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Author SHA1 Message Date
Nate Coraor 9e6afea498 Security fixes for tool shed repository browsing 2016-02-24 11:18:24 -05:00
Nate Coraor ffcd4fe192 Remove sample tracking manual external service transfer due to security concerns 2016-02-24 11:18:24 -05:00
Nate Coraor 7c4b8ff747 Security fixes for object store paths 2016-02-24 11:18:24 -05:00
Nate Coraor 61b59b2082 Security fixes for history imports 2016-02-24 11:18:24 -05:00
Nate Coraor 1f530b45b3 Merge branch 'release_16.01' into dev 2016-02-24 10:58:54 -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 2a64fac0c7 Merge pull request #1760 from remimarenco/html_refactoring 
Refactor the Html Datatype Class into text.py instead of images.py
 2016-02-23 17:43:40 -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
Dannon Baker 805b5906b2 Merge pull request #1772 from jmchilton/python26_drop 
[16.01] Deprecation notice - Python 2.6.
 2016-02-23 16:43:21 -05:00
Daniel Blankenberg 3621d6f221 Merge pull request #1784 from carlfeberhard/fix.fa 
[16.01] Fix chrome-only intermittent rendering error of font awesome icons th…
 2016-02-23 16:33:33 -05:00
Eric Rasche a41f475017 Merge pull request #1783 from guerler/fix_sections_000 
Fix tool form rendering of sections
 2016-02-23 15:23:13 -06:00
carlfeberhard 9acbfdf3c3 Fix chrome-only intermittent rendering error of font awesome icons that have their sizes changed by overriding 4.2 font-size inheritance rule from core.less 2016-02-23 15:46:00 -05:00
guerler dda851def5 Fix sections 2016-02-23 14:17:13 -05:00
Nicola Soranzo 390d3b7eb7 Merge branch 'release_16.01' into dev 
Conflicts:
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js
	static/scripts/bundled/libs.bundled.js.map
 2016-02-23 18:13:22 +00:00
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 4c815a7d05 Merge pull request #1778 from nsoranzo/release_16.01_fix_download_file 
[16.01] Strip URL of download_file and download_by_url install actions.
 2016-02-23 16:50:16 +00:00
Daniel Blankenberg f06b820589 Merge pull request #1775 from nsoranzo/release_16.01_fix_download_file 
[16.01] Strip URL of download_file and download_by_url install actions.
 2016-02-23 10:34:06 -05:00
Daniel Blankenberg 5b720b4a02 Merge pull request #1774 from jmchilton/wf_fixes 
[16.01] Workaround for #1739 - fixing up subworkflow input connections.
 2016-02-23 10:11:04 -05:00
Nicola Soranzo 5ce771b70e Strip URL of download_file and download_by_url install actions. 2016-02-23 14:47:23 +00:00
Eric Rasche 4498c50f90 Merge pull request #1770 from mvdbeek/fix_ies 
Use "Gateway" from docker inspect as default docker_hostname
 2016-02-22 16:42:26 -06:00
John Chilton dbab6f5b97 Workaround for #1739 - fixing up subworkflow inut connections. 
Do the same relaxed thing we do for inputs of type 'input' as we do for outputs of this type. Someday we should have better tracking, but such a change is probably not wise for a release branch.
 2016-02-22 21:46:03 +00:00
Marius van den Beek e718e8ebac docstring fixes 2016-02-22 17:44:19 +01:00
Marius van den Beek bad1aca5a9 Split out inspect and container_port_mapping / container_gateway_ip recovery, fix typo. 2016-02-22 17:32:48 +01:00
Nicola Soranzo 1b25944a5d Merge pull request #1731 from mvdbeek/python_2_3_string_handling 
Python 2/3 string handling
 2016-02-22 12:34:29 +00:00
John Chilton f2a27acff8 Drop Python 2.6 with 16.04. 
xref #1596
 2016-02-22 11:40:01 +00:00
Marius van den Beek a47a4f40b4 Remove len(stderr), breaks on recent docker versions 2016-02-22 11:56:21 +01:00
Marius van den Beek 5d37f9b103 missing quotes 2016-02-21 23:51:42 +01:00
Marius van den Beek aa27fcf75b better default than localhost 2016-02-21 23:42:17 +01:00
Eric Rasche 4e73d56bf1 Merge pull request #1769 from mvdbeek/fix_ies 
Remove len(stderr), breaks on recent docker versions
 2016-02-21 13:31:52 -06:00
Marius van den Beek ecd6ca8a2f Remove len(stderr), breaks on recent docker versions 2016-02-21 20:23:14 +01:00
mvdbeek 92fe009f96 fix bad rebase 2016-02-20 13:01:05 +01:00
mvdbeek f706ed7e86 properly encode column_filter 2016-02-20 13:01:05 +01:00
mvdbeek 66bce36a40 Indentation fixes, import json_fix from galaxy.util.json 2016-02-20 13:01:05 +01:00
Marius van den Beek 6653bcb63b remove unncessary if statements 2016-02-20 13:01:05 +01:00
Marius van den Beek 8ee38f64f3 Do not test if text_type instance before calling unicodify() 2016-02-20 13:01:05 +01:00
Marius van den Beek 0028ac2636 need binary type 2016-02-20 13:01:05 +01:00
Marius van den Beek da9cd12ae6 Use unicodify 2016-02-20 13:01:05 +01:00
Marius van den Beek fbc40f69f6 use six's text_type 2016-02-20 13:01:05 +01:00
Marius van den Beek a22af161ad For python2/3 compatibility, replace basestring with six's string_types, unicode with six's text_type. 2016-02-20 13:01:05 +01:00
Martin Cech d7eb315f72 Merge pull request #1610 from jmchilton/discovered_dataset_keys 
Improve dbkey handling for discovered datasets.
 2016-02-19 13:28:23 -05:00
carlfeberhard 040fb8185b Merge pull request #1751 from martenson/libraries-refactor 
various libraries refactoring and bugfixes
 2016-02-19 11:57:10 -05:00
Martin Cech 0988a6e7d7 Merge pull request #1565 from davebx/ts_api_all_metadata 
Add API endpoint for fetching all metadata for a repository.
 2016-02-19 10:34:19 -05:00
Dave Bouvier 8132d5bfe4 Fix failing test. 2016-02-19 09:13:25 -05:00
Nicola Soranzo 975304ac59 Merge branch 'release_16.01' into dev 2016-02-19 11:42:48 +00:00
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
John Chilton 5ff028a9d0 Merge pull request #1711 from guerler/revise_states_000 
Revise tool parameter handling, remove redundancies
 2016-02-18 20:12:54 -05:00
guerler 5041c80d85 Fix optional column parameter handling and accept_default tag 2016-02-18 19:17:07 -05:00
guerler 5a82468784 Use regular dataset matching for selected values 2016-02-18 17:41:41 -05:00
guerler 664ae0c8df Attempt to strip legacy collection handling, fixes 2016-02-18 17:41:41 -05:00
guerler 9423283e83 Fix ftp handling 2016-02-18 17:41:41 -05:00