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21,286 Commits 63 Branches 243 Tags
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Commit Graph
11155 Commits
Author SHA1 Message Date
Dannon Baker 6442cbc3d4 Fix downgrade attempting to drop parent_workflow_id off the wrong table. 2016-03-07 09:53:07 -05:00
Dannon Baker 0e0c1caec4 Fixing subworkflow migration (0131) to work with mysql 2016-03-07 09:53:01 -05:00
guerler 0445fcda51 Add workflow building mode check to collection parameter handling 2016-03-04 09:26:16 -05:00
John Chilton e0ce68cc58 Fix lack of output when discovering large collections... 
Example log statement collected for each dataset:

```
galaxy.tools.parameters.output_collect DEBUG 2016-03-03 11:47:31,302 (8) Created dynamic collection dataset for path [/home/john/workspace/galaxy/database/job_working_directory/000/8/oe2_ie2.fq] with element identifier [oe2:ie2] for output [list_output].
```
 2016-03-03 11:48:56 +00:00
Nate Coraor a494011897 Improve dataset error log message 2016-03-02 11:40:45 -05:00
Dannon Baker 7534182d7a Add a default logger prior to full logging configuration. We currently attempt to log at various places in config parsing/etc that fail with 'No handlers could be found for logger ...', and this resolves that. 2016-03-01 08:59:14 -05:00
Dannon Baker 16280c6323 Only attempt to read/load sanitize_whitelist_file when starting an actual galaxy application. 2016-03-01 08:01:14 -05:00
Dannon Baker 93494a833e This silences logging when display whitelist isn't explicitly defined and the default file doesn't exist. Explicit usage still logs a failure. 2016-03-01 08:01:05 -05:00
John Chilton 56076db848 Disable command isolation for Pulsar... 
... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better.
 2016-02-26 12:15:56 +00:00
Nate Coraor 5677c2ee4f Update version to 16.01 2016-02-24 15:29:14 -05:00
Nate Coraor e845d649c6 Security fixes for tool shed hg push and capsule/tarball uploads 2016-02-24 11:18:23 -05:00
Nate Coraor e4a1d57278 Security fixes for tool shed repository browsing 2016-02-24 11:18:23 -05:00
Nate Coraor cd8b96553f Remove sample tracking manual external service transfer due to security concerns 2016-02-24 11:18:23 -05:00
Nate Coraor 5da91bddcd Security fixes for object store paths 2016-02-24 11:18:23 -05:00
Nate Coraor bf1c77d171 Security fixes for history imports 2016-02-24 11:18:23 -05:00
Nate Coraor f540a16768 Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory 2016-02-24 11:18:23 -05:00
Daniel Blankenberg 6bb43aa4af Merge pull request #1786 from jmchilton/format_source_restrictive 
[16.01] format_source in workflow editor is too restrictive.
 2016-02-23 17:57:47 -05:00
John Chilton a5c30c563e Merge pull request #1771 from mvdbeek/16.01_fix_ies 
[16.01] Remove len(stderr), breaks on recent docker versions
 2016-02-23 17:42:27 -05:00
John Chilton b402093479 format_source in workflow editor is too restrictive. 
Case made well by @erasche on #1746, fixes #1746.

To resolve this more correctly (and many other potential type problems) - the workflow editor should be significantly reworked to track the datatype (or a range of datatypes) on each terminal (the way it does for collection mapping information). The change would be a weeks worth of development effort and inappropriate to apply to a release branch.
 2016-02-23 17:16:27 +00:00
Nicola Soranzo 5ce771b70e Strip URL of download_file and download_by_url install actions. 2016-02-23 14:47:23 +00:00
Marius van den Beek a47a4f40b4 Remove len(stderr), breaks on recent docker versions 2016-02-22 11:56:21 +01:00
Nicola Soranzo b5e91d2377 Merge branch 'release_15.10' into release_16.01 
Conflicts:
	lib/galaxy/util/__init__.py
 2016-02-19 11:41:10 +00:00
Nicola Soranzo ef93629719 Fix pretty_print_time_interval for MySQL. Fix #1619. 2016-02-18 20:08:14 +00:00
Daniel Blankenberg b4c823f2cd Merge pull request #1758 from jmchilton/ts_section_fix 
[16.01] Fix updating in-memory tools for tool shed installs into sections.
 2016-02-18 15:03:52 -05:00
Nicola Soranzo 3f34131ff5 Merge branch 'release_15.10' into release_16.01 
Conflicts:
	lib/galaxy/version.py
 2016-02-18 19:40:14 +00:00
Nicola Soranzo 587d450402 Fix installation of Tool Shed repositories containing non-ASCII characters in the description. Fix #1702. 2016-02-18 17:44:08 +00:00
John Chilton 4c0993cc42 Fix updating in-memory tools for tool shed installs into sections. 2016-02-18 13:04:18 +00:00
Dannon Baker 37b98b773e Load whitelist regardless of whether the setting is explicit in config. 
This is a sensible enough default, and requiring the option to be set in
galaxy.ini is cumbersome and unnecessary since it's admin-only
functionality.
 2016-02-17 09:29:29 -05:00
John Chilton 4a566b6db8 Improved debug message in workflow scheduling. 2016-02-16 12:25:15 +00:00
Marius van den Beek 75a3797d0f Also fix legacy export. 2016-02-15 14:05:45 +01:00
John Chilton e0ee1203c6 Fix problem with legacy workflows and duplicate output labels. 
Fixes #1704 - many thanks to @tzk and @mvdbeek.
 2016-02-12 11:02:51 +00:00
Martin Cech 776180ab80 show all available information for current library and the opened folder 2016-02-09 10:24:02 -05:00
Martin Cech 5301269fbb update docs of the data libraries API 2016-02-05 12:12:53 -05:00
Martin Cech e7b6b4b13b Revert "delete the 'payload' if it is in kwd so it is not supplied twice" 
This reverts commit 134d792c1f.
 2016-02-05 11:32:37 -05:00
Martin Cech 134d792c1f delete the 'payload' if it is in kwd so it is not supplied twice 2016-02-05 11:06:19 -05:00
Martin Cech 170c83e6c2 fix unused imports and unused vars 2016-02-04 22:45:33 -05:00
Martin Cech b46636a53f remove deletion of the payload dict item 
it is not necessary and the key does not have to exist
 2016-02-04 20:42:45 -05:00
Martin Cech a4c2098da0 allow PATCHing with payload in urlparams 2016-02-04 15:54:30 -05:00
Martin Cech 7867f3e083 accept json as input for setting permissions; 
fix inconsistency by leveraging role_manager
 2016-02-04 15:51:57 -05:00
Martin Cech c288b43627 allow creating folders with JSON payload 2016-02-04 15:10:02 -05:00
Martin Cech 4b51be57d1 allow specifying DELETE params in JSON 2016-02-04 15:04:42 -05:00
Martin Cech 0398aafb1c fix updating library API to not require payload 
and to properly handle optional params
 2016-02-04 15:00:14 -05:00
Martin Cech edd8b222ac catch value errors from id decoding 2016-02-04 14:43:45 -05:00
Martin Cech 5dd839960e unify api for library creation; support POST with url params 2016-02-04 14:30:31 -05:00
Martin Cech 530501c682 fix setting library permissions to accept JSON correctly 2016-02-04 14:23:15 -05:00
Martin Cech ada39dea6a handle correctly application/json pased in POST 2016-02-04 13:05:24 -05:00
Aysam Guerler bb95a65b22 Merge pull request #1666 from martenson/correct-datatype-typo 
[16.01] correct typo in text datatype
 2016-02-03 13:27:22 -05:00
Nate Coraor cd3f3b330d Merge pull request #1638 from dannon/pysam_84_update 
Pysam 84 update [16.01]
 2016-02-03 13:04:10 -05:00
Martin Cech bf989f6051 correct typo in text datatype 2016-02-03 12:44:26 -05:00
John Chilton a95827751f Merge pull request #1637 from guerler/fix_optional_001 
[16.01] Prevent optional test parameters in conditionals
 2016-02-02 19:12:13 -05:00