💾 Archived View for thebird.nl › gn-gemtext-threads › issues › rqtl-mapping-throws-JSONDecodeError.g… captured on 2023-01-29 at 03:13:02. Gemini links have been rewritten to link to archived content
-=-=-=-=-=-=-
When we have a deployment problem R/qtl throws this error. It comes from the GN3 API and it means there is some problem with the R code. Obviously GN2 should show a proper error message. Not only that, there should be a hint in the logs and we should test for regressions.
These have been fixed by Zach and Pjotr
Now qtlreaper works. That suggests a problem with R. Zach says there is a problem with the load path in
./genenetwork3/scripts/rqtl_wrapper.R
The current Guix profile is in
export GN2_PROFILE=/home/zas1024/opt/gn-latest-20221206
So we can run a shell
source /home/zas1024/opt/gn-latest-20221206/etc/profile
and test the script with
gn2@tux01:~/production$ Rscript ./genenetwork3/scripts/rqtl_wrapper.R
This works fine, so there is no path problem that I can tell. At least with the load path.
Now, on production we have two flask servers running on port 8081 and 8087. According to production settings the last is used, probably in a tmux. Zach has written
../topics/starting_gn2_and_gn3.gmi
which uses the same startup profile but uses a different port number(!)
After restarting GN3 properly we are getting errors on R/qtl
Fatal error: cannot open file 'None': No such file or directory
[2022-12-23 16:39:30,575] ERROR in app: Exception on /api/rqtl/compute [POST]
Traceback (most recent call last):
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 2077, in wsgi_app
response = self.full_dispatch_request()
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1525, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request
rv = self.dispatch_request()
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1509, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
File "/home/gn2/gn3_production/genenetwork3/gn3/api/rqtl.py", line 55, in compute
rqtl_output['results'] = process_rqtl_mapping(rqtl_cmd.get('output_file'))
File "/home/gn2/gn3_production/genenetwork3/gn3/computations/rqtl.py", line 65, in process_rqtl_mapping
with open(
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/output/d41d8cd98f00b204e9800998ecf8427eLnBwXfCEpZ9SqYsOI0dPtAvGj6hf+TA2Ra7FIrlrT4Pw-output.csv'
Some issues there. First of all, why are we using /tmp? TMPDIR should be set to something that gets cleaned up. It looks like /tmp/output is not created(!?). Trying
mkdir /tmp/output
Gives the same error, suggesting that R has not done its thing.
Another error shows up
[2022-12-23 16:42:14,906] ERROR in app: Exception on /api/search/ [GET]
Traceback (most recent call last):
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 2077, in wsgi_app
response = self.full_dispatch_request()
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1525, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1523, in full_dispatch_request
rv = self.dispatch_request()
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/flask/app.py", line 1509, in dispatch_request
return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
File "/home/gn2/gn3_production/genenetwork3/gn3/api/search.py", line 45, in search_results
with xapian_database(current_app.config["XAPIAN_DB_PATH"]) as db:
File "/gnu/store/qar3sks5fwzm91bl3d3ngyrvxs7ipj5z-python-3.9.9/lib/python3.9/contextlib.py", line 119, in __enter__
return next(self.gen)
File "/home/gn2/gn3_production/genenetwork3/gn3/db_utils.py", line 55, in xapian_database
db = xapian.Database(path)
File "/gnu/store/lj173vcx5w60mzp203x17p7yhcz5ifwx-profile/lib/python3.9/site-packages/xapian/__init__.py", line 8483, in __init__
_xapian.Database_swiginit(self, _xapian.new_Database(*args))
xapian.DatabaseOpeningError: Couldn't stat 'xapian' (No such file or directory)
A test has been added to sheepdog using a POST request. See