warrenstephens commented on issue #15607:
URL: https://github.com/apache/airflow/issues/15607#issuecomment-875024881
This is from the annotate.py.log. Looks like some sort of bizarre import
error to me.
```
[2021-07-06 16:23:52,806] {scheduler_job.py:182} INFO - Started process
(PID=40) to work on /opt/airflow/dags/annotate.py
[2021-07-06 16:23:52,810] {scheduler_job.py:629} INFO - Processing file
/opt/airflow/dags/annotate.py for tasks to queue
[2021-07-06 16:23:52,828] {logging_mixin.py:104} INFO - [2021-07-06
16:23:52,828] {dagbag.py:448} INFO - Filling up the DagBag from
/opt/airflow/dags/annotate.py
[2021-07-06 16:24:22,863] {logging_mixin.py:104} INFO - [2021-07-06
16:24:22,856] {timeout.py:36} ERROR - Process timed out, PID: 40
[2021-07-06 16:24:22,916] {logging_mixin.py:104} INFO - [2021-07-06
16:24:22,873] {dagbag.py:305} ERROR - Failed to import:
/opt/airflow/dags/annotate.py
Traceback (most recent call last):
File
"/home/airflow/.local/lib/python3.8/site-packages/airflow/models/dagbag.py",
line 302, in _load_modules_from_file
loader.exec_module(new_module)
File "<frozen importlib._bootstrap_external>", line 783, in exec_module
File "<frozen importlib._bootstrap>", line 219, in
_call_with_frames_removed
File "/opt/airflow/dags/annotate.py", line 5, in <module>
from dug_helpers.dug_utils import DugUtil, get_topmed_files,
get_dbgap_files
File "/opt/airflow/dags/dug_helpers/dug_utils.py", line 21, in <module>
from roger.core import Util
File "/opt/airflow/dags/roger/core.py", line 14, in <module>
from bmt import Toolkit
File "/home/airflow/.local/lib/python3.8/site-packages/bmt/__init__.py",
line 1, in <module>
from bmt.toolkit import Toolkit
File "/home/airflow/.local/lib/python3.8/site-packages/bmt/toolkit.py",
line 5, in <module>
from biolinkml.meta import SchemaDefinition, Element, Definition,
ClassDefinition, SlotDefinition
File "/home/airflow/.local/lib/python3.8/site-packages/biolinkml/meta.py",
line 16, in <module>
from biolinkml.utils.metamodelcore import empty_list, empty_dict, bnode
File
"/home/airflow/.local/lib/python3.8/site-packages/biolinkml/utils/metamodelcore.py",
line 9, in <module>
from ShExJSG.ShExJ import IRIREF, PN_PREFIX
File
"/home/airflow/.local/lib/python3.8/site-packages/ShExJSG/__init__.py", line 1,
in <module>
from ShExJSG.SchemaWithContext import Schema
File
"/home/airflow/.local/lib/python3.8/site-packages/ShExJSG/SchemaWithContext.py",
line 3, in <module>
from ShExJSG import ShExJ
File "/home/airflow/.local/lib/python3.8/site-packages/ShExJSG/ShExJ.py",
line 55, in <module>
class PN_PREFIX(jsg.JSGString):
File "/home/airflow/.local/lib/python3.8/site-packages/ShExJSG/ShExJ.py",
line 56, in PN_PREFIX
pattern =
jsg.JSGPattern(r'({PN_CHARS_BASE})((({PN_CHARS})|\.)*({PN_CHARS}))?'.format(PN_CHARS=PN_CHARS.pattern,
PN_CHARS_BASE=PN_CHARS_BASE.pattern))
File
"/home/airflow/.local/lib/python3.8/site-packages/pyjsg/jsglib/jsg_strings.py",
line 18, in __init__
self.pattern_re = re.compile(pattern, flags=re.DOTALL)
File "/usr/local/lib/python3.8/re.py", line 252, in compile
return _compile(pattern, flags)
File "/usr/local/lib/python3.8/re.py", line 304, in _compile
p = sre_compile.compile(pattern, flags)
File "/usr/local/lib/python3.8/sre_compile.py", line 768, in compile
code = _code(p, flags)
File "/usr/local/lib/python3.8/sre_compile.py", line 604, in _code
_compile_info(code, p, flags)
File "/usr/local/lib/python3.8/sre_compile.py", line 590, in _compile_info
charset, hascased = _optimize_charset(charset)
File "/usr/local/lib/python3.8/sre_compile.py", line 312, in
_optimize_charset
charmap[i] = 1
File
"/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/timeout.py",
line 37, in handle_timeout
raise AirflowTaskTimeout(self.error_message)
airflow.exceptions.AirflowTaskTimeout: DagBag import timeout for
/opt/airflow/dags/annotate.py after 30.0s, PID: 40
[2021-07-06 16:24:22,925] {scheduler_job.py:641} WARNING - No viable dags
retrieved from /opt/airflow/dags/annotate.py
[2021-07-06 16:24:23,127] {scheduler_job.py:190} INFO - Processing
/opt/airflow/dags/annotate.py took 30.356 seconds
[2021-07-06 16:24:54,072] {scheduler_job.py:182} INFO - Started process
(PID=50) to work on /opt/airflow/dags/annotate.py
```
--
This is an automated message from the Apache Git Service.
To respond to the message, please log on to GitHub and use the
URL above to go to the specific comment.
To unsubscribe, e-mail: [email protected]
For queries about this service, please contact Infrastructure at:
[email protected]
