mvdbeek
b2454dcafe
Use TagHandlerSession in ModelPersistenceContext
...
Eliminates an unnecessary flush
2021-10-18 11:42:41 +02:00
mvdbeek
f0092c9926
Use TagHandlerSession to avoid flushes
2021-10-18 11:42:41 +02:00
mvdbeek
0f685ab65c
Now that we don't flush when adding hids we can do it earlier
2021-10-18 11:42:41 +02:00
mvdbeek
ee6ec264c4
Flush just once per import
...
That might mean we accumulate a lot of items in memory, but if we don't
do this we need to assign hids for every flush (which is possible).
2021-10-18 11:42:41 +02:00
mvdbeek
f63dc3b9df
Do not explicitly begin a new transaction when getting next_hid
...
There is no transactional state, so it seems unncessary. Not starting an
explicit transaction means sqlalchemy won't flush the current session,
which means we're not committing a HDA/HDCA to the database that doesn't
have a hid yet.
2021-10-18 11:42:41 +02:00
mvdbeek
cfdd6e9dfb
Also raise eception if item has no hid
2021-10-18 11:42:41 +02:00
mvdbeek
6c15c1334c
Fix copy action
2021-10-18 11:42:41 +02:00
mvdbeek
00a274c26a
Explicitly pass history into DatasetCollectionManager.create
2021-10-18 11:42:40 +02:00
mvdbeek
53e3cf56c3
Fix hda_manager.copy so it doesn't flush datasets without a history_id
2021-10-18 11:42:40 +02:00
mvdbeek
bf7cc9072c
Always set item.history to self
...
What I've observed is that for a job with a immediate post job action
(e.g setting a dataset tag within https://github.com/galaxyproject/galaxy/blob/202bff420761c63fc30ac933630d72dd40496248/lib/galaxy_test/api/test_workflows.py#L3605 )
something is resetting hda.history_id. I have no idea how this happens.
Possibly https://github.com/galaxyproject/galaxy/blob/f66520e4a6f6b71516c48861f473c1b430ad967f/lib/galaxy/tools/actions/__init__.py#L557
fetches a new HDA from a different sqlalchemy session and modifies it ??
2021-10-18 11:42:40 +02:00
mvdbeek
b4befd02b5
Raise exception for if we're saving a historyless HDA
2021-10-18 11:42:39 +02:00
mvdbeek
ea40edf1b7
Merge branch 'release_21.05' into release_21.09
2021-10-18 11:08:01 +02:00
Marius van den Beek
6fcdc5c44d
Merge pull request #12731 from mvdbeek/fix_bad_merge
...
[21.05] Fix bad merge
2021-10-18 11:06:21 +02:00
mvdbeek
f162322b35
Fix bad merge
...
we've changed the import
2021-10-18 10:16:17 +02:00
mvdbeek
9c4b6305b9
Merge branch 'release_21.05' into release_21.09
2021-10-18 08:29:12 +02:00
mvdbeek
2a4cd49083
Merge branch 'release_21.01' into release_21.05
2021-10-18 08:28:04 +02:00
mvdbeek
14b6579eb1
Merge branch 'release_20.09' into release_21.01
2021-10-18 08:23:32 +02:00
mvdbeek
b60e5ea76d
Merge branch 'release_20.05' into release_20.09
2021-10-18 08:22:04 +02:00
David López
aee63e5aba
Merge pull request #12728 from jmchilton/show_page_pdf_fixes
...
[21.09] Various show page PDF bug fixes.
2021-10-17 20:03:36 +02:00
John Chilton
5cd46c3d5e
Various show page PDF bug fixes.
...
- In FastAPI mode GET /api/pages/{id}.pdf was being masked by /api/pages/{id} and the tested 400 was an invalid ID error.
- trans.response was being used in the service layer and was unavailable under FastAPI - moved setting response type back up into the controller.
- API tests should skip if the Galaxy configuration is invalid - it wasn't doing this.
While I was in there I also tweaked the exception handling a bit to indicate that this is not a USER FORBIDDEN (403) operation so much as an optional SERVER configuration NOT IMPLEMENTED (501).
2021-10-16 15:00:59 -04:00
Marius van den Beek
bf4dc3bd46
Merge pull request #12722 from mvdbeek/fix_recursively_deleting_hdcas
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[20.05] Continue deleting dataset collection if member HDA has no history
2021-10-16 11:09:54 +02:00
mvdbeek
0aaef9c93e
Continue deleting dataset collection if member HDA has no history
...
These can be cleaned up with pgcleanup.
2021-10-15 19:09:59 +02:00
Dannon
0c1c0be38b
Merge pull request #12702 from guerler/reduce_flickering
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[21.09] Reduce number of Tool Form requests in Workflow Editor, improve visibility of Tool Infos
2021-10-15 10:58:31 -04:00
Nicola Soranzo
bb96d2df96
Merge pull request #12718 from bernt-matthias/topic/vg-gz
2021-10-15 14:00:19 +01:00
Matthias Bernt
6d14b2b73d
make vg a subclass of CompressedArchive
...
the test data in IUC's vg repo is (`file test-data/*vg`):
- test-data/hla.vg: data
- test-data/x.vg: Blocked GNU Zip Format (BGZF; gzip compatible), block length 2909
this makes https://github.com/galaxyproject/tools-iuc/pull/4070
fail because the x.vg file is decompressed during upload
2021-10-15 12:44:42 +02:00
guerler
9e672c0805
Add tool footer test to verify proper handling of citations
2021-10-14 16:57:03 -04:00
guerler
dec3e5c89d
Add test case for promise queue
2021-10-14 14:50:35 -04:00
guerler
3adbb84e79
Refresh citation details if tool node changes, augment workflow loading alert.
2021-10-14 08:40:16 -04:00
guerler
a8701a3402
Consolidate render wait calls in workflow editor tests
2021-10-14 06:50:40 -04:00
guerler
88dcba87af
Adjust selenium and jest tests
2021-10-14 06:32:18 -04:00
guerler
1849568754
Enable multiple arguments in promise queue
2021-10-14 00:57:45 -04:00
guerler
1b22fa5046
Throttle number of workflow editor form requests to one per second
2021-10-14 00:42:23 -04:00
guerler
f5921df8a9
Add a non-jquery promise queue to reduce form update requests (particularly useful for sliders in the workflow forms)
2021-10-14 00:21:41 -04:00
guerler
11ece208ef
Use paused state background for info alerts
2021-10-13 23:18:02 -04:00
guerler
7e2a6b11bf
Reduce flickering by removing the spinning card icon and increasing background opacity
2021-10-13 22:04:20 -04:00
Dannon
ef6b0c3b66
Merge pull request #12641 from OlegZharkov/fix-remote-data-dialog
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[21.09] Fix ambiguity in remote file upload
2021-10-13 14:01:57 -04:00
Oleg Zharkov
b040e3cdb8
fix test_history_import_export_ftp Selenium test
2021-10-12 20:00:00 +02:00
Oleg Zharkov
41b49dda3b
fix selenium tests and cleanup
2021-10-12 17:08:37 +02:00
Oleg Zharkov
852b328c2d
fix linting
2021-10-12 16:17:22 +02:00
Oleg Zharkov
d8fed97115
fix jest unit test
2021-10-11 20:45:53 +02:00
Björn Grüning
4c6ad48048
Merge pull request #12619 from natefoo/update-sorter
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[21.09] Modernize sorter (sort1) tool
2021-10-10 16:28:14 +02:00
mvdbeek
0c5a2a51c1
Add sort1 to list of workflow-safe built-in tool updates
2021-10-10 11:13:05 +02:00
Dannon
bd5eb1f78d
Merge pull request #12681 from guerler/turn_to_wait
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[21.09] Set wait instead of not-allowed cursor to indicate tool form loading
2021-10-09 16:51:27 -04:00
guerler
6cd2f0e19d
Set wait instead of not-allowed cursor to indicate tool form loading
2021-10-09 06:40:04 -04:00
mvdbeek
bfe7999c1e
Merge branch 'release_21.05' into release_21.09
2021-10-09 09:17:19 +02:00
Marius van den Beek
d5cca9c254
Merge pull request #12675 from davelopez/fix_fsources_anonymous_expression
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[21.05] Fix possible None in TokenContainedEvaluator
2021-10-09 09:05:46 +02:00
Dannon
dadfdb59de
Merge pull request #12669 from mvdbeek/show_error_message_on_tool_load_error
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[21.09] Show loading error in tool form
2021-10-08 20:03:09 -04:00
Dannon
ba5f76d7af
Merge pull request #12677 from mvdbeek/fix_toolshed_console_alerts
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[21.09] Don't change panel view after installing repositories, clean up provider
2021-10-08 19:44:21 -04:00
Dannon
08b635eef7
Merge pull request #12639 from guerler/welcome_update
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[21.09] Adjust appearance of new user welcome page
2021-10-08 14:52:43 -04:00
mvdbeek
cacbeeea27
Prevent duplicate alter messages in card and form
2021-10-08 20:25:11 +02:00
mvdbeek