| e2460bd | John Chilton | 04 July 2020, 13:47:17 UTC | Version 20.5.0 of objectstore (tag galaxy-objectstore-20.5.0). | 04 July 2020, 13:47:17 UTC |
| b0a7e65 | John Chilton | 04 July 2020, 13:46:52 UTC | Prep 20.05 release of galaxy-objectstore. | 04 July 2020, 13:46:52 UTC |
| 2ecbaa0 | Nicola Soranzo | 04 July 2020, 00:23:52 UTC | Merge pull request #9952 from jmchilton/release_20.05_packages_0 [20.05] Various small fixes for galaxy packages. | 04 July 2020, 00:23:52 UTC |
| b883856 | John Chilton | 03 July 2020, 16:37:12 UTC | Fix galaxy-containers unit tests. | 03 July 2020, 17:43:49 UTC |
| 78fb5e2 | John Chilton | 03 July 2020, 16:29:57 UTC | Fix Makefile test command for packages | 03 July 2020, 16:29:57 UTC |
| 1dc11a2 | John Chilton | 03 July 2020, 16:29:36 UTC | Fix requirements for galaxy-objectstore. | 03 July 2020, 16:29:48 UTC |
| fa06468 | John Chilton | 03 July 2020, 16:20:00 UTC | Starting work on util 20.5.1 | 03 July 2020, 16:20:00 UTC |
| 92bd1d9 | John Chilton | 03 July 2020, 16:19:37 UTC | Version 20.5.0 of util (tag galaxy-util-20.5.0). | 03 July 2020, 16:19:37 UTC |
| 26d007f | John Chilton | 03 July 2020, 16:18:40 UTC | Prep galaxy-util 20.5.0. | 03 July 2020, 16:18:40 UTC |
| 462f77b | Nicola Soranzo | 03 July 2020, 15:26:25 UTC | Merge pull request #9950 from jmchilton/20_05_packages_1 [20.05] Fixes to package dependency declarations. | 03 July 2020, 15:26:25 UTC |
| be8855a | John Chilton | 03 July 2020, 12:34:29 UTC | Update packages/test_driver/requirements.txt Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 03 July 2020, 12:34:29 UTC |
| 2041a65 | John Chilton | 02 July 2020, 20:32:16 UTC | Update packages/test_driver/requirements.txt Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 02 July 2020, 20:32:16 UTC |
| 6866e79 | John Chilton | 02 July 2020, 15:13:32 UTC | Fixes for package dependency lists. | 02 July 2020, 16:38:46 UTC |
| b3782e8 | John Chilton | 02 July 2020, 15:04:00 UTC | Fix typo. | 02 July 2020, 16:38:46 UTC |
| 811f5a2 | mvdbeek | 30 June 2020, 16:27:42 UTC | Update version to 20.05 | 30 June 2020, 16:27:42 UTC |
| cc19fc7 | Martin Cech | 30 June 2020, 15:53:51 UTC | Merge pull request #9940 from mvdbeek/20.05_release_notes [20.05] Update 20.05 release notes with later PRs | 30 June 2020, 15:53:51 UTC |
| ba3a07a | Nicola Soranzo | 30 June 2020, 15:23:13 UTC | Small fixes | 30 June 2020, 15:23:13 UTC |
| c683013 | mvdbeek | 30 June 2020, 14:58:03 UTC | Merge branch 'release_20.01' into release_20.05 | 30 June 2020, 14:58:03 UTC |
| aadc914 | Dannon | 26 June 2020, 11:59:11 UTC | Update lib/galaxy/web/framework/base.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 30 June 2020, 14:37:35 UTC |
| 56b40e2 | Dannon Baker | 25 June 2020, 22:29:04 UTC | Fix, split imports | 30 June 2020, 14:37:35 UTC |
| 9911c59 | Dannon Baker | 25 June 2020, 22:28:51 UTC | Drop paste usage in cookie handling | 30 June 2020, 14:37:35 UTC |
| 2f12a20 | Dannon Baker | 25 June 2020, 21:49:23 UTC | Initial hack to fix cookie handling that changed with py3. Cookie handling used to be more robust, allowing invalid values to be set without breaking the whole thing. | 30 June 2020, 14:37:35 UTC |
| 93e0200 | mvdbeek | 30 June 2020, 11:24:18 UTC | Update release notes with later PRs | 30 June 2020, 14:32:37 UTC |
| 3157929 | Nicola Soranzo | 30 June 2020, 12:31:17 UTC | Merge pull request #9936 from mvdbeek/backport_sqlite_sniffing_fix | 30 June 2020, 12:31:17 UTC |
| 38e1c38 | Marius van den Beek | 30 June 2020, 11:32:05 UTC | Merge pull request #9921 from dannon/fix-py3-cookie-robustitude [20.01] Make cookie handling more robust | 30 June 2020, 11:32:05 UTC |
| 6fe1ce3 | mvdbeek | 19 June 2020, 09:48:50 UTC | Fix Chira sniffer | 30 June 2020, 09:48:09 UTC |
| 7fb4fc8 | Marius van den Beek | 30 June 2020, 09:46:49 UTC | Merge pull request #9925 from blankenberg/regex-valid-list-20.05 [20.05] Enable regex validator to validate lists of values. | 30 June 2020, 09:46:49 UTC |
| 34b4fcc | John Chilton | 29 June 2020, 20:21:49 UTC | Merge pull request #9931 from almahmoud/patch-1 [20.05] Explicitly cast oidc providers to a list | 29 June 2020, 20:21:49 UTC |
| fb8cf65 | John Chilton | 29 June 2020, 20:20:44 UTC | Merge pull request #9932 from nsoranzo/release_20.05_fix_9929 [20.05] Move the `--debug` flag after the conda subcommand | 29 June 2020, 20:20:44 UTC |
| 95d8ede | Nicola Soranzo | 29 June 2020, 18:38:36 UTC | Merge branch 'release_20.01' into release_20.05 | 29 June 2020, 18:38:36 UTC |
| 6f2bf92 | Nicola Soranzo | 29 June 2020, 18:30:37 UTC | Move the `--debug` flag after the conda subcommand Fix https://github.com/galaxyproject/galaxy/issues/9929 . Also: - Better variable names - Do not use list as argument default | 29 June 2020, 18:33:40 UTC |
| a37af15 | Marius van den Beek | 29 June 2020, 18:31:10 UTC | Merge pull request #9920 from nsoranzo/release_20.01_fix_check_html [20.01] Rewrite `check_html()` and `Text.count_data_lines()` to read a chunk of each line | 29 June 2020, 18:31:10 UTC |
| 4b6e611 | Alexandru Mahmoud | 29 June 2020, 17:45:45 UTC | explicitly cast oidc providers to a list Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 29 June 2020, 17:57:37 UTC |
| b195db8 | Daniel Blankenberg | 29 June 2020, 13:23:19 UTC | Add unit test to regex validator | 29 June 2020, 13:23:19 UTC |
| daa6715 | Daniel Blankenberg | 26 June 2020, 20:25:07 UTC | Enable regex validator to validate lists of values. | 26 June 2020, 20:25:07 UTC |
| 975ba91 | Nicola Soranzo | 26 June 2020, 17:14:46 UTC | Read a chunk of each line in `Text.count_data_lines()` Prevent out-of-memory issues when setting metadata of files with very long lines, e.g. ftp://ftp.ensembl.org/pub/current_json/homo_sapiens/homo_sapiens.json | 26 June 2020, 17:14:49 UTC |
| a9b7a4a | John Chilton | 26 June 2020, 12:43:46 UTC | Merge pull request #9907 from dannon/handler_assignment_bugfix [20.01] Fix incorrect variable assignment | 26 June 2020, 12:43:46 UTC |
| 3d2eae5 | Dannon | 26 June 2020, 11:59:11 UTC | Update lib/galaxy/web/framework/base.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 26 June 2020, 11:59:11 UTC |
| 663b793 | Nicola Soranzo | 26 June 2020, 00:01:13 UTC | Rewrite `check_html()` to read a chunk of each line Fix the following traceback during upload of files with very long lines (e.g. JSON from Ensembl): ``` Traceback (most recent call last): File "/srv/galaxy/tools/data_source/upload.py", line 326, in <module> __main__() File "/srv/galaxy/tools/data_source/upload.py", line 319, in __main__ metadata.append(add_file(dataset, registry, output_path)) File "/srv/galaxy/tools/data_source/upload.py", line 128, in add_file convert_spaces_to_tabs=dataset.space_to_tab, File "/srv/galaxy/lib/galaxy/datatypes/upload_util.py", line 54, in handle_upload convert_spaces_to_tabs=convert_spaces_to_tabs, File "/srv/galaxy/lib/galaxy/datatypes/sniff.py", line 749, in handle_uploaded_dataset_file_internal if not is_binary and check_content and check_html(converted_path): File "/srv/galaxy/lib/galaxy/util/checkers.py", line 42, in check_html line = util.unicodify(line) File "/srv/galaxy/lib/galaxy/util/__init__.py", line 1042, in unicodify raise Exception(msg) Exception: Value '...' could not be coerced to Unicode: MemoryError('') ``` Also: - Use `with` statement to open/close files inside archives - Add tests | 26 June 2020, 02:08:27 UTC |
| 9b56449 | Dannon Baker | 25 June 2020, 22:29:04 UTC | Fix, split imports | 25 June 2020, 22:29:04 UTC |
| cb94255 | Dannon Baker | 25 June 2020, 22:28:51 UTC | Drop paste usage in cookie handling | 25 June 2020, 22:28:51 UTC |
| b418b17 | Dannon Baker | 25 June 2020, 21:49:23 UTC | Initial hack to fix cookie handling that changed with py3. Cookie handling used to be more robust, allowing invalid values to be set without breaking the whole thing. | 25 June 2020, 21:49:23 UTC |
| 9b757c0 | Nicola Soranzo | 25 June 2020, 21:47:31 UTC | Add original exception details in error message | 25 June 2020, 21:47:31 UTC |
| aeb92db | Nicola Soranzo | 24 June 2020, 20:30:10 UTC | Merge branch 'release_20.01' into release_20.05 | 24 June 2020, 20:30:10 UTC |
| 6d29cb3 | Nicola Soranzo | 24 June 2020, 19:22:15 UTC | Merge pull request #9913 from nuwang/fix_user_prefs_leak [20.01] Fix extra preference values leaking between requests | 24 June 2020, 19:22:15 UTC |
| 780f860 | Nuwan Goonasekera | 24 June 2020, 17:44:47 UTC | Fix extra preference values leaking between requests | 24 June 2020, 17:44:47 UTC |
| 9a8be72 | Nuwan Goonasekera | 23 June 2020, 19:55:05 UTC | Fix incorrect variable assignment | 23 June 2020, 22:28:22 UTC |
| 580c36a | Dannon | 23 June 2020, 15:45:26 UTC | Merge pull request #9892 from mvdbeek/tsv_sra_manifest [20.05] Output SRA manifest as tabular dataset | 23 June 2020, 15:45:26 UTC |
| 845b02c | mvdbeek | 23 June 2020, 15:25:06 UTC | Allow sra_manifest upload, so that we can test with planemo | 23 June 2020, 15:25:06 UTC |
| b8dc6d7 | mvdbeek | 23 June 2020, 14:24:12 UTC | Set comment_lines to 1 for SraManifest | 23 June 2020, 14:24:12 UTC |
| 049956b | Marius van den Beek | 23 June 2020, 08:14:03 UTC | Merge pull request #9897 from nsoranzo/release_20.05_py3_only [20.05] Python 2.7 is officially unsupported on 20.05 | 23 June 2020, 08:14:03 UTC |
| f39f6bd | John Chilton | 22 June 2020, 19:44:25 UTC | Merge pull request #9898 from dannon/fix-webpack-import-proxy-prefix [20.05] Fix webpack import proxy prefix | 22 June 2020, 19:44:25 UTC |
| 2a2957d | Dannon Baker | 22 June 2020, 15:50:03 UTC | Eslint global declaration and unused-vars conflict; simply disable rule for a single line instead of declaring. | 22 June 2020, 15:50:03 UTC |
| eaaf0cb | Marius van den Beek | 22 June 2020, 15:06:21 UTC | Merge pull request #9896 from nsoranzo/release_20.05_flake8_fixes [20.05] Fixes for flake8 3.8 and bugbear | 22 June 2020, 15:06:21 UTC |
| 278a033 | mvdbeek | 18 June 2020, 16:51:46 UTC | Add SraManifest datatype This datatype auto-generates its column_names from the first line of the dataset, since the user can choose which columns to include. | 22 June 2020, 15:03:26 UTC |
| c9942e3 | mvdbeek | 18 June 2020, 16:48:21 UTC | Display up to 100 columns Bumping this up from 50 so that we can display the manifest coming from the SRA nicely. | 22 June 2020, 15:01:36 UTC |
| 52138db | mvdbeek | 18 June 2020, 16:46:05 UTC | Allow datatypes to specify data_line_offset If set, the first ``data_line_offset`` lines won't be rendered. This is useful if the column_names are specified in the first line. Otherwise these would be rendered twice, once as the header and once as the data. | 22 June 2020, 15:01:36 UTC |
| ee8d9f0 | mvdbeek | 15 June 2020, 09:53:38 UTC | Update sra_source tool to outut sra_manifest.tabular | 22 June 2020, 15:01:36 UTC |
| 693e115 | John Chilton | 22 June 2020, 12:58:07 UTC | Merge pull request #9894 from dannon/custos_wording_tweak [20.05] Custos login notice wording tweak | 22 June 2020, 12:58:07 UTC |
| 5ee0a00 | Dannon Baker | 21 June 2020, 01:48:59 UTC | Declare webpack global for linting, swap to explicit <root>/static/dist, which should always be correct. | 22 June 2020, 11:49:02 UTC |
| bf2df2a | Dannon Baker | 20 June 2020, 20:19:19 UTC | Move publicPath setting to its own module | 21 June 2020, 01:18:51 UTC |
| bc553e3 | Dannon Baker | 20 June 2020, 18:44:40 UTC | Prettier.? | 20 June 2020, 18:44:40 UTC |
| 919d919 | Dannon Baker | 20 June 2020, 18:44:11 UTC | Fix webpack dynamic imports when serving Galaxy at a prefix | 20 June 2020, 18:44:11 UTC |
| e8466d0 | Nicola Soranzo | 20 June 2020, 18:04:57 UTC | Python 2.7 is officially unsupported on 20.05 | 20 June 2020, 18:04:57 UTC |
| f1f5bea | Nicola Soranzo | 20 June 2020, 17:16:28 UTC | Drop use of removed config option In commit c8c34fa2f766c78cf7753c532e699eb39a22c726 `enable_beta_mulled_containers` was replaced by `enable_mulled_containers`, which defaults to `true`. xref. https://github.com/galaxyproject/galaxy/pull/8195#pullrequestreview-284244354 | 20 June 2020, 17:16:30 UTC |
| 8154413 | Nicola Soranzo | 20 June 2020, 17:11:47 UTC | Fix broken symlink | 20 June 2020, 17:11:47 UTC |
| 41af684 | Nicola Soranzo | 20 June 2020, 17:10:54 UTC | Fixes for flake8 3.8 and bugbear | 20 June 2020, 17:10:54 UTC |
| 691e78c | Dannon Baker | 19 June 2020, 14:36:17 UTC | Minor wording/link tweak (custos privacy policy coming soon, will also be linked here) | 19 June 2020, 14:36:17 UTC |
| bc99000 | Marius van den Beek | 19 June 2020, 11:17:14 UTC | Merge pull request #9890 from OlegZharkov/release_20.05 [20.05] hide expression tools | 19 June 2020, 11:17:14 UTC |
| 87db25d | Dannon Baker | 18 June 2020, 20:32:18 UTC | We don't use the myproxy scope and don't need this language. | 18 June 2020, 20:32:30 UTC |
| 4185a43 | Dannon | 18 June 2020, 17:21:25 UTC | Merge pull request #9889 from dannon/custos-tweaks [20.05] Custos spec fixes | 18 June 2020, 17:21:25 UTC |
| 251821d | Dannon Baker | 18 June 2020, 14:46:36 UTC | Minor verbiage tweaks | 18 June 2020, 14:46:36 UTC |
| ed535ab | Oleg Zharkov | 08 June 2020, 17:15:13 UTC | hide expression tools | 18 June 2020, 14:35:53 UTC |
| 2894cf5 | Dannon Baker | 18 June 2020, 14:31:56 UTC | Drop idphint from custos sample; allowlist will provide this functionality in the future. | 18 June 2020, 14:31:56 UTC |
| 48aae69 | Dannon Baker | 18 June 2020, 14:25:36 UTC | Icon isn't used for custos | 18 June 2020, 14:25:36 UTC |
| 778d79d | Dannon Baker | 18 June 2020, 14:23:21 UTC | Swap enable_idp_logout in sample to default (false) | 18 June 2020, 14:23:21 UTC |
| 6684f70 | Dannon Baker | 18 June 2020, 13:36:42 UTC | Formatting of test data | 18 June 2020, 13:36:42 UTC |
| fc324f7 | Dannon Baker | 18 June 2020, 13:29:51 UTC | Fix custos authnz tests with more request mocks | 18 June 2020, 13:29:51 UTC |
| 1b184ac | Dannon Baker | 18 June 2020, 12:46:52 UTC | Update sample to include default custos url | 18 June 2020, 12:46:52 UTC |
| 94c55ba | Dannon Baker | 18 June 2020, 12:41:54 UTC | Refactor credential loading for custos, compose credential URL instead of requiring specification (TODO: Should be in well-known eventually?) | 18 June 2020, 12:41:59 UTC |
| a14f282 | Dannon Baker | 18 June 2020, 12:41:26 UTC | Swap custos to use composed well-known URL | 18 June 2020, 12:41:26 UTC |
| c0db660 | Dannon | 17 June 2020, 18:31:15 UTC | Merge pull request #9730 from dannon/fix-authnz-provider-naming [20.05] oidc-based authnz provider overhaul; breaking changes for keycloak | 17 June 2020, 18:31:15 UTC |
| b490eaf | Dannon Baker | 17 June 2020, 16:05:25 UTC | Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 | 17 June 2020, 16:05:25 UTC |
| 79e5634 | Nicola Soranzo | 17 June 2020, 15:57:05 UTC | Merge pull request #9884 from dannon/fix-workflow-input-format-spec [20.01] Input dataset module format filtering fix; | 17 June 2020, 15:57:05 UTC |
| 29018e0 | Dannon Baker | 17 June 2020, 13:03:37 UTC | Minor tweak. | 17 June 2020, 13:03:37 UTC |
| f6f579f | Dannon Baker | 17 June 2020, 13:02:33 UTC | Refactor fetching/loading well-known oidc config for custos/keycloak | 17 June 2020, 13:02:33 UTC |
| 78c934f | Dannon Baker | 17 June 2020, 11:30:53 UTC | Input dataset module format filtering fix; this would previously turn `fasta` into `f,,,,a,,,,s,,,...` and so on when you actually tried to run a workflow using this functionality. It would increasingly proliferate commas on runs to the point where it crashed a webserver. | 17 June 2020, 12:41:08 UTC |
| b56ca26 | Nicola Soranzo | 17 June 2020, 12:37:22 UTC | Split imports for future additions | 17 June 2020, 12:37:22 UTC |
| aeed0f7 | Dannon Baker | 17 June 2020, 12:34:55 UTC | Adjust unit test cases to match reality. | 17 June 2020, 12:34:55 UTC |
| 482131a | Dannon Baker | 17 June 2020, 12:18:35 UTC | Add lookup of keycloak/custos backends instead of using ors everywhere | 17 June 2020, 12:18:35 UTC |
| eb69186 | Marius van den Beek | 17 June 2020, 11:19:47 UTC | Merge pull request #9870 from mvdbeek/fix_tool_not_getting_update [20.05] Only cache xml tool files | 17 June 2020, 11:19:47 UTC |
| 674b6be | Dannon Baker | 16 June 2020, 22:18:56 UTC | Backport a small bit of an InteractiveTools test fix to get things green (8d2d8bbc4d2380f4e3745b7d0de734b166a5dc5d) | 16 June 2020, 22:20:07 UTC |
| e915c78 | Dannon Baker | 11 June 2020, 11:39:35 UTC | Minor typo in oidc backends sample | 16 June 2020, 22:20:07 UTC |
| 32fbd22 | Dannon Baker | 11 June 2020, 11:38:56 UTC | Drop commented code related to oidc config loading | 16 June 2020, 22:20:07 UTC |
| 7b5effa | almahmoud | 11 June 2020, 01:24:38 UTC | Adding Keycloak provider to sample oidc backends | 16 June 2020, 22:20:07 UTC |
| ebabfd3 | almahmoud | 11 June 2020, 00:58:40 UTC | Add Keycloak IDP and standardize URL and well-known formation for Keycloak and Custos | 16 June 2020, 22:20:07 UTC |
| ab46011 | Dannon Baker | 06 May 2020, 17:02:53 UTC | Consistently use provider.lower in configuration. Custos != custos. | 16 June 2020, 22:20:07 UTC |
| 3bed894 | Martin Cech | 16 June 2020, 16:21:33 UTC | Merge pull request #9838 from galaxyproject/20.05_release_notes Release notes for 20.05 | 16 June 2020, 16:21:33 UTC |
| 7b99755 | Martin Cech | 16 June 2020, 10:06:13 UTC | include RN in index and add minor changes to them | 16 June 2020, 10:06:13 UTC |
| ccb6657 | John Chilton | 15 June 2020, 12:37:52 UTC | Merge pull request #9878 from mvdbeek/9869_backport [20.05] Improved UploadModal state handling during initialization. | 15 June 2020, 12:37:52 UTC |
