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Author SHA1 Message Date
Marius van den Beek 76bf9bfccf Merge pull request #13764 from natefoo/distributed-no-search 
[22.01] Add an option to disable searching for distributed object store datasets that don't have an object_store_id
 2022-04-22 10:46:31 +02:00
Martin Cech 5aad013172 Merge pull request #13718 from mvdbeek/fix_quay_io_cache_use 
[22.01] Fix persistent mulled cache unused for repo_has_name
 2022-04-22 10:45:55 +02:00
Marius van den Beek 1db61fc5ae Merge pull request #13773 from kxk302/main_irods_fixes 
Added exist_ok flag to other object stores
 2022-04-22 10:21:50 +02:00
cat-bro 8c44fce0c9 pass app.toolbox from reindex_tool_function instead of using stored toolbox 2022-04-21 14:27:02 +10:00
Nate CoraorandSergey Golitsynskiy 5dc725c7f9 Update lib/galaxy/objectstore/__init__.py 
Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
 2022-04-20 11:51:33 -04:00
Nate Coraor 8a81038701 Add an option to disable searching for distributed object store datasets 
that don't have an object_store_id
 2022-04-20 11:50:58 -04:00
Kaivan Kamali d99f26decd Added exist_ok flag to other object stores 2022-04-20 09:57:11 -04:00
Marius van den Beek f5c511beed Merge pull request #13768 from kxk302/main_irods_fixes 
[22.01] Fix race condition in object store dir creation
 2022-04-20 10:20:35 +02:00
Kaivan Kamali 5dcb129490 Added exist_ok flag so creating an directory that already exists does not error out 2022-04-19 16:39:01 -04:00
David LópezandNicola Soranzo 5e8eea6759 Add type hint suggestion 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-04-19 15:44:44 -04:00
davelopez 99025c770b Fix mypy error 2022-04-19 15:44:38 -04:00
Kaivan Kamali e83a691293 Update python-irodsclient 2022-04-19 11:43:34 -04:00
Kaivan Kamali d3afc0b6a1 Merge branch 'release_22.01' of https://github.com/galaxyproject/galaxy into release_22.01 2022-04-19 11:40:40 -04:00
Kaivan Kamali b621f83d0e Update python-irodsclient 2022-04-19 11:38:44 -04:00
mvdbeek da61e77068 Fix persistent mulled cache unused for repo_has_name 2022-04-14 12:10:42 +02:00
Nicola Soranzo bb6aaef8ab Merge pull request #12375 from muon-spectroscopy-computational-project/eli/add-data-types 
[22.01] Add new molecule datatypes
 2022-04-13 20:49:35 +01:00
elichad d72aab5322 convert is_periodic to bool in XYZ 2022-04-13 16:41:17 +00:00
elichadandNicola Soranzo 4de5883388 Convert is_periodic to bool in Cell and CIF 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-04-13 16:27:47 +01:00
Nicola Soranzo 8adc7ec870 Merge branch 'release_21.09' into release_22.01 2022-04-11 19:03:41 +01:00
Matthias Bernt 98b324ade0 refactor: do not store intermediate lists 2022-04-08 19:38:39 +02:00
Matthias Bernt c01f9d47b4 fix sorting for recursively discovered datasets 
files in subdirectories were not subject to sort
 2022-04-08 19:38:23 +02:00
elichad acb0e2a588 Merge branch 'eli/add-data-types' of https://github.com/muon-spectroscopy-computational-project/muon-galaxy into eli/add-data-types 2022-04-08 16:17:02 +00:00
elichad 2adef05e12 change elemen _symbols toclass attribute 2022-04-08 16:16:48 +00:00
elichadandNicola Soranzo cfeb89a466 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-04-08 17:01:14 +01:00
davelopez 0d272ba256 Allow admins to run tools on private datasets 2022-04-06 10:32:00 +02:00
Marius van den Beek 4aa985e16e Merge pull request #13669 from jmchilton/2201_fix_upload_calls 
[22.01] Correct data fetch API call in the client.
 2022-04-05 11:28:00 +02:00
Marius van den Beek d4001d1851 Merge pull request #13665 from nsoranzo/release_22.01_update_uvicorn 
[22.01] Update uvicorn from broken 0.17.1
 2022-04-05 01:14:22 +02:00
John Chilton 8cd1503860 Correct data fetch API in the client. 
More defensive backend to prevent these errors.
 2022-04-04 15:58:44 -04:00
Marius van den Beek d4e0d3dc4c Merge pull request #13668 from dannon/toolshed-style-loading-fix 
[22.01] Fix toolshed style loading
 2022-04-04 20:09:59 +02:00
Nicola Soranzo b5fb285ca7 Update mypy to 0.942 . Fix new mypy errors. 
Remove unused `optional()` decorator function that had an annotation issue.
 2022-04-04 18:04:01 +01:00
mvdbeek d5e9901f3f Forward type annotation of depends 2022-04-04 18:04:01 +01:00
Nicola Soranzo 112d34f32c Update uvicorn from broken 0.17.1 
Fix issue found when testing planemo in
https://github.com/galaxyproject/planemo/pull/1224#issuecomment-1086201126 :

```
2022-04-01T14:44:05.3964452Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received.
2022-04-01T14:44:05.3964583Z Traceback (most recent call last):
2022-04-01T14:44:05.3965087Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events
2022-04-01T14:44:05.3965218Z     event = self.conn.next_event()
2022-04-01T14:44:05.3965652Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 443, in next_event
2022-04-01T14:44:05.3965801Z     exc._reraise_as_remote_protocol_error()
2022-04-01T14:44:05.3966277Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 76, in _reraise_as_remote_protocol_error
2022-04-01T14:44:05.3966383Z     raise self
2022-04-01T14:44:05.3966831Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 425, in next_event
2022-04-01T14:44:05.3966977Z     event = self._extract_next_receive_event()
2022-04-01T14:44:05.3967445Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 367, in _extract_next_receive_event
2022-04-01T14:44:05.3967588Z     event = self._reader(self._receive_buffer)
2022-04-01T14:44:05.3968049Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_readers.py", line 73, in maybe_read_from_IDLE_client
2022-04-01T14:44:05.3968225Z     request_line_re, lines[0], "illegal request line: {!r}", lines[0]
2022-04-01T14:44:05.3968629Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_util.py", line 88, in validate
2022-04-01T14:44:05.3968781Z     raise LocalProtocolError(msg)
2022-04-01T14:44:05.3969215Z h11._util.RemoteProtocolError: illegal request line: bytearray(b'--a250a2c0546542508998e4e0ac8f1001')
2022-04-01T14:44:05.3969497Z [2022-04-01 14:41:23 +0000] [6904] [WARNING] Invalid HTTP request received.
2022-04-01T14:44:05.3969623Z Traceback (most recent call last):
2022-04-01T14:44:05.3970105Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 136, in handle_events
2022-04-01T14:44:05.3970231Z     event = self.conn.next_event()
2022-04-01T14:44:05.3970655Z   File "/tmp/planemo-test-workspace/gx_venv_3/lib/python3.7/site-packages/h11/_connection.py", line 423, in next_event
2022-04-01T14:44:05.3971003Z     raise RemoteProtocolError("Can't receive data when peer state is ERROR")
2022-04-01T14:44:05.3971287Z h11._util.RemoteProtocolError: Can't receive data when peer state is ERROR
```
 2022-04-04 18:04:00 +01:00
Nicola Soranzo 88f3d6d509 Merge branch 'release_21.09' into release_22.01 2022-04-04 18:02:42 +01:00
Dannon Baker de71354678 Drop debugging commentary from base mako 2022-04-04 12:44:53 -04:00
Dannon Baker cd5128b7bd Fix toolshed style loading 2022-04-04 12:42:29 -04:00
Nicola Soranzo 48a01454e4 Add missing pin for rich, dependency of refgenconf 0.12.0 
Pinning to the version that was current when
https://github.com/galaxyproject/galaxy/pull/12435
was merged to fix the following traceback with rich 12.1.0:

```
2022-04-04T14:16:19.5073158Z   File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/data/__init__.py", line 21, in <module>
2022-04-04T14:16:19.5073535Z     import refgenconf
2022-04-04T14:16:19.5074393Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/__init__.py", line 6, in <module>
2022-04-04T14:16:19.5074853Z     from .populator import looper_refgenie_populate
2022-04-04T14:16:19.5075535Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/populator.py", line 9, in <module>
2022-04-04T14:16:19.5075970Z     from . import refgenconf
2022-04-04T14:16:19.5076607Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/refgenconf.py", line 27, in <module>
2022-04-04T14:16:19.5077091Z     from rich.progress import BarColumn, Progress, TextColumn
2022-04-04T14:16:19.5077768Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/progress.py", line 43, in <module>
2022-04-04T14:16:19.5078272Z     from .console import Console, JustifyMethod, RenderableType, Group
2022-04-04T14:16:19.5078956Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/console.py", line 46, in <module>
2022-04-04T14:16:19.5079437Z     from ._log_render import FormatTimeCallable, LogRender
2022-04-04T14:16:19.5080105Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_log_render.py", line 5, in <module>
2022-04-04T14:16:19.5124479Z     from .text import Text, TextType
2022-04-04T14:16:19.5130069Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/text.py", line 5, in <module>
2022-04-04T14:16:19.5134858Z     from rich.emoji import EmojiVariant
2022-04-04T14:16:19.5139847Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/emoji.py", line 4, in <module>
2022-04-04T14:16:19.5144648Z     from .jupyter import JupyterMixin
2022-04-04T14:16:19.5147478Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/jupyter.py", line 4, in <module>
2022-04-04T14:16:19.5150060Z     from .segment import Segment
2022-04-04T14:16:19.5152862Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/segment.py", line 19, in <module>
2022-04-04T14:16:19.5155442Z     from .cells import (
2022-04-04T14:16:19.5158112Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/cells.py", line 6, in <module>
2022-04-04T14:16:19.5159612Z     from ._lru_cache import LRUCache
2022-04-04T14:16:19.5161691Z   File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_lru_cache.py", line 8, in <module>
2022-04-04T14:16:19.5163233Z     from typing_extensions import OrderedDict
2022-04-04T14:16:19.5165289Z ImportError: cannot import name 'OrderedDict' from 'typing_extensions' (/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/typing_extensions.py)
```
 2022-04-04 15:43:43 +01:00
Nicola Soranzo c7ce60a351 Merge branch 'release_21.05' into release_21.09 2022-04-04 15:11:17 +01:00
Nicola Soranzo 2cbbf1ea50 Check GitHub API rate limit in GitHubSearch. Deprecate get_json() search 
Follow-up on https://github.com/galaxyproject/galaxy/pull/13509 .
 2022-04-04 12:56:07 +01:00
Nicola Soranzo 58d7e3cd96 Raise exception if GET request returned an unsuccessful status code 2022-04-04 12:40:16 +01:00
elichad c5195fbd61 choose a scipy version compatible with py3.7 2022-04-01 15:41:53 +00:00
elichad 0d7143472e update ase dependencies for newer pip 2022-04-01 15:27:01 +00:00
elichad 31e20ebe46 add only ase dependencies 2022-04-01 14:14:54 +00:00
elichad 753619454f Revert "add ase to dev-dependencies" 
This reverts commit b03d7dca19.
 2022-04-01 13:20:29 +00:00
elichad 6388315df1 avoid setting any metadata if ase not present 2022-04-01 10:42:55 +00:00
elichad b03d7dca19 add ase to dev-dependencies 2022-04-01 09:35:04 +00:00
elichadandMarius van den Beek 6c1e7a7d00 Apply suggestions from code review 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-01 09:35:04 +00:00
elichad 96c33b0373 avoid raising errors 2022-04-01 09:35:04 +00:00
elichad 36f54df6ff don't fail basic set_meta for xyz 2022-04-01 09:35:04 +00:00
elichad d8ada266df clarify relationship between CIF and STAR 2022-04-01 09:35:04 +00:00
elichad ccc13777ab change to sniff_prefix for cif,xyz,extxyz 2022-04-01 09:35:04 +00:00