Greg Von Kuster
8f6e8213a0
Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.
2009-11-11 15:59:41 -05:00
Nate Coraor
0e700a29fd
Fix for the broken test I just committed
2009-11-10 16:02:49 -05:00
Nate Coraor
baea4439d1
Add test for library tarball downloads
2009-11-10 15:10:43 -05:00
Ramkrishna Chakrabarty
c3878e925f
Fixed a bug in the view requesttype page.
...
Now barcodes are visible in the request details page itself.
2009-11-10 12:35:00 -05:00
Nate Coraor
2f97633eb6
Don't display diff during tests if it contains non-ascii characters
2009-11-10 10:10:29 -05:00
Greg Von Kuster
00c3f84f40
Incorporate latest grid features into managing users, groups and roles from the admin view.
2009-11-09 23:00:55 -05:00
Ramkrishna Chakrabarty
6dce23d603
Fixed some functional tests related to the previous commit
2009-11-09 16:40:59 -05:00
Ramkrishna Chakrabarty
a5c0f9305f
Fixed a checkbox bug in request & user_info
...
Resolved bitbucket issue 221: now there is a reject option for an admin to move a request to an unsubmitted state
2009-11-09 16:15:52 -05:00
James Taylor
905a6e503b
Fix closure in creation of generated test methods, otherwise the last testdef is used for every test
2009-11-06 00:25:02 -05:00
James Taylor
6fdcd4ba08
Fix for tools with multiple tests
2009-11-05 17:55:14 -05:00
Ramkrishna Chakrabarty
7a441130bb
Refactored the new address functional test
2009-11-05 14:19:45 -05:00
James Taylor
1bc08c9546
Fix tool test specification by id
2009-11-04 11:35:50 -05:00
Ramkrishna Chakrabarty
11368df068
Fixed the ordering in selectboxes
...
Fixed a bug in editing samples in the request page
2009-11-04 10:16:20 -05:00
Nate Coraor
87aa7e2287
merge heads
2009-11-03 13:04:35 -05:00
Jeremy Goecks
ec3674f5f0
Improved search functionality for history grid: (a) generic free text search box and (b) advanced search using name, tag, deleted status, and shared status.
2009-11-03 12:58:13 -05:00
Nate Coraor
8d96c8d979
imported patch alchemy05_fixes_02
2009-11-03 12:52:01 -05:00
Ramkrishna Chakrabarty
d552d41a9b
Changed the test user emails in the user_info functional tests
2009-11-03 07:58:24 -05:00
Ramkrishna Chakrabarty
26c91e40d3
Fixed the functional test to create new user as admin
2009-11-02 16:12:31 -05:00
Ramkrishna Chakrabarty
07aafbd6c9
User information forms first pass.
...
- added a foreign key in the galaxy_user table to the form_values table
- separate user info page for viewing/editing user info
- user addresses added to user info page
2009-11-02 13:30:17 -05:00
Greg Von Kuster
29b55b8707
Make sqlalchemy queries use sa_session.query( object ) rather than object.query(). This eliminates the need for the _monkeypatch_query_method() in assignmapper.py. Also eliminate the need for the _monkeypatch_session_method() for everything except object.flush() - I just ran out of time and will handle flush() asap. I also eliminated the .all() call on several queries where it was not necessary - should improve performance. I fixed several bugs I found as well.
2009-10-22 23:02:28 -04:00
James Taylor
4cf17c1961
Fix for tool tests. Comment out get_peek test, doesn't appear correct (result is unicode and forced to multiple lines, when did this change?)
2009-10-21 15:45:01 -04:00
James Taylor
2c1e959a94
New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.
...
[mq]: functional-test-harness
2009-10-20 13:08:29 -04:00
Kanwei Li
1e69d3b5ad
Show encoded URL, while still allowing unencoded ids for backward compatibility. Revert to "display" displaying whole file.
2009-10-20 15:34:47 -04:00
Greg Von Kuster
9f6ceaef1c
Fixes and new functional tests for uploading multi-byte character files and fixes for displaying multi-byte character dataset peek.
2009-10-15 20:10:32 -04:00
Ramkrishna Chakrabarty
45739d03c5
Forms & request controllers
...
- refactored to work on main
- cleanup
Added more functional tests
2009-10-14 02:22:11 -04:00
Greg Von Kuster
f77e0e03f4
Add new functional tests for uploading composite data types lped and pbed - handles ticket # 173.
2009-10-13 16:37:20 -04:00
James Taylor
d9072184f3
Backed out changeset 037374950cc9
2009-10-10 14:03:08 -04:00
Kanwei Li
91e873f1a7
Encode HDA ids when peeking and saving. Fixes #110
2009-10-09 16:59:35 -04:00
Jeremy Goecks
4c401cddc1
Enables viewing of an importable/sharable history. Using the syntax /history/view?id=<encoded_history_id> produces a page that renders a history for viewing. A user need not be logged in to view the history.
2009-10-08 13:38:32 -04:00
Kelly Vincent
53d6ccf8f3
Removed sniff method from fastqsanger datatype
2009-10-08 10:45:31 -04:00
Kelly Vincent
7263afac9f
Added fastq (generic) datatype and deleted fastqsolexa datatype
2009-10-07 12:43:15 -04:00
Greg Von Kuster
6e236907c6
Bug fix for adding a new folder template ( fixes # 193 ), more functioanl test coverage for folder templates, more code mering and cleanup in the library controllers, shortened the table buttons on the brose library grid and template.
2009-10-06 14:13:31 -04:00
Greg Von Kuster
72f972afc2
Fix forms and request functional test - broke with my last commit.
2009-10-02 09:30:50 -04:00
Greg Von Kuster
ff1ab81c32
A couple bug fixes, additional functional tests for the Data Libraries features.
2009-10-02 08:55:01 -04:00
Greg Von Kuster
6d573a9870
Only allow 'uload files' option when replacing a dataset with a new version, more code merging, a few bugs fixes and additional functional tests for libraries.
2009-10-01 15:07:22 -04:00
Greg Von Kuster
ef356a857b
If you populate a history before logging in, then login, your current history will be the one you populated before logging in - fixes ticket number 163. Also added additional functional tests to cover scenario.
2009-09-30 14:47:17 -04:00
Ramkrishna Chakrabarty
19a36f8c15
Requests functional tests: fixed a hack in user address creation
2009-09-30 11:40:09 -04:00
Ramkrishna Chakrabarty
d28e921362
More functional tests for Requests
2009-09-30 10:40:08 -04:00
Greg Von Kuster
96d78e08a7
Functional test fixes for uploading and sniffing metadata - not sure when the behavior for these changed.
2009-09-30 08:28:31 -04:00
Greg Von Kuster
baa64fc6a7
Refactored the library_dataset_dataset_association methods in the library_admin and library controllers, renamed the library_dataset controller to be library_common and moved several common methods to it, and some other code cleanup.
2009-09-30 05:16:17 -04:00
Nate Coraor
87db3952d3
Real Job(tm) support for the library upload tool. Does not include iframe upload for the library side yet.
2009-09-25 14:36:12 -04:00
Greg Von Kuster
8d6652853a
Eliminate the encode data functional test.
2009-09-22 14:47:47 -04:00
Greg Von Kuster
de1ea7ae0a
Eliminate the use of the genetrack controller, merge the template code for uploading library datasets, and several bug fixes:
...
- The genetrack controller is no longer used ( I'll delete it soon ), so the GeneTrack application is now loosely coupled
- Merge the 2 new_dataset.mako templates into one common code module name library_dataset_common.mako
- Rename all of the library upload form fields to have the same names as the history upload form fields
- Eliminate a 2nd runtool_btn from being rendered on the same form in tool_form.mako
- Fix bug and add functional tests to cover uploading a library dataset that does not include a template
2009-09-22 14:04:48 -04:00
Greg Von Kuster
2cd2c865ad
Template fixes: get current FormDefinition when inheriting templates, and use filter then retrieving FormDeinition for library templates. A few other miscellaneous bug fixes as well. Functional tests should now pass.
2009-09-20 11:48:51 -04:00
Greg Von Kuster
0f294b742c
Bug fixes, enhancements, code refactoring and re-introduction of functional tests for library templates.
...
- Fixed bug where exception was thrown when chosing a role in the admin view
- The contents of inherited templates will no longer be displayed in the inherited container
- Old versions of library datasets will not be displayed in the lbrary browser
- Added the job.traceback information to the dataset error report
- Moved the get_form_wigets method the forms.py to the FormDefinition class, renaming it to get_wigets
2009-09-19 00:25:14 -04:00
Ramkrishna Chakrabarty
6b92bf6eb8
Galaxy AMQP Listener, first pass
...
Added a check for testing completed requests in Requests functional tests
2009-09-18 15:18:57 -04:00
Greg Von Kuster
3d6f94d323
Use a grid for admin user management, still needs some polishing, but a good start.
2009-09-16 14:06:14 -04:00
Ramkrishna Chakrabarty
cf99c114a7
Forms:
...
- 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
Greg Von Kuster
715dc77d5d
Move the data library admin methods to a separate library_admin controller.
2009-09-14 11:05:36 -04:00
Greg Von Kuster
3eab20f513
Streamline history sharing, add a "Manage shared histories" section to the History options menu. Also use a better approach to setting peek on datasets.
2009-09-10 21:24:06 -04:00
Greg Von Kuster