feat: download dicomweb data to local file system

.gitignore

@@ -6,6 +6,7 @@ yarn-debug.log*
 yarn-error.log*
 lerna-debug.log*
 .pnpm-debug.log*
+studies/
 
 # Diagnostic reports (https://nodejs.org/api/report.html)
 report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json

README.md

@@ -3,8 +3,9 @@
 To install, clone the directory and run:
 
 ```
-yarn install
-yarn link:exec
+bun install
+bun run build
+bun run link:exec
 ```
 
 # dcmjs commands
@@ -29,13 +30,25 @@ dicomwebjs dump https://d33do7qe4w26qo.cloudfront.net/dicomweb/studies/1.3.6.1.4
 dicomwebjs dump testdata/studies/1.2.276.1.74.1.2.132733202464108492637644434464108492/series/2.16.840.1.113883.3.8467.132733202477512857637644434477512857/metadata.gz
 ```
 
-## File Locations
-Files dicomweb can be paths to JSON files.  However, tree structure data must follow the Static DICOMweb format, specifically starting at `studies/` relative to the base directory, and containing some/all of the ones below.
+## download `url`
+
+dicomwebjs can be used to download a directory of file locations. By default it will fetch everything at and below the specified URL, plus referenced bulkdata. Bulkdata will be
+placed in the `studies/<studyUID>/bulkdata` directory, with metadata references to the bulkdata using the `../../bulkdata/<path>` relative URI locations.
+
+### Example Commands
+
+```
+dicomwebjs download https://d33do7qe4w26qo.cloudfront.net/dicomweb/studies/1.3.6.1.4.1.14519.5.2.1.4792.2001.105216574054253895819671475627 -d ~/dicomweb
+```
+
+### File Locations
+
+Files dicomweb can be paths to JSON files. However, tree structure data must follow the Static DICOMweb format, specifically starting at `studies/` relative to the base directory, and containing some/all of the ones below.
 Note that un-compressed files are acceptable as well, but will not be found on a search.
 
-* `studies/index.json.gz` - an index in DICOMweb QIDO response format for the studies
-* `studies/<studyUID>/index.json.gz` - the index entry of this study
-* `studies/<studyUID>/series/index.json.gz` - the series QIDO response
-* `studies/<studyUID>/series/<seriesUID>/metadata.gz` - the metadata WADO response
-* `studies/<studyUID>/bulkdata/...` - bulkdata files
-* `studies/<studyUID>/series/<seriesUID>/instances/<instanceUID>/frame/<frameNumber>` - compressed frame data
+- `studies/index.json.gz` - an index in DICOMweb QIDO response format for the studies
+- `studies/<studyUID>/index.json.gz` - the index entry of this study
+- `studies/<studyUID>/series/index.json.gz` - the series QIDO response
+- `studies/<studyUID>/series/<seriesUID>/metadata.gz` - the metadata WADO response
+- `studies/<studyUID>/bulkdata/...` - bulkdata files
+- `studies/<studyUID>/series/<seriesUID>/instances/<instanceUID>/frame/<frameNumber>` - compressed frame data

bin/cliDownload.js

@@ -0,0 +1,52 @@
+import { DicomAccess } from "@dcmjs/commands";
+
+const action = async (url, options) => {
+  try {
+    const destination = await DicomAccess.createInstance(options.directory, {
+      ...options,
+      scheme: "file",
+    });
+
+    // Create access instance (currently supports only DICOMweb)
+    console.debug(
+      "🔌 Creating DICOM access instance...",
+      url,
+      "to",
+      options.directory
+    );
+    const access = await DicomAccess.createInstance(url, options);
+
+    const { StudyInstanceUID: studyUID } = options;
+    if (!studyUID) {
+      console.warn("Please provide a studyUID");
+      return -2;
+    }
+    const srcStudy = await access.queryStudy(studyUID);
+
+    await destination.store(srcStudy, options);
+
+    console.log(
+      `🎉 Download complete. Study saved to: ${options.directory}/studies/${studyUID}`
+    );
+  } catch (err) {
+    console.warn("❌ An error occurred during download:", err);
+    process.exit(1);
+  }
+
+  process.exit(0);
+};
+
+// CLI registration
+export default async function cliDownload(program) {
+  program
+    .command("download")
+    .description("Download a full DICOM study from any supported source")
+    .argument("<url>", "DICOMweb URL or local path (e.g. ./study, scp://...)")
+    .option(
+      "-S, --StudyInstanceUID <StudyInstanceUID>",
+      "StudyInstanceUID to download"
+    )
+    .option("-d, --directory <targetDir>", "Download to local directory", ".")
+    .option("--debug", "Enable debug logging")
+    .action(action);
+}

bin/dicomwebjs.js

@@ -1,35 +1,46 @@
-#!/usr/bin/env node
-import { Command } from 'commander';
-import { dicomweb, instanceDicom, dumpDicom } from '../src/index.js';
+#!/usr/bin/env bun
+import { Command } from "commander";
+import { dicomweb, instanceDicom, dumpDicom } from "../src/index.js";
+import cliDownload from "./cliDownload.js";
 
 const program = new Command();
 
+program.option(
+  "-s, --study <studyInstanceUID>",
+  "Download a specific study instance UID"
+);
+
 program
-  .name('dicomwebjs')
-  .description('dicomwebjs based tools for manipulation of DICOMweb')
-  .version('0.0.1')
-  .option('--seriesUID <seriesUID>', 'For a specific seriesUID');
+  .name("dicomwebjs")
+  .description("dicomwebjs based tools for manipulation of DICOMweb")
+  .version("0.0.1")
+  .option("--seriesUID <seriesUID>", "For a specific seriesUID");
 
-program.command('dump')
-  .description('Dump a dicomweb file')
-  .argument('<dicomwebUrl>', 'dicomweb URL or file location')
+program
+  .command("dump")
+  .description("Dump a dicomweb file")
+  .argument("<dicomwebUrl>", "dicomweb URL or file location")
+  .option("--debug", "Set debug level logging")
   .action(async (fileName, options) => {
     const qido = await dicomweb.readDicomWeb(fileName, options);
     for (const dict of qido) {
       dumpDicom({ dict });
     }
   });
 
-program.command('instance')
-  .description('Write the instance data')
-  .argument('<part10>', 'part 10 file')
-  .option('-p, --pretty', 'Pretty print')
+program
+  .command("instance")
+  .description("Write the instance data")
+  .argument("<part10>", "part 10 file")
+  .option("-p, --pretty", "Pretty print")
+  .option("--debug", "Set debug level logging")
   .action(async (fileName, options) => {
     const qido = await dicomweb.readDicomWeb(fileName, options);
     for (const dict of qido) {
       instanceDicom({ dict }, options);
     }
-  })
+  });
 
+cliDownload(program);
 
-program.parse();
+program.parse();