T; commonFields?: Array; - // @FIXME: this property is not used. - // eslint-disable-next-line react/no-unused-prop-types url?: string | null; extraHeaderAction?: ReactNode; commonFieldsClassName?: string; fieldsClassName?: string; onDownload?: (entity: T) => void; + isEditing?: boolean; + onEditToggle?: () => void; + onSave?: () => void; + onFieldChange?: (fieldName: string, value: unknown) => void; }) { return (
- detail={detail} extraHeaderAction={extraHeaderAction} onDownload={onDownload} /> + + detail={detail} + extraHeaderAction={extraHeaderAction} + onDownload={onDownload} + isEditing={isEditing} + onEditToggle={onEditToggle} + onSave={onSave} + />
- {commonFields.length > 0 && ( -
- {commonFields.map(({ className, field }) => ( - - ))} -
+ {isEditing ? ( + <> + {commonFields.length > 0 && ( +
+ {commonFields.map(({ className, field }) => ( + + key={field} + className={className} + field={field} + data={detail} + onFieldChange={onFieldChange!} + /> + ))} +
+ )} +
+ {fields.map(({ className, field }) => ( + + key={field} + className={className} + field={field} + data={detail} + onFieldChange={onFieldChange!} + /> + ))} +
+ + ) : ( + <> + {commonFields.length > 0 && ( +
+ {commonFields.map(({ className, field }) => ( + key={field} className={className} field={field} data={detail} /> + ))} +
+ )} +
+ {fields.map(({ className, field }) => ( + key={field} className={className} field={field} data={detail} /> + ))} +
+ )} -
- {fields.map(({ className, field }) => ( - - ))} -
); diff --git a/src/features/details-view/summary.tsx b/src/features/details-view/summary.tsx index b067b3578..1cfb23e86 100644 --- a/src/features/details-view/summary.tsx +++ b/src/features/details-view/summary.tsx @@ -25,8 +25,11 @@ import type { TypeSummaryProps } from '@/entity-configuration/definitions/view-d import type { EntityCoreIdentifiableNamed } from '@/api/entitycore/types/shared/global'; import type { DetailViewUrlParams } from '@/types/explore-section/application'; import { downloadArchive } from '@/services/entity-download'; +import { EntityCoreFields } from '@/entity-configuration/definitions/fields-defs/enums'; -export default function Summary({ +export default function Summary< + T extends EntityCoreIdentifiableNamed & Partial>, +>({ payload, showViewMode, extraHeaderAction, @@ -50,12 +53,15 @@ export default function Summary({ const memoizedDetailAtom = useMemo(() => { const detailFetchAtom = detailFamily({ id, virtualLabId, projectId, dataType, ...params }); return conditionalAtom(payload, detailFetchAtom); - // eslint-disable-next-line react-hooks/exhaustive-deps - }, [payload, id, virtualLabId, projectId, dataType, JSON.stringify(params)]); + }, [payload, id, virtualLabId, projectId, dataType, params]); const detail = useAtomValue(memoizedDetailAtom); - const onDownload = useCallback((entity: T) => downloadArchive(entity.type, [entity.id]), []); + const onDownload = useCallback( + (entity: EntityCoreIdentifiableNamed & Partial>) => + downloadArchive(entity.type, [entity.id]), + [] + ); useEffect(() => { setBrainRegionSidebarIsCollapsed(true); From 537cfd09160eb08a06c6952a1e5f37663dd711f0 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 08:10:05 +0200 Subject: [PATCH 24/44] updated with feedback --- .../morphology/small-microcircuit.module.css | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100755 src/features/contribute/morphology/small-microcircuit.module.css diff --git a/src/features/contribute/morphology/small-microcircuit.module.css b/src/features/contribute/morphology/small-microcircuit.module.css new file mode 100755 index 000000000..0a4777633 --- /dev/null +++ b/src/features/contribute/morphology/small-microcircuit.module.css @@ -0,0 +1,32 @@ +div.threeColumns { + display: grid; + grid-template-columns: minmax(0, 1fr) minmax(0, 1fr) minmax(0, 2fr); + gap: 5px; + height: calc(100% - 100px); +} + +div.threeColumns > div { + min-height: 0; + height: 100%; +} + +div.threeColumns > div.scrollable { + overflow-y: auto; + overflow-x: visible; +} + +div.threeColumns > div:first-child { + display: grid; + grid-template-rows: 1fr auto; + gap: 1em; + overflow: unset; +} + +header.header { + display: flex; + flex-wrap: nowrap; + flex-direction: row; + justify-content: space-between; + align-items: center; + gap: 1em; +} From f0991406aa8935566c0e8cb5faaba871be3042cb Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 08:14:21 +0200 Subject: [PATCH 25/44] updated with feedback --- .../morphology/_components/tooltip/index.ts | 1 + .../_components/tooltip/tooltip.module.css | 39 +++++++++ .../_components/tooltip/tooltip.tsx | 20 +++++ .../#button-edit-metadata.css# | 80 +++++++++++++++++++ .../button-edit-metadata.module.css | 78 ++++++++++++++++++ .../button-edit-metadata.tsx | 43 ++++++++++ .../button-edit-metadata/index.ts | 1 + 7 files changed, 262 insertions(+) create mode 100644 src/features/contribute/morphology/_components/tooltip/index.ts create mode 100644 src/features/contribute/morphology/_components/tooltip/tooltip.module.css create mode 100644 src/features/contribute/morphology/_components/tooltip/tooltip.tsx create mode 100644 src/features/details-view/button-edit-metadata/#button-edit-metadata.css# create mode 100644 src/features/details-view/button-edit-metadata/button-edit-metadata.module.css create mode 100644 src/features/details-view/button-edit-metadata/button-edit-metadata.tsx create mode 100644 src/features/details-view/button-edit-metadata/index.ts diff --git a/src/features/contribute/morphology/_components/tooltip/index.ts b/src/features/contribute/morphology/_components/tooltip/index.ts new file mode 100644 index 000000000..bb106e207 --- /dev/null +++ b/src/features/contribute/morphology/_components/tooltip/index.ts @@ -0,0 +1 @@ +export { default } from './tooltip'; diff --git a/src/features/contribute/morphology/_components/tooltip/tooltip.module.css b/src/features/contribute/morphology/_components/tooltip/tooltip.module.css new file mode 100644 index 000000000..a4e563aa8 --- /dev/null +++ b/src/features/contribute/morphology/_components/tooltip/tooltip.module.css @@ -0,0 +1,39 @@ +.tooltipContainer { + position: relative; + overflow: visible; +} + +.tooltip { + position: relative; + background: #0050b3ee; + color: #fff; + padding: 0.5em 1em; + border-radius: 0.25em; + position: absolute; + left: 0; + right: 0; + bottom: 0; + width: 100%; + pointer-events: none; + z-index: 9; + transform: translateY(calc(100% + 16px)); + transition: all 0.2s; + opacity: 0; +} + +.tooltipContainer:hover .tooltip { + opacity: 1; +} + +.tooltip::after { + content: ''; + border: 16px solid transparent; + border-bottom: 16px solid #0050b3ee; + position: absolute; + top: -16px; + left: 50%; + width: 0; + height: 0; + margin: -16px; + transform: scale(0.5, 1); +} diff --git a/src/features/contribute/morphology/_components/tooltip/tooltip.tsx b/src/features/contribute/morphology/_components/tooltip/tooltip.tsx new file mode 100644 index 000000000..45a1501f4 --- /dev/null +++ b/src/features/contribute/morphology/_components/tooltip/tooltip.tsx @@ -0,0 +1,20 @@ +import React from 'react'; + +import { classNames } from '@/util/utils'; + +import styles from './tooltip.module.css'; + +interface TooltipProps { + className?: string; + value?: React.ReactNode; + children: React.ReactNode; +} + +export default function Tooltip({ className, value, children }: TooltipProps) { + return ( +
+ {children} + {value &&
{value}
} +
+ ); +} diff --git a/src/features/details-view/button-edit-metadata/#button-edit-metadata.css# b/src/features/details-view/button-edit-metadata/#button-edit-metadata.css# new file mode 100644 index 000000000..c4baa6891 --- /dev/null +++ b/src/features/details-view/button-edit-metadata/#button-edit-metadata.css# @@ -0,0 +1,80 @@ +.buttonEditMetadata { + margin: 0; + padding: 0; + position: relative; + overflow: visible; +} + padding: 0; + position: relative; + +.buttonEditMetadata, +.buttonEditMetadata > button.actualButton { + cursor: pointer; +} + +.buttonEditMetadata:hover > button.actualButton:hover { + color: #0352b3; +} + +.tooltip { + position: absolute; + left: 50%; + bottom: -2.5em; + width: auto; + height: 2em; + color: #fffe; + background-color: #003a8c; + z-index: 9999; + display: grid; + place-items: center; + margin-left: -50%; + padding: 0 1em; + pointer-events: none; + opacity: 0; + transition: opacity 0.2s; +} + +.buttonEditMetadata.copied .tooltip { + display: none; +} + +.buttonEditMetadata:hover .tooltip { + opacity: 1; +} + +.tooltip::after { + content: ''; + background-color: transparent; + position: absolute; + left: 50%; + top: -1em; + width: 0; + height: 0; + border-width: 0.5em; + border-color: transparent; + border-bottom: 0.5em solid #003a8c; +} + +.copiedLabel { + position: absolute; + left: 0; + top: 0; + width: 100%; + height: 100%; + display: flex; + flex-wrap: nowrap; + flex-direction: row; + justify-content: center; + align-items: center; + gap: 1em; + opacity: 0; + pointer-events: none; +} + +.buttonEditMetadata.copied .copiedLabel { + opacity: 1; +} + +.buttonEditMetadata.copied > button.actualButton { + opacity: 0; +} diff --git a/src/features/details-view/button-edit-metadata/button-edit-metadata.module.css b/src/features/details-view/button-edit-metadata/button-edit-metadata.module.css new file mode 100644 index 000000000..81dd62528 --- /dev/null +++ b/src/features/details-view/button-edit-metadata/button-edit-metadata.module.css @@ -0,0 +1,78 @@ +.buttonEditMetadata { + margin: 0; + padding: 0; + position: relative; + overflow: visible; +} + +.buttonEditMetadata, +.buttonEditMetadata > button.actualButton { + cursor: pointer; +} + +.buttonEditMetadata:hover > button.actualButton:hover { + color: #0352b3; +} + +.tooltip { + position: absolute; + left: 50%; + bottom: -2.5em; + width: auto; + height: 2em; + color: #fffe; + background-color: #003a8c; + z-index: 9999; + display: grid; + place-items: center; + margin-left: -50%; + padding: 0 1em; + pointer-events: none; + opacity: 0; + transition: opacity 0.2s; +} + +.buttonEditMetadata.copied .tooltip { + display: none; +} + +.buttonEditMetadata:hover .tooltip { + opacity: 1; +} + +.tooltip::after { + content: ''; + background-color: transparent; + position: absolute; + left: 50%; + top: -1em; + width: 0; + height: 0; + border-width: 0.5em; + border-color: transparent; + border-bottom: 0.5em solid #003a8c; +} + +.copiedLabel { + position: absolute; + left: 0; + top: 0; + width: 100%; + height: 100%; + display: flex; + flex-wrap: nowrap; + flex-direction: row; + justify-content: center; + align-items: center; + gap: 1em; + opacity: 0; + pointer-events: none; +} + +.buttonEditMetadata.copied .copiedLabel { + opacity: 1; +} + +.buttonEditMetadata.copied > button.actualButton { + opacity: 0; +} diff --git a/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx b/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx new file mode 100644 index 000000000..01d1b268a --- /dev/null +++ b/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx @@ -0,0 +1,43 @@ +import React from 'react'; +import { Button } from 'antd'; +import { EditOutlined, EyeOutlined } from '@ant-design/icons'; + +import { classNames } from '@/util/utils'; + +import styles from './button-edit-metadata.module.css'; + +interface ButtonEditMetadataProps { + className?: string; + label?: string; + tooltip?: string; + isEditing: boolean; + onClick: () => void; +} + +export function ButtonEditMetadata({ + className, + label = 'Edit Metadata', + isEditing, + onClick, +}: ButtonEditMetadataProps) { + return ( +
+ +
+ ); +} diff --git a/src/features/details-view/button-edit-metadata/index.ts b/src/features/details-view/button-edit-metadata/index.ts new file mode 100644 index 000000000..4226d5370 --- /dev/null +++ b/src/features/details-view/button-edit-metadata/index.ts @@ -0,0 +1 @@ +export * from './button-edit-metadata'; From 7f1d0556339ceaf3f103fc496e7a5cee8ddeb39e Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 08:49:11 +0200 Subject: [PATCH 26/44] updated with feedback --- .../interactive/add/experimental/morphology/page.tsx | 12 +++--------- .../morphology/_components/hooks/schema.ts | 1 - src/features/contribute/morphology/index.tsx | 4 +--- 3 files changed, 4 insertions(+), 13 deletions(-) diff --git a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx index 74df5228a..73400c1b2 100755 --- a/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx +++ b/src/app/app/virtual-lab/lab/[virtualLabId]/project/[projectId]/explore/interactive/add/experimental/morphology/page.tsx @@ -4,17 +4,11 @@ import { useParams } from 'next/navigation'; import ContributeMorphologyConfiguration from '@/features/contribute/morphology'; import { WorkspaceContext } from '@/types/common'; -type Params = WorkspaceContext & { circuit_id: string }; +type Params = WorkspaceContext; export default function MorphologyPage() { const params = useParams(); - const { virtualLabId, projectId, circuit_id } = params; + const { virtualLabId, projectId } = params; - return ( - - ); + return ; } diff --git a/src/features/contribute/morphology/_components/hooks/schema.ts b/src/features/contribute/morphology/_components/hooks/schema.ts index f09d4543d..825f9bc51 100644 --- a/src/features/contribute/morphology/_components/hooks/schema.ts +++ b/src/features/contribute/morphology/_components/hooks/schema.ts @@ -143,7 +143,6 @@ export function resolveKey( } export function useObioneJsonConfigurationSchema( - circuitId: string, notification: NotificationInstance, setSchema: React.Dispatch>, setAtomsMap: (atomsMap: AtomsMap) => void diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index 64840df58..8caf5ef37 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -30,13 +30,11 @@ import { classNames } from '@/util/utils'; import styles from './small-microcircuit.module.css'; export default function ContributeMorphologyConfiguration({ - circuitId, virtualLabId, projectId, initialCampaignId, initialConfig, }: { - circuitId: string; virtualLabId: string; projectId: string; initialCampaignId?: string; @@ -127,7 +125,7 @@ export default function ContributeMorphologyConfiguration({ return validate.errors ?? []; }, [validate, config]); - useObioneJsonConfigurationSchema(circuitId, notification, setSchema, setAtomsMap); + useObioneJsonConfigurationSchema(notification, setSchema, setAtomsMap); const canSubmit = !errors.length && !loading && !readOnly && selectedFile && formValidation.isValid; From 1040e896d8eb515a4ef8db3625ad70e1f4849c79 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 10:24:25 +0200 Subject: [PATCH 27/44] updated with feedback --- src/features/contribute/index.tsx | 656 ------------------ .../morphology/_components/components.tsx | 190 +++-- .../morphology/_components/hooks/schema.ts | 138 +--- .../morphology/_components/section.tsx | 82 ++- src/features/contribute/morphology/index.tsx | 175 ++--- src/features/contribute/morphology/types.ts | 9 +- .../button-edit-metadata.tsx | 1 - src/features/details-view/overview.tsx | 28 +- 8 files changed, 277 insertions(+), 1002 deletions(-) delete mode 100755 src/features/contribute/index.tsx diff --git a/src/features/contribute/index.tsx b/src/features/contribute/index.tsx deleted file mode 100755 index 78aa0b8a4..000000000 --- a/src/features/contribute/index.tsx +++ /dev/null @@ -1,656 +0,0 @@ -'use client'; - -import { - LoadingOutlined, - UploadOutlined, - CheckCircleFilled, - WarningFilled, - RightOutlined, -} from '@ant-design/icons'; -import Ajv, { AnySchema } from 'ajv'; -import { atom } from 'jotai'; -import { Fragment, useMemo, useRef, useState, KeyboardEvent, useEffect } from 'react'; -import { Config, ConfigValue, JSONSchemaForm } from './_components/components'; -import { useConfigAtom } from './_components/hooks/config-atom'; -import { - isRootCategory, - resolveKey, - useObioneJsonConfigurationSchema, -} from './_components/hooks/schema'; -import { Section } from './_components/section'; -import { CATEGORIES, isAtom, ORDERING } from './_components/utils'; -import { AtomsMap, JSONSchema } from './types'; -import { resolveDataKey } from '@/utils/key-builder'; -import { useBrainRegionHierarchy } from '@/features/brain-region-hierarchy/context'; -import ApiError from '@/api/error'; -import authFetch from '@/authFetch'; -import { useAppNotification } from '@/components/notification'; -import { classNames } from '@/util/utils'; -import styles from './small-microcircuit.module.css'; - -export default function ContributeMorphologyConfiguration({ - circuitId, - virtualLabId, - projectId, - initialCampaignId, - initialConfig, -}: { - circuitId: string; - virtualLabId: string; - projectId: string; - initialCampaignId?: string; - initialConfig?: Config; -}) { - if (!!initialCampaignId !== !!initialConfig) { - throw new Error('Both or none of initialCampaignId, initialConfigId should be passed'); - } - - const { node } = useBrainRegionHierarchy({ - dataKey: resolveDataKey({ section: 'explore', projectId }), - }); - - const [configTab, setConfigTab] = useState('info'); - const [editing, setEditing] = useState(true); - const [schema, setSchema] = useState(null); - const [selectedCategory, setSelectedCategory] = useState(''); - const [selectedItemIdx, setSelectedItemIdx] = useState(null); - const [loading, setLoading] = useState(false); - const [showConfig, setShowConfig] = useState(false); - const [selectedFile, setSelectedFile] = useState(null); - const [fileStatus, setFileStatus] = useState<{ - message?: string; - }>({}); - const [newJsonPayload, setNewJsonPayload] = useState(null); - const notification = useAppNotification(); - const [campaignId, setCampaignId] = useState(initialCampaignId ?? ''); - const initialConfigValidated = useRef(false); - - // Add success state - const [isSuccess, setIsSuccess] = useState(false); - - // Add validation state - const [formValidation, setFormValidation] = useState<{ - isValid: boolean; - errors: string[]; - }>({ - isValid: true, - errors: [], - }); - - // Debug log to verify selectedFile state - useEffect(() => { - console.log('selectedFile state:', selectedFile); - }, [selectedFile]); - - const selectedCatSchema = schema?.properties?.[configTab]?.additionalProperties?.anyOf?.find( - (s) => s.properties?.type.const === selectedCategory - ); - - const handleAddReferenceClick = (referenceTab: string) => { - setConfigTab(referenceTab); - setEditing(true); - setSelectedCategory(''); - }; - - // Handle validation changes from the form - const handleValidationChange = (isValid: boolean, errors: string[]) => { - setFormValidation({ isValid, errors }); - }; - - const readOnly = initialConfig !== undefined; - - const validate = useMemo(() => { - const ajv = new Ajv({ strictSchema: false, allErrors: true }); - if (!schema) { - return; - } - return ajv.compile(schema as AnySchema); - }, [schema]); - - const [atomsMap, setAtomsMap] = useState({}); - - const config = useConfigAtom(schema, atomsMap, node.id, configTab); - - if (validate && initialConfig && !initialConfigValidated.current) { - initialConfigValidated.current = true; - validate(initialConfig); - if (validate.errors) { - throw new Error('Invalid Simulation Campaign Configuration'); - } - } - - const errors = useMemo(() => { - if (validate) { - validate(config); - } - return validate?.errors; - }, [validate, config]); - - useObioneJsonConfigurationSchema(circuitId, notification, setSchema, setAtomsMap); - - // Update the submit button condition - const canSubmit = - !errors?.length && !loading && !readOnly && selectedFile && formValidation.isValid; - - // Show success page if upload was successful - if (isSuccess) { - return ( -
-
-
- ✓ Morphology created successfully -
- -
-
- ); - } - - if (!schema) { - return ( -
- -
- ); - } - - return ( -
-
-
-
-
- {/* ... form validation */} -
Assets
-
{ - setConfigTab('assets'); - setEditing(true); - setSelectedCategory(''); - setSelectedItemIdx(null); - }} - onKeyDown={(e: KeyboardEvent) => { - if (e.key === 'Enter' || e.key === ' ') { - setConfigTab('assets'); - setEditing(true); - setSelectedCategory(''); - setSelectedItemIdx(null); - } - }} - > - Assets -
- {selectedFile ? ( - <> - - - - ) : ( - <> - - - - )} -
-
- {CATEGORIES.filter((c) => c !== 'Assets').map((c) => ( - -
{c}
- {schema.properties && - Object.entries(schema.properties) - .filter(([k]) => k !== 'type' && ORDERING[k]?.category === c) - .sort((a, b) => { - const order = (k: string) => ORDERING[k]?.order ?? 999; - return order(a[0]) - order(b[0]); - }) - .map(([k, v]) => ( -
- ))} - - ))} -
- {!readOnly && ( - - )} -
-
- {configTab === 'assets' && editing && ( -
-
- UPLOAD MORPHOLOGY FILE -
-
- One reference file should be loaded. -
-
-
- - {fileStatus?.message && ( - {fileStatus.message} - )} -
-
-
- )} - {schema.properties && - schema.properties?.[configTab]?.additionalProperties?.anyOf && - !selectedCategory && - editing && - configTab !== 'assets' && ( -
- {schema.properties[configTab].additionalProperties.anyOf.map((o) => ( -
{ - if (isRootCategory(schema, configTab)) return; - setSelectedCategory(o.properties?.type.const ?? ''); - const initial: Record = {}; - if (o.properties) { - Object.entries(o.properties).forEach(([subkey, subValue]) => { - initial[subkey] = - subkey === 'type' - ? (subValue.const ?? null) - : (subValue.default ?? null); - }); - } - const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => - parseInt(subkey.split('_')[1], 10) - ); - itemIndexes.sort((a, b) => a - b); - const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; - setSelectedItemIdx(itemIdx); - setAtomsMap({ - ...atomsMap, - [configTab]: { - ...atomsMap[configTab], - [resolveKey(schema, configTab, itemIdx)]: - atom>(initial), - }, - }); - }} - onKeyDown={(e: KeyboardEvent) => { - if (e.key === 'Enter' || e.key === ' ') { - if (isRootCategory(schema, configTab)) return; - setSelectedCategory(o.properties?.type.const ?? ''); - const initial: Record = {}; - if (o.properties) { - Object.entries(o.properties).forEach(([subkey, subValue]) => { - initial[subkey] = - subkey === 'type' - ? (subValue.const ?? null) - : (subValue.default ?? null); - }); - } - const itemIndexes = Object.keys(atomsMap[configTab]).map((subkey) => - parseInt(subkey.split('_')[1], 10) - ); - itemIndexes.sort((a, b) => a - b); - const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; - setSelectedItemIdx(itemIdx); - setAtomsMap({ - ...atomsMap, - [configTab]: { - ...atomsMap[configTab], - [resolveKey(schema, configTab, itemIdx)]: - atom>(initial), - }, - }); - } - }} - > -
{o.title}
-
{o.description}
-
- ))} -
- )} - {schema.properties && - schema.properties?.[configTab] && - editing && - (isRootCategory(schema, configTab) || selectedCatSchema) && - configTab !== 'assets' && ( - - )} -
-
- {showConfig && ( -
-
-
-

New Record JSON

- -
- - 
-              {JSON.stringify(newJsonPayload, null, 2)}
-
- -
- -
-
-
- )} -
- ); -} diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index d3d654541..469d263de 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -1,4 +1,3 @@ -// src/features/contribute/morphology/_components/components.tsx import { useEffect, useState } from 'react'; import { useAtom, PrimitiveAtom } from 'jotai'; import { InputNumber, Input, Select } from 'antd'; @@ -131,8 +130,8 @@ const processData = async (token: string): Promise => { const urlSpecies = 'https://staging.openbraininstitute.org/api/entitycore/subject'; const urlStrain = 'https://staging.openbraininstitute.org/api/entitycore/strain'; - let json_data_species: SpeciesData = { data: [] }; - let json_data_strain: StrainData = { data: [] }; + let jsonDataSpecies: SpeciesData = { data: [] }; + let jsonDataStrain: StrainData = { data: [] }; try { const [responseSpecies, responseStrain] = await Promise.all([ @@ -147,18 +146,17 @@ const processData = async (token: string): Promise => { throw new Error(`Strain request failed with status code: ${responseStrain.status}`); } - json_data_species = await responseSpecies.json(); - json_data_strain = await responseStrain.json(); - } catch (error) { - console.error((error as Error).message); + jsonDataSpecies = await responseSpecies.json(); + jsonDataStrain = await responseStrain.json(); + } catch { return null; } - json_data_species.data.push({ + jsonDataSpecies.data.push({ id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', name: 'Generic Mus musculus', }); - json_data_species.data.push({ + jsonDataSpecies.data.push({ id: '3b1c2a25-b4fb-468d-98d2-d2d431ac8b4a', name: 'Generic Rattus norvegicus', }); @@ -169,27 +167,25 @@ const processData = async (token: string): Promise => { strains: Record; }> = []; - for (const species_record of json_data_species.data) { - if (species_record.name === 'Unknown') { + for (const speciesRecord of jsonDataSpecies.data) { + if (speciesRecord.name === 'Unknown') { continue; } - const filtered_data = json_data_strain.data.filter( - (item) => item.species_id === species_record.id - ); + const filteredData = jsonDataStrain.data.filter((item) => item.species_id === speciesRecord.id); const strains: Record = {}; - for (const strain of filtered_data) { + for (const strain of filteredData) { strains[strain.name] = strain.id; } - const species_entry = { - species_id: species_record.id, - species_name: species_record.name, + const speciesEntry = { + species_id: speciesRecord.id, + species_name: speciesRecord.name, strains, }; - speclist.push(species_entry); + speclist.push(speciesEntry); } return JSON.stringify(speclist, null, 2); @@ -208,17 +204,16 @@ const fetchAgents = async (token: string): Promise | null if (!response.ok) { throw new Error(`Agent request failed with status code: ${response.status}`); } - const json_data_person: PersonData = await response.json(); + const jsonDataPerson: PersonData = await response.json(); - const person_dict: Record = {}; - for (const item of json_data_person.data) { + const personDict: Record = {}; + for (const item of jsonDataPerson.data) { if (item.pref_label) { - person_dict[item.pref_label] = item.id; + personDict[item.pref_label] = item.id; } } - return person_dict; - } catch (error) { - console.error((error as Error).message); + return personDict; + } catch { return null; } }; @@ -236,17 +231,16 @@ const fetchRoles = async (token: string): Promise | null> if (!response.ok) { throw new Error(`Role request failed with status code: ${response.status}`); } - const json_data_role: RoleData = await response.json(); + const jsonDataRole: RoleData = await response.json(); - const role_dict: Record = {}; - for (const item of json_data_role.data) { + const roleDict: Record = {}; + for (const item of jsonDataRole.data) { if (item.name) { - role_dict[item.name] = item.id; + roleDict[item.name] = item.id; } } - return role_dict; - } catch (error) { - console.error((error as Error).message); + return roleDict; + } catch { return null; } }; @@ -266,21 +260,20 @@ const fetchSubjects = async ( if (!response.ok) { throw new Error(`Subject request failed with status code: ${response.status}`); } - const json_data_subject: SubjectData = await response.json(); + const jsonDataSubject: SubjectData = await response.json(); - const subject_list: Array<{ label: string; value: string }> = []; - for (const item of json_data_subject.data) { + const subjectList: Array<{ label: string; value: string }> = []; + for (const item of jsonDataSubject.data) { if (item.name) { - const subject_entry = { + const subjectEntry = { label: item.name, value: item.id, }; - subject_list.push(subject_entry); + subjectList.push(subjectEntry); } } - return subject_list; - } catch (error) { - console.error((error as Error).message); + return subjectList; + } catch { return null; } }; @@ -300,21 +293,20 @@ const fetchLicenses = async ( if (!response.ok) { throw new Error(`License request failed with status code: ${response.status}`); } - const json_data_license: LicenseData = await response.json(); + const jsonDataLicense: LicenseData = await response.json(); - const license_list: Array<{ label: string; value: string }> = []; - for (const item of json_data_license.data) { + const licenseList: Array<{ label: string; value: string }> = []; + for (const item of jsonDataLicense.data) { if (item.label && item.label !== 'undefined') { - const license_entry = { + const licenseEntry = { label: item.label, value: item.id, }; - license_list.push(license_entry); + licenseList.push(licenseEntry); } } - return license_list; - } catch (error) { - console.error((error as Error).message); + return licenseList; + } catch { return null; } }; @@ -334,23 +326,21 @@ const fetchMtypes = async ( if (!response.ok) { throw new Error(`MTYPE request failed with status code: ${response.status}`); } - const json_data_mtype: MtypeData = await response.json(); + const jsonDataMtype: MtypeData = await response.json(); - const mtype_list: Array<{ mtype_pref_label: string; mtype_id: string }> = []; - for (const item of json_data_mtype.data) { + const mtypeList: Array<{ mtype_pref_label: string; mtype_id: string }> = []; + for (const item of jsonDataMtype.data) { if (item.pref_label) { - const alt_label = item.alt_label ? ` ${item.alt_label}` : ''; - const mtype_entry = { - mtype_pref_label: item.pref_label + alt_label, + const altLabel = item.alt_label ? ` ${item.alt_label}` : ''; + const mtypeEntry = { + mtype_pref_label: item.pref_label + altLabel, mtype_id: item.id, }; - mtype_list.push(mtype_entry); + mtypeList.push(mtypeEntry); } } - - return mtype_list; - } catch (error) { - console.error('fetchMtypes: Error', (error as Error).message); + return mtypeList; + } catch { return null; } }; @@ -368,10 +358,9 @@ const fetchBrainRegion = async (token: string, brainRegionId: string): Promise; nodeId?: string; - currentCategory?: string; }) { const skip = ['type']; @@ -423,45 +411,41 @@ export function JSONMorphologySchemaForm({ const session = await getSessionWithCheck(); if (!session) return; - try { - const [speciesData, agentsData, rolesData, subjectsData, licensesData, mtypesData] = - await Promise.all([ - processData(session.accessToken), - fetchAgents(session.accessToken), - fetchRoles(session.accessToken), - fetchSubjects(session.accessToken), - fetchLicenses(session.accessToken), - fetchMtypes(session.accessToken), - ]); - - let brainRegionName = null; - if (nodeId) { - brainRegionName = await fetchBrainRegion(session.accessToken, nodeId); - } - - if (speciesData) { - const parsedData = JSON.parse(speciesData); - setAllSpeciesStrains(parsedData); - } - if (agentsData) { - setAllAgents(agentsData); - } - if (rolesData) { - setAllRoles(rolesData); - } - if (subjectsData) { - setAllSubjects(subjectsData); - } - if (licensesData) { - setAllLicenses(licensesData); - } - if (mtypesData) { - setAllMtypes(mtypesData); - } - setBrainRegionName(brainRegionName); - } catch (error) { - console.error('Failed to fetch data:', error); + const [speciesData, agentsData, rolesData, subjectsData, licensesData, mtypesData] = + await Promise.all([ + processData(session.accessToken), + fetchAgents(session.accessToken), + fetchRoles(session.accessToken), + fetchSubjects(session.accessToken), + fetchLicenses(session.accessToken), + fetchMtypes(session.accessToken), + ]); + + let brainRegionName = null; + if (nodeId) { + brainRegionName = await fetchBrainRegion(session.accessToken, nodeId); + } + + if (speciesData) { + const parsedData = JSON.parse(speciesData); + setAllSpeciesStrains(parsedData); + } + if (agentsData) { + setAllAgents(agentsData); + } + if (rolesData) { + setAllRoles(rolesData); + } + if (subjectsData) { + setAllSubjects(subjectsData); + } + if (licensesData) { + setAllLicenses(licensesData); + } + if (mtypesData) { + setAllMtypes(mtypesData); } + setBrainRegionName(brainRegionName); }; fetchData(); diff --git a/src/features/contribute/morphology/_components/hooks/schema.ts b/src/features/contribute/morphology/_components/hooks/schema.ts index 825f9bc51..3e2c68d25 100644 --- a/src/features/contribute/morphology/_components/hooks/schema.ts +++ b/src/features/contribute/morphology/_components/hooks/schema.ts @@ -1,4 +1,3 @@ -// src/features/contribute/morphology/_components/hooks/schema.ts import React from 'react'; import { atom, PrimitiveAtom } from 'jotai'; import { NotificationInstance } from 'antd/es/notification/interface'; @@ -7,22 +6,31 @@ import $RefParser from '@apidevtools/json-schema-ref-parser'; import { AtomsMap, JSONMorphologySchema } from '../../types'; import { ConfigValue, Config } from '../components'; import { isPlainObject, isAtom } from '../utils'; -import { assertErrorMessage } from '@/util/utils'; // Define a type for the OpenAPI schema to include components interface OpenAPISchema { components?: { schemas?: { - SimulationsForm?: JSONMorphologySchema; - ContributeMorphologyForm?: JSONMorphologySchema; + [key: string]: JSONMorphologySchema; }; }; } -export function useObioneJsonMorphologySchema( +/** + * A generic hook to fetch and dereference a JSON schema from the OpenAPI spec. + * It also initializes Jotai atoms based on the schema properties. + * + * @param notification Antd notification instance. + * @param setSchema React state setter for the schema. + * @param setAtomsMap React state setter for the atoms map. + * @param schemaName The name of the schema to fetch (e.g., 'ContributeMorphologyForm'). + * @param initialConfig Optional initial configuration to populate the atoms. + */ +export function useObioneJsonSchema( notification: NotificationInstance, setSchema: React.Dispatch>, setAtomsMap: (atomsMap: AtomsMap) => void, + schemaName: string, initialConfig?: Config ) { React.useEffect(() => { @@ -31,25 +39,13 @@ export function useObioneJsonMorphologySchema( const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); const json = await res.json(); const dereferenced = (await $RefParser.dereference(json)) as OpenAPISchema; - const theSchema = dereferenced.components?.schemas?.SimulationsForm as - | JSONMorphologySchema - | undefined; + const theSchema = dereferenced.components?.schemas?.[schemaName]; if (!theSchema || !theSchema.properties) { - console.warn('useObioneJsonMorphologySchema: Schema has no properties', theSchema); - notification.error({ message: 'Schema has no properties' }); + notification.error({ message: `Schema "${schemaName}" has no properties` }); return; } - console.log( - 'useObioneJsonMorphologySchema: Loaded schema', - JSON.stringify(theSchema, null, 2) - ); - console.log( - 'useObioneJsonMorphologySchema: schema.properties.morphology', - theSchema.properties.morphology - ); - setSchema(theSchema); const map: AtomsMap = {}; @@ -59,27 +55,20 @@ export function useObioneJsonMorphologySchema( .filter(([k]) => isRootCategory(theSchema, k)) .forEach(([k, v]) => { if (isPlainObject(v)) { - const initial: Record = {}; - Object.entries(v).forEach(([subKey, subValue]) => { - initial[subKey] = subValue as ConfigValue; - }); - map[k] = atom>(initial); + map[k] = atom>(v as Record); } }); Object.entries(initialConfig) .filter(([k]) => !isRootCategory(theSchema, k)) .forEach(([k, v]) => { - if (!isPlainObject(v)) return; + if (!isPlainObject(v) || isAtom(map[k])) return; map[k] = {}; Object.entries(v).forEach(([subK, subV]) => { - if (!isPlainObject(subV) || isAtom(map[k])) return; - const initial: Record = {}; - Object.entries(subV).forEach(([innerKey, innerValue]) => { - initial[innerKey] = innerValue as ConfigValue; - }); - (map[k] as Record>>)[subK] = - atom>(initial); + if (!isPlainObject(subV)) return; + (map[k] as Record>>)[subK] = atom< + Record + >(subV as Record); }); }); } else { @@ -100,25 +89,17 @@ export function useObioneJsonMorphologySchema( } }); } - - console.log('useObioneJsonMorphologySchema: Initialized atomsMap', map); setAtomsMap(map); - } catch (e) { - console.error( - 'useObioneJsonMorphologySchema: Failed to fetch schema:', - assertErrorMessage(e) - ); - notification.error({ message: assertErrorMessage(e) }); + } catch { + notification.error({ message: `Failed to fetch schema "${schemaName}"` }); } } - fetchSpec(); - }, [notification, setAtomsMap, setSchema, initialConfig]); + }, [notification, setAtomsMap, setSchema, schemaName, initialConfig]); } export function isRootCategory(schema: JSONMorphologySchema | null, key: string) { - const isRoot = schema?.properties?.[key] && !schema.properties[key].additionalProperties; - console.log(`isRootCategory: key=${key}, isRoot=${isRoot}`); + const isRoot = !!schema?.properties?.[key] && !schema.properties[key].additionalProperties; return isRoot; } @@ -129,80 +110,11 @@ export function resolveKey( ) { if (itemIdx === null) throw new Error('Invalid itemIdx'); if (!schema || !schema.properties || !schema.properties[tabKey]?.singular_name) { - console.warn(`resolveKey: Using fallback key for ${tabKey}_${itemIdx} due to missing schema`); return `${tabKey}_${itemIdx}`; } if (isRootCategory(schema, tabKey)) { - console.log(`resolveKey: ${tabKey} is a root category, returning ${tabKey}`); return tabKey; } - const key = `${schema.properties[tabKey].singular_name.replaceAll(' ', '')}_${itemIdx}`; - console.log(`resolveKey: Generated key ${key} for tabKey=${tabKey}, itemIdx=${itemIdx}`); return key; } - -export function useObioneJsonConfigurationSchema( - notification: NotificationInstance, - setSchema: React.Dispatch>, - setAtomsMap: (atomsMap: AtomsMap) => void -) { - React.useEffect(() => { - async function fetchSpec() { - try { - const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); - const json = await res.json(); - const dereferenced = (await $RefParser.dereference(json)) as OpenAPISchema; - const theSchema = dereferenced.components?.schemas?.ContributeMorphologyForm as - | JSONMorphologySchema - | undefined; - - if (!theSchema || !theSchema.properties) { - console.warn('useObioneJsonConfigurationSchema: Schema has no properties', theSchema); - notification.error({ message: 'Schema has no properties' }); - return; - } - - console.log( - 'useObioneJsonConfigurationSchema: Loaded schema', - JSON.stringify(theSchema, null, 2) - ); - console.log( - 'useObioneJsonConfigurationSchema: schema.properties.morphology', - theSchema.properties.morphology - ); - - setSchema(theSchema); - - const map: AtomsMap = {}; - Object.entries(theSchema.properties).forEach(([k, v]) => { - if (!v.additionalProperties) { - const initial: Record = {}; - if (v.properties) { - Object.entries(v.properties).forEach(([subkey, subValue]) => { - initial[subkey] = - subkey === 'type' - ? (subValue.const ?? undefined) - : (subValue.default ?? undefined); - }); - } - map[k] = atom>(initial); - } else { - map[k] = {}; - } - }); - - console.log('useObioneJsonConfigurationSchema: Initialized atomsMap', map); - setAtomsMap(map); - } catch (e) { - console.error( - 'useObioneJsonConfigurationSchema: Failed to fetch schema:', - assertErrorMessage(e) - ); - notification.error({ message: assertErrorMessage(e) }); - } - } - - fetchSpec(); - }, [notification, setAtomsMap, setSchema]); -} diff --git a/src/features/contribute/morphology/_components/section.tsx b/src/features/contribute/morphology/_components/section.tsx index 5aa607b2a..f7ed8868b 100644 --- a/src/features/contribute/morphology/_components/section.tsx +++ b/src/features/contribute/morphology/_components/section.tsx @@ -1,32 +1,38 @@ -import { Dispatch, SetStateAction } from 'react'; +import { Dispatch, SetStateAction, KeyboardEvent } from 'react'; import { RightOutlined } from '@ant-design/icons'; -import { JSONMorphologySchema, AtomsMap } from '../types'; -import { classNames } from '@/util/utils'; +import isNil from 'lodash/isNil'; import { ErrorObject } from 'ajv'; -import { Config } from './components'; + +import { AtomsMap, JSONMorphologySchema, Config } from '../types'; +import { classNames } from '@/util/utils'; type Props = { k: string; - schema: JSONMorphologySchema; sectionSchema: JSONMorphologySchema | undefined; + schema: JSONMorphologySchema; + config: Config; + errors: ErrorObject, unknown>[]; // Fixed to avoid no-explicit-any atomsMap: AtomsMap; - setAtomsMap: Dispatch>; // Updated to Dispatch type + setAtomsMap: Dispatch>; configTab: string; setConfigTab: (tab: string) => void; - config: Config; - campaignId?: string; - loading?: boolean; - errors: ErrorObject, unknown>[] | null | undefined; - selectedItemIdx?: number | null; setSelectedItemIdx: (idx: number | null) => void; setEditing: (editing: boolean) => void; setSelectedCategory: (category: string) => void; + campaignId: string; + loading: boolean; + selectedItemIdx: number | null; }; export function Section({ k, - sectionSchema, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + schema, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + config, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + errors, atomsMap, setAtomsMap, configTab, @@ -34,14 +40,13 @@ export function Section({ setSelectedItemIdx, setEditing, setSelectedCategory, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + campaignId, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + loading, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + selectedItemIdx, }: Props) { - console.log(`Section ${k}:`, { - key: k, - sectionSchema: JSON.stringify(sectionSchema, null, 2), - isSectionSchemaValid: - sectionSchema && sectionSchema.type === 'object' && sectionSchema.properties, - }); - const fallbackSchema: JSONMorphologySchema = { type: 'object', title: k, @@ -53,26 +58,37 @@ export function Section({ const buttonText = k === 'subject' ? 'Subject' : schemaToUse.title || k; + const handleClick = () => { + setConfigTab(k); + setEditing(true); + setSelectedCategory(''); + setSelectedItemIdx(null); + + if (isNil(atomsMap[k])) { + setAtomsMap({ + ...atomsMap, + [k]: {}, + }); + } + }; + + const handleKeyDown = (e: KeyboardEvent) => { + if (e.key === 'Enter' || e.key === ' ') { + e.preventDefault(); + handleClick(); + } + }; + return (
{ - console.log(`Clicked section: ${k}`); - setConfigTab(k); - setEditing(true); - setSelectedCategory(''); - setSelectedItemIdx(null); - - if (!atomsMap[k]) { - setAtomsMap({ - ...atomsMap, - [k]: {}, - }); - } - }} + onClick={handleClick} + onKeyDown={handleKeyDown} + role="button" + tabIndex={0} > {buttonText}
diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index 8caf5ef37..70e2b0e47 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -1,4 +1,3 @@ -// src/features/contribute/morphology/index.tsx 'use client'; import { @@ -13,11 +12,7 @@ import { atom, useAtom, PrimitiveAtom } from 'jotai'; import { Fragment, useMemo, useRef, useState, KeyboardEvent, useEffect } from 'react'; import { Config, ConfigValue, JSONMorphologySchemaForm } from './_components/components'; import { useConfigAtom } from './_components/hooks/config-atom'; -import { - isRootCategory, - resolveKey, - useObioneJsonConfigurationSchema, -} from './_components/hooks/schema'; +import { isRootCategory, resolveKey, useObioneJsonSchema } from './_components/hooks/schema'; import { Section } from './_components/section'; import { CATEGORIES, ORDERING } from './_components/utils'; import { AtomsMap, JSONMorphologySchema } from './types'; @@ -125,7 +120,7 @@ export default function ContributeMorphologyConfiguration({ return validate.errors ?? []; }, [validate, config]); - useObioneJsonConfigurationSchema(notification, setSchema, setAtomsMap); + useObioneJsonSchema(notification, setSchema, setAtomsMap, 'ContributeMorphologyForm'); const canSubmit = !errors.length && !loading && !readOnly && selectedFile && formValidation.isValid; @@ -172,6 +167,15 @@ export default function ContributeMorphologyConfiguration({ ); } + // Fallback schema for when selectedCatSchema is undefined + const fallbackSchema: JSONMorphologySchema = { + type: 'object', + properties: {}, + required: [], + title: 'Default Schema', + description: 'Fallback schema when no specific schema is selected', + }; + return (
@@ -375,7 +379,7 @@ export default function ContributeMorphologyConfiguration({ }); } - const mtype_request_body = { + const mtypeRequestBody = { authorized_public: true, entity_id: newEntityId, mtype_class_id: mtypeConfig?.mtype_class_id ?? undefined, @@ -391,7 +395,7 @@ export default function ContributeMorphologyConfiguration({ { method: 'POST', headers: fileUploadMtypeHeaders, - body: JSON.stringify(mtype_request_body), + body: JSON.stringify(mtypeRequestBody), } ); const fileResponseMtypeText = await fileResponseMtype.text(); @@ -402,7 +406,7 @@ export default function ContributeMorphologyConfiguration({ }); } - const contribution_request_body = { + const contributionRequestBody = { entity_id: newEntityId, agent_id: contributionConfig?.agent_id ?? undefined, role_id: contributionConfig?.role_id ?? undefined, @@ -418,7 +422,7 @@ export default function ContributeMorphologyConfiguration({ { method: 'POST', headers: fileUploadContributionHeaders, - body: JSON.stringify(contribution_request_body), + body: JSON.stringify(contributionRequestBody), } ); const fileResponseContributionText = await fileResponseContribution.text(); @@ -521,42 +525,71 @@ export default function ContributeMorphologyConfiguration({
)} - {schema?.properties && - configTab !== 'assets' && + {configTab !== 'assets' && editing && ( + >) + : ( + atomsMap[configTab] as Record< + string, + PrimitiveAtom> + > + )[resolveKey(schema, configTab, selectedItemIdx)] + } + nodeId={node?.id} + /> + )} + {configTab !== 'assets' && editing && - (isRootCategory(schema, configTab) ? ( - >} - nodeId={node?.id} - currentCategory={configTab} - /> - ) : selectedCatSchema ? ( - > - > - )[resolveKey(schema, configTab, selectedItemIdx)] - } - nodeId={node?.id} - currentCategory={configTab} - /> - ) : ( - schema.properties[configTab]?.additionalProperties?.anyOf && ( -
- {schema.properties[configTab].additionalProperties.anyOf.map((o) => ( -
{ + !isRootCategory(schema, configTab) && + !selectedCatSchema && + schema.properties[configTab]?.additionalProperties?.anyOf && ( +
+ {schema.properties[configTab].additionalProperties.anyOf.map((o) => ( +
{ + if (isRootCategory(schema, configTab)) return; + setSelectedCategory(o.properties?.type.const ?? ''); + const initial: Record = {}; + if (o.properties) { + Object.entries(o.properties).forEach(([subkey, subValue]) => { + initial[subkey] = + subkey === 'type' + ? (subValue.const ?? undefined) + : (subValue.default ?? undefined); + }); + } + const itemIndexes = Object.keys(atomsMap[configTab] || {}).map((subkey) => + parseInt(subkey.split('_')[1], 10) + ); + itemIndexes.sort((a, b) => a - b); + const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; + setSelectedItemIdx(itemIdx); + setAtomsMap((prev) => ({ + ...prev, + [configTab]: { + ...(prev[configTab] as Record< + string, + PrimitiveAtom> + >), + [resolveKey(schema, configTab, itemIdx)]: + atom>(initial), + }, + })); + }} + onKeyDown={(e: KeyboardEvent) => { + if (e.key === 'Enter' || e.key === ' ') { if (isRootCategory(schema, configTab)) return; setSelectedCategory(o.properties?.type.const ?? ''); const initial: Record = {}; @@ -585,47 +618,15 @@ export default function ContributeMorphologyConfiguration({ atom>(initial), }, })); - }} - onKeyDown={(e: KeyboardEvent) => { - if (e.key === 'Enter' || e.key === ' ') { - if (isRootCategory(schema, configTab)) return; - setSelectedCategory(o.properties?.type.const ?? ''); - const initial: Record = {}; - if (o.properties) { - Object.entries(o.properties).forEach(([subkey, subValue]) => { - initial[subkey] = - subkey === 'type' - ? (subValue.const ?? undefined) - : (subValue.default ?? undefined); - }); - } - const itemIndexes = Object.keys(atomsMap[configTab] || {}).map((subkey) => - parseInt(subkey.split('_')[1], 10) - ); - itemIndexes.sort((a, b) => a - b); - const itemIdx = (itemIndexes.at(-1) ?? -1) + 1; - setSelectedItemIdx(itemIdx); - setAtomsMap((prev) => ({ - ...prev, - [configTab]: { - ...(prev[configTab] as Record< - string, - PrimitiveAtom> - >), - [resolveKey(schema, configTab, itemIdx)]: - atom>(initial), - }, - })); - } - }} - > -
{o.title}
-
{o.description}
-
- ))} -
- ) - ))} + } + }} + > +
{o.title}
+
{o.description}
+
+ ))} +
+ )} {showConfig && (
diff --git a/src/features/contribute/morphology/types.ts b/src/features/contribute/morphology/types.ts index 04d46bc6d..257132571 100755 --- a/src/features/contribute/morphology/types.ts +++ b/src/features/contribute/morphology/types.ts @@ -1,4 +1,3 @@ -// src/features/contribute/morphology/types.ts import { PrimitiveAtom } from 'jotai'; import { ConfigValue } from './_components/components'; @@ -34,3 +33,11 @@ export type AtomsMap = Record< >; export type TabType = 'configuration' | 'simulations'; + +export type Config = { + morphology?: Record; + license?: Record; + mtype?: Record; + contribution?: Record; + [key: string]: ConfigValue | Record | ConfigValue[]; +}; diff --git a/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx b/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx index 01d1b268a..89b3b67ef 100644 --- a/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx +++ b/src/features/details-view/button-edit-metadata/button-edit-metadata.tsx @@ -9,7 +9,6 @@ import styles from './button-edit-metadata.module.css'; interface ButtonEditMetadataProps { className?: string; label?: string; - tooltip?: string; isEditing: boolean; onClick: () => void; } diff --git a/src/features/details-view/overview.tsx b/src/features/details-view/overview.tsx index cb5a99d68..8a44dad48 100644 --- a/src/features/details-view/overview.tsx +++ b/src/features/details-view/overview.tsx @@ -54,6 +54,7 @@ function EditField< }) { const fieldObj = getFieldDefinition(field); const value = data[field]; + const inputId = `input-${field}`; // Unique ID for accessibility return (
@@ -62,8 +63,11 @@ function EditField<
{Object.keys(value).map((key) => (
- + ) : ( - onFieldChange(field, e.target.value)} - /> + <> + + onFieldChange(field, e.target.value)} + /> + )}
); @@ -98,11 +108,12 @@ export default function DetailHeader< onEditToggle, onSave, onFieldChange, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + url, }: { fields: Array; detail: T; commonFields?: Array; - url?: string | null; extraHeaderAction?: ReactNode; commonFieldsClassName?: string; fieldsClassName?: string; @@ -111,6 +122,7 @@ export default function DetailHeader< onEditToggle?: () => void; onSave?: () => void; onFieldChange?: (fieldName: string, value: unknown) => void; + url?: string; // Made optional to fix error in single-neuron-simulation.tsx }) { return (
From e54a535deef629152970a181f189b1e0bc5eaebe Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 10:34:02 +0200 Subject: [PATCH 28/44] updated with feedback --- .../contribute/morphology/_components/components.tsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index 469d263de..fb6acc40f 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -421,9 +421,9 @@ export function JSONMorphologySchemaForm({ fetchMtypes(session.accessToken), ]); - let brainRegionName = null; + let fetchedBrainRegionName = null; // Renamed to avoid shadowing if (nodeId) { - brainRegionName = await fetchBrainRegion(session.accessToken, nodeId); + fetchedBrainRegionName = await fetchBrainRegion(session.accessToken, nodeId); } if (speciesData) { @@ -445,7 +445,7 @@ export function JSONMorphologySchemaForm({ if (mtypesData) { setAllMtypes(mtypesData); } - setBrainRegionName(brainRegionName); + setBrainRegionName(fetchedBrainRegionName); }; fetchData(); From a9db8353ab1ffa895cd3bcb37e654b0ed1c4c8b3 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 11:23:04 +0200 Subject: [PATCH 29/44] add dependencies --- package.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/package.json b/package.json index a6520184b..f9eba45ff 100644 --- a/package.json +++ b/package.json @@ -134,7 +134,6 @@ "react-markdown": "^9.1.0", "react-pdf": "^9.2.1", "react-plotly.js": "^2.6.0", - "react-query": "link:@types/@tanstack/react-query", "react-resizable": "^3.0.5", "react-select": "^5.7.3", "react-syntax-highlighter": "^15.6.1", @@ -154,6 +153,8 @@ "zod": "^3.22.4" }, "devDependencies": { + "@opentelemetry/auto-instrumentations-node": "^0.64.1", + "@opentelemetry/sdk-node": "^0.205.0", "@playwright/test": "^1.51.1", "@sanity/types": "^3.93.0", "@tailwindcss/postcss": "^4.1.3", @@ -196,10 +197,12 @@ "knip": "^5.61.3", "lefthook": "^1.11.12", "msw": "^2.0.5", + "plotly.js": "^3.1.0", "postcss": "^8.5.3", "prettier": "^3.2.4", "prettier-plugin-tailwindcss": "^0.6.11", "raw-loader": "^4.0.2", + "sass": "^1.92.1", "tailwindcss": "^4.1.3", "typescript": "^5.8.3", "vite-tsconfig-paths": "^5.1.4", From 26295be8cf38ea800391a1d7fe0889c3af4e2396 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 11:27:41 +0200 Subject: [PATCH 30/44] add dependencies --- pnpm-lock.yaml | 1768 +++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 1446 insertions(+), 322 deletions(-) diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index ce6c2cf1a..1943698c7 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -19,7 +19,7 @@ importers: version: 6.0.0(react-dom@19.1.0(react@19.1.0))(react@19.1.0) '@ant-design/nextjs-registry': specifier: ^1.0.2 - version: 1.0.2(@ant-design/cssinjs@1.23.0(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(antd@5.24.6(date-fns@4.1.0)(moment@2.30.1)(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react-dom@19.1.0(react@19.1.0))(react@19.1.0) + version: 1.0.2(@ant-design/cssinjs@1.23.0(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(antd@5.24.6(date-fns@4.1.0)(moment@2.30.1)(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react-dom@19.1.0(react@19.1.0))(react@19.1.0) '@ant-design/v5-patch-for-react-19': specifier: ^1.0.3 version: 1.0.3(antd@5.24.6(date-fns@4.1.0)(moment@2.30.1)(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(react-dom@19.1.0(react@19.1.0))(react@19.1.0) @@ -154,7 +154,7 @@ importers: version: 3.94.2(@types/react@19.1.0)(debug@4.4.0) '@sentry/nextjs': specifier: ^9.12.0 - version: 9.12.0(@opentelemetry/context-async-hooks@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/core@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/instrumentation@0.57.2(@opentelemetry/api@1.9.0))(@opentelemetry/sdk-trace-base@1.30.1(@opentelemetry/api@1.9.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react@19.1.0)(webpack@5.99.5(esbuild@0.25.5)) + version: 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5.1.4(typescript@5.8.3)(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1)) + vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) + vite-tsconfig-paths: 5.1.4(typescript@5.8.3)(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1)) ws: 8.18.2 xdg-basedir: 5.1.0 transitivePeerDependencies: @@ -16624,7 +17778,7 @@ snapshots: optionalDependencies: '@sanity/types': 3.94.2(@types/react@19.1.0)(debug@4.4.0) - '@sanity/visual-editing@2.15.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3)': + '@sanity/visual-editing@2.15.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3)': dependencies: '@sanity/comlink': 3.0.5 '@sanity/icons': 3.7.0(react@19.1.0) @@ -16647,7 +17801,7 @@ snapshots: xstate: 5.19.2 optionalDependencies: '@sanity/client': 7.6.0(debug@4.4.0) - next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2) + next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1) transitivePeerDependencies: - '@emotion/is-prop-valid' - '@sanity/types' @@ -16766,7 +17920,7 @@ snapshots: '@sentry/core@9.12.0': {} - '@sentry/nextjs@9.12.0(@opentelemetry/context-async-hooks@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/core@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/instrumentation@0.57.2(@opentelemetry/api@1.9.0))(@opentelemetry/sdk-trace-base@1.30.1(@opentelemetry/api@1.9.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react@19.1.0)(webpack@5.99.5(esbuild@0.25.5))': + '@sentry/nextjs@9.12.0(@opentelemetry/context-async-hooks@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/core@1.30.1(@opentelemetry/api@1.9.0))(@opentelemetry/instrumentation@0.57.2(@opentelemetry/api@1.9.0))(@opentelemetry/sdk-trace-base@1.30.1(@opentelemetry/api@1.9.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react@19.1.0)(webpack@5.99.5(esbuild@0.25.5))': dependencies: '@opentelemetry/api': 1.9.0 '@opentelemetry/semantic-conventions': 1.32.0 @@ -16779,7 +17933,7 @@ snapshots: '@sentry/vercel-edge': 9.12.0 '@sentry/webpack-plugin': 3.2.4(webpack@5.99.5(esbuild@0.25.5)) chalk: 3.0.0 - next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2) + next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1) resolve: 1.22.8 rollup: 4.35.0 stacktrace-parser: 0.1.11 @@ -17108,6 +18262,8 @@ snapshots: '@types/aria-query@5.0.4': {} + '@types/aws-lambda@8.10.152': {} + '@types/babel__core@7.20.5': dependencies: '@babel/parser': 7.27.0 @@ -17131,6 +18287,10 @@ snapshots: '@types/base16@1.0.5': {} + '@types/bunyan@1.8.11': + dependencies: + '@types/node': 22.16.4 + '@types/canvas-confetti@1.9.0': {} '@types/chroma-js@2.4.5': {} @@ -17343,8 +18503,6 @@ snapshots: '@types/katex@0.16.7': {} - '@types/less@3.0.8': {} - '@types/lodash-es@4.17.12': dependencies: '@types/lodash': 4.17.16 @@ -17365,6 +18523,10 @@ snapshots: dependencies: '@types/unist': 3.0.3 + '@types/memcached@2.2.10': + dependencies: + '@types/node': 22.16.4 + '@types/minimist@1.2.5': {} '@types/ms@2.1.0': {} @@ -17373,6 +18535,10 @@ snapshots: dependencies: '@types/node': 22.14.0 + '@types/mysql@2.15.27': + dependencies: + '@types/node': 22.16.4 + '@types/node@20.17.30': dependencies: undici-types: 6.19.8 @@ -17389,6 +18555,10 @@ snapshots: '@types/offscreencanvas@2019.7.3': {} + '@types/oracledb@6.5.2': + dependencies: + '@types/node': 22.16.4 + '@types/parse-json@4.0.2': {} '@types/pbf@3.0.5': {} @@ -17397,6 +18567,12 @@ snapshots: dependencies: '@types/pg': 8.6.1 + '@types/pg@8.15.5': + dependencies: + '@types/node': 22.16.4 + pg-protocol: 1.8.0 + pg-types: 2.2.0 + '@types/pg@8.6.1': dependencies: '@types/node': 22.14.0 @@ -17442,10 +18618,6 @@ snapshots: dependencies: csstype: 3.1.3 - '@types/sass@1.45.0': - dependencies: - sass: 1.89.2 - '@types/shallow-equals@1.0.3': {} '@types/shimmer@1.2.0': {} @@ -17460,10 +18632,6 @@ snapshots: '@types/stylis@4.2.5': {} - '@types/stylus@0.48.43': - dependencies: - '@types/node': 22.16.4 - '@types/supercluster@7.1.3': dependencies: '@types/geojson': 7946.0.16 @@ -17697,7 +18865,7 @@ snapshots: '@vercel/stega@0.1.2': {} - '@vitejs/plugin-react@4.5.2(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1))': + '@vitejs/plugin-react@4.5.2(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1))': dependencies: '@babel/core': 7.27.4 '@babel/plugin-transform-react-jsx-self': 7.27.1(@babel/core@7.27.4) @@ -17705,11 +18873,11 @@ snapshots: '@rolldown/pluginutils': 1.0.0-beta.11 '@types/babel__core': 7.20.5 react-refresh: 0.17.0 - vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) transitivePeerDependencies: - supports-color - '@vitejs/plugin-react@4.6.0(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1))': + '@vitejs/plugin-react@4.6.0(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1))': dependencies: '@babel/core': 7.27.4 '@babel/plugin-transform-react-jsx-self': 7.27.1(@babel/core@7.27.4) @@ -17717,7 +18885,7 @@ snapshots: '@rolldown/pluginutils': 1.0.0-beta.19 '@types/babel__core': 7.20.5 react-refresh: 0.17.0 - vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) transitivePeerDependencies: - supports-color @@ -17728,14 +18896,14 @@ snapshots: chai: 5.2.0 tinyrainbow: 2.0.0 - '@vitest/mocker@3.1.1(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1))': + '@vitest/mocker@3.1.1(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1))': dependencies: '@vitest/spy': 3.1.1 estree-walker: 3.0.3 magic-string: 0.30.17 optionalDependencies: msw: 2.7.3(@types/node@22.14.0)(typescript@5.8.3) - vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) '@vitest/pretty-format@3.1.1': dependencies: @@ -18277,6 +19445,8 @@ snapshots: big.js@5.2.2: {} + bignumber.js@9.3.1: {} + binary-extensions@2.3.0: {} binary-search-bounds@2.0.5: {} @@ -18783,19 +19953,6 @@ snapshots: css-global-keywords@1.0.1: {} - css-loader@7.1.2(webpack@5.99.5(esbuild@0.25.5)): - dependencies: - icss-utils: 5.1.0(postcss@8.5.6) - postcss: 8.5.6 - postcss-modules-extract-imports: 3.1.0(postcss@8.5.6) - postcss-modules-local-by-default: 4.2.0(postcss@8.5.6) - postcss-modules-scope: 3.2.1(postcss@8.5.6) - postcss-modules-values: 4.0.0(postcss@8.5.6) - postcss-value-parser: 4.2.0 - semver: 7.7.2 - optionalDependencies: - webpack: 5.99.5(esbuild@0.25.5) - css-select@5.1.0: dependencies: boolbase: 1.0.0 @@ -18823,8 +19980,6 @@ snapshots: csscolorparser@1.0.3: {} - cssesc@3.0.0: {} - cssom@0.3.8: {} cssom@0.5.0: {} @@ -19548,15 +20703,6 @@ snapshots: transitivePeerDependencies: - supports-color - esbuild-style-plugin@1.6.3: - dependencies: - '@types/less': 3.0.8 - '@types/sass': 1.45.0 - '@types/stylus': 0.48.43 - glob: 10.4.5 - postcss: 8.5.6 - postcss-modules: 6.0.1(postcss@8.5.6) - esbuild@0.25.2: optionalDependencies: '@esbuild/aix-ppc64': 0.25.2 @@ -20226,9 +21372,25 @@ snapshots: functions-have-names@1.2.3: {} - generic-names@4.0.0: + gaxios@6.7.1: + dependencies: + extend: 3.0.2 + https-proxy-agent: 7.0.6 + is-stream: 2.0.1 + node-fetch: 2.7.0 + uuid: 9.0.1 + transitivePeerDependencies: + - encoding + - supports-color + + gcp-metadata@6.1.1: dependencies: - loader-utils: 3.3.1 + gaxios: 6.7.1 + google-logging-utils: 0.0.2 + json-bigint: 1.0.0 + transitivePeerDependencies: + - encoding + - supports-color gensync@1.0.0-beta.2: {} @@ -20515,6 +21677,8 @@ snapshots: through2: 2.0.5 xtend: 4.0.2 + google-logging-utils@0.0.2: {} + gopd@1.2.0: {} graceful-fs@4.2.11: {} @@ -20791,10 +21955,6 @@ snapshots: dependencies: safer-buffer: 2.1.2 - icss-utils@5.1.0(postcss@8.5.6): - dependencies: - postcss: 8.5.6 - ieee754@1.2.1: {} ignore@5.3.2: {} @@ -21663,6 +22823,10 @@ snapshots: jsesc@3.1.0: {} + json-bigint@1.0.0: + dependencies: + bignumber.js: 9.3.1 + json-bignum@0.0.3: {} json-buffer@3.0.1: {} @@ -21896,8 +23060,6 @@ snapshots: emojis-list: 3.0.0 json5: 2.2.3 - loader-utils@3.3.1: {} - locate-path@3.0.0: dependencies: p-locate: 3.0.0 @@ -21973,6 +23135,8 @@ snapshots: chalk: 5.4.1 is-unicode-supported: 1.3.0 + long@5.3.2: {} + longest-streak@3.1.0: {} loose-envify@1.4.0: @@ -22716,13 +23880,13 @@ snapshots: neo-async@2.6.2: {} - next-auth@4.24.11(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react-dom@19.1.0(react@19.1.0))(react@19.1.0): + next-auth@4.24.11(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react-dom@19.1.0(react@19.1.0))(react@19.1.0): dependencies: '@babel/runtime': 7.27.0 '@panva/hkdf': 1.2.1 cookie: 0.7.2 jose: 4.15.9 - next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2) + next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1) oauth: 0.9.15 openid-client: 5.7.1 preact: 10.26.5 @@ -22731,27 +23895,27 @@ snapshots: react-dom: 19.1.0(react@19.1.0) uuid: 8.3.2 - next-sanity-client@1.0.8(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2)): + next-sanity-client@1.0.8(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1)): dependencies: - next: 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next-sanity@9.12.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/icons@3.7.4(react@19.1.0))(@sanity/types@3.94.2(@types/react@19.1.0))(@sanity/ui@2.16.2(@emotion/is-prop-valid@1.2.2)(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0)))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(sanity@3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1))(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3): + next-sanity@9.12.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/icons@3.7.4(react@19.1.0))(@sanity/types@3.94.2(@types/react@19.1.0))(@sanity/ui@2.16.2(@emotion/is-prop-valid@1.2.2)(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0)))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(sanity@3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1))(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3): dependencies: '@portabletext/react': 3.2.1(react@19.1.0) '@sanity/client': 7.6.0(debug@4.4.0) '@sanity/icons': 3.7.4(react@19.1.0) - '@sanity/next-loader': 1.6.2(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react@19.1.0) + '@sanity/next-loader': 1.6.2(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react@19.1.0) '@sanity/preview-kit': 6.1.1(@sanity/types@3.94.2(@types/react@19.1.0))(react@19.1.0) '@sanity/preview-url-secret': 2.1.11(@sanity/client@7.6.0) '@sanity/types': 3.94.2(@types/react@19.1.0)(debug@4.4.0) '@sanity/ui': 2.16.2(@emotion/is-prop-valid@1.2.2)(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0)) - '@sanity/visual-editing': 2.15.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3) + '@sanity/visual-editing': 2.15.0(@emotion/is-prop-valid@1.2.2)(@sanity/client@7.6.0)(@sanity/types@3.94.2(@types/react@19.1.0))(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react-dom@19.1.0(react@19.1.0))(react-is@18.3.1)(react@19.1.0)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(typescript@5.8.3) groq: 3.92.0 history: 5.3.0 - next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2) + next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1) react: 19.1.0 react-dom: 19.1.0(react@19.1.0) - sanity: 3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1) + sanity: 3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1) styled-components: 6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0) transitivePeerDependencies: - '@emotion/is-prop-valid' @@ -22765,7 +23929,7 @@ snapshots: next-tick@1.1.0: {} - next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2): + next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1): dependencies: '@next/env': 15.4.1 '@swc/helpers': 0.5.15 @@ -22785,7 +23949,7 @@ snapshots: '@next/swc-win32-x64-msvc': 15.4.1 '@opentelemetry/api': 1.9.0 '@playwright/test': 1.51.1 - sass: 1.89.2 + sass: 1.92.1 sharp: 0.34.3 transitivePeerDependencies: - '@babel/core' @@ -22852,12 +24016,12 @@ snapshots: dependencies: is-finite: 1.1.0 - nuqs@2.4.1(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2))(react@19.1.0): + nuqs@2.4.1(next@15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1))(react@19.1.0): dependencies: mitt: 3.0.1 react: 19.1.0 optionalDependencies: - next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2) + next: 15.4.1(@babel/core@7.27.4)(@opentelemetry/api@1.9.0)(@playwright/test@1.51.1)(babel-plugin-macros@3.1.0)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1) nwsapi@2.2.20: {} @@ -23218,12 +24382,13 @@ snapshots: plotly.js-dist-min@2.35.3: {} - plotly.js@3.0.1(mapbox-gl@1.13.3)(webpack@5.99.5(esbuild@0.25.5)): + plotly.js@3.1.0(mapbox-gl@1.13.3): dependencies: '@plotly/d3': 3.8.2 '@plotly/d3-sankey': 0.7.2 '@plotly/d3-sankey-circular': 0.33.1 '@plotly/mapbox-gl': 1.13.4(mapbox-gl@1.13.3) + '@plotly/regl': 2.1.2 '@turf/area': 7.2.0 '@turf/bbox': 7.2.0 '@turf/centroid': 7.2.0 @@ -23234,7 +24399,6 @@ snapshots: color-parse: 2.0.0 color-rgba: 3.0.0 country-regex: 1.1.0 - css-loader: 7.1.2(webpack@5.99.5(esbuild@0.25.5)) d3-force: 1.2.1 d3-format: 1.4.5 d3-geo: 1.12.1 @@ -23243,7 +24407,6 @@ snapshots: d3-interpolate: 3.0.1 d3-time: 1.1.0 d3-time-format: 2.3.0 - esbuild-style-plugin: 1.6.3 fast-isnumeric: 1.1.4 gl-mat4: 1.2.0 gl-text: 1.4.0 @@ -23259,13 +24422,11 @@ snapshots: point-in-polygon: 1.1.0 polybooljs: 1.2.2 probe-image-size: 7.2.3 - regl: '@plotly/regl@2.1.2' regl-error2d: 2.0.12 regl-line2d: 3.1.3 regl-scatter2d: 3.3.1 regl-splom: 1.0.14 strongly-connected-components: 1.0.1 - style-loader: 4.0.0(webpack@5.99.5(esbuild@0.25.5)) superscript-text: 1.0.0 svg-path-sdf: 1.1.3 tinycolor2: 1.6.0 @@ -23274,10 +24435,8 @@ snapshots: webgl-context: 2.2.0 world-calendars: 1.0.4 transitivePeerDependencies: - - '@rspack/core' - mapbox-gl - supports-color - - webpack pluralize-esm@9.0.5: {} @@ -23291,44 +24450,6 @@ snapshots: possible-typed-array-names@1.1.0: {} - postcss-modules-extract-imports@3.1.0(postcss@8.5.6): - dependencies: - postcss: 8.5.6 - - postcss-modules-local-by-default@4.2.0(postcss@8.5.6): - dependencies: - icss-utils: 5.1.0(postcss@8.5.6) - postcss: 8.5.6 - postcss-selector-parser: 7.1.0 - postcss-value-parser: 4.2.0 - - postcss-modules-scope@3.2.1(postcss@8.5.6): - dependencies: - postcss: 8.5.6 - postcss-selector-parser: 7.1.0 - - postcss-modules-values@4.0.0(postcss@8.5.6): - dependencies: - icss-utils: 5.1.0(postcss@8.5.6) - postcss: 8.5.6 - - postcss-modules@6.0.1(postcss@8.5.6): - dependencies: - generic-names: 4.0.0 - icss-utils: 5.1.0(postcss@8.5.6) - lodash.camelcase: 4.3.0 - postcss: 8.5.6 - postcss-modules-extract-imports: 3.1.0(postcss@8.5.6) - postcss-modules-local-by-default: 4.2.0(postcss@8.5.6) - postcss-modules-scope: 3.2.1(postcss@8.5.6) - postcss-modules-values: 4.0.0(postcss@8.5.6) - string-hash: 1.1.3 - - postcss-selector-parser@7.1.0: - dependencies: - cssesc: 3.0.0 - util-deprecate: 1.0.2 - postcss-value-parser@4.2.0: {} postcss@8.4.31: @@ -23349,12 +24470,6 @@ snapshots: picocolors: 1.1.1 source-map-js: 1.2.1 - postcss@8.5.6: - dependencies: - nanoid: 3.3.11 - picocolors: 1.1.1 - source-map-js: 1.2.1 - postgres-array@2.0.0: {} postgres-bytea@1.0.0: {} @@ -23466,6 +24581,21 @@ snapshots: property-information@7.0.0: {} + protobufjs@7.5.4: + dependencies: + '@protobufjs/aspromise': 1.1.2 + '@protobufjs/base64': 1.1.2 + '@protobufjs/codegen': 2.0.4 + '@protobufjs/eventemitter': 1.1.0 + '@protobufjs/fetch': 1.1.0 + '@protobufjs/float': 1.0.2 + '@protobufjs/inquire': 1.1.0 + '@protobufjs/path': 1.1.2 + '@protobufjs/pool': 1.1.0 + '@protobufjs/utf8': 1.1.0 + '@types/node': 22.16.4 + long: 5.3.2 + protocol-buffers-schema@3.6.0: {} proxy-from-env@1.1.0: {} @@ -24001,9 +25131,9 @@ snapshots: optionalDependencies: '@types/react': 19.1.0 - react-plotly.js@2.6.0(plotly.js@3.0.1(mapbox-gl@1.13.3)(webpack@5.99.5(esbuild@0.25.5)))(react@19.1.0): + react-plotly.js@2.6.0(plotly.js@3.1.0(mapbox-gl@1.13.3))(react@19.1.0): dependencies: - plotly.js: 3.0.1(mapbox-gl@1.13.3)(webpack@5.99.5(esbuild@0.25.5)) + plotly.js: 3.1.0(mapbox-gl@1.13.3) prop-types: 15.8.1 react: 19.1.0 @@ -24556,7 +25686,7 @@ snapshots: safer-buffer@2.1.2: {} - sanity@3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.89.2)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1): + sanity@3.94.2(@emotion/is-prop-valid@1.2.2)(@types/node@22.14.0)(@types/react@19.1.0)(immer@10.1.1)(jiti@2.4.2)(lightningcss@1.29.2)(react-dom@19.1.0(react@19.1.0))(react@19.1.0)(sass@1.92.1)(styled-components@6.1.17(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1): dependencies: '@dnd-kit/core': 6.3.1(react-dom@19.1.0(react@19.1.0))(react@19.1.0) '@dnd-kit/modifiers': 6.0.1(@dnd-kit/core@6.3.1(react-dom@19.1.0(react@19.1.0))(react@19.1.0))(react@19.1.0) @@ -24570,7 +25700,7 @@ snapshots: '@rexxars/react-json-inspector': 9.0.1(react@19.1.0) '@sanity/asset-utils': 2.2.1 '@sanity/bifur-client': 0.4.1 - '@sanity/cli': 3.94.2(@types/node@22.14.0)(@types/react@19.1.0)(lightningcss@1.29.2)(react@19.1.0)(sass@1.89.2)(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1) + '@sanity/cli': 3.94.2(@types/node@22.14.0)(@types/react@19.1.0)(lightningcss@1.29.2)(react@19.1.0)(sass@1.92.1)(terser@5.43.1)(typescript@5.8.3)(yaml@2.7.1) '@sanity/client': 7.6.0(debug@4.4.0) '@sanity/color': 3.0.6 '@sanity/comlink': 3.0.5 @@ -24607,7 +25737,7 @@ snapshots: '@types/tar-stream': 3.1.3 '@types/use-sync-external-store': 1.5.0 '@types/which': 3.0.4 - '@vitejs/plugin-react': 4.6.0(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1)) + '@vitejs/plugin-react': 4.6.0(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1)) '@xstate/react': 6.0.0(@types/react@19.1.0)(react@19.1.0)(xstate@5.20.0) archiver: 7.0.1 arrify: 2.0.1 @@ -24695,7 +25825,7 @@ snapshots: use-hot-module-reload: 2.0.0(react@19.1.0) use-sync-external-store: 1.5.0(react@19.1.0) uuid: 11.1.0 - vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) which: 5.0.0 xstate: 5.20.0 yargs: 17.7.2 @@ -24721,7 +25851,7 @@ snapshots: - utf-8-validate - yaml - sass@1.89.2: + sass@1.92.1: dependencies: chokidar: 4.0.3 immutable: 5.1.3 @@ -25071,8 +26201,6 @@ snapshots: string-convert@0.2.1: {} - string-hash@1.1.3: {} - string-length@4.0.2: dependencies: char-regex: 1.0.2 @@ -25196,10 +26324,6 @@ snapshots: strongly-connected-components@1.0.1: {} - style-loader@4.0.0(webpack@5.99.5(esbuild@0.25.5)): - dependencies: - webpack: 5.99.5(esbuild@0.25.5) - style-to-js@1.1.16: dependencies: style-to-object: 1.0.8 @@ -25927,13 +27051,13 @@ snapshots: '@types/unist': 3.0.3 vfile-message: 4.0.2 - vite-node@3.1.1(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1): + vite-node@3.1.1(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1): dependencies: cac: 6.7.14 debug: 4.4.0(supports-color@8.1.1) es-module-lexer: 1.6.0 pathe: 2.0.3 - vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) transitivePeerDependencies: - '@types/node' - jiti @@ -25948,18 +27072,18 @@ snapshots: - tsx - yaml - vite-tsconfig-paths@5.1.4(typescript@5.8.3)(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1)): + vite-tsconfig-paths@5.1.4(typescript@5.8.3)(vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1)): dependencies: debug: 4.4.0(supports-color@8.1.1) globrex: 0.1.2 tsconfck: 3.1.5(typescript@5.8.3) optionalDependencies: - vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) transitivePeerDependencies: - supports-color - typescript - vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1): + vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1): dependencies: esbuild: 0.25.2 postcss: 8.5.3 @@ -25969,11 +27093,11 @@ snapshots: fsevents: 2.3.3 jiti: 2.4.2 lightningcss: 1.29.2 - sass: 1.89.2 + sass: 1.92.1 terser: 5.43.1 yaml: 2.7.1 - vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1): + vite@6.3.5(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1): dependencies: esbuild: 0.25.5 fdir: 6.4.6(picomatch@4.0.2) @@ -25986,14 +27110,14 @@ snapshots: fsevents: 2.3.3 jiti: 2.4.2 lightningcss: 1.29.2 - sass: 1.89.2 + sass: 1.92.1 terser: 5.43.1 yaml: 2.7.1 - vitest@3.1.1(@types/debug@4.1.12)(@types/node@22.14.0)(jiti@2.4.2)(jsdom@26.1.0)(lightningcss@1.29.2)(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1): + vitest@3.1.1(@types/debug@4.1.12)(@types/node@22.14.0)(jiti@2.4.2)(jsdom@26.1.0)(lightningcss@1.29.2)(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1): dependencies: '@vitest/expect': 3.1.1 - '@vitest/mocker': 3.1.1(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1)) + '@vitest/mocker': 3.1.1(msw@2.7.3(@types/node@22.14.0)(typescript@5.8.3))(vite@6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1)) '@vitest/pretty-format': 3.1.1 '@vitest/runner': 3.1.1 '@vitest/snapshot': 3.1.1 @@ -26009,8 +27133,8 @@ snapshots: tinyexec: 0.3.2 tinypool: 1.0.2 tinyrainbow: 2.0.0 - vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) - vite-node: 3.1.1(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.89.2)(terser@5.43.1)(yaml@2.7.1) + vite: 6.2.6(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) + vite-node: 3.1.1(@types/node@22.14.0)(jiti@2.4.2)(lightningcss@1.29.2)(sass@1.92.1)(terser@5.43.1)(yaml@2.7.1) why-is-node-running: 2.3.0 optionalDependencies: '@types/debug': 4.1.12 From 7ba5656a2f92d531104c7010cc16a432c0613bc1 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 12:03:45 +0200 Subject: [PATCH 31/44] package fixes --- src/features/details-view/summary.tsx | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/features/details-view/summary.tsx b/src/features/details-view/summary.tsx index 1cfb23e86..e164948a4 100644 --- a/src/features/details-view/summary.tsx +++ b/src/features/details-view/summary.tsx @@ -44,16 +44,17 @@ export default function Summary< dataType: DataType; children?: (detail: T) => ReactNode; }) { - const { id, virtualLabId, projectId, ...params } = useParams(); + const allParams = useParams(); + const { virtualLabId, projectId } = allParams; const setBrainRegionSidebarIsCollapsed = useSetAtom(brainRegionSidebarIsCollapsedAtom); const fields = getViewDefinitionByLegacyType(dataType)?.summaryViewFields; const path = usePathname(); const memoizedDetailAtom = useMemo(() => { - const detailFetchAtom = detailFamily({ id, virtualLabId, projectId, dataType, ...params }); + const detailFetchAtom = detailFamily({ ...allParams, dataType }); return conditionalAtom(payload, detailFetchAtom); - }, [payload, id, virtualLabId, projectId, dataType, params]); + }, [payload, dataType, allParams]); const detail = useAtomValue(memoizedDetailAtom); From 15856472db603ef3ecdce2059d9338909974cb1b Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 13:16:26 +0200 Subject: [PATCH 32/44] default license update --- .../contribute/morphology/_components/components.tsx | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index fb6acc40f..fea52ddba 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -421,7 +421,7 @@ export function JSONMorphologySchemaForm({ fetchMtypes(session.accessToken), ]); - let fetchedBrainRegionName = null; // Renamed to avoid shadowing + let fetchedBrainRegionName = null; if (nodeId) { fetchedBrainRegionName = await fetchBrainRegion(session.accessToken, nodeId); } @@ -441,6 +441,10 @@ export function JSONMorphologySchemaForm({ } if (licensesData) { setAllLicenses(licensesData); + if (!state.license_id) { + const defaultLicenseId = 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7'; + setState((prev) => ({ ...prev, license_id: defaultLicenseId })); + } } if (mtypesData) { setAllMtypes(mtypesData); @@ -449,7 +453,7 @@ export function JSONMorphologySchemaForm({ }; fetchData(); - }, [nodeId]); + }, [nodeId, state.license_id, setState]); const markFieldTouched = (field: string) => { setTouchedFields((prev) => new Set([...prev, field])); From e112ef5848200691394092f611b5aadccc736943 Mon Sep 17 00:00:00 2001 From: dkeller9 Date: Fri, 12 Sep 2025 16:19:53 +0200 Subject: [PATCH 33/44] Update components.tsx --- src/features/contribute/morphology/_components/components.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index fea52ddba..91c702829 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -127,7 +127,7 @@ const processData = async (token: string): Promise => { Authorization: `Bearer ${token}`, }; - const urlSpecies = 'https://staging.openbraininstitute.org/api/entitycore/subject'; + const urlSpecies = 'https://staging.openbraininstitute.org/api/entitycore/species'; const urlStrain = 'https://staging.openbraininstitute.org/api/entitycore/strain'; let jsonDataSpecies: SpeciesData = { data: [] }; From 6f46820cfd9d5e3e2cb0fdbffb8e98b74d658940 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 16:57:52 +0200 Subject: [PATCH 34/44] cleanup --- .../contribute/_components/atoms/index.ts | 170 ---- .../circuit-details/circuit-details.tsx | 22 - .../_components/circuit-details/index.ts | 1 - .../circuit-name/circuit-name.module.css | 50 - .../circuit-preview.module.css | 14 - .../circuit-preview/circuit-preview.tsx | 25 - .../_components/circuit-preview/index.ts | 1 - .../contribute/_components/components.tsx | 949 ------------------ .../_components/file-viewer/index.tsx | 81 -- .../contribute/_components/hooks/circuit.ts | 88 -- .../_components/hooks/config-atom.ts | 30 - .../contribute/_components/hooks/schema.ts | 149 --- .../contribute/_components/section.tsx | 221 ---- .../_components/simulation-files/index.tsx | 198 ---- .../_components/simulation-status/index.tsx | 50 - .../_components/tabs-selector/index.ts | 1 - .../tabs-selector/tabs-selector.tsx | 43 - .../contribute/_components/tooltip/index.ts | 1 - .../_components/tooltip/tooltip.module.css | 39 - .../_components/tooltip/tooltip.tsx | 20 - src/features/contribute/_components/utils.ts | 73 -- src/features/contribute/error-registry.ts | 7 - .../contribute/small-microcircuit.module.css | 32 - src/features/contribute/types.ts | 35 - 24 files changed, 2300 deletions(-) delete mode 100644 src/features/contribute/_components/atoms/index.ts delete mode 100644 src/features/contribute/_components/circuit-details/circuit-details.tsx delete mode 100644 src/features/contribute/_components/circuit-details/index.ts delete mode 100644 src/features/contribute/_components/circuit-name/circuit-name.module.css delete mode 100644 src/features/contribute/_components/circuit-preview/circuit-preview.module.css delete mode 100644 src/features/contribute/_components/circuit-preview/circuit-preview.tsx delete mode 100644 src/features/contribute/_components/circuit-preview/index.ts delete mode 100644 src/features/contribute/_components/components.tsx delete mode 100644 src/features/contribute/_components/file-viewer/index.tsx delete mode 100644 src/features/contribute/_components/hooks/circuit.ts delete mode 100644 src/features/contribute/_components/hooks/config-atom.ts delete mode 100644 src/features/contribute/_components/hooks/schema.ts delete mode 100644 src/features/contribute/_components/section.tsx delete mode 100644 src/features/contribute/_components/simulation-files/index.tsx delete mode 100644 src/features/contribute/_components/simulation-status/index.tsx delete mode 100644 src/features/contribute/_components/tabs-selector/index.ts delete mode 100644 src/features/contribute/_components/tabs-selector/tabs-selector.tsx delete mode 100644 src/features/contribute/_components/tooltip/index.ts delete mode 100644 src/features/contribute/_components/tooltip/tooltip.module.css delete mode 100644 src/features/contribute/_components/tooltip/tooltip.tsx delete mode 100644 src/features/contribute/_components/utils.ts delete mode 100755 src/features/contribute/error-registry.ts delete mode 100755 src/features/contribute/small-microcircuit.module.css delete mode 100755 src/features/contribute/types.ts diff --git a/src/features/contribute/_components/atoms/index.ts b/src/features/contribute/_components/atoms/index.ts deleted file mode 100644 index 25ceed256..000000000 --- a/src/features/contribute/_components/atoms/index.ts +++ /dev/null @@ -1,170 +0,0 @@ -import { atom } from 'jotai'; -import { atomWithRefresh } from 'jotai/utils'; -import isEqual from 'lodash/isEqual'; - -import { downloadAsset } from '@/api/entitycore/queries/assets'; -import { getCircuit } from '@/api/entitycore/queries/model/circuit'; -import { getCircuitSimulations } from '@/api/entitycore/queries/simulation/circuit-simulation'; -import { getCircuitSimulationExecutions } from '@/api/entitycore/queries/simulation/circuit-simulation-execution'; -import { getCircuitSimulationResult } from '@/api/entitycore/queries/simulation/circuit-simulation-result'; -import { EntityTypeValue } from '@/api/entitycore/types'; -import { ICircuit } from '@/api/entitycore/types/entities/circuit'; -import { ICircuitSimulation } from '@/api/entitycore/types/entities/circuit-simulation'; -import { ICircuitSimulationExecution } from '@/api/entitycore/types/entities/circuit-simulation-execution'; -import { ICircuitSimulationResult } from '@/api/entitycore/types/entities/circuit-simulation-result'; -import { getLatestSimExecStatus } from '@/features/small-microcircuit/_components/utils'; -import { SimExecStatusMap } from '@/features/small-microcircuit/types'; -import { WorkspaceContext } from '@/types/common'; -import { atomFamilyWithExpiration, readAtomFamilyWithExpiration } from '@/util/atoms'; - -const simExecBySimIdAtomFamily = readAtomFamilyWithExpiration( - ({ simulationId, context }: { simulationId: string; context: WorkspaceContext }) => - atom>(async () => { - const simulationExecutionFilters = { used__id: simulationId }; - const res = await getCircuitSimulationExecutions({ - filters: simulationExecutionFilters, - context, - }); - - return res.data[0]; - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -export const simExecRemoteStatusMapAtomFamily = atomFamilyWithExpiration( - ({ simulationIds, context }: { simulationIds: string[]; context: WorkspaceContext }) => - atomWithRefresh>(async () => { - const simulationExecutionFilters = { used__id__in: simulationIds.join(',') }; - const res = await getCircuitSimulationExecutions({ - filters: simulationExecutionFilters, - context, - }); - - return res.data.reduce( - (map, simExec) => map.set(simExec.used[0].id, simExec.status), - new Map() - ); - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -type SimExecStatusMapAtomFamilyArg = { simulationIds: string[]; context: WorkspaceContext }; - -export const simExecStatusMapAtomFamily = atomFamilyWithExpiration( - ({ simulationIds, context }: SimExecStatusMapAtomFamilyArg) => { - const simExecRemoteStatusMapAtom = simExecRemoteStatusMapAtomFamily({ - simulationIds, - context, - }); - - const localStatusMapAtom = atom(new Map()); - - return atom, [SimExecStatusMap], void>( - async (get) => { - const remoteStatusMap = await get(simExecRemoteStatusMapAtom); - const localStatusMap = get(localStatusMapAtom); - - const simIds = Array.from(new Set([...remoteStatusMap.keys(), ...localStatusMap.keys()])); - const statusMap = simIds.reduce((map, simId) => { - const remoteStatus = remoteStatusMap.get(simId); - const localStatus = localStatusMap.get(simId); - // If both are set we take the latest possible one, - // because the status change in a particular sequence. - // See definition of getLatestSimExecStatus - const status = - remoteStatus && localStatus - ? getLatestSimExecStatus(remoteStatus, localStatus) - : (localStatus ?? remoteStatus); - return map.set(simId, status); - }, new Map()); - - return statusMap; - }, - (get, set, newStatusMap) => set(localStatusMapAtom, new Map(newStatusMap)) - ); - }, - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -export const simResultBySimIdAtomFamily = readAtomFamilyWithExpiration( - ({ simulationId, context }: { simulationId: string; context: WorkspaceContext }) => - atom>(async (get) => { - const execution = await get(simExecBySimIdAtomFamily({ simulationId, context })); - - if (!execution?.generated?.[0]) { - throw new Error('Simulation Result not found'); - } - - return getCircuitSimulationResult({ id: execution.generated[0].id, context }); - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -export const simulationsByCampaignIdAtomFamily = readAtomFamilyWithExpiration( - ({ campaignId, context }: { campaignId: string; context: WorkspaceContext }) => - atom>(async () => { - const filters = { simulation_campaign_id: campaignId }; - const res = await getCircuitSimulations({ filters, context }); - - return res.data; - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -export const circuitAtomFamily = readAtomFamilyWithExpiration( - ({ circuitId, context }: { circuitId: string; context: WorkspaceContext }) => - atom>(async () => { - return getCircuit({ id: circuitId, context }); - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); - -export const fileAtomFamily = readAtomFamilyWithExpiration( - ({ - id, - entityId, - entityType, - assetPath, - context, - }: { - id: string; - entityId: string; - entityType: EntityTypeValue; - assetPath?: string; - context: WorkspaceContext; - }) => - atom>(async () => { - const res = await downloadAsset({ - ctx: context, - entityId, - id, - entityType, - assetPath, - asRawResponse: true, - }); - - return res.json(); - }), - { - ttl: 120000, // 2 minutes - areEqual: isEqual, - } -); diff --git a/src/features/contribute/_components/circuit-details/circuit-details.tsx b/src/features/contribute/_components/circuit-details/circuit-details.tsx deleted file mode 100644 index f8f856fd3..000000000 --- a/src/features/contribute/_components/circuit-details/circuit-details.tsx +++ /dev/null @@ -1,22 +0,0 @@ -import React from 'react'; -import { Input } from 'antd'; - -import Tooltip from '../tooltip'; - -import { ICircuit } from '@/api/entitycore/types/entities/circuit'; - -interface CircuitDetailsProps { - className?: string; - circuit: ICircuit; -} - -export default function CircuitDetails({ className, circuit }: CircuitDetailsProps) { - return ( -
- - - - -
- ); -} diff --git a/src/features/contribute/_components/circuit-details/index.ts b/src/features/contribute/_components/circuit-details/index.ts deleted file mode 100644 index 42451142f..000000000 --- a/src/features/contribute/_components/circuit-details/index.ts +++ /dev/null @@ -1 +0,0 @@ -export { default } from './circuit-details'; diff --git a/src/features/contribute/_components/circuit-name/circuit-name.module.css b/src/features/contribute/_components/circuit-name/circuit-name.module.css deleted file mode 100644 index 61b1f9711..000000000 --- a/src/features/contribute/_components/circuit-name/circuit-name.module.css +++ /dev/null @@ -1,50 +0,0 @@ -.circuitName { - position: relative; - text-align: end; -} - -.circuitName > .name svg { - margin-left: 1em; - color: #005; -} - -.name { - font-weight: bold; - font-variant: small-caps; -} - -.description { - margin-top: 16px; - white-space: pre-wrap; - position: absolute; - background: #0050b3ee; - color: #fff; - padding: 0.5em 1em; - border-radius: 0.25em; - position: absolute; - left: 0; - right: 0; - width: 100%; - pointer-events: none; - z-index: 9; - text-align: start; - transition: all 0.3s; - opacity: 0; -} - -.circuitName:hover .description { - opacity: 1; -} - -.description::after { - content: ''; - border: 16px solid transparent; - border-bottom: 16px solid #0050b3ee; - position: absolute; - top: -16px; - left: 50%; - width: 0; - height: 0; - margin: -16px; - transform: scale(0.5, 1); -} diff --git a/src/features/contribute/_components/circuit-preview/circuit-preview.module.css b/src/features/contribute/_components/circuit-preview/circuit-preview.module.css deleted file mode 100644 index 2e4f7d702..000000000 --- a/src/features/contribute/_components/circuit-preview/circuit-preview.module.css +++ /dev/null @@ -1,14 +0,0 @@ -div.circuitPreview { - width: 100%; - height: 100%; - min-height: 0; - overflow: visible; -} - -.circuitPreview > .image { - background: #fff; - border-radius: 1em; - box-shadow: 0 2px 8px #0002; - width: 100%; - height: 100%; -} diff --git a/src/features/contribute/_components/circuit-preview/circuit-preview.tsx b/src/features/contribute/_components/circuit-preview/circuit-preview.tsx deleted file mode 100644 index 8862833f2..000000000 --- a/src/features/contribute/_components/circuit-preview/circuit-preview.tsx +++ /dev/null @@ -1,25 +0,0 @@ -/* eslint-disable @next/next/no-img-element */ -import React from 'react'; - -import { useCircuitImageURL } from '../hooks/circuit'; -import { classNames } from '@/util/utils'; -import { ICircuit } from '@/api/entitycore/types/entities/circuit'; -import ZoomableImage from '@/components/zoomable-image'; - -import styles from './circuit-preview.module.css'; - -interface CircuitPreviewProps { - className?: string; - circuit: ICircuit | undefined | null; -} - -export default function CircuitPreview({ className, circuit }: CircuitPreviewProps) { - const url = useCircuitImageURL(circuit?.id); - - return ( -
- {/* Circuit preview */} - -
- ); -} diff --git a/src/features/contribute/_components/circuit-preview/index.ts b/src/features/contribute/_components/circuit-preview/index.ts deleted file mode 100644 index 677278f17..000000000 --- a/src/features/contribute/_components/circuit-preview/index.ts +++ /dev/null @@ -1 +0,0 @@ -export { default } from './circuit-preview'; diff --git a/src/features/contribute/_components/components.tsx b/src/features/contribute/_components/components.tsx deleted file mode 100644 index cbf36e002..000000000 --- a/src/features/contribute/_components/components.tsx +++ /dev/null @@ -1,949 +0,0 @@ -import { useEffect, useState, useRef } from 'react'; -import { atom, useAtom } from 'jotai'; -import { InputNumber, Input, Select, Button } from 'antd'; -import { CheckCircleOutlined, CloseCircleOutlined, PlusCircleOutlined } from '@ant-design/icons'; -import isNil from 'lodash/isNil'; - -import { JSONSchema } from '../types'; -import { isPlainObject } from './utils'; -import CircuitDetails from './circuit-details'; -import Tooltip from './tooltip'; - -import { ICircuit } from '@/api/entitycore/types/entities/circuit'; -import { classNames } from '@/util/utils'; - -type Primitive = null | boolean | number | string; -interface Object { - [key: string]: Primitive | Primitive[] | Object; -} - -export type ConfigValue = Primitive | Primitive[] | Object; - -export type Config = Record; - -// Updated structure for MTYPE classification -const MTYPE_CLASSES = [ - { mtype_pref_label: 'L23_NBC', mtype_id: '6605787b-ba14-43fd-a954-de9cff4b15a0' }, - { mtype_pref_label: 'L23_NGC', mtype_id: 'dd16dca0-e567-416b-b8b7-f8fbcaa05af0' }, - { mtype_pref_label: 'L23_PC', mtype_id: '0791edc9-7ad4-4a94-a4a5-feab9b690d7e' }, - { mtype_pref_label: 'L23_PTPC', mtype_id: '52ea242f-6591-425a-8eae-962fa0b4dfe0' }, - { mtype_pref_label: 'L23_SBC', mtype_id: 'fbb8b577-92f4-4c93-b355-0982af5a3c7c' }, - { mtype_pref_label: 'L23_STPC', mtype_id: '93be8237-9861-4870-9977-ff1cf9e7462c' }, - { mtype_pref_label: 'L2_ChC', mtype_id: '91ba3deb-1139-4bc6-a12f-6a64a0ed0e92' }, - { mtype_pref_label: 'L2_IPC', mtype_id: 'e55f12e1-807c-42f6-ba98-91d6d30c57d7' }, - { mtype_pref_label: 'L2_MC', mtype_id: 'ea51f2c8-95fc-4940-a400-c37a3ff2d9eb' }, - { mtype_pref_label: 'L2_PC', mtype_id: 'dd73956b-423e-42c5-87d9-9e2cc84356b9' }, - { mtype_pref_label: 'L2_TPC', mtype_id: '7abf03d5-30b0-41ae-a02b-1f4e26c243a8' }, - { mtype_pref_label: 'L2_TPC:A', mtype_id: '9b04acb1-4737-4088-8d22-0658414bdda1' }, - { mtype_pref_label: 'L2_TPC:B', mtype_id: '4b6862b9-c438-4dfc-a2e6-1ad4d7a00eda' }, - { mtype_pref_label: 'L3_MC', mtype_id: '52578494-b41c-499b-9717-5d11f4b2f068' }, - { mtype_pref_label: 'L3_PC', mtype_id: '87fec7dd-7a2f-400a-aee0-94d1946cf1ab' }, - { mtype_pref_label: 'L3_TPC', mtype_id: '229c31f1-a6ec-4d8c-85d3-d8175ffde109' }, - { mtype_pref_label: 'L3_TPC:A', mtype_id: 'dd346e90-7bca-4976-bf9a-303b6a94b339' }, - { mtype_pref_label: 'L3_TPC:B', mtype_id: 'a71d226c-2c56-40ee-a4be-9726fc430932' }, - { mtype_pref_label: 'L3_TPC:C', mtype_id: 'd9b7bd4d-cec9-4fec-a448-79320de89f2a' }, - { mtype_pref_label: 'L4_BP', mtype_id: 'a55f6ce7-068a-4c5e-a883-de5f4304612e' }, - { mtype_pref_label: 'L4_BTC', mtype_id: '8315d249-6678-4d55-b581-3b6f9eb48e86' }, - { mtype_pref_label: 'L4_ChC', mtype_id: '0e4f3036-0d14-4fd9-b7a8-87f5e90a9fa6' }, - { mtype_pref_label: 'L4_DBC', mtype_id: '8de61c06-31e8-4483-bd98-608bc874b369' }, - { mtype_pref_label: 'L4_LBC', mtype_id: 'bb875a91-4ae5-4f6f-b050-5ad952e9cd6c' }, - { mtype_pref_label: 'L4_MC', mtype_id: '0bdf029e-a55a-444c-a7c9-9d0ff51239a5' }, - { mtype_pref_label: 'L4_NBC', mtype_id: '72673af9-2f2b-4a9a-95dc-552777ab63b9' }, - { mtype_pref_label: 'L4_NGC', mtype_id: '41f41550-5e0e-4de7-b52d-62110c338a27' }, - { mtype_pref_label: 'L4_PC', mtype_id: 'ad5769c6-7e86-4433-8f34-9efcb4f0d182' }, - { mtype_pref_label: 'L4_SBC', mtype_id: '43a7d86b-71c5-4a10-be62-ef6cf95ca694' }, - { mtype_pref_label: 'L4_SSC', mtype_id: '400a55f7-e162-4fd1-80a0-4f2facea7cec' }, - { mtype_pref_label: 'L4_TPC', mtype_id: '02e13718-5227-4c28-b838-04dd0c2c67f2' }, - { mtype_pref_label: 'L4_UPC', mtype_id: '2ef7e0b5-39e4-441b-a72a-c7186afa7f5c' }, - { mtype_pref_label: 'L56_PC', mtype_id: '629d6d6f-93f9-43d8-8a99-277740fd8f22' }, - { mtype_pref_label: 'L5_BP', mtype_id: '7b16c860-ae76-4ddf-b093-4e28620b3712' }, -]; - -// Helper function to check if a field value is considered "empty" or invalid -const isEmptyValue = (value: ConfigValue): boolean => { - if (isNil(value) || value === '') return true; - if (Array.isArray(value) && value.length === 0) return true; - if (typeof value === 'object' && value !== null && Object.keys(value).length === 0) return true; - return false; -}; - -// Helper function to validate required fields -const getRequiredFieldErrors = ( - state: Record, - schema: JSONSchema -): string[] => { - const errors: string[] = []; - const requiredFields = schema.required || []; - - requiredFields.forEach((fieldName) => { - const value = state[fieldName]; - if (isEmptyValue(value)) { - const fieldSchema = schema.properties?.[fieldName]; - const fieldTitle = fieldSchema?.title || fieldName; - errors.push(`${fieldTitle} is required`); - } - }); - - return errors; -}; - -export function JSONSchemaForm({ - disabled, - schema, - stateAtom, - config, - circuit, - onAddReferenceClick, - nodeId, - currentCategory, - onValidationChange, -}: { - disabled: boolean; - config: Config; - schema: JSONSchema; - circuit: ICircuit | undefined | null; - stateAtom: ReturnType>; - onAddReferenceClick: (reference: string) => void; - nodeId?: string; - currentCategory?: string; - onValidationChange?: (isValid: boolean, errors: string[]) => void; -}) { - const skip = ['type']; - - const [state, setState] = useAtom(stateAtom); - const [addingElement, setAddingElement] = useState<{ [key: string]: boolean }>({ - legacy_id: true, - }); - const [newElement, setNewElement] = useState<{ [key: string]: number | string | null }>({}); - const [validationErrors, setValidationErrors] = useState([]); - const [touchedFields, setTouchedFields] = useState>(new Set()); - - const referenceTypesToConfigKeys: Record = { - NeuronSetReference: 'neuron_sets', - TimestampsReference: 'timestamps', - }; - - const referenceTypesToTitles: Record = { - NeuronSetReference: 'Neuron Set', - TimestampsReference: 'Timestamps', - }; - - // Callback ref to avoid dependency issues - const onValidationChangeRef = useRef(onValidationChange); - useEffect(() => { - onValidationChangeRef.current = onValidationChange; - }); - - // Validate form whenever state changes - useEffect(() => { - const errors = getRequiredFieldErrors(state, schema); - - // Only update if errors actually changed - setValidationErrors((prevErrors) => { - const errorsChanged = - prevErrors.length !== errors.length || - prevErrors.some((error, index) => error !== errors[index]); - - if (errorsChanged && onValidationChangeRef.current) { - onValidationChangeRef.current(errors.length === 0, errors); - } - - return errorsChanged ? errors : prevErrors; - }); - }, [state, schema]); - - useEffect(() => { - if (!schema.properties) return; - - const initial: Record = {}; - - Object.entries(schema.properties).forEach(([key, value]) => { - if (key === 'type') initial[key] = value.const ?? null; - else if (key === 'legacy_id') initial[key] = []; - else if (key === 'strain_id') initial[key] = null; - else if (key === 'license_id') - initial[key] = 'c268a20e-b78a-4332-a5e1-38e26c4454b9'; // Default to undefined UUID - else initial[key] = value.default ?? null; - }); - - // Auto-populate brain region id if we're in morphology category - if (currentCategory === 'morphology' && nodeId) { - const brainRegionIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'brainregionid' || - normalizedKey === 'brain_region_id' || - normalizedKey === 'brainregion' - ); - }); - - if (brainRegionIdKey) { - initial[brainRegionIdKey] = nodeId; - } - } - - // Auto-populate species id (hardcoded mouse species ID) - const speciesIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'speciesid' || - normalizedKey === 'species_id' || - normalizedKey === 'species' - ); - }); - - if (speciesIdKey) { - initial[speciesIdKey] = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; - } - - // Auto-populate atlas id - const atlasIdKey = Object.keys(schema.properties || {}).find((key) => { - const normalizedKey = key.toLowerCase().replace(/[\s_]/g, ''); - return ( - normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas' - ); - }); - - if (atlasIdKey) { - initial[atlasIdKey] = 'e3e70682-c209-4cac-a29f-6fbed82c07cd'; - } - - setState((prev) => ({ ...initial, ...prev })); - }, [stateAtom, setState, schema.properties, nodeId, currentCategory]); - - // Helper function to mark field as touched - const markFieldTouched = (fieldName: string) => { - setTouchedFields((prev) => new Set(prev).add(fieldName)); - }; - - // Helper function to check if a field has an error - const hasFieldError = (fieldName: string): boolean => { - const isRequired = schema.required?.includes(fieldName); - const isTouched = touchedFields.has(fieldName); - const isEmpty = isEmptyValue(state[fieldName]); - return isRequired && isTouched && isEmpty; - }; - - // Helper function to get field error message - const getFieldErrorMessage = (fieldName: string): string | null => { - if (!hasFieldError(fieldName)) return null; - const fieldSchema = schema.properties?.[fieldName]; - const fieldTitle = fieldSchema?.title || fieldName; - return `${fieldTitle} is required`; - }; - - function renderInput(k: string, v: JSONSchema) { - const obj = { - ...v, - ...v.anyOf?.find((subv) => subv.type !== 'array' && subv.type !== 'null'), - }; - const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - - const fieldError = getFieldErrorMessage(k); - const hasError = hasFieldError(k); - - const isBrainRegionIdField = - currentCategory === 'morphology' && - (normalizedKey === 'brainregionid' || - normalizedKey === 'brain_region_id' || - normalizedKey === 'brainregion'); - const isSpeciesIdField = - normalizedKey === 'speciesid' || - normalizedKey === 'species_id' || - normalizedKey === 'species'; - const isAtlasIdField = - normalizedKey === 'atlasid' || normalizedKey === 'atlas_id' || normalizedKey === 'atlas'; - const isExperimentDateField = - normalizedKey === 'experimentdate' || - normalizedKey === 'experiment_date' || - normalizedKey === 'date' || - v.title?.toLowerCase().includes('date'); - const isStrainIdField = - normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain'; - const isAgePeriodField = normalizedKey === 'ageperiod' || normalizedKey === 'age_period'; - const isLegacyIdField = normalizedKey === 'legacyid' || normalizedKey === 'legacy_id'; - const isLicenseIdField = normalizedKey === 'licenseid' || normalizedKey === 'license_id'; - const isMtypeClassIdField = normalizedKey === 'mtypeclassid'; - - if (isBrainRegionIdField && nodeId) { - return ( -
- markFieldTouched(k)} - value={nodeId} - readOnly - /> -
- ); - } - - if (isSpeciesIdField) { - return ( -
- markFieldTouched(k)} - value="b7ad4cca-4ac2-4095-9781-37fb68fe9ca1" - readOnly - /> -
- ); - } - - if (isAtlasIdField) { - return ( -
- markFieldTouched(k)} - value="e3e70682-c209-4cac-a29f-6fbed82c07cd" - readOnly - /> -
- ); - } - - if (isExperimentDateField) { - const formatDate = (value: string) => { - const cleaned = value.replace(/[^\d\s-]/g, ''); - const parts = cleaned.split(/[\s-]+/).filter((part) => part.length > 0); - if (parts.length === 0) return ''; - if (parts.length === 1) return parts[0]; - if (parts.length === 2) return `${parts[0]} ${parts[1]}`; - return parts.slice(0, 3).join(' '); - }; - - const validateDateFormat = (value: string) => { - if (!value) return true; - const parts = value.split(' '); - if (parts.length !== 3) return false; - const [day, month, year] = parts; - const dayNum = parseInt(day, 10); - const monthNum = parseInt(month, 10); - const yearNum = parseInt(year, 10); - return ( - dayNum >= 1 && - dayNum <= 31 && - monthNum >= 1 && - monthNum <= 12 && - yearNum >= 1900 && - yearNum <= new Date().getFullYear() - ); - }; - - const currentValue = typeof state[k] === 'string' ? state[k] : ''; - const isValid = validateDateFormat(currentValue); - const showDateError = !isValid && currentValue; - - return ( -
- markFieldTouched(k)} - value={currentValue} - className={`w-full ${hasError || showDateError ? 'border-red-500' : ''}`} - onChange={(e) => { - const formatted = formatDate(e.currentTarget.value); - setState({ ...state, [k]: formatted }); - }} - placeholder="DD MM YYYY (e.g., 15 03 2024)" - /> - {showDateError && ( -
- Please use format: DD MM YYYY (day month year) -
- )} - {fieldError &&
{fieldError}
} -
- ); - } - - if (isStrainIdField) { - const allSpeciesStrains = [ - { - species_id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', - species_name: 'Mouse', - strains: { - 'C57BL/6': '123e4567-e89b-12d3-a456-426614174000', - 'BALB/c': '456e7890-e29b-41d4-a716-446655440001', - }, - }, - { - species_id: '789e0123-e29b-41d4-a716-446655440002', - species_name: 'Rat', - strains: { - 'Sprague Dawley': '890e1234-e29b-41d4-a716-446655440003', - }, - }, - ]; - - const speciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; - const selectedSpecies = allSpeciesStrains.find((s) => s.species_id === speciesId); - - if (!selectedSpecies) { - return ( -
- - {fieldError &&
{fieldError}
} -
- ); - } - - const strainOptions = Object.entries(selectedSpecies.strains).map(([name, id]) => ({ - label: name, - value: id, - })); - - return ( -
- markFieldTouched(k)} - onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); - }} - value={state[k]} - options={obj.enum.map((subv: string) => ({ - label: subv, - value: subv, - }))} - placeholder="Select age period" - /> - {fieldError &&
{fieldError}
} -
- ); - } - return ( -
- markFieldTouched(k)} - value={typeof state[k] === 'string' ? state[k] : ''} - onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); - }} - placeholder="Enter age period" - /> - {fieldError &&
{fieldError}
} -
- ); - } - - if (isLegacyIdField) { - return ( -
-
-
- {Array.isArray(state[k]) && - state[k].map((e) => ( -
- {e}{' '} - {!disabled && ( - { - const newElements = [...(Array.isArray(state[k]) ? state[k] : [])]; - newElements.splice(newElements.indexOf(e), 1); - setState({ ...state, [k]: newElements }); - markFieldTouched(k); - }} - /> - )} -
- ))} -
- {!addingElement[k] && !disabled && ( - setAddingElement({ ...addingElement, [k]: true })} - className="text-primary-8" - /> - )} - {addingElement[k] && !disabled && ( -
- setNewElement({ ...newElement, [k]: e.currentTarget.value })} - placeholder="Enter legacy ID" - /> - {newElement[k] && ( - { - setState({ - ...state, - [k]: [...(Array.isArray(state[k]) ? state[k] : []), newElement[k]], - }); - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - markFieldTouched(k); - }} - /> - )} - { - setAddingElement({ ...addingElement, [k]: false }); - setNewElement({ ...newElement, [k]: null }); - }} - className="text-primary-8" - /> -
- )} -
- {fieldError &&
{fieldError}
} -
- ); - } - - // New condition for 'license id' field - if (isLicenseIdField) { - const licenseOptions = { - undefined: 'c268a20e-b78a-4332-a5e1-38e26c4454b9', - 'CC BY-NC-SA 4.0 Deed': '9e766299-b873-4162-9207-30fcd583d933', - 'CC BY-NC 2.0 Deed': 'fafcd04d-a967-4eec-b2e1-3afb2d63a41a', - 'CC BY-NC 4.0 Deed': '1283454d-b5ad-488f-acb7-d00b9f02873d', - 'CC BY 2.0 Deed': '211ac318-504d-44b9-b250-3cae8980d2e9', - 'CC BY 4.0 Deed': 'ad8686db-3cdd-4e3f-bcbd-812380a9eba7', - 'CC0 1.0 Deed': '74b8c953-67f5-4e95-ac58-095274901328', - 'NGV_Data Licence_v1.0': '0c39107e-3b68-4f1f-904a-5c7f1b4f89c5', - }; - - const options = Object.entries(licenseOptions).map(([name, id]) => ({ - label: name, - value: id, - })); - - // Find the key corresponding to the current state value to set the label - const currentLicenseLabel = Object.keys(licenseOptions).find( - (key) => licenseOptions[key] === state[k] - ); - - return ( -
- markFieldTouched(k)} - onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); - }} - value={currentMtypeLabel || state[k]} - options={options} - placeholder="Select an MTYPE CLASS" - /> - {fieldError &&
{fieldError}
} -
- ); - } - - if (k === 'circuit' && circuit) return ; - - if (v.is_block_reference && v.properties && typeof v.properties.type.const === 'string') { - const referenceKey = referenceTypesToConfigKeys[v.properties.type.const]; - const referenceTitle = referenceTypesToTitles[v.properties.type.const]; - if (!referenceKey) return null; - const referenceConfig = config[referenceKey]; - if (!isPlainObject(referenceConfig)) return null; - - const referees = Object.entries(referenceConfig).filter(([, val]) => { - return isPlainObject(val); - }); - - if (referees.length === 0) { - return ( -
- - {fieldError &&
{fieldError}
} -
- ); - } - - const defaultV = - isPlainObject(state[k]) && typeof state[k].block_name === 'string' - ? state[k].block_name - : null; - - return ( -
- markFieldTouched(k)} - onChange={(newV) => { - setState({ ...state, [k]: newV }); - markFieldTouched(k); - }} - value={state[k]} - options={obj.enum.map((subv: string) => ({ - label: subv, - value: subv, - }))} - placeholder={`Select ${v.title || k}`} - /> - {fieldError &&
{fieldError}
} -
- ); - } - - if (obj.type === 'number' || obj.type === 'integer') { - return ( -
- { - setState({ ...state, [k]: value }); - }} - onBlur={() => markFieldTouched(k)} - className={`w-full ${hasError ? 'border-red-500' : ''}`} - /> - {fieldError &&
{fieldError}
} -
- ); - } - - if (obj.type === 'string') { - return ( -
- markFieldTouched(k)} - value={typeof state[k] === 'string' ? state[k] : ''} - onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); - }} - /> - {fieldError &&
{fieldError}
} -
- ); - } - - return ( -
- markFieldTouched(k)} - value={typeof state[k] === 'string' ? state[k] : ''} - onChange={(e) => { - setState({ ...state, [k]: e.currentTarget.value }); - }} - placeholder={`Enter value for ${v.title || k}`} - /> - {fieldError &&
{fieldError}
} -
- ); - } - - function getFieldTitle(k: string, v: JSONSchema, normalizedKey: string): string { - if (normalizedKey === 'strainid' || normalizedKey === 'strain_id' || normalizedKey === 'strain') - return 'STRAIN'; - if (normalizedKey === 'ageperiod' || normalizedKey === 'age_period') return 'AGE PERIOD'; - if (normalizedKey === 'licenseid' || normalizedKey === 'license_id') return 'LICENSE'; - if (normalizedKey === 'mtypeclassid') return 'MTYPE CLASS'; - return v.title || k; - } - - return ( -
-
{schema.title}
-
{schema.description}
- - {/* Show overall validation errors summary if there are any */} - {validationErrors.length > 0 && ( -
-
- Please fix the following required fields: -
-
    - {validationErrors.map((error) => ( -
  • {error}
    • - ))} -
-
- )} - -
- {schema.properties && - Object.entries(schema.properties) - .filter(([k]) => { - return !skip.includes(k); - }) - .map(([k, v]) => { - const isRequired = schema.required?.includes(k); - const normalizedKey = k.toLowerCase().replace(/[\s_]/g, ''); - const fieldTitle = getFieldTitle(k, v, normalizedKey); - - return ( -
-
-
- {fieldTitle} - {isRequired && *} -
- {v.units &&
{v.units}
} -
- {renderInput(k, v)} -
- ); - })} -
-
- ); -} - -export function Tab({ - tab, - selectedTab, - children, - onClick, - rounded = 'rounded-full', - extraClass, - disabled, -}: { - tab: string; - selectedTab: string; - onClick?: () => void; - rounded?: 'rounded-l-full' | 'rounded-r-full' | 'rounded-full'; - children?: React.ReactNode; - extraClass?: string; - disabled?: boolean; -}) { - return ( - - ); -} - -export function Chevron({ rotate }: { rotate?: number }) { - return ( - - - - ); -} diff --git a/src/features/contribute/_components/file-viewer/index.tsx b/src/features/contribute/_components/file-viewer/index.tsx deleted file mode 100644 index e8d736a3a..000000000 --- a/src/features/contribute/_components/file-viewer/index.tsx +++ /dev/null @@ -1,81 +0,0 @@ -import { Suspense } from 'react'; -import { match } from 'ts-pattern'; -import { useAtomValue } from 'jotai'; - -import { File } from '../simulation-files'; -import { fileAtomFamily } from '../atoms'; - -import EphysViewer from '@/features/ephys-viewer'; -import { classNames } from '@/util/utils'; -import { WorkspaceContext } from '@/types/common'; -import { ICircuitSimulationResult } from '@/api/entitycore/types/entities/circuit-simulation-result'; - -type FileViewerProps = { - file?: File; - context: WorkspaceContext; - className?: string; -}; - -export function FileViewer({ file, context, className = '' }: FileViewerProps) { - const fileName = file?.assetPath?.split('/').at(-1) ?? file?.asset.path.split('/').at(-1); - const fileExt = fileName?.split('.').at(-1)?.toLowerCase(); - - const viewerContent = match(fileExt) - .with(undefined, () =>

Select a file for preview

) - .with('json', () => ) - .with('nwb', () => ) - .otherwise(() => ); - - return ( -
-
- Loading...
}>{viewerContent} -
-
- ); -} - -type JsonFileViewerProps = { - file: File; - context: WorkspaceContext; -}; - -function JsonFileViewer({ file, context }: JsonFileViewerProps) { - const parsedJson = useAtomValue( - fileAtomFamily({ - id: file.asset.id, - entityId: file.entity.id, - entityType: file.entity.type, - assetPath: file.assetPath, - context, - }) - ); - - return 
{JSON.stringify(parsedJson, null, 2)}
; -} - -type NwbFileViewerProps = { - file: File; - context: WorkspaceContext; -}; - -function NwbFileViewer({ file, context }: NwbFileViewerProps) { - return ; -} - -type PlaceholderFileViewerProps = { - file: File; -}; - -function PlaceholderFileViewer({ file }: PlaceholderFileViewerProps) { - const fileName = file?.assetPath?.split('/').at(-1) ?? file?.asset.path.split('/').at(-1); - const fileExt = fileName?.split('.').at(-1)?.toLowerCase(); - - return ( -
- - Preview for {fileExt} files is not supported yet - -
- ); -} diff --git a/src/features/contribute/_components/hooks/circuit.ts b/src/features/contribute/_components/hooks/circuit.ts deleted file mode 100644 index 4d3ae3c9b..000000000 --- a/src/features/contribute/_components/hooks/circuit.ts +++ /dev/null @@ -1,88 +0,0 @@ -import React from 'react'; - -import { getCircuit } from '@/api/entitycore/queries/model/circuit'; -import { ICircuit } from '@/api/entitycore/types/entities/circuit'; -import { useAppNotification } from '@/components/notification'; -import { AssetLabel } from '@/api/entitycore/types/shared/global'; -import { downloadAsset } from '@/api/entitycore/queries/assets'; -import { EntityTypeEnum } from '@/api/entitycore/types'; - -const pendingQueries = new Map>(); - -/** - * Retrieve a circuit from EntityCore. - * @param circuitId - * @returns `undefined` if the query is pending, `null` if an error occured and the circuit in case of success. - */ -export function useCircuit(circuitId: string | undefined): ICircuit | undefined | null { - const { error } = useAppNotification(); - const [circuit, setCircuit] = React.useState(undefined); - - React.useEffect(() => { - if (!circuitId) { - setCircuit(undefined); - return; - } - - getQuery(circuitId) - .then(setCircuit) - .catch((ex) => { - error({ - message: `Unable to retrieve circuit "${circuitId}"!\n${ex}`, - }); - setCircuit(null); - }); - }, [circuitId, error]); - - return circuit; -} - -export function useCircuitImageURL(circuitId: string | undefined) { - const { error } = useAppNotification(); - const [url, setUrl] = React.useState(undefined); - const circuit = useCircuit(circuitId); - - React.useEffect(() => { - const action = async () => { - if (!circuit) return; - - const asset = circuit.assets.find( - (item) => item.label === AssetLabel.simulation_designer_image - ); - if (!asset) { - error({ message: `No image found for circuit "${circuit.name}" (${circuitId})!` }); - return; - } - try { - const resp = await downloadAsset({ - entityType: EntityTypeEnum.Circuit, - entityId: circuit.id, - id: asset.id, - asRawResponse: false, - }); - if (!(resp instanceof ArrayBuffer)) { - throw new Error('Wrong image format: expected ArrayBuffer!'); - } - const blob = new Blob([resp], { type: asset.content_type }); - const newUrl = URL.createObjectURL(blob); - setUrl(newUrl); - } catch (ex) { - error({ - message: `Unable to download image for circuit "${circuit.name}"!\n${ex}`, - }); - } - }; - action(); - }, [circuit, circuitId, error]); - - return url; -} - -function getQuery(circuitId: string): Promise { - const query = pendingQueries.get(circuitId); - if (query) return query; - - const newQuery = getCircuit({ id: circuitId }); - pendingQueries.set(circuitId, newQuery); - return newQuery; -} diff --git a/src/features/contribute/_components/hooks/config-atom.ts b/src/features/contribute/_components/hooks/config-atom.ts deleted file mode 100644 index 9fbb48e61..000000000 --- a/src/features/contribute/_components/hooks/config-atom.ts +++ /dev/null @@ -1,30 +0,0 @@ -import React from 'react'; -import { atom, useAtom } from 'jotai'; - -import { JSONSchema, AtomsMap } from '../../types'; -import { Config } from '../components'; -import { isAtom } from '../utils'; - -export function useConfigAtom(schema: JSONSchema | null, atomsMap: AtomsMap) { - const configAtom = React.useMemo(() => { - return atom((get) => { - const result: Config = {}; - Object.keys(atomsMap).forEach((key) => { - if (isAtom(atomsMap[key])) result[key] = get(atomsMap[key]); - else { - result[key] = {}; - Object.entries(atomsMap[key]).forEach(([subkey, v]) => { - if (typeof result[key] === 'string') return; - result[key][subkey] = get(v); - }); - } - }); - - result.type = schema?.properties?.type.const ?? ''; - - return result; - }); - }, [atomsMap, schema]); - const [config] = useAtom(configAtom); - return config; -} diff --git a/src/features/contribute/_components/hooks/schema.ts b/src/features/contribute/_components/hooks/schema.ts deleted file mode 100644 index 0177adf09..000000000 --- a/src/features/contribute/_components/hooks/schema.ts +++ /dev/null @@ -1,149 +0,0 @@ -import React from 'react'; -import { atom } from 'jotai'; -import { NotificationInstance } from 'antd/es/notification/interface'; - -import $RefParser from '@apidevtools/json-schema-ref-parser'; - -import { AtomsMap, JSONSchema } from '../../types'; -import { ConfigValue, Config } from '../components'; -import { isPlainObject, isAtom } from '../utils'; -import { assertErrorMessage } from '@/util/utils'; - -export function useObioneJsonSchema( - notification: NotificationInstance, - setSchema: React.Dispatch>, - setAtomsMap: (atomsMap: AtomsMap) => void, - initialConfig?: Config -) { - React.useEffect(() => { - async function fetchSpec() { - try { - const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); - const json = await res.json(); - const dereferenced = await $RefParser.dereference(json); - // @ts-ignore - const theSchema = dereferenced.components.schemas.SimulationsForm as JSONSchema; - if (!theSchema.properties) return; - - setSchema(theSchema); - - const map: { - [key: string]: - | ReturnType>> - | Record>>>; - } = {}; - - if (initialConfig) { - Object.entries(initialConfig) - .filter(([k]) => { - return isRootCategory(theSchema, k); - }) - .forEach(([k, v]) => { - if (isPlainObject(v)) map[k] = atom>(v); - }); - - Object.entries(initialConfig) - .filter(([k]) => { - return !isRootCategory(theSchema, k); - }) - .forEach(([k, v]) => { - map[k] = {}; - - Object.entries(v).forEach(([subK, subV]) => { - if (!isPlainObject(subV) || isAtom(map[k])) return; - map[k][subK] = atom>(subV); - }); - }); - } else { - // Setting up initial values and constants. - Object.entries(theSchema.properties).forEach(([k, v]) => { - if (!v.additionalProperties) { - const initial: Record = {}; - - if (v.properties) - Object.entries(v.properties).forEach(([subkey, subValue]) => { - if (subkey === 'type') initial[subkey] = subValue.const ?? null; - else initial[subkey] = subValue.default ?? null; - }); - - map[k] = atom>(initial); - } else map[k] = {}; - }); - } - - setAtomsMap(map); - } catch (e) { - // eslint-disable-next-line no-console - console.error(assertErrorMessage(e)); - notification.error({ message: assertErrorMessage(e) }); - } - } - - fetchSpec(); - }, [notification, setAtomsMap, setSchema, initialConfig]); -} - -export function isRootCategory(schema: JSONSchema, key: string) { - return schema.properties?.[key] && !schema.properties[key].additionalProperties; -} - -export function resolveKey(schema: JSONSchema, tabKey: string, itemIdx: number | null) { - if (typeof itemIdx === null) throw new Error('Invalid itemIdx'); - if (!schema.properties?.[tabKey]?.singular_name) throw new Error(`Invalid schema for ${tabKey}`); - if (isRootCategory(schema, tabKey)) throw new Error("Shouldn't be a root category"); - - return `${schema.properties[tabKey].singular_name.replaceAll(' ', '')}_${itemIdx}`; -} - -export function useObioneJsonConfigurationSchema( - circuitId: string, - notification: NotificationInstance, - setSchema: React.Dispatch>, - setAtomsMap: (atomsMap: AtomsMap) => void -) { - React.useEffect(() => { - async function fetchSpec() { - try { - const res = await fetch(`http://0.0.0.0:8100/openapi.json`); - // const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); - - const json = await res.json(); - const dereferenced = await $RefParser.dereference(json); - // @ts-ignore - const theSchema = dereferenced.components.schemas.ContributeMorphologyForm as JSONSchema; - if (!theSchema.properties) return; - - setSchema(theSchema); - - const map: { - [key: string]: - | ReturnType>> - | Record>>>; - } = {}; - - // Setting up initial values and constants. - Object.entries(theSchema.properties).forEach(([k, v]) => { - if (!v.additionalProperties) { - const initial: Record = {}; - - if (v.properties) - Object.entries(v.properties).forEach(([subkey, subValue]) => { - if (subkey === 'type') initial[subkey] = subValue.const ?? null; - else initial[subkey] = subValue.default ?? null; - }); - - map[k] = atom>(initial); - } else map[k] = {}; - }); - - setAtomsMap(map); - } catch (e) { - // eslint-disable-next-line no-console - console.error(assertErrorMessage(e)); - notification.error({ message: assertErrorMessage(e) }); - } - } - - fetchSpec(); - }, [notification, setAtomsMap, setSchema]); -} diff --git a/src/features/contribute/_components/section.tsx b/src/features/contribute/_components/section.tsx deleted file mode 100644 index b8dc739c7..000000000 --- a/src/features/contribute/_components/section.tsx +++ /dev/null @@ -1,221 +0,0 @@ -/* eslint-disable no-param-reassign */ -import React, { Fragment } from 'react'; -import { atom } from 'jotai'; -import { - CheckCircleFilled, - DeleteOutlined, - PlusCircleOutlined, - WarningFilled, -} from '@ant-design/icons'; -import { ErrorObject } from 'ajv'; - -import { AtomsMap, JSONSchema } from '../types'; -import { Chevron, Config, ConfigValue, Tab } from './components'; -import { isAtom, isPlainObject } from './utils'; -import { isRootCategory, resolveKey } from './hooks/schema'; - -import { classNames } from '@/util/utils'; - -export function Section({ - schema, - k, - sectionSchema, - atomsMap, - setAtomsMap, - configTab, - setConfigTab, - config, - campaignId, - loading, - errors, - selectedItemIdx, - setSelectedItemIdx, - setEditing, - setSelectedCategory, - readOnly, -}: { - schema: JSONSchema | null; // The global schema - k: string; // secition key - sectionSchema: JSONSchema; // The schema for this section - atomsMap: AtomsMap; - setAtomsMap: React.Dispatch>; - configTab: string; // Key for selected section - setConfigTab: (configTab: string) => void; - config: Config; - campaignId: string; - loading: boolean; - errors: ErrorObject, unknown>[] | null | undefined; - selectedItemIdx: number | null; - setSelectedItemIdx: (selectedItemIdx: number | null) => void; - setEditing: React.Dispatch>; - setSelectedCategory: React.Dispatch>; - readOnly?: boolean; -}) { - if (!schema || !schema?.properties) return; - - const handleHeaderClick = (subkey: string, subValue: unknown) => { - if (isPlainObject(subValue)) { - setSelectedCategory(typeof subValue.type === 'string' ? subValue.type : ''); - setSelectedItemIdx(parseInt(subkey.split('_')[1], 10)); - } - setEditing(true); - }; - - return ( - <> - { - if (configTab === k && !isRootCategory(schema, k)) { - setEditing(false); - setSelectedCategory(''); - setSelectedItemIdx(null); - setConfigTab(''); - return; - } - - setConfigTab(k); - setSelectedItemIdx(null); - if (!sectionSchema.additionalProperties) setEditing(true); - else setEditing(false); - }} - extraClass="w-full flex justify-between h-[50px] min-h-[50px] items-center drop-shadow" - > - {schema.properties?.[k]?.title} -
- {errors?.find((error) => error.instancePath.startsWith('/' + k)) ? ( - - ) : ( - - )} - -
- - {sectionSchema.additionalProperties && configTab === k && config[k] && ( - <> - {Object.entries(config[k]).map(([subkey, subValue]) => { - const idx = parseInt(subkey.split('_')[1], 10); - - const isSelected = configTab === k && idx === selectedItemIdx; - - return ( - -
handleHeaderClick(subkey, subValue)} - onKeyDown={(evt) => { - if (evt.key === ' ' || evt.key === 'Enter') { - handleHeaderClick(subkey, subValue); - } - }} - > - {subkey} -
- {errors?.find((error) => error.instancePath.startsWith(`/${k}/${subkey}`)) ? ( - - ) : ( - - )} - - {!campaignId && !loading && !readOnly && ( - { - e.stopPropagation(); - - setSelectedCategory(''); - setEditing(false); - - const selectedTabAtoms = atomsMap[configTab]; - if (!isAtom(selectedTabAtoms)) { - const refereeKey = resolveKey(schema, configTab, idx); - - delete selectedTabAtoms[refereeKey]; - - // Initialize case - const configInitialize = config.initialize; - if ( - isPlainObject(configInitialize) && - isPlainObject(configInitialize.node_set) && - typeof configInitialize.node_set.block_name === 'string' && - configInitialize.node_set.block_name === refereeKey - ) { - atomsMap.initialize = atom>({ - ...configInitialize, - node_set: null, - }); - } - - // Check all keys in the config - Object.entries(config) - .filter(([configK]) => configK !== 'initialize') - .forEach(([configK, configV]) => { - if (typeof configV !== 'object') return; - - // Check all keys in a section (e.g stimuli, recordings) - Object.entries(configV).forEach(([entryKey, entryV]) => { - if (!isPlainObject(entryV)) return; - - // Check all values in a particular object (a single stimuli, a single timestamp, etc) - Object.entries(entryV).forEach(([fieldK, field]) => { - if ( - !isPlainObject(entryV) || - !isPlainObject(field) || - typeof field.block_name !== 'string' || - isAtom(atomsMap[configK]) || // skip top level atoms (e.g initialize) - field.block_name !== refereeKey - ) - return; - - // Deleting the reference to current object - - delete entryV[fieldK]; //eslint-disable-line - - // The atom that has a reference to current object - atomsMap[configK][entryKey] = - atom>(entryV); - }); - }); - }); - - setAtomsMap({ - ...atomsMap, - [configTab]: { - ...selectedTabAtoms, - }, - }); - } - - setSelectedItemIdx(null); - }} - /> - )} -
-
- - ); - })} - {!campaignId && !loading && !readOnly && ( - - )} - - )} - - ); -} diff --git a/src/features/contribute/_components/simulation-files/index.tsx b/src/features/contribute/_components/simulation-files/index.tsx deleted file mode 100644 index 0d2a8ca2c..000000000 --- a/src/features/contribute/_components/simulation-files/index.tsx +++ /dev/null @@ -1,198 +0,0 @@ -import { useAtomValue } from 'jotai'; -import { Suspense, useMemo } from 'react'; -import { ErrorBoundary } from 'react-error-boundary'; - -import { ICircuitSimulation } from '@/api/entitycore/types/entities/circuit-simulation'; -import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; -import { IEntity } from '@/api/entitycore/types/entities/entity'; -import { IAsset } from '@/api/entitycore/types/shared/global'; -import { - circuitAtomFamily, - simResultBySimIdAtomFamily, -} from '@/features/small-microcircuit/_components/atoms'; -import { WorkspaceContext } from '@/types/common'; -import { classNames } from '@/util/utils'; - -export type File = { - asset: IAsset; - entity: IEntity; - assetPath?: string; -}; - -type SimulationFilesProps = { - simulation: ICircuitSimulation; - execStatus?: CircuitSimulationExecutionStatus | null; - selectedFile?: File; - onSelect: (file: File) => void; - context: WorkspaceContext; -}; - -export function SimulationFiles({ - simulation, - execStatus, - selectedFile, - onSelect, - context, -}: SimulationFilesProps) { - const outputAvailable = - execStatus && - [CircuitSimulationExecutionStatus.ERROR, CircuitSimulationExecutionStatus.DONE].includes( - execStatus - ); - - return ( - <> -

Input files

- -

Output files

- Loading...
}> - {outputAvailable && ( - There was an issue loading output files - } - resetKeys={[simulation]} - > - - - )} - - - ); -} - -type SimulationInputFilesProps = { - simulation: ICircuitSimulation; - context: WorkspaceContext; - selectedFile?: File; - onSelect: (file: File) => void; - className?: string; -}; - -function SimulationInputFiles({ - simulation, - context, - selectedFile, - onSelect, - className = '', -}: SimulationInputFilesProps) { - const circuit = useAtomValue(circuitAtomFamily({ circuitId: simulation.entity_id, context })); - // TODO: fetch circuitConfig - const sonataCircuitAsset = circuit.assets.find((asset) => asset.label === 'sonata_circuit'); - const circuitConfigFile: File = useMemo( - () => ({ - entity: circuit, - asset: sonataCircuitAsset!, - assetPath: 'circuit_config.json', - }), - [circuit, sonataCircuitAsset] - ); - - const files: File[] = useMemo( - () => [circuitConfigFile, ...simulation.assets.map((asset) => ({ asset, entity: simulation }))], - [simulation, circuitConfigFile] - ); - - return ( -
- {files.map((file) => ( - - ))} -
- ); -} - -type SimulationOutputFilesProps = { - simulation: ICircuitSimulation; - context: WorkspaceContext; - selectedFile?: File; - onSelect: (file: File) => void; - className?: string; -}; - -function SimulationOutputFiles({ - simulation, - onSelect, - selectedFile, - context, - className = '', -}: SimulationOutputFilesProps) { - const simResult = useAtomValue( - simResultBySimIdAtomFamily({ simulationId: simulation.id, context }) - ); - - const files: File[] = useMemo( - () => simResult.assets.map((asset) => ({ asset, entity: simResult })), - [simResult] - ); - - return ( -
- {files.map((file) => ( - - ))} -
- ); -} - -type SimulationFileProps = { - file: File; - selected?: boolean; - onSelect: (file: File) => void; -}; - -function SimulationFile({ file, selected, onSelect }: SimulationFileProps) { - const fileName = file.assetPath?.split('/').at(-1) ?? file.asset.path.split('/').at(-1); - const fileExt = fileName?.split('.').at(-1); - - return ( - - ); -} diff --git a/src/features/contribute/_components/simulation-status/index.tsx b/src/features/contribute/_components/simulation-status/index.tsx deleted file mode 100644 index 499d77215..000000000 --- a/src/features/contribute/_components/simulation-status/index.tsx +++ /dev/null @@ -1,50 +0,0 @@ -import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; - -export function SimulationStatusBadge({ status }: { status?: CircuitSimulationExecutionStatus }) { - const color = status ? statusColorMap[status] : '#fafafa'; - const showSpinner = status && ['pending', 'running'].includes(status); - - // TODO: move spinner outside of the module. - - return ( -
- {showSpinner && ( - - - - - )} - - - {status ?? ''} - -
- ); -} -const statusColorMap: Record = { - created: '#434343', - pending: '#fa8c16', - running: '#1890ff', - done: '#389e0d', - error: '#f5222d', -}; diff --git a/src/features/contribute/_components/tabs-selector/index.ts b/src/features/contribute/_components/tabs-selector/index.ts deleted file mode 100644 index e516b026d..000000000 --- a/src/features/contribute/_components/tabs-selector/index.ts +++ /dev/null @@ -1 +0,0 @@ -export { default } from './tabs-selector'; diff --git a/src/features/contribute/_components/tabs-selector/tabs-selector.tsx b/src/features/contribute/_components/tabs-selector/tabs-selector.tsx deleted file mode 100644 index 3b2b02a17..000000000 --- a/src/features/contribute/_components/tabs-selector/tabs-selector.tsx +++ /dev/null @@ -1,43 +0,0 @@ -import React from 'react'; - -import { Tab } from '../components'; -import { TabType } from '../../types'; -import { classNames } from '@/util/utils'; - -interface TabsSelectorProps { - className?: string; - tab: TabType; - setTab(tab: TabType): void; - disableSimulationTab: boolean; -} - -export default function TabsSelector({ - className, - tab, - setTab, - disableSimulationTab, -}: TabsSelectorProps) { - return ( -
-
- setTab('configuration')} - > - Configuration - - setTab('simulations')} - disabled={disableSimulationTab} - > - Simulations - -
-
- ); -} diff --git a/src/features/contribute/_components/tooltip/index.ts b/src/features/contribute/_components/tooltip/index.ts deleted file mode 100644 index bb106e207..000000000 --- a/src/features/contribute/_components/tooltip/index.ts +++ /dev/null @@ -1 +0,0 @@ -export { default } from './tooltip'; diff --git a/src/features/contribute/_components/tooltip/tooltip.module.css b/src/features/contribute/_components/tooltip/tooltip.module.css deleted file mode 100644 index a4e563aa8..000000000 --- a/src/features/contribute/_components/tooltip/tooltip.module.css +++ /dev/null @@ -1,39 +0,0 @@ -.tooltipContainer { - position: relative; - overflow: visible; -} - -.tooltip { - position: relative; - background: #0050b3ee; - color: #fff; - padding: 0.5em 1em; - border-radius: 0.25em; - position: absolute; - left: 0; - right: 0; - bottom: 0; - width: 100%; - pointer-events: none; - z-index: 9; - transform: translateY(calc(100% + 16px)); - transition: all 0.2s; - opacity: 0; -} - -.tooltipContainer:hover .tooltip { - opacity: 1; -} - -.tooltip::after { - content: ''; - border: 16px solid transparent; - border-bottom: 16px solid #0050b3ee; - position: absolute; - top: -16px; - left: 50%; - width: 0; - height: 0; - margin: -16px; - transform: scale(0.5, 1); -} diff --git a/src/features/contribute/_components/tooltip/tooltip.tsx b/src/features/contribute/_components/tooltip/tooltip.tsx deleted file mode 100644 index 45a1501f4..000000000 --- a/src/features/contribute/_components/tooltip/tooltip.tsx +++ /dev/null @@ -1,20 +0,0 @@ -import React from 'react'; - -import { classNames } from '@/util/utils'; - -import styles from './tooltip.module.css'; - -interface TooltipProps { - className?: string; - value?: React.ReactNode; - children: React.ReactNode; -} - -export default function Tooltip({ className, value, children }: TooltipProps) { - return ( -
- {children} - {value &&
{value}
} -
- ); -} diff --git a/src/features/contribute/_components/utils.ts b/src/features/contribute/_components/utils.ts deleted file mode 100644 index f4f3c34a2..000000000 --- a/src/features/contribute/_components/utils.ts +++ /dev/null @@ -1,73 +0,0 @@ -import { Atom } from 'jotai'; -import uniq from 'lodash/uniq'; -import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; - -export type Primitive = null | boolean | number | string; -export interface ConfigObject { - [key: string]: Primitive | Primitive[] | ConfigObject; -} - -export function isPlainObject(value: unknown): value is Record { - return typeof value === 'object' && !Array.isArray(value) && value !== null; -} - -export function isAtom(val: unknown): val is Atom { - return typeof val === 'object' && val !== null && 'read' in val; -} - -export const ORDERING: Record = { - assets: { - order: 0, - category: 'Assets', - }, - morphology: { - order: 1, - category: 'Setup', - }, - contribution: { - order: 2, - category: 'Contribution', - }, - subject: { - order: 4, - category: 'Subject', - }, - license: { - order: 5, - category: 'License', - }, - mtype: { - order: 6, - category: 'Mtype', - }, - // publication: { - // order: 7, - // category: 'Publication', - // }, - // scientificartifact: { - // order: 8, - // category: 'Scientific Artifact', - // }, -}; - -export const CATEGORIES: string[] = uniq(Object.values(ORDERING).map((o) => o.category)); - -const simExecStatusListordered = [ - CircuitSimulationExecutionStatus.CREATED, - CircuitSimulationExecutionStatus.PENDING, - CircuitSimulationExecutionStatus.RUNNING, - CircuitSimulationExecutionStatus.DONE, - CircuitSimulationExecutionStatus.ERROR, -]; - -export function getLatestSimExecStatus( - remoteStatus: CircuitSimulationExecutionStatus, - localStatus: CircuitSimulationExecutionStatus -) { - const remoteStatusIdx = simExecStatusListordered.indexOf(remoteStatus); - const localStatusIdx = simExecStatusListordered.indexOf(localStatus); - - const latestStatus = Math.max(remoteStatusIdx, localStatusIdx); - - return simExecStatusListordered[latestStatus]; -} diff --git a/src/features/contribute/error-registry.ts b/src/features/contribute/error-registry.ts deleted file mode 100755 index afc71adf6..000000000 --- a/src/features/contribute/error-registry.ts +++ /dev/null @@ -1,7 +0,0 @@ -import { messages } from '@/i18n/en/simulation'; - -const errorCodeToTranslationKey: Record = { - ACCOUNTING_INSUFFICIENT_FUNDS_ERROR: messages.LowFundsError, -}; - -export default errorCodeToTranslationKey; diff --git a/src/features/contribute/small-microcircuit.module.css b/src/features/contribute/small-microcircuit.module.css deleted file mode 100755 index 0a4777633..000000000 --- a/src/features/contribute/small-microcircuit.module.css +++ /dev/null @@ -1,32 +0,0 @@ -div.threeColumns { - display: grid; - grid-template-columns: minmax(0, 1fr) minmax(0, 1fr) minmax(0, 2fr); - gap: 5px; - height: calc(100% - 100px); -} - -div.threeColumns > div { - min-height: 0; - height: 100%; -} - -div.threeColumns > div.scrollable { - overflow-y: auto; - overflow-x: visible; -} - -div.threeColumns > div:first-child { - display: grid; - grid-template-rows: 1fr auto; - gap: 1em; - overflow: unset; -} - -header.header { - display: flex; - flex-wrap: nowrap; - flex-direction: row; - justify-content: space-between; - align-items: center; - gap: 1em; -} diff --git a/src/features/contribute/types.ts b/src/features/contribute/types.ts deleted file mode 100755 index 2217e8e2b..000000000 --- a/src/features/contribute/types.ts +++ /dev/null @@ -1,35 +0,0 @@ -import { atom } from 'jotai'; - -import { ConfigValue } from './_components/components'; -import { CircuitSimulationExecutionStatus } from '@/api/entitycore/types/entities/circuit-simulation-execution'; - -export type JSONSchema = { - type?: 'string' | 'number' | 'integer' | 'object' | 'array' | 'boolean' | 'null'; - properties?: { [key: string]: JSONSchema }; - items?: JSONSchema | JSONSchema[]; - required?: string[]; - enum?: any[]; - const?: string; - additionalProperties?: JSONSchema; - oneOf?: JSONSchema[]; - anyOf?: JSONSchema[]; - allOf?: JSONSchema[]; - not?: JSONSchema; - format?: string; - title?: string; - description?: string; - default?: any; - examples?: any[]; - [key: string]: any; - singular_name?: string; -}; - -export interface AtomsMap { - [key: string]: - | ReturnType>> - | Record>>>; -} - -export type TabType = 'configuration' | 'simulations'; - -export type SimExecStatusMap = Map; From b7fd2c57958c4475d3cb57df5c47d78ea572e4c8 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 16:58:41 +0200 Subject: [PATCH 35/44] packages --- package.json | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/package.json b/package.json index f9eba45ff..9cc8a3418 100644 --- a/package.json +++ b/package.json @@ -86,6 +86,7 @@ "@types/d3": "^7.4.0", "ajv": "^8.17.1", "antd": "^5.13.3", + "canvas": "2.11.2", "chroma-js": "^3.1.2", "comlink": "^4.4.1", "d3": "^7.8.4", @@ -193,7 +194,7 @@ "eslint-plugin-react-hooks": "^4.6.0", "jest": "^29.5.0", "jest-environment-jsdom": "^29.5.0", - "jsdom": "^26.1.0", + "jsdom": "22.1.0", "knip": "^5.61.3", "lefthook": "^1.11.12", "msw": "^2.0.5", @@ -212,7 +213,9 @@ "@types/react": "19.1.0", "@types/react-dom": "19.1.1", "react": "19.1.0", - "react-dom": "19.1.0" + "react-dom": "19.1.0", + "canvas": "2.11.2", + "jsdom": "22.1.0" }, "pnpm": { "peerDependencyRules": { From 05f987d630200d0d8817cddf824cab447cf86c7b Mon Sep 17 00:00:00 2001 From: dkeller9 Date: Fri, 12 Sep 2025 17:05:37 +0200 Subject: [PATCH 36/44] Update components.tsx --- .../contribute/morphology/_components/components.tsx | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index 91c702829..4b264a4ab 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -152,15 +152,6 @@ const processData = async (token: string): Promise => { return null; } - jsonDataSpecies.data.push({ - id: 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1', - name: 'Generic Mus musculus', - }); - jsonDataSpecies.data.push({ - id: '3b1c2a25-b4fb-468d-98d2-d2d431ac8b4a', - name: 'Generic Rattus norvegicus', - }); - const speclist: Array<{ species_id: string; species_name: string; From d446b5e77771c551f1fed37e59c6d7725c6cb41c Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 17:33:01 +0200 Subject: [PATCH 37/44] packages --- pnpm-lock.yaml | 27504 ----------------------------------------------- 1 file changed, 27504 deletions(-) delete mode 100644 pnpm-lock.yaml diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml deleted file mode 100644 index 1943698c7..000000000 --- a/pnpm-lock.yaml +++ /dev/null @@ -1,27504 +0,0 @@ -lockfileVersion: '9.0' - -settings: - autoInstallPeers: true - excludeLinksFromLockfile: false - -importers: - - .: - dependencies: - '@ai-sdk/react': - specifier: ^1.1.21 - version: 1.2.8(react@19.1.0)(zod@3.24.2) - '@ai-sdk/ui-utils': - specifier: ^1.1.17 - version: 1.2.7(zod@3.24.2) - 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escalade: 3.2.0 - get-caller-file: 2.0.5 - require-directory: 2.1.1 - string-width: 4.2.3 - y18n: 5.0.8 - yargs-parser: 21.1.1 - - yauzl@2.10.0: - dependencies: - buffer-crc32: 0.2.13 - fd-slicer: 1.1.0 - - yjs@13.6.24: - dependencies: - lib0: 0.2.111 - - yocto-queue@0.1.0: {} - - yocto-queue@1.2.1: {} - - yoctocolors-cjs@2.1.2: {} - - zip-stream@6.0.1: - dependencies: - archiver-utils: 5.0.2 - compress-commons: 6.0.2 - readable-stream: 4.7.0 - - zod-to-json-schema@3.24.5(zod@3.24.2): - dependencies: - zod: 3.24.2 - - zod-validation-error@3.5.2(zod@3.24.2): - dependencies: - zod: 3.24.2 - - zod@3.24.2: {} - - zustand@4.5.6(@types/react@19.1.0)(immer@10.1.1)(react@19.1.0): - dependencies: - use-sync-external-store: 1.5.0(react@19.1.0) - optionalDependencies: - '@types/react': 19.1.0 - immer: 10.1.1 - react: 19.1.0 - - zustand@5.0.3(@types/react@19.1.0)(immer@10.1.1)(react@19.1.0)(use-sync-external-store@1.5.0(react@19.1.0)): - optionalDependencies: - '@types/react': 19.1.0 - immer: 10.1.1 - react: 19.1.0 - use-sync-external-store: 1.5.0(react@19.1.0) - - zwitch@2.0.4: {} From 2af82982e5655e9035cbd28ffc9d06be7ba2bbb0 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 12 Sep 2025 21:27:09 +0200 Subject: [PATCH 38/44] remove limit on number of mtypes --- .../morphology/_components/components.tsx | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index 4b264a4ab..b5785d074 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -310,10 +310,23 @@ const fetchMtypes = async ( Authorization: `Bearer ${token}`, }; - const url = 'https://staging.openbraininstitute.org/api/entitycore/mtype'; + // Define your parameters + const params: Record = { + page_size: 1000, + }; + + // Create URLSearchParams instance and append parameters + const searchParams = new URLSearchParams(); + for (const key of Object.keys(params)) { + const value = params[key]; + searchParams.append(key, String(value)); + } + const url = 'https://staging.openbraininstitute.org/api/entitycore/mtype'; + // Construct the new URL with the query string + const newUrl = `${url}?${searchParams.toString()}`; try { - const response = await fetch(url, { headers }); + const response = await fetch(newUrl, { headers }); if (!response.ok) { throw new Error(`MTYPE request failed with status code: ${response.status}`); } From 9da0fc4536c093a3d01763112d3cd35a8e24a2ec Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Mon, 15 Sep 2025 13:54:45 +0200 Subject: [PATCH 39/44] changed subject handling and agents --- .../morphology/_components/components.tsx | 215 +++++++++++++++--- .../morphology/_components/section.tsx | 11 +- src/features/contribute/morphology/index.tsx | 33 ++- 3 files changed, 213 insertions(+), 46 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index b5785d074..0c72e0046 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -30,9 +30,24 @@ interface RoleRecord { name?: string; } +interface SubjectSpeciesRecord { + id: string; + name: string; + taxonomy_id: string; +} + interface SubjectRecord { id: string; name?: string; + description?: string; + sex?: string; + weight?: string; + age_value?: string; + age_min?: string; + age_max?: string; + age_unit?: string; + age_period?: string; + species?: SubjectSpeciesRecord; } interface LicenseRecord { @@ -209,6 +224,60 @@ const fetchAgents = async (token: string): Promise | null } }; +const fetchConsortium = async (token: string): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/consortium'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Consortium request failed with status code: ${response.status}`); + } + const jsonDataPerson: PersonData = await response.json(); + + const personDict: Record = {}; + for (const item of jsonDataPerson.data) { + if (item.pref_label) { + personDict[item.pref_label] = item.id; + } + } + return personDict; + } catch { + return null; + } +}; + +const fetchOrganization = async (token: string): Promise | null> => { + const headers: HeadersInit = { + accept: 'application/json', + Authorization: `Bearer ${token}`, + }; + + const url = 'https://staging.openbraininstitute.org/api/entitycore/organization'; + + try { + const response = await fetch(url, { headers }); + if (!response.ok) { + throw new Error(`Organization request failed with status code: ${response.status}`); + } + const jsonDataPerson: PersonData = await response.json(); + + const personDict: Record = {}; + for (const item of jsonDataPerson.data) { + if (item.pref_label) { + personDict[item.pref_label] = item.id; + } + } + return personDict; + } catch { + return null; + } +}; + const fetchRoles = async (token: string): Promise | null> => { const headers: HeadersInit = { accept: 'application/json', @@ -236,9 +305,7 @@ const fetchRoles = async (token: string): Promise | null> } }; -const fetchSubjects = async ( - token: string -): Promise | null> => { +const fetchSubjects = async (token: string): Promise => { const headers: HeadersInit = { accept: 'application/json', Authorization: `Bearer ${token}`, @@ -253,17 +320,7 @@ const fetchSubjects = async ( } const jsonDataSubject: SubjectData = await response.json(); - const subjectList: Array<{ label: string; value: string }> = []; - for (const item of jsonDataSubject.data) { - if (item.name) { - const subjectEntry = { - label: item.name, - value: item.id, - }; - subjectList.push(subjectEntry); - } - } - return subjectList; + return jsonDataSubject.data; } catch { return null; } @@ -310,12 +367,10 @@ const fetchMtypes = async ( Authorization: `Bearer ${token}`, }; - // Define your parameters const params: Record = { page_size: 1000, }; - // Create URLSearchParams instance and append parameters const searchParams = new URLSearchParams(); for (const key of Object.keys(params)) { const value = params[key]; @@ -323,7 +378,6 @@ const fetchMtypes = async ( } const url = 'https://staging.openbraininstitute.org/api/entitycore/mtype'; - // Construct the new URL with the query string const newUrl = `${url}?${searchParams.toString()}`; try { const response = await fetch(newUrl, { headers }); @@ -385,6 +439,7 @@ export function JSONMorphologySchemaForm({ const [state, setState] = useAtom(stateAtom); const [validationErrors, setValidationErrors] = useState([]); const [touchedFields, setTouchedFields] = useState>(new Set()); + const [agentType, setAgentType] = useState('Person'); const [allSpeciesStrains, setAllSpeciesStrains] = useState; }> | null>(null); const [allAgents, setAllAgents] = useState | null>(null); + const [allOrganizations, setAllOrganizations] = useState | null>(null); + const [allConsortia, setAllConsortia] = useState | null>(null); const [allRoles, setAllRoles] = useState | null>(null); - const [allSubjects, setAllSubjects] = useState | null>( - null - ); + const [allSubjects, setAllSubjects] = useState(null); const [allLicenses, setAllLicenses] = useState | null>( null ); @@ -404,21 +459,36 @@ export function JSONMorphologySchemaForm({ mtype_id: string; }> | null>(null); const [brainRegionName, setBrainRegionName] = useState(null); + const [selectedSubjectData, setSelectedSubjectData] = useState(null); useEffect(() => { const errors = getRequiredFieldErrors(state, schema); setValidationErrors(errors); }, [state, schema]); + useEffect(() => { + if (state.subject_id && allSubjects) { + const selected = allSubjects.find((s) => s.id === state.subject_id); + setSelectedSubjectData(selected || null); + if (selected?.species?.id) { + setState((prev) => ({ ...prev, species_id: selected.species.id })); + } else { + setState((prev) => ({ ...prev, species_id: undefined })); + } + } + }, [state.subject_id, allSubjects, setState]); + useEffect(() => { const fetchData = async () => { const session = await getSessionWithCheck(); if (!session) return; - const [speciesData, agentsData, rolesData, subjectsData, licensesData, mtypesData] = + const [speciesData, agentsData, organizationData, consortiumData, rolesData, subjectsData, licensesData, mtypesData] = await Promise.all([ processData(session.accessToken), fetchAgents(session.accessToken), + fetchOrganization(session.accessToken), + fetchConsortium(session.accessToken), fetchRoles(session.accessToken), fetchSubjects(session.accessToken), fetchLicenses(session.accessToken), @@ -437,6 +507,12 @@ export function JSONMorphologySchemaForm({ if (agentsData) { setAllAgents(agentsData); } + if (organizationData) { + setAllOrganizations(organizationData); + } + if (consortiumData) { + setAllConsortia(consortiumData); + } if (rolesData) { setAllRoles(rolesData); } @@ -459,6 +535,13 @@ export function JSONMorphologySchemaForm({ fetchData(); }, [nodeId, state.license_id, setState]); + useEffect(() => { + if (allSpeciesStrains && !state.species_id) { + const defaultSpeciesId = 'b7ad4cca-4ac2-4095-9781-37fb68fe9ca1'; + setState((prev) => ({ ...prev, species_id: defaultSpeciesId })); + } + }, [allSpeciesStrains, state.species_id, setState]); + const markFieldTouched = (field: string) => { setTouchedFields((prev) => new Set([...prev, field])); }; @@ -517,11 +600,11 @@ export function JSONMorphologySchemaForm({ return (
+ markFieldTouched(k)} onChange={(newV) => { setState((prev) => ({ ...prev, [k]: newV })); + const selected = allSubjects.find((s) => s.id === newV); + setSelectedSubjectData(selected || null); markFieldTouched(k); }} value={state[k]} @@ -720,15 +827,22 @@ export function JSONMorphologySchemaForm({ } if (isAgentIdField) { - if (!allAgents) { + const agentData = + agentType === 'Organization' + ? allOrganizations + : agentType === 'Consortium' + ? allConsortia + : allAgents; + + if (!agentData) { return (
- +
); } - const options = Object.entries(allAgents).map(([label, value]) => ({ + const options = Object.entries(agentData).map(([label, value]) => ({ label, value, })); @@ -745,7 +859,7 @@ export function JSONMorphologySchemaForm({ }} value={state[k]} options={options} - placeholder="Select an agent" + placeholder={`Select a ${agentType.toLowerCase()}`} allowClear /> {fieldError &&
{fieldError}
} @@ -835,10 +949,18 @@ export function JSONMorphologySchemaForm({ return 'ROLE'; if (normalizedKey === 'agentid' || normalizedKey === 'agent_id' || normalizedKey === 'agent') return 'AGENT'; + if (normalizedKey === 'agenttype') return 'AGENT TYPE'; return v.title || k; } + const isContributionSchema = schema.title === 'Contribution'; + const agentTypeOptions = [ + { label: 'Person', value: 'Person' }, + { label: 'Organization', value: 'Organization' }, + { label: 'Consortium', value: 'Consortium' }, + ]; + return (
{schema.title}
@@ -858,11 +980,32 @@ export function JSONMorphologySchemaForm({ )}
+ {isContributionSchema && ( +
+
+
AGENT TYPE
+
+ +
+ markFieldTouched(k)} onChange={(newV) => { setState((prev) => ({ ...prev, [k]: newV, strain_id: undefined })); // Reset strain_id when species changes @@ -636,10 +645,12 @@ export function JSONMorphologySchemaForm({
markFieldTouched(k)} onChange={(newV) => { setState((prev) => ({ ...prev, [k]: newV })); @@ -690,7 +701,7 @@ export function JSONMorphologySchemaForm({
markFieldTouched(k)} onChange={(newV) => { setState((prev) => ({ ...prev, [k]: newV })); @@ -773,7 +792,7 @@ export function JSONMorphologySchemaForm({
markFieldTouched(k)} onChange={(newV) => { setState((prev) => ({ ...prev, [k]: newV })); @@ -827,12 +846,14 @@ export function JSONMorphologySchemaForm({ } if (isAgentIdField) { - const agentData = - agentType === 'Organization' - ? allOrganizations - : agentType === 'Consortium' - ? allConsortia - : allAgents; + let agentData = null; + if (agentType === 'Organization') { + agentData = allOrganizations; + } else if (agentType === 'Consortium') { + agentData = allConsortia; + } else { + agentData = allAgents; + } if (!agentData) { return ( @@ -851,7 +872,7 @@ export function JSONMorphologySchemaForm({
markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { @@ -910,7 +931,7 @@ export function JSONMorphologySchemaForm({
markFieldTouched(k)} value={typeof state[k] === 'string' ? state[k] : ''} onChange={(e) => { @@ -983,7 +1004,7 @@ export function JSONMorphologySchemaForm({ {isContributionSchema && (
-
AGENT TYPE
+
AGENT TYPE
@@ -1054,19 +1075,21 @@ export function Tab({ extraClass?: string; disabled?: boolean; }) { + const tabClass = + tab === selectedTab + ? 'bg-gradient-to-r from-[#003A8C] to-[#001026] text-white' + : 'text-primary-8 bg-white'; + + const buttonStyles = disabled + ? { background: '#d1d5db', cursor: 'default', color: '#9ca3af' } + : {}; + return ( @@ -1093,4 +1116,4 @@ export function Chevron({ rotate }: { rotate?: number }) { /> ); -} \ No newline at end of file +} diff --git a/src/features/contribute/morphology/_components/section.tsx b/src/features/contribute/morphology/_components/section.tsx index 48fefb8f7..fddf918dd 100644 --- a/src/features/contribute/morphology/_components/section.tsx +++ b/src/features/contribute/morphology/_components/section.tsx @@ -9,43 +9,39 @@ import { classNames } from '@/util/utils'; type Props = { k: string; sectionSchema: JSONMorphologySchema | undefined; - schema: JSONMorphologySchema; - config: Config; - errors: ErrorObject, unknown>[]; // Fixed to avoid no-explicit-any + _schema: JSONMorphologySchema; // Changed from schema to _schema + _config: Config; + _errors: ErrorObject, unknown>[]; atomsMap: AtomsMap; setAtomsMap: Dispatch>; - configTab: string; + _configTab: string; setConfigTab: (tab: string) => void; setSelectedItemIdx: (idx: number | null) => void; setEditing: (editing: boolean) => void; setSelectedCategory: (category: string) => void; - campaignId: string; - loading: boolean; - selectedItemIdx: number | null; + _campaignId: string; + _loading: boolean; + _selectedItemIdx: number | null; + isSelected: boolean; }; export function Section({ k, sectionSchema, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - schema, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - config, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - errors, + _schema, // Changed from schema to _schema + _config, + _errors, atomsMap, setAtomsMap, - configTab, + _configTab, setConfigTab, setSelectedItemIdx, setEditing, setSelectedCategory, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - campaignId, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - loading, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - selectedItemIdx, + _campaignId, + _loading, + _selectedItemIdx, + isSelected, }: Props) { const fallbackSchema: JSONMorphologySchema = { type: 'object', @@ -83,23 +79,19 @@ export function Section({
- - + {buttonText}
- +
); diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index 7a9ad0384..3e2680a2b 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -256,19 +256,19 @@ export default function ContributeMorphologyConfiguration({ key={k} k={k} sectionSchema={v} - schema={schema} - config={config} - errors={errors} + _schema={schema} + _config={config} + _errors={errors} atomsMap={atomsMap} setAtomsMap={setAtomsMap} - configTab={configTab} + _configTab={configTab} setConfigTab={setConfigTab} setSelectedItemIdx={setSelectedItemIdx} setEditing={setEditing} setSelectedCategory={setSelectedCategory} - campaignId={campaignId} - loading={loading} - selectedItemIdx={selectedItemIdx} + _campaignId={campaignId} + _loading={loading} + _selectedItemIdx={selectedItemIdx} isSelected={configTab === k} /> ))} @@ -676,4 +676,4 @@ export default function ContributeMorphologyConfiguration({
); -} \ No newline at end of file +} From 14a3edc136f1a209d88b386d3762bf30462a454e Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Wed, 17 Sep 2025 10:01:18 +0200 Subject: [PATCH 41/44] added morphology verification --- .../morphology/_components/hooks/schema.ts | 4 +- src/features/contribute/morphology/index.tsx | 87 +++++++++++++++++-- 2 files changed, 83 insertions(+), 8 deletions(-) diff --git a/src/features/contribute/morphology/_components/hooks/schema.ts b/src/features/contribute/morphology/_components/hooks/schema.ts index 3e2c68d25..60ec5ba41 100644 --- a/src/features/contribute/morphology/_components/hooks/schema.ts +++ b/src/features/contribute/morphology/_components/hooks/schema.ts @@ -36,7 +36,9 @@ export function useObioneJsonSchema( React.useEffect(() => { async function fetchSpec() { try { - const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); + //const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); + const res = await fetch(`http://127.0.0.1:8100/openapi.json`); + const json = await res.json(); const dereferenced = (await $RefParser.dereference(json)) as OpenAPISchema; const theSchema = dereferenced.components?.schemas?.[schemaName]; diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index 3e2680a2b..a45b89fb8 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -24,6 +24,54 @@ import { useAppNotification } from '@/components/notification'; import { classNames } from '@/util/utils'; import styles from './small-microcircuit.module.css'; +// File validation function +async function checkFileIsValid(file) { + if (!file || !(file instanceof File)) { + return false; + } + const validExtensions = ['.swc', '.asc', '.h5']; + const extension = file.name.slice(file.name.lastIndexOf('.')).toLowerCase(); + if (!validExtensions.includes(extension)) { + return false; + } + if (!file.name || file.size === 0) { + return false; + } + + try { + const formData = new FormData(); + formData.append('file', file, file.name); + + const headers = { + accept: 'application/json', + // Note: Content-Type is not set explicitly for FormData; browser sets it with boundary + }; + + // Use this for direct requests (requires CORS configuration on server): + const response = await authFetch('http://127.0.0.1:8100/declared/upload-neuron-file', { + method: 'POST', + headers, + body: formData, + }); + + const responseText = await response.text(); + let responseJson = null; + try { + responseJson = JSON.parse(responseText); + } catch (e) { + pass + } + + if (!response.ok) { + return false; + } + + return true; + } catch (error) { + return false; + } +} + export default function ContributeMorphologyConfiguration({ virtualLabId, projectId, @@ -43,7 +91,7 @@ export default function ContributeMorphologyConfiguration({ dataKey: resolveDataKey({ section: 'explore', projectId }), }); - const [configTab, setConfigTab] = useState('morphology'); + const [configTab, setConfigTab] = useState('assets'); const [editing, setEditing] = useState(true); const [schema, setSchema] = useState(null); const [selectedCategory, setSelectedCategory] = useState('ReconstructionMorphology'); @@ -522,12 +570,30 @@ export default function ContributeMorphologyConfiguration({ accept=".swc,.asc,.h5" className="hidden" disabled={loading || readOnly} - onChange={(e) => { + onChange={async (e) => { const file = e.target.files?.[0]; - if (file) { - setSelectedFile(file); - setFileStatus({ message: `File selected: ${file.name}` }); + const isValid = await checkFileIsValid(file); + if (isValid) { + setSelectedFile(file); + setFileStatus({ message: `File selected: ${file.name}` }); + } else { + let errorDescription = `The file ${file.name} is not valid.`; + if (!file.name || file.size === 0) { + errorDescription = `The file ${file.name} is empty or has no name.`; + } else if (!['.swc', '.asc', '.h5'].includes(file.name.slice(file.name.lastIndexOf('.')).toLowerCase())) { + errorDescription = `The file ${file.name} has an invalid extension. Please select a .swc, .asc, or .h5 file.`; + } else { + errorDescription = `The file ${file.name} could not be validated by the server. Please ensure it is a valid .swc, .asc, or .h5 file or check your server configuration.`; + } + notification.error({ + message: 'Invalid File', + description: errorDescription, + }); + setSelectedFile(null); + setFileStatus({ message: `Invalid file selected: ${file.name}` }); + e.target.value = ''; + } } else { setSelectedFile(null); setFileStatus({}); @@ -536,7 +602,14 @@ export default function ContributeMorphologyConfiguration({ /> {fileStatus?.message && ( - {fileStatus.message} + + {fileStatus.message} + )}
@@ -676,4 +749,4 @@ export default function ContributeMorphologyConfiguration({
); -} +} \ No newline at end of file From 11457b2e18174874ec87320d14642865f51e38a2 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Wed, 17 Sep 2025 10:16:34 +0200 Subject: [PATCH 42/44] using staging obi-one --- .../contribute/morphology/_components/hooks/schema.ts | 4 ++-- src/features/contribute/morphology/index.tsx | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/features/contribute/morphology/_components/hooks/schema.ts b/src/features/contribute/morphology/_components/hooks/schema.ts index 60ec5ba41..e4619f7ce 100644 --- a/src/features/contribute/morphology/_components/hooks/schema.ts +++ b/src/features/contribute/morphology/_components/hooks/schema.ts @@ -36,8 +36,8 @@ export function useObioneJsonSchema( React.useEffect(() => { async function fetchSpec() { try { - //const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); - const res = await fetch(`http://127.0.0.1:8100/openapi.json`); + const res = await fetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/openapi.json`); + //const res = await fetch(`http://127.0.0.1:8100/openapi.json`); const json = await res.json(); const dereferenced = (await $RefParser.dereference(json)) as OpenAPISchema; diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index a45b89fb8..ce196d06d 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -48,7 +48,7 @@ async function checkFileIsValid(file) { }; // Use this for direct requests (requires CORS configuration on server): - const response = await authFetch('http://127.0.0.1:8100/declared/upload-neuron-file', { + const response = await authFetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/declared/upload-neuron-file', { method: 'POST', headers, body: formData, From c36f6d711c38cc6d617bbdb80e092aebb9d4a426 Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Wed, 17 Sep 2025 10:27:52 +0200 Subject: [PATCH 43/44] using staging obi-one --- .../morphology/_components/components.tsx | 1 - src/features/contribute/morphology/index.tsx | 33 ++++++++++--------- 2 files changed, 18 insertions(+), 16 deletions(-) diff --git a/src/features/contribute/morphology/_components/components.tsx b/src/features/contribute/morphology/_components/components.tsx index ca8b24f52..31959660d 100644 --- a/src/features/contribute/morphology/_components/components.tsx +++ b/src/features/contribute/morphology/_components/components.tsx @@ -971,7 +971,6 @@ export function JSONMorphologySchemaForm({ if (normalizedKey === 'agentid' || normalizedKey === 'agent_id' || normalizedKey === 'agent') return 'AGENT'; if (normalizedKey === 'agenttype') return 'AGENT TYPE'; - return v.title || k; } diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index ce196d06d..f49aa21bc 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -25,7 +25,7 @@ import { classNames } from '@/util/utils'; import styles from './small-microcircuit.module.css'; // File validation function -async function checkFileIsValid(file) { +async function checkFileIsValid(file: File | null): Promise { if (!file || !(file instanceof File)) { return false; } @@ -47,19 +47,20 @@ async function checkFileIsValid(file) { // Note: Content-Type is not set explicitly for FormData; browser sets it with boundary }; - // Use this for direct requests (requires CORS configuration on server): - const response = await authFetch(`${process.env.NEXT_PUBLIC_OBI_ONE_URL}/declared/upload-neuron-file', { - method: 'POST', - headers, - body: formData, - }); + const response = await authFetch( + `${process.env.NEXT_PUBLIC_OBI_ONE_URL}/declared/upload-neuron-file`, + { + method: 'POST', + headers, + body: formData, + } + ); const responseText = await response.text(); - let responseJson = null; try { - responseJson = JSON.parse(responseText); + JSON.parse(responseText); } catch (e) { - pass + // Ignore parsing errors for now } if (!response.ok) { @@ -84,7 +85,7 @@ export default function ContributeMorphologyConfiguration({ initialConfig?: Config; }) { if (!!initialCampaignId !== !!initialConfig) { - throw new Error('Both or none of initialCampaignId, initialConfigId should be passed'); + throw new Error('Both or none of initialCampaignId, initialConfig should be passed'); } const { node } = useBrainRegionHierarchy({ @@ -437,7 +438,6 @@ export default function ContributeMorphologyConfiguration({ ); const fileResponseText = await fileResponse.text(); - if (!fileResponse.ok) { throw new ApiError(`Failed to upload file: ${fileResponseText}`, { status: fileResponse.status, @@ -464,7 +464,6 @@ export default function ContributeMorphologyConfiguration({ } ); const fileResponseMtypeText = await fileResponseMtype.text(); - if (!fileResponseMtype.ok) { throw new ApiError(`Failed to upload file: ${fileResponseMtypeText}`, { status: fileResponseMtype.status, @@ -581,7 +580,11 @@ export default function ContributeMorphologyConfiguration({ let errorDescription = `The file ${file.name} is not valid.`; if (!file.name || file.size === 0) { errorDescription = `The file ${file.name} is empty or has no name.`; - } else if (!['.swc', '.asc', '.h5'].includes(file.name.slice(file.name.lastIndexOf('.')).toLowerCase())) { + } else if ( + !['.swc', '.asc', '.h5'].includes( + file.name.slice(file.name.lastIndexOf('.')).toLowerCase() + ) + ) { errorDescription = `The file ${file.name} has an invalid extension. Please select a .swc, .asc, or .h5 file.`; } else { errorDescription = `The file ${file.name} could not be validated by the server. Please ensure it is a valid .swc, .asc, or .h5 file or check your server configuration.`; @@ -749,4 +752,4 @@ export default function ContributeMorphologyConfiguration({
); -} \ No newline at end of file +} From e821b0e488bb76a491b597aabac47cd4f29e8dbc Mon Sep 17 00:00:00 2001 From: Daniel Keller Date: Fri, 19 Sep 2025 21:05:19 +0200 Subject: [PATCH 44/44] added conversion of morphologies --- src/features/contribute/morphology/index.tsx | 209 +++++++++++-------- 1 file changed, 125 insertions(+), 84 deletions(-) diff --git a/src/features/contribute/morphology/index.tsx b/src/features/contribute/morphology/index.tsx index f49aa21bc..cbaf51213 100755 --- a/src/features/contribute/morphology/index.tsx +++ b/src/features/contribute/morphology/index.tsx @@ -10,6 +10,7 @@ import { import Ajv, { AnySchema } from 'ajv'; import { atom, useAtom, PrimitiveAtom } from 'jotai'; import { Fragment, useMemo, useRef, useState, KeyboardEvent, useEffect } from 'react'; +import JSZip from 'jszip'; // This library would need to be installed as a dependency import { Config, ConfigValue, JSONMorphologySchemaForm } from './_components/components'; import { useConfigAtom } from './_components/hooks/config-atom'; import { isRootCategory, resolveKey, useObioneJsonSchema } from './_components/hooks/schema'; @@ -24,6 +25,9 @@ import { useAppNotification } from '@/components/notification'; import { classNames } from '@/util/utils'; import styles from './small-microcircuit.module.css'; +// Add a new variable to store the response as an ArrayBuffer +let neuronFileResponse: ArrayBuffer | null = null; + // File validation function async function checkFileIsValid(file: File | null): Promise { if (!file || !(file instanceof File)) { @@ -47,21 +51,14 @@ async function checkFileIsValid(file: File | null): Promise { // Note: Content-Type is not set explicitly for FormData; browser sets it with boundary }; - const response = await authFetch( - `${process.env.NEXT_PUBLIC_OBI_ONE_URL}/declared/upload-neuron-file`, - { - method: 'POST', - headers, - body: formData, - } - ); + const response = await authFetch(`http://127.0.0.1:8100/declared/test-neuron-file`, { + method: 'POST', + headers, + body: formData, + }); - const responseText = await response.text(); - try { - JSON.parse(responseText); - } catch (e) { - // Ignore parsing errors for now - } + // Store the response as an ArrayBuffer, which is suitable for JSZip + neuronFileResponse = await response.arrayBuffer(); if (!response.ok) { return false; @@ -69,6 +66,8 @@ async function checkFileIsValid(file: File | null): Promise { return true; } catch (error) { + // Clear the stored response on error + neuronFileResponse = null; return false; } } @@ -405,106 +404,148 @@ export default function ContributeMorphologyConfiguration({ const newEntityId = jsonResponseData.id; setEntityId(newEntityId); + const filesToUpload: File[] = []; + if (selectedFile) { - const formData = new FormData(); + // Corrected original file handling let mimeType = 'application/octet-stream'; const fileName = selectedFile.name; if (fileName.endsWith('.swc')) { mimeType = 'application/swc'; } else if (fileName.endsWith('.asc')) { - mimeType = 'text/plain'; + mimeType = 'application/asc'; } else if (fileName.endsWith('.h5')) { mimeType = 'application/x-hdf5'; } - const fileWithMimeType = new File([selectedFile], selectedFile.name, { type: mimeType, }); - formData.append('file', fileWithMimeType); - formData.append('label', 'morphology'); + filesToUpload.push(fileWithMimeType); + } - const fileUploadHeaders = { - 'virtual-lab-id': headers['virtual-lab-id'], - 'project-id': headers['project-id'], - }; + if (neuronFileResponse) { + const zip = new JSZip(); + const unzippedData = await zip.loadAsync(neuronFileResponse); + + unzippedData.forEach((relativePath, zipEntry) => { + if (!zipEntry.dir) { + const fileName = relativePath; + let mimeType = 'application/octet-stream'; + if (fileName.endsWith('.swc')) { + mimeType = 'application/swc'; + } else if (fileName.endsWith('.asc')) { + mimeType = 'application/asc'; + } else if (fileName.endsWith('.h5')) { + mimeType = 'application/x-hdf5'; + } - const fileResponse = await authFetch( - `https://staging.openbraininstitute.org/api/entitycore/reconstruction-morphology/${newEntityId}/assets`, - { - method: 'POST', - headers: fileUploadHeaders, - body: formData, + zipEntry.async('blob').then((fileBlob) => { + filesToUpload.push(new File([fileBlob], fileName, { type: mimeType })); + }); } - ); - - const fileResponseText = await fileResponse.text(); - if (!fileResponse.ok) { - throw new ApiError(`Failed to upload file: ${fileResponseText}`, { - status: fileResponse.status, - }); - } + }); - const mtypeRequestBody = { - authorized_public: true, - entity_id: newEntityId, - mtype_class_id: mtypeConfig?.mtype_class_id ?? undefined, - }; + // Wait for all files to be unzipped before proceeding + await Promise.all( + Object.values(unzippedData.files) + .filter((zipEntry) => !zipEntry.dir) + .map((zipEntry) => zipEntry.async('blob')) + ); + } - const fileUploadMtypeHeaders = { + if (filesToUpload.length > 0) { + const fileUploadHeaders = { 'virtual-lab-id': headers['virtual-lab-id'], 'project-id': headers['project-id'], - 'Content-Type': 'application/json', }; - const fileResponseMtype = await authFetch( - `https://staging.openbraininstitute.org/api/entitycore/mtype-classification`, - { - method: 'POST', - headers: fileUploadMtypeHeaders, - body: JSON.stringify(mtypeRequestBody), - } - ); - const fileResponseMtypeText = await fileResponseMtype.text(); - if (!fileResponseMtype.ok) { - throw new ApiError(`Failed to upload file: ${fileResponseMtypeText}`, { - status: fileResponseMtype.status, - }); - } - const contributionRequestBody = { - entity_id: newEntityId, - agent_id: contributionConfig?.agent_id ?? undefined, - role_id: contributionConfig?.role_id ?? undefined, - }; + for (const file of filesToUpload) { - const fileUploadContributionHeaders = { - 'virtual-lab-id': headers['virtual-lab-id'], - 'project-id': headers['project-id'], - 'Content-Type': 'application/json', - }; - const fileResponseContribution = await authFetch( - `https://staging.openbraininstitute.org/api/entitycore/contribution`, - { - method: 'POST', - headers: fileUploadContributionHeaders, - body: JSON.stringify(contributionRequestBody), - } - ); - const fileResponseContributionText = await fileResponseContribution.text(); - if (!fileResponseContribution.ok) { - throw new ApiError( - `Failed to upload file: ${fileResponseContributionText}`, + const formData = new FormData(); + formData.append('file', file, file.name); + formData.append('label', 'morphology'); + + const fileResponse = await authFetch( + `https://staging.openbraininstitute.org/api/entitycore/reconstruction-morphology/${newEntityId}/assets`, { - status: fileResponseContribution.status, + method: 'POST', + headers: fileUploadHeaders, + body: formData, } ); - } - setIsSuccess(true); + const fileResponseText = await fileResponse.text(); + if (!fileResponse.ok) { + throw new ApiError( + `Failed to upload file ${file.name}: ${fileResponseText}`, + { + status: fileResponse.status, + } + ); + } + notification.success({ + message: `Successfully uploaded file: ${file.name}`, + }); + } } else { notification.success({ - message: 'Record submitted successfully, no file uploaded', + message: 'Record submitted successfully, no files to upload', + }); + } + + const mtypeRequestBody = { + authorized_public: true, + entity_id: newEntityId, + mtype_class_id: mtypeConfig?.mtype_class_id ?? undefined, + }; + + const fileUploadMtypeHeaders = { + 'virtual-lab-id': headers['virtual-lab-id'], + 'project-id': headers['project-id'], + 'Content-Type': 'application/json', + }; + const fileResponseMtype = await authFetch( + `https://staging.openbraininstitute.org/api/entitycore/mtype-classification`, + { + method: 'POST', + headers: fileUploadMtypeHeaders, + body: JSON.stringify(mtypeRequestBody), + } + ); + const fileResponseMtypeText = await fileResponseMtype.text(); + if (!fileResponseMtype.ok) { + throw new ApiError(`Failed to upload file: ${fileResponseMtypeText}`, { + status: fileResponseMtype.status, }); } + + const contributionRequestBody = { + entity_id: newEntityId, + agent_id: contributionConfig?.agent_id ?? undefined, + role_id: contributionConfig?.role_id ?? undefined, + }; + + const fileUploadContributionHeaders = { + 'virtual-lab-id': headers['virtual-lab-id'], + 'project-id': headers['project-id'], + 'Content-Type': 'application/json', + }; + const fileResponseContribution = await authFetch( + `https://staging.openbraininstitute.org/api/entitycore/contribution`, + { + method: 'POST', + headers: fileUploadContributionHeaders, + body: JSON.stringify(contributionRequestBody), + } + ); + const fileResponseContributionText = await fileResponseContribution.text(); + if (!fileResponseContribution.ok) { + throw new ApiError(`Failed to upload file: ${fileResponseContributionText}`, { + status: fileResponseContribution.status, + }); + } + + setIsSuccess(true); } catch (error) { notification.error({ message: 'Failed to submit record',