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Author SHA1 Message Date
Daniel Blankenberg 8444da7bc7 Merge pull request #8 from bgruening/it 
migrating a few more interactive environments to interactive tools
 2019-08-14 10:32:24 -04:00
Daniel Blankenberg 6953bfae06 update migration script version 2019-08-14 10:09:23 -04:00
Daniel Blankenberg 764e28f812 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-14 10:08:44 -04:00
Daniel Blankenberg 0ba4ca5175 cleanup comments 2019-08-14 10:08:40 -04:00
Marius van den Beek a86ed8a064 Merge pull request #8414 from jmchilton/record_job_tool_version 
Record Galaxy version job was created with.
 2019-08-14 08:11:38 -04:00
Marius van den Beek 0c3e21fdd7 Merge pull request #8455 from selten/gitlab-error-reporting-update 
Implement #8183 for further GitLab integration.
 2019-08-14 07:30:53 -04:00
Björn Grüning c34fce8a5e add some more comments 2019-08-14 09:36:27 +02:00
Björn Grüning 2fd4c13aba enhance documentation for developers 2019-08-14 09:32:05 +02:00
Bjoern Gruening 24c7c76379 remove complexity from ipython wrapper, not needed for this version 2019-08-14 09:15:09 +02:00
Peter Selten 72678dfb18 Implement #8183 for further GitLab integration. Allow toggling of the proxy functionality, add automatic assignment to the last person that commited to the repository. 2019-08-13 22:17:40 +02:00
Daniel Blankenberg 5ed5ff6d49 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-13 14:47:53 -04:00
Daniel Blankenberg 0e5892c5ca Update galaxy.yml.realtime example with outputs_to_working_directory: true 2019-08-13 14:45:39 -04:00
Björn Grüning 01c23ce705 Merge pull request #75 from abretaud/it_askoko 
Fixes for askomics IT
 2019-08-13 15:53:40 +02:00
Anthony Bretaudeau 22edfcc11e fixes for askomics IT 2019-08-13 15:07:11 +02:00
Marius van den Beek 5ebfb6a4da Merge pull request #8451 from bernt-matthias/topic/fix-drmaa-memstatement 
fix memory statement for drmaa (SGE/UNIVA)
 2019-08-13 07:51:43 -04:00
M Bernt d303bf72dc fix memory statement for drmaa (SGE/UNIVA) 
The environment variable `SGE_HGR_h_vmem` turns out to be the
total memory for all slots (cores).

In the original implementation I was unfortunatelly tricked by the
fact that the ressouce request parameter `-l h_vmem` needs to be
specified per core.
 2019-08-13 11:00:35 +02:00
Björn Grüning 986b0baa71 Merge pull request #73 from blankenberg/patch-1 
Fix websockets in interactive_tool_bam_iobio.xml
 2019-08-13 08:48:48 +02:00
Daniel Blankenberg 5655ace083 Fix websockets in interactive_tool_bam_iobio.xml 2019-08-12 15:41:23 -04:00
Björn Grüning 717d94997c Merge pull request #72 from blankenberg/patch-1 
Add API_KEY, GALAXY_URL, and fix HISTORY_ID envars
 2019-08-12 19:04:28 +02:00
Daniel Blankenberg 29e1173f6c Add API_KEY, GALAXY_URL, and fix HISTORY_ID envars 
in interactive_tool_juypter_notebook.xml
 2019-08-12 12:23:38 -04:00
Bjoern Gruening 3689d857df some small changes 2019-08-11 21:28:04 +02:00
Bjoern Gruening 04b1e8f79c add a bunch of ITs 2019-08-11 16:42:49 +02:00
John Chilton 04f196439d Merge pull request #8431 from natefoo/fix-manage-db 
Fix config file finding for the manage_db script
 2019-08-09 14:56:53 -04:00
John Chilton 72d978be63 Merge pull request #8437 from erasche/undocumented 
document undocumented workflow_schedulers_config_file
 2019-08-09 13:17:41 -04:00
John Chilton e6280d4e49 Merge pull request #8433 from ic4f/fix_var_naming 
Improve variable naming
 2019-08-09 10:30:26 -04:00
Helena Rasche af5ecc487d rewrite 2019-08-09 16:14:32 +02:00
Helena Rasche 82c417d6e4 document workflow_schedulers_config_file 2019-08-09 15:19:43 +02:00
Marius van den Beek 8ef1fc46f6 Merge pull request #8426 from jmchilton/xml_macros_opts 
Remove seemingly unneeded deepcopy's in macro expansion.
 2019-08-09 07:02:09 -04:00
Sergey Golitsynskiy b03d9c3d5d Improve variable naming 2019-08-08 12:05:39 -04:00
John Chilton f1c4bafbdc Record version of Galaxy job was created with. 
We have so much job code dependant on what version of Galaxy created a job. This should help keep track of that without having to hit the job directory and guess.
 2019-08-08 11:52:28 -04:00
John Chilton 736c1e9b6d Merge pull request #8430 from martenson/optimize-libperms 
optimize unrestricted library dataset permission checks
 2019-08-08 11:13:17 -04:00
Martin CechandNicola Soranzo cef66191c7 remove debug 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-08 09:22:57 -04:00
Martin CechandNicola Soranzo 2a048300c1 fix typo 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-08 09:22:40 -04:00
Nate Coraor 395d98857b Fix config file finding for the manage_db script 2019-08-07 16:33:40 -04:00
Martin Cech 689ef6757c dataset is not private if unrestricted 2019-08-07 16:00:43 -04:00
Nate Coraor acbc8d9ca1 Merge remote-tracking branch 'upstream/release_19.05' into dev 2019-08-07 15:45:20 -04:00
Nate Coraor 9071402e31 Merge pull request #8418 from jmchilton/fix_too_many_records 
[19.05] Try to fix too many workflow step output associations.
 2019-08-07 15:35:49 -04:00
Marius van den Beek ca70a2a1d3 Merge pull request #8421 from jmchilton/speed_tool_shed_cache 
Speed up tool shed cache.
 2019-08-07 15:32:40 -04:00
John Chilton 0b789135d2 Remove seemingly unneeded deepcopy's in macro expansion. 
Before:

```
load_with_references (/Users/john/workspace/galaxy/lib/galaxy/util/xml_macros.py:11)
function called 14 times

         26836 function calls (23318 primitive calls) in 0.028 seconds

   Ordered by: cumulative time, internal time, call count
   List reduced from 121 to 40 due to restriction <40>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       14    0.000    0.000    0.028    0.002 xml_macros.py:11(load_with_references)
    44/14    0.000    0.000    0.018    0.001 xml_macros.py:127(_expand_macros)
    30/27    0.000    0.000    0.017    0.001 xml_macros.py:141(_expand_macro)
  1608/78    0.004    0.000    0.010    0.000 copy.py:145(deepcopy)
```

After:

```
load_with_references (/Users/john/workspace/galaxy/lib/galaxy/util/xml_macros.py:11)
function called 14 times

         18269 function calls (15767 primitive calls) in 0.020 seconds

   Ordered by: cumulative time, internal time, call count
   List reduced from 121 to 40 due to restriction <40>

   ncalls  tottime  percall  cumtime  percall filename:lineno(function)
       14    0.000    0.000    0.020    0.001 xml_macros.py:11(load_with_references)
    44/14    0.000    0.000    0.011    0.001 xml_macros.py:127(_expand_macros)
    30/27    0.000    0.000    0.009    0.000 xml_macros.py:141(_expand_macro)
       15    0.000    0.000    0.007    0.000 xml_macros.py:311(_parse_xml)
       14    0.000    0.000    0.007    0.000 xml_macros.py:51(raw_xml_tree)
       15    0.000    0.000    0.006    0.000 ElementTree.py:1180(parse)
       15    0.000    0.000    0.006    0.000 ElementTree.py:644(parse)
   672/30    0.002    0.000    0.005    0.000 copy.py:145(deepcopy)
```
 2019-08-07 14:33:48 -04:00
John Chilton d9100e25f3 Add more tests for XML macro expansion. 2019-08-07 14:30:41 -04:00
John Chilton f95a4271f3 Try again to hack around failing test. 2019-08-07 13:51:54 -04:00
John Chilton f4388a3d11 [19.05] Try to fix too many workflow step output associations. 
Certain entries on main have hundreds of thousands of such records because they're being created at each iteration of workflow scheduling. This leads to serious memory and runtime issues over time.

Cleanup extra rows with:

```sql
DELETE FROM workflow_invocation_step_output_dataset_association
WHERE id NOT IN (

SELECT max(w.id) FROM
workflow_invocation_step_output_dataset_association as w GROUP BY workflow_invocation_step_id, dataset_id, output_name

)
```
 2019-08-07 13:21:53 -04:00
John Chilton 2c7493221a Fallback - just to see if this helps the tests. 2019-08-07 10:58:18 -04:00
John Chilton b2632c19e8 Simplify logic thanks to @nsoranzo. 2019-08-07 10:57:20 -04:00
mvdbeek 3d11c6aa9e When adding new repo to cache also add it to repos_by_tuple 2019-08-07 06:04:20 -04:00
Marius van den Beek c4fa198d0b Merge pull request #8423 from martenson/backport-speedup 
[19.05] Backport tool search index building speedup
 2019-08-07 05:50:25 -04:00
Martin Cech 42d1a1fb1f drop unused import 2019-08-06 19:00:41 -04:00
John Chilton 3de99087d9 Don't parse HTML for tool help search index. 
Just use the simpler raw rST (or Markdown in the future). This should prevent all rst_to_html loading from happening at Galaxy startup - the existing caching should allow it to just be loaded and cached on first use.
 2019-08-06 19:00:33 -04:00
Martin Cech 587749968d Merge pull request #8422 from jmchilton/speed_help 
Don't parse HTML for tool help search index.
 2019-08-06 18:58:42 -04:00
Martin Cech 901a9da826 drop unused import 2019-08-06 16:55:17 -04:00