🧐 Detects working links as not working for danielecook/Awesome-Bioinformatics

[tgotwig]

Hello there 🙋‍♂️

This Action doesn't work very well with https://github.com/TGotwig/Awesome-Bioinformatics/tree/patch-2

The output is sometimes quite random from run to run and has always working links showing as not working 🤔

 ERROR: 25 dead links found!
[✖] http://nextflow.io → Status: 0
[✖] https://software.broadinstitute.org/gatk → Status: 403
[✖] https://github.com/arq5x/bedtools2 → Status: 429
[✖] https://github.com/adamewing/bamsurgeon → Status: 429
[✖] https://github.com/lh3/wgsim → Status: 429
[✖] https://github.com/teamdfir/sift → Status: 429
[✖] https://github.com/pcingola/SnpEff → Status: 429
[✖] https://github.com/brentp/cruzdb → Status: 429
[✖] https://github.com/openvax/pyensembl → Status: 429
[✖] https://github.com/cokelaer/bioservices → Status: 429
[✖] https://github.com/arq5x/cyvcf → Status: 429
[✖] https://github.com/jamescasbon/PyVCF → Status: 429
[✖] https://github.com/brentp/cyvcf2 → Status: 429
[✖] https://github.com/daler/pybedtools → Status: 429
[✖] https://github.com/arq5x/bedtools → Status: 429
[✖] https://github.com/mdshw5/pyfaidx → Status: 429
[✖] https://github.com/pysam-developers/pysam → Status: 429
[✖] https://github.com/Lab41/squiggle → Status: 429
[✖] https://github.com/dasmoth/dalliance → Status: 429
[✖] https://github.com/biojs/biojs → Status: 429
[✖] http://biojs.net/ → Status: 0
[✖] https://github.com/jonathancrabtree/Circleator → Status: 429
[✖] https://github.com/drio/dnaism → Status: 429
[✖] https://github.com/igvteam/igv → Status: 429
[✖] http://watson.nci.nih.gov/cran_mirror/web/packages/RCircos/index.html → Status: 0

What it should look like:

 ERROR: 2 dead links found!
[✖] http://biojs.net/ → Status: 522
[✖] http://watson.nci.nih.gov/cran_mirror/web/packages/RCircos/index.html → Status: 

[gaurav-nelson]

Thanks @TGotwig GitHub (and some other sites) return a Status: 429: Too Many Requests

To fix this, just accept the status 429 as alive, use the config-file option and specify the following in your mlc_config.json file:

{
  "aliveStatusCodes":[200, 206, 429]
}

[gaurav-nelson]

@TGotwig before you try that, just re-run the check again, I've updated the markdown-link-check dependency to the latest version and that might resolve the issue. Please confirm if it does, otherwise try the solution in my previous comment. :+1:

[tgotwig]

Ahh yeah makes sense!

So now I still get:

ERROR: 4 dead links found!
[✖] http://nextflow.io → Status: 0
[✖] https://software.broadinstitute.org/gatk → Status: 403
[✖] http://biojs.net/ → Status: 0
[✖] http://watson.nci.nih.gov/cran_mirror/web/packages/RCircos/index.html → Status: 0

Hmm the first two are working fine 🤔

[gaurav-nelson]

@TGotwig looks correct to me.

• :x: https://www.isitdownrightnow.com/nextflow.io.html (Seems down)
• ¯\(ツ)/¯ https://software.broadinstitute.org/gatk sometimes failed and sometimes sent me to https://gatk.broadinstitute.org/hc/en-us
• :x: https://www.isitdownrightnow.com/biojs.net.html
• :x: http://watson.nci.nih.gov/cran_mirror/web/packages/RCircos/index.html

[tgotwig]

This gif proves that the first two are working 🧐 But yeah sometimes the second one loads very slow 🐌

[gaurav-nelson]

Thanks @TGotwig for the GIF. I still can't reach out to http://nextflow.io. Maybe ignore these domains if you think they are working.

{
    "ignorePatterns": [
        {
            "pattern": "^http://nextflow.io",
            "pattern": ".*(broadinstitute.org).*"
        }
    ]
}

[tgotwig]

Hmm maybe this is country specific or so, thanks for the tip with ignorePatterns 👍

[tgotwig]

Because of ignorePatterns, why are there two keys with the same name pattern? Wouldn't it be better when passing raw strings into ignorePatterns?

With that I still get:

ERROR: 3 dead links found!
[✖] http://nextflow.io → Status: 0
[✖] http://biojs.net/ → Status: 0
[✖] http://watson.nci.nih.gov/cran_mirror/web/packages/RCircos/index.html → Status: 0

[gaurav-nelson]

PS: https://github.com/gaurav-nelson/github-action-markdown-link-check#too-many-requests

Its an issue with the underlying library.