opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
53,056 Commits 63 Branches 243 Tags
b29cd4e824268b72012694fdc6353bbeac78ce2e
Commit Graph
53056 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
guerler b29cd4e824 Remove unused import 2021-04-19 13:52:56 -04:00
guerler 2208de874a Parse history name to page client, post import request to histories api 2021-04-19 13:46:45 -04:00
guerler 54a927af7c Add new element to pages, allow history import 2021-04-19 12:51:52 -04:00
John Chilton 5c6b738fc5 Merge pull request #11861 from rhpvorderman/patch-3 
BUGFIX: Also check for boolean True, not just string 'True' when evaluating conditional dependencies.
 2021-04-19 10:01:42 -04:00
Ruben Vorderman 4361e1001d Also check for boolean True, not just string 'True' when evaluating conditional dependencies. 
When people know how actual yaml works they might have

    galaxy:
        watch_tools: true

as their config. Which signifies an actual Boolean value. This should be considered by the script as well.
 2021-04-19 14:12:02 +02:00
Marius van den Beek 7cf7e1b737 Merge pull request #11844 from simonbray/wf-check-tools 
Do not invoke workflow if not all tools are available
 2021-04-19 09:34:05 +02:00
Marius van den Beek 87a71e061f Merge pull request #11856 from davelopez/unify_security_decode_id_exceptions 
Unify security decode id exceptions
 2021-04-19 09:15:37 +02:00
davelopez 37f32c444d Remove helper _decode_id in resource_parser 2021-04-17 21:23:48 +02:00
David LópezandNicola Soranzo 1c41c8d8af Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-17 20:49:16 +02:00
davelopez cc4847e4fd Replace helpers with direct call as suggested by code review 2021-04-17 20:08:21 +02:00
Simon Bray 51ee555b40 do not invoke workflow if not all tools are available 2021-04-17 15:41:50 +02:00
David LópezandNicola Soranzo 1a456b1624 Update lib/galaxy/managers/folders.py 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-04-17 14:56:58 +02:00
Marius van den Beek c8f881f0ba Merge pull request #11852 from jmchilton/less_transfer 
Test a better Pulsar configuration for extended metadata.
 2021-04-17 09:24:40 +02:00
Marius van den Beek 796f3a1d24 Merge pull request #11693 from Nerdinacan/hcp-scrolling-fixes 
Beta History scrolling behavior and polling efficiency tuning
 2021-04-17 09:22:58 +02:00
John Chilton 7c77975b58 Merge pull request #11831 from gregvonkuster/relion_star 
Add support for the Relion STAR data format
 2021-04-16 11:46:47 -04:00
John Chilton 0e1c17c382 Merge pull request #11846 from davelopez/fix_10178 
Improve error handling when creating a new History with the master API key
 2021-04-16 11:45:05 -04:00
MasonandMarius van den Beek 3537e8dd34 Update client/src/components/History/providers/CollectionContentProvider/CollectionContentProvider.js 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-04-16 08:17:57 -07:00
MasonandMarius van den Beek efcb4bccab Update client/src/components/History/CurrentCollection/Panel.vue 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-04-16 08:17:45 -07:00
MasonandMarius van den Beek c334ce2449 Update client/src/components/History/History.vue 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-04-16 08:17:40 -07:00
davelopez 2158498371 Add specific exception 2021-04-16 15:57:29 +02:00
davelopez ebe6e30d1a Check for bootstrap admin user (master API key) specifically 2021-04-16 15:57:29 +02:00
davelopez cb3bd5047f Check session when creating history using the API. 
This will return a BadRequest instead of a InternalServerError when trying to create a history with the master API key.
 2021-04-16 15:57:29 +02:00
davelopez 92092ce975 Add API test to create history without session 2021-04-16 15:57:29 +02:00
davelopez 62de18fc35 Fix HistoryDeserializerTestCase::test_sharable to use expected exception 2021-04-16 15:35:12 +02:00
Marius van den Beek 4b749fc891 Merge pull request #11847 from Nerdinacan/upload-button-beta-history 
fixes upload link in beta history empty history message
 2021-04-16 15:11:20 +02:00
davelopez 3eb10b69f5 Remove unused __decode_id function 2021-04-16 14:03:16 +02:00
davelopez ebb68213cb Slightly enhance decode_id error message 2021-04-16 13:59:35 +02:00
davelopez 4c9ffef89c Remove redundant decode_id exception checks 2021-04-16 13:57:56 +02:00
Marius van den Beek 5b0fe015ff Merge pull request #11843 from nsoranzo/restore_triggers 
Restore triggers dropped in #10821
 2021-04-16 13:44:20 +02:00
davelopez 639fe87b92 Raise MalformedId exception when IdEncodingHelper.decode_id() fails 2021-04-16 13:08:54 +02:00
John Chilton b52c78ac1e Merge pull request #11845 from OlegZharkov/folder-change-fix 
fix data stickiness on folder change
 2021-04-15 15:10:57 -04:00
John Chilton cc41f30af6 Better extended metadata configuration for Pulsar (don't copy outputs) 2021-04-15 15:01:28 -04:00
Mason Houtz 315d0772cd fixes upload link in beta history empty history message 2021-04-15 09:24:25 -07:00
John Chilton 289862d384 Merge pull request #11716 from OlegZharkov/library-collections-test 
[Selenium] Library collections export
 2021-04-15 10:31:16 -04:00
John Chilton 51c9c3af08 Merge pull request #11840 from jmchilton/seperate_pulsar_tests 
Separate tests for "remote" and "remote + extended" metadata.
 2021-04-15 09:53:31 -04:00
Oleg Zharkov 47bad1c4b8 fix data stickiness on folder change 2021-04-15 16:10:32 +03:00
Nicola Soranzo ef03871a74 Add migration to re-add the triggers 
Make sure that any BEFORE/AFTER trigger is removed.
 2021-04-15 12:09:21 +01:00
Nicola Soranzo a414444a59 Restore triggers dropped in #10821 
Partially revert commit 33883fe5eb .

Also:
- Update `update_time` on target (i.e. `history`) table AFTER HDA/HDCA
  insert/update/delete
- Use f-strings instead of templates
- Use `CURRENT_TIMESTAMP` also in PostgreSQL (it's equivalent but standard
  SQL)
- Code cleanups
 2021-04-15 12:09:21 +01:00
Mason Houtz e041bc2791 adjusted update grouping, clarifications 2021-04-14 21:11:28 -07:00
greg 767b90c757 Improve approach to sniffing STAR data 2021-04-14 18:22:17 -04:00
John Chilton a73962871e Merge pull request #11839 from mvdbeek/fix_converter_tests 
Fix attribute error in converter tests
 2021-04-14 14:54:09 -04:00
John Chilton d9ca2ed983 Transfer fewer files when using extended + remote metadata. 2021-04-14 13:21:15 -04:00
John Chilton 59fac33d06 Separate tests for "remote" and "remote + extended" metadata. 
We should be testing both these scenarios and ensure they both continue to work.
 2021-04-14 13:21:15 -04:00
mvdbeek 73aeb4c363 Minor fix, don't need to manage handler assignment methods like this 2021-04-14 17:58:45 +02:00
John Chilton e557f3eb60 Merge pull request #11826 from rhpvorderman/smallerimage 
Make k8s container 39 MB smaller by using vim-tiny
 2021-04-14 10:01:22 -04:00
Ruben Vorderman 4c028d5b95 Use a tiny nano as well 2021-04-14 08:13:22 +02:00
Mason Houtz 671002873a fixed collection scrolling 2021-04-13 22:31:01 -07:00
Mason Houtz 367b43c34f loader subject for collection content provider was never firing a completed message 2021-04-13 20:11:53 -07:00
Mason Houtz 8ffb41e8d6 new hcp and scroller implementation 2021-04-13 20:11:53 -07:00
Marius van den Beek 6c098b6226 Merge pull request #11830 from Nerdinacan/fix-upload-link 
Fixed uploader link on tool list and legacy empty history message
 2021-04-13 20:43:11 +02:00