Kanwei Li
2d1eca1c13
Fix trackster error handling for job errors
2011-01-10 20:18:36 -05:00
Jeremy Goecks
cead324e72
Improve display of page numbers on grids so that not all page numbers are always shown. Add parameter 'num_page_links' to grid framework so that grid can control how many page links are shown.
2011-01-10 15:14:16 -05:00
Ramkrishna Chakrabarty
7fe6167d94
More instances of sequencer renamed to external service
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Form type in form_definition table changed to 'external service info form' from 'sequencer info form'
The sequencer tag in the external_services xml changed to external_service.
'do_not_encode' option removed from the build_select_field utility method in form_builder
2011-01-10 14:06:10 -05:00
Jeremy Goecks
41f937d166
Cleanup from changeset 4815:761738c53c8f: (1) fix bug that was loading jquery twice and hence causing problems; and (2) move setting of modal's min-width from init function into modal code itself.
2011-01-10 11:21:08 -05:00
Ramkrishna Chakrabarty
15f2571928
Bug fix in the migration script to support workaround for deleting a column in sqlite
2011-01-10 10:02:22 -05:00
Jeremy Goecks
b089e5872d
Use grids to enable selection of datasets for trackster using a hierarchical approach: user first selects a history and then datasets to add. Grid framework enhancements include: (a) grid title can be changed and (b) show_item_checkboxes is a proper grid parameter.
2011-01-07 16:52:32 -05:00
Ramkrishna Chakrabarty
dfbe729f8c
Tweaks to migration script
2011-01-07 16:27:57 -05:00
Ramkrishna Chakrabarty
f7a35e13cb
Renamed sequencer to external_service and sequencer_type to external_service_type.
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Added table to associate external services to a request type.
Enhanced UI to support selection of multiple external services for a request type.
2011-01-07 16:12:36 -05:00
Greg Von Kuster
bb6d5fe0d3
Add menu items to display / hide items pointing to a library dataset's disk file instead of always displaying them.
2011-01-07 13:12:27 -05:00
Greg Von Kuster
2275c15c28
Add support for several types of authentication to the demo sequencer, including browser login. Add menu options for using, editing and unusing run details templates for a sample, and fix several bugs related to upating template information.
2011-01-07 10:47:47 -05:00
Jeremy Goecks
c5705c0f6f
Fix read length bugs in trackster BAM data provider that were causing bad data to be sent to track browser. Also add documentation to BAM data provider.
2011-01-06 14:50:25 -05:00
Jeremy Goecks
76b8710677
Enhancements to visual analytics: (1) refactoring of tracks controller to enable more efficient dataset indexing and reuse of code; (2) new features in track browser: custom wait times, programmatic track renaming, strict synchronization b/t slider and parameter values, and labeling for tracking parameter values.
2011-01-06 12:12:43 -05:00
Daniel Blankenberg
0adf8f72c3
Change method of accessing additional fields by name for dynamically generated select lists which was added in 4784:7be369e7cc6f.
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Access now takes the form similar to ${param.fields.path}.
2011-01-05 14:57:05 -05:00
Ramkrishna Chakrabarty
e993ddad83
Minor fix in sequencer controller
2011-01-05 07:11:04 -05:00
Ramkrishna Chakrabarty
812d108495
Fixed a bug rendering the sequencer_type selectfield
2011-01-05 07:06:48 -05:00
Ramkrishna Chakrabarty
bb140c9fd0
Minor tweaks to the migration script to fix single quote escape issues
2011-01-04 14:54:50 -05:00
Ramkrishna Chakrabarty
b72c2406c8
Fixed user_info and sample_tracking functional tests.
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Refactored getting form values into a separate method in controller.py.
Changed request type access into a restrict permission.
Added a check when sequencer_types are not loaded.
2011-01-04 07:11:12 -05:00
Kanwei Li
867c40ae15
Copy datasets feature:
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- Simplified destination interface by using a single select box by default, but also providing a link to show checkboxes for multiple destination histories
- Use newly imported Inflector library to get correct plural/singular nouns on actions
- Added arrow between source and destination
- Removed checkbox for copying to a new history. Instead, create new history if new history field is not blank
2011-01-03 18:32:02 -05:00
Nate Coraor
174dad27e8
Deal with MySQL's 1000-character limit on INDEXes on BLOBs and SQLAlchemy's lack of interface to create compatible indexes.
2011-01-03 14:59:52 -05:00
Nate Coraor
b2b891d52d
Do away with the https->http rewrite hack for display at UCSC since the browser supports https now.
2011-01-03 11:11:52 -05:00
Greg Von Kuster
5e2d7e83f1
Eliminate the use of the 'editing_samples' flag by adding the code needed to add new samples without calling the edit_samples method or mako template. Decoupling the different features makes them much cleaner and easier to maintain.
2011-01-03 11:11:00 -05:00
Nate Coraor
04072aa87a
Force correct platform when running 32-bit Python on 64-bit Linux.
2011-01-03 10:54:57 -05:00
Daniel Blankenberg
46d9369f7b
Enhance select parameter wrapper objects to provide access to additional fields by name for dynamically generated select lists (i.e. dynamic_options).
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Allows simplified access to e.g. a path field when the path is not the name or value. The value for the 'path' column in a parameter 'param' could be accessed as:
${param.get_field( 'path' )}
2011-01-03 10:37:35 -05:00
Jeremy Goecks
06d7ba44a4
Visual analytics: enable users to click on and type in values for tool parameters.
2010-12-22 16:11:58 -05:00
Jeremy Goecks
277362ea29
Refactored and enhanced trackster dataset conversion code so that all conversions are started when data from a dataset is requested rather than iteratively.
2010-12-22 11:04:40 -05:00
Kanwei Li
a69e00e635
Clean up and improve the interface to copy datasets between histories:
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-- New "Copy Datasets" link added under History Options dropdown
-- Dataset and history IDs are now encoded
-- JS dropdown used to change source history, so you no longer have to switch desired source history to be "active"
-- Remove link in "edit attributes" of datasets
2010-12-21 21:10:10 -05:00
Ramkrishna Chakrabarty
e1d5a0efd3
Merge with 26a78858dd2d1a67e2bb2fbd479e4a5d84b9ad0a
2010-12-21 13:37:30 -05:00
Ramkrishna Chakrabarty
be6239f545
Applying Brad's patch: Do not remove quotes when porting over form content
2010-12-21 13:34:10 -05:00
Jeremy Goecks
3e98171846
Speed and usability improvements for visual analytics. New track now appears immediately when user runs tool, and track data is pulled directly from file to avoid indexing delay.
2010-12-21 13:23:18 -05:00
Ramkrishna Chakrabarty
d4f484e9ae
Moving sample state and dataset transfer status update api methods to the samples api controller.
2010-12-20 16:05:08 -05:00
Ramkrishna Chakrabarty
08c17e17df
More tweaks in the migrate script to handle boolean values in sqlite
2010-12-20 12:11:30 -05:00
Ramkrishna Chakrabarty
6f21492e18
bug fix in sequencer types config settings
2010-12-20 11:07:16 -05:00
Ramkrishna Chakrabarty
43fac3717b
Tweaked the migrate script to populate the sequencer table
2010-12-20 10:57:44 -05:00
Ramkrishna Chakrabarty
7858868650
First pass of the new sequencer_type & sequencer framework
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- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
2010-12-20 10:50:50 -05:00
Greg Von Kuster
788bc29f56
Eliminate the temporary update_sample_run_details method from the request_common contrller and add new Galaxy API methods to handle the request. Fix a bug copying a new sample from an existing sample introduced when FormValues.content was changed from a list to a dict. A bit of miscellaneous code cleanup.
2010-12-17 15:52:47 -05:00
Nate Coraor
82ed4cbd5d
A couple more bugfixes for the deferred job queue and transfer manager.
2010-12-17 14:22:31 -05:00
Nate Coraor
7bc80bd6b5
Fix a bug from my last commit that prevented the app from starting, which is probably a bit of a problem.
2010-12-17 13:41:37 -05:00
Nate Coraor
30915f5c71
Commit of the initial work on the deferred job queue and transfer manager. This code is for reference only and is unfinished. The deferred job queue mostly works, the transfer manager may barely work, but neither have much error handling. Stability of all interfaces should be considered experimental.
2010-12-17 13:17:10 -05:00
Kanwei Li
dc9a5f6f6e
trackster: Fix BAM reads without cigar string. Second attempt at segfault fix.
2010-12-16 18:05:17 -05:00
Kanwei Li
166ceec8b6
trackster: Fix tracks fetching from data provider when indexer returned None. Possibly fix a segfault with pysam in some cases.
2010-12-16 15:12:27 -05:00
Enis Afgan
90b0d461ba
An addendum to the previous commit; using strict Bourne syntax now
2010-12-16 14:43:15 -05:00
Enis Afgan
c1a076ca83
A more general package dependency injection command line composition.
2010-12-16 14:22:28 -05:00
Greg Von Kuster
37b68d6621
Missed cleaning up the base controller in my last commit, so here it is again.
2010-12-15 17:05:19 -05:00
Greg Von Kuster
11957ed5fa
Fixed as many of the issues as could be found throughout the framework due to the migration of FormValues.content from a list to a dictionary in change set 4744 b73ad3906e24.
2010-12-15 17:00:29 -05:00
Greg Von Kuster
5ecf61ab9b
Bug fix for generating unique job ids in the demo sequencer.
2010-12-14 12:58:46 -05:00
Ramkrishna Chakrabarty
3fdf16b208
Fixed contents default value in FormDefinition.get_widgets
2010-12-14 11:23:49 -05:00
Ramkrishna Chakrabarty
72878479f7
FIxed the edit request form bug caused by the previous commit
2010-12-14 10:29:18 -05:00
Ramkrishna Chakrabarty
84e18119d7
More tweaks added to the previous migration script
2010-12-13 18:37:55 -05:00
Ramkrishna Chakrabarty
b34ef29442
Adding a 'name' attribute in the field dict for form_definitions. In the 'form_values'
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table, the 'content' column is now a JSON dict instead of a list. Made appropriate code changes.
2010-12-13 17:29:23 -05:00
Greg Von Kuster
8a30d03783
Rearrange the tool shed grid columns per user request. Code cleanup and fixes for the tool shed upload form; if uploading a new version of a tool or tool suite, the correct type is automatically selected on the upload form.
2010-12-13 15:20:50 -05:00
Kanwei Li