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0bc41e0b8978f40655c23f3786f4ed0bda7c558e
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28833 Commits
Author SHA1 Message Date
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
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 25ba40ee9c Merge pull request #13203 from simonbray/patch-2 2022-01-19 19:20:53 +00:00
Nicola Soranzo 178d97222d Merge pull request #13202 from mvdbeek/fix_metadata_source_access 2022-01-19 18:40:47 +00:00
guerler 2ed8cf644d Consistently parse content id for workflow modules when updating states 2022-01-19 18:18:27 +01:00
Simon Bray ee62798b0c fix error getting toolshed repo metadata when no repo found 2022-01-19 17:54:31 +01:00
mvdbeek 98b7b120b5 Fix metadata source access in tool shed 
Fixes:
```
Unexpected HTTP status code: 500: {"err_msg": "Metadata may have been defined for some items in revision '8f1b150a2487'.  Correct the following problems if necessary and reset metadata.<br/><b>abyss-pe.xml<\/b> - 'NoneType' object has no attribute 'get_biotools_metadata'<br/>"}
```
in https://github.com/galaxyproject/tools-iuc/runs/4792653893?check_suite_focus=true
 2022-01-19 17:32:47 +01:00
mvdbeek d5b31ee55a Fix tool id not getting updated on tool update 2022-01-19 14:46:31 +01:00
Marius van den Beek 6c354e2203 Merge pull request #13182 from kxk302/release_21.09 
[21.09] Backport of iRODS Object Store path name fix in #13080
 2022-01-18 18:57:46 +01:00
Kaivan Kamali 2b70e34a61 Revised code based on code review 2022-01-18 10:14:35 -05:00
mvdbeek faddbeeca9 Use job.get_user_email systematically 2022-01-18 14:21:09 +01:00
Ruben Vorderman 9e546f7d97 Catch exceptions when job.user is None 
prevents the following error:

galaxy.web.framework.decorators ERROR 2022-01-17 14:52:09,619 [p:18,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
  File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
    rval = func(self, trans, *args, **kwargs)
  File "lib/galaxy/webapps/galaxy/api/jobs.py", line 113, in index
    j['user_email'] = job.user.email
AttributeError: 'NoneType' object has no attribute 'email'
 2022-01-18 14:21:08 +01:00
Björn Grüning 48e725717a Merge pull request #13176 from mvdbeek/fix_yaml_downloaded_in_preview 
[21.09] Show yaml files in preview
 2022-01-17 12:27:08 +01:00
mvdbeek ea24c7c93e Show yaml files in preview 
The `application/yaml` mediatype might be the logical mediatype for yaml
(there's no standard yet), but we want to see a textual preview (in the
absence of a viewer).
Fixes https://github.com/galaxyproject/galaxy/issues/13168
 2022-01-17 10:15:57 +01:00
Björn Grüning 53ec65f59d Merge pull request #13157 from mvdbeek/fix_hiding_on_rerun 
[21.09] Fix re-run with rerun_remap_job_id hiding collection
 2022-01-14 17:02:25 +01:00
mvdbeek fc8fb85530 Set collection update_time when replacing failed elements 
That allows the new history to update the collection.
 2022-01-14 12:59:36 +01:00
mvdbeek bf712670f2 Drop refresh argument of get_installed_repository 2022-01-13 13:35:36 +01:00
Marius van den Beek afd94218f0 Don't need to use a joinedload anymore 
The cache is only used on startup, not during dependency resolution.
Also rename _rebuild, since we only use it once now.
 2022-01-13 12:26:56 +01:00
mvdbeek a327e34c89 Limit lifetime of repository cache 2022-01-13 12:26:55 +01:00
mvdbeek 855e9f9f2f Fix re-run with rerun_remap_job_id hiding collection 
Fixes https://github.com/galaxyproject/galaxy/issues/13052
 2022-01-12 20:10:08 +01:00
mvdbeek 74a7ef06d0 Strip trailing slash from cookie path 2022-01-09 19:00:00 +01:00
Marius van den BeekandNicola Soranzo 2086ce9a01 Check response status code 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-08 08:51:46 +01:00
mvdbeek a2ede0331e Fix history import for datasets with tags 
and tag dataset used for history import/export tests
 2022-01-07 17:16:45 +01:00
Bryan Raubenolt 34cdf6da3d added description of inpcrd and prmtop 2022-01-06 10:57:00 -05:00
Marius van den Beek 4beeac336d Merge pull request #13096 from mvdbeek/trim_stdout_stderr 
[21.09] Limit possible size of info field, read only 100 MB of stdio
 2021-12-21 09:48:29 +01:00
mvdbeek 11c5a1923e Limit possible size of info field, read only 100 MB of stdio 2021-12-20 17:53:42 +01:00
Björn Grüning 8f841a7b9c Merge pull request #13076 from mvdbeek/yield_per 
[21.09] Use yield_per option to limit amount of ORM objects loaded into memory
 2021-12-17 17:57:39 +01:00
mvdbeek 9e52fb6ac7 Disable eagerload of job pja relationship 2021-12-17 12:08:07 +01:00
mvdbeek aa73b52a20 Use yield_per option to limit amount of ORM objects loaded into memory 
I've applied it only to non-legacy code where we don't need the entire
list up-front.

This might help with

>  I have an issue with the job handlers from a few days. Randomly one of them gets trapped in a death loop. It starts to monitor jobs, the memory ramps up until the systemd limit of 12GB and then is killed by sytemd

report by @gmauro on usegalaxy.eu
 2021-12-17 11:54:07 +01:00
John Chilton 9a20f43040 Merge pull request #13059 from abretaud/sanit_fix 
[21.09] Fixes for HTML sanitization
 2021-12-15 10:37:51 -05:00
Marius van den Beek 799a94fbdd Merge pull request #13056 from davelopez/fix_private_history_publishing 
[21.09] Fix private history publishing
 2021-12-14 16:32:17 +01:00
Anthony Bretaudeau bfd97c1bc0 fix wrong data when a tool specified in the allow list is not installed 2021-12-14 13:07:35 +01:00
Anthony Bretaudeau 47d0e6232b ignore empty lines 2021-12-14 13:04:31 +01:00
davelopez 13221ddaba Make datasets public when pubishing or link access history 2021-12-13 19:12:42 +01:00
davelopez d364d8b775 Add API test for private histories 2021-12-13 19:09:09 +01:00
mvdbeek dd60630588 Merge branch 'release_21.05' into release_21.09 2021-12-13 15:20:05 +01:00
mvdbeek b4238f9717 Merge branch 'release_21.01' into release_21.05 2021-12-13 15:18:13 +01:00
mvdbeek b4a29f2600 Only check profile version in Galaxy 
Should fix https://github.com/galaxyproject/galaxy/issues/13008
 2021-12-13 12:49:50 +01:00
Marius van den Beek 8ec119eebb Merge pull request #13050 from cat-bro/add-to-implicitly-required-tool-files-for-pulsar 
add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py
 2021-12-12 17:39:02 +01:00
Björn Grüning d6e6235687 Merge pull request #13021 from mvdbeek/copy_hdas_within_hdcas_on_import 
[21.09] Copy HDCA member items to new history when copying history
 2021-12-11 22:41:23 +01:00
cat-bro 9a0978102e add tools to IMPLICITLY_REQUIRED_TOOL_FILES in tools/__init__.py 2021-12-08 20:30:56 +11:00
Dannon 7ef39f676d Merge pull request #12985 from OlegZharkov/fixhistoryerror 
[21.09] fix showing history error
 2021-12-07 10:09:05 -05:00
Oleg Zharkov dbcf1e8e98 expose api to expose api anonymous 2021-12-06 19:28:34 +01:00
mvdbeek 5810adb3e6 Add minimize_copies mode for coying histories 2021-12-02 19:13:48 +01:00
Nate Coraor 9146fcc981 Make dataset display route sessionless as well as anonymous. 2021-12-02 12:29:42 -05:00
mvdbeek 483e5658c0 Use HDCA dataset instance hid to skip unnecesary new HDAs 2021-12-02 18:05:27 +01:00
mvdbeek dd806f0993 Copy HDCA member items to new history when copying history 2021-12-02 16:22:15 +01:00
Nate Coraor 9b293ac438 Refactor Sentry middleware/client changes for Tool Shed 2021-11-30 15:04:32 -05:00
Björn Grüning 5793a1c325 Merge pull request #12989 from mvdbeek/install_model_sessionfactory 
[21.09] Reconstruct separate scoped session for ToolShedRepositoryCache
 2021-11-26 16:45:49 +01:00