diff options
| -rw-r--r-- | issues/rqtl-mapping-throws-JSONDecodeError.gmi | 102 | ||||
| -rw-r--r-- | topics/starting_gn2_and_gn3.gmi | 19 |
2 files changed, 119 insertions, 2 deletions
diff --git a/issues/rqtl-mapping-throws-JSONDecodeError.gmi b/issues/rqtl-mapping-throws-JSONDecodeError.gmi new file mode 100644 index 0000000..8eb4cc6 --- /dev/null +++ b/issues/rqtl-mapping-throws-JSONDecodeError.gmi @@ -0,0 +1,102 @@ +# R/qtl JSONDecodeError + +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. + +* [ ] Give informative message +* [ ] Log in error log +* [X] Add test regressions + +## Info + +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(!) + +## GN3 + +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 + +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) +``` + +## Test regression + +A test has been added to sheepdog using a POST request. See + +=> ../topics/testing/using-curl.gmi diff --git a/topics/starting_gn2_and_gn3.gmi b/topics/starting_gn2_and_gn3.gmi index d0065e4..2ce6aed 100644 --- a/topics/starting_gn2_and_gn3.gmi +++ b/topics/starting_gn2_and_gn3.gmi @@ -12,7 +12,9 @@ See also GN2 depends on GN3 for REST services and libraries. -1. Set PATH/PYTHONPATH/GN2_PROFILE environment variables +## Environment + +Set PATH/PYTHONPATH/GN2_PROFILE environment variables Example: @@ -22,12 +24,25 @@ export PATH=$GN2_PROFILE/bin:$PATH export PYTHONPATH="$GN2_PROFILE/lib/python3.9/site-packages" ``` -2. Start GN3 from the relevant directory (in this case production +## Start development on port 8081 + +Start GN3 from the relevant directory ``` env FLASK_DEBUG=1 FLASK_APP="main.py" CORS_ORIGINS="http://gn2-zach.genenetwork.org:*,https://gn2-zach.genenetwork.org:*,http://genenetwork.org:*,https://genenetwork.org:*" flask run --port=8081 ``` +## Start production on port 8087 + +``` +gn2@tux01: +cd ~/gn3_production/genenetwork3 +gunicorn --bind 0.0.0.0:8087 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app +``` + +Note I had to comment out some oauth stuff on the latest. + + # GN2 1. Just run /home/gn2/production/run_production.sh |