JSONDecodeError
Im trying to process L343252 as calibrator. Im using native installation, since Docker version crashed even earlier (BTW: is udocker required?). I realize Prefacotr CWL is not yet released, but this looks like a real error so maybe it would be good to report it.
As far as I understand my .json file was parsed OK and later something happened.
I attach .json file and full log.pack.zip
30 (function(){return ((JSON.parse(self[0].contents).file));})()
stdout was: ''
stderr was: 'evalmachine.<anonymous>:30
(function(){return ((JSON.parse(self[0].contents).file));})()
^
TypeError: Cannot read properties of undefined (reading 'contents')
at evalmachine.<anonymous>:30:41
at evalmachine.<anonymous>:30:60
at Script.runInContext (node:vm:139:12)
at Script.runInNewContext (node:vm:144:17)
at Object.runInNewContext (node:vm:298:38)
at Socket.<anonymous> ([eval]:11:57)
at Socket.emit (node:events:390:28)
at addChunk (node:internal/streams/readable:324:12)
at readableAddChunk (node:internal/streams/readable:293:11)
at Socket.Readable.push (node:internal/streams/readable:234:10)'
[0m
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/cwltool/sandboxjs.py", line 384, in execjs
return cast(CWLOutputType, json.loads(stdout))
File "/usr/lib/python3.8/json/__init__.py", line 357, in loads
return _default_decoder.decode(s)
File "/usr/lib/python3.8/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/usr/lib/python3.8/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.8/dist-packages/cwltool/expression.py", line 393, in do_eval
return interpolate(
File "/usr/local/lib/python3.8/dist-packages/cwltool/expression.py", line 297, in interpolate
e = evaluator(
File "/usr/local/lib/python3.8/dist-packages/cwltool/expression.py", line 232, in evaluator
return execjs(
File "/usr/local/lib/python3.8/dist-packages/cwltool/sandboxjs.py", line 386, in execjs
raise JavascriptException(
cwltool.sandboxjs.JavascriptException: Expecting value: line 1 column 1 (char 0)
script was:
01 "use strict";
02 var inputs = {
03 "msin": {
04 "class": "Directory",
05 "location": "file:///storage/akurek/N4449_mozaik/3C196/L343252_SB000_uv.dppp.MS",
06 "basename": "L343252_SB000_uv.dppp.MS",
07 "path": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/43msnskv/stg7dd219e3-9b44-4dd7-ade2-a0e71ccae9fa/L343252_SB000_uv.dppp.MS",
08 "dirname": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/43msnskv/stg7dd219e3-9b44-4dd7-ade2-a0e71ccae9fa"
09 },
10 "skymodels": {
11 "class": "Directory",
12 "location": "file:///usr/local/share/prefactor/skymodels",
13 "basename": "skymodels",
14 "path": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/43msnskv/stge8e34d64-ee09-4616-9ed0-9790cf684b36/skymodels",
15 "dirname": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/43msnskv/stge8e34d64-ee09-4616-9ed0-9790cf684b36"
16 },
17 "max_separation_arcmin": 1.0,
18 "skymodels_extension": null
19 };
20 var self = [];
21 var runtime = {
22 "cores": 1,
23 "ram": 256,
24 "tmpdirSize": 1024,
25 "outdirSize": 1024,
26 "exitCode": 1,
27 "tmpdir": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/snuvmw7z",
28 "outdir": "/storage/akurek/N4449_mozaik/L343256_DR2_pref_CWL/tmpdir/pjelbeoi"
29 };
30 (function(){return ((JSON.parse(self[0].contents).file));})()
stdout was: ''
stderr was: 'evalmachine.<anonymous>:30
(function(){return ((JSON.parse(self[0].contents).file));})()
^
TypeError: Cannot read properties of undefined (reading 'contents')
at evalmachine.<anonymous>:30:41
at evalmachine.<anonymous>:30:60
at Script.runInContext (node:vm:139:12)
at Script.runInNewContext (node:vm:144:17)
at Object.runInNewContext (node:vm:298:38)
at Socket.<anonymous> ([eval]:11:57)
at Socket.emit (node:events:390:28)
at addChunk (node:internal/streams/readable:324:12)
at readableAddChunk (node:internal/streams/readable:293:11)
at Socket.Readable.push (node:internal/streams/readable:234:10)'