@openneuro/app 4.30.2 → 4.31.0-alpha.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (58) hide show
  1. package/package.json +5 -5
  2. package/src/assets/activity-icon.png +0 -0
  3. package/src/assets/icon-archived.png +0 -0
  4. package/src/assets/icon-saved.png +0 -0
  5. package/src/assets/icon-unread.png +0 -0
  6. package/src/client.jsx +1 -1
  7. package/src/scripts/datalad/dataset/dataset-query-fragments.js +4 -14
  8. package/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap +4 -304
  9. package/src/scripts/dataset/components/ValidationBlock.tsx +13 -15
  10. package/src/scripts/dataset/components/__tests__/ValidationBlock.spec.tsx +2 -0
  11. package/src/scripts/dataset/draft-container.tsx +2 -1
  12. package/src/scripts/dataset/files/__tests__/__snapshots__/file-tree.spec.jsx.snap +1 -9
  13. package/src/scripts/dataset/fragments/__tests__/{dataset-alert-draft.spec.tsx → dataset-alert.spec.tsx} +33 -1
  14. package/src/scripts/dataset/fragments/{dataset-alert-draft.tsx → dataset-alert.tsx} +30 -18
  15. package/src/scripts/dataset/routes/delete-page.tsx +72 -39
  16. package/src/scripts/dataset/routes/snapshot.tsx +23 -17
  17. package/src/scripts/dataset/routes/tab-routes-draft.tsx +5 -2
  18. package/src/scripts/dataset/snapshot-container.tsx +11 -0
  19. package/src/scripts/search/__tests__/search-params-ctx.spec.tsx +3 -0
  20. package/src/scripts/search/initial-search-params.tsx +2 -0
  21. package/src/scripts/search/inputs/__tests__/nihselect.spec.tsx +36 -0
  22. package/src/scripts/search/inputs/index.ts +2 -0
  23. package/src/scripts/search/inputs/nih-select.tsx +63 -0
  24. package/src/scripts/search/search-container.tsx +20 -12
  25. package/src/scripts/search/search-params-ctx.tsx +2 -0
  26. package/src/scripts/search/search-routes.tsx +14 -6
  27. package/src/scripts/search/use-search-results.tsx +15 -0
  28. package/src/scripts/types/user-types.ts +72 -0
  29. package/src/scripts/uploader/upload-issues.tsx +2 -2
  30. package/src/scripts/users/__tests__/datasest-card.spec.tsx +201 -0
  31. package/src/scripts/users/__tests__/user-card.spec.tsx +30 -3
  32. package/src/scripts/users/__tests__/user-query.spec.tsx +6 -0
  33. package/src/scripts/users/__tests__/user-routes.spec.tsx +42 -18
  34. package/src/scripts/users/components/user-dataset-filters.tsx +157 -0
  35. package/src/scripts/users/dataset-card.tsx +121 -0
  36. package/src/scripts/users/fragments/query.js +42 -0
  37. package/src/scripts/users/scss/datasetcard.module.scss +153 -0
  38. package/src/scripts/users/scss/usernotifications.module.scss +159 -0
  39. package/src/scripts/users/user-account-view.tsx +1 -12
  40. package/src/scripts/users/user-card.tsx +1 -14
  41. package/src/scripts/users/user-container.tsx +1 -17
  42. package/src/scripts/users/user-datasets-view.tsx +58 -43
  43. package/src/scripts/users/user-notification-accordion.tsx +160 -0
  44. package/src/scripts/users/user-notification-list.tsx +27 -0
  45. package/src/scripts/users/user-notifications-tab-content.tsx +85 -0
  46. package/src/scripts/users/user-notifications-view.tsx +102 -4
  47. package/src/scripts/users/user-query.tsx +6 -14
  48. package/src/scripts/users/user-routes.tsx +18 -19
  49. package/src/scripts/utils/__tests__/user-datasets.spec.tsx +86 -0
  50. package/src/scripts/utils/gtag.js +3 -2
  51. package/src/scripts/utils/user-datasets.tsx +60 -0
  52. package/src/scripts/validation/__tests__/__snapshots__/validation-issues.spec.tsx.snap +1 -122
  53. package/src/scripts/validation/validation-results-query.ts +44 -0
  54. package/src/scripts/validation/validation-results.tsx +31 -7
  55. package/src/scripts/validation/validation.tsx +58 -49
  56. package/src/scripts/workers/schema.worker.ts +2 -7
  57. package/tsconfig.json +1 -2
  58. package/vite.config.js +1 -0
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
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  "name": "@openneuro/app",
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- "version": "4.30.2",
3
+ "version": "4.31.0-alpha.1",
4
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  "description": "React JS web frontend for the OpenNeuro platform.",
5
5
  "license": "MIT",
6
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  "main": "public/client.js",
@@ -16,11 +16,11 @@
16
16
  "dependencies": {
17
17
  "@apollo/client": "3.11.8",
18
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  "@artsy/fresnel": "^1.3.1",
19
- "@bids/validator": "npm:@jsr/bids__validator@^2.0.0",
19
+ "@bids/validator": "npm:@jsr/bids__validator@^2.0.2",
20
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  "@emotion/react": "11.11.1",
21
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  "@emotion/styled": "11.11.0",
22
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  "@niivue/niivue": "0.45.1",
23
- "@openneuro/components": "^4.30.2",
23
+ "@openneuro/components": "^4.31.0-alpha.1",
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  "@sentry/react": "^8.25.0",
25
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  "@tanstack/react-table": "^8.9.3",
26
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  "buffer": "^6.0.3",
@@ -68,11 +68,11 @@
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  "sass": "^1.32.8",
69
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  "stream-browserify": "^3.0.0",
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  "typescript": "5.6.3",
71
- "vite": "5.4.8",
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+ "vite": "5.4.12",
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  "vitest": "2.1.2"
73
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  },
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  "publishConfig": {
75
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  "access": "public"
76
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  },
77
- "gitHead": "7a6abc827a38daa177038e85fd1130daa810fbd0"
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+ "gitHead": "48a348e9accee0109c46516b704b643a2d5b4f4b"
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  }
package/src/assets/activity-icon.png ADDED
Binary file
package/src/assets/icon-archived.png ADDED
Binary file
package/src/assets/icon-saved.png ADDED
Binary file
package/src/assets/icon-unread.png ADDED
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package/src/client.jsx CHANGED
@@ -1,5 +1,5 @@
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  /**
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- * Browser client entrypoint - see server.tsx for SSR entrypoint
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+ * Browser client entrypoint
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  */
4
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  import "./scripts/utils/global-polyfill"
5
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  import "./scripts/sentry"
package/src/scripts/datalad/dataset/dataset-query-fragments.js CHANGED
@@ -135,13 +135,8 @@ export const DATASET_ISSUES = gql`
135
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  ${ISSUE_FIELDS}
136
136
  }
137
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  validation {
138
- codeMessages {
139
- code
140
- message
141
- }
142
- issues {
143
- ${VALIDATION_FIELDS}
144
- }
138
+ errors
139
+ warnings
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  }
146
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  }
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  }
@@ -154,13 +149,8 @@ export const SNAPSHOT_ISSUES = gql`
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  ${ISSUE_FIELDS}
155
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  }
156
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  validation {
157
- codeMessages {
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- code
159
- message
160
- }
161
- issues {
162
- ${VALIDATION_FIELDS}
163
- }
152
+ errors
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+ warnings
164
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  }
165
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  }
166
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  `
package/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap CHANGED
@@ -181,124 +181,7 @@ exports[`SnapshotContainer component > renders successfully 1`] = `
181
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  </div>
182
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  <div
183
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  class="accordion-item collapsed "
184
- >
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- <div
186
- class="accordion-content"
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- >
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- <div>
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- <span
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- class="message error fade-in"
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- >
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- We found
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- <strong>
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- 1 Warning
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- </strong>
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- in your dataset. You are not required to fix warnings, but doing so will make your dataset more BIDS compliant.
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- </span>
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- </div>
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- <br />
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- <div
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- class="validation-messages on-accordion-wrapper"
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- >
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- <article
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- class="plain accordion fade-in upload-panel warning-wrap"
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- >
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- <div
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- class="accordion-title "
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- role="switch"
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- >
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- <span>
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- view 1 warning in 1 file
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- </span>
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- </div>
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- <div
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- class="accordion-item collapsed "
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- >
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- <div
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- class="accordion-content"
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- >
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- <div
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- class=" on-accordion-wrapper"
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- >
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- <article
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- class="plain accordion validation-error fade-in"
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- >
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- <div
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- class="accordion-title "
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- role="switch"
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- >
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- <span
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- class="file-header"
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- >
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- <h4
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- class="em-header"
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- >
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- <strong
237
- class="em-header "
238
- >
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- Warning: 1
240
- </strong>
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- <span
242
- class="file-issue-count"
243
- >
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- 1 file
245
- </span>
246
- </h4>
247
- Tabular file contains custom columns not described in a data dictionary
248
- </span>
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- </div>
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- <div
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- class="accordion-item collapsed "
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- >
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- <div
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- class="accordion-content"
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- >
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- <div
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- class="em-body"
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- >
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- <span
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- class="e-meta"
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- >
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- <span>
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- <label>
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- Location:
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- </label>
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- <p>
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- /participants.tsv
268
- </p>
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- </span>
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- </span>
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- <span
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- class="e-meta"
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- >
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- <label>
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- Reason:
276
- </label>
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- <p>
278
- Tabular file contains custom columns not described in a data dictionary
279
- </p>
280
- </span>
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- <span
282
- class="e-meta"
283
- >
284
- <label>
285
- Evidence:
286
- </label>
287
- <p>
288
- Columns: sex, age not defined, please define in: /participants.json
289
- </p>
290
- </span>
291
- </div>
292
- </div>
293
- </div>
294
- </article>
295
- </div>
296
- </div>
297
- </div>
298
- </article>
299
- </div>
300
- </div>
301
- </div>
184
+ />
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185
  </article>
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  </div>
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  </div>
@@ -670,174 +553,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
670
553
  </div>
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  <div
672
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  class="accordion-item collapsed "
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- >
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- <div
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- class="accordion-content"
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- >
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- <ul
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- class="child-files"
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- >
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- <li
681
- class="clearfix filetree-item filetree-file"
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- >
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- <span
684
- aria-label=""
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- class=" on-icon "
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- role="img"
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- style="color: orange;"
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- >
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- <i
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- class="fas fa-file-alt"
691
- />
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- </span>
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-   CHANGES
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- <span
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- class="filetree-editfile"
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- />
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- </li>
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- <li
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- class="clearfix filetree-item filetree-file"
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- >
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- <span
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- aria-label=""
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- class=" on-icon "
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- role="img"
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- style="color: deepskyblue;"
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- >
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- <i
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- class="fab fa-markdown"
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- />
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- </span>
711
-   README
712
- <span
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- class="filetree-editfile"
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- />
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- </li>
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- <li
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- class="clearfix filetree-item filetree-file"
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- >
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- <span
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- aria-label=""
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- class=" on-icon "
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- role="img"
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- style="color: limegreen;"
724
- >
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- <i
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- class="fab fa-node-js"
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- />
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- </span>
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-   T1w.json
730
- <span
731
- class="filetree-editfile"
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- />
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- </li>
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- <li
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- class="clearfix filetree-item filetree-file"
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- >
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- <span
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- aria-label=""
739
- class=" on-icon "
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- role="img"
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- style="color: limegreen;"
742
- >
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- <i
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- class="fab fa-node-js"
745
- />
746
- </span>
747
-   dataset_description.json
748
- <span
749
- class="filetree-editfile"
750
- />
751
- </li>
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- <li
753
- class="clearfix filetree-item filetree-file"
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- >
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- <span
756
- aria-label=""
757
- class=" on-icon "
758
- role="img"
759
- style="color: lightgreen;"
760
- >
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- <i
762
- class="fas fa-file-excel"
763
- />
764
- </span>
765
-   participants.tsv
766
- <span
767
- class="filetree-editfile"
768
- />
769
- </li>
770
- <li
771
- class="clearfix filetree-item filetree-dir"
772
- >
773
- <article
774
- class="file-tree accordion "
775
- >
776
- <div
777
- class="accordion-title "
778
- role="switch"
779
- >
780
- <span
781
- aria-label="sub-01"
782
- class="file-icon on-icon icon-text "
783
- role="img"
784
- >
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- <i
786
- class="fas fa-folder"
787
- />
788
- sub-01
789
- </span>
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- </div>
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- <div
792
- class="accordion-item collapsed "
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- >
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- <div
795
- class="accordion-content"
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- >
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- <div>
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- Loading...
799
- </div>
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- </div>
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- </div>
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- </article>
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- </li>
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- <li
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- class="clearfix filetree-item filetree-dir"
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- >
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- <article
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- class="file-tree accordion "
809
- >
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- <div
811
- class="accordion-title "
812
- role="switch"
813
- >
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- <span
815
- aria-label="sub-02"
816
- class="file-icon on-icon icon-text "
817
- role="img"
818
- >
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- <i
820
- class="fas fa-folder"
821
- />
822
- sub-02
823
- </span>
824
- </div>
825
- <div
826
- class="accordion-item collapsed "
827
- >
828
- <div
829
- class="accordion-content"
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- >
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- <div>
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- Loading...
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- </div>
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- </div>
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- </div>
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- </article>
837
- </li>
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- </ul>
839
- </div>
840
- </div>
556
+ />
841
557
  </article>
842
558
  </div>
843
559
  </div>
@@ -1003,15 +719,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1003
719
  </div>
1004
720
  <div
1005
721
  class="accordion-item collapsed "
1006
- >
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- <div
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- class="accordion-content"
1009
- >
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- <div>
1011
- Loading...
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- </div>
1013
- </div>
1014
- </div>
722
+ />
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  </article>
1016
724
  </li>
1017
725
  <li
@@ -1037,15 +745,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1037
745
  </div>
1038
746
  <div
1039
747
  class="accordion-item collapsed "
1040
- >
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- <div
1042
- class="accordion-content"
1043
- >
1044
- <div>
1045
- Loading...
1046
- </div>
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- </div>
1048
- </div>
748
+ />
1049
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  </article>
1050
750
  </li>
1051
751
  </ul>
package/src/scripts/dataset/components/ValidationBlock.tsx CHANGED
@@ -1,7 +1,6 @@
1
1
  import React from "react"
2
- import { Validation } from "../../validation/validation"
2
+ import { Validation, ValidationPending } from "../../validation/validation"
3
3
  import LegacyValidation from "../../validation-legacy/validation.jsx"
4
- import { DatasetIssues } from "@bids/validator/issues"
5
4
  import type { Issue } from "@bids/validator/issues"
6
5
 
7
6
  // TODO - Generate from GraphQL
@@ -14,10 +13,13 @@ interface CodeMessageInput {
14
13
  interface ValidationFragment {
15
14
  issues: Issue[]
16
15
  codeMessages: CodeMessageInput[]
16
+ warnings: number
17
+ errors: number
17
18
  }
18
19
 
19
20
  export interface ValidationBlockProps {
20
21
  datasetId: string
22
+ version?: string
21
23
  issues?: object
22
24
  validation?: ValidationFragment
23
25
  }
@@ -29,6 +31,7 @@ export interface ValidationBlockProps {
29
31
  */
30
32
  export const ValidationBlock: React.FC<ValidationBlockProps> = ({
31
33
  datasetId,
34
+ version,
32
35
  issues,
33
36
  validation,
34
37
  }) => {
@@ -40,26 +43,21 @@ export const ValidationBlock: React.FC<ValidationBlockProps> = ({
40
43
  )
41
44
  } else {
42
45
  // If data exists, populate this. Otherwise we show pending.
43
- if (validation?.issues) {
44
- // Reconstruct DatasetIssues from JSON
45
- const datasetIssues = new DatasetIssues()
46
- datasetIssues.issues = validation.issues
47
- datasetIssues.codeMessages = validation.codeMessages.reduce(
48
- (acc, curr) => {
49
- acc.set(curr.code, curr.message)
50
- return acc
51
- },
52
- new Map<string, string>(),
53
- )
46
+ if (validation?.warnings + validation?.errors > 0) {
54
47
  return (
55
48
  <div className="validation-accordion">
56
- <Validation issues={datasetIssues} />
49
+ <Validation
50
+ datasetId={datasetId}
51
+ version={version}
52
+ warnings={validation.warnings}
53
+ errors={validation.errors}
54
+ />
57
55
  </div>
58
56
  )
59
57
  } else {
60
58
  return (
61
59
  <div className="validation-accordion">
62
- <Validation issues={null} />
60
+ <ValidationPending />
63
61
  </div>
64
62
  )
65
63
  }
package/src/scripts/dataset/components/__tests__/ValidationBlock.spec.tsx CHANGED
@@ -26,6 +26,8 @@ describe("ValidationBlock component", () => {
26
26
  codeMessages: [
27
27
  { code: "JSON_KEY_RECOMMENDED", message: "message" },
28
28
  ],
29
+ warnings: 1,
30
+ errors: 0,
29
31
  }
30
32
  render(
31
33
  <ValidationBlock
package/src/scripts/dataset/draft-container.tsx CHANGED
@@ -13,7 +13,7 @@ import {
13
13
  hasEditPermissions,
14
14
  } from "../authentication/profile"
15
15
  import { useCookies } from "react-cookie"
16
- import { DatasetAlertDraft } from "./fragments/dataset-alert-draft"
16
+ import { DatasetAlertDraft } from "./fragments/dataset-alert"
17
17
  import { CloneDropdown } from "./components/CloneDropdown"
18
18
  import { DatasetGitAccess } from "./components/DatasetGitAccess"
19
19
  import { DatasetHeader } from "./components/DatasetHeader"
@@ -135,6 +135,7 @@ const DraftContainer: React.FC<DraftContainerProps> = ({ dataset }) => {
135
135
  <div className="dataset-validation">
136
136
  <ValidationBlock
137
137
  datasetId={dataset.id}
138
+ version={dataset.draft.head}
138
139
  issues={dataset.draft.issues}
139
140
  validation={dataset.draft.validation}
140
141
  />
package/src/scripts/dataset/files/__tests__/__snapshots__/file-tree.spec.jsx.snap CHANGED
@@ -21,15 +21,7 @@ exports[`FileTree component > renders with default props 1`] = `
21
21
  </div>
22
22
  <div
23
23
  class="accordion-item collapsed "
24
- >
25
- <div
26
- class="accordion-content"
27
- >
28
- <ul
29
- class="child-files"
30
- />
31
- </div>
32
- </div>
24
+ />
33
25
  </article>
34
26
  </DocumentFragment>
35
27
  `;
package/src/scripts/dataset/fragments/__tests__/{dataset-alert-draft.spec.tsx → dataset-alert.spec.tsx} RENAMED
@@ -1,7 +1,7 @@
1
1
  import React from "react"
2
2
  import { render, screen } from "@testing-library/react"
3
3
  import { MemoryRouter } from "react-router-dom"
4
- import { DatasetAlertDraft } from "../dataset-alert-draft"
4
+ import { DatasetAlertDraft, DatasetAlertPrivate } from "../dataset-alert"
5
5
 
6
6
  describe("DatasetAlertDraft component", () => {
7
7
  it("renders the correct text for private drafts with changes", () => {
@@ -69,3 +69,35 @@ describe("DatasetAlertDraft component", () => {
69
69
  ).toBeInTheDocument()
70
70
  })
71
71
  })
72
+
73
+ describe("DatasetAlertPrivate component", () => {
74
+ it("renders the correct text for private snapshots with no changes", () => {
75
+ render(
76
+ <DatasetAlertPrivate
77
+ datasetId="test00001"
78
+ hasDraftChanges={false}
79
+ />,
80
+ { wrapper: MemoryRouter },
81
+ )
82
+
83
+ expect(
84
+ screen.queryByText(/this dataset has not been published/i),
85
+ ).toBeInTheDocument()
86
+ expect(
87
+ screen.queryByText(/there have been changes to the draft/i),
88
+ ).not.toBeInTheDocument()
89
+ })
90
+ it("renders the correct text for private snapshots with changes", () => {
91
+ render(
92
+ <DatasetAlertPrivate
93
+ datasetId="test00001"
94
+ hasDraftChanges
95
+ />,
96
+ { wrapper: MemoryRouter },
97
+ )
98
+
99
+ expect(
100
+ screen.queryByText(/there have been changes to the draft/i),
101
+ ).toBeInTheDocument()
102
+ })
103
+ })
package/src/scripts/dataset/fragments/{dataset-alert-draft.tsx → dataset-alert.tsx} RENAMED
@@ -2,6 +2,11 @@ import React from "react"
2
2
  import { Link } from "react-router-dom"
3
3
  import { DatasetAlert } from "../components/DatasetAlert"
4
4
 
5
+ export interface DatasetAlertPrivateProps {
6
+ datasetId: string
7
+ hasDraftChanges: boolean
8
+ }
9
+
5
10
  export interface DatasetAlertDraftProps {
6
11
  isPrivate: boolean
7
12
  datasetId: string
@@ -9,6 +14,30 @@ export interface DatasetAlertDraftProps {
9
14
  hasSnapshot: boolean
10
15
  }
11
16
 
17
+ export const DatasetAlertPrivate: React.FC<DatasetAlertPrivateProps> = ({
18
+ datasetId,
19
+ hasDraftChanges,
20
+ }) => {
21
+ return (
22
+ <DatasetAlert
23
+ alert="This dataset has not been published!"
24
+ footer={hasDraftChanges &&
25
+ "* There have been changes to the draft since your last version"}
26
+ level="warning"
27
+ >
28
+ <>
29
+ <Link
30
+ className="dataset-tool"
31
+ to={"/datasets/" + datasetId + "/publish"}
32
+ >
33
+ Publish this dataset
34
+ </Link>
35
+ &#32; to make all versions available publicly.
36
+ </>
37
+ </DatasetAlert>
38
+ )
39
+ }
40
+
12
41
  export const DatasetAlertDraft: React.FC<DatasetAlertDraftProps> = ({
13
42
  isPrivate,
14
43
  datasetId,
@@ -17,24 +46,7 @@ export const DatasetAlertDraft: React.FC<DatasetAlertDraftProps> = ({
17
46
  }) => {
18
47
  if (isPrivate) {
19
48
  if (hasSnapshot) {
20
- return (
21
- <DatasetAlert
22
- alert="This dataset has not been published!"
23
- footer={hasDraftChanges &&
24
- "* There have been changes to the draft since your last version"}
25
- level="warning"
26
- >
27
- <>
28
- <Link
29
- className="dataset-tool"
30
- to={"/datasets/" + datasetId + "/publish"}
31
- >
32
- Publish this dataset
33
- </Link>
34
- &#32; to make all versions available publicly.
35
- </>
36
- </DatasetAlert>
37
- )
49
+ return DatasetAlertPrivate({ datasetId, hasDraftChanges })
38
50
  } else {
39
51
  return (
40
52
  <DatasetAlert