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11816 Commits
Author SHA1 Message Date
Dannon Baker 118e223027 Merge pull request #2089 from jmchilton/cleanup_job 
Fix job_wrapper.cleanup_job.
 2016-04-05 13:15:15 -04:00
Dave Bouvier 77353902ee Move scripts out of lib/tool_shed. 2016-04-05 13:04:44 -04:00
Martin Cech cce822cfd6 make new beta TS tools installation via API configurable 
we probably need more testing on Test/real Galaxies to rely on it fully
 2016-04-05 11:27:24 -04:00
John Chilton 2346b32331 Fix job_wrapper.cleanup_job. 
Broken in 16.04 with 81b5ca564a in PR #1688.

Minor.
 2016-04-05 11:07:14 -04:00
Björn Grüning e377613466 Merge pull request #1807 from erasche/gie-go-proxy-2 
Implement new GIE proxy
 2016-04-05 16:40:17 +02:00
Martin Cech 1543f0d925 Merge pull request #1959 from jmchilton/optimize_dataset_collection_discovery 
Optimization for discovering datasets for dynamic output collection.
 2016-04-05 10:27:34 -04:00
Marius van den Beek ab264ebeb4 Remove version by slicing tool_id before last slash 
As pointed out by @nsoranzo, this  may avoid conflicts when the version string
appears more than once in tool_id.
 2016-04-05 15:45:06 +02:00
Marius van den Beek 9b7be814b3 Build tool lineage for versionless toolshed tool_ids 
The tool_id for a toolshed tool contains the version as last element
(<toolshed>/<name>/<owner>/<id>/<version>). This means that looking up a tool
lineage using a tools' tool_id does not work if the tool is installed in a different
version than referenced by the tool_id. To allow this, we register the
tool_lineage also under a tool_id that is stripped of the version.
 2016-04-05 14:29:45 +02:00
Marius van den Beek 99cb27557f Fix reversed workflow upgrade message 2016-04-05 14:15:32 +02:00
John Chilton bdb41005c8 Fix pulsar_conf/pulsar_config problem. 
One was being validated and the other was being read and documented.
 2016-04-04 20:08:55 -04:00
John Chilton 3bd802268d Merge pull request #2039 from dannon/fluent_tweaks 
Fix fluent query log serialization when datetime types are in use.
 2016-04-04 13:26:27 -04:00
John Chilton aee38feeb4 Merge remote-tracking branch 'galaxyproject/dev' into gie-generic 
Conflicts:
	static/maps/layout/menu.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/layout/menu.js
 2016-04-04 13:00:21 -04:00
John Chilton 3b31f23eb6 Fix deps.command.download_command on Mac OS X. 
Previously -O- and --recursive would be used together - this doesn't seem to be possible on Mac OS X.

See issue https://github.com/galaxyproject/planemo/issues/431.
 2016-04-04 12:04:01 -04:00
Dannon Baker 46e4308f7c Fix pbs runner file touch. 2016-04-04 11:57:30 -04:00
Dannon Baker 3ecd4e94cf Merge pull request #2060 from nitesh1989/workflow_sharing_menu 
Simplify Workflow sharing menu
 2016-04-04 11:14:19 -04:00
Martin Cech 65a7ebee23 Merge pull request #2072 from mvdbeek/backport_1738 
[16.01] backport #1738
 2016-04-04 09:34:02 -04:00
Marius van den Beek 20f61e6a2f workaround for error message in case original toolshed had been disabled 2016-04-04 12:28:46 +02:00
John Chilton b3881f86c1 For non-shed tool data - read loc from sample if available. 2016-04-01 17:25:47 -04:00
Nate Coraor 1c201a8630 Merge pull request #2057 from jmchilton/pulsar_overhaul 
Implement an Embedded Pulsar Job Runner
 2016-04-01 17:19:40 -04:00
Nate Coraor 991d7282c7 Merge pull request #2052 from jmchilton/pulsar-deps 
Pulsar-As-A-Dependency
 2016-04-01 17:14:34 -04:00
Martin Cech a03e64268a Merge pull request #2061 from davebx/api_install_performance 
Disable install button if changeset is installed.
 2016-04-01 15:57:39 -04:00
Nicola Soranzo 26569c3ec4 Merge pull request #2066 from jmchilton/static_tool_conf 
Allow tool confs with a tool_path to not be interpreted as shed confs.
 2016-04-01 18:03:56 +01:00
Martin Cech 18596a2bb4 Merge pull request #2055 from davebx/url_join 
Replace common_util.url_join with util.build_url.
 2016-04-01 11:18:21 -04:00
John Chilton 34e3b7f1c2 Rename shed_conf attribute to is_shed_conf. 
Per discussion with @nsoranzo.
 2016-04-01 10:01:54 -04:00
Nicola Soranzo 205850586e Use a stricter regexp for microseconds. 2016-04-01 14:46:30 +01:00
John Chilton 569b87dc00 Merge pull request #2029 from mvdbeek/element_identifier_in_repeat 
Better element_identifier handling in repeat sections
 2016-04-01 09:29:57 -04:00
John Chilton cb5e786aa9 Allow tool confs with a tool_path to not be interpreted as shed confs. 2016-04-01 09:28:46 -04:00
John Chilton 4b7e86fa43 Clean up docstrings in lib/galaxy/tools/toolbox/parser.py. 2016-04-01 09:02:08 -04:00
Dannon Baker ff48ad9b54 Merge pull request #2063 from dannon/dryrun 
Change user disk usage pgcalc function up a bit to make a slightly sa…
 2016-03-31 18:52:32 -04:00
Dannon Baker ec83fb6494 Change user disk usage pgcalc function up a bit to make a slightly safer dry-run, since it doesn't appear that in some environments (not sure why) the rollback isn't actually happening. 2016-03-31 17:15:12 -04:00
carlfeberhard 46b4e8d94c Managers: remove UTC zone when parsing dates 
This change creates a more complete regex for parsing dates used in filters. MySQL in particular errored when the UTC zone character 'Z' was appended to a valid iso 8601 date (because it's MySQL). The FilterParser.parse_date method now:
- strips both the separator 'T' and any ending 'Z'
- one space are allowed as the date/time separator
- milliseconds are permitted
- both time and time with milliseconds are optional
- any added timezone (besides the UTC Z) will cause an error
- feedback was made more clear
- tests were added (and should make the above more clear)
 2016-03-31 15:00:50 -04:00
Dave Bouvier 71f473b165 Disable install button if changeset is installed. 2016-03-31 14:39:26 -04:00
John Chilton 5fd5343d07 Merge pull request #2045 from martenson/update_mercurial_wheel 
upgrade mercurial wheel to latest (fixing CVE issues)
 2016-03-31 14:26:21 -04:00
John Chilton 90b95dc665 Merge pull request #2043 from martenson/update_mercurial_wheel 
[16.01] upgrade mercurial wheel to latest (fixing CVE issues)
 2016-03-31 14:26:02 -04:00
nitesh1989 827d175e43 removed commeted code 2016-03-31 13:55:03 -04:00
Dave Bouvier d885367955 Fix indent broken with search/replace. 2016-03-31 13:52:43 -04:00
nitesh1989 0ea13c957a cleaning comments 2016-03-31 13:38:03 -04:00
Dannon Baker 829c84c8cb Merge branch 'release_16.01' into dev 2016-03-31 13:35:39 -04:00
John Chilton cc17d5304c Implement a Pulsar embedded job runner. 
Closes #1378.
 2016-03-31 11:37:45 -04:00
John Chilton 32b945f063 Fix pulsar import order. 2016-03-31 11:25:33 -04:00
Nicola Soranzo 7d08d1b069 Specify default value when getting disable_push 2016-03-31 11:11:08 -04:00
Martin Cech dc4d4cbce7 disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#deprecation-notices 2016-03-31 11:10:58 -04:00
Dave Bouvier 494384171f Do the same for tool_shed_get. 2016-03-31 11:05:31 -04:00
Dave Bouvier 7d378792cc Replace common_util.url_join with util.build_url. 2016-03-31 10:59:16 -04:00
carlfeberhard 10db8ec8fe Merge pull request #2042 from nsoranzo/fix_for_2037 
Remove microseconds when parsing datetimes for MySQL.
 2016-03-31 10:09:42 -04:00
John Chilton d629822912 Docstring fixes for lib/galaxy/jobs/runners/pulsar.py. 2016-03-31 08:30:39 -04:00
John Chilton 07eb322e8c Fix Pulsar effective working directory for #1688. 2016-03-31 08:17:06 -04:00
John Chilton 51f63a7d3e Replace embedded Pulsar code with dependency. 
Pulsar's setup.py has been parameterized to allow it build a special wheel that doesn't depend on galaxy-lib (https://github.com/galaxyproject/pulsar/commit/ce9d4f9e80936407fe4f793afa6688d75635e827) and instead expects it to come from the environment.

This special dependency has been published to PyPI here (https://pypi.python.org/pypi/pulsar-galaxy-lib) and added to StarForge here (https://github.com/galaxyproject/starforge/pull/79). These are now available on wheels.galaxyproject.org.

In addition to removing the source dirctories - I have removed doc and CI references to these directories.
 2016-03-31 08:17:06 -04:00
John Chilton b160cd52f3 Merge pull request #2046 from martenson/jstree-dictobj 
use dictobj as standard dependency
 2016-03-30 20:25:52 -04:00
nitesh1989 0609fe056f Need to make changes to consolidate sharing.mako file 2016-03-30 18:49:23 -04:00