Website file tree contains broken links

[github-actions]

Summary

Status	Count
🔍 Total	828
✅ Successful	685
⏳ Timeouts	0
🔀 Redirected	0
👻 Excluded	28
❓ Unknown	0
🚫 Errors	115

Errors per input

Errors in _build/html/runtime-docs-as-html/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?

👉 This is a false positive. This web page is a rendered version of this Python notebook. The author of the notebook is instructing the reader to start up a server locally and then visit that localhost URL.

Errors in _build/html/home-docs-as-html/404.html

• [ERROR] file:///howto_guides/portal_guide.html | Cannot find file
• [ERROR] file:///_static/favicon.ico | Cannot find file
• [ERROR] file:///explanation/community_conversations.html | Cannot find file
• [ERROR] file:///_static/css/theme.css%3Fv=e59714d7 | Cannot find file
• [ERROR] file:///runtime.html | Cannot find file
• [ERROR] file:///reference/data_portal.html | Cannot find file
• [ERROR] file:///tutorials/run_workflows.html | Cannot find file
• [ERROR] file:///genindex.html | Cannot find file
• [ERROR] file:///_static/pygments.css%3Fv=b86133f3 | Cannot find file
• [ERROR] file:///explanation/fair_data.html | Cannot find file
• [ERROR] file:///_static/css/custom.css%3Fv=d4ef3e3c | Cannot find file
• [ERROR] file:///howto_guides/globus.html | Cannot find file
• [ERROR] file:///index.html | Cannot find file
• [ERROR] file:///search.html | Cannot find file
• [ERROR] file:///_static/nmdc-logo-bg-white.png | Cannot find file
• [ERROR] file:///howto_guides/data_plan.html | Cannot find file
• [ERROR] file:///tutorials/submission_portal.html | Cannot find file
• [ERROR] file:///howto_guides/submit2nmdc.html | Cannot find file
• [ERROR] file:///howto_guides/api_gui.html | Cannot find file
• [ERROR] file:///workflows.html | Cannot find file
• [ERROR] file:///tutorials/nav_data_portal.html | Cannot find file
• [ERROR] file:///howto_guides/run_workflows.html | Cannot find file

Errors in _build/html/runtime-docs-as-html/tutorials/json/index.html

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

Errors in _build/html/runtime-docs-as-html/nb/wf_automation/index.html

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

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

• [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/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/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?
• [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?

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

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

Errors in _build/html/runtime-docs-as-html/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/workflow-docs-as-html/chapters/5_Metagenome_and_Metatranscriptome_Annotation/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/readsqc_output/SRR11678315-int-0.1_filtered.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/annotation_output/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/assembly_output/SRR11678315-int-0.1_contigs.fna | Network error: Service Unavailable
• [403] https://journals.asm.org/doi/10.1128/msystems.00804-20 | Network error: Forbidden
• [503] https://portal.nersc.gov/project/m3408//test_data/metaT/SRR11678315.fastq.gz | Network error: Service Unavailable

Errors in _build/html/home-docs-as-html/howto_guides/run_workflows.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int-0.1.fastq.gz | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/6_Metagenome_Assembled_Genome/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaMAGs_test_dataset.tgz | Network error: Service Unavailable
• [403] https://doi.org/10.1093/bioinformatics/btz848 | Network error: Forbidden

Errors in _build/html/runtime-docs-as-html/404.html

• [ERROR] file:///runtime/nb/api_access_via_python | Cannot find file
• [ERROR] file:///runtime | Cannot find file
• [ERROR] file:///runtime/howto-guides/improving-search-api | Cannot find file
• [ERROR] file:///runtime/howto-guides/update-sensors-ops | Cannot find file
• [ERROR] file:///runtime/admin | Cannot find file
• [ERROR] file:///runtime/stylesheets/extra.css | Cannot find file
• [ERROR] file:///runtime/assets/stylesheets/palette.06af60db.min.css | Cannot find file
• [ERROR] file:///runtime/nb/get_data | Cannot find file
• [ERROR] file:///runtime/tutorials/metadata-in | Cannot find file
• [ERROR] file:///runtime/howto-guides/claim-and-run-jobs | Cannot find file
• [ERROR] file:///runtime/nb/queue_and_trigger_data_jobs | Cannot find file
• [ERROR] file:///runtime/howto-guides/jobs/gold-translation-etl | Cannot find file
• [ERROR] file:///runtime/nb/wf_automation | Cannot find file
• [ERROR] file:///runtime/howto-guides/release-process | Cannot find file
• [ERROR] file:///runtime/assets/images/favicon.ico | Cannot find file
• [ERROR] file:///runtime/assets/stylesheets/main.a40c8224.min.css | Cannot find file
• [ERROR] file:///runtime/howto-guides/author-changesheets | Cannot find file
• [ERROR] file:///runtime/explanation/journeys | Cannot find file
• [ERROR] file:///runtime/tutorials/json | Cannot find file
• [ERROR] file:///runtime/tutorials/translators | Cannot find file
• [ERROR] file:///runtime/explanation/identifiers | Cannot find file
• [ERROR] file:///runtime/contributing-docs | Cannot find file
• [ERROR] file:///runtime/howto-guides/create-triggers | Cannot find file
• [ERROR] file:///runtime/tutorials/exporters | Cannot find file
• [ERROR] file:///runtime/tutorials/auth | Cannot find file

Errors in _build/html/home-docs-as-html/tutorials/run_workflows.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int-0.1.fastq.gz | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/1_Metagenome_Workflow_Overview/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR8553641/SRR8553641.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_1.fastq.gz | Network error: Service Unavailable

Errors in _build/html/runtime-docs-as-html/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/partitions-schedules-sensors/schedules | Network error: Not Found
• [404] https://docs.dagster.io/concepts/repositories-workspaces/repositories | Network error: Not Found
• [404] https://docs.dagster.io/_apidocs/solids#legacy-solids | Network error: Not Found
• [404] https://docs.dagster.io/concepts/repositories-workspaces/workspaces | 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/home-docs-as-html/genindex.html

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

Errors in _build/html/workflow-docs-as-html/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/workflow-docs-as-html/chapters/10_Metatranscriptome_Expression/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/readcounts_output/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/annotation_output/SRR11678315-int-0.1_functional_annotation.gff | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/assembly_output/SRR11678315-int-0.1_pairedMapped_sorted.bam | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/annotation_output/SRR11678315-int-0.1_contig_names_mapping.tsv | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/2_Read_Based_Taxonomy/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR8553641/SRR8553641.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_1.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_2.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int-0.1.fastq.gz | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/3_Metagenome_Reads_QC/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int-0.1.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_1.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/ReadsQC_small_test_data.tgz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR13128014.pacbio.subsample.ccs.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_2.fastq.gz | Network error: Service Unavailable

Errors in _build/html/runtime-docs-as-html/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/workflow-docs-as-html/chapters/7_Metatranscriptome_Workflow_Overview/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/ | Network error: Service Unavailable
• [404] https://pythonhosted.org/gffutils/ | Network error: Not Found
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678313.fastq.gz | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/9_Metatranscriptome_Assembly/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/SRR11678315.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/readsqc_output/SRR11678315-int-0.1_filtered.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/assembly_output/ | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/8_Metatranscriptome_Reads_QC/index.html

• [503] https://portal.nersc.gov/project/m3408//test_data/metaT/SRR11678315.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315/readsqc_output/ | Network error: Service Unavailable

Errors in _build/html/workflow-docs-as-html/chapters/4_Metagenome_Assembly/index.html

• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaAssembly_small_test_data.tgz | Network error: Service Unavailable
• [ERROR] https://cab.spbu.ru/software/spades/ | Network error: error sending request for url (https://cab.spbu.ru/software/spades/) Maybe a certificate error?
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR13128014.pacbio.subsample.ccs.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884_1.fastq.gz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/ | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/metaAssembly_large_test_data.tgz | Network error: Service Unavailable
• [503] https://portal.nersc.gov/cfs/m3408/test_data/SRR7877884/SRR7877884-int.fastq.gz | Network error: Service Unavailable
  Full Github Actions output

[eecavanna]

Some of these may be false positives (TBD).

[eecavanna]

Also, CFS is down this week, which may be affecting links to NERSC-hosted files.

[eecavanna]

The "Error 404" pages that are dynamically generated by some Sphinx plugin, contain some problematic links; for example:

[ERROR] file:///howto_guides/portal_guide.html | Cannot find file

[eecavanna]

There are, indeed, some broken HTTP links in the list; for example:

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

[eecavanna]

Replaced by #186