Jeremy Goecks
3dffeafdea
Update tool template's chrom_info to correctly point to len file for custom builds defined by len files. This was broken was len files were moved from the len_file directory to HDAs.
2014-01-23 15:29:14 -05:00
Martin Cech
7af8b1a4c7
removed bug in libraries API (prepending ‘F’ to library id, should be only for folders)
2014-01-23 10:05:09 -05:00
Greg Von Kuster
13908bda0b
Pep-8 fixes for the base admin controller.
2014-01-22 16:52:18 -05:00
Dannon Baker
da5be14d18
Use url_for with webhelpers + reinstate previous absolute path w/ slash.
2014-01-22 16:03:57 -05:00
John Chilton
33fb5fa773
Make normalizing remote user e-mail optional (off by default).
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I don't think we can make this change as is in case other institutions have configured their proxies to supply consistent e-mail addresses or other identifiers and these identifiers are not uniformly lower case. In such cases these changes (Pull Request 144) would break Galaxy's existing user management.
2014-01-17 01:10:58 -06:00
Galaxy
b627c3d061
lower case external remote user - canonicalise email address
2013-03-27 12:32:29 +13:00
Jeremy Goecks
7954e0e4c4
Fix for 9bc3fa1 to allow path rewrites; old Webhelper functions stripped preceding '/' but current functions do not.
2014-01-22 14:09:09 -05:00
John Chilton
89e959bb1a
Allow adjusting the reset password length in unvierse_wsgi.ini.
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Purposely not annotated in universe_wsgi.ini.sample - though could be persuaded to add it.
2014-01-22 11:06:26 -06:00
John Chilton
427ad65d9a
Adjust logic related to_posix_lines to make optionally specified.
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Fixes library uploads and restores backward-compatiblity to create_paramfile interface to rest of Galaxy. This is an alternative to pull request #305 .
2014-01-22 10:35:31 -06:00
Nate Coraor
7f58614225
Point rsync at a cname rather than scofield.
2014-01-22 11:28:49 -05:00
Daniel Blankenberg
25f0640f6a
Fix for installing migrated tools with dependencies.
2014-01-22 11:13:13 -05:00
Daniel Blankenberg
5c64af0270
Fix for upload tool importing from ftp uploaded file.
2014-01-21 17:21:04 -05:00
Daniel Blankenberg
5650037d79
Handle errors uploading files to a toolshed repository using mercurial clone by presenting an error message to the user.
2014-01-21 16:42:39 -05:00
Greg Von Kuster
fe7a7e0a7c
Fix typos in error messages displayed when importing repository capsules into a tool shed.
2014-01-21 16:04:34 -05:00
Nate Coraor
3c98a976b3
Merge stable.
2014-01-21 12:40:58 -05:00
Nate Coraor
09ecc02a17
Add missing requirement tags to converters, fixes Trello #1349 .
2014-01-21 12:39:35 -05:00
Daniel Blankenberg
c6e0023c71
Add a space between keywords.
2014-01-21 12:06:15 -05:00
Daniel Blankenberg
c7ae3e1c28
Merged in BjoernGruening/galaxy-central-bgruening/external_display_application (pull request #303 )
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fix display_application with login_required=True
2014-01-21 11:54:24 -05:00
Bjoern Gruening
efd3ac9b66
fix display_application with login_required=True
2014-01-21 17:28:35 +01:00
Bjoern Gruening
331a182079
In case of proxy-prefix configuration the $PATH_TO_IMAGES is not correctly converted. Removing the beginning Slash solves it for proxy-prefix configurations and other are not affected.
2014-01-21 15:42:35 +01:00
Greg Von Kuster
7e883fb968
Eliminate the recently introduced restriction on uninstalling repositories that are dependencies of other installed items, but keep the beneficial feature that displays dependent items that will be affected if a repository is uninstalled.
2014-01-20 16:07:08 -05:00
John Chilton
e67ae76526
Small refactor to ToolDataParameter.
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Break out logic for computing and asserting existence of history - simplifies get_html_field, get_initial_value_from_history_prevent_repeat, reduces code duplication, and eases some downstream merges changes I making.
2014-01-20 12:39:50 -06:00
Greg Von Kuster
e01cc26dd1
Fixes and code cleanup for the tool shed's install and test framework.
2014-01-20 11:48:05 -05:00
Greg Von Kuster
0bb74156d4
Merged in saketkc/galaxy-central-gsoc2013 (pull request #299 )
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Add ProxyHandler to auto-detect system proxies
2014-01-20 09:42:05 -05:00
John Chilton
e45e22caa9
Merged in jmchilton/galaxy-central-fork-1 (pull request #300 )
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Potential DRMAA fixes.
2014-01-17 16:04:39 -06:00
Greg Von Kuster
ac120fb0d1
Dict url entry changes and improved logging for the Tool Shed api.
2014-01-17 16:35:05 -05:00
Daniel Blankenberg
ca07eb79e9
Change log.error to log.debug.
2014-01-17 15:45:04 -05:00
Greg Von Kuster
a48cc46574
Enhance setting tool shed repository metadata to support tool dependency recipes that define installation of a binary but do not also include a recipe for installing and compiling from source.
2014-01-17 13:49:10 -05:00
Martin Cech
5137176626
library history ‘back’ button bug removal
2014-01-17 12:19:04 -05:00
John Chilton
766fbee77b
Handle subclassed DRMAA exceptions properly.
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No clue if this was a problem, but realized it might be.
2014-01-17 09:48:17 -06:00
John Chilton
ae96c90894
Provide item style access to runner params.
2014-01-17 09:48:17 -06:00
Martin Cech
2404aca0bf
Merge
2014-01-17 09:55:27 -05:00
John Chilton
658ea5966c
Merge pull request 171.
2014-01-16 23:57:43 -06:00
Saket Choudhary
f1190a8d37
Add ProxyHandler to auto-detect system proxies
2014-01-17 05:24:23 +05:30
Daniel Blankenberg
2752bc74de
Fix for api/tools/show/ when no id is provided.
2014-01-16 16:52:39 -05:00
Daniel Blankenberg
de2e6d3f79
Use toolbox.get_tool instead of toolbox.tools_by_id.get in tools api show().
2014-01-16 16:21:41 -05:00
Daniel Blankenberg
fddb4b0ba6
Use toolbox.get_tool instead of toolbox.tools_by_id.get in tools api show().
2014-01-16 16:21:41 -05:00
Greg Von Kuster
9d49a65e60
Forgot None in my last commit
2014-01-16 16:13:47 -05:00
Greg Von Kuster
78b6229584
Re-include deprecated repositories when resetting metadata since they can be dependencies of installable repositories.
2014-01-16 16:02:39 -05:00
Martin Cech
0508ce36ff
Merge
2014-01-16 14:13:15 -05:00
Martin Cech
0d08258c11
PEP8 tweaks
2014-01-16 14:08:58 -05:00
Greg Von Kuster
212aa39901
Fixes in the tool shed api for mapping the repository user_id and for handling repository_dependency changeset_revision values that have been updated.
2014-01-16 14:07:28 -05:00
John Chilton
fc17db50cc
Fix database engine options when verifying tools using separate install database.
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Bug report and fix thanks to Jim Johnson.
2014-01-16 13:00:30 -06:00
Martin Cech
a9b39936d6
remove doubled import
2014-01-16 13:35:51 -05:00
Martin Cech
34976050e5
removed obvious bugs in api_key retrieval through API using basic authentication
2014-01-16 13:30:53 -05:00
Martin Cech
e1ed16b74b
api_key retrieval through API using basic authentication
2014-01-16 13:20:10 -05:00
John Chilton
994ac18d73
Rearrange __handle_execute and handle_input in Tool...
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Slightly cleaner this way (fewer exit points) and will enable extensions I am making downstream.
2014-01-16 09:30:01 -06:00
Dannon Baker
33f83e1b77
Explicitly require UsesAnnotations mixin for the annotations api controller *after* UsesStoredWorkflowMixin.
2014-01-16 09:56:31 -05:00
Nicola Soranzo
966a7911e1
Add /api/workflows/import method to import a workflow shared by other users.
2014-01-15 18:28:21 +01:00
Nicola Soranzo
9953a948d6
Move core code for importing a shared workflow to UsesStoredWorkflowMixin.
2014-01-15 18:17:24 +01:00
Jeremy Goecks