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Author SHA1 Message Date
M Bernt ce13eef805 Completed filter type docs 2019-08-18 20:32:38 +02:00
M Bernt c093cf9fa0 add regexp to filters in xsd 
and further work on filter documentation
 2019-08-18 18:22:03 +02:00
M Bernt 96db74d0f4 add tests for static_value and regexp filter 2019-08-18 16:22:06 +02:00
M Bernt db4dce21b7 added few comments 2019-08-17 01:13:40 +02:00
M Bernt 64deb4dbc0 extend test for dbkey filtering 
code suggest that column names can be used, lets try
 2019-08-16 17:15:44 +02:00
M Bernt 57cd9f369e filters: add regexp filter and efficient sort 
- also started to add docs
- use likely more efficient implementation of the sort filter.
  used insertion sort before which is n^2 (n^3 if the insertions
  take linear time)
 2019-08-14 23:35:23 +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 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
John Chilton 5fc358f7cb Merge pull request #8405 from martenson/client-build 
client auto format
 2019-08-05 10:27:29 -04:00
John Chilton 6b3fec0a92 Merge pull request #8404 from martenson/nginx-docs 
mention IGB in the docs
 2019-08-05 10:26:58 -04:00
John Chilton 2a49c2f64f Merge pull request #8410 from mvdbeek/add_tool_linter_unit_test 
Add basic unit test for lint_inputs
 2019-08-05 10:23:04 -04:00
mvdbeek 5e9dd557d5 Add basic unit test for lint_inputs 
This could of course be extended much more.
 2019-08-04 11:58:39 +02:00
John Chilton 281ccaa189 Merge pull request #8407 from martenson/mysql-depre 
docs - change mysql support to deprecated
 2019-08-02 14:23:30 -04:00
Martin Cech 8c01ae716d change mysql support to deprecated 
until we fix migrations at least
 2019-08-02 11:12:44 -04:00
Martin Cech 1bdbb77044 client auto format 2019-08-02 09:41:03 -04:00
Martin Cech cb3c5b7a5e mention IGB in the docs 2019-08-02 09:36:37 -04:00
Helena Rasche d50cec0866 Improve color relationships between text and background (#8388) 
Improve color relationships between text and background
 2019-08-02 09:53:25 +02:00
Martin Cech 1376d96510 Merge pull request #8331 from janani-prasad/favbtn_toggle 
Issue#8105: Make tool favourite query a toggle
 2019-08-01 15:10:54 -04:00
Martin Cech 8d7280db4b use standard naming and format 2019-08-01 15:09:55 -04:00
guerler 00a9d7caf4 Use text color for dark gray 2019-08-01 14:08:27 -04:00
guerler 41e8b04e29 Determine dark grays from text colors 2019-08-01 11:53:32 -04:00
guerler e236758f50 Move text colors below brand colors in theme file to highlight settings 2019-08-01 11:31:56 -04:00