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
Daniel Blankenberg
786c544b41
Fix tabs to spaces.
2012-10-15 16:01:13 -04:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
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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
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
d354a1ce35
Abstract the code supporting data library templates so templates can be used in sample tracking as well. These templates now provide support for handling information about sample runs. A RequestType can have a single association to a Run, with the run details template made available to all samples. A Sample can have many associations to Runs.
2010-12-09 14:52:27 -05:00
Ramkrishna Chakrabarty
c22691a2af
Forms refactoring first pass.
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sample tracking data transfer selection UI css bug fixed
2010-11-23 00:00:03 -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
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
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
Kanwei Li
52459bceb0
Refactored refresh_on_change javascript code to run in galaxy.base when the page is loaded. Fixed bug with autocomplete_select: when switching from a value within refresh_on_change_values to a value outside of it, the page did not refresh. Removed duplicate code from templates.
2010-10-01 16:20:34 -04:00
Greg Von Kuster
858349cb63
Rewrite the functional tests that cover all Galaxy forms related behavior. Clean up / fix bugs in several sample run request templates. Fix a bug introduced in change set a8cdece11998 which incorrectly generated selected options in a select list in the data library framework.
2010-09-22 16:38:49 -04:00
Greg Von Kuster
f7334104a0
Move the upload_option (ie., file, directory, filesystem paths, import from history) into a select list on the data library upload form. Selecting an upload_option now performs a refresh_on_change on the upload form so that any form contents entered before selecting the option are now retained. Improvements and bug fixes were made throughout the pieces of the framework that support this.
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Major improvements and very significant code cleanup to the entire functional test framework was done in this change set as well.
2010-09-17 15:23:58 -04:00
Greg Von Kuster
77b1a84769
Move toward standardizing the way messages are displayed on Galaxy forms by using params 'message' and 'status' instead of 'msg' and 'messagetype'.
2010-04-02 16:06:43 -04:00
Greg Von Kuster
1a239e9c67
Add the ability to edit library templates and make library template inheritance optional.  Fix another bug in the form builder's CheckboxField.is_checked() method, and clean up some library code. With regard to template inheritance, a LibraryFolder is a special case because if it inherited the template from it's parent, we want to set inheritable to True for it's info_association.  This allows for the default inheritance to be False for each level in the Library hierarchy unless we're creating a new level in the hierarchy, in which case we'll inherit the "inheritable" setting from the parent level.
2010-02-11 14:26:25 -05:00
Ramkrishna Chakrabarty
cea3324bbb
Sequencer data acquisition for LIMS
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- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer
Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine
2010-02-04 11:01:45 -05:00
Ramkrishna Chakrabarty
c73610de9d
Adding grids to forms, requests & request types pages. Resolves issue #231 .
2009-11-17 14:28:34 -05:00
Ramkrishna Chakrabarty
1a9209d5bf
Fixed a form definition editing bug
2009-10-19 09:53:04 -04:00
Ramkrishna Chakrabarty
45739d03c5
Forms & request controllers
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- refactored to work on main
- cleanup
Added more functional tests
2009-10-14 02:22:11 -04:00
Ramkrishna Chakrabarty
d28e921362
More functional tests for Requests
2009-09-30 10:40:08 -04:00
Ramkrishna Chakrabarty
8c26cb39dd
Sample Form definitions:
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- layout details added to csv file importer
- form preview
2009-09-28 13:37:14 -04:00
Ramkrishna Chakrabarty
cf99c114a7
Forms:
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- Added 'type' and 'layout' columns to the form_definition table
- Added types to forms; Request, Sample & Library info template
- Added layouts to sample form definition to support multiple grids while rendering
Requests:
- Added 'folder_id' column to the request table
- Added the Data Library Folder selectbox when creating a new request
- Moved the 4 request_type methods to requests_admin from admin controller
Updated the functional tests
2009-09-16 12:39:57 -04:00
Ramkrishna Chakrabarty
1a912d6cc0
First pass of the functional tests for forms & requests
2009-08-14 15:47:13 -04:00
Ramkrishna Chakrabarty
e467fa7bba
Added browse button on csv importers in LIMS
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Fixed a bug in creating request types
2009-08-11 13:21:20 -04:00
Greg Von Kuster
63696f000e
Re-introduce library templates which are now based on the new Galaxy forms. A library template can be added to a library item ( library, folder, library dataset ), and will be inherited downward in the library hierarchy. A new template can be added to a library item as long as no template field contents have previously been filled in. If template field contents were previously filled in, that template must remain for the current time.
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More work is needed on for this feature, including additional work on the forms. Functional tests are under way, but much more work is needed here as well.
2009-08-07 16:11:14 -04:00
Ramkrishna Chakrabarty
d9c56f360f
LIMS enhancements
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- Requests page now displays all samples in grid layout
- New samples UI
- Requests states added
- CSV import for samples
- User address management
- New AddressField in form_builder
- Deletion added for forms, request types, requests & samples
- Editing added for requests and samples
- Grid filtering added for requests, forms, request types
2009-08-06 09:52:59 -04:00
Ramkrishna Chakrabarty
a01cbf917d
More LIMS changes
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- Request page now includes all its samples (both Admin & User perspective)
- Sample page removed and samples UI overhaul
- DB changes
- new 'submitted' column in request table
- new 'bar_code' column in sample table
- CSV importer to create forms
2009-07-23 17:08:21 -04:00
Ramkrishna Chakrabarty
7dafb15077
First pass of the new Galaxy forms components including requests which based on form definitions and samples.
2009-07-10 11:37:28 -04:00
Martin Cech