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29938 Commits
Author SHA1 Message Date
Marius van den Beek a68b716743 Merge pull request #13178 from bernt-matthias/topic/stdio/exit-code-parsing 
Fix stdio parsing
 2022-01-25 12:40:02 +01:00
Simon Bray a8e85bf0e8 change display_in_upload to true for PHAR datatype 2022-01-25 09:21:47 +01:00
Dannon 6df67a9038 Merge pull request #13228 from itisAliRH/Remove-jquery.complexify-from-everywhere 
Remove `jquery.complexify` from everywhere
 2022-01-24 23:06:36 -05:00
Alireza Heidari f23f5d9cc7 Remove toolshed password strength from register and change password 2022-01-25 02:49:03 +03:30
Marius van den Beek 98734112e7 Merge pull request #12900 from galaxyproject/dependabot/pip/lib/galaxy/dependencies/tensorflow-2.5.2 
Bump tensorflow from 2.5.1 to 2.5.2 in /lib/galaxy/dependencies
 2022-01-24 20:34:41 +01:00
Alireza Heidari 98d2a34acc Update change_password.mako 2022-01-24 23:04:25 +03:30
Alireza Heidari c41b890a19 Replace check password strength in toolshed register 2022-01-24 23:04:25 +03:30
Alireza Heidari 04ed8f123c Replace check password strength in toolshed change_password 2022-01-24 23:04:25 +03:30
Dannon b69e656b12 Merge pull request #13219 from wm75/patch-1 
Enable display of BAM data without sequence info
 2022-01-24 14:21:02 -05:00
Dannon 976cbebe6c Merge pull request #13159 from davelopez/fix_libraries_non_admin_permissions 
Assorted Data Libraries fixes
 2022-01-24 13:50:07 -05:00
Marius van den Beek 1bb557c74a Merge pull request #13003 from galaxyproject/dependabot/pip/lib/galaxy/dependencies/python-ldap-3.4.0 
Bump python-ldap from 3.2.0 to 3.4.0 in /lib/galaxy/dependencies
 2022-01-24 18:49:44 +01:00
Marius van den Beek 5df80bd0b7 Merge pull request #13171 from ic4f/dev_sa20warning 
Enable setting SQLALCHEMY_WARN_20
 2022-01-24 18:47:35 +01:00
mvdbeek 64d395862e Merge branch 'release_21.09' into dev 2022-01-24 09:28:08 +01:00
mvdbeek f7fde81b9c Print exception 2022-01-23 13:43:06 +01:00
mvdbeek f66b67346e Drop indented, fenced galaxy blocks from test 
https://github.com/galaxyproject/galaxy/issues/13181
 2022-01-23 10:48:22 +01:00
mvdbeek 65b3157c02 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.
 2022-01-23 10:48:22 +01:00
mvdbeek bb2c6ba481 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
 2022-01-23 10:48:21 +01:00
mvdbeek f6ce2f6f5a Merge branch 'release_21.09' into dev 2022-01-22 16:35:43 +01:00
Marius van den Beek 59393dc133 Merge pull request #13216 from mvdbeek/fix_unique_constraint_exceptions 
[21.09] Handle unique tag name constraints
 2022-01-22 16:26:47 +01:00
mvdbeek f0baddd905 Merge branch 'release_21.09' into dev 2022-01-21 16:38:36 +01:00
mvdbeek 29f8b1807f Handle unique tag name constraints 
The idea is to create the tag one by one in a separate session, and
catch any violations.
 2022-01-21 14:50:16 +01:00
Marius van den Beek 851bc56e89 Merge pull request #13210 from mvdbeek/backport_non_data_map_over_fix 
[21.09] Backport allow mapping of collection outputs to parameter inputs
 2022-01-21 13:09:19 +01:00
Wolfgang Maier bc9bd0538f Enable display of BAM data without sequence info 
Unaligned BAM files like produced, e.g., by picard FastqToSam will not have sequence information present in their header.
This change should allow Galaxy to display such files instead of just a
```
Could not display BAM file, error was:
file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
```
message.
 2022-01-21 09:44:56 +01:00
Sergey Golitsynskiy 262c30a4d5 Wrap drop_table in db revision 180 in try/except 2022-01-20 23:11:17 -05:00
davelopez 0bc41e0b89 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
 2022-01-20 19:39:03 +01:00
davelopez 4f104cfbd7 Add API test for dataset collections batch update 
When merging forward replace `_raw_update_batch` to `_update_batch`
 2022-01-20 19:25:45 +01:00
John Chilton 9f8223d845 Merge pull request #10304 from bernt-matthias/topic/test-sort-order-multiple 
Reimplement collection order test, add wrong order, add `expect_test_failure` attribute
 2022-01-20 12:31:01 -05:00
mvdbeek 7f0ce0ec84 Add selenium test to check map over state for parameter steps 2022-01-20 16:20:31 +01:00
Dannon d34e43d3ce Merge pull request #12571 from natefoo/fix-nested-object-store-example 
Update and correct sample object store config file
 2022-01-20 09:31:15 -05:00
Dannon 529ca10e09 Merge pull request #13209 from cat-bro/admin-user-list-sort-by-last-login_rebased 
make admin user list sortable by last login
 2022-01-20 09:23:15 -05:00
cat-bro 7bfeddf57d sort admin user list by last login 2022-01-20 21:21:16 +11:00
mvdbeek 15d4d2952d Fix ToolApp 2022-01-20 08:39:20 +01:00
Nicola Soranzo a8f1a900a1 Merge pull request #13147 from mvdbeek/mako_fix 2022-01-19 23:00:15 +00:00
Aysam Guerler 6805a345d7 Merge pull request #13196 from mvdbeek/fix_tool_id_update 
[21.09] Fix tool id update when updating tool shed tools in editor
 2022-01-19 16:26:14 -05:00
Nicola Soranzo c6058f126b Merge branch 'release_21.09' into dev 2022-01-19 19:22:05 +00:00
Nicola Soranzo 25ba40ee9c Merge pull request #13203 from simonbray/patch-2 2022-01-19 19:20:53 +00:00
Nicola Soranzo 5390a07224 Merge branch 'release_21.09' into dev 2022-01-19 19:05:56 +00:00
Nicola Soranzo 178d97222d Merge pull request #13202 from mvdbeek/fix_metadata_source_access 2022-01-19 18:40:47 +00:00
Nicola Soranzo 60976ec69b Use importlib.resources.files() for ToolShed config_schema.yml 2022-01-19 18:20:21 +00:00
Nicola Soranzo bcc505cbbd Drop remaining uses of template_path config 2022-01-19 18:20:20 +00:00
Nicola Soranzo 6bb9d87d7e Use super() 2022-01-19 18:20:20 +00:00
Marius van den BeekandNicola Soranzo f6915cf9cf Replace only use of app_template_path 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-19 18:20:19 +00:00
mvdbeek 817272085e Move uwsgi_schema.yml as well 2022-01-19 18:20:18 +00:00
mvdbeek f1e62b1e0d Fix template resolition for tool shed 2022-01-19 18:20:17 +00:00
mvdbeek 03e218df68 Fix config schema packaging 2022-01-19 18:20:16 +00:00
mvdbeek d3cfb72266 Use importlib_resources 2022-01-19 18:20:16 +00:00
mvdbeek 19e9e55ca3 Fix uvloop message 2022-01-19 18:20:15 +00:00
mvdbeek 01a5cbba37 Fix resolving mako paths for installed Galaxy 2022-01-19 18:20:15 +00:00
mvdbeek f403fd8fcd Fix resolving path to config_schema.yml for installed Galaxy 2022-01-19 18:20:14 +00:00
guerler 2ed8cf644d Consistently parse content id for workflow modules when updating states 2022-01-19 18:18:27 +01:00