Merge pull request #2222 from broadinstitute/jb-bed-file-upload

Correctly identify bundled files in upload wizard (SCP-5941)

Author: bistline

app/javascript/components/upload/upload-utils.js

@@ -111,7 +111,7 @@ export function findBundleChildren(file, files) {
       f.study_file_bundle_id
     ]
     return parentFields.includes(file._id) ||
-      file.study_file_bundle_id && parentFields.includes(file.study_file_bundle_id)
+      file.study_file_bundle_id && parentFields.includes(file.study_file_bundle_id) && f._id !== file._id
   })
 }
 

test/js/upload-wizard/file-info-responses.js

@@ -323,7 +323,7 @@ export const RAW_COUNTS_MTX_FILE = {
     ''
   ],
   'status': 'uploaded',
-  'study_file_bundle_id': 'null',
+  'study_file_bundle_id': '618bd61acc7ba038ac7cb091',
   'study_id': {
     '$oid': '60a2b9f4cc7ba082358b5448'
   },
@@ -368,7 +368,7 @@ export const BARCODES_FILE = {
   remote_location: '',
   spatial_cluster_associations: [''],
   status: 'uploaded',
-  study_file_bundle_id: { $oid: '618bd61acc7ba038ac7cb091' },
+  study_file_bundle_id: '618bd61acc7ba038ac7cb091',
   study_id: { $oid: '618aacbfcc7ba038ac7cb00f' },
   taxon_id: null,
   updated_at: '2021-11-10T09:24:57.640-05:00',
@@ -408,7 +408,7 @@ export const FEATURES_FILE = {
   remote_location: '',
   spatial_cluster_associations: [''],
   status: 'uploaded',
-  study_file_bundle_id: { $oid: '618bd61acc7ba038ac7cb091' },
+  study_file_bundle_id: '618bd61acc7ba038ac7cb091',
   study_id: { $oid: '618aacbfcc7ba038ac7cb00f' },
   taxon_id: null,
   updated_at: '2021-11-10T09:24:57.640-05:00',
@@ -430,6 +430,70 @@ export const FEATURES_FILE = {
   _id: { $oid: '618bd61acc7ba038ac22334' }
 }
 
+export const BED_FILE =   {
+  _id: { $oid: "668360b1fb648e9c7c7d3380" },
+  parse_status: "unparsed",
+  x_axis_label: "",
+  y_axis_label: "",
+  z_axis_label: "",
+  spatial_cluster_associations: [""],
+  remote_location: "pbmc_3k_atac_fragments.possorted.bed.gz",
+  options: { upload_trigger: "bucket" },
+  study_id: { $oid: "66835832771a5b0202fcfeae" },
+  human_data: false,
+  use_metadata_convention: false,
+  is_spatial: false,
+  queued_for_deletion: false,
+  taxon_id: { $oid: '604009b7cc7ba03e1b277a38' },
+  genome_assembly_id: { $oid: '604009b7cc7ba03e1b277a39' },
+  name: "pbmc_3k_atac_fragments.possorted.bed.gz",
+  description: "",
+  file_type: "BED",
+  human_fastq_url: "",
+  data_dir: "b2695100728ad64155d462d59e57bfd7c2200e979114dbc534c17866b935067f",
+  status: "uploaded",
+  upload_file_name: "pbmc_3k_atac_fragments.possorted.bed.gz",
+  upload_content_type: "application/x-gzip",
+  upload_file_size: 539109524,
+  generation: "1719884843494138",
+  updated_at: "2024-07-02T02:07:19.309Z",
+  created_at: "2024-07-02T02:07:07.182Z",
+  version: 2,
+  study_file_bundle_id: "668360d7771a5b0202fcff56",
+  is_complete: true
+}
+
+export const BED_INDEX_FILE = {
+  _id: { $oid: "668360bdb51a86c2885fd5e6" },
+  parse_status: "unparsed",
+  x_axis_label: "",
+  y_axis_label: "",
+  z_axis_label: "",
+  spatial_cluster_associations: [""],
+  remote_location: "pbmc_3k_atac_fragments.possorted.bed.gz.tbi",
+  options: { upload_trigger: "bucket", bed_id: "668360b1fb648e9c7c7d3380" },
+  study_id: { $oid: "66835832771a5b0202fcfeae" },
+  human_data: false,
+  use_metadata_convention: false,
+  is_spatial: false,
+  queued_for_deletion: false,
+  name: "pbmc_3k_atac_fragments.possorted.bed.gz",
+  description: "",
+  file_type: "Tab Index",
+  human_fastq_url: "",
+  data_dir: "b2695100728ad64155d462d59e57bfd7c2200e979114dbc534c17866b935067f",
+  status: "uploaded",
+  upload_file_name: "pbmc_3k_atac_fragments.possorted.bed.gz.tbi",
+  upload_content_type: null,
+  upload_file_size: 645077,
+  generation: "1719884679213326",
+  updated_at: "2024-07-02T02:07:19.316Z",
+  created_at: "2024-07-02T02:07:19.287Z",
+  version: 2,
+  study_file_bundle_id: "668360d7771a5b0202fcff56",
+  is_complete: true
+}
+
 export const IMAGE_FILE = {
   created_at: '2021-11-15T18:31:41.598Z',
   data_dir: '71e1a89e5c5d9300aabd0e757d1b569eb66644872b40bcbb720e2b39bc7e3822',

test/js/upload-wizard/validations.test.js

@@ -1,4 +1,5 @@
-import { validateFile } from 'components/upload/upload-utils'
+import { validateFile, findBundleChildren } from 'components/upload/upload-utils'
+import { BED_FILE, BED_INDEX_FILE, RAW_COUNTS_MTX_FILE, FEATURES_FILE, BARCODES_FILE } from './file-info-responses'
 
 describe('upload file validation name checks', () => {
   it('allows files with unique names and valid extensions', async () => {
@@ -162,3 +163,18 @@ describe('it checks presence of required fields', () => {
     expect(msgs['expression_file_info.biosample_input_type']).toEqual('You must specify: biosample input type')
   })
 })
+
+describe('it finds bundled files', () => {
+  it('find sequence index files', () => {
+    const serverFiles = [BED_FILE, BED_INDEX_FILE]
+    const bundledIndex = findBundleChildren(BED_FILE, serverFiles)[0]
+    expect(bundledIndex.upload_file_name).toEqual(BED_INDEX_FILE.upload_file_name)
+  })
+
+  it('finds features/barcodes files for MTX', () => {
+    const serverFiles = [RAW_COUNTS_MTX_FILE, FEATURES_FILE, BARCODES_FILE]
+    const bundledFiles = findBundleChildren(RAW_COUNTS_MTX_FILE, serverFiles)
+    const fileNames = bundledFiles.map(f => { return f.upload_file_name })
+    expect(fileNames).toEqual([FEATURES_FILE.upload_file_name, BARCODES_FILE.upload_file_name])
+  })
+})