GitHub Actions: check-links job is failing

[eecavanna]

The check-links job is failing.

I checked the "Actions" tab on GitHub to see when the most recent passing run occurred, and did not see any passing runs.

https://github.com/microbiomedata/NMDC_documentation/actions/workflows/link-check.yaml

---

This section was added on September 7, 2023: Here's the failure list from the latest run. In this list, I manually (via regex replacement) formatted the file:/// links, added 🔒 emojis to (at least some) private GitHub links, and added checkboxes.

Summary

Status	Count
🔍 Total	8623
✅ Successful	7527
⏳ Timeouts	12
🔀 Redirected	0
👻 Excluded	1022
❓ Unknown	0
🚫 Errors	62

Errors per input

Errors in ./docs/reference/metadata/index.md

• http://insdc.org/country.html: Failed: Network error
• http://purl.obolibrary.org/obo/EO_0007147: Failed: Network error
• http://www.cropontology.org/ontology/CO_715/Crop%20Research: Failed: Network error
• http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups: Failed: Network error

Errors in ./docs/howto_guides/submit2nmdc.md

• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/howto_guides/portal_guide/submision_context.png: Failed: Cannot find file

Errors in ./docs/reference/metadata/fao_class.md

• http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups: Failed: Network error

Errors in ./docs/reference/metadata/growth_facil.md

• http://www.cropontology.org/ontology/CO_715/Crop%20Research: Failed: Network error

Errors in ./docs/reference/metadata/combined_schema_docs.md

• https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf: Timeout
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/reference/_static/jsonschema/nmdc.schema.json: Failed: Cannot find file
• http://insdc.org/country.html: Failed: Network error
• http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups: Failed: Network error
• http://purl.obolibrary.org/obo/ENVO: Failed: Network error
• http://www.cropontology.org/ontology/CO_715/Crop%20Research: Failed: Network error
• http://dmk-brain.ecn.uiowa.edu/pVOGs/: Timeout
• http://purl.obolibrary.org/obo/EO_0007147: Failed: Network error
• http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/: Failed: Network error
• document mapping between NMDC-style GFF3 and schema annotation component nmdc-metadata#184: Failed: Network error 🔒
• https://pypi.org/proje../_static/jsonschema/: Failed: Network error
• http://www.ontobee.org/ontology/GAZ: Timeout
• decide on structure of IDs generated as part of workflows nmdc-metadata#195: Failed: Network error 🔒
• https://gensc.org/mixs: Failed: Network error
• https://github.com/microbiomedata/nmdc-metadata: Failed: Network error 🔒
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/reference/_static/jsonschema/nmdc.context.jsonld: Failed: Cannot find file

Errors in ./docs/reference/metadata/Metadata_Documentation_Overview.md

• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img2.png: Failed: Cannot find file
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img4.png: Failed: Cannot find file
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img3.png: Failed: Cannot find file
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img5.png: Failed: Cannot find file
• https://github.com/microbiomedata/nmdc-metadata: Cached: Error (cached) 🔒
• https://gensc.org/mixs: Cached: Error (cached)
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img6.png: Failed: Cannot find file
• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/_static/images/NMDC_metadata_img1.png: Failed: Cannot find file

Errors in ./docs/reference/metadata/salinity_category.md

• issue-291: Fix schema to match mixs.yaml nmdc-metadata#297: Failed: Network error 🔒

Errors in ./docs/reference/metadata/identifiers.md

• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/reference/metadata/jsonschema/nmdc.context.jsonld: Failed: Cannot find file
• decide on structure of IDs generated as part of workflows nmdc-metadata#195: Cached: Error (cached) 🔒
• document mapping between NMDC-style GFF3 and schema annotation component nmdc-metadata#184: Cached: Error (cached) 🔒

Errors in ./docs/reference/metadata/Biosample.md

• http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups: Failed: Network error
• http://insdc.org/country.html: Failed: Network error

Errors in ./docs/reference/metadata/plant_growth_med.md

• http://purl.obolibrary.org/obo/EO_0007147: Failed: Network error

Errors in ./docs/reference/metadata/geo_loc_name.md

• http://insdc.org/country.html: Failed: Network error

Errors in ./docs/reference/metadata/Environment.md

• http://insdc.org/country.html: Failed: Network error

Errors in ./docs/reference/metadata/NMDC_MIxS_Soil_documentation.md

• http://dmk-brain.ecn.uiowa.edu/pVOGs/: Timeout
• http://purl.obolibrary.org/obo/ENVO: Failed: Network error
• http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/: Cached: Error (cached)
• http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/: Failed: Network error
• http://insdc.org/country.html: Failed: Network error
• https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf: Timeout
• http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups: Failed: Network error
• http://www.ontobee.org/ontology/GAZ: Timeout

Errors in ./docs/explanation/publications.md

• https://www.sciencedirect.com/science/article/pii/S0966842X16000482?via%3Dihub: Failed: Network error
• https://journals.asm.org/doi/10.1128/mSystems.01194-20: Failed: Network error

Errors in ./docs/reference/metadata/types/ExternalIdentifier.md

• file:///home/runner/work/NMDC_documentation/NMDC_documentation/docs/reference/metadata/types/types/Uriorcurie.md: Failed: Cannot find file

Errors in ./docs/reference/data_portal.md

• https://rancher2.spin.nersc.gov/p/c-fwj56:p-nlxq2/workload/deployment:nmdc-dev:worker: Failed: Network error

Errors in ./docs/reference/metadata/README.md

• https://collector.githubapp.com/github-external/browser_event: Failed: Network error
• https://api.github.com/_private/browser/errors: Failed: Network error
• https://api.github.com/_private/browser/stats: Failed: Network error
• https://collector.githubapp.com/github/collect: Failed: Network error
• https://github-cloud.s3.amazonaws.com/: Failed: Network error
• https://user-images.githubusercontent.com/: Failed: Network error
• https://api.github.com/_private/browser/optimizely_client/errors: Failed: Network error
• https://github.com/microbiomedata/nmdc-schema/blob/main/docs/README.md: Failed: Network error
• https://github.com/microbiomedata/nmdc-schema/blob/%7B%7B%20urlEncodedRefName%20%7D%7D/docs/README.md: Failed: Network error

Errors in ./docs/reference/metadata/schema-validation.md

• https://pypi.org/_static/jsonschema/: Failed: Network error

[eecavanna]

Each run takes 1-2 minutes.

Here's a link to information about GitHub Actions "minutes" quotas:

https://docs.github.com/en/billing/managing-billing-for-github-actions/about-billing-for-github-actions#included-storage-and-minutes

[eecavanna]

I think at least some of the file:/// link failures could be fixed by using absolute URLs to those files (e.g. https://example.com/path/to/file.png) instead of relative paths (e.g. ../../file.png). For example, here:

NMDC_documentation/docs/reference/metadata/schema-validation.md

Line 31 in ae70391

The JSON-Schema for NMDC is maintained in this github repo, under [jsonschema/nmdc.schema.json](../../_static/jsonschema/nmdc.schema.json)

That might not be what the authors want when the docs are deployed to a different server, though. With that in mind, I wonder whether lychee (the link checker) can be configured to interpret these particular links differently (e.g. preprocessing them by adding a prefix before checking them).

[eecavanna]

I think the failing https://pypi.org/proje../_static/jsonschema/ hyperlink contains a typo (i.e. a copy/paste error):

NMDC_documentation/docs/reference/metadata/combined_schema_docs.md

Line 1397 in ae70391

There are a variety of json schema validators, these will give the same results. There are web playgrounds for this. But for simplicity we recommend the Python [jsonschema package](https://pypi.org/proje../_static/jsonschema/)