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11881 Commits
Author SHA1 Message Date
carlfeberhard 4c7f367680 (merge conflicts with dev) 2016-04-15 15:23:08 -04:00
carlfeberhard 89cb03a037 History contents manager: improve contents query 
Serializers in the index_v2 of history_contents were re-
querying the database for mapped model attributes.

- eagerload collection on hdcas
- undefer _metadata on hdas
- eaglerload tags and annotations for both
- rework annotatable manager mixin to cycle through annotations
bypassing the get_item_annotation_str call (which would bypass
item.annotations even if already loaded)

Anecdotally provides significant speed up.
 2016-04-15 14:47:45 -04:00
Nicola Soranzo 58f510fda9 Merge branch 'release_16.04' into dev 2016-04-15 09:47:45 +01:00
Nicola Soranzo 7488e3b7be Merge branch 'release_16.01' into release_16.04 
Conflicts:
	lib/galaxy/web/framework/helpers/grids.py
 2016-04-15 09:45:32 +01:00
John Chilton 88db9e6a0f Merge pull request #2120 from guerler/fix_hidden_001 
Hide hidden data parameters in workflow editor
 2016-04-14 20:17:20 -04:00
John Chilton 411e33194b Merge pull request #2171 from dannon/mostats 
Stats prefix configurability and conditional wheel req.
 2016-04-14 20:12:38 -04:00
Dannon Baker 18c00899a3 Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135 
[16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters
 2016-04-14 17:20:23 -04:00
Dannon Baker fbf894ef14 Merge pull request #2168 from jmchilton/ftp_upload 
More documentation and flexibility for FTP imports.
 2016-04-14 16:40:34 -04:00
Dannon Baker 238b90a7f5 Support configurable statsd prefix (was formerly just 'galaxy', which remains the default) 2016-04-14 15:51:41 -04:00
Dannon Baker 44a337ab6f Add conditional statsd requirement. Wheel is live on wheels.galaxyproject.org. 2016-04-14 15:49:37 -04:00
Eric Rasche 4ffee71969 Merge pull request #2165 from jmchilton/single_user 
Implement ``single_user = <email>`` config option.
 2016-04-14 19:34:18 +00:00
carlfeberhard 1e04025819 Merge branch 'release_16.04' into dev 2016-04-14 14:50:59 -04:00
carlfeberhard 8b49814859 Merge 16.01 into 16.04 2016-04-14 14:49:07 -04:00
John Chilton e81448c62a Merge pull request #2146 from mvdbeek/reorder_job_template 
Place $headers before integrity_check
 2016-04-14 14:23:49 -04:00
carlfeberhard 570baa5bb6 Fix bad merge: when HTTP_GX_SECRET is None 2016-04-14 14:06:13 -04:00
carlfeberhard e26bff23ed Merge 'release_15.10' with 'release_16.01' 2016-04-14 12:59:05 -04:00
John Chilton 2546030c66 Do not require use_remote_user to be explicitly set if single_user is set. 
Based on comments from @erasche - https://github.com/galaxyproject/galaxy/pull/2165#issuecomment-210048830.
 2016-04-14 12:41:18 -04:00
John Chilton e67506802d Implement config.single_user = <email> option. 
Let Planemo and other such applications serve a full-fledged Galaxy instance without having to worry about logins, etc....
 2016-04-14 12:41:18 -04:00
John Chilton 997b53f3ae Implement option to prevent FTP uploads from being deleted on import. 
- Simply set `ftp_upload_purge` to `False` in galaxy.ini to enable this.
 - xref http://dev.list.galaxyproject.org/Data-removal-after-ftp-import-td4667111.html
 - slight xref http://dev.list.galaxyproject.org/Uploading-files-to-galaxy-from-a-folder-td4664614.html
 2016-04-14 11:34:21 -04:00
John Chilton f95cbf8f38 More documentation and flexibility for configuring FTP imports. 
- Add missing documentation for the ftp_upload_dir_identifier option.
 - Add ftp_upload_dir_template option to configure how to combine identifier and base directory to generate an ftp upload directory.
 2016-04-14 11:34:21 -04:00
John Chilton 54173807e5 Re-use `trans` logic for calculating user_ftp_dir. 2016-04-14 11:34:20 -04:00
Nate Coraor a919e98be3 Merge branch 'release_16.04' into dev 2016-04-14 11:15:43 -04:00
Nicola Soranzo 148d4ee88d Merge pull request #2145 from mvdbeek/pbs_ncpu 
Use "$NCPUS" if defined to set GALAXY_SLOTS
 2016-04-14 15:50:06 +01:00
Nate Coraor 84ef4fd99f Update pulsar-galaxy-lib in pinned-requirements.txt (it was already 
updated in requirements.txt).
 2016-04-14 10:09:26 -04:00
Nate Coraor 9bb5978d53 Merge pull request #2156 from guerler/fix_data_001 
[16.04] Add tool parameters back to parameters and expose for certain tools
 2016-04-14 09:56:29 -04:00
guerler a889e19af7 Fix parameter wrapping 2016-04-14 07:23:06 -04:00
Eric Rasche 3d5663e97f Remove double escaping 2016-04-13 21:35:50 +00:00
guerler ac14139714 Add blank line 2016-04-13 15:50:44 -04:00
guerler 82e9ce827c Add tool parameters back to parameters 2016-04-13 15:34:11 -04:00
Martin Cech f85aaa4a27 port of middleware fix for TS (#2106) 2016-04-13 15:22:35 -04:00
Eric Rasche dd05f0ab24 Escape everything 2016-04-13 18:36:36 +00:00
Eric Rasche 6ce9bd8220 Minor touch up for consistency 2016-04-13 18:21:19 +00:00
Eric Rasche 4d729ff890 Typo 2016-04-13 17:27:14 +00:00
Eric Rasche a3e925cc1b Fix second nitpick 2016-04-13 17:24:26 +00:00
Eric Rasche cba10c812b Fix nitpick 2016-04-13 17:23:32 +00:00
Eric Rasche df481dabe0 Remove unused import 2016-04-13 16:34:26 +00:00
Eric Rasche a6d95d0909 Fix flake8 by reverting a previous commit 2016-04-13 16:32:37 +00:00
Marius van den Beek b93b62ae77 Place $headers before integrity_check 
PBS needs the resource selection (which will be filled in using $headers) to
appear before anything else (except the shebang), so this changes the order.
 2016-04-13 12:35:20 +02:00
Marius van den Beek 3c97d30cd6 Use "$NCPUS" if defined to set GALAXY_SLOTS 
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
 2016-04-13 10:39:43 +02:00
Eric Rasche 5923a67301 Fix sanitization completely 2016-04-13 00:48:09 +00:00
Eric Rasche c2cff25826 Use CGI for escaping 2016-04-13 00:38:25 +00:00
Eric Rasche e9823573e3 Add HTML Template 2016-04-13 00:25:31 +00:00
Eric Rasche 024ae7a286 bail earlier if no SMTP server is configured 2016-04-12 23:40:39 +00:00
carlfeberhard b5580c23f6 Merge remote-tracking branch 'upstream/dev' into history-contents.limiting 2016-04-12 15:48:57 -04:00
Nicola Soranzo cde04ad52d markupsafe.escape() in Python2 does not work on str containing non-ASCII characters. 
Fix #2135.
 2016-04-12 15:52:01 +01:00
Nicola Soranzo 408827e251 Merge branch 'release_16.04' into dev 2016-04-12 14:35:37 +01:00
Nate Coraor f03c037556 Merge pull request #2122 from jmchilton/pulsar_metadata 
[16.04] Rev Pulsar to 0.7.0.dev3.
 2016-04-12 09:01:27 -04:00
guerler c78887c4ae Use elif, do not require hidden attribute 2016-04-11 17:20:21 -04:00
Nicola Soranzo baf1bd639f Merge branch 'release_16.04' into dev 2016-04-11 20:26:42 +01:00
Nicola Soranzo 6317297cad Merge branch 'release_16.01' into release_16.04 2016-04-11 20:24:46 +01:00