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japonicusdb / japonicus-config

Configuration for JaponicusDB
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Fix broken links in JaponicusDB documentation #92

Closed kimrutherford closed 1 year ago

kimrutherford commented 2 years ago

Found with:

./etc/check_docs_broken_links.pl japonicus-config/japonicus_site_config.json src/docs src/assets

Mostly left over pombe stuff.

Examples:

src/docs/community/index.md:3:  community/fission-yeast-community-curation-project
   - [Community curation project](community/fission-yeast-community-curation-project), including the old *S. pombe* [pilot project](community/fission-yeast-community-curation-pilot-project)

src/docs/datasets/index.md:37:  faq/how-can-i-find-s.-pombe-ortholog-s-human-gene
   [Orthologs](${base_url}/data/orthologs/)|Manually curated ortholog sets for [human](/faq/how-can-i-find-s.-pombe-ortholog-s-human-gene) and [*S. cerevisiae*](faq/how-can-i-search-s.-cerevisiae-ortholog-s-homolog-s-s.-pombe-gene); also see [documentation](/documentation/orthologs) 

src/docs/faq/how-can-i-use-artemis-to-browse-the-genome.JaponicusDB.md:22:  faq/can-i-generate-comprehensive-restriction-enzyme-map-genome-pombase
       "[restriction enzyme map](/faq/can-i-generate-comprehensive-restriction-enzyme-map-genome-pombase)" FAQ)

src/docs/faq/how-can-i-find-all-of-the-genes-that-have-a-given-mutant-phenotype.md:23:  faq/can-i-get-list-essential-pombe-genes
   Also see the FAQ on [finding essential genes](/faq/can-i-get-list-essential-pombe-genes).

src/docs/faq/how-can-i-search-for-the-s-cerevisiae-ortholog-s-homolog-s-of-an-s-pombe-gene.md:18:  faq/how-do-i-receive-updates-list-s.-cerevisiae-and-s.-pombe-orthologs
   Also see the [FAQ on downloading the full set of orthologs](/faq/how-do-i-receive-updates-list-s.-cerevisiae-and-s.-pombe-orthologs).

src/docs/faq/how-can-i-find-protein-localization-data.md:25:  faq/there-list-protein-complexes-s.-pombe-and-their-subunits
   [FAQ](faq/there-list-protein-complexes-s.-pombe-and-their-subunits)).

src/docs/faq/can-i-download-all-s-pombe-phenotype-data.md:11:  faq/can-i-get-list-essential-pombe-genes
   [essential genes FAQ](/faq/can-i-get-list-essential-pombe-genes).

src/docs/faq/can-i-get-a-file-with-a-specific-set-of-genome-features.md:12:  faq/can-i-access-pombase-via-api
   "[Can I access ${database_name} via an API?](/faq/can-i-access-pombase-via-api)"
kimrutherford commented 1 year ago

I've fixed all those problems and the link checking script is now run for the japonicus docs on each push to GitHub.