genomicsstandardsconsortium / mixs6.2_release_candidate Goto Github PK

see also

• GenomicsStandardsConsortium#685
• GenomicsStandardsConsortium#714

Will change them to CompoundWordEnum

@cmungall suggested getting more community input

• linkml/linkml#1652

will elaborate later

and keep track of the run time

started ~ 19:30 ET

finished ~ 20:40

We should aim to have all changes into the YAML file by the next CIG meeting on Sep. 26. At that point, no more conversions from the old spreadsheets to YAML should happen.

At the CIG meeting, the TWG will present the MIxS 6.2 release with YAML as SOT. If approved by TWG, we can proceed with the release.

After the 6.2 release, we will implement conversion to schema sheets as SOT, as per issue GenomicsStandardsConsortium#715 .

note, this repo was previously forked from https://github.com/GenomicsStandardsConsortium/mixs and all of that content was removed in a pus to main

I.e. don't merge this, but make a new branch, empty it out, repopulate with the official cookiecutter, and move the generated schema into the cookiecutter's expected schema source directory.

May also want to copy over some of the QC utilities, but not the schema generation code.

Could also check in the last batch of logs

see also

• #27

Haven't decided about enums yet.

see GenomicsStandardsConsortium#610

npm run build -- \
  --outDir ../dist/__data_harmonizer \
  --base /mixs6.2_release_candidate/__data_harmonizer/

2023-10-03T14:50:31.7455664Z shell: /usr/bin/bash -e {0}
2023-10-03T14:50:31.7455936Z env:
2023-10-03T14:50:31.7456235Z pythonLocation: /opt/hostedtoolcache/Python/3.9.18/x64
2023-10-03T14:50:31.7456610Z LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.18/x64/lib
2023-10-03T14:50:31.7456914Z VENV: .venv/bin/activate
2023-10-03T14:50:31.7457142Z ##[endgroup]
2023-10-03T14:50:36.8080841Z
2023-10-03T14:50:36.8082077Z > [email protected] build
2023-10-03T14:50:36.8082892Z > vite build --outDir ../dist/__data_harmonizer --base /mixs6.2_release_candidate/__data_harmonizer/
2023-10-03T14:50:36.8083181Z
2023-10-03T14:50:37.0252115Z �[36mvite v3.0.4 �[32mbuilding for production...�[36m�[39m
2023-10-03T14:50:37.0902595Z transforming...
2023-10-03T14:50:40.3690301Z �[32m✓�[39m 10 modules transformed.
2023-10-03T14:50:40.3695634Z �[31m[vite:json] Failed to parse JSON file, invalid JSON syntax found at line 1655660�[39m
2023-10-03T14:50:40.3696692Z file: �[36m/home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/schemas/mixs_6_2_rc.json�[39m
2023-10-03T14:50:40.3721431Z �[31merror during build:
2023-10-03T14:50:40.3722112Z Error: Failed to parse JSON file, invalid JSON syntax found at line 1655660
2023-10-03T14:50:40.3723287Z at error (file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/rollup/dist/es/shared/rollup.js:1858:30)
2023-10-03T14:50:40.3724133Z at throwPluginError (file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/rollup/dist/es/shared/rollup.js:21587:12)
2023-10-03T14:50:40.3724913Z at Object.error (file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/rollup/dist/es/shared/rollup.js:22541:20)
2023-10-03T14:50:40.3725664Z at Object.error (file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/rollup/dist/es/shared/rollup.js:21764:42)
2023-10-03T14:50:40.3726819Z at Object.transform (file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/vite/dist/node/chunks/dep-71eb12cb.js:38838:22)
2023-10-03T14:50:40.3728189Z at file:///home/runner/work/mixs6.2_release_candidate/mixs6.2_release_candidate/data_harmonizer/node_modules/rollup/dist/es/shared/rollup.js:22748:40�[39m

but remember, the target notes/keywords comes from config/curated-slot-notes-by-text-mining.tsv

@cmungall has suggested switching to a more sustainable topic detector

And do we really want the filename hard-coded into scripts/term_list_generator.py ?

• linkml/linkml#1652

Review changes in https://github.com/GenomicsStandardsConsortium/mixs6.2_release_candidate/blob/main/conflict-reports/conflict-repair-report.tsv

They are changes already made in the fork. Changes are based on the configuration files: Instructions: https://github.com/GenomicsStandardsConsortium/mixs6.2_release_candidate/blob/main/config/mixs-tables-stage-modifications.tsv

[tool.poetry]
name = "mixs-envo-struct-knowl-extraction"

So I used redirection

schema-derivatives/$(RC_PREFIX).owl.ttl: $(SOURCE_SCHEMA_PATH)
	$(RUN) gen-owl \
		--output $@ \
		--format ttl \
		--metadata-profile rdfs $< > $@

see also

• #17

see

• #49

The latest deployment of the MIXS documentation pages has links to the following sections on its index/landing page:

• Checklists
• Packages
• Combinations
• Enumerations
• Types
• Subsets

We should update/refresh the table of contents section to include only the following three links rather than including links to LinkML element pages like enums, subsets, etc.

• Checklists
• Packages
• Combinations

What are your thoughts on this @turbomam @cmungall?

I think this is OK on my local machine now. Trying to rebuild into GH pages now.

The term table list that we see being rendered correctly locally after running the Makefile documentation steps is not working in production due to GitHub Actions oddities.

The old for the schema was set to: https://microbiomedata.github.io/mixs-6-2-release-candidate/mixs_6_2_rc/ (https://w3id.org/mixs-6-2-rc/mixs_6_2_rc)

Change the id so that it has this new URL: https://genomicsstandardsconsortium.github.io/mixs6.2_release_candidate/ (https://w3id.org/mixs-6-2-rc)

This repo is really meant for a one time bulk conversion, so unit tests have been de-prioritized.

e.g. linkml2schemasheets-template, called by
make schemasheets-usage-output/mixs_6_2_rc.yaml.concise.schemasheet.tsv

see

• linkml/linkml#1643