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103 Commits
Author SHA1 Message Date
Martin Cech ba13435838 none of the requests & forms controllers used escaping so I escaped the variables exclusively in the templates 2014-12-01 17:38:24 -05:00
Dannon Baker 21eb0edea3 Web helpers (${h.*}) in mako used to_json_string, now dumps. 2014-09-08 17:03:22 -04:00
Dave Bouvier 5bdb75aa82 Correct usage of "it's" versus "its". 2014-04-17 15:49:32 -04:00
Aysam Guerler 7fbe750594 Grids: Unify operation handling, use new popups, refactor, bug fixes 2013-11-23 16:14:59 -05:00
Jeremy Goecks 7b19a84ba8 UI framework enhancements: (a) upgrade to jQuery UI 1.9.1; (b) remove version information from jQuery UI file names; (c) add generic jQueryUI search+select combobox widget; (d) use combobox widget for choosing dbkey in Trackster visualizations. Also pack scripts. 2012-10-30 09:07:29 -04:00
Daniel Blankenberg 303ab46812 Fix tabs to spaces. 2012-10-15 16:01:14 -04:00
Daniel Blankenberg 495e341598 Fix tabs to spaces. 2012-10-15 16:01:14 -04:00
Scott McManus 53236fa933 Moved galaxy.web.controllers references to galaxy.webapps.galaxy.controllers 2012-10-04 21:43:15 -04:00
Jeremy Goecks e7b7853dd2 jQuery UI enhancements: (a) update to v1.8.23; (b) remove core script and replace with script that includes core, autocomplete, sliders, and dependencies; (c) replace overcast theme with smoothness theme; and (d) add directory for jQuery UI styles. 2012-09-05 09:35:21 -04:00
Jeremy Goecks 2a4012e03d Final JS reorg to rename and move files so that all files follow standard conventions. 2012-08-21 17:08:35 -04:00
Jeremy Goecks 44d37d7eee Move most jQuery files into own libs directory. 2012-08-21 15:52:50 -04:00
Ross Lazarus d53c3e984f Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository 
This is a backout of commit 5765
 2011-07-06 09:44:56 +10:00
Ross Lazarus 86b55bb0c0 branch merge 2011-07-05 12:40:43 +10:00
Greg Von Kuster 9102fc3472 1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set. 
2.  Clean up the code that renders the jquery file browser plugin - things work much cleaner now.  One remaining item is handing the issue where rsh / ssh keys are not set.  Also clean up a lot of code related to manual file transfers in the requests_admin controller.

3.  In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.

4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
 2011-04-13 13:52:05 -04:00
Greg Von Kuster d839983f21 Bug fixes and code cleanup related to recently implemented external services. 2011-01-13 16:14:25 -05:00
Ramkrishna Chakrabarty 7fe6167d94 More instances of sequencer renamed to external service 
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
Ramkrishna Chakrabarty f7a35e13cb Renamed sequencer to external_service and sequencer_type to external_service_type. 
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
Ramkrishna Chakrabarty 7858868650 First pass of the new sequencer_type & sequencer framework 
- 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 87c645dc0e Rename the sequencer controller to be named request_type. 2010-12-09 15:59:14 -05:00
Ramkrishna Chakrabarty d295688300 Added async update of sample dataset transfer status on admin manage datasets grid page for a sample. 2010-11-24 13:30:48 -05:00
Ramkrishna Chakrabarty 4999fc4742 Added async update of sample dataset transfer status on user dataset view page. 
Fixed user info functional tests
 2010-11-23 13:54:09 -05:00
Ramkrishna Chakrabarty c22691a2af Forms refactoring first pass. 
sample tracking data transfer selection UI css bug fixed
 2010-11-23 00:00:03 -05:00
Ramkrishna Chakrabarty d220a8c791 sample tracking functional tests 
- data transfer selection, renaming initiation
- new address at request creation
- request lifecycle, rejection
Fixed ui bugs
 2010-11-19 10:52:49 -05:00
Greg Von Kuster efed83a828 Move the sequencer interface ( RequestType ) components from the requests_admin controller to a new sequencer controller. 2010-11-19 10:14:08 -05:00
Greg Von Kuster c3afe4cb34 Code fixes and cleanup for adding and viewing sequencer configurations ( RequestTypes ). Move the request_type templates from the requests folder to their own request_type folder. Add the ability to edit sequencer configurations. 2010-11-18 14:16:39 -05:00
Ramkrishna Chakrabarty 9e6d11bc46 removed unused mako template 2010-11-17 16:24:12 -05:00
Ramkrishna Chakrabarty b8652ecc4e - added the change data library sample operation functional test. 
- renaming dataset now checks for incorrect filename characters
- fixed bugs
 2010-11-17 11:33:54 -05:00
Greg Von Kuster c3c7c89c5d More miscellaneous Sample Tracking cleanup and bug fixes, move supported form_builder field types from form_builder.BaseField to Request.model and Sample.model. 2010-11-17 10:25:12 -05:00
Ramkrishna Chakrabarty cb46f92b43 Replaced request with 'sequencing request' in sample tracking ui. 
Show the request page instead of the request grid after submitting the request
 2010-11-16 10:48:37 -05:00
Ramkrishna Chakrabarty b32a47fe4b minor ui fixes in sample tracking 2010-11-16 09:12:15 -05:00
Greg Von Kuster 212a7e65cf First pass at cleaning up the Galaxy Form Definition UI ( forms controller still needs a re-write ). 2010-11-15 11:46:39 -05:00
Greg Von Kuster 162c2b0a26 Make sure samples have associated target libraries befoe enabling ability to transfer datasets, use better naming convention for request history code and templates, eliminate the ability to submit a request unless it has samples. 2010-11-11 15:36:23 -05:00
Greg Von Kuster 90964a467b A few more bug fixes in the new sample tracking code. 2010-11-10 17:17:25 -05:00
Greg Von Kuster 88e22fa6a1 Bug fixes and more UI streamlining for sample tracking. 2010-11-10 17:03:40 -05:00
Greg Von Kuster a6d8e4a58b Streamline the sample tracking UI in selecting and transferring sample datasets. 2010-11-08 23:10:08 -05:00
Ramkrishna Chakrabarty 45c6515b8b sample tracking 
- new file browser for selecting datasets in the sequencer
 2010-11-03 01:02:27 -04:00
Greg Von Kuster fa8a352dcd Significant cleanup for the Sample Tracking UI. Things are more streamlined and Galaxy UI standards are now followed. 2010-11-01 18:16:50 -04:00
Ramkrishna Chakrabarty 6a9ab2813a sample_tracking: 
- added web api methods to update requests, samples using restful api
- removed the old ad-doc web api
- modified the data transfer code to use this api
- code cleanup
 2010-10-26 10:00:23 -04:00
Ramkrishna Chakrabarty 83b1fba835 sample tracking 
- create request search+select box bug fixed.
- sample datasets grid operations fixed
 2010-10-15 08:51:30 -04:00
Ramkrishna Chakrabarty 4631710431 sample_tracking fixes 2010-10-14 00:24:56 -04:00
Ramkrishna Chakrabarty 381b72258a sample tracking bug fixes 2010-10-13 16:07:06 -04:00
Greg Von Kuster 2942a66c90 Clean up the code in the request_admin controller. 2010-10-12 15:36:22 -04:00
Ramkrishna Chakrabarty fe791cbdc7 sample_tracking: 
- bug fix in method to set library permissions for the data transfer user
- code cleanup
 2010-10-12 15:06:00 -04:00
Ramkrishna Chakrabarty d4610fa444 sample tracking bug fixes: 
- dataset select page now fixed
- find samples page now fixed for regular user
 2010-10-12 09:17:04 -04:00
Greg Von Kuster 81c76fdb96 First pass at Galaxy sample tracking re-write. Highlights: lots of code cleanup with several not-needed methods removed, many mthods and mako templates have been renamed clarify what they do, all object ids are now encoded, methods in the requests_common controller that include features requiring an admin user are now secured. More work is needed in the requests_admin controller which will be in the next commit. 2010-10-11 16:35:57 -04:00
Ramkrishna Chakrabarty 0c1f60ce78 lims: ui improvements 
removed dbg stmt
 2010-09-20 15:08:30 -04:00
Ramkrishna Chakrabarty 95e2a635ba lims: changed the name 'request type' to 'sequencer configuration' in UI. In the code it is still called request_type. 2010-09-03 09:20:52 -04:00
Ramkrishna Chakrabarty f0a3f224d4 lims: show last update date/time in the transfer datasets grid 2010-08-09 16:33:15 -04:00
Ramkrishna Chakrabarty 397db8d2f4 lims: 
- fixed couple of broken links
- comminting the db migrate script (0052) skipped in the previous commit
 2010-07-29 11:10:55 -04:00
Ramkrishna Chakrabarty c925dc1f2c lims: 
- added a new table 'sample_dataset' to store sample datasets & their info when they are transfered from the sequencer
- the datasets transfer page now uses a grid to facilitate bulk renaming
- bulk renaming possible to fix the problem with the way SOLiD generates datasets
- the remote file browser is now independent of a specific sample, the user may select any sample when transferring datasets from the sequencer
 2010-07-29 10:55:08 -04:00