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Author SHA1 Message Date
John Chilton 47d46c626e Merge pull request #8452 from erasche/faster-quota 
Replace in-python quota calc with a SQL query
 2019-08-14 14:40:12 -04:00
John Chilton 404bf6bbc0 Merge pull request #8458 from bgruening/pgp 
add pgp and osw filetype as used in OpenSWATH experiments
 2019-08-14 14:38:52 -04:00
Nicola Soranzo 561f3cd377 Add pointer to client/README.md (#8457) 
Add pointer to client/README.md
 2019-08-14 17:08:52 +01:00
Helena Rasche 16c13ad62e refresh session 2019-08-14 16:41:10 +02:00
Helena Rasche 887aae2ab3 Refactor into model 2019-08-14 16:15:49 +02:00
Björn Grüning 851ef559b3 add osw datatype 2019-08-14 16:11:02 +02:00
Helena Rasche 58f4f65a4a new method 2019-08-14 16:08:04 +02:00
Helena Rasche c501c092a5 replace both with pgcalc 2019-08-14 16:07:24 +02:00
Björn Grüning d3a578b71a add pgp filetype as used in OpenSWATH experiments 2019-08-14 16:01:57 +02:00
Dannon Baker 877bd322d6 Add pointer to client/README.md to address 'https://github.com/galaxyproject/galaxy/commit/8bb2b6bfbcac89910ec6b5cc58e23243571ab879#commitcomment-34259049' 2019-08-14 09:59:55 -04:00
Helena Rasche 52bd23cacf revert changes to original, move to pgcalc 2019-08-14 15:55:51 +02:00
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
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
Helena Rasche 7830c54a60 rewrite query again 2019-08-13 16:20:02 +02:00
Helena Rasche 686e912097 fix linting errors 2019-08-13 14:40:49 +02:00
Helena Rasche 4976e77957 Replace in-python quota calc with a SQL query 2019-08-13 14:10:47 +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
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
John Chilton f42bdb4f60 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 16:33:51 -04:00
John Chilton 88426db37c Speed up tool shed cache. 
Cache the cache for more cached caching.
 2019-08-06 16:27:08 -04:00
Martin Cech fa1c10a7e9 Merge pull request #8394 from bernt-matthias/topic/cleanup-logging 
make cleanup script use logging instead of print
 2019-08-06 15:18:55 -04:00