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Evaluate Handbook / website for broken links #1759

Closed sr320 closed 2 months ago

sr320 commented 9 months ago

Should be a program for that...

kubu4 commented 9 months ago

I run a GitHub action on my notebook that checks for broken URLs. However, the output isn't totally clear on which URLs are passing and which are failing, nor which files the URLs are identified from. I'll investigate more to see if there are more options for these and then possibly implement this for the Handbook.

kubu4 commented 9 months ago

Out put from url-checker GitHub action:

🤔 Uh oh... The following urls did not pass:
/github/workspace/docs/bio-Gene-expression.md:
     ❌️ https://robertslab.github.io/sams-notebook/2022/08/10/Splice-Site-Identification-S.namaycush-Liver-Parasitized-and-Non-Parasitized-SRA-RNAseq-Using-Hisat2-Stingtie-with-Genome-GCF_016432855.1.html
     ❌️ https://robertslab.github.io/sams-notebook/2022/09/14/RNAseq-Alignments-P.generosa-Alignments-and-Alternative-Transcript-Identification-Using-Hisat2-and-StringTie-on-Mox.html
/github/workspace/docs/Onboarding.md:
     ❌️ https://environment.uw.edu/students/student-resources/scholarships-funding/student-travel-meeting-fund/
     ❌️ https://environment.uw.edu/students/student-resources/graduate-student-resources/
/github/workspace/docs/mox_Logging-In.md:
     ❌️ http://wiki.hyak.uw.edu/
/github/workspace/docs/bio-Annotation.md:
     ❌️ http://swcarpentry.github.io/shell-novice/01-intro/
     ❌️ https://rest.uniprot.org/uniprotkb/search?compressed=true&
/github/workspace/docs/mox_RStudio-Server.md:
     ❌️ https://cran.rstudio.com/src/contrib/matrixStats_0.61.0.tar.gz
     ❌️ http://localhost:8787
/github/workspace/docs/bio_DNA-methylation.md:
     ❌️ https://rawgit.com/FelixKrueger/Bismark/master/Docs/Bismark_User_Guide.htm
     ❌️ http://felixkrueger.github.io/Bismark/Docs/
/github/workspace/docs/Data-Management.md:
     ❌️ http://gannet.fish.washington.edu/your_folder
     ❌️ https://doi.org/10.7287/peerj.preprints.3183v
/github/workspace/docs/Purchasing-and-Reimbursement.md:
     ❌️ http://128.95.12.98:88/stores/dataSearch.asp
/github/workspace/docs/Lab-Safety.md:
     ❌️ https://cspc.admin.uw.edu/mychem/default.aspx
/github/workspace/docs/DEI-Resources.md:
     ❌️ https://www.washingtonpost.com/local/education/the-science-divide-why-do-latino-and-black-students-leave-stem-majors-at-higher-rates/2019/05/03/e386d318-4b32-11e9-93d0-64dbcf38ba41_story.html
     ❌️ https://www.adventure-journal.com/2020/06/these-orgs-could-use-your-help-to-bring-more-diversity-to-the-outdoors/
     ❌️ https://environment.uw.edu/about/diversity-equity-inclusion/college-diversity-committee/
     ❌️ https://grad.uw.edu/equity-inclusion-and-diversity/programs-resources/for-faculty-and-staff/departmental-diversity-committees/
     ❌️ https://compliance.uw.edu/titleIX
/github/workspace/docs/Lab-Protocols.md:
     ❌️ https://geneseesci.com/shop-online/product-details/923/?product=22-178A
/github/workspace/docs/Pubathon.md:
     ❌️ https://github.com/grace-ac/paper-bitter-crab
     ❌️ https://app.sparkmailapp.com/web-share/loJcna4ywGWcWsnmOZ9L2GGv2-ioeexS6jolWxv-
/github/workspace/docs/bio_Transcriptome-assembly.md:
     ❌️ https://robertslab.github.io/sams-notebook/2020/03/30/Transcriptome-Assembly-C.bairdi-with-MEGAN6-Taxonomy-specific-Reads-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2022/02/07/Transcriptome-Assembly-Genome-guided-C.virginica-Adult-Gonad-OA-RNAseq-Using-Trinity-on-Mox.html
/github/workspace/docs/mox_Adding-a-User.md:
     ❌️ http://wiki.cac.washington.edu/display/hyakusers/Hyak+Account+Creation
/github/workspace/docs/code_Snippets.md:
     ❌️ https://drive.google.com/uc?id=1Yanmb5yBXn-D4b_fzkR2GSxP
/github/workspace/docs/Genomic-Resources.md:
     ❌️ http://onsnetwork.org/kubu4/2018/08/28/transposable-element-mapping-crassostrea-virginica-genome-cvirginica_v300-using-repeatmasker-4-07/
     ❌️ https://robertslab.github.io/sams-notebook/2020/03/31/Transcriptome-Assessment-BUSCO-Metazoa-on-Hematodinium-MEGAN-Transcriptome.html
     ❌️ https://gannet.fish.washington.edu/Atumefaciens/20210308_hemat_trinity_v1.6_v1.7/hemat_transcriptome_v1.6.fasta_trinity_out_dir/hemat_transcriptome_v1.7.fasta
     ❌️ https://robertslab.github.io/sams-notebook/2020/06/05/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v3.1.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/03/30/Transcriptome-Assembly-C.bairdi-with-MEGAN6-Taxonomy-specific-Reads-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/27/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v1.7.html
     ❌️ https://robertslab.github.io/sams-notebook/2021/12/09/Data-Wrangling-C.virginica-NCBI-GCF_002022765.2-GFF-to-Gene-BED-File.html
     ❌️ https://robertslab.github.io/sams-notebook/2019/07/10/Genome-Assessment-BUSCO-Metazoa-on-Pgenerosa_v074-on-Mox.html
     ❌️ http://onsnetwork.org/halfshell/2015/02/27/re-defining-cgigas-canonical-features/
     ❌️ https://gannet.fish.washington.edu/Atumefaciens/20210309_hemat_trinotate_transcriptome-v1.7/20210309.hemat_transcriptome_v1.7.fasta.trinotate.go_annotations.txt
     ❌️ https://robertslab.github.io/sams-notebook/2018/05/08/bs-seq-mapping-olympia-oyster-bisulfite-sequencing-trimgalore-fastqc-bismark.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/09/23/Data-Wrangling-Subsetting-cbai_genome_v1.0-Assembly-with-faidx.html
     ❌️ https://robertslab.github.io/sams-notebook/2021/03/09/Transcriptome-Annotation-Trinotate-Hematodinium-v1.6-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/01/23/Transcriptome-Annotation-C.bairdi-MEGAN-Trinity-Assembly-Using-DIAMOND-BLASTx-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/18/Transcriptome-Assembly-C.bairdi-All-Pooled-RNAseq-Data-Without-Taxonomic-Filters-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/04/08/Transcriptome-Annotation-C.bairdi-MEGAN-Trinity-Assembly-Using-DIAMOND-BLASTx-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2023/01/31/Genome-Indexing-P.verrucosa-v1.0-Assembly-with-HiSat2-on-Mox.html
     ❌️ http:/owl.fish.washington.edu/halfshell/genomic-databank/Olurida_v081_TE-Cg.gff
     ❌️ https://robertslab.github.io/sams-notebook/2019/06/25/Data-Wrangling-FastA-Subsetting-of-Pgenerosa_v070.fa-Using-samtools-faidx.html
     ❌️ http://onsnetwork.org/kubu4/2018/07/03/transposable-element-mapping-olympia-oyster-genome-assembly-olurida_v081-using-repeatmasker-4-07/
     ❌️ https://robertslab.github.io/sams-notebook/2023/02/17/Data-Wrangling-C.goreaui-Genome-GFF-to-GTF-Using-gffread.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/09/17/Genome-Assembly-C.bairdi-cbai_v1.0-Using-All-NanoPore-Data-With-Flye-on-Mox.html
     ❌️ https://owl.fish.washington.edu/halfshell/genomic-databank/cbai_transcriptome_v1.0.fasta.fasta.fai
     ❌️ https://robertslab.github.io/sams-notebook/2020/01/22/Transcriptome-Assembly-Hematodinium-with-MEGAN6-Taxonomy-specific-Reads-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2019/09/28/Genome-Annotation-Pgenerosa_v074-a4-Using-GenSAS.html
     ❌️ https://robertslab.github.io/sams-notebook/2023/01/27/Data-Wrangling-P.verrucosa-Genome-GFF-to-GTF-Using-gffread.html
     ❌️ https://gannet.fish.washington.edu/Atumefaciens/20200331_hemat_diamond_blastx_megan/20200408.hemat.megan.Trinity.fasta.blastx.outfmt6
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/19/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v3.0.html
     ❌️ https://robertslab.github.io/sams-notebook/2022/08/18/Data-Wrangling-Convert-S.namaycush-NCBI-GFF-to-genes-only-BED-file-for-Use-in-Ballgown-Analysis.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/09/24/Assembly-Assessment-BUSCO-C.bairdi-Genome-v1.01-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2021/03/09/Transcriptome-Annotation-Trinotate-Hematodinium-v1.7-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/02/07/Transcriptome-Assessment-BUSCO-Metazoa-on-Hematodinium-MEGAN-Transcriptome.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/04/07/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-MEGAN-Transcriptome.html
     ❌️ https://robertslab.github.io/sams-notebook/2023/05/26/Repeats-Identification-P.meandrina-Using-RepeatMasker-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2023/01/26/Data-Wrangling-P.acuta-Genome-GFF-to-GTF-Conversion-Using-gffread.html
     ❌️ https://robertslab.github.io/sams-notebook/2021/03/08/Transcriptome-Assembly-Hematodinium-Transcriptomes-v1.6-and-v1.7-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/08/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-v2.0-Transcriptome.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/02/Transcriptome-Assembly-C.bairdi-All-RNAseq-Data-Without-Taxonomic-Filters-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2021/03/17/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v4.0-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/08/14/Transcriptome-Annotation-Hematodinium-Transcriptomes-v1.6-v1.7-v2.1-v3.1-with-DIAMOND-BLASTx-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/01/22/Transcriptome-Assembly-C.bairdi-with-MEGAN6-Taxonomy-specific-Reads-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2019/02/21/Data-Management-Create-C.gigas-Bisulfite-Genome-with-Bismark-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/08/14/Transcriptome-Assessment-BUSCO-Metazoa-on-Hematodinium-v1.6-v1.7-v2.1-and-v3.1-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/27/Transcriptome-Assembly-C.bairdi-All-Pooled-Arthropoda-only-RNAseq-Data-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/09/18/Assembly-Assessment-BUSCO-C.bairdi-Genome-v1.0-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2019/11/05/Data-Wrangling-Rename-Pgenerosa_v074-Files-and-Scaffolds.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/06/05/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v2.1.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/03/30/Transcriptome-Assembly-Hematodinium-with-MEGAN6-Taxonomy-specific-Reads-with-Trinity-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2018/09/04/transcriptome-assembly-geoduck-rnaseq-data.html
     ❌️ https://robertslab.github.io/sams-notebook/2019/02/21/Data-Management-Create-C.virginica-Bisulfite-Genome-wit-Bismark-on-Mox.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/05/19/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-Transcriptome-v1.6.html
     ❌️ https://robertslab.github.io/sams-notebook/2023/01/27/Data-Wrangling-M.capitata-Genome-GFF-to-GTF-Using-gffread.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/06/05/Sequence-Extractions-C.bairdi-Transcriptomes-v2.0-and-v3.0-Excluding-Alveolata-with-MEGAN6-on-Swoose.html
     ❌️ https://robertslab.github.io/sams-notebook/2020/02/07/Transcriptome-Assessment-BUSCO-Metazoa-on-C.bairdi-MEGAN-Transcriptome.html
/github/workspace/docs/bio_Basics.md:
     ❌️ http://swcarpentry.github.io/shell-novice/01-intro/
/github/workspace/docs/Lab-Notebooks.md:
     ❌️ https://github.com/shellytrigg
     ❌️ https://shellytrigg.github.io/notebook/
/github/workspace/docs/Code-of-Conduct.md:
     ❌️ http://2012.jsconf.us/#/about
/github/workspace/docs/Lab-Software.md:
     ❌️ http://172.25.149.12:8787
/github/workspace/docs/Publications.md:
     ❌️ http://www.springerlink.com/content/j051782638k7n058/
     ❌️ http://www.springerlink.com/content/u975017n6763324n/
     ❌️ https://10.1093/bfgp/elt054
     ❌️ http://faculty.washington.edu/sr320/wordpress/wp-content/uploads/2012/03/Meztger_JSR.pdf
     ❌️ http://ajpendo.physiology.org/content/292/2/E371.full
     ❌️ http://faculty.washington.edu/sr320/wordpress/wp-content/uploads/2012/07/Thraustochtrid_Lyons.pdf
     ❌️ http://doi.org/10.3389/fmars.2020.56641
     ❌️ http://www.springerlink.com/content/v106205xn62ju541/?MUD=MP
     ❌️ https://dl.dropboxusercontent.com/u/115356/Gavery_Roberts_context2013.pdf
     ❌️ http://fish.washington.edu/research/publications/ms_phd/Metzger_D_MS_Sp12.pdf
     ❌️ http://www.fish.washington.edu/research/genefish/reprints/GCE2004biga.pdf
     ❌️ http://faculty.washington.edu/sr320/wordpress/wp-content/uploads/2012/03/Snapshot-102712-953-AM.png
     ❌️ https://dl.dropboxusercontent.com/u/115356/docs/Storer2013.pdf
     ❌️ http://dx.doi.org/10.6084/m9.figshare.95828
     ❌️ http://www.nwfsc.noaa.gov/assets/2/7809_08032011_103552_Moser.and.Roberts.1999-rev.pdf
     ❌️ http://www.springerlink.com/content/435447rxg52h7152/
     ❌️ http://c43[1376](https://github.com/RobertsLab/resources/actions/runs/7183597204/job/19562733032#step:4:1377).r76.cf2.rackcdn.com/19155/fphys-02-00116-HTML/image_m/fphys-02-00116-g002.jpg
/github/workspace/docs/External-Communication-and-Funding.md:
     ❌️ https://environment.uw.edu/students/student-resources/scholarships-funding/student-travel-meeting-fund/
     ❌️ https://pcsga.org/events/list/
     ❌️ https://grad.uw.edu/graduate-student-funding/funding-information-for-departments/awards-and-funding-resources/graduate-student-conference-travel-awards/
kubu4 commented 9 months ago

lab-website

/github/workspace/posts/sr320-spencer-paper/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/frontpage/sr320-DM/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/frontpage/sr320-george-paper/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/frontpage/sr320-fhl/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/frontpage/sr320-marineomics/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/mytilus-genome/index.qmd:
     ❌️ https://robertslab.info
/github/workspace/posts/cool-paper/index.qmd:
     ❌️ https://github.com/sr320/paper-oly-mbdbs-gen/blob/master/oly-epigen-gen-cover-letter.pdf
/github/workspace/posts/aquamine/index.qmd:
     ❌️ https://robertslab.info
kubu4 commented 9 months ago

I've updated a bunch of URLs in resources. If anyone wants to work on this, they should probably go to the repo and then select the "Actions" tab to view the output of the most recent run to see what's still broken (i.e. don't rely on what's pasted in this issue).