Website file tree contains broken links (35)

[github-actions]

Summary

Status	Count
🔍 Total	828
✅ Successful	765
⏳ Timeouts	0
🔀 Redirected	0
👻 Excluded	28
❓ Unknown	0
🚫 Errors	35

Errors per input

Errors in _build/html/genindex.html

• [404] https://github.com/microbiomedata/docs/blob/main/content/home/src/genindex | Network error: Not Found

Errors in _build/html/workflows/chapters/8_Metatranscriptome_Reads_QC/index.html

• [404] https://portal.nersc.gov/project/m3408//test_data/metaT/SRR11678315.fastq.gz | Network error: Not Found

Errors in _build/html/runtime/admin/index.html

* [404] https://rancher2.spin.nersc.gov/p/c-fwj56:p-nlxq2/secrets/nmdc-runtime-dev:mongo-root-password | Network error: Not Found

Errors in _build/html/workflows/chapters/2_Read_Based_Taxonomy/index.html

• [404] https://portal.nersc.gov/cfs/m3408/test_data/SRR8553641/SRR8553641.fastq.gz | Network error: Not Found

Errors in _build/html/runtime/howto-guides/author-changesheets/index.html

• [404] https://microbiomedata.github.io/nmdc-schema/doi/ | Network error: Not Found

Errors in _build/html/workflows/chapters/4_Metagenome_Assembly/index.html

• [ERROR] https://cab.spbu.ru/software/spades/ | Network error: error sending request for url (https://cab.spbu.ru/software/spades/) Maybe a certificate error?

Errors in _build/html/runtime/howto-guides/release-process/index.html

• [404] https://github.com/microbiomedata/NMDC_documentation/blob/main/decisions/0007-mongo-migration-scripts.md | Network error: Not Found

Errors in _build/html/workflows/chapters/7_Metatranscriptome_Workflow_Overview/index.html

• [404] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315.fastq.gz | Network error: Not Found
• [404] https://pythonhosted.org/gffutils/ | Network error: Not Found

Errors in _build/html/workflows/chapters/6_Metagenome_Assembled_Genome/index.html

• [403] http://www.microbesonline.org/fasttree/FastTree.c | Network error: Forbidden
• [403] https://doi.org/10.1093/bioinformatics/btz848 | Network error: Forbidden
• [403] http://www.microbesonline.org/fasttree/ | Network error: Forbidden

Errors in _build/html/runtime/howto-guides/jobs/gold-translation-etl/index.html

* [ERROR] http://localhost:3000/workspace | Network error: error sending request for url (http://localhost:3000/workspace) Maybe a certificate error?

Errors in _build/html/runtime/howto-guides/update-sensors-ops/index.html

• [404] https://docs.dagster.io/concepts/dagit/dagit | Network error: Not Found
• [404] https://docs.dagster.io/concepts/repositories-workspaces/repositories | Network error: Not Found
• [404] https://docs.dagster.io/concepts/partitions-schedules-sensors/schedules | Network error: Not Found
• [404] https://docs.dagster.io/concepts/repositories-workspaces/workspaces | Network error: Not Found
• [404] https://docs.dagster.io/_apidocs/solids#legacy-solids | Network error: Not Found
• [ERROR] https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/jobs/apply_changesheet/ | Network error: error sending request for url (https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/jobs/apply_changesheet/) Maybe a certificate error?

Errors in _build/html/runtime/tutorials/json/index.html

• [404] https://api.microbiomedata.org/nmdcschema/biosample_set/gold:Gb0115217 | Network error: Not Found

Errors in _build/html/workflows/chapters/1_Metagenome_Workflow_Overview/index.html

• [404] https://portal.nersc.gov/cfs/m3408/test_data/SRR8553641/SRR8553641.fastq.gz | Network error: Not Found

Errors in _build/html/runtime/howto-guides/claim-and-run-jobs/index.html

• [404] https://docs.dagster.io/concepts/repositories-workspaces/repositories | Network error: Not Found

Errors in _build/html/404.html

• [ERROR] file:///_static/pygments.css%3Fv=b86133f3 | Cannot find file
• [ERROR] file:///_static/css/theme.css%3Fv=e59714d7 | Cannot find file
• [ERROR] file:///_static/css/custom.css%3Fv=d4ef3e3c | Cannot find file

Errors in _build/html/workflows/chapters/14_Lipidomics/index.html

• [404] https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst | Network error: Not Found

Errors in _build/html/workflows/chapters/12_Metabolomics/index.html

• [404] https://github.com/microbiomedata/metaMS/blob/master/docs/index.rst | Network error: Not Found

Errors in _build/html/runtime/tutorials/metadata-in/index.html

• [ERROR] https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/sensors/process_workflow_job_triggers | Network error: error sending request for url (https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/sensors/process_workflow_job_triggers) Maybe a certificate error?
• [ERROR] https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/instance/runs | Network error: error sending request for url (https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/instance/runs) Maybe a certificate error?
• [404] https://api.microbiomedata.org/nmdcschema/biosample_set/fake | Network error: Not Found
• [ERROR] https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/jobs/apply_metadata_in/runs | Network error: error sending request for url (https://dagit-readonly.nmdc-runtime-dev.polyneme.xyz/workspace/repo@nmdc_runtime.site.repository:repo/jobs/apply_metadata_in/runs) Maybe a certificate error?
• [ERROR] https://dagit.dev.microbiomedata.org/ | Network error: error sending request for url (https://dagit.dev.microbiomedata.org/) Maybe a certificate error?

Errors in _build/html/runtime/nb/wf_automation/index.html

• [404] https://microbiomedata.github.io/nmdc-schema/Activity/ | Network error: Not Found

Errors in _build/html/workflows/chapters/5_Metagenome_and_Metatranscriptome_Annotation/index.html

• [403] https://journals.asm.org/doi/10.1128/msystems.00804-20 | Network error: Forbidden
• [404] https://portal.nersc.gov/project/m3408//test_data/metaT/SRR11678315.fastq.gz | Network error: Not Found
  Full Github Actions output

[eecavanna]

Next steps

• For the errors under headings that start with "Errors in _build/html/runtime/", create a single ticket in nmdc-runtime listing all those errors
• For the errors under headings that start with "Errors in _build/html/workflows/", create tickets in the respective workflow repos
• Address the errors in the sections that start with "Errors in _build/html/genindex.html" and "Errors in _build/html/404.html"

[eecavanna]

Here's a link to the section of Lychee's documentation about ignoring links: https://lychee.cli.rs/recipes/excluding-links/

We could configure Lychee to ignore localhost:{port} links and password-protected Dagit links, for example.

[eecavanna]

On second thought, I'm not familiar with those Dagit links. Some are on the polyneme domain.