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Fix Rqtl paths #845

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Fix Rqtl paths #845

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@pjotrp pjotrp commented May 11, 2024

Sync with gn3 production fix.

pjotrp and others added 14 commits March 2, 2024 17:19
@pjotrp
Disable GNQA "button" for now
1abea13
@pjotrp
Disable GNQA URL
dfcf455
Disable CaseAttributeId - because it needs an update to the database
4539ef0 
and it is not clear why. @bonfacem.
@pjotrp
Merge branch 'testing' into prod
2c122f9
@pjotrp
URL error on result of
42b37bb 
=> https://fallback.genenetwork.org/show_trait?trait_id=5581148&dataset=UMUTAffyExon_0209_RMA

```
      GeneNetwork 2.11-rc2  https://fallback.genenetwork.org/run_mapping (10:01AM UTC Mar 22, 2024)
Traceback (most recent call last):
  File "/gnu/store/a39cgbdawj9vp24nsz9q25sf9g5vda7c-profile/lib/python3.10/site-packages/requests/models.py", line 434, in prepare_url
    scheme, auth, host, port, path, query, fragment = parse_url(url)
  File "/gnu/store/a39cgbdawj9vp24nsz9q25sf9g5vda7c-profile/lib/python3.10/site-packages/urllib3/util/url.py", line 397, in parse_url
    return six.raise_from(LocationParseError(source_url), None)
  File "<string>", line 3, in raise_from
urllib3.exceptions.LocationParseError: Failed to parse: http://localhost:8893api/rqtl/compute
```

The error points out a missing slash in the local URL: http://localhost:8893api/rqtl/compute

Grepping machines we get:

```
gn3-port 8893
("GN3_LOCAL_URL" ,(string-append "http://localhost:" (number->string gn3-port)))
```

On production we set a trailing slash

```
GN3_LOCAL_URL = "http://localhost:8081/"
```

and in the code we mostly see another addition of the slash - except for this particular link. Arguably the slash is not part of the URL prefix (it is part of the path), so I think setting GN3_LOCAL_URL without the trailing slash is preferred. See also

=> https://en.wikipedia.org/wiki/URL
@pjotrp
JOSS logo is defunct
20256eb
@pjotrp
Bump version
2d2c84b
@pjotrp
Bump version
9308493
@pjotrp
Avoid loading fontawesome twice (it is in base) and change button cla…
b850685 
…ss for purescript browser
@pjotrp
Remove JS d3panels package - we are moving that to guix-bioinformatics
dee74b6
@pjotrp
Fix d3panels load path to use Guix
ea9c4f8
@pjotrp
Remove gnqa from global HTML
fd3de3d
@pjotrp
Bump D3 to version 7 for pair scan
56bca57
@pjotrp
Introduce recent D3
95e634c
@robwwilliams
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robwwilliams commented May 11, 2024 via email

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