Closed TBI-YMN closed 5 years ago
michael-kotliar
commented
5 years ago Hi @mina-theragenetex,
Thank you for using cwl-airflow. To help me solve your problem, please check if you have the same error when running airflow initdb command. Also, could you tell me the version of cwl-airflow you use by typing pip show cwl-airflow
TBI-YMN
commented
5 years ago $ airflow initdb [2019-07-04 11:20:09,446] {init.py:45} INFO - Using executor SequentialExecutor DB: sqlite:////Users/mina/airflow/airflow.db [2019-07-04 11:20:09,861] {db.py:312} INFO - Creating tables INFO [alembic.runtime.migration] Context impl SQLiteImpl. INFO [alembic.runtime.migration] Will assume non-transactional DDL. Traceback (most recent call last): File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 348, in _revision_for_ident revision = self._revision_map[resolved_id] KeyError: '939bb1e647c8'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 138, in _catch_revision_errors
yield
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 329, in _upgrade_revs
revs = list(revs)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 641, in _iterate_revisions
requested_lowers = self.get_revisions(lower)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in get_revisions
return sum([self.get_revisions(id_elem) for idelem in id], ())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/miniconda2/envs/cwl-airflow3.6/bin/airflow", line 27, in
$ pip show cwl-airflow Name: cwl-airflow Version: 1.0.16 Summary: Python package to extend Airflow functionality with CWL v1.0 support Home-page: https://github.com/Barski-lab/cwl-airflow Author: Michael Kotliar Author-email: misha.kotliar@gmail.com License: Apache-2.0 Location: /usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages Requires: apache-airflow, uuid, cwltool, jsonmerge Required-by:
michael-kotliar
commented
5 years ago Unfortunately I cannot replicate this error in my version of Python, but I would recommend you to manually drop the Airflow's database and to run cwl-airflow init one more time. The problem seems to be similar to the one mentioned here https://stackoverflow.com/a/32356600/8808721
Also, I would try to run airflow resetdb or airflow upgradedb (please, share the log of these commands). Another options is to install CWL-Airflow not in the Python from Miniconda, but the one that you have in your OS by default. Additionally, you can download DMG file with the latest release of CWL-Airflow and install it as Application. Please note, that the documentation for the latest release is still in progress and may not correspond to the latest changes. Feel free to post here all the issues you have. It will help us to make our program better.
TBI-YMN
commented
5 years ago Thank you
I tried to remove existing db and ~/airflow also
and then I run cwl-airflow init It works!
michael-kotliar
commented
5 years ago Cool! I'm glad I could help you!
Hi
I got error when I typed "cwl-airflow init". I installed today and python version is 3.6.5 on mac os x. please help me.
[2019-07-03 17:51:51,809] {main.py:129} INFO Init Airflow DB Traceback (most recent call last): File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 348, in _revision_for_ident revision = self._revision_map[resolved_id] KeyError: '939bb1e647c8'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 138, in _catch_revision_errors yield File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 329, in _upgrade_revs revs = list(revs) File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 641, in _iterate_revisions requested_lowers = self.get_revisions(lower) File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in get_revisions return sum([self.get_revisions(id_elem) for idelem in id], ()) File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in
return sum([self.get_revisions(id_elem) for idelem in id], ())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 303, in get_revisions
for rev_id in resolved_id)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 303, in
for rev_id in resolved_id)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 358, in _revision_for_ident
resolved_id)
alembic.script.revision.ResolutionError: No such revision or branch '939bb1e647c8'
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/usr/local/miniconda2/envs/cwl-airflow3.6/bin/cwl-airflow", line 10, in
sys.exit(main())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/cwl_airflow/main.py", line 156, in main
args.func(args)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/cwl_airflow/main.py", line 131, in run_init
initdb(argparse.Namespace())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/airflow/bin/cli.py", line 897, in initdb
db_utils.initdb()
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/airflow/utils/db.py", line 103, in initdb
upgradedb()
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/airflow/utils/db.py", line 320, in upgradedb
command.upgrade(config, 'heads')
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/command.py", line 174, in upgrade
script.run_env()
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 416, in run_env
util.load_python_file(self.dir, 'env.py')
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/util/pyfiles.py", line 93, in load_python_file
module = load_module_py(module_id, path)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/util/compat.py", line 68, in load_module_py
module_id, path).load_module(module_id)
File "", line 399, in _check_name_wrapper
File "", line 823, in load_module
File "", line 682, in load_module
File "", line 265, in _load_module_shim
File "", line 684, in _load
File "", line 665, in _load_unlocked
File "", line 678, in exec_module
File "", line 219, in _call_with_frames_removed
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/airflow/migrations/env.py", line 86, in
run_migrations_online()
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/airflow/migrations/env.py", line 81, in run_migrations_online
context.run_migrations()
File "", line 8, in run_migrations
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/runtime/environment.py", line 807, in run_migrations
self.get_context().run_migrations(**kw)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/runtime/migration.py", line 312, in run_migrations
for step in self._migrations_fn(heads, self):
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/command.py", line 163, in upgrade
return script._upgrade_revs(revision, rev)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 333, in _upgrade_revs
for script in reversed(list(revs))
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/contextlib.py", line 99, in exit
self.gen.throw(type, value, traceback)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 169, in _catch_revision_errors
compat.raise_from_cause(util.CommandError(resolution))
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/util/compat.py", line 121, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=exc_value)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/util/compat.py", line 114, in reraise
raise value.with_traceback(tb)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 138, in _catch_revision_errors
yield
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/base.py", line 329, in _upgrade_revs
revs = list(revs)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 641, in _iterate_revisions
requested_lowers = self.get_revisions(lower)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in get_revisions
return sum([self.get_revisions(id_elem) for idelem in id], ())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 298, in
return sum([self.get_revisions(id_elem) for idelem in id], ())
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 303, in get_revisions
for rev_id in resolved_id)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 303, in
for rev_id in resolved_id)
File "/usr/local/miniconda2/envs/cwl-airflow3.6/lib/python3.6/site-packages/alembic/script/revision.py", line 358, in _revision_for_ident
resolved_id)
alembic.util.exc.CommandError: Can't locate revision identified by '939bb1e647c8'