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galaxyproject / pulsar

Distributed job execution application built for Galaxy
https://pulsar.readthedocs.io
Apache License 2.0
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[WIP] Restrict tests to get some output. #308

Closed jmchilton closed 1 year ago

jmchilton commented 1 year ago

Ahhh... yeah... that sort of makes sense as a culprit at least!

galaxy.jobs.runners DEBUG 2022-10-04 13:23:04,187 [pN:main,p:2484,tN:PulsarJobRunner.work_thread-3] execution of external set_meta for job 3 finished
galaxy.jobs ERROR 2022-10-04 13:23:04,188 [pN:main,p:2484,tN:PulsarJobRunner.work_thread-3] problem importing job outputs. stdout [] stderr []
Traceback (most recent call last):
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/__init__.py", line 1811, in finish
    tag_handler=self.app.tag_handler.create_tag_handler_session(),
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/model/store/__init__.py", line 1230, in get_import_model_store_for_directory
    f"Could not find import model store for directory [{archive_dir}] (full path [{os.path.abspath(archive_dir)}])"
Exception: Could not find import model store for directory [/tmp/tmp2ogmvj7n/tmpey17f16k/tmpuzzcovtu/database/job_working_directory_kfjv0wzj/000/3/metadata/outputs_populated] (full path [/tmp/tmp2ogmvj7n/tmpey17f16k/tmpuzzcovtu/database/job_working_directory_kfjv0wzj/000/3/metadata/outputs_populated])
galaxy.jobs.runners.pulsar ERROR 2022-10-04 13:23:04,191 [pN:main,p:2484,tN:PulsarJobRunner.work_thread-3] Job wrapper finish method failed
Traceback (most recent call last):
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 663, in finish_job
    job_metrics_directory=job_metrics_directory,
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/__init__.py", line 1811, in finish
    tag_handler=self.app.tag_handler.create_tag_handler_session(),
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/model/store/__init__.py", line 1230, in get_import_model_store_for_directory
    f"Could not find import model store for directory [{archive_dir}] (full path [{os.path.abspath(archive_dir)}])"
Exception: Could not find import model store for directory [/tmp/tmp2ogmvj7n/tmpey17f16k/tmpuzzcovtu/database/job_working_directory_kfjv0wzj/000/3/metadata/outputs_populated] (full path [/tmp/tmp2ogmvj7n/tmpey17f16k/tmpuzzcovtu/database/job_working_directory_kfjv0wzj/000/3/metadata/outputs_populated])
INFO:     127.0.0.1:50214 - "GET /api/jobs/d9abeb[986](https://github.com/galaxyproject/pulsar/actions/runs/3182415169/jobs/5188326790#step:8:987)49a6a7e HTTP/1.1" 200 OK
INFO:     127.0.0.1:50224 - "GET /api/jobs/d9abeb98649a6a7e HTTP/1.1" 200 OK
INFO:     127.0.0.1:50234 - "GET /api/jobs/d9abeb98649a6a7e?full=true HTTP/1.1" 200 OK
INFO:     127.0.0.1:50248 - "GET /api/jobs/d9abeb98649a6a7e?full=true HTTP/1.1" 200 OK
INFO:     127.0.0.1:50264 - "GET /api/jobs/d9abeb98649a6a7e HTTP/1.1" 200 OK
INFO:     127.0.0.1:50272 - "GET /api/jobs/d9abeb98649a6a7e?full=true HTTP/1.1" 200 OK
----------------------------- Captured stderr call -----------------------------
WARNING:galaxy.metadata.set_metadata:Failed to find tool_stdout or tool_stderr for this job, cannot collect metadata. Working dir contents [['metadata', 'inputs', 'working', 'outputs']], output directory contents [[]]
Traceback (most recent call last):
  File "metadata/set.py", line 1, in <module>
    from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/metadata/set_metadata.py", line 130, in set_metadata
    set_metadata_portable()
  File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/metadata/set_metadata.py", line 247, in set_metadata_portable
    raise Exception(error_desc)
Exception: Failed to find tool_stdout or tool_stderr for this job, cannot collect metadata
mvdbeek commented 1 year ago

I assume we don't need this anymore