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Author SHA1 Message Date
Kaivan Kamali ef38ff5390 Minor revision 2020-06-25 15:02:23 -04:00
Kaivan Kamali 88a76cd65a Added page documenting steps that happen during Galaxy startup. 2020-06-25 15:02:23 -04:00
Sergey Golitsynskiy 327f58fd6b Merge pull request #9902 from ic4f/dev_inflection 
Trim the inflector
 2020-06-24 09:51:57 -04:00
Nicola Soranzo 5d2e5a0ddf Merge pull request #9909 from gmauro/patch-3 2020-06-24 10:43:03 +01:00
Gianmauro Cuccuru c8182b7e21 generated files from make config-rebuild 2020-06-24 10:11:43 +02:00
Gianmauro Cuccuru f3eb6c62d5 Typo in the uWSGI default umask description 
Typo
 2020-06-24 09:28:26 +02:00
Sergey Golitsynskiy f625d487f0 Fix incorrect variable name 2020-06-23 15:15:57 -04:00
Sergey GolitsynskiyandNicola Soranzo b89eda6f01 Update lib/galaxy/util/inflection.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-23 14:40:09 -04:00
Sergey GolitsynskiyandNicola Soranzo 7e85a8f360 Update lib/galaxy/util/inflection.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-23 14:39:59 -04:00
Sergey GolitsynskiyandNicola Soranzo 733dfd8383 Update lib/galaxy/util/inflection.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-23 14:39:43 -04:00
John Chilton 12f1f22e2f Merge pull request #9802 from mvdbeek/dce_for_jobs 
Allow tool submission with DatasetCollectionElements / make build_for_rerun consumable by API
 2020-06-23 14:20:51 -04:00
John Chilton cf210c5f92 Merge pull request #9782 from davebx/selenium_test_toolbox_filters 
Add selenium test for user toolbox filters.
 2020-06-23 14:16:21 -04:00
Sergey Golitsynskiy 6f9b65619d Use suffix comparison to identify nonchanging words 
As per code review.
 2020-06-23 14:15:27 -04:00
Nicola Soranzo 7ded4170ce Merge branch 'release_20.05' into dev 2020-06-23 10:25:25 +01:00
Marius van den Beek 049956b4f4 Merge pull request #9897 from nsoranzo/release_20.05_py3_only 
[20.05] Python 2.7 is officially unsupported on 20.05
 2020-06-23 10:14:03 +02:00
Sergey Golitsynskiy d8cab1c268 Fix lint error 2020-06-23 03:35:23 -04:00
Sergey Golitsynskiy 9fdea64f57 Add missing test; refactor last bit 2020-06-23 03:32:34 -04:00
Sergey Golitsynskiy fd2759a635 Simplify inflector: 
1. Remove unused methods (that are not covered by tests)
2. Simplify. YAGNI.
 2020-06-23 02:59:42 -04:00
Sergey Golitsynskiy 0c9065bb11 Refactor, modify inflection; add tests 
Linguistic edits:
- plural for virus is viruses, not viri
- plural for fish can be fish or fishes depending on context
- elfs vs elves is infrequent, but not incorrect
- plural for dwarf is dwarfs; "dwarves" was popularized by J.R.R.Tolkien
- saves is not the plural for safe

Refactoring:
- do not instantiate (and modify!) a list of lists to
  pluralize/singularize every single word
- for nonchanging words, do not replace suffix - replace entire word
  (example: a bug would happen for 'heep' because it would match the
  suffix for 'sheep', but the plural for 'heep' is 'heeps')
- get rid of misc. duplication
 2020-06-23 02:36:14 -04:00
Nicola Soranzo 28b292e460 Merge branch 'release_20.05' into dev 2020-06-22 23:14:38 +01:00
John Chilton f39f6bd6c4 Merge pull request #9898 from dannon/fix-webpack-import-proxy-prefix 
[20.05] Fix webpack import proxy prefix
 2020-06-22 15:44:25 -04:00
Dannon Baker 2a2957def4 Eslint global declaration and unused-vars conflict; simply disable rule for a single line instead of declaring. 2020-06-22 11:50:03 -04:00
Marius van den Beek eaaf0cb161 Merge pull request #9896 from nsoranzo/release_20.05_flake8_fixes 
[20.05] Fixes for flake8 3.8 and bugbear
 2020-06-22 17:06:21 +02:00
John Chilton 693e115202 Merge pull request #9894 from dannon/custos_wording_tweak 
[20.05] Custos login notice wording tweak
 2020-06-22 08:58:07 -04:00
Dannon Baker 5ee0a0061d Declare webpack global for linting, swap to explicit <root>/static/dist, which should always be correct. 2020-06-22 07:49:02 -04:00
Sergey Golitsynskiy 5f3a2c4ce4 Merge pull request #9899 from nsoranzo/fix_inflection 
Fix DeprecationWarning: Flags not at the start of the expression
 2020-06-21 15:19:49 -04:00
Nicola Soranzo 0d499b9bb2 Merge pull request #9874 from assuntad23/feature/9669-sort-collection-for-paired-collections 
Feature/9669 sort collection for paired collections
 2020-06-21 03:05:32 +01:00
Nicola Soranzo 8e05787395 Fix DeprecationWarning: Flags not at the start of the expression 
Fix:

```
lib/galaxy/util/inflection.py:188: DeprecationWarning: Flags not at the start of the expression '^(?i)(ox)$'
    match = re.search(rules[rule][0], word, re.IGNORECASE)
```

Also modernise the code a bit.
 2020-06-21 02:40:13 +01:00
Dannon Baker bf2df2ac0f Move publicPath setting to its own module 2020-06-20 21:18:51 -04:00
Nicola Soranzo 0681af64d1 Fix tool test syntax 2020-06-20 23:34:31 +01:00
Nicola Soranzo 4361d2c001 Remove spaces 2020-06-20 22:26:12 +01:00
assuntad23 0962c768f4 updating sort_collection_list test 2020-06-20 14:54:06 -04:00
Dannon Baker bc553e3331 Prettier.? 2020-06-20 14:44:40 -04:00
Dannon Baker 919d919d31 Fix webpack dynamic imports when serving Galaxy at a prefix 2020-06-20 14:44:11 -04:00
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Nicola Soranzo f1f5beaa6a Drop use of removed config option 
In commit c8c34fa2f7
`enable_beta_mulled_containers` was replaced by
`enable_mulled_containers`, which defaults to `true`.

xref. https://github.com/galaxyproject/galaxy/pull/8195#pullrequestreview-284244354
 2020-06-20 18:16:30 +01:00
Nicola Soranzo 815441314c Fix broken symlink 2020-06-20 18:11:47 +01:00
Nicola Soranzo 41af684cc2 Fixes for flake8 3.8 and bugbear 2020-06-20 18:10:54 +01:00
assuntad23 48ef3bb4c4 updating sort_collection_list test 2020-06-19 18:40:33 -04:00
Dannon Baker 691e78c961 Minor wording/link tweak (custos privacy policy coming soon, will also be linked here) 2020-06-19 10:36:17 -04:00
Marius van den Beek bc99000d6a Merge pull request #9890 from OlegZharkov/release_20.05 
[20.05] hide expression tools
 2020-06-19 13:17:14 +02:00
Marius van den Beek 4e80f6495d Merge pull request #9712 from pvanheus/ncbi_taxonomy_sqlite 
Add NcbiTaxonomySQlite class to describe NCBI Taxonomy SQLite databases
 2020-06-19 12:37:36 +02:00
mvdbeek 331321e1ae Add NcbiTaxonomySQlite before SQLite sniffer 2020-06-19 11:53:32 +02:00
mvdbeek 2c90d1e497 Fix Chira sniffer 2020-06-19 11:48:50 +02:00
Peter van Heusden a3893f2c41 Add sample of ncbitaxonomy.sqlite data type 2020-06-18 23:31:24 +02:00
Dannon Baker 87db25d1aa We don't use the myproxy scope and don't need this language. 2020-06-18 16:32:30 -04:00
Dannon Baker a8126ee5f6 Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-06-18 13:21:57 -04:00
Dannon 4185a43293 Merge pull request #9889 from dannon/custos-tweaks 
[20.05] Custos spec fixes
 2020-06-18 13:21:25 -04:00
Dannon a80eb05166 Merge pull request #9891 from Nerdinacan/fix_webpack_hmr_script 
Added missing dev flag to hot module reload script, sourcemaps work now
 2020-06-18 12:58:34 -04:00
Mason 04d561c747 added dev flag to webpack dev server launch 2020-06-18 09:36:05 -07:00