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Merged
merged 5 commits into from
Aug 25, 2022
Merged

Restructured tests for library schema with Defs #82

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a5326f1
Added additional test data to bids.spec
VisLab Aug 25, 2022
62aedb6
Merge branch 'library-schemas' of https://github.com/hed-standard/hed…
VisLab Aug 25, 2022
dc4ac90
Updated the tests for def and libraries
VisLab Aug 25, 2022
78d73b0
Merging the tests for def with libraries
VisLab Aug 25, 2022
b59fd13
Updated the tests for BIDS datasets with libraries including definitions
VisLab Aug 25, 2022
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273 changes: 197 additions & 76 deletions tests/bids.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ describe('BIDS datasets', () => {
},
},
{
// Just library
// Just library no defs
event_type: {
HED: {
show_face: 'ts:Sensory-event, ts:Visual-presentation',
Expand All @@ -173,6 +173,54 @@ describe('BIDS datasets', () => {
},
},
},
{
// Just score as base
event_type: {
HED: {
show_face: 'Manual-eye-closure, Drowsiness',
left_press: 'Wicket-spikes, Frequency',
},
},
},
{
// Just score as a library
event_type: {
HED: {
show_face: 'sc:Manual-eye-closure, sc:Drowsiness',
left_press: 'sc:Wicket-spikes, sc:Frequency',
},
},
},
{
// Testlib with Defs as base
event_type: {
HED: {
show_face: 'Sensory-event, Visual-presentation',
left_press: 'Press, Def/My-def1, Def/My-def2/3',
},
},
dummy_defs: {
HED: {
def1: '(Definition/My-def1, (Red, Blue))',
def2: '(Definition/My-def2/#, (Green, Label/#))',
},
},
},
{
// Testlib with defs with as library
event_type: {
HED: {
show_face: 'ts:Sensory-event, ts:Visual-presentation',
left_press: 'ts:Press, ts:Def/My-def1, ts:Def/My-def2/3',
},
},
dummy_defs: {
HED: {
def1: '(ts:Definition/My-def1, (ts:Red, ts:Blue))',
def2: '(ts:Definition/My-def2/#, (ts:Green, ts:Label/#))',
},
},
},
],
]

Expand Down Expand Up @@ -566,6 +614,74 @@ describe('BIDS datasets', () => {
path: '/sub06/sub06_task-test_run-1_events.tsv',
},
),
new BidsEventFile(
'/sub03/sub06_task-test_run-1_events.tsv',
['/sub03/sub06_task-test_run-1_events.json'],
sidecars[4][3],
{
headers: ['onset', 'duration', 'event_type', 'size'],
rows: [
['onset', 'duration', 'event_type', 'size'],
['7', 'n/a', 'show_face', '6'],
['7', 'n/a', 'left_press', '7'],
],
},
{
relativePath: '/sub06/sub06_task-test_run-1_events.tsv',
path: '/sub06/sub06_task-test_run-1_events.tsv',
},
),
new BidsEventFile(
'/sub03/sub06_task-test_run-1_events.tsv',
['/sub03/sub06_task-test_run-1_events.json'],
sidecars[4][4],
{
headers: ['onset', 'duration', 'event_type', 'size'],
rows: [
['onset', 'duration', 'event_type', 'size'],
['7', 'n/a', 'show_face', '6'],
['7', 'n/a', 'left_press', '7'],
],
},
{
relativePath: '/sub06/sub06_task-test_run-1_events.tsv',
path: '/sub06/sub06_task-test_run-1_events.tsv',
},
),
new BidsEventFile(
'/sub03/sub06_task-test_run-1_events.tsv',
['/sub03/sub06_task-test_run-1_events.json'],
sidecars[4][5],
{
headers: ['onset', 'duration', 'event_type', 'size'],
rows: [
['onset', 'duration', 'event_type', 'size'],
['7', 'n/a', 'show_face', '6'],
['7', 'n/a', 'left_press', '7'],
],
},
{
relativePath: '/sub06/sub06_task-test_run-1_events.tsv',
path: '/sub06/sub06_task-test_run-1_events.tsv',
},
),
new BidsEventFile(
'/sub03/sub06_task-test_run-1_events.tsv',
['/sub03/sub06_task-test_run-1_events.json'],
sidecars[4][6],
{
headers: ['onset', 'duration', 'event_type', 'size'],
rows: [
['onset', 'duration', 'event_type', 'size'],
['7', 'n/a', 'show_face', '6'],
['7', 'n/a', 'left_press', '7'],
],
},
{
relativePath: '/sub06/sub06_task-test_run-1_events.tsv',
path: '/sub06/sub06_task-test_run-1_events.tsv',
},
),
],
]

Expand All @@ -574,9 +690,12 @@ describe('BIDS datasets', () => {
[
{ Name: 'OnlyBase', BIDSVersion: '1.7.0', HEDVersion: '8.1.0' },
{ Name: 'BaseAndTest', BIDSVersion: '1.7.0', HEDVersion: ['8.1.0', 'ts:testlib_1.0.2'] },
{ Name: 'OnlyTest', BIDSVersion: '1.7.0', HEDVersion: ['ts:testlib_1.0.2'] },
{ Name: 'OnlyTestAsLib', BIDSVersion: '1.7.0', HEDVersion: ['ts:testlib_1.0.2'] },
{ Name: 'BaseAndTwoTests', BIDSVersion: '1.7.0', HEDVersion: ['8.1.0', 'ts:testlib_1.0.2', 'bg:testlib_1.0.2'] },
{ Name: 'TwoTests', BIDSVersion: '1.7.0', HEDVersion: ['ts:testlib_1.0.2', 'bg:testlib_1.0.2'] },
{ Name: 'OnlyScoreAsBase', BIDSVersion: '1.7.0', HEDVersion: 'score_0.0.1' },
{ Name: 'OnlyScoreAsLib', BIDSVersion: '1.7.0', HEDVersion: 'sc:score_0.0.1' },
{ Name: 'OnlyTestAsBase', BIDSVersion: '1.7.0', HEDVersion: 'testlib_1.0.2' },
],
[
{ Name: 'NonExistentLibrary', BIDSVersion: '1.7.0', HEDVersion: ['8.1.0', 'ts:badlib_1.0.2'] },
Expand Down Expand Up @@ -632,20 +751,6 @@ describe('BIDS datasets', () => {
}, datasetDescriptions)
})

// /**
// * Create a schema spec for .
// * @param {list} specList The datasets to test with.
// * @return {SchemasSpec}
// */
// const getSchemaSpecs = (specList) =>{
// const specs = new SchemasSpec()
// for (let i=0; i < specList.length; i++) {
// const spec = specList[i]
// specs.addSchemaSpec(spec.nickname, spec)
// }
// return specs
// }

/**
* Validate the test datasets.
* @param {Object<string,BidsDataset>} testDatasets The datasets to test with.
Expand Down Expand Up @@ -853,78 +958,94 @@ describe('BIDS datasets', () => {
})

describe('HED 3 library schema tests', () => {
let goodEvents0, goodEvents1, goodEvents2
let goodEvents
let goodDatasetDescriptions, badDatasetDescriptions

beforeAll(() => {
goodEvents0 = [bidsTsvFiles[5][0]]
goodEvents1 = [bidsTsvFiles[5][1]]
goodEvents2 = [bidsTsvFiles[5][2]]
goodEvents = bidsTsvFiles[5]
goodDatasetDescriptions = bidsDatasetDescriptions[0]
badDatasetDescriptions = bidsDatasetDescriptions[1]
})

describe('HED 3 library schema good tests', () => {
it('should validate HED 3 in BIDS event with json and a dataset description and no version spec', () => {
const testDatasets = {
just_base: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[0]),
just_base2: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[1]),
just_base3: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[3]),
just_library: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[1]),
just_library2: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[3]),
just_library3: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[4]),
basestd_with_std_no_defs: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[0]),
basestd_with_std_and_libtestlib_nodefs: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[1]),
basestd_with_std_and_two_libtestlibs_nodefs: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[3]),
libtestlib_with_basestd_and_libtestlib_nodefs: new BidsDataset(
[goodEvents[1]],
[],
goodDatasetDescriptions[1],
),
libtestlib_with_basestd_and_two_libtestlibs_nodefs: new BidsDataset(
[goodEvents[1]],
[],
goodDatasetDescriptions[3],
),
libtestlib_with_two_libtestlibs_nodefs: new BidsDataset([goodEvents[1]], [], goodDatasetDescriptions[4]),
basestd_libtestlib_with_basestd_and_libtestlib_defs: new BidsDataset(
[goodEvents[0]],
[],
goodDatasetDescriptions[1],
),
basestd_libtestlib_with_basestd_and_two_libtestlib_defs: new BidsDataset(
[goodEvents[0]],
[],
goodDatasetDescriptions[3],
),
basescore_with_basescore_no_defs: new BidsDataset([goodEvents[3]], [], goodDatasetDescriptions[5]),
libscore_with_libscore_nodefs: new BidsDataset([goodEvents[4]], [], goodDatasetDescriptions[6]),
basetestlib_with_basetestlib_with_defs: new BidsDataset([goodEvents[5]], [], goodDatasetDescriptions[7]),
libtestlib_with_basestd_and_libtestlib_with_defs: new BidsDataset(
[goodEvents[6]],
[],
goodDatasetDescriptions[1],
),
// libtestlib_with_libtestlib_with_defs:
// new BidsDataset([goodEvents[6]], [], goodDatasetDescriptions[2]),
libtestlib_with_basestd_and_two_libtestlib_with_defs: new BidsDataset(
[goodEvents[6]],
[],
goodDatasetDescriptions[3],
),
// libtestlib_with_two_libtestlib_with_defs:
// new BidsDataset([goodEvents[6]], [], goodDatasetDescriptions[4]),
}
const expectedIssues = {
just_base: [],
just_base2: [],
just_base3: [],
just_library: [],
just_library2: [],
just_library3: [],
basestd_with_std_no_defs: [],
basestd_with_std_and_libtestlib_nodefs: [],
basestd_with_std_and_two_libtestlibs_nodefs: [],
libtestlib_with_basestd_and_libtestlib_nodefs: [],
libtestlib_with_basestd_and_two_libtestlibs_nodefs: [],
libtestlib_with_two_libtestlibs_nodefs: [],
basestd_libtestlib_with_basestd_and_libtestlib_defs: [],
basestd_libtestlib_with_basestd_and_two_libtestlib_defs: [],
basescore_with_basescore_no_defs: [],
libscore_with_libscore_nodefs: [],
basetestlib_with_basetestlib_with_defs: [],
libtestlib_with_basestd_and_libtestlib_with_defs: [],
libtestlib_with_libtestlib_with_defs: [],
libtestlib_with_basestd_and_two_libtestlib_with_defs: [],
libtestlib_with_two_libtestlib_with_defs: [],
}
return validator(testDatasets, expectedIssues, null)
}, 10000)

it('should validate HED 3 in BIDS event files sidecars and libraries using dataset descriptions', () => {
const testDatasets1 = {
library_and_defs_base_ignored: new BidsDataset(goodEvents0, [], goodDatasetDescriptions[1]),
library_and_defs_no_base: new BidsDataset(goodEvents0, [], goodDatasetDescriptions[3]),
library_only_with_extra_base: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[1]),
library_only: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[1]),
just_base2: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[0]),
library_not_needed1: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[1]),
library_not_needed2: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[3]),
library_and_base_with_extra_schema: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[3]),
}
const expectedIssues1 = {
library_and_defs_base_ignored: [],
library_and_defs_no_base: [],
library_only_with_extra_base: [],
library_only: [],
library_only_extra_schema: [],
only_libraries: [],
just_base2: [],
library_not_needed1: [],
library_not_needed2: [],
library_and_base_with_extra_schema: [],
}
return validator(testDatasets1, expectedIssues1, null)
}, 10000)
})

describe('HED 3 library schema bad tests', () => {
it('should not validate when library schema specifications are invalid', () => {
const testDatasets = {
unknown_library: new BidsDataset(goodEvents2, [], badDatasetDescriptions[0]),
leading_colon: new BidsDataset(goodEvents2, [], badDatasetDescriptions[1]),
bad_nickname: new BidsDataset(goodEvents2, [], badDatasetDescriptions[2]),
multipleColons1: new BidsDataset(goodEvents2, [], badDatasetDescriptions[3]),
multipleColons2: new BidsDataset(goodEvents2, [], badDatasetDescriptions[4]),
noLibraryName: new BidsDataset(goodEvents2, [], badDatasetDescriptions[5]),
badVersion1: new BidsDataset(goodEvents2, [], badDatasetDescriptions[6]),
badVersion2: new BidsDataset(goodEvents2, [], badDatasetDescriptions[7]),
badRemote1: new BidsDataset(goodEvents2, [], badDatasetDescriptions[8]),
badRemote2: new BidsDataset(goodEvents2, [], badDatasetDescriptions[9]),
unknown_library: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[0]),
leading_colon: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[1]),
bad_nickname: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[2]),
multipleColons1: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[3]),
multipleColons2: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[4]),
noLibraryName: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[5]),
badVersion1: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[6]),
badVersion2: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[7]),
badRemote1: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[8]),
badRemote2: new BidsDataset([goodEvents[2]], [], badDatasetDescriptions[9]),
}

const expectedIssues = {
Expand Down Expand Up @@ -1013,14 +1134,14 @@ describe('BIDS datasets', () => {
const [specs3] = parseSchemasSpec(['8.1.0', 'ts:testlib_1.0.2', 'bg:testlib_1.0.2'])
const [specs4] = parseSchemasSpec(['ts:testlib_1.0.2', 'bg:testlib_1.0.2'])
const testDatasets1 = {
library_and_defs_base_ignored: new BidsDataset(goodEvents0, [], goodDatasetDescriptions[1]),
library_and_defs_no_base: new BidsDataset(goodEvents0, [], goodDatasetDescriptions[3]),
library_only_with_extra_base: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[1]),
library_only: new BidsDataset(goodEvents1, [], goodDatasetDescriptions[1]),
just_base2: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[0]),
library_not_needed1: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[1]),
library_not_needed2: new BidsDataset(goodEvents2, [], goodDatasetDescriptions[3]),
library_and_base_with_extra_schema: new BidsDataset(goodEvents0, [], goodDatasetDescriptions[1]),
library_and_defs_base_ignored: new BidsDataset([goodEvents[0]], [], goodDatasetDescriptions[1]),
library_and_defs_no_base: new BidsDataset([goodEvents[0]], [], goodDatasetDescriptions[3]),
library_only_with_extra_base: new BidsDataset([goodEvents[1]], [], goodDatasetDescriptions[1]),
library_only: new BidsDataset([goodEvents[1]], [], goodDatasetDescriptions[1]),
just_base2: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[0]),
library_not_needed1: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[1]),
library_not_needed2: new BidsDataset([goodEvents[2]], [], goodDatasetDescriptions[3]),
library_and_base_with_extra_schema: new BidsDataset([goodEvents[0]], [], goodDatasetDescriptions[1]),
}
const expectedIssues1 = {
library_and_defs_base_ignored: [],
Expand Down