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usegalaxy-au / infrastructure

Galaxy Australia's Ansible scripts
MIT License
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use type: swift instead of type: boto3 for nectar_test in object store #2256

Closed cat-bro closed 1 month ago

cat-bro commented 1 month ago

This is trying to be like Galaxy Main's entry here: https://github.com/galaxyproject/usegalaxy-playbook/blob/33fac17ea40efe05a11e68204f1d5f079b5ed775/env/main/group_vars/all/galaxy_config_vars.yml#L181-L203

cat-bro commented 1 month ago 
Traceback (most recent call last):
  File "/Users/cat/dev/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 68, in app_pair
    app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs)
  File "/Users/cat/dev/galaxy/lib/galaxy/app.py", line 698, in __init__
    super().__init__(fsmon=True, **kwargs)
  File "/Users/cat/dev/galaxy/lib/galaxy/app.py", line 550, in __init__
    super().__init__(**kwargs)
  File "/Users/cat/dev/galaxy/lib/galaxy/app.py", line 283, in __init__
    self._configure_object_store(fsmon=True)
  File "/Users/cat/dev/galaxy/lib/galaxy/app.py", line 448, in _configure_object_store
    self.object_store = build_object_store_from_config(self.config, **kwds)
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1651, in build_object_store_from_config
    return objectstore_class(config=config, config_dict=config_dict, **objectstore_constructor_kwds)
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1118, in __init__
    backend = build_object_store_from_config(config, config_dict=backend_def, fsmon=fsmon)
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/__init__.py", line 1651, in build_object_store_from_config
    return objectstore_class(config=config, config_dict=config_dict, **objectstore_constructor_kwds)
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/s3.py", line 190, in __init__
    self._initialize()
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/s3.py", line 210, in _initialize
    self._bucket = self._get_bucket(self.bucket)
  File "/Users/cat/dev/galaxy/lib/galaxy/objectstore/s3.py", line 253, in _get_bucket
    bucket = self.conn.get_bucket(bucket_name)
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/s3/connection.py", line 509, in get_bucket
    return self.head_bucket(bucket_name, headers=headers)
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/s3/connection.py", line 528, in head_bucket
    response = self.make_request('HEAD', bucket_name, headers=headers)
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/s3/connection.py", line 667, in make_request
    return super(S3Connection, self).make_request(
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/connection.py", line 1070, in make_request
    return self._mexe(http_request, sender, override_num_retries,
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/connection.py", line 1030, in _mexe
    raise ex
  File "/Users/cat/dev/galaxy/.venv/lib/python3.10/site-packages/boto/connection.py", line 944, in _mexe
    response = connection.getresponse()
  File "/Users/cat/.pyenv/versions/3.10.5/lib/python3.10/http/client.py", line 1374, in getresponse
    response.begin()
  File "/Users/cat/.pyenv/versions/3.10.5/lib/python3.10/http/client.py", line 318, in begin
    version, status, reason = self._read_status()
  File "/Users/cat/.pyenv/versions/3.10.5/lib/python3.10/http/client.py", line 287, in _read_status
    raise RemoteDisconnected("Remote end closed connection without"
http.client.RemoteDisconnected: Remote end closed connection without response
cat-bro commented 1 month ago

With the above commit this shouldn't break galaxy anymore. I'm trying the data fetch job on the localhost galaxy to see if it will work.