John Chilton
cf4c1539df
Improved logic for determining if something is a GIE directory.
2016-02-26 00:38:47 +00:00
Eric Rasche
efcbfe6a0c
Make flake8 happy
2016-02-24 19:22:25 -06:00
Eric Rasche
4bf14db042
Correct the format statement for mounting
2016-02-24 19:16:51 -06:00
Eric Rasche
ba6b06cecb
Merge in master
2016-02-24 16:49:46 -06:00
Eric Rasche
590b75597e
Move viz plugin into templates and lib
2016-02-24 16:46:35 -06:00
Nate Coraor
b14e35f48b
Add a safe_relpath util function for ensuring a path does not reference an absolute or parent directory
2016-02-24 16:39:15 -05:00
Nate Coraor
3a006766d3
Security fixes for tool shed hg push and capsule/tarball uploads
2016-02-24 11:18:24 -05:00
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
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
guerler
dda851def5
Fix sections
2016-02-23 14:17:13 -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
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
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
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
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
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
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
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
guerler
6ffa104cb3
Use visit inputs to set runtime config, remove conflicting booleans
2016-02-18 17:41:41 -05:00
guerler
89759a00c1
Remove DummyDataset
2016-02-18 17:41:41 -05:00
guerler
25c6eda06e
Remove regular tool handling from editor_form_post
2016-02-18 17:41:40 -05:00
guerler
032ecd1e6e
Remove former update state
2016-02-18 17:41:40 -05:00
John Chilton