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8337 Commits
Author SHA1 Message Date
Nicola Soranzo e5f0a8c4eb Merge branch 'release_24.0' into release_24.1 2024-12-10 10:51:03 +00:00
mvdbeek 2d7667d958 Add regression test for #18927 2024-11-27 18:34:41 +01:00
mvdbeek 974d7e58bf Tighten conversion target input 
This way we test that conversion to txt occurs via fasta, not the fasta
to tabular converter.
 2024-11-19 17:33:58 +01:00
mvdbeek a42496e8ec Disable locking when opening h5 files, add missing with 2024-10-12 09:26:54 +02:00
mvdbeek b5d46aa943 Test workflow module building with dynamic parameters 
and parameter references and validators.
 2024-09-30 13:48:03 +02:00
mvdbeek 69a3cda018 Fix history import when parent_hda not serialized 
and make sure we include the parent_hda when exporting histories.
Fixes
https://sentry.galaxyproject.org/share/issue/20ee27f675ef476588bbe8ff273eaee7/:
```
KeyError: '31e7840b5aedca43523bfcc8e2e9e56f'
  File "galaxy/jobs/__init__.py", line 2039, in finish
    task_wrapper = self.tool.exec_after_process(
  File "galaxy/tools/__init__.py", line 3100, in exec_after_process
    JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job()
  File "galaxy/tools/imp_exp/__init__.py", line 81, in cleanup_after_job
    model_store.perform_import(new_history, job=job, new_history=True)
  File "galaxy/model/store/__init__.py", line 416, in perform_import
    self._import_implicit_dataset_conversions(object_import_tracker)
  File "galaxy/model/store/__init__.py", line 1280, in _import_implicit_dataset_conversions
    idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]]
```
 2024-09-23 11:07:20 +02:00
mvdbeek 2bbae08220 Merge branch 'release_24.0' into release_24.1 2024-09-20 08:27:18 +02:00
mvdbeek e1d6c93a21 Fix discovered outputs with directory metadata and distributed object 
stores

The problem is that `object_store.is_private` would check in which
object store the dataset is stored, and that fails if we haven't written
to the object store yet (which is why extended metadata is a
workaround).

Fixes https://github.com/galaxyproject/galaxy/issues/17208
 2024-09-19 19:51:51 +02:00
John Davis 4a85cb3280 Merge pull request #18775 from bernt-matthias/topic/quota-desctiption-update 
[24.1] Allow to change only the description of a quota
 2024-09-19 09:48:27 -04:00
M BerntandMarius van den Beek fc9d2f1dc7 remove assert 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-09-19 09:39:08 +02:00
Matthias Bernt 1d9a61132c add test for updating quota description 2024-09-19 09:39:08 +02:00
mvdbeek 64e74b8b48 Tighten TRS url check 
Fixes
https://sentry.galaxyproject.org/share/issue/5b8d495edd6545278d4d93d0ed69ac3a/:
```
Message
Uncaught exception in exposed API method:
Stack Trace

Newest

gaierror: [Errno -2] Name or service not known
  File "urllib3/connection.py", line 174, in _new_conn
    conn = connection.create_connection(
  File "urllib3/util/connection.py", line 72, in create_connection
    for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
  File "socket.py", line 962, in getaddrinfo
    for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known
  File "urllib3/connectionpool.py", line 715, in urlopen
    httplib_response = self._make_request(
  File "urllib3/connectionpool.py", line 416, in _make_request
    conn.request(method, url, **httplib_request_kw)
  File "urllib3/connection.py", line 244, in request
    super(HTTPConnection, self).request(method, url, body=body, headers=headers)
  File "http/client.py", line 1286, in request
    self._send_request(method, url, body, headers, encode_chunked)
  File "http/client.py", line 1332, in _send_request
    self.endheaders(body, encode_chunked=encode_chunked)
  File "http/client.py", line 1281, in endheaders
    self._send_output(message_body, encode_chunked=encode_chunked)
  File "http/client.py", line 1041, in _send_output
    self.send(msg)
  File "http/client.py", line 979, in send
    self.connect()
  File "urllib3/connection.py", line 205, in connect
    conn = self._new_conn()
  File "urllib3/connection.py", line 186, in _new_conn
    raise NewConnectionError(
MaxRetryError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known'))
  File "requests/adapters.py", line 486, in send
    resp = conn.urlopen(
  File "urllib3/connectionpool.py", line 799, in urlopen
    retries = retries.increment(
  File "urllib3/util/retry.py", line 592, in increment
    raise MaxRetryError(_pool, url, error or ResponseError(cause))
ConnectionError: HTTPConnectionPool(host='https', port=80): Max retries exceeded with url: //training.galaxyproject.org/training-material//api/ga4gh/trs/v2/tools/variant-analysis-microbial-variants/versions/microbial_variant_calling/GALAXY/descriptor (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7f8e35406450>: Failed to establish a new connection: [Errno -2] Name or service not known'))
  File "galaxy/web/framework/decorators.py", line 346, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/api/workflows.py", line 261, in create
    archive_data = server.get_version_descriptor(trs_tool_id, trs_version_id)
  File "galaxy/workflow/trs_proxy.py", line 115, in get_version_descriptor
    return self._get(trs_api_url)["content"]
  File "galaxy/workflow/trs_proxy.py", line 126, in _get
    response = requests.get(url, params=params, timeout=DEFAULT_SOCKET_TIMEOUT)
  File "galaxy/util/requests.py", line 29, in wrapper
    rval = f(*args, **kwargs)
  File "requests/api.py", line 73, in get
    return request("get", url, params=params, **kwargs)
  File "requests/api.py", line 59, in request
    return session.request(method=method, url=url, **kwargs)
  File "requests/sessions.py", line 589, in request
    resp = self.send(prep, **send_kwargs)
  File "requests/sessions.py", line 703, in send
    r = adapter.send(request, **kwargs)
  File "requests/adapters.py", line 519, in send
    raise ConnectionError(e, request=request)
```
which happened for https://usegalaxy.org/workflows/trs_import?run_form=true&trs_url=http%3A%2F%2Flocalhost%3A4000%2F%2Ftraining-material%2F%2Fapi%2Fga4gh%2Ftrs%2Fv2%2Ftools%2Fvariant-analysis-microbial-variants%2Fversions%2Fmicrobial_variant_calling"
 2024-09-18 10:31:23 +02:00
Marius van den Beek 310cbd976c Merge pull request #18809 from mvdbeek/collect_job_metrics_also_when_job_failed 
[24.1] Collect job metrics also when job failed
 2024-09-13 17:40:18 +02:00
mvdbeek 4a5b3dd0bb Fix job metric collection when job fails 2024-09-13 14:36:12 +02:00
mvdbeek 14909829f7 Test metric collection when runner fails 2024-09-13 12:37:14 +02:00
mvdbeek ee63214516 Fix wrong extension on pick data output 
This fixes https://github.com/galaxyproject/galaxy/issues/18795
 2024-09-11 12:21:33 +02:00
mvdbeek 1dce8cf75b Add test for keeping picked dataset's extension in place 2024-09-10 18:50:12 +02:00
mvdbeek 302328f05f Merge branch 'release_24.0' into release_24.1 2024-08-09 15:57:24 +02:00
davelopez d9051005bc Remove unnecessary assert for file_size 
The file_size should be preserved in the database for traceability and other uses.
 2024-08-09 14:03:53 +02:00
Marius van den Beek f8175ef771 Merge pull request #18552 from dannon/update-h5web 
[24.1] Update h5web
 2024-08-06 18:00:56 +02:00
Dannon Baker ab90c943ff Load h5 datatype in reduced test datatypes set 2024-08-05 10:58:22 -04:00
Matthias Bernt 262b4b69ca remove test for actions from collection_creates_pair_format 
now in metadata_column_names
 2024-07-30 13:01:51 +02:00
Matthias Bernt 3cdbb8f64c test actions in statically defined collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt eeab749ef6 Revert "add test for filters in statically defined collection elements" 
This reverts commit c0ce2a7eb6beaacaf65a389273cae12244103591.
 2024-07-30 13:01:51 +02:00
Matthias Bernt 7b0972598b add test for filters in statically defined collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt 85d4b4235b add test for output actions for collection elements 2024-07-30 13:01:51 +02:00
Matthias Bernt 3b3a65d1d2 extend tool test for change_format in statically defined collection elements 2024-07-30 13:01:51 +02:00
mvdbeek a5960ee262 Fix map over calculation for runtime inputs 
Fixes https://github.com/galaxyproject/galaxy/issues/18506
 2024-07-14 20:53:52 +02:00
Nicola Soranzo 49f820da8b Merge branch 'release_24.0' into release_24.1 2024-07-08 20:11:56 +01:00
mvdbeek e395ea7d6d Stabilize test_purge_while_job_running test 
In the extended_metadata + remote tool_evaluation_strategy the
commandline is templated as part of the job, so we need to give the test
more time to start running before we delete outputs (as then we can't
template the command line anymore).
 2024-07-04 17:35:57 +02:00
Ahmed Hamid AwanandJohn Davis 077832bc29 Update test/unit/app/managers/test_UserManager.py 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-07-01 13:56:50 -05:00
Ahmed Awan a6e70816f3 adjust test_reset_email_user_deleted for None instead of str 2024-07-01 13:42:44 -05:00
mvdbeek 33f27d5456 Merge branch 'release_24.0' into release_24.1 2024-07-01 18:23:55 +02:00
Marius van den Beek 444ae58736 Merge pull request #18446 from mvdbeek/when_upgrade_fix 
[24.0] Fix dropped when_expression on step upgrade
 2024-07-01 18:19:18 +02:00
Jonathan Laperle beb705428a fix indentation 2024-06-28 12:50:32 -04:00
Jonathan Laperle e69d7b2f8b Prevent deleted users from reseting password 2024-06-28 08:01:25 -04:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
Marius van den Beek 8a52443a0a Merge pull request #18428 from mvdbeek/replace_busybox 
[24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
 2024-06-28 09:22:30 +02:00
mvdbeek ed8dc4b8e2 Fix dropped when_expression on workflow/tool_upgrade 
Fixes https://github.com/galaxyproject/galaxy/issues/18441
 2024-06-27 15:31:30 +02:00
mvdbeek 5050ccde3d Add test to make sure when_expression is not lost on refactoring 2024-06-27 15:31:29 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
Nicola Soranzo 08d42ea24f Merge branch 'release_24.0' into release_24.1 2024-06-19 13:14:15 +01:00
mvdbeek 111d5632ff Run make format 2024-06-19 10:24:55 +02:00
Martin Cech 2891489cad Merge pull request #18389 from mvdbeek/ensure_data_extension_if_no_extension_specified 
[24.0] Assign default ``data`` extension on discovered collection output
 2024-06-18 17:21:20 +02:00
mvdbeek ed2369f9a0 Merge branch 'release_24.0' into release_24.1 2024-06-18 17:19:55 +02:00
M Bernt 5297fa3137 Apply suggestions from code review 2024-06-18 09:59:33 +02:00
Matthias Bernt a2d1a5d2e6 really allow in-range validator for txt 
just enabling the linter
https://github.com/galaxyproject/galaxy/pull/18403 was not sufficient
 2024-06-17 14:57:56 +02:00
mvdbeek 6551f31671 Implement default format on collection level 2024-06-13 13:02:51 +02:00
mvdbeek dd171fe34d Add test tool for default ext handling in discovered collections 2024-06-13 12:53:28 +02:00
mvdbeek b8e2bfc9c7 Merge branch 'release_24.0' into release_24.1 2024-06-11 13:42:48 +02:00