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J uranic/publication nextgen dir schema (#1288)
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* Update publication-v2.yaml

Update to next-gen directory schema

* Update CHANGELOG.md

* Docs: Update publication directory schema

---------

Co-authored-by: Juan Puerto <=>
Co-authored-by: jpuerto-psc <[email protected]>
j-uranic and jpuerto-psc authored Jan 19, 2024

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2 changes: 1 addition & 1 deletion CHANGELOG.md
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@@ -12,7 +12,7 @@
- Refactor Upload to avoid validating the same contributors.tsv multiple times / running plugins over files multiple times
- Add entry for segmentation-mask
- Modify directory schema validation such that it takes empty directories into account

- Add Publication next-gen directory schema

## v0.0.16

5 changes: 4 additions & 1 deletion docs/publication/current/index.md
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@@ -28,6 +28,9 @@ Excel and TSV templates for this schema will be available when the draft next-ge

| pattern | required? | description |
| --- | --- | --- |
| <code>TODO</code> || Directory structure not yet specified. |
| <code>extras\/.*</code> || Folder for general lab-specific files related to the dataset. [Exists in all assays] |
| <code>data\/.+</code> (example: <code>data/file1.ext</code>) || Supplementary data files for the publication. All files referenced by the Vitessce visualization configurations in the vignettes must be included in this directory. |
| <code>vignettes\/.*</code> || Subdirectory containing Vitessce visualization files and a description of those files. |
| <code>vignettes\/vignette_\d+\/[^\/]+\.json</code> (example: <code>vignettes/vignette_01/file1.json</code>) | | Vitessce visualization configuration files. One or more visualization configurations can be provided per vignette. |
| <code>vignettes\/vignette_\d+\/description\.md</code> (example: <code>vignettes/vignette_02/description.md</code>) | | Description of the vignette and titles for the visualization configuration files. |

23 changes: 19 additions & 4 deletions src/ingest_validation_tools/directory-schemas/publication-v2.yaml
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files:
-
pattern: 'TODO'
description: 'Directory structure not yet specified.'
required: True
-
pattern: extras\/.*
required: True
description: Folder for general lab-specific files related to the dataset. [Exists in all assays]
-
pattern: data\/.+
required: True
description: Supplementary data files for the publication. All files referenced by the Vitessce visualization configurations in the vignettes must be included in this directory.
example: data/file1.ext
-
pattern: vignettes\/.*
required: True
description: Subdirectory containing Vitessce visualization files and a description of those files.
-
pattern: vignettes\/vignette_\d+\/[^\/]+\.json
required: False
description: Vitessce visualization configuration files. One or more visualization configurations can be provided per vignette.
example: vignettes/vignette_01/file1.json
-
pattern: vignettes\/vignette_\d+\/description\.md
required: False
description: Description of the vignette and titles for the visualization configuration files.
example: vignettes/vignette_02/description.md

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