Removed timecourse from types and added to biomaterial core. Fixes #1511 #1529
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willrockout
requested review from
ESapenaVentura,
amnonkhen,
NoopDog,
hannes-ucsc and
ncalvanese1
Fixed description to be more general. Co-authored-by: Hannes Schmidt <[email protected]>
docs/jsonBrowser/core.md
Outdated
| @@ -61,6 +61,7 @@ supplementary_files | A list of filenames of biomaterial-level supplementary fil | |||
| biosamples_accession | A BioSamples accession. | string | no | | BioSamples accession | | SAMN00000000 | |||
| insdc_sample_accession | An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. | string | no | | INSDC sample accession | | SRS0000000 | |||
| HDBR_accession | A Human Developmental Biology Resource (HDBR) sample accession. | string | no | | HDBR accession | | 34526; 14758, 2, liver | |||
| timecourse | Information relating to a timecourse associated with this cell line. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | | |||
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| timecourse | Information relating to a timecourse associated with this cell line. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | | |
| timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | [See module timecourse](module.md#timecourse) | Timecourse | | |
I thought the documentation was automatically generated from the schema, so making the schema change I proposed in my previous review should have automatically caused this line to be updated, too.
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I believe it is automatically created with Git hooks upon a push but I'm not 100%. It seems to not work from a GitHub commit.
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It seems to not work from a GitHub commit.
Well, that's a problem.
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Procedural comment: The author shouldn't resolve reviewer comments. Reviewers resolve their own comments when they feel they have been addressed.
From the SOP:
If you accept the PR author's response to a comment made by the reviewer, mark the comment thread as resolved on Github.
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@ESapenaVentura, in my experience, commit hooks aren't a good enforcement mechanism, simply because they can easily be bypassed. What we do in our projects is make the code/doc generation part of our build process and then have a validation step in our GitHub Actions workflow that tests for a dirty working copy. If the author of a change forgets to run the code/doc generation and commit the result, the code generation will dirty the working copy on CI/CD and fail the GitHub Actions workflow. This has worked very well for us in a number of different scenarios. For example, we also detect stale transitive Python dependencies that way. |
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@ESapenaVentura Yes I changed it from the command line on my local copy then committed and pushed the change but for the change to the biomaterial_core.json I made the change on Git Hub. |
willrockout
deleted the
ws-add-timecourse-to-biomaterial-core-Issue1511
branch
Release notes
This is a remake of PR #1513 to clean up the commit tree.
For core/biomaterial/biomaterial_core.json schema:
-Added timecourse module
For type/biomaterial/donor_organism.json schema:
-Removed timecourse module
For type/biomaterial/cell_suspension.json schema:
-Removed timecourse module
For type/biomaterial/cell_line.json schema:
-Removed timecourse module
Reviews requested
-Major change, removing timecourse module from donor_organism, cell_line, and cell_suspension.
-Minor change, adding timecourse module to biomaterial core.