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df481dabe092ff49e97619138e111d57eafb871b
Commit Graph
11816 Commits
Author SHA1 Message Date
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
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
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
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
Martin Cech f759961a29 mention planemo in the error message for disabled TS pushing 
rephrase to Norwegian
 2016-04-11 12:56:42 -04:00
carlfeberhard 99c2a6b623 API: add server_starttime to api/configuration 
Adds key server_starttime to the JSON returned from api/configuration.
This is the epoch time since the last server restart and may be
convenient for use in client-side caching.

This moves server_starttime from web/framework/helpers/__init__.py
(for use in script cache-busting) to web/framework/base.py.

On the client, this should be available to all pages as:
Galaxy.config.server_starttime.
 2016-04-11 10:38:20 -04:00
John Chilton 84ad9c2ee2 Rev Pulsar to 0.7.0.dev3. 
- Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory.
 - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04).
 - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this.
 2016-04-10 23:54:02 -04:00
John Chilton 5739f25003 Update version to 16.07.dev 2016-04-08 14:00:47 -04:00
John Chilton 579846fdfb Update version to 16.04.rc1 2016-04-08 13:59:37 -04:00
John Chilton 0945809099 Merge remote-tracking branch 'upstream/release_16.01' into dev 2016-04-08 13:22:03 -04:00
John Chilton ce27863086 Merge pull request #2099 from davebx/shed_model_trim 
Consolidate duplicated method in tool_shed/model.
 2016-04-08 13:21:59 -04:00
John Chilton 0d616af28a Merge pull request #2106 from davebx/hg_middleware 
Workaround for the toolshed's hgweb.
 2016-04-08 13:20:22 -04:00
John Chilton 6f6554ea8c Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency 
Updated to Dependency change in b167a741a4
 2016-04-08 13:18:26 -04:00
Dave Bouvier 5ead1c089f Remove refactoring that belongs in a different PR. 2016-04-08 12:38:56 -04:00
John Chilton be10253b69 Remove stray print statements. 
Not Python 3 compat.
 2016-04-08 10:28:09 -04:00
John Chilton 2744d5541f Merge pull request #2093 from davebx/move_scripts 
Move scripts out of lib/tool_shed.
 2016-04-08 09:54:44 -04:00
John Chilton ef604a75e5 Merge pull request #2102 from natefoo/global-drmaa-session 
Convert the DRMAA runner to use Pulsar's DRMAA session wrapper
 2016-04-08 09:47:24 -04:00
John Chilton 40953369e6 Merge pull request #2107 from ThomasWollmann/master 
Fix cli runner: use embed_metadata_in_job parameter
 2016-04-08 09:44:53 -04:00
Thomas Wollmann fb26d27b97 fixed lint error 2016-04-08 13:48:13 +02:00
Thomas Wollmann bf8292ecc1 fixed lint error 2016-04-08 12:30:56 +02:00
Thomas Wollmann 0548e8ed30 added missing import 2016-04-08 12:20:50 +02:00
Thomas Wollmann 4e15dc4e74 typo 2016-04-08 12:17:36 +02:00
Thomas Wollmann 91c4ccfc90 added default DEFAULT_EMBED_METADATA_IN_JOB value 2016-04-08 12:09:58 +02:00
Thomas Wollmann 987aac34bb removed comment 2016-04-08 11:00:34 +02:00
Thomas Wollmann ab242a84b1 fixed bug with cli runner analogous to https://github.com/dpryan79/galaxy/commit/3536ff923cf736b2dbefab3e04b7fcd79b909d22 2016-04-08 11:00:13 +02:00
Dave Bouvier 2a76eb19c1 Remove unused import, restore used import. 2016-04-07 20:38:11 -04:00
Martin Cech 50268cb8ca fix missing call; add docs and refactor a bit 2016-04-07 18:22:42 -04:00
Dave Bouvier b4e768b828 Workaround for the toolshed's hgweb. 2016-04-07 16:54:43 -04:00
Nate Coraor edd23f7c7a Bump pulsar-galaxy-lib version 2016-04-07 12:31:41 -04:00
Nicola Soranzo a85d6d5566 Merge pull request #1968 from jmchilton/csv_fix 
Improve tabular datatypes.
 2016-04-07 16:48:32 +01:00
Dave Bouvier 4b8b7b4647 Update which method is used in API. 2016-04-07 09:31:28 -04:00
Christian-B c720c0fde8 Updated to Dependency change in b167a741a4 2016-04-07 14:30:49 +01:00
John Chilton 0029949ed2 More fixups for specialized, more correct tabular datatypes. 
Followed through with @nsoranzo's comment:

1. overwrite CSV.sniff() and CSV.set_meta() methods with the ones from BaseCSV
2. remove BaseCSV class and rename CSV to BaseCSV
3. rename ExcelCSV class to CSV

Also renamed ExcelTSV to TSV and corrected another bug in sample datatypes noticed by @nsoranzo.
 2016-04-07 09:04:49 -04:00
Nate Coraor a6af938ea4 Fix linting errors 2016-04-06 16:39:08 -04:00
Martin Cech 0882b4d8fb use proper method for detecting admin 2016-04-06 15:32:52 -04:00
Nate Coraor febadeae65 Convert the DRMAA runner to use Pulsar's DRMAA session wrapper 2016-04-06 15:32:37 -04:00
John Chilton 7129726e8f Merge pull request #2088 from martenson/make-beta-install-config 
make new beta TS tools installation via API configurable
 2016-04-06 14:47:17 -04:00
Martin Cech 9ecf99c227 make dependencies browsable again 
it would be denied previously as the dependency folder is
outside of the repository (symlink protection)
 2016-04-06 13:55:32 -04:00
Martin Cech 204627c935 Merge pull request #2082 from mvdbeek/tool_lineage_map 
tool lineage for versionless toolshed tool_ids
 2016-04-06 11:15:04 -04:00
Dave Bouvier 4df7e45f61 Consolidate duplicated method. 2016-04-06 11:09:02 -04:00
Marius van den Beek 753b302df0 Merge pull request #2094 from natefoo/local-set-meta 
Run external local set_metadata jobs in the job's working directory
 2016-04-06 10:54:17 +02:00
Martin Cech 4138860bfd Merge pull request #2075 from jmchilton/conda_download_fixes 
Fix deps.command.download_command on Mac OS X.
 2016-04-05 16:25:23 -04:00
Nate Coraor d6d216c92e Merge pull request #2078 from jmchilton/embed_dev 
Enhancements for Pulsar Embedded Runner
 2016-04-05 15:09:43 -04:00
Nate Coraor 7cf0a80d19 Run external local set_metadata jobs in the job's working directory, 
because metadata temp files will be created in the cwd. Previously this
would most likely be the Galaxy root directory, Which Was Bad.
 2016-04-05 14:52:50 -04:00