907130d | mvdbeek | 21 February 2022, 09:28:38 UTC | Fix repository uploads with remove_repo_files_not_in_tar This fixes erroneously deleting the just uploaded files, which otherwise happens in ``` if full_name not in filenames_in_archive: files_to_remove.append(full_name) ``` | 21 February 2022, 09:28:41 UTC |
76a8e12 | Marius van den Beek | 10 February 2022, 10:19:20 UTC | Merge pull request #13325 from mvdbeek/remap_fix_sentry [21.09] Fix resuming job when job has optional data parameters | 10 February 2022, 10:19:20 UTC |
76d2f63 | Nicola Soranzo | 08 February 2022, 16:04:13 UTC | Merge pull request #13326 from dannon/backport-blame-ignore-revs | 08 February 2022, 16:04:13 UTC |
9cb0c45 | Dannon Baker | 08 February 2022, 14:57:50 UTC | Add .git-blame-ignore-revs to 21.09. Without this, if you have set the file up in git config blame will blow up with something like `could not open object name list: .git-blame-ignore-revs`. I only included the relevant hashes here, will need to handle a merge as it goes forward. | 08 February 2022, 14:57:50 UTC |
bec9d4b | mvdbeek | 08 February 2022, 11:36:28 UTC | Fix resuming job when job has optional data parameters This fixes ``` ERROR galaxy.tools.actions:__init__.py:683 Cannot remap rerun dependencies. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 664, in _remap_job_on_rerun self.__remap_parameters(job_to_remap, jtid, jtod, out_data) File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in __remap_parameters input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters} File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/actions/__init__.py", line 694, in <dictcomp> input_values = {p.name: json.loads(p.value) for p in job_to_remap.parameters} File "/usr/local/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 339, in loads raise TypeError(f'the JSON object must be str, bytes or bytearray, ' TypeError: the JSON object must be str, bytes or bytearray, not NoneType ``` Optional data inputs or optional selects are stored as `None` (super inconsistent, since most other parameters are stored as JOSN. We should create "basic_2.py" using pydantic at one point not too far into the future ...). This means we can't call `json.loads` on these. Fortunately this is the only place we do it, and we don't need to consider optional parameters here anyway. | 08 February 2022, 14:45:01 UTC |
00b0846 | Nicola Soranzo | 08 February 2022, 12:05:23 UTC | Merge branch 'release_21.05' into release_21.09 | 08 February 2022, 13:29:08 UTC |
d27ded4 | Nicola Soranzo | 08 February 2022, 11:14:26 UTC | Merge pull request #13315 from mvdbeek/restore_metadata_size_limit | 08 February 2022, 11:14:26 UTC |
e5455a4 | Marius van den Beek | 07 February 2022, 14:29:56 UTC | Merge pull request #13316 from mvdbeek/fix_failure_to_fail_job [21.09] Make __link_file_check more robust | 07 February 2022, 14:29:56 UTC |
83c0683 | mvdbeek | 07 February 2022, 10:12:54 UTC | Restore Metadata size limit Broke in https://github.com/galaxyproject/galaxy/pull/11902 | 07 February 2022, 14:02:02 UTC |
37846b2 | mvdbeek | 07 February 2022, 10:32:00 UTC | Make __link_file_check more robust There's no need to load the job and job parameters if the tool isn't upload1. This should fix https://github.com/galaxyproject/galaxy/issues/13311 | 07 February 2022, 10:33:18 UTC |
44644a0 | Björn Grüning | 04 February 2022, 12:46:28 UTC | Merge pull request #13304 from mvdbeek/fix_stopping_its_slurm [21.09] Fix stopping ITs on slurm | 04 February 2022, 12:46:28 UTC |
bb299b9 | Marius van den Beek | 04 February 2022, 12:13:46 UTC | Merge pull request #13301 from Smithsonian/Fixfor13297 [21.09] Fix univa job runner setup without nativeSpecification | 04 February 2022, 12:13:46 UTC |
a60a898 | mvdbeek | 04 February 2022, 09:44:17 UTC | Fix stopping ITs on slurm If slurm decided the job is in error. There are configurations of slurm that error out when cancelling the job monitor script, and others that don't do this. | 04 February 2022, 09:44:19 UTC |
10a6db4 | ajs6f | 03 February 2022, 16:46:42 UTC | Fix for traceback: ``` Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 707, in monitor self.check_watched_items() File "lib/galaxy/jobs/runners/drmaa.py", line 338, in check_watched_items if self._complete_terminal_job(ajs, drmaa_state=state) is not None: File "lib/galaxy/jobs/runners/univa.py", line 85, in _complete_terminal_job time_granted, mem_granted = _parse_native_specs(ajs.job_id, native_spec) File "lib/galaxy/jobs/runners/univa.py", line 572, in _parse_native_specs m = re.search(r"rt=([0-9:]+)[\s,]*", native_spec) File "/pool/spare/galaxy/galaxy/.venv/lib64/python3.6/re.py", line 182, in search return _compile(pattern, flags).search(string) TypeError: expected string or bytes-like object ``` See https://github.com/galaxyproject/galaxy/issues/13297 reported by @ajs6f fix from @mvdbeek | 03 February 2022, 16:46:42 UTC |
213f6ee | Dannon | 02 February 2022, 00:03:10 UTC | Merge pull request #13290 from mvdbeek/fix_dataset_details_and_drag_and_drop [21.09] Fix dataset details and drag and drop | 02 February 2022, 00:03:10 UTC |
04c340a | Marius van den Beek | 01 February 2022, 22:58:39 UTC | Drop leftover debug log Co-authored-by: Dannon <dannon.baker@gmail.com> | 01 February 2022, 22:58:39 UTC |
69c635b | mvdbeek | 01 February 2022, 19:52:12 UTC | Fix link to dataset details for datasets in running collection | 01 February 2022, 19:57:54 UTC |
51bca9d | mvdbeek | 01 February 2022, 19:50:58 UTC | Fix drag and drop of unexpanded collection elements | 01 February 2022, 19:54:41 UTC |
81f27cb | Marius van den Beek | 27 January 2022, 17:20:52 UTC | Merge pull request #13254 from davelopez/fix_edit_imported_subworkflow [21.09] Fix imported sub-workflows cannot be edited | 27 January 2022, 17:20:52 UTC |
6cb59a5 | davelopez | 27 January 2022, 13:24:54 UTC | Fix imported subworkflows cannot be edited There may be no StoredWorkflow associated with the imported subworkflow yet, so trying to edit the subworkflow without it will fail. xref https://github.com/galaxyproject/galaxy/pull/10160 | 27 January 2022, 14:25:06 UTC |
004d69f | Nicola Soranzo | 26 January 2022, 19:36:56 UTC | Merge pull request #13249 from mvdbeek/hgutil_fix | 26 January 2022, 19:36:56 UTC |
2d70fa5 | mvdbeek | 26 January 2022, 15:54:42 UTC | Fix one usage of hg_util.remove_file I missed this one in https://github.com/galaxyproject/galaxy/pull/13230 | 26 January 2022, 15:54:45 UTC |
5845b3d | Dannon | 25 January 2022, 13:32:38 UTC | Merge pull request #13230 from mvdbeek/fix_mercurial_new_file [21.09] Fix adding new files via tarball upload | 25 January 2022, 13:32:38 UTC |
0f59f70 | Marius van den Beek | 24 January 2022, 14:38:59 UTC | Merge pull request #13231 from simonbray/wf-au-fix [21.09] Ensure tool_id/content_id is updated when refactoring workflows | 24 January 2022, 14:38:59 UTC |
381d218 | Simon Bray | 24 January 2022, 12:37:59 UTC | ensure tool_id/content_id is updated when refactoring workflows | 24 January 2022, 12:39:27 UTC |
5c39169 | mvdbeek | 24 January 2022, 11:25:14 UTC | Partial unit tests for hgutil.py | 24 January 2022, 11:28:06 UTC |
956ad81 | mvdbeek | 24 January 2022, 10:10:59 UTC | Fix adding new files via tarball upload The API of `repo.dirstate.write` has changed and takes a `tr` parameter now. I've removed the whole fallback since it fails and uses internals of mercurial that we should probably not be using anyway. Instead we're going to delete untracked files in hg_util.remove_file() | 24 January 2022, 10:58:30 UTC |
f2c6666 | Marius van den Beek | 24 January 2022, 08:17:12 UTC | Merge pull request #13174 from mvdbeek/fix_display_in_upload_false_connections [21.09] Fix workflow connections for outputs that are not displayed in uploads | 24 January 2022, 08:17:12 UTC |
15e1158 | Marius van den Beek | 23 January 2022, 12:43:55 UTC | Merge pull request #13227 from mvdbeek/drop_unnecessary_tests [21.09] Skip non-Selenium tests if only lib/galaxy_test/selenium is touched | 23 January 2022, 12:43:55 UTC |
31f0cb4 | mvdbeek | 23 January 2022, 12:40:57 UTC | Don't sort array in place, fixes infinite update loop | 23 January 2022, 12:43:06 UTC |
f7fde81 | mvdbeek | 23 January 2022, 10:13:55 UTC | Print exception | 23 January 2022, 12:43:06 UTC |
f66b673 | mvdbeek | 21 January 2022, 16:15:55 UTC | Drop indented, fenced galaxy blocks from test https://github.com/galaxyproject/galaxy/issues/13181 | 23 January 2022, 09:48:22 UTC |
036dddc | mvdbeek | 18 January 2022, 13:07:14 UTC | Wait for data and datatype before rendering HistoryDatasetsDisplay | 23 January 2022, 09:48:22 UTC |
65b3157 | mvdbeek | 16 January 2022, 17:35:27 UTC | Search datatype before selecting it We now return more datatypes in the list, so bam fell out of the intial items that select2 displays without scrolling. | 23 January 2022, 09:48:22 UTC |
bb2c6ba | mvdbeek | 16 January 2022, 16:03:46 UTC | Fix workflow connections for outputs that are not displayed in uploads and apply the same fix for tool recommendations. Fixes https://github.com/galaxyproject/galaxy/issues/13173 | 23 January 2022, 09:48:21 UTC |
6c7f4b0 | mvdbeek | 17 January 2022, 08:31:26 UTC | Skip api tests if lib/galaxy_test/selenium is touched (and other unrelated test). | 23 January 2022, 09:42:34 UTC |
59393dc | Marius van den Beek | 22 January 2022, 15:26:47 UTC | Merge pull request #13216 from mvdbeek/fix_unique_constraint_exceptions [21.09] Handle unique tag name constraints | 22 January 2022, 15:26:47 UTC |
296b31e | Dannon | 21 January 2022, 20:42:18 UTC | Merge pull request #13193 from davelopez/fix_wf_invocation_name_overflow [21.09] Fix workflow invocation name overflow | 21 January 2022, 20:42:18 UTC |
29f8b18 | mvdbeek | 20 January 2022, 18:02:15 UTC | Handle unique tag name constraints The idea is to create the tag one by one in a separate session, and catch any violations. | 21 January 2022, 13:50:16 UTC |
ad9b422 | davelopez | 21 January 2022, 13:45:56 UTC | Fix column text overflow after wrapping in div And slightly enhance switch to history tooltip | 21 January 2022, 13:45:56 UTC |
bac2cc2 | davelopez | 21 January 2022, 13:26:24 UTC | Move `toggle-invocation-details` class to expand column | 21 January 2022, 13:26:24 UTC |
407c04d | davelopez | 21 January 2022, 12:44:28 UTC | Fix tooltip position The tooltip was ignoring the text-overflow when the full name was truncated and was positioned in the center of where the full text would be. Putting the tooltip into a wrapping div seems to solve the issue. | 21 January 2022, 12:44:28 UTC |
36a0f56 | davelopez | 21 January 2022, 12:42:08 UTC | Truncate history name too | 21 January 2022, 12:42:08 UTC |
851bc56 | Marius van den Beek | 21 January 2022, 12:09:19 UTC | Merge pull request #13210 from mvdbeek/backport_non_data_map_over_fix [21.09] Backport allow mapping of collection outputs to parameter inputs | 21 January 2022, 12:09:19 UTC |
10fc135 | Marius van den Beek | 21 January 2022, 12:08:53 UTC | Merge pull request #13214 from davelopez/fix_hide_collection_batch [21.09] Fix hide collections in batch | 21 January 2022, 12:08:53 UTC |
de633e9 | davelopez | 21 January 2022, 11:43:14 UTC | Fix column index in unit tests After adding a new "first" column for expanding | 21 January 2022, 11:43:14 UTC |
5e603a9 | davelopez | 21 January 2022, 11:28:34 UTC | Add explicit row expand button - Makes more obvious that the row can be expanded. - Allows to display the full name in the tooltip when truncated. | 21 January 2022, 11:28:34 UTC |
71e3fd4 | davelopez | 21 January 2022, 11:26:40 UTC | Add min-width to table This will prevent the workflow name column to completely dissapear in small resolutions | 21 January 2022, 11:26:40 UTC |
0bc41e0 | davelopez | 20 January 2022, 18:30:00 UTC | Fix dataset collections not hiding when updating in batch NOTE: this commit can be dropped when merging forward as this is already refactored and fixed in the dev branch | 20 January 2022, 18:39:03 UTC |
4f104cf | davelopez | 20 January 2022, 18:25:45 UTC | Add API test for dataset collections batch update When merging forward replace `_raw_update_batch` to `_update_batch` | 20 January 2022, 18:25:45 UTC |
2a005df | guerler | 20 January 2022, 03:16:04 UTC | Separate qunit test cases for data and parameter input terminals | 20 January 2022, 15:20:32 UTC |
f7fb4ed | guerler | 19 January 2022, 05:58:35 UTC | Remove currently unused options from qunit terminal creation helpers | 20 January 2022, 15:20:32 UTC |
b5f35c7 | guerler | 19 January 2022, 04:57:03 UTC | Add test to validate correct mapping of parameter input terminals | 20 January 2022, 15:20:32 UTC |
dce483e | guerler | 19 January 2022, 04:15:46 UTC | Call setMapOver routine in input parameter terminals to detect mapped collections | 20 January 2022, 15:20:31 UTC |
7f0ce0e | mvdbeek | 20 January 2022, 10:31:49 UTC | Add selenium test to check map over state for parameter steps | 20 January 2022, 15:20:31 UTC |
6805a34 | Aysam Guerler | 19 January 2022, 21:26:14 UTC | Merge pull request #13196 from mvdbeek/fix_tool_id_update [21.09] Fix tool id update when updating tool shed tools in editor | 19 January 2022, 21:26:14 UTC |
25ba40e | Nicola Soranzo | 19 January 2022, 19:20:53 UTC | Merge pull request #13203 from simonbray/patch-2 | 19 January 2022, 19:20:53 UTC |
178d972 | Nicola Soranzo | 19 January 2022, 18:40:47 UTC | Merge pull request #13202 from mvdbeek/fix_metadata_source_access | 19 January 2022, 18:40:47 UTC |
b920bfb | davelopez | 19 January 2022, 17:36:50 UTC | Set table columns widths as suggested in comments | 19 January 2022, 17:36:50 UTC |
9ba9783 | davelopez | 19 January 2022, 17:35:26 UTC | Use break-word on overflow-wrap | 19 January 2022, 17:35:26 UTC |
2ed8cf6 | guerler | 19 January 2022, 15:58:28 UTC | Consistently parse content id for workflow modules when updating states | 19 January 2022, 17:18:27 UTC |
ee62798 | Simon Bray | 19 January 2022, 16:44:25 UTC | fix error getting toolshed repo metadata when no repo found | 19 January 2022, 16:54:31 UTC |
98b7b12 | mvdbeek | 13 January 2022, 12:39:05 UTC | Fix metadata source access in tool shed Fixes: ``` Unexpected HTTP status code: 500: {"err_msg": "Metadata may have been defined for some items in revision '8f1b150a2487'. Correct the following problems if necessary and reset metadata.<br/><b>abyss-pe.xml<\/b> - 'NoneType' object has no attribute 'get_biotools_metadata'<br/>"} ``` in https://github.com/galaxyproject/tools-iuc/runs/4792653893?check_suite_focus=true | 19 January 2022, 16:32:47 UTC |
d3d6c60 | mvdbeek | 19 January 2022, 14:49:05 UTC | Fix embedding subworkflow | 19 January 2022, 14:49:05 UTC |
d5b31ee | mvdbeek | 19 January 2022, 13:33:25 UTC | Fix tool id not getting updated on tool update | 19 January 2022, 13:46:31 UTC |
97c5f8d | guerler | 18 January 2022, 19:25:12 UTC | Properly replace tool version in tool identifer string | 19 January 2022, 11:34:19 UTC |
60cd5fc | davelopez | 19 January 2022, 10:26:35 UTC | Fix workflow invocation name overflow This will force wrapping the name of the workflow when it overflows | 19 January 2022, 10:44:58 UTC |
6c354e2 | Marius van den Beek | 18 January 2022, 17:57:46 UTC | Merge pull request #13182 from kxk302/release_21.09 [21.09] Backport of iRODS Object Store path name fix in #13080 | 18 January 2022, 17:57:46 UTC |
043371e | Marius van den Beek | 18 January 2022, 17:57:17 UTC | Merge pull request #13179 from rhpvorderman/patch-5 [21.09] Catch exceptions when job.user is None | 18 January 2022, 17:57:17 UTC |
2b70e34 | Kaivan Kamali | 06 January 2022, 14:41:28 UTC | Revised code based on code review | 18 January 2022, 15:14:35 UTC |
28423d2 | Kaivan Kamali | 13 January 2022, 20:19:10 UTC | Clear the cache before fetching a file from irods object store, to verify file is fetched from the object store, not from the cache | 18 January 2022, 14:51:56 UTC |
faddbee | mvdbeek | 18 January 2022, 13:20:50 UTC | Use job.get_user_email systematically | 18 January 2022, 13:21:09 UTC |
9e546f7 | Ruben Vorderman | 17 January 2022, 15:02:01 UTC | Catch exceptions when job.user is None prevents the following error: galaxy.web.framework.decorators ERROR 2022-01-17 14:52:09,619 [p:18,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 282, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/jobs.py", line 113, in index j['user_email'] = job.user.email AttributeError: 'NoneType' object has no attribute 'email' | 18 January 2022, 13:21:08 UTC |
48e7257 | Björn Grüning | 17 January 2022, 11:27:08 UTC | Merge pull request #13176 from mvdbeek/fix_yaml_downloaded_in_preview [21.09] Show yaml files in preview | 17 January 2022, 11:27:08 UTC |
ea24c7c | mvdbeek | 17 January 2022, 09:14:28 UTC | Show yaml files in preview The `application/yaml` mediatype might be the logical mediatype for yaml (there's no standard yet), but we want to see a textual preview (in the absence of a viewer). Fixes https://github.com/galaxyproject/galaxy/issues/13168 | 17 January 2022, 09:15:57 UTC |
53ec65f | Björn Grüning | 14 January 2022, 16:02:25 UTC | Merge pull request #13157 from mvdbeek/fix_hiding_on_rerun [21.09] Fix re-run with rerun_remap_job_id hiding collection | 14 January 2022, 16:02:25 UTC |
fc8fb85 | mvdbeek | 14 January 2022, 10:49:04 UTC | Set collection update_time when replacing failed elements That allows the new history to update the collection. | 14 January 2022, 11:59:36 UTC |
2a76f41 | Marius van den Beek | 13 January 2022, 15:10:40 UTC | Merge pull request #13154 from mvdbeek/limit_repository_cache_lifetime [21.09] Limit lifetime of repository cache | 13 January 2022, 15:10:40 UTC |
bf71267 | mvdbeek | 13 January 2022, 12:35:36 UTC | Drop refresh argument of get_installed_repository | 13 January 2022, 12:35:36 UTC |
afd9421 | Marius van den Beek | 12 January 2022, 18:48:16 UTC | Don't need to use a joinedload anymore The cache is only used on startup, not during dependency resolution. Also rename _rebuild, since we only use it once now. | 13 January 2022, 11:26:56 UTC |
a327e34 | mvdbeek | 12 January 2022, 11:07:15 UTC | Limit lifetime of repository cache | 13 January 2022, 11:26:55 UTC |
855e9f9 | mvdbeek | 12 January 2022, 19:00:37 UTC | Fix re-run with rerun_remap_job_id hiding collection Fixes https://github.com/galaxyproject/galaxy/issues/13052 | 12 January 2022, 19:10:08 UTC |
a2c4f12 | Björn Grüning | 12 January 2022, 16:40:09 UTC | Merge pull request #13156 from mvdbeek/fix_logo_url [21.09] Fix staticUrlToPrefixed url rewriting | 12 January 2022, 16:40:09 UTC |
817a2d4 | mvdbeek | 12 January 2022, 14:12:14 UTC | Fix staticUrlToPrefixed url rewriting | 12 January 2022, 14:12:14 UTC |
1e889ad | Dannon | 10 January 2022, 23:06:17 UTC | Merge pull request #13138 from mvdbeek/prefix_fixes_backports [21.09] Backport of prefix fixes | 10 January 2022, 23:06:17 UTC |
89c814d | mvdbeek | 06 January 2022, 16:07:14 UTC | Fix logo link when using prefix | 09 January 2022, 18:06:19 UTC |
2af7abd | mvdbeek | 05 January 2022, 12:10:32 UTC | Fix Save and View url | 09 January 2022, 18:01:34 UTC |
0c27185 | mvdbeek | 04 January 2022, 20:56:33 UTC | Fix (per-domain) favicon url | 09 January 2022, 18:01:18 UTC |
8e1e225 | mvdbeek | 26 December 2021, 09:20:40 UTC | Fix old-style page editor load when using prefix | 09 January 2022, 18:00:51 UTC |
ab6e245 | mvdbeek | 25 December 2021, 21:09:15 UTC | Fix tour builder for instances with prefix | 09 January 2022, 18:00:43 UTC |
ba33eca | mvdbeek | 25 December 2021, 19:45:39 UTC | Fix tagService for url prefix | 09 January 2022, 18:00:20 UTC |
74a7ef0 | mvdbeek | 24 December 2021, 13:23:41 UTC | Strip trailing slash from cookie path | 09 January 2022, 18:00:00 UTC |
1328b45 | Nicola Soranzo | 08 January 2022, 10:23:25 UTC | Merge pull request #13134 from mvdbeek/fix_import_of_history_archives_with_tag [21.09] Fix history import for datasets with tags | 08 January 2022, 10:23:25 UTC |
2086ce9 | Marius van den Beek | 08 January 2022, 07:51:46 UTC | Check response status code Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 08 January 2022, 07:51:46 UTC |
a2ede03 | mvdbeek | 07 January 2022, 15:33:11 UTC | Fix history import for datasets with tags and tag dataset used for history import/export tests | 07 January 2022, 16:16:45 UTC |
7fecc4b | Marius van den Beek | 07 January 2022, 09:04:48 UTC | Merge pull request #13126 from thepineapplepirate/master added description of inpcrd and prmtop | 07 January 2022, 09:04:48 UTC |
34cdf6d | Bryan Raubenolt | 06 January 2022, 15:57:00 UTC | added description of inpcrd and prmtop | 06 January 2022, 15:57:00 UTC |
3f8bb2d | Björn Grüning | 28 December 2021, 16:33:08 UTC | Merge pull request #13092 from mvdbeek/fix_dataset_details_prefix [21.09] Fix dataset details button when using prefix | 28 December 2021, 16:33:08 UTC |
4beeac3 | Marius van den Beek | 21 December 2021, 08:48:29 UTC | Merge pull request #13096 from mvdbeek/trim_stdout_stderr [21.09] Limit possible size of info field, read only 100 MB of stdio | 21 December 2021, 08:48:29 UTC |
11c5a19 | mvdbeek | 20 December 2021, 16:39:04 UTC | Limit possible size of info field, read only 100 MB of stdio | 20 December 2021, 16:53:42 UTC |