| 186a2f6 | Dannon | 10 August 2022, 17:17:16 UTC | Merge pull request #14428 from mvdbeek/update_gravity_pylibmagic [22.05] Update pylibmagic and gravity | 10 August 2022, 17:17:16 UTC |
| 728ceeb | mvdbeek | 10 August 2022, 13:30:20 UTC | Fix nested archive unzipping on windows We need the directory markers in order for the default windows zip utility to be able to extract the archives. Also requires https://github.com/evanmiller/mod_zip/commit/51cf45d3e9f51e02224af017b235d1d30fbf28fb or newer on the mod_zip side. | 10 August 2022, 15:33:29 UTC |
| f83aefd | mvdbeek | 09 August 2022, 09:01:39 UTC | Calculate CRC32 for files in size between 1444 and 1459 bytes | 10 August 2022, 15:33:25 UTC |
| b3c8e38 | Marius van den Beek | 10 August 2022, 15:09:25 UTC | Fix typo in sample variable Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 10 August 2022, 15:09:25 UTC |
| 0eff482 | mvdbeek | 10 August 2022, 14:51:19 UTC | Pass --cleanenv by default to singularity command | 10 August 2022, 14:52:59 UTC |
| fc86a42 | mvdbeek | 10 August 2022, 14:12:17 UTC | Update pylibmagic and gravity | 10 August 2022, 14:12:17 UTC |
| a22d62e | davelopez | 10 August 2022, 13:26:37 UTC | Ignore case when filtering using `contains` The `contains` function is case sensitive so we must apply first `func.lower` to the column and the value. I tried this first but it doesn't work... so replacing contains with `ilike` made the trick, but I don't like it at all... | 10 August 2022, 13:26:37 UTC |
| cf32b54 | davelopez | 10 August 2022, 13:14:53 UTC | Add API test for history contents filtering Filtering history contents by name should be case insensitive | 10 August 2022, 13:14:53 UTC |
| 1316285 | Marius van den Beek | 10 August 2022, 08:33:53 UTC | Merge pull request #14424 from dannon/fix-workflow-step-insertion [22.05] Fix workflow direct step insertion in workflow editor | 10 August 2022, 08:33:53 UTC |
| fbd52b9 | Dannon Baker | 10 August 2022, 00:18:03 UTC | Drop test for delegation -- this is part of the component (for now). | 10 August 2022, 00:18:03 UTC |
| 566e00d | Dannon Baker | 10 August 2022, 00:12:13 UTC | Fix vue-attributes-order | 10 August 2022, 00:12:13 UTC |
| 3c1d6f2 | Dannon Baker | 10 August 2022, 00:09:31 UTC | Eliminate SaveAs old modal usage in the workflow editor, swapping to b-modal. needs refactoring, modal should probably be split out, but this is mvp | 10 August 2022, 00:09:31 UTC |
| 58597e1 | Dannon Baker | 09 August 2022, 20:34:11 UTC | Swap back to 10 nodes as the threshold for confirmation; cleanup. | 09 August 2022, 20:34:11 UTC |
| ccc781f | Dannon Baker | 09 August 2022, 20:31:00 UTC | Use standard bootstrap modal for copyIntoWorkflow; yagni w/ utilities -- keep action with component. Separation wasn't remotely clean anyway, with it taking the component instance as the first argument to operate on. | 09 August 2022, 20:31:37 UTC |
| 6090fb1 | Marius van den Beek | 09 August 2022, 16:42:30 UTC | Merge pull request #14406 from davelopez/support_quoted_strings_in_bool_expression [22.05] Support quoted strings in bool expressions | 09 August 2022, 16:42:30 UTC |
| 858c57d | Dannon | 09 August 2022, 15:27:15 UTC | Merge pull request #14343 from dannon/fix-oldstyle-dataset-display [22.05] Fix oldstyle dataset display | 09 August 2022, 15:27:15 UTC |
| 31c3826 | Dannon Baker | 09 August 2022, 14:50:40 UTC | Raise threshold for workflow insertion confirmation to 10 steps | 09 August 2022, 14:50:40 UTC |
| f19e19c | Dannon Baker | 09 August 2022, 14:49:43 UTC | In workflow step insertion from saved workflow, swap to browser standard (jquery-free, whew) confirmation for now, as a bugfix -- we eventually want this to be a proper vue-confirm modal. | 09 August 2022, 14:49:43 UTC |
| c6a967e | Marius van den Beek | 09 August 2022, 14:30:57 UTC | Merge pull request #14420 from dannon/tool-success-njobs-fix [22.05] Fix number of jobs submitted display in tool success. | 09 August 2022, 14:30:57 UTC |
| 55bb5e0 | Dannon Baker | 09 August 2022, 12:53:50 UTC | Fix number of jobs submitted display in tool success. | 09 August 2022, 12:54:27 UTC |
| 2c5c4bb | Marius van den Beek | 09 August 2022, 12:06:18 UTC | Merge pull request #14418 from davelopez/22.05_dataset_details_additional_fixes [22.05] Fix additional errors when requesting dataset details in history contents | 09 August 2022, 12:06:18 UTC |
| 9c63cb6 | davelopez | 09 August 2022, 10:05:04 UTC | Avoid possible empty IDs in expanded datasets In some unknown situations, the expanded items IDs contains just blank spaces and provoke a Bad Request. | 09 August 2022, 10:05:04 UTC |
| ef9da34 | davelopez | 09 August 2022, 10:01:48 UTC | Handle history index params validation properly Instead of trying to raise an error for each possible case, just wrap the ValidationError with our custom exceptions. This will finally return a 400 instead of 500 error code when any query parameter is invalid. | 09 August 2022, 10:01:48 UTC |
| b46b1ae | davelopez | 09 August 2022, 09:58:14 UTC | Add more API tests for errors in dataset details | 09 August 2022, 09:58:14 UTC |
| e6b64e8 | Marius van den Beek | 08 August 2022, 16:06:01 UTC | Merge pull request #14414 from mvdbeek/work_around_python_not_on_path [22.05] Fix first startup when only python3 is on PATH | 08 August 2022, 16:06:01 UTC |
| da334f1 | mvdbeek | 08 August 2022, 14:27:04 UTC | Fix first startup when only python3 is on PATH | 08 August 2022, 14:28:26 UTC |
| 1238d29 | Dannon | 05 August 2022, 20:48:52 UTC | Merge pull request #14403 from dannon/backport-fix-dataset-links [22.05] Fix dataset list operation to switch between histories | 05 August 2022, 20:48:52 UTC |
| bcff4a1 | davelopez | 05 August 2022, 13:56:21 UTC | Update integration test Test boolean expression with group names containing spaces and surrounded by single quotes | 05 August 2022, 13:56:21 UTC |
| 4846d04 | davelopez | 05 August 2022, 13:54:04 UTC | Add unit test for quoted strings with spaces | 05 August 2022, 13:54:04 UTC |
| aff0c5d | davelopez | 05 August 2022, 13:53:16 UTC | Add quoted string support to boolean expressions | 05 August 2022, 13:53:16 UTC |
| 574c8f8 | Dannon | 05 August 2022, 01:35:49 UTC | Merge pull request #14358 from hexylena/fix-tool-encoding [22.05] Fix handling + encoding of spaces in tool names | 05 August 2022, 01:35:49 UTC |
| f274283 | guerler | 04 August 2022, 02:49:50 UTC | Fix dataset list operation to switch between histories | 04 August 2022, 18:59:18 UTC |
| 954012a | David López | 04 August 2022, 17:13:01 UTC | Merge pull request #14402 from dannon/copy-datasets-always-available [22.05] Always allow 'copy datasets' action in history, even when empty. | 04 August 2022, 17:13:01 UTC |
| 3f3f7b8 | Marius van den Beek | 04 August 2022, 15:53:41 UTC | Merge pull request #14395 from davelopez/fix_dataset_details_validation [22.05] Fix validation issue for dataset_details | 04 August 2022, 15:53:41 UTC |
| 0c6c939 | Dannon Baker | 04 August 2022, 13:21:25 UTC | Allow 'Copy Datasets' action in history even when the current history is empty. This action can be used to copy datasets *into* the history as well, so is appropriate. | 04 August 2022, 13:21:25 UTC |
| 083978d | davelopez | 04 August 2022, 11:59:52 UTC | Raise exception when details contains empty IDs Otherwise the pydantic validation will raise an unhandled exception with a rather cryptic error message | 04 August 2022, 11:59:52 UTC |
| e2cec35 | davelopez | 04 August 2022, 11:58:11 UTC | Add API test for history content details With empty ids it should return a 400 Bad Request a not just a 500 error | 04 August 2022, 11:58:11 UTC |
| d66bbe2 | davelopez | 04 August 2022, 09:29:42 UTC | Avoid requesting details for invalid item IDs In some circumstances the item ID might be undefined or empty and the request will fail with a rather cryptic validation error. ``` Aug 03 10:44:54 sn06.galaxyproject.eu gunicorn[2458098]: pydantic.error_wrappers.ValidationError: 2 validation errors for HistoryContentsIndexParams Aug 03 10:44:54 sn06.galaxyproject.eu gunicorn[2458098]: dataset_details -> 1 Aug 03 10:44:54 sn06.galaxyproject.eu gunicorn[2458098]: Invalid characters in encoded ID (type=value_error) Aug 03 10:44:54 sn06.galaxyproject.eu gunicorn[2458098]: dataset_details Aug 03 10:44:54 sn06.galaxyproject.eu gunicorn[2458098]: unhashable type: 'set' (type=type_error) ``` | 04 August 2022, 09:29:42 UTC |
| af949c2 | davelopez | 04 August 2022, 09:23:31 UTC | Revert adding __hash__ to BaseDatabaseIdField | 04 August 2022, 09:23:31 UTC |
| 6dec9a0 | Dannon | 02 August 2022, 14:44:38 UTC | Merge pull request #14388 from davelopez/22.05_fix_unhashable_type [22.05] Fix unhashable type in history contents API | 02 August 2022, 14:44:38 UTC |
| e5b11bb | davelopez | 02 August 2022, 09:10:35 UTC | Add unit tests for DabaseIdFields hashing | 02 August 2022, 09:10:35 UTC |
| 0c4b68f | davelopez | 01 August 2022, 08:49:21 UTC | Fix unhashable type in history contents API Add __hash__ function to BaseDatabaseIdField | 02 August 2022, 09:09:05 UTC |
| 8810ccb | David López | 30 July 2022, 21:26:26 UTC | Merge pull request #14386 from bgruening/remove_debug_statements [22.05] remove debug statements from tool search | 30 July 2022, 21:26:26 UTC |
| 7f82cad | Björn Grüning | 30 July 2022, 21:14:29 UTC | remove unused import | 30 July 2022, 21:14:29 UTC |
| d9c3afa | Bjoern Gruening | 30 July 2022, 19:42:23 UTC | remove debug statements from tool search | 30 July 2022, 19:42:23 UTC |
| 4b06817 | Dannon | 29 July 2022, 12:12:52 UTC | Merge pull request #14372 from neoformit/tool-search-backend-cam [22.05] Tool search backend bug fixes | 29 July 2022, 12:12:52 UTC |
| 38b8207 | Dannon | 29 July 2022, 01:59:12 UTC | Merge pull request #14375 from davelopez/history_contents_detailed_only_for_expanded [22.05] Optimize History watcher to request detailed information only for expanded items | 29 July 2022, 01:59:12 UTC |
| 98c7395 | Cameron Hyde | 28 July 2022, 15:43:07 UTC | Fix linting | 28 July 2022, 22:32:32 UTC |
| c1d3259 | Cameron Hyde | 28 July 2022, 15:33:34 UTC | Fix linting | 28 July 2022, 22:32:32 UTC |
| 23c6ef6 | Cameron Hyde | 28 July 2022, 15:22:44 UTC | Fix linting | 28 July 2022, 22:32:32 UTC |
| 03e3386 | Cameron Hyde | 28 July 2022, 15:09:14 UTC | Fix linting | 28 July 2022, 22:32:32 UTC |
| 112d663 | Cameron Hyde | 26 July 2022, 20:07:14 UTC | Minor refactor for linter | 28 July 2022, 22:32:32 UTC |
| 00e4658 | Cameron Hyde | 26 July 2022, 19:37:04 UTC | Fix type error | 28 July 2022, 22:32:32 UTC |
| cdf982a | Cameron Hyde | 26 July 2022, 19:29:59 UTC | Fix type hint error | 28 July 2022, 22:32:32 UTC |
| ffb9b34 | Cameron Hyde | 26 July 2022, 19:29:48 UTC | Update config schema descriptions for tool search | 28 July 2022, 22:32:32 UTC |
| c476d65 | Cameron Hyde | 26 July 2022, 16:30:40 UTC | Fix syntax error | 28 July 2022, 22:32:32 UTC |
| 2900b1d | Cameron Hyde | 26 July 2022, 00:44:13 UTC | Fix config_schema type error | 28 July 2022, 22:32:32 UTC |
| 406db82 | Cameron Hyde | 26 July 2022, 00:42:28 UTC | Fix type hinting error | 28 July 2022, 22:32:32 UTC |
| 852a7a8 | Cameron Hyde | 26 July 2022, 00:32:08 UTC | Remove redundant config argument | 28 July 2022, 22:32:32 UTC |
| f2cde6d | Cameron Hyde | 26 July 2022, 00:30:53 UTC | Replace get_or_create_index function | 28 July 2022, 22:32:32 UTC |
| fb2cd59 | Cameron Hyde | 25 July 2022, 22:11:18 UTC | Refactor ToolPanelViewSearch.build_index | 28 July 2022, 22:32:32 UTC |
| c8e589d | Cameron Hyde | 25 July 2022, 22:10:18 UTC | Add fallback generic name field when ngrams are disabled | 28 July 2022, 22:32:31 UTC |
| e5d6b3c | Cameron Hyde | 25 July 2022, 22:05:43 UTC | Re-implement OR grouping to work around StopFiltered words | 28 July 2022, 22:32:31 UTC |
| 90bdaea | Cameron Hyde | 25 July 2022, 22:04:42 UTC | Add tool search docstring | 28 July 2022, 22:32:31 UTC |
| e952095 | Cameron Hyde | 23 July 2022, 21:38:52 UTC | Switch tool search score logging to debug | 28 July 2022, 22:32:31 UTC |
| bfa786a | Cameron Hyde | 23 July 2022, 21:38:01 UTC | Update call to Toolbox.search to pass config variables as object | 28 July 2022, 22:32:07 UTC |
| c1b3e7d | Cameron Hyde | 23 July 2022, 21:36:34 UTC | Remove dumping of tool search index to JSON | 28 July 2022, 22:29:59 UTC |
| 7b28f27 | Cameron Hyde | 23 July 2022, 21:36:05 UTC | Add field id_exact to permit exact match against tool_id field | 28 July 2022, 22:29:59 UTC |
| 11cb30d | Cameron Hyde | 23 July 2022, 21:35:07 UTC | Limit tool search by config variable tool_search_limit | 28 July 2022, 22:29:58 UTC |
| ee58450 | Cameron Hyde | 23 July 2022, 21:29:54 UTC | Pass config to tool search with config reference. Remove description ngram search. | 28 July 2022, 22:29:58 UTC |
| 1e058ea | Cameron Hyde | 23 July 2022, 21:25:05 UTC | Remove redundancy and refactor for readability | 28 July 2022, 22:29:58 UTC |
| 2ca6e73 | Cameron Hyde | 23 July 2022, 20:38:56 UTC | Add new config params for tool search | 28 July 2022, 22:29:58 UTC |
| 476daef | Cameron Hyde | 23 July 2022, 16:59:32 UTC | Remove wildcard search query and boost exact name matches | 28 July 2022, 22:29:58 UTC |
| f64ebbe | Cameron Hyde | 23 July 2022, 15:20:08 UTC | Add json tool search index for debugging | 28 July 2022, 22:29:58 UTC |
| bcabd5d | Cameron Hyde | 22 July 2022, 22:39:18 UTC | Refactor tool search: ngrams, remove OR search, fix boost | 28 July 2022, 22:29:58 UTC |
| 7ba6d26 | Cameron Hyde | 22 July 2022, 17:18:20 UTC | Logging scores for tool search api | 28 July 2022, 22:29:58 UTC |
| 4021281 | Cameron Hyde | 22 July 2022, 17:16:42 UTC | Change from BM25F to Frequency search algorithm | 28 July 2022, 22:29:58 UTC |
| e383e59 | Nicola Soranzo | 27 July 2022, 14:38:19 UTC | Merge branch 'release_22.01' into release_22.05 | 27 July 2022, 14:38:19 UTC |
| 0e4e318 | David López | 27 July 2022, 10:17:40 UTC | Merge pull request #14376 from dannon/fix-history-sync [22.05] Fix incorrect history swapping in some cases where we swap on the client but the server is never notified. | 27 July 2022, 10:17:40 UTC |
| c0b80f3 | Dannon Baker | 26 July 2022, 14:57:47 UTC | Fix incorrect history swapping / see more in #14173 | 26 July 2022, 15:07:33 UTC |
| 6c43d66 | Marius van den Beek | 26 July 2022, 12:26:15 UTC | Merge pull request #14373 from cat-bro/fix-IMPLICITLY_REQUIRED_TOOL_FILES-for-maxquant [22.01] Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 26 July 2022, 12:26:15 UTC |
| fc940e1 | davelopez | 26 July 2022, 11:57:14 UTC | Optimize history watcher for detailed contents This will requests the detailed view only for those items that are currently expanded in the history panel instead of all of them. | 26 July 2022, 11:57:14 UTC |
| 9b3bfe0 | davelopez | 26 July 2022, 11:53:47 UTC | Refactor history watcher to use axios params | 26 July 2022, 11:53:47 UTC |
| 8ec4fa4 | davelopez | 26 July 2022, 11:48:18 UTC | Allow to optionally set axios params in `urlData` | 26 July 2022, 11:48:18 UTC |
| 25e847e | cat-bro | 22 July 2022, 15:54:36 UTC | Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 25 July 2022, 17:07:36 UTC |
| 8b6030f | Nicola Soranzo | 25 July 2022, 02:04:44 UTC | Merge pull request #14371 from mr-c/tool_utils_types_22.05 | 25 July 2022, 02:04:44 UTC |
| a20d796 | Marius van den Beek | 24 July 2022, 16:22:21 UTC | Merge pull request #14332 from bernt-matthias/topic/options-var [22.01] fix `startswith` attribute of `<options>` | 24 July 2022, 16:22:21 UTC |
| 1b5ba60 | Marius van den Beek | 24 July 2022, 16:19:16 UTC | Merge pull request #14325 from davelopez/22.05_allow_dataset_actions_in_new_tab [22.05] Add HREF links to some history item actions | 24 July 2022, 16:19:16 UTC |
| 53744eb | Marius van den Beek | 24 July 2022, 16:18:16 UTC | Merge pull request #14364 from dannon/fix-tool-search-config-ngram [22.05] Fix tool search config defaults | 24 July 2022, 16:18:16 UTC |
| 21a7ad2 | Marius van den Beek | 24 July 2022, 16:17:39 UTC | Merge pull request #14363 from davelopez/fix_enable_account_interface [22.01] Fix enable_account_interface option hiding too much | 24 July 2022, 16:17:39 UTC |
| f902d3c | Michael R. Crusoe | 24 July 2022, 08:29:08 UTC | Apply suggestions from code review Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 24 July 2022, 08:29:08 UTC |
| e955f87 | Michael R. Crusoe | 22 July 2022, 20:35:29 UTC | pin schema-salad version | 23 July 2022, 18:59:20 UTC |
| 8d38d52 | Michael R. Crusoe | 22 July 2022, 18:58:38 UTC | type hints that cwltool used to carry | 23 July 2022, 18:59:20 UTC |
| 37826a1 | Dannon Baker | 22 July 2022, 16:25:06 UTC | Update remaining uses of config.get in tool service | 22 July 2022, 16:25:06 UTC |
| f2bdee4 | davelopez | 22 July 2022, 16:11:14 UTC | Display correct description in Manage Information | 22 July 2022, 16:11:14 UTC |
| b004c32 | davelopez | 22 July 2022, 16:10:19 UTC | Display Manage Cloud Auth user preferences always | 22 July 2022, 16:10:19 UTC |
| e775648 | davelopez | 22 July 2022, 16:09:23 UTC | Disable only specific inputs in user information | 22 July 2022, 16:09:23 UTC |
| b00a070 | Dannon Baker | 22 July 2022, 15:16:22 UTC | Fix default for tool search ngrams | 22 July 2022, 16:06:31 UTC |
| 3dd75a8 | Dannon | 21 July 2022, 20:13:44 UTC | Merge pull request #14340 from mvdbeek/dont_hit_disk_in_serializer [22.05] Don't hit object store when getting size | 21 July 2022, 20:13:44 UTC |
| 57645b1 | John Chilton | 21 July 2022, 14:33:19 UTC | Merge pull request #14329 from jdavcs/release_22.05_dbinit_error Improve handling of non-existent or uninitialized database when running upgrade script | 21 July 2022, 14:33:19 UTC |
