Check UPPMAX scripts for broken links

[richelbilderbeek]

Your suggestion

Currently, we put our documentation at this website. There, all (hopefully!) links are checked.

However, the tools on UPPMAX may have not been updated.

Check if these tools refer to existing pages.

[richelbilderbeek]

I created the container as decribed at https://docs.uppmax.uu.se/software/create_singularity_container_from_docker_pull/ called lychee.sif (instead of my_container.sif) and put it in /staff/proj/richel.

It works, although these links are not ours:

[richel@rackham3 richel]$ ./lychee.sif /sw/apps/bioinfo/beast2/
  165/165 ━━━━━━━━━━━━━━━━━━━━ Finished extracting links                                                                           Issues found in 12 inputs. Find details below.

[/sw/apps/bioinfo/beast2/2.7.4/rackham/jre/legal/java.xml/xalan.md]:
↻ [ERR] http://www.lotus.com/ | Cached: Error (cached)

[/sw/apps/bioinfo/beast2/2.7.4/rackham/jre/Welcome.html]:
✗ [404] https://docs.azul.com/core/zulu-openjdk/release-notes.html | Failed: Network error: Not Found

[/sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/beasy.html]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/beasystudio.png | Failed: Cannot find file
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/dag.png | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/beasy.html]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/beasystudio.png | Failed: Cannot find file
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/dag.png | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/html/about.html]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/html/images/Bee_2D.jpeg | Failed: Cannot find file
✗ [404] https://commons.wikimedia.org/w/index.php?curid=58241551 | Failed: Network error: Not Found
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/html/style.css | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/html/about.html]:
✗ [404] https://commons.wikimedia.org/w/index.php?curid=58241551 | Failed: Network error: Not Found
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/html/images/Bee_2D.jpeg | Failed: Cannot find file
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.3/rackham/packages/Beasy/doc/html/style.css | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/beasy.html]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/beasystudio.png | Failed: Cannot find file
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/share/beast/2.6/Beasy/doc/dag.png | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.7.4/rackham/packages/lphybeast/README.md]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.7.4/rackham/packages/lphybeast/DEV_NOTE.md | Failed: Cannot find file
✗ [404] https://github.com/LinguaPhylo/linguaPhylo/blob/master/examples/hkyCoalescent.lphy | Failed: Network error: Not Found

[/sw/apps/bioinfo/beast2/2.7.3/rackham/jre/legal/java.xml/xalan.md]:
✗ [ERR] http://www.lotus.com/ | Failed: Network error: error sending request for url (http://www.lotus.com/)

[/sw/apps/bioinfo/beast2/2.7.3/rackham/jre/Welcome.html]:
✗ [404] https://docs.azul.com/core/zulu-openjdk/release-notes.html | Failed: Network error: Not Found

[/sw/apps/bioinfo/beast2/2.7.4/rackham/packages/phylonco/README.md]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.7.4/rackham/packages/phylonco/phylonco-lphybeast/version.xml | Failed: Cannot find file

[/sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/html/about.html]:
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/html/images/Bee_2D.jpeg | Failed: Cannot find file
✗ [ERR] file:///sw/apps/bioinfo/beast2/2.6.2/rackham/packages/Beasy/doc/html/style.css | Failed: Cannot find file
✗ [404] https://commons.wikimedia.org/w/index.php?curid=58241551 | Failed: Network error: Not Found

🔍 165 Total (in 3s) ✅ 127 OK 🚫 22 Errors 💤 16 Excluded
💡 There were issues with GitHub URLs. You could try setting a GitHub token and running lychee again.[richel@rackham3 richel]$ ./lychee.sif /sw/apps/bioinfo/beast2/

[richelbilderbeek]

There we have useful things:

grep -R http /usr/local/bin/ > ~/tmp.txt ; /proj/staff/richel/lychee.sif ~/tmp.txt

grep: /usr/local/bin/quota.sh: Permission denied
  6/6 ━━━━━━━━━━━━━━━━━━━━ Finished extracting links                                                                               Issues found in 1 input. Find details below.

[/home/richel/tmp.txt]:
✗ [404] https://www.uppmax.uu.se/support/user-guides/setting-up-two-factor-authentication/ | Failed: Network error: Not Found
✗ [404] http://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/ | Failed: Network error: Not Found
✗ [400] https://verify.uppmax.uu.se/verify.py?user=%USER%&code=%FACTOR% | Failed: Network error: Bad Request
✗ [ERR] https://docs.uppmax.uu.se/ | Failed: Network error: error sending request for url (https://docs.uppmax.uu.se/)
⧖ [TIMEOUT] http://computer-programming-forum.com/53-perl/74f89dee1a92c3e3.htm | Timeout

[richelbilderbeek]

Contacted @dahlo with the question:

Can I just modify these files and fix their links? It feel weird without version control and without a testing environment to do so ...

[richelbilderbeek]

Contacted him again, we was probably fixing things elsewhere 👍

[richelbilderbeek]

I will make the list of files with broken links, and it will be sent to the sysexperts.