@openneuro/app 4.11.0 → 4.12.0-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 (18) hide show
  1. package/package.json +4 -5
  2. package/src/scripts/apm.js +0 -2
  3. package/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap +48 -68
  4. package/src/scripts/dataset/download/download-native.js +77 -30
  5. package/src/scripts/dataset/download/download-query.js +3 -1
  6. package/src/scripts/dataset/download/native-file-toast.jsx +24 -6
  7. package/src/scripts/dataset/files/__tests__/file-tree-unloaded-directory.spec.jsx +4 -16
  8. package/src/scripts/dataset/files/__tests__/file-tree.spec.jsx +104 -33
  9. package/src/scripts/dataset/files/file-tree-unloaded-directory.jsx +26 -31
  10. package/src/scripts/dataset/files/file-tree.tsx +158 -0
  11. package/src/scripts/dataset/files/file.tsx +2 -2
  12. package/src/scripts/dataset/files/{files.jsx → files.tsx} +21 -12
  13. package/src/scripts/types/dataset-file.ts +11 -0
  14. package/src/scripts/dataset/files/__tests__/file-tree-loading.spec.jsx +0 -18
  15. package/src/scripts/dataset/files/__tests__/flat-to-tree.spec.js +0 -55
  16. package/src/scripts/dataset/files/file-tree-loading.jsx +0 -65
  17. package/src/scripts/dataset/files/file-tree.jsx +0 -126
  18. package/src/scripts/dataset/files/flat-to-tree.js +0 -49
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
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  {
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  "name": "@openneuro/app",
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- "version": "4.11.0",
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+ "version": "4.12.0-alpha.1",
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  "description": "React JS web frontend for the OpenNeuro platform.",
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  "license": "MIT",
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  "main": "public/client.js",
@@ -20,8 +20,8 @@
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  "@emotion/react": "11.6.0",
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  "@emotion/styled": "11.6.0",
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  "@niivue/niivue": "0.23.1",
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- "@openneuro/client": "^4.11.0",
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- "@openneuro/components": "^4.11.0",
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+ "@openneuro/client": "^4.12.0-alpha.1",
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+ "@openneuro/components": "^4.12.0-alpha.1",
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  "bids-validator": "1.9.9",
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  "bytes": "^3.0.0",
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  "comlink": "^4.0.5",
@@ -39,7 +39,6 @@
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  "react-dom": "^17.0.1",
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  "react-helmet": "6.1.0",
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  "react-router-dom": "6.3.0",
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- "react-spring": "^8.0.27",
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  "react-toastify": "6.0.9",
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  "react-usestateref": "^1.0.5",
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  "react-virtualized": "remorses/react-virtualized-fixed-import.git#9.22.3",
@@ -105,5 +104,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "4795359e0756b2f6d83f385172a80d9b26b5fdc8"
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+ "gitHead": "9350a34292c3222e7a68940d5397fce87fa1469b"
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  }
package/src/scripts/apm.js CHANGED
@@ -15,8 +15,6 @@ export function setupApm() {
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  serviceVersion: version,
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  environment: config.sentry.environment,
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  })
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- } else {
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- apm = {}
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  }
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  }
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package/src/scripts/dataset/__tests__/__snapshots__/snapshot-container.spec.tsx.snap CHANGED
@@ -624,13 +624,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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;"
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+ style="color: deepskyblue;"
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  >
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  <i
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- class="fab fa-node-js"
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+ class="fab fa-markdown"
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  />
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  </span>
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-   dataset_description.json
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+   README
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  <span
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  class="filetree-editfile"
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  >
@@ -647,7 +647,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/dataset_description.json"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/README"
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  >
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  <i
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  class="fa fa-eye"
@@ -664,13 +664,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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: lightgreen;"
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+ style="color: limegreen;"
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  >
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  <i
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- class="fas fa-file-excel"
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+ class="fab fa-node-js"
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  />
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  </span>
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-   participants.tsv
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+   T1w.json
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  <span
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  class="filetree-editfile"
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  >
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/participants.tsv"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/T1w.json"
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  >
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  <i
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  class="fa fa-eye"
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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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+ style="color: limegreen;"
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  >
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- class="fab fa-markdown"
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+ class="fab fa-node-js"
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  />
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-   README
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+   dataset_description.json
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  <span
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  class="filetree-editfile"
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  >
@@ -727,7 +727,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/README"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/dataset_description.json"
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  >
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  <i
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  class="fa fa-eye"
@@ -744,13 +744,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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;"
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+ style="color: lightgreen;"
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  >
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- class="fab fa-node-js"
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+ class="fas fa-file-excel"
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  />
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  </span>
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-   T1w.json
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+   participants.tsv
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  <span
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  class="filetree-editfile"
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  >
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/T1w.json"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/participants.tsv"
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  >
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  <i
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  class="fa fa-eye"
@@ -803,13 +803,8 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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="css-t3f89n"
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- >
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- <div
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- class="css-b1x83q"
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- style="width: 0%;"
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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>
@@ -841,13 +836,8 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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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- >
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- style="width: 0%;"
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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>
@@ -974,13 +964,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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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- class="fab fa-node-js"
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+ class="fab fa-markdown"
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  />
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  </span>
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-   dataset_description.json
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+   README
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  <span
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  class="filetree-editfile"
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  >
@@ -990,7 +980,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <span
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  class=" "
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  data-flow="up"
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- data-tooltip="Download: 172B"
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+ data-tooltip="Download: 709B"
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  >
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  <span
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  class="edit-file download-file"
@@ -998,7 +988,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <a
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  aria-label="download file"
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  download=""
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- href="/crn/datasets/ds001032/snapshots/1.0.0/files/dataset_description.json"
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+ href="/crn/datasets/ds001032/snapshots/1.0.0/files/README"
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  >
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  <i
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  class="fa fa-download"
@@ -1017,7 +1007,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/dataset_description.json"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/README"
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  >
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  <i
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  class="fa fa-eye"
@@ -1034,13 +1024,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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: lightgreen;"
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+ style="color: limegreen;"
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  >
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  <i
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- class="fas fa-file-excel"
1030
+ class="fab fa-node-js"
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  />
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  </span>
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-   participants.tsv
1033
+   T1w.json
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  <span
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  class="filetree-editfile"
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  >
@@ -1050,7 +1040,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <span
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  class=" "
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  data-flow="up"
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- data-tooltip="Download: 36B"
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+ data-tooltip="Download: 196B"
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  >
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  <span
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  class="edit-file download-file"
@@ -1058,7 +1048,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <a
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  aria-label="download file"
1060
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  download=""
1061
- href="/crn/datasets/ds001032/snapshots/1.0.0/files/participants.tsv"
1051
+ href="/crn/datasets/ds001032/snapshots/1.0.0/files/T1w.json"
1062
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  >
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  <i
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  class="fa fa-download"
@@ -1077,7 +1067,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1077
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  >
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  <a
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  aria-label="view file"
1080
- href="/datasets/ds001032/versions/1.0.0/file-display/participants.tsv"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/T1w.json"
1081
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  >
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  <i
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  class="fa fa-eye"
@@ -1094,13 +1084,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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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+ style="color: limegreen;"
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  >
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  <i
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- class="fab fa-markdown"
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+ class="fab fa-node-js"
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  />
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  </span>
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-   README
1093
+   dataset_description.json
1104
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  <span
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  class="filetree-editfile"
1106
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  >
@@ -1110,7 +1100,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <span
1111
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  class=" "
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  data-flow="up"
1113
- data-tooltip="Download: 709B"
1103
+ data-tooltip="Download: 172B"
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1104
  >
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  <span
1116
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  class="edit-file download-file"
@@ -1118,7 +1108,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1118
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  <a
1119
1109
  aria-label="download file"
1120
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  download=""
1121
- href="/crn/datasets/ds001032/snapshots/1.0.0/files/README"
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+ href="/crn/datasets/ds001032/snapshots/1.0.0/files/dataset_description.json"
1122
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  >
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  <i
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  class="fa fa-download"
@@ -1137,7 +1127,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1137
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  >
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  <a
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  aria-label="view file"
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- href="/datasets/ds001032/versions/1.0.0/file-display/README"
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+ href="/datasets/ds001032/versions/1.0.0/file-display/dataset_description.json"
1141
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  >
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  <i
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  class="fa fa-eye"
@@ -1154,13 +1144,13 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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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;"
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+ style="color: lightgreen;"
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  >
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  <i
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- class="fab fa-node-js"
1150
+ class="fas fa-file-excel"
1161
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  />
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  </span>
1163
-   T1w.json
1153
+   participants.tsv
1164
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  <span
1165
1155
  class="filetree-editfile"
1166
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  >
@@ -1170,7 +1160,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
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  <span
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  class=" "
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  data-flow="up"
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- data-tooltip="Download: 196B"
1163
+ data-tooltip="Download: 36B"
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  >
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@@ -1178,7 +1168,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1178
1168
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1179
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  aria-label="download file"
1180
1170
  download=""
1181
- href="/crn/datasets/ds001032/snapshots/1.0.0/files/T1w.json"
1171
+ href="/crn/datasets/ds001032/snapshots/1.0.0/files/participants.tsv"
1182
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  >
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  <i
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  class="fa fa-download"
@@ -1197,7 +1187,7 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1197
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  >
1198
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1199
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  aria-label="view file"
1200
- href="/datasets/ds001032/versions/1.0.0/file-display/T1w.json"
1190
+ href="/datasets/ds001032/versions/1.0.0/file-display/participants.tsv"
1201
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  >
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  <i
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  class="fa fa-eye"
@@ -1233,13 +1223,8 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1233
1223
  <div
1234
1224
  class="accordion-content"
1235
1225
  >
1236
- <div
1237
- class="css-t3f89n"
1238
- >
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1240
- class="css-b1x83q"
1241
- style="width: 0%;"
1242
- />
1226
+ <div>
1227
+ Loading...
1243
1228
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1244
1229
  </div>
1245
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  </div>
@@ -1271,13 +1256,8 @@ OCI-1131441 (R. Poldrack, PI) in any publications.
1271
1256
  <div
1272
1257
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1273
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  >
1274
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1275
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1276
- >
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+ <div>
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+ Loading...
1281
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  </div>
1283
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  </div>
package/src/scripts/dataset/download/download-native.js CHANGED
@@ -40,30 +40,90 @@ class DownloadAbortError extends Error {
40
40
  }
41
41
  }
42
42
 
43
+ let downloadCanceled
44
+
43
45
  /**
44
- * Downloads a dataset via the native file API, skipping expensive compression if the browser supports it
45
- * @param {string} datasetId Accession number string for a dataset
46
- * @param {string} snapshotTag Snapshot tag name
46
+ * Recursive download for file trees via browser file access API
47
47
  */
48
- export const downloadNative = (datasetId, snapshotTag, client) => async () => {
48
+ const downloadTree = async (
49
+ { datasetId, snapshotTag, client, apmTransaction, dirHandle, toastId },
50
+ path = '',
51
+ tree = null,
52
+ ) => {
49
53
  const filesToDownload = await downloadDataset(client)({
50
54
  datasetId,
51
55
  snapshotTag,
56
+ tree,
52
57
  })
58
+ for (const [index, file] of filesToDownload.entries()) {
59
+ const downloadPath = path ? `${path}/${file.filename}` : file.filename
60
+ if (file.directory) {
61
+ // Next tree level
62
+ await downloadTree(
63
+ {
64
+ datasetId,
65
+ snapshotTag,
66
+ client,
67
+ apmTransaction,
68
+ dirHandle,
69
+ toastId,
70
+ },
71
+ downloadPath,
72
+ file.id,
73
+ )
74
+ } else {
75
+ // Regular file
76
+ if (downloadCanceled) {
77
+ throw new DownloadAbortError('Download canceled by user request')
78
+ }
79
+ const fileHandle = await openFileTree(
80
+ dirHandle,
81
+ path ? `${path}/${file.filename}` : file.filename,
82
+ )
83
+ // Skip files which are already complete
84
+ if (fileHandle.size == file.size) continue
85
+ const writable = await fileHandle.createWritable()
86
+ const { body, status, statusText } = await fetch(file.urls.pop())
87
+ let loaded = 0
88
+ const progress = new TransformStream({
89
+ transform(chunk, controller) {
90
+ downloadToastUpdate(toastId, loaded / file.size, {
91
+ datasetId,
92
+ snapshotTag,
93
+ downloadPath,
94
+ dirName: dirHandle.name,
95
+ })
96
+ loaded += chunk.length
97
+ controller.enqueue(chunk)
98
+ },
99
+ })
100
+ if (status === 200) {
101
+ await body.pipeThrough(progress).pipeTo(writable)
102
+ } else {
103
+ apmTransaction.captureError(statusText)
104
+ return requestFailureToast(file.filename)
105
+ }
106
+ }
107
+ }
108
+ }
53
109
 
110
+ /**
111
+ * Downloads a dataset via the native file API, skipping expensive compression if the browser supports it
112
+ * @param {string} datasetId Accession number string for a dataset
113
+ * @param {string} snapshotTag Snapshot tag name
114
+ */
115
+ export const downloadNative = (datasetId, snapshotTag, client) => async () => {
54
116
  // Try trackDownload but don't worry if it fails
55
117
  try {
56
118
  trackDownload(client, datasetId, snapshotTag)
57
119
  } catch (err) {
58
120
  apm.captureError(err)
59
121
  }
60
- const apmTransaction = apm.startTransaction(
61
- `download:${datasetId}`,
62
- 'download',
63
- )
122
+ const apmTransaction =
123
+ apm && apm.startTransaction(`download:${datasetId}`, 'download')
64
124
  if (apmTransaction)
65
125
  apmTransaction.addLabels({ datasetId, snapshot: snapshotTag })
66
- let downloadCanceled = false
126
+ downloadCanceled = false
67
127
  let toastId
68
128
  try {
69
129
  const apmSelect =
@@ -77,27 +137,14 @@ export const downloadNative = (datasetId, snapshotTag, client) => async () => {
77
137
  () => (downloadCanceled = true),
78
138
  )
79
139
  apmSelect && apmSelect.end()
80
- for (const [index, file] of filesToDownload.entries()) {
81
- const apmDownload =
82
- apmTransaction &&
83
- apmTransaction.startSpan(`download ${file.filename}:${file.size}`)
84
- if (downloadCanceled) {
85
- throw new DownloadAbortError('Download canceled by user request')
86
- }
87
- const fileHandle = await openFileTree(dirHandle, file.filename)
88
- // Skip files which are already complete
89
- if (fileHandle.size == file.size) continue
90
- const writable = await fileHandle.createWritable()
91
- const { body, status, statusText } = await fetch(file.urls.pop())
92
- if (status === 200) {
93
- await body.pipeTo(writable)
94
- } else {
95
- apmDownload && apmDownload.captureError(statusText)
96
- return requestFailureToast()
97
- }
98
- apmDownload && apmDownload.end()
99
- downloadToastUpdate(toastId, index / filesToDownload.length)
100
- }
140
+ await downloadTree({
141
+ datasetId,
142
+ snapshotTag,
143
+ client,
144
+ apmTransaction,
145
+ dirHandle,
146
+ toastId,
147
+ })
101
148
  downloadCompleteToast(dirHandle.name)
102
149
  } catch (err) {
103
150
  if (err.name === 'AbortError') {
package/src/scripts/dataset/download/download-query.js CHANGED
@@ -2,13 +2,14 @@ import { datasets } from '@openneuro/client'
2
2
 
3
3
  export const downloadDataset =
4
4
  client =>
5
- async ({ datasetId, snapshotTag }) => {
5
+ async ({ datasetId, snapshotTag, tree = null }) => {
6
6
  if (snapshotTag) {
7
7
  const { data } = await client.query({
8
8
  query: datasets.downloadSnapshot,
9
9
  variables: {
10
10
  datasetId,
11
11
  tag: snapshotTag,
12
+ tree: tree,
12
13
  },
13
14
  })
14
15
  return data.snapshot.files
@@ -17,6 +18,7 @@ export const downloadDataset =
17
18
  query: datasets.downloadDataset,
18
19
  variables: {
19
20
  datasetId,
21
+ tree,
20
22
  },
21
23
  })
22
24
  return data.dataset.draft.files
package/src/scripts/dataset/download/native-file-toast.jsx CHANGED
@@ -41,10 +41,13 @@ export const nativeErrorToast = () => {
41
41
  )
42
42
  }
43
43
 
44
- export const requestFailureToast = () => {
44
+ export const requestFailureToast = filename => {
45
45
  toast.error(
46
46
  <ToastContent title="Download Error" body="A file failed to download">
47
- <p>You may not have access to download this dataset.</p>
47
+ <p>
48
+ {filename} failed. Retry your download to reattempt downloading this
49
+ file.
50
+ </p>
48
51
  </ToastContent>,
49
52
  )
50
53
  }
@@ -70,8 +73,8 @@ export const downloadCompleteToast = dirName => {
70
73
  */
71
74
  export const downloadToast = (dirName, datasetId, snapshotId, onClose) => {
72
75
  const downloadMessage = snapshotId
73
- ? `Copying ${datasetId} snapshot ${snapshotId} to local folder ${dirName}`
74
- : `Copying ${datasetId} to local folder ${dirName}`
76
+ ? `${datasetId} snapshot ${snapshotId} to local folder ${dirName}`
77
+ : `${datasetId} to local folder ${dirName}`
75
78
  return toast(
76
79
  <ToastContent title={'Downloading'} body={downloadMessage}></ToastContent>,
77
80
  {
@@ -84,7 +87,22 @@ export const downloadToast = (dirName, datasetId, snapshotId, onClose) => {
84
87
  )
85
88
  }
86
89
 
87
- export const downloadToastUpdate = (toastId, progress) =>
88
- toast.update(toastId, { progress })
90
+ export const downloadToastUpdate = (
91
+ toastId,
92
+ progress,
93
+ { datasetId, snapshotTag, downloadPath, dirName },
94
+ ) => {
95
+ const downloadMessage = snapshotTag
96
+ ? `${datasetId} snapshot ${snapshotTag} to local folder ${dirName}`
97
+ : `${datasetId} to local folder ${dirName}`
98
+ toast.update(toastId, {
99
+ render: (
100
+ <ToastContent title={'Downloading'} body={downloadMessage}>
101
+ {downloadPath}
102
+ </ToastContent>
103
+ ),
104
+ progress,
105
+ })
106
+ }
89
107
 
90
108
  export const downloadToastDone = toastId => toast.done(toastId)
package/src/scripts/dataset/files/__tests__/file-tree-unloaded-directory.spec.jsx CHANGED
@@ -32,37 +32,25 @@ describe('FileTreeUnloadedDirectory component', () => {
32
32
  const dir = { filename: 'sub-01', directory: true }
33
33
  const a = { id: '1234', filename: 'a', directory: false }
34
34
  const b = { id: '5678', filename: 'b', directory: false }
35
- const c = { id: '91011', filename: 'sub-01/c', directory: false }
35
+ const c = { id: '91011', filename: 'c', directory: false }
36
36
  const defaultObj = { dataset: { draft: { files: [a, b] } } }
37
37
  const updatedObj = { dataset: { draft: { files: [c] } } }
38
38
  expect(
39
39
  mergeNewFiles(dir)(defaultObj, { fetchMoreResult: updatedObj }).dataset
40
40
  .draft.files,
41
- ).toEqual([a, b, c])
42
- })
43
- it('removes the existing directory facade when merging lists', () => {
44
- const dir = { filename: 'sub-01', directory: true }
45
- const a = { id: '1234', filename: 'a', directory: false }
46
- const b = { id: '5678', filename: 'b', directory: false }
47
- const c = { id: '91011', filename: 'sub-01/c', directory: false }
48
- const defaultObj = { dataset: { draft: { files: [dir, a, b] } } }
49
- const updatedObj = { dataset: { draft: { files: [c] } } }
50
- expect(
51
- mergeNewFiles(dir)(defaultObj, { fetchMoreResult: updatedObj }).dataset
52
- .draft.files,
53
- ).toEqual([a, b, c])
41
+ ).toEqual([a, b, { ...c, filename: 'sub-01:c' }])
54
42
  })
55
43
  it('works with snapshots', () => {
56
44
  const dir = { filename: 'sub-01', directory: true }
57
45
  const a = { id: '1234', filename: 'a', directory: false }
58
46
  const b = { id: '5678', filename: 'b', directory: false }
59
- const c = { id: '91011', filename: 'sub-01/c', directory: false }
47
+ const c = { id: '91011', filename: 'c', directory: false }
60
48
  const defaultObj = { snapshot: { files: [dir, a, b] } }
61
49
  const updatedObj = { snapshot: { files: [c] } }
62
50
  expect(
63
51
  mergeNewFiles(dir, '1.0.0')(defaultObj, { fetchMoreResult: updatedObj })
64
52
  .snapshot.files,
65
- ).toEqual([a, b, c])
53
+ ).toEqual([dir, a, b, { ...c, filename: 'sub-01:c' }])
66
54
  })
67
55
  })
68
56
  })