Greg Von Kuster
b94de80659
Add the ability to move data library items within a data library or between data libraries.
2011-03-08 15:50:19 -05:00
Ramkrishna Chakrabarty
a97da4abcf
Add import statement for binascii
2011-03-08 14:35:26 -05:00
Ramkrishna Chakrabarty
5bfdb9443b
Added the postgres9 json sniffnfix method to the migration script instead of importing it from custom_types.py
2011-03-08 14:08:07 -05:00
Ramkrishna Chakrabarty
a20d7738b6
Fixes the data corruption caused in the form_values table (content field) by the migrate script 65.
2011-03-08 12:42:26 -05:00
Jeremy Goecks
4b78ad9765
Fix bug in GFF/GTF feature parser: new feature starts when transcript_id _or_ gene_id changes.
2011-03-07 15:40:24 -05:00
Nate Coraor
c83d376e42
If the referer is the logout page, redirect to base analysis interface after login instead of back to the logout page. Fixes issue #486 .
2011-03-07 13:30:29 -05:00
Dannon Baker
95545a8973
Add basic security to workflows api.
2011-03-05 16:32:41 -05:00
Dannon Baker
5b2f58bb14
Adjust ColumnListParameter tests to account for the new return from History.add_dataset.
2011-03-05 16:15:55 -05:00
Dannon Baker
e62494e2b0
Initial commit of workflows API. Supports simple execution, multiple input datasets. Does not support runtime tool parameter modification.
2011-03-05 11:47:12 -05:00
Dannon Baker
77eace152f
Removed invalid parameter in History.add_dataset, added return of dataset to the method.
...
Add APIItem to StoredWorkflow.
2011-03-05 11:31:41 -05:00
Daniel Blankenberg
1af6e33966
Add a 'subclass' flag to datatype definitions in datatypes_conf.xml that allows dynamic creation of a subclass.
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For example, to create a datatype that has the attributes of a Tabular file, but is more 'specific':
<datatype extension="more_than_tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" />
2011-03-04 10:28:04 -05:00
Ramkrishna Chakrabarty
cef8e1cc70
Backed out of changeset 5173:ac6b14ffc984
2011-03-04 09:59:06 -05:00
Ramkrishna Chakrabarty
3e7e8c2238
Fixes the data corruption caused in the form_values table (content field) by the migrate script 65.
2011-03-04 07:28:23 -05:00
Kanwei Li
cb076fdd9a
trackster: Fix summary_tree and error messages
2011-03-03 16:32:04 -05:00
Jeremy Goecks
c01a15b638
Set message type to error when history deletion fails due to sharing. Fixes #477
2011-03-02 17:31:09 -05:00
Daniel Blankenberg
2935741194
Allow FromParamToolOutputActionOption and ParamValueToolOutputActionOptionFilter to access attributes of parameter values.
2011-03-02 11:34:36 -05:00
Daniel Blankenberg
ad3f55b5b0
Allow DataToolParameter to be filtered on attributes other than dbkey.
2011-03-02 11:34:03 -05:00
Greg Von Kuster
4bdc069c4d
Clarify what's being searched in the tool shed.
2011-03-02 09:59:24 -05:00
Nate Coraor
3fc4c7c4f8
Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
2011-03-01 15:46:35 -05:00
Daniel Blankenberg
4eb1b0a79f
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
2011-02-28 12:16:28 -05:00
Nate Coraor
b4506597e6
Require ctypes egg before pysam on Python 2.4
2011-02-28 09:35:36 -05:00
Ramkrishna Chakrabarty
5ddadf7921
Fixed adding an external service to a request type in edit_request_type
2011-02-25 16:25:54 -05:00
Kanwei Li
ac2d5a8f69
Only lowercase columns if starting with "c".. fixes issue where "None" was lowercased to "none". Fixes subtract_query tests
2011-02-24 19:07:41 -05:00
Jeremy Goecks
39bfd3c89d
Add options to Tophat wrapper to support v1.2.0 functionality: (a) allow indel search; (b) max insertion and max deletion lengths; and (c) library type. Update functional tests to tests new options. Also update function that checks from_work_dir output attribute to use real path to prevent mishandling of symbolic links.
2011-02-24 15:24:52 -05:00
Ramkrishna Chakrabarty
47a61afa18
Adding ftype attribute to vcf tool tests
2011-02-24 12:16:33 -05:00
Ramkrishna Chakrabarty
0e7e0241fb
Bug fix: checkbox values were not getting saved for samples in the sample grid. Issue #476
2011-02-23 11:56:16 -05:00
Jeremy Goecks
85a065cd5b
Enhance GFF reader to handle headers and comments.
2011-02-23 10:40:30 -05:00
Kanwei Li
4660370320
Copy datasets feature:
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- Fix functional tests
- Populate previously selected target history if attempt fails
2011-02-22 17:14:16 -05:00
Greg Von Kuster
b34afd146f
(no commit message)
2011-02-22 10:38:35 -05:00
Jeremy Goecks
e85d70ffa4
Trackster refactoring: (a) move ReadTrack-specific code out of FeatureTrack and into ReadTrack; (b) move VCFTrack-specific code of out FeatureTrack and into VcfTTrack. This makes it easier to modify drawing for each track type but creates some repeated code in draw_tile() for different classes that needs to be cleaned up.
2011-02-21 15:54:22 -05:00
Nate Coraor
a7a048cd0f
Don't use 'python -ES' when scrambling eggs due to '-S' breaking virtualenv.
2011-02-21 09:46:54 -05:00
Kanwei Li
a3b48f8d5d
Update distutils egg to 0.7, and use the provided HTML output writer to do rst->html conversion. Remove old code that previously did this. This fixes a bug where an extra "</div>" was appended after every output, resulting in the tool config not showing in workflows, in IE.
2011-02-18 17:47:07 -05:00
Ramkrishna Chakrabarty
0186ef38e6
renamed 'samples' to 'sample_widgets' in __save_samples
2011-02-18 14:46:16 -05:00
Nate Coraor
64ff3f715d
Don't copy ez_setup.py to egg build directories anymore, and provide a more useful error message when an egg is missing a dependency with a version conflict.
2011-02-18 13:22:31 -05:00
Daniel Blankenberg
bde479e1f1
Do not print summary information in FASTQ groomer when grooming an empty file.
2011-02-18 12:07:27 -05:00
Greg Von Kuster
cc72c1103b
Fix for changing the selected data library and folder for a checked list of samples ( a subset of the entire list of the request's samples ).
2011-02-18 12:04:26 -05:00
Ramkrishna Chakrabarty
0b935e7956
Backed out of changeset 5085:0ce482e2ec78
2011-02-18 11:18:52 -05:00
Ramkrishna Chakrabarty
37cd10cb27
bug fix: bulk operations on samples for changing target data libraries was broken
2011-02-18 10:49:46 -05:00
Kanwei Li
6670d7a7f2
Add a "format_source" attribute to the ToolConfig output data element [JJ Johnson]. Closes #470
2011-02-17 15:35:07 -05:00
Dannon Baker
a078966558
Adjustment to dataset line estimation.
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Estimate is now rounded to only the first two digits, like: ~65,000 lines, to make it clearer that it's an estimate.
Will no longer try to estimate for small files, however they ended up without lines set.
2011-02-17 12:05:39 -05:00
Dannon Baker
e9d1d07192
Quick fix for postgres9 JSONType/MetadataType hex decoding issues.
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Todo: Postgres9 might be configurable to do this natively, postgres8 does not have the issue.
2011-02-16 13:50:30 -05:00
Greg Von Kuster
57d2f8168e
Fix bug when rendering the contents of a data library - render the options for acting on multiple datasets if the library includes accessible datasets at any level in the hierarchy rather than if it only includes them in the root folder.
2011-02-16 09:54:49 -05:00
Kanwei Li
c075b3d119
trackster: For feature/bam tracks, new option in dropdown to list chroms/contigs that have data for that dataset. Tweak popup menu system to use a $.data variable that is bound to the anchor link, allowing options to be modified after the first initialization.
2011-02-15 19:09:38 -05:00
Nate Coraor
f66a193b94
lazy load jobs for job recovery and a bugfix for administrative job stops when tracking jobs in the database.
2011-02-15 16:52:16 -05:00
Kanwei Li
4cade49419
Add len_file_path configurable to specify where chrom .len files are stored
2011-02-15 13:53:16 -05:00
Greg Von Kuster
00c6be5124
Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.
2011-02-14 14:54:07 -05:00
Nate Coraor
b5927f9e4e
Fix for PBS job runner importing itself instead of pbs_python.
2011-02-14 10:56:06 -05:00
Nate Coraor
fc893e7859
Fix infinite loop setting up locales.
2011-02-14 09:08:04 -05:00
Kanwei Li
09e5692b27
trackster:
...
- Fix bug where tiles were not aligning correctly because of inconsistent w_scale
- Fix tracks with errors or no data not having right background
- Refactoring
2011-02-11 16:55:14 -05:00
Nate Coraor
9dfe03493d
Instead of raising in exception, default to english if a locale is set by the client but not installed on the server.
2011-02-11 16:15:18 -05:00
Greg Von Kuster