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 |
f566c87 | John Chilton | 22 May 2020, 13:33:00 UTC | Improved UploadModal state handling during initialization. Track whether datatypes and genomes have been set and use the LoadingSpan component to display information about this wait if the component is not yet ready. | 15 June 2020, 10:24:47 UTC |
9bc4c53 | mvdbeek | 12 June 2020, 11:33:05 UTC | Only cache xml files | 12 June 2020, 11:33:05 UTC |
9de73a8 | Nicola Soranzo | 12 June 2020, 00:59:37 UTC | Merge pull request #9866 from mvdbeek/fix_tool_not_getting_update [20.05] Invalidate tool cache when tool modified outside of Galaxy | 12 June 2020, 00:59:37 UTC |
ff492b6 | mvdbeek | 11 June 2020, 17:23:34 UTC | Add source_path property to YamlToolSource and CwlToolSource | 11 June 2020, 17:23:34 UTC |
cdf1036 | mvdbeek | 11 June 2020, 15:28:33 UTC | Make tool_source and macro_path properties, move paths_and_modtimes to interface | 11 June 2020, 15:38:08 UTC |
72f7f14 | Nicola Soranzo | 11 June 2020, 15:00:51 UTC | Fix typo | 11 June 2020, 15:00:51 UTC |
bcc7cc6 | mvdbeek | 11 June 2020, 14:50:12 UTC | Don't store path_and_modtimes since we don't re-use it | 11 June 2020, 14:50:12 UTC |