diff options
| -rw-r--r-- | issues/systems/fallback-errors.gmi | 76 | ||||
| -rw-r--r-- | topics/guix/guix-system-containers-and-how-we-use-them.gmi | 6 |
2 files changed, 81 insertions, 1 deletions
diff --git a/issues/systems/fallback-errors.gmi b/issues/systems/fallback-errors.gmi index 5dca461..dc424fb 100644 --- a/issues/systems/fallback-errors.gmi +++ b/issues/systems/fallback-errors.gmi @@ -19,6 +19,7 @@ Note that some issues may be related to produciton (i.e. the same). * [X] 502 timeout errors * [ ] Rqtl2 not working * [ ] 413 error +* [ ] Monitor service - both systemd and sheepdog ## 502 timeout errors @@ -39,10 +40,83 @@ Traceback (most recent call last): 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 + +# R/qtl JSONDecodeError + +After adding the slash to GN3 URLs (see above) led to the next error: + +``` +simplejson.errors.JSONDecodeError: Expecting value: line 1 column 1 (char 0) +``` + +This looks similar to the earlier documented + +=> ../rqtl-mapping-throws-JSONDecodeError +suggesting a missing path for R. In the container log GN3 actually gives the error + +``` +2024-03-24 08:02:24 return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args) +2024-03-24 08:02:24 File "/gnu/store/yi76sybwqql4ky60yahv91z57srb2fr0-profile/lib/python3.10/site-packages/gn3/api/rqtl.py", line 25, in compute +2024-03-24 08:02:24 raise FileNotFoundError +2024-03-24 08:02:24 FileNotFoundError +``` + +Now two things are bad here becuase there is no context other than the error lines! For FileNotFound pass in the filename as suggested here: + +=> https://stackoverflow.com/questions/36077266/how-do-i-raise-a-filenotfounderror-properly + +Patched in + +=> https://github.com/genenetwork/genenetwork3/commit/b615df8c65d4fb6c8f08cf653e920c360c136552 + +That should help clarify the missing path or file. + +``` + File "/export/source/fallback-debug/genenetwork3/gn3/fs_helpers.py", line 21, in assert_paths_exist + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path) +FileNotFoundError: [Errno 2] No such file or directory: '/tmp/gn2/83f0831af5911ab6dc62cbbd37d13741.csv' ``` -Gemma works though +So, GN2 is miscommunicating the path to GN3. + +This also led to documenting how one should test GN2 and GN3 in a running VM: + +=> /topics/guix/guix-system-containers-and-how-we-use-them.gmi + +## QTLReaper showing font problem + +Try HK on + +=> https://fallback.genenetwork.org/show_trait?trait_id=5581148&dataset=UMUTAffyExon_0209_RMA + +``` + File "/gnu/store/hvv0r5nzhbbsnd9s68cmx5q0sznjhnrp-profile/lib/python3.10/site-packages/PIL/ImageFont.py", line 956, in freetype + return FreeTypeFont(font, size, index, encoding, layout_engine) + File "/gnu/store/hvv0r5nzhbbsnd9s68cmx5q0sznjhnrp-profile/lib/python3.10/site-packages/PIL/ImageFont.py", line 247, in __init__ + self.font = core.getfont( +OSError: cannot open resource +``` ## 413 Request Entity Too Large diff --git a/topics/guix/guix-system-containers-and-how-we-use-them.gmi b/topics/guix/guix-system-containers-and-how-we-use-them.gmi index f9d7253..0ceac71 100644 --- a/topics/guix/guix-system-containers-and-how-we-use-them.gmi +++ b/topics/guix/guix-system-containers-and-how-we-use-them.gmi @@ -101,3 +101,9 @@ Probably worth reading the Here we focus on the production server setup running on test01: => https://git.genenetwork.org/gn-machines/tree/production.scm + +# Debugging and development + +See + +=> /topics/systems/debug-and-developing-code-with-genenetwork-system-container |