Fixes #2725 clm-cl.owl component edits #2763
Conversation
|
Looks good, but maybe some unrelated edits here too - e.g. on taxon constraints? |
There was a problem hiding this comment.
On the addition of the clm-cl.owl component itself, no problem except that at some point we will need to make the downloading of the component conditional, so that it is only refreshed when a refresh is explicitly required and not when running the QC pipelines (#2644). But this is out of scope of this PR.
The real issue here is the overwriting of our custom QC workflow file (.github/workflows/qc.yml), which must be reverted.
| env: | ||
| DEFAULT_BRANCH: master | ||
| run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false | ||
|
|
||
| - name: Reason over taxon constraints |
There was a problem hiding this comment.
All changes to that file should not have been committed.
When running make update_repo, the ODK automatically updates a bunch of files, including the .github/workflows/qc.yml file. But in CL, we are running a customised version of the QC check (in which we additionally check for taxon constraint violations), so our own qc.yml file should not be replaced by the ODK-generated one.
So, after running make update_repo, all changes to .github/workflows/qc.yml should be reverted so as to leave our original file unchanged.
| @@ -1,7 +1,7 @@ | |||
| # ---------------------------------------- | |||
| # Makefile for cl | |||
| # Generated using ontology-development-kit | |||
| # ODK Version: v1.5.3 | |||
| # ODK Version: v1.5.2 | |||
There was a problem hiding this comment.
You are running the ODK 1.5.2. This is not a problem here, but please note that CL’s QC and release workflows now require the ODK 1.5.3.
| @@ -313,6 +313,14 @@ CELLXGENE_SUBSET_URL="https://raw.githubusercontent.com/hkir-dev/cellxgene-cell- | |||
| $(TEMPLATEDIR)/cellxgene_subset.tsv: | |||
| wget $(CELLXGENE_SUBSET_URL) -O $@ | |||
|
|
|||
| # CellMark reference subset | |||
| CLM_CL_URL="https://raw.githubusercontent.com/Cellular-Semantics/CellMark/main/clm-cl.owl" | |||
| $(TMPDIR)/clm-cl.owl: | |||
There was a problem hiding this comment.
This is in line with how we “manage“ the already existing components, so it’s fine for now.
But this will need to be changed at some point to uncouple the refreshing of components from the release and QC processes (#2644).
Unfortunately it won’t be practical to do this starting from this PR, since the changes to Better to actually start anew in a completely distinct PR. I can take care of that. |
clm-cl.owl component edits - This work was done under the supervision of @hkir-dev
blocked by Cellular-Semantics/CellMark#9.