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Sharing plan issue 106 #110

Merged
merged 25 commits into from
Jul 2, 2024
Merged

Sharing plan issue 106 #110

merged 25 commits into from
Jul 2, 2024

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Bankso
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@Bankso Bankso commented Jun 28, 2024

Fixes #106 (again)

Changelog

  • Adds Dataset Sharing Plan and attributes
  • Adds controlled vocab for new attribute Dataset Level
  • Moved some shared vocab terms from module/dataset --> module/shared
  • Update build-jsonld to schematic 24.5.1 and address dependency issue with ipython==8.18.1
  • Update a few erroneous entries

Bankso and others added 17 commits June 28, 2024 14:45
@Bankso
Fixing unexpected merge (#109)
935dd18 
* build jsonld

* Revert "build jsonld"

This reverts commit 3365dfe.

* Revert "Address typing_extensions issue with ipython"

This reverts commit ce22e3f.

* Revert "Bump schematic to version 24.5.1"

This reverts commit d4e1daa.

* Revert "Collate model CSV and convert to JSON-LD"

This reverts commit 0111969.

* Revert "Update valid values"

This reverts commit 2830a66.

* Revert "Remove unnecessary double quotes"

This reverts commit f791a93.

* Revert "Update annotationProperty.csv"

This reverts commit c0c5409.

* Revert "Removed misspelled Project attribute"

This reverts commit 3122359.

* Revert "Update shared attributes"

This reverts commit 47b324f.

* Revert "Remove Project dependency loop"

This reverts commit 29c6090.

* Revert "Create processLevel.csv"

This reverts commit 22846e7.

* Revert "Change folder reference for DSP"

This reverts commit b755a98.

* Revert "Update and add valid value mappings"

This reverts commit 824437d.

* Revert "Add shared attribute Data Use Codes"

This reverts commit cc73994.

* Revert "Move dataset valid values to shared"

This reverts commit c3e0807.

* Revert "Add DUO terms to model as valid values"

This reverts commit 5a032df.

* Revert "Add initial version of Dataset Sharing Plan model"

This reverts commit 3749b3b.

---------

Co-authored-by: mc2center-bot[bot] <[email protected]>
@Bankso
Add initial version of Dataset Sharing Plan model
6a05873
@Bankso
Add DUO terms to model as valid values
3c3aa8c
@Bankso
Move dataset valid values to shared
e3f1a09
@Bankso
Add shared attribute Data Use Codes
8b58464
@Bankso
Update and add valid value mappings
61526ad 
- update dataset mappings
- add DSP mappings
- add Data Use Code mapping
@Bankso
Change folder reference for DSP
8ef560b
@Bankso
Create processLevel.csv
8025707
@Bankso
Remove Project dependency loop
63345f1 
Project Type dependency on Project is not necessary and is flagged by schematic as circular. Removing produces a true directed acyclic graph (DAG)
@Bankso
Update shared attributes
64fd709
@Bankso
Removed misspelled Project attribute
d87248c
@Bankso
Update annotationProperty.csv
ac7023f
@Bankso
Remove unnecessary double quotes
21dd74f
@Bankso
Update valid values
ebdc7da
@Bankso
Collate model CSV and convert to JSON-LD
c46693a 
Schematic 24.5.1
@Bankso
Bump schematic to version 24.5.1
da91825
@Bankso
Address typing_extensions issue with ipython
813cacf
@vpchung vpchung added the minor PR label for a minor update label Jun 28, 2024
vpchung
vpchung approved these changes Jun 28, 2024
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@vpchung vpchung left a comment •
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Saving this as a TODO for a separate PR, but:

Since some of the module files have been moved and the template files have been updated from XLSX to CSV, we will also need to update the doc markdowns in order to reflect their new filepaths/filenames.

@Bankso
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Bankso commented Jun 28, 2024

Since some of the module files have been moved and the template files have been updated from XLSX to CSV, we will also need to update the doc markdowns in order to reflect their new filepaths/filenames.

Thank you for pointing this out! Since I'm the one breaking things, I will make those updates 😁

@vpchung
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vpchung commented Jun 29, 2024

@Bankso thank you!! I don't mind doing it either, so if you have other pressing things to do, just lmk!

@Bankso Bankso mentioned this pull request Jul 1, 2024
Merged
@Bankso
Doc updates issue 106 (#111)
e4348e5 
* Update template refs from xlsx --> csv

* Update dataset cv refs to new 'shared' path

* Create DataDSP.md

* Add valid values md for DSP

* Add DSP content to nav config

* Rename Dataset Type to Assay

For consistency with DatasetView model

* Add sharingPlans folder to hooks

* Update Dataset Type to Assay in CV mapping

* Add DSP Url and update schema definition

* Update DataDSP.csv
@Bankso Bankso requested a review from aclayton555 as a code owner July 1, 2024 20:18
@Bankso
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Bankso commented Jul 1, 2024

@aditigopalan could you please take a quick look at the current DataDSP model implementation? I just want to make sure things look reasonable before we merge

Bankso added 3 commits July 1, 2024 15:36
@Bankso
Add DSP Data Use Codes as attribute
ad969e5 
Instead of using a single Data Use Codes attribute, differentiate for DSP model. This allows it to show up in our documentation
@Bankso
Update mapping to use DSP Data Use Codes
899f493
@Bankso
Add DSP Data Use Codes to vocab section
aebc3cc
@aditigopalan
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@aditigopalan could you please take a quick look at the current DataDSP model implementation? I just want to make sure things look reasonable before we merge

Looks good to me!

@Bankso Bankso merged commit 0da76df into main Jul 2, 2024
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@Bankso Bankso deleted the sharing-plan-issue-106 branch July 2, 2024 16:05
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@aditigopalan aditigopalan aditigopalan approved these changes

@vpchung vpchung vpchung approved these changes

@aclayton555 aclayton555 Awaiting requested review from aclayton555 aclayton555 is a code owner

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Data sharing plan - refactor and model implementation
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@Bankso @vpchung @aditigopalan