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3579 Commits
Author SHA1 Message Date
mvdbeek a42496e8ec Disable locking when opening h5 files, add missing with 2024-10-12 09:26:54 +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 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
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 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
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
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 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 b8e2bfc9c7 Merge branch 'release_24.0' into release_24.1 2024-06-11 13:42:48 +02:00
Marius van den Beek 96c9be32ce Merge pull request #18342 from mvdbeek/fix_copying_purged_files 
[24.0] Do not copy purged outputs to object store
 2024-06-11 13:35:10 +02:00
Marius van den Beek 2585d1e604 Merge pull request #18291 from jmchilton/cleanup_user_data_indexing 
[24.1] More structured indexing for user data objects.
 2024-06-10 13:27:26 +02:00
mvdbeek a2fdcb3c72 Merge branch 'release_24.0' into release_24.1 2024-06-08 15:54:19 +02:00
mvdbeek c6930fff72 Merge branch 'release_23.2' into release_24.0 2024-06-08 15:53:41 +02:00
John Chilton 821b31c3b2 More structured indexing for user data objects. 
I think I clung to the idea of having two ways to do this too long. I did a bunch of testing with the old way (exposing integer references based on numeric database primary keys). Having a config option that if changed would break everything exisiting is also a symptom of maybe me clinging too hard for too long.

The result of dropping this option is a much cleaner API schema, simpler API objects, and better typing throughout. We can also be more certain of how things entering the Vault are stored - I think being more strucutured about this is good.

Ultimately, the future facing stuff (e.g. OAuth 2.0) is going to require UUIDs so that I can store things like refresh tokens in the store before the object has been fully created.
 2024-06-07 19:20:11 -04:00
mvdbeek dff6307e91 Allow DCE as outer input to to_cwl 2024-06-07 17:29:07 +02:00
mvdbeek 87124a396a Don't copy from_work_dir outputs to purged path in shell fragment 2024-06-07 15:20:44 +02:00
mvdbeek 0122cdb16e Merge branch 'release_24.0' into release_24.1 2024-06-05 17:43:18 +02:00
mvdbeek 7228c5aad1 Merge branch 'release_23.2' into release_24.0 2024-06-05 15:25:29 +02:00
mvdbeek 9681d8647f Fix one more tool shed unit test 2024-06-05 14:44:04 +02:00
mvdbeek 54a27a19e6 Fix tool_shed package unit tests 2024-06-05 12:15:46 +02:00
mvdbeek fed2294c1b Merge branch 'release_23.1' into release_23.2 2024-06-05 10:03:56 +02:00
mvdbeek 992777edee Fix typo 2024-06-04 17:00:43 +02:00
Marius van den Beek b3835bbefe Merge pull request #18246 from jmchilton/backport_user_data_1 
[24.1] Small bug fixes for user data plugins
 2024-06-04 09:43:17 +02:00
mvdbeek 2e8c0df88b Test and lint fixes 2024-06-03 17:52:27 +02:00
Nicola Soranzo 1174bbe8f4 Fix packages' dependencies and MANIFEST.in files 
Also:
- Add missing `graphene` and `graphql-core` dependencies to
  `pyproject.toml` (already installed as other dependencies' deps,
  but explicitly imported by ToolShed code).
- Move `test_tool_validation.py` unit tests to the galaxy-tool-shed
  package.
 2024-06-02 19:56:20 +01:00
Nicola Soranzo b2076ee5f9 Move carbon data loading to `GalaxyManagerApplication` 
Fix the galaxy-config package wrongly depending on galaxy-app.
Also move the carbon_emissions unit tests to the `app/` subdirectory.

Refines @mvdbeek's proposed patch from https://github.com/galaxyproject/galaxy/pull/17159#issuecomment-1850276194 .

Close https://github.com/galaxyproject/galaxy/pull/17159 .
 2024-06-02 19:56:20 +01:00
mvdbeek b2097db85d Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-05-31 15:27:27 +02:00
Marius van den Beek fd1cb2726a Merge pull request #18252 from bernt-matthias/revert/17656 
[24.1] Remove linter for unstripped text content for tool xml leaves
 2024-05-31 10:03:52 +02:00
Nicola Soranzo 3ea8de4ce5 Merge branch 'release_23.2' into release_24.0 2024-05-30 16:45:28 +01:00
Nicola Soranzo 6d068ca5f9 Add `hgweb_repo_prefix attribute to TestToolShedConfig` 
Fix the following error in unit tests:

```
AttributeError: 'TestToolShedConfig' object has no attribute 'hgweb_repo_prefix'
```

caused by merging commit b00beec3d2
forward.
 2024-05-30 15:16:38 +01:00
Nicola Soranzo 6ef6fc911f Merge branch 'release_24.0' into release_24.1 2024-05-30 13:03:12 +01:00
Matthias Bernt c201daa7a8 remove linter for unstripped text content for tool xml leaves 
reverts #17656

we have to many xml nodes where this is allowed (e.g. command)
and limiting the linter to a statically defined list of node types
seemed difficult to maintain

replaced this with a change in the xsd that should lead to the
automatic removal of surplus white spaces (leading/trailing are removed,
multiple whitespaces are replaced by a single space) for some of the
node types that were the original motivation for the linter
(if this proves useful this could be used for more node types).
 2024-05-29 15:29:00 +02:00
mvdbeek ce1582f46a Move assertions out request error handling 2024-05-29 13:50:29 +02:00
Marius van den BeekandNicola Soranzo 5d2ccdfbe7 Use variable 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2024-05-29 13:49:10 +02:00
mvdbeek d8379a79a1 Also skip unit test 2024-05-29 13:39:26 +02:00
mvdbeek 229b1c5bcb Skip doi unit test if request fails 2024-05-29 13:30:22 +02:00
John Chilton 77e6df4303 Fill out missing file source management tests. 2024-05-28 11:31:35 -04:00