Daniel Blankenberg
183c2d3d13
Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
...
Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
2010-06-07 15:34:20 -04:00
Kelly Vincent
f9f54848ed
Add SAM indel filter tool to tool_conf.xml.sample
2010-06-07 15:30:20 -04:00
Kelly Vincent
19f6b34ad2
merged SAM indel filter tool commit
2010-06-07 15:27:45 -04:00
Kelly Vincent
78b17cbb9c
Adding SAM indel filter tool with test files
2010-06-07 15:23:32 -04:00
Greg Von Kuster
db04e55560
Yet another fix fo creating the history link on the library dataset information page - since it is possible to have an hda that does not have an associated history, we need to handle it.
2010-06-07 13:14:07 -04:00
Greg Von Kuster
05fcb04122
Being extremely cautious when displaying history atibutes associated with an hda in the library dataset info page.
2010-06-07 12:51:38 -04:00
Nate Coraor
506699c31a
Bugfix for 4fb747f317d0, open tar file as stream
2010-06-07 11:57:47 -04:00
Nate Coraor
20a9badd9c
Fix bug in 48ec25db21c3
2010-06-07 11:36:09 -04:00
Nate Coraor
fe3873752c
Add RGENETICS section label to main tool conf
2010-06-07 11:26:52 -04:00
Nate Coraor
e987084f3d
Allow disabling of library download compression types
2010-06-07 11:25:10 -04:00
Nate Coraor
5eaf2c7e20
When using gzip compression in the upstream proxy, do not gzip compress library tar.gz or zip archives. bz2 then remains as the only compression perfomed in Galaxy itself.
2010-06-07 11:24:09 -04:00
Jeremy Goecks
474ea363b6
Fix model_class typo.
2010-06-07 11:06:07 -04:00
Kanwei Li
47407f39ad
Fix autocomplete select not closing after dragging text inside, and holding arrow keys not triggering multiple times in firefox. Cleanup JS
2010-06-06 18:55:09 -04:00
Jeremy Goecks
af04947287
Better handling of return key in search+select.
2010-06-05 12:00:10 -04:00
Kanwei Li
4fe3713429
Prevent workflow forms from being submitted twice when dynamic options are refreshed, resulting in AJAX error and inability to savewq
2010-06-04 18:27:50 -04:00
Greg Von Kuster
1e727e2534
Fix for library dataset information page, link to history items using hda.history_id rather than hda.history.id.
2010-06-04 18:03:10 -04:00
Greg Von Kuster
15abe33231
Add the CBI Rice Mart data source tool to the distribution.
2010-06-04 15:49:58 -04:00
Greg Von Kuster
ce5e865a84
Add the ratmine datasource tool to main's tool config.
2010-06-04 14:45:02 -04:00
Greg Von Kuster
4bfd300326
I forgot to change the disk file size from 0 back to 4 gb for the systems report before may last commit.
2010-06-04 14:30:57 -04:00
Greg Von Kuster
bc8c2f65e1
Fixes and enhancements to the reports webapp:
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0) The report that is initially displayed is now the number of jobs per day for the current month rather than the grid displaying all jobs for today.
1) Eliminate eagerloading when querying jobs so that queries are much faster
2) Fix the disk space ( system ) report, and add a new feature that displays all active ( undeleted ) hda and ldda pointers to a specific dataset.
3) Standardize request parameters so that queries can more easily be built using parameters from the request.
4) A few other miscellaneous bug fixes in the reports.
2010-06-04 13:29:14 -04:00
Ramkrishna Chakrabarty
fff52c9c64
lims: added new feature where the datasets are be automatically renamed using a setting with the request_type. This makes solves the same dataset name problem on SOLiD
2010-06-04 13:18:56 -04:00
Greg Von Kuster
0e76adfeb8
Add a temporary fix to grid_common.mako, eliminating the use of the categorical-filter style for grid StateColumns so that the request will not be mangled before it reaches the server. Added several TODOs in the grid Javascript code outlining the problem.
2010-06-04 13:14:30 -04:00
Dannon Baker
248cdc408d
BUGFIX: Removed console.logs from page and workflow editors.
2010-06-04 11:04:33 -04:00
Jeremy Goecks
efe2ba46d8
Filter datasets grid so that datasets in deleted histories are not shown.
2010-06-04 09:43:06 -04:00
Jeremy Goecks
3d5d6b2e32
Update cufflinks wrapper and tests. Expression output files are now tabular and all outputs are evaluated in functional test.
2010-06-04 09:19:36 -04:00
Kanwei Li
0bcd4656bd
trackster: Implemented drag-zooming by letting you drag a region in the top label track (where chrom position is shown). Refactored to not use zoom levels anymore.
2010-06-03 17:58:58 -04:00
Jeremy Goecks
6f8aaecaa6
Bug fix for importing a history archive.
2010-06-03 17:04:31 -04:00
Jeremy Goecks
92588a9004
Improvements to history import/export archive: (a) use python tar file support (which may be more widely available than pax) and (b) perform some simple security checks to ensure that uploaded archive files are not malicious.
2010-06-03 15:59:19 -04:00
Daniel Blankenberg
3abcf309a9
Minor fix for changing datatype test.
2010-06-03 13:31:54 -04:00
Jeremy Goecks
6f68a41a53
Add history import and export functionality to Galaxy. Options for exporting the current history to a file or importing a history from a file are now listed in the history options menu. Also modified the form builder to support file inputs.
2010-06-03 12:17:34 -04:00
Daniel Blankenberg
f0357e375f
Resync Annotation Profiler tests to current cached data.
2010-06-02 16:40:39 -04:00
Greg Von Kuster
983b198fff
Enhancements for the library dataset information page: display all metadata elements, and if in the admin view, display all undeleted history items and other undeleted library datasets that use the current library dataset's disk file.
2010-06-02 14:29:19 -04:00
Greg Von Kuster
3135ffa5fc
Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.
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Add a get_display_name() method to the LibraryDatasetDatasetAssociation class.
Fix for the test_forms_and_requests.py functional test script, purge all created libraries created during the tests so following test runs will test correctly.
2010-06-02 14:24:48 -04:00
Nate Coraor
cb70efddd8
add fly_modencode, worm_modencode, and wormbase tools to main
2010-06-01 11:19:30 -04:00
Greg Von Kuster
e96b597b26
Fix the test_forms_and_requests.py functional test script to purge the group named "Group One" from the database in the reset data method so that later tests that create a group with the same name will pass. All library functional tests should now pass.
2010-06-01 10:02:34 -04:00
Nate Coraor
7a804317ef
When use_remote_user = True, still display the logged in user in the User menu
2010-06-01 09:44:42 -04:00
Jeremy Goecks
89aa0dd8bf
Search/select sorts only dbkey selects; others are unsorted.
2010-05-31 15:18:32 -04:00
Kanwei Li
64baf696f5
trackster: Can manually set display modes for tracks. Move buttons to the headers.
2010-05-28 21:13:25 -04:00
Greg Von Kuster
e79bf72fbe
Enhancements for the reports webapp:
...
In case you do not know about the Galaxy reports, make any changes you want to reports_wsgi.ini.sample and copy it to reports_wsgi.ini ( you'll have to do this anyway since there are changes in this change set )...
...then start them up with:
sh run_reports.sh
There is more work necessary, but this is a good start.  This is such a huge overhaul, that I'm sure there will be some issues.  Let me know and I'll fix them!
Here are the current fixes:
1) Use grids for rendering pages whose queries return lots of rows.
2) By using grids, we can:
 a) search for jobs whose state or tool id match a standard search filter
b) search for a specific job id using the advanced search filter
c) filter on job.state in the Advanced Search window
d) sort on id, state, tool_id or create_time in the grid
e) eliminate many of the complex old-style SQL select commands
3) Eliminate all unnecessary templates due to the use of grids, and move remaining templates to the proper loation
4) Eliminate the duplicated static files and use those from the Galaxy webapp
2010-05-28 16:30:16 -04:00
Ramkrishna Chakrabarty
c222bcb215
lims:
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- ui enhancements to the remote file browser: file details available on demand & the browser saves state after each transfer
- code cleanup
2010-05-28 16:06:57 -04:00
Greg Von Kuster
c55c40a243
Enhancements to the grid framework:
...
1) Change the name of the apply_default_filter() method to be apply_query_filter() to eliminate confusion about it being at all related to the default_filter dictionary attribute ( which it is not )
2) Add the kwd param to the method signatures of the handle_operation(), get_current_item() and build_initial_query() methods.  For build_initial_query(), this enables using request params as filters to be added to the query.
3) Add a new IntegerColumn column type to enable advanced search on integer column types.
4) Add a new StateColumn column type to enable filtering on an object's state values.
2010-05-28 10:04:30 -04:00
Greg Von Kuster
8670adafc2
Fix form.mako and message.mako to use the correct webapp version of base_panels.mako.
2010-05-28 09:51:57 -04:00
Greg Von Kuster
e99828e3b9
Change references to "public user name" to just be "publi name" on the user registration and user information pages.
2010-05-28 09:40:42 -04:00
Greg Von Kuster
355b914b02
Enhancement to the data libraries grid: display the file size of each library dataset in the grid.
2010-05-28 08:38:06 -04:00
Ramkrishna Chakrabarty
d4ebde01d1
lims:
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- fixed sample deletion bug. now alongwith the sample itself, the form_value row which stores the field values for that sample, is also deleted.
2010-05-27 16:31:19 -04:00
Daniel Blankenberg
0b2ad8d04b
Add a jar directory / bin which is accessible to tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar which has been placed in / linked to 'GALAXY_ROOT/tool-data/shared/jars' (by default; $GALAXY_DATA_INDEX_DIR can be configured to point elsewhere [value of 'tool_data_path' configuration variable in universe_wsgi.ini]).
...
The setup.sh script has been modified to create this directory when not present.
2010-05-27 16:01:25 -04:00
Nate Coraor
e6c1e39cf7
add tip about downloading individual library files
2010-05-27 15:53:56 -04:00
Jeremy Goecks
a4fd878207
Add test data necessary for tophat and cuffdiff functional tests.
2010-05-27 13:28:18 -04:00
Kanwei Li
275f8fd79a
-Fix icon positioning of datasets not ready to be viewed during upload
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-Fix CSS generator scripts, recreate sprites with new icons
2010-05-27 12:57:40 -04:00
Nate Coraor
133caa6170
Add missing location files for buildbot
2010-05-27 12:22:27 -04:00
Daniel Blankenberg