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Author SHA1 Message Date
James Taylor d7bb37c95c Merging due to sloppy commit order. 2008-12-16 17:32:20 -05:00
James Taylor d2dfd2db26 Allow workflows to recognize "data_meta" filters in dynamic options as 
forcing runtime validation.
 2008-12-16 17:30:19 -05:00
James Taylor 54385c8313 Allow workflows to recognize "data_meta" filters in dynamic options as 
forcing runtime validation.
 2008-12-16 17:05:28 -05:00
James Taylor 9ca2331917 One more fix for running workflows involving conditional params. 2008-12-16 16:38:46 -05:00
James Taylor 274cc3f1c5 Two fixes for inputs inside conditionals when building and running workflows. 2008-12-16 16:26:03 -05:00
Nate Coraor 5994eb7055 merging heads 2008-12-16 14:32:13 -05:00
Nate Coraor cbaf4609d9 Update bx-python to r459 2008-12-16 14:31:00 -05:00
Greg Von Kuster 36e3f21d7e merging from central 2008-12-16 10:07:10 -05:00
Greg Von Kuster ae84867027 Server errors thrown when switching between Galaxy and reports in the same browser was due to the id_secret being different in the Galaxy config and the reports config, so add comments to ensure this is not repeated. 2008-12-16 10:04:30 -05:00
Nate Coraor 8243eee012 Fix functional tests broken by my last commit 2008-12-15 17:08:35 -05:00
Greg Von Kuster c730aad62c Some code cleanup in framework/__init__.py 2008-12-15 17:04:06 -05:00
Greg Von Kuster 769efedc5e merging from central 2008-12-15 17:03:31 -05:00
Nate Coraor b6d561fb42 Allow users to download a selection of datasets directly from the library in an archive format of their choosing. 2008-12-15 16:37:54 -05:00
Greg Von Kuster 4e48d41c8a Add a necessary closing </div> tag for the library browser, caused indendation problems in Safari, but now fixed. 2008-12-15 14:13:34 -05:00
Greg Von Kuster c90a09e782 Fix for the users reports. 2008-12-15 11:25:47 -05:00
Greg Von Kuster a80cbe30b8 merging from central 2008-12-15 11:25:11 -05:00
Greg Von Kuster dfd5e9827f Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server. 2008-12-15 10:37:39 -05:00
Greg Von Kuster d3b2a27cee merging from central 2008-12-15 10:37:16 -05:00
Greg Von Kuster 7ecfd7c61e Reset functional test port which somehow got committed when attempting to merge conflicts. 2008-12-15 09:06:11 -05:00
Greg Von Kuster bff56d118e merging from central 2008-12-15 09:05:20 -05:00
Greg Von Kuster e858742d73 merging from central 2008-12-15 09:01:37 -05:00
Greg Von Kuster 7a5203fd65 Attempting to merge conflicts. 2008-12-15 08:58:33 -05:00
Greg Von Kuster b432fd166d merging heads 2008-12-15 08:55:16 -05:00
Greg Von Kuster 0b85700945 merging from central 2008-12-13 23:36:47 -05:00
Greg Von Kuster 2647f72e4a Add ability for data_source tools to append parameters passed in the initial response to the value of URL prior to Galaxy's post to the URL. This is a cleaner method for Biomart and also gets GBrowse to wrok. 2008-12-13 23:35:29 -05:00
Greg Von Kuster 394c26fa1f Fix for __get_or_create_remote_user, show an error message if the user's account has been deleted instead of automatically undeleting it. 2008-12-12 14:56:35 -05:00
Greg Von Kuster dbf2479cc8 merging from central 2008-12-12 14:36:23 -05:00
Greg Von Kuster 89fa876175 Fix for showing deleted datasets in a history, also yet another fix for the new users report, users are now sorted descending by last login, as the report states. 2008-12-12 14:33:51 -05:00
Guruprasad Anada 7d48102b82 merging heads 2008-12-12 12:16:41 -05:00
Guruprasad Anada 9a0953f1f1 Added more test-cases to GOPS JOIN to include cases with different cut-offs for overlap. 2008-12-12 12:12:59 -05:00
Greg Von Kuster 797b6e1d87 Filter out deleted users from report in security branch. 2008-12-12 11:58:23 -05:00
Greg Von Kuster ecb5436d71 Bug fix for users report controller, some users may not yet have logged in. 2008-12-12 11:53:06 -05:00
Greg Von Kuster eafbffe917 merging from central 2008-12-12 11:53:00 -05:00
Greg Von Kuster 40a55c1832 Add ability ot rename roles and groups, 2 fixes for filtering out deleted roles, some code cleanup and additional functional tests to cover new features. 2008-12-12 11:27:37 -05:00
Nate Coraor 533b4cf9e5 merging from central 2008-12-12 10:17:47 -05:00
Nate Coraor 47471ed40a Update bx-python to r458 2008-12-12 10:15:37 -05:00
Greg Von Kuster 6d00bd4f17 merging from central 2008-12-12 09:47:08 -05:00
Greg Von Kuster c58bacce7f New report showing last login for users, a few bug fixes and some code cleanup for the reports as well. 2008-12-12 09:43:42 -05:00
Daniel Blankenberg 739921bda9 Merging Heads 2008-12-11 16:00:34 -05:00
Daniel Blankenberg 16e783267c Update Fasta.sniff() 
Rules for sniffing as True:
    We don't care about line length (other than empty lines).
    The first non-empty line must start with '>' and the Very Next line.strip() must have sequence data and not be a header.
        'sequence data' here is loosely defined as non-empty lines which do not start with '>'
        This will cause Color Space FASTA (csfasta) to be detected as True (they are, after all, still FASTA files - they have a header line followed by sequence data)
            Previously this method did some checking to determine if the sequence data had integers (presumably to differentiate between fasta and csfasta)
            This should be done through sniff order, where csfasta (currently has a null sniff function) is detected for first (stricter definition) followed sometime after by fasta
    We will only check that the first purported sequence is correctly formatted.
 2008-12-11 16:00:06 -05:00
Nate Coraor 68728e0a9c merging heads 2008-12-11 15:14:20 -05:00
Nate Coraor 075357caf3 merged from central 2008-12-11 15:14:07 -05:00
Nate Coraor 87f81c24b1 Comment out logging for remote_user creation as a temporary fix 2008-12-11 15:09:37 -05:00
Daniel Blankenberg 2c05491514 A script to update a pre-security/library Galaxy database with necessary schema changes and set default roles/permissions for users and their histories and datasets. 
It will reset permissions on histories and datasets if they are already set (i.e. script was run on a database which already has security/library tables).

This has been tested with Postgres, SQLite, and MySQL databases.

Due to limitations of SQLite this script is unable to add foreign keys to existing SQLite tables (fks are ignored anyway).

*** Remember to backup your database before running. ***
 2008-12-11 14:10:11 -05:00
Greg Von Kuster 918b43177c merging from central 2008-12-11 12:23:50 -05:00
Greg Von Kuster 6416e095a0 Fix a development problem that I inadvertently left in the code. 2008-12-11 12:18:00 -05:00
Greg Von Kuster 5213175431 Requires DB schema change: change TEXT column types with indexes to VARCHAR. 
SQL commands to change db schema:
ALTER TABLE galaxy_group ALTER COLUMN name TYPE VARCHAR(255);
ALTER TABLE role ALTER COLUMN name TYPE VARCHAR(255);
ALTER TABLE role ALTER COLUMN type TYPE VARCHAR(40);
ALTER TABLE library ALTER COLUMN name TYPE VARCHAR(255);
 2008-12-11 12:09:09 -05:00
James Taylor 8e8693a616 Template for running workflows from analysis view. 2008-12-11 10:18:46 -05:00
Greg Von Kuster 34ec0e8cbf Functional test coverage now fairly complete for current dataset security and library features. 2008-12-10 10:35:47 -05:00
Daniel Blankenberg a9cd55a62f Merging heads 2008-12-09 15:51:34 -05:00