Nate Coraor
da2475b3e0
'fields' is apparently reserved in MySQL 4, fix migration scripts that use it unaliased. Thanks John Eppley.
2011-06-02 12:11:53 -04:00
Daniel Blankenberg
90aeffb5e6
Import patch contributed by Jim Johnson that supports sub directories in extra_files_path for displaying and downloading.
...
"Numerous applications create html files with a directory hierarchy. I\'m including a patch support the display and download of datasets that include subdirs in their extra_files_path."
2011-06-02 11:46:49 -04:00
Nate Coraor
c229b70b4c
Another fix for uploading datasets to a library without a history.
2011-06-02 11:40:06 -04:00
Nate Coraor
91a484c259
Fix for library upload when there is no current history.
2011-06-02 11:06:08 -04:00
Nate Coraor
b91ca79851
Set a catchall content-type (application/octet-stream) on metadata file downloads so Safari doesn't consider them to be html.
2011-06-01 16:27:28 -04:00
Greg Von Kuster
7c5e57f774
Fix the ToolParamSanitizer unit test. Since mercurial imports locale.getpreferredencoding(), which is part of the Python stdlib, the behavior of python strings is re-sorted, so we have to sort them back...
2011-06-01 16:21:12 -04:00
Greg Von Kuster
95ffc3243f
Fixes for editing role name, descriptionn, and renaming groups. Resolves issue #539 .
2011-06-01 15:47:04 -04:00
Greg Von Kuster
72dfb35375
Several data library bug fixes:
...
- Determiining if an accessible dataset exists somewhere in the data library hierarchy now works all the time ( I believe ). It used to work most of the time, but under corner conditions, it would break.
- When importing dataset from a history into a data library, the dataset permissions are now correctly applied to the library dataset. The DATASET_MANAGE_PERMISSIONS permission is a spoecial case in that if it exists on the dataset, the LIBRARY_MANAGE permission must be applied to the library dataset.
- Fix for message display and db flushing when importing library dataset into a history.
- Do not render the folder pop-up menu option for selecting library dataset to import into histories if the folder does not contain any accessible library datasets.
2011-06-01 15:20:43 -04:00
Nate Coraor
51aeadf8e5
Fix the user create/login links in the FTP upload form
2011-06-01 15:12:12 -04:00
Daniel Blankenberg
05242912c7
Minor reformatting for 5609:f530dbdde1f5
2011-06-01 11:40:38 -04:00
Daniel Blankenberg
0a47db9aa4
Allow VCF parser to accept unknown values for QUAL field.
2011-06-01 11:29:07 -04:00
Greg Von Kuster
9dede7be76
Fix for importing library datasets into a new named history. Library datasets will no longer be imported into both the current history and the new named history ( only the latter ) in this scenario.
2011-05-31 12:03:52 -04:00
Jeremy Goecks
71cc5195d1
Fix bugs in reading and visualizing GFF3 datasets.
2011-05-28 01:07:06 +02:00
Kanwei Li
d270433ccc
Remove debug
2011-05-26 08:27:52 -04:00
Kanwei Li
5f36576880
Fix user/create from direct URL access
2011-05-26 08:20:37 -04:00
Kanwei Li
2037dc102d
Sanitize defaults
2011-05-25 16:39:43 +02:00
Kanwei Li
68a514d789
Fix a few XSS issues in workflow/history
2011-05-25 11:31:26 +02:00
Nate Coraor
5dbf59c2fc
Fix the non-working default="true" for checkboxes, thanks Louise-Amélie Schmitt.
2011-05-24 05:33:07 -04:00
Greg Von Kuster
212433fe2c
First pass of the next-gen Galaxy tool shed. See it demonsrated and discussed at the 2011 Gallaxy Community Conference in Lunteren on May 24,25,26.
2011-05-20 16:04:30 -04:00
Daniel Blankenberg
ef795f04e0
Fix typo (val to value).
2011-05-20 06:17:35 +01:00
Jeremy Goecks
8db5b83322
Clone annotation and tags when cloning workflows.
2011-05-18 16:48:02 -04:00
Kanwei Li
d340c2ab22
Fix data.py typo. Fixes #543
2011-05-17 18:41:12 -04:00
Kanwei Li
5caf51ddaa
trackster: Refactor LineTrack overflow, fix it to work better for Line and Filled modes
2011-05-16 17:08:06 -04:00
Kanwei Li
3275e4558c
trackster: tweak resolution, fix LineTrack data bug
2011-05-13 16:49:43 -04:00
Jeremy Goecks
649bd62af7
Trackster: enable chaining of filters.
2011-05-13 10:02:28 -04:00
Jeremy Goecks
3eb0c50ae4
Trackster: enable dynamic filters to be run on complete dataset using filter tools.
2011-05-12 17:12:01 -04:00
Kanwei Li
efe0cba6d8
trackster: Fix border and error not lining up at right place
2011-05-11 15:43:33 -04:00
Jeremy Goecks
01ec149d82
Add support for comment handling to gff_to_interval_index tool.
2011-05-11 15:38:57 -04:00
Kanwei Li
a706fc3796
Show details: now works even when tool is obsolete. Show inheritance chain where the dataset came from if it was copied from a history or library
2011-05-11 11:36:22 -04:00
Kanwei Li
5b5b243b9b
trackster: Greatly improve LineTrack performance as it was fetching an unoptimal amount of data, decreasing performance by orders of magnitude
2011-05-06 16:02:25 -04:00
Nate Coraor
fb99bf73f1
Standardize naming of reserved/predefined values in the param_dict. Old values are maintaned as well.
2011-05-06 11:49:02 -04:00
Jeremy Goecks
86826cc91d
Trackster: use GTF metadata to create dynamic filters.
2011-05-05 19:05:39 -04:00
Jeremy Goecks
1d03c82144
Enable GFF filter attributes tool to accept arbitrary conditions.
2011-05-05 16:51:56 -04:00
Jeremy Goecks
c7cfc3d67f
Add metadata for GTF attribute values.
2011-05-04 16:45:10 -04:00
Jeremy Goecks
faafc762bf
Trackster: enable a tool to be run on complete dataset or a visible region.
2011-05-04 10:20:54 -04:00
Jeremy Goecks
5e350f9208
Fix bugs in tracks/run_tool.
2011-05-02 15:14:53 -04:00
Jeremy Goecks
1e0b6bb5c3
Make gops intersect tool compatible with GFF features rather than GFF lines.
2011-05-02 13:59:49 -04:00
Daniel Blankenberg
5c7daee0f0
Only allow a user to rerun if they have access permissions on the dataset.
2011-04-29 16:51:51 -04:00
Greg Von Kuster
2749ab91b0
Apply patch from taoliu - ticket #529 - Missing controller when creating user with require_login & allow_user_creatio is on.
2011-04-29 15:32:04 -04:00
Nate Coraor
e7c5ff5c08
Minor fix for setting the username during user creation under use_remote_user = True. Converts the user portion of the user's email to lowercase and replaces invalid characters with '-' as per the public name format requirements.
2011-04-29 10:35:42 -04:00
Ross Lazarus
899de56e61
tweaks to fasta locations for tests for ASM and insertsize
2011-04-28 19:30:48 -04:00
Kanwei Li
f52f8fcada
trackster: Fix filters, restore name of IntervalIndex provider
2011-04-28 13:17:51 -04:00
Nate Coraor
41730ac15b
Set and allow modification of the public username if use_remote_user = True
2011-04-28 11:33:07 -04:00
Kanwei Li
2e3c767ec4
trackster: Restore interval_index as Gff indexer for now due to sorting issues
2011-04-27 19:08:31 -04:00
Kanwei Li
19e18e1899
trackster: Fix incorrect "end" calculation
2011-04-27 17:33:08 -04:00
Kanwei Li
43de1e17ce
Fix GTF for trackster
2011-04-27 15:41:25 -04:00
Daniel Blankenberg
f9c267f406
When label text for a static option in a SelectToolParameter is not provided, default to using the 'value'.
2011-04-26 11:25:54 -04:00
Kanwei Li
8e2f6f4c8f
trackster:
...
- Make GFF, Bed and Vcf use Tabix data provider instead of interval_index. PLEASE UPDATE with new entries in datatypes_conf.xml.sample
- Refactoring for data providers
2011-04-25 18:59:37 -04:00
Daniel Blankenberg
1f9abea3fe
Bug fix for 5454:2379785017d7
2011-04-25 17:21:21 -04:00
Daniel Blankenberg
129448a30c
Fix for dynamic options when referencing a DataToolParameter that has already been wrapped.
2011-04-25 14:41:54 -04:00
Nate Coraor