Greg Von Kuster
e508256568
merging from central
2009-01-06 11:38:37 -05:00
Greg Von Kuster
3ed821a39d
Better exception handling, messaging for upload utility.
2009-01-06 11:35:49 -05:00
Greg Von Kuster
4216601beb
Fixes to enable multiple test runs that test security and libraries.
2009-01-05 11:36:57 -05:00
Greg Von Kuster
7308a73429
Code cleanup, new functional tests for sharing histories with private datasets.
2008-12-23 16:06:01 -05:00
Greg Von Kuster
db1c1fb660
merging from central
2008-12-18 16:44:34 -05:00
Greg Von Kuster
42ca95a373
Enhance the tool panel, now supports following tags:
...
<toolbox>
<tool file="data_source/upload.xml"/> # tools outside sections
<label text="Basic Tools" id="basic_tools" /> # labels outside sections
<workflow id="529fd61ab1c6cc36" /> # workflows outside sections
<section name="Get Data" id="getext"> # sections
<tool file="data_source/biomart.xml" /> # tools inside sections
<label text="In Section" id="in_section" /> # labels inside sections
<workflow id="adb5f5c93f827949" /> # workflows inside sections
</section>
</toolbox>
2008-12-18 16:35:26 -05:00
Nate Coraor
8243eee012
Fix functional tests broken by my last commit
2008-12-15 17:08:35 -05:00
Greg Von Kuster
7ecfd7c61e
Reset functional test port which somehow got committed when attempting to merge conflicts.
2008-12-15 09:06:11 -05:00
Greg Von Kuster
bff56d118e
merging from central
2008-12-15 09:05:20 -05:00
Greg Von Kuster
e858742d73
merging from central
2008-12-15 09:01:37 -05:00
Greg Von Kuster
b432fd166d
merging heads
2008-12-15 08:55:16 -05:00
Greg Von Kuster
40a55c1832
Add ability ot rename roles and groups, 2 fixes for filtering out deleted roles, some code cleanup and additional functional tests to cover new features.
2008-12-12 11:27:37 -05:00
Greg Von Kuster
34ec0e8cbf
Functional test coverage now fairly complete for current dataset security and library features.
2008-12-10 10:35:47 -05:00
Greg Von Kuster
9f48fed903
Fixes, code cleanup, new functional tests for accessing libraries from the analysis view.
2008-12-08 16:55:52 -05:00
Greg Von Kuster
ca2a5a4e69
New features and functional tests for security and libraries, multiple functional test runs should once again work without purging the data.
2008-12-08 11:47:05 -05:00
Greg Von Kuster
77791e96e9
Better functional test coverage, a couple new features, several fixes and code cleanup for security and libraries.
2008-12-05 16:59:14 -05:00
Greg Von Kuster
d400506970
A bunch of bug fixes, a few new features and functional tests fixes for the security and library stuff, getting closer, but a bit more work left.
2008-12-03 16:14:36 -05:00
Greg Von Kuster
ca43dadc1b
Fixes and new functional tests for dataset security and libraries - now should be able to have multiple test runs without purging the database.
2008-12-01 16:40:11 -05:00
Greg Von Kuster
0073f3e42c
Fixes for functional tests for sharing a history.
2008-11-28 16:59:49 -05:00
Greg Von Kuster
6b0712c8ee
Bug fix for my last commit.
2008-11-28 15:39:47 -05:00
Greg Von Kuster
ed90f0f683
Fixes and new features for data security and libraries, requires db schema change and new config setting.
...
- add ability for an admin to reset another user's password
- add ability for an admin user to delete another user's account ( requires config setting to display feature )
- add ability for an admin user to manage deleted users ( undelete / purge )
- more code cleanup in the admin controller
- several new functional tests and existing functional test improvements
SQL commands to alter db schema:
ALTER TABLE galaxy_user ADD COLUMN deleted BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_galaxy_user_deleted ON galaxy_user USING btree (deleted);
ALTER TABLE galaxy_user ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_galaxy_user_purged ON galaxy_user USING btree (purged);
New config setting:
# Can an admin user delete user accounts?
#allow_user_deletion = False
2008-11-28 15:32:15 -05:00
Greg Von Kuster
8b3666a0a8
Fixes and functional tests:
...
- move admin method for creating new user account to admin controller
- fixes and functional tests for initial settings of DefaultUserPermissions and DefaultHistoryPermissions when accounts and histories created
- fixes and functional tests for changing DefaultHistoryPermissions for the current history
- fixes and functional tests for Changing DefaultHistoryPermissions for new histories
2008-11-24 14:44:39 -05:00
Greg Von Kuster
eeeab78b32
Fixes for accessing libraries from the analysis view.
2008-11-21 09:21:39 -05:00
Greg Von Kuster
e3f07d5f45
More bug fixes, functional tests for data security and libraries.
2008-11-20 17:00:34 -05:00
Greg Von Kuster
0a94eb20cd
Fixes in security and libraries: standard messaging, more functional tests, better GUI flow, 2 new mappers, miscellaneous bug fixes.
2008-11-19 16:42:54 -05:00
Greg Von Kuster
a8cd7a9118
Streamline the process of adding datasets to a library and then updating roles and permissions on them, improve admin GUI flow, more functional tests.
2008-11-18 17:10:16 -05:00
Greg Von Kuster
dd6d0f9737
Fixes for deleting / purging libraries, improvements in functional tests.
2008-11-14 15:12:50 -05:00
Greg Von Kuster
34cda87570
Add ability to manage deleted libraries, requires db schema change, commands are:
...
ALTER TABLE library ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_library_purged ON library USING btree (purged);
ALTER TABLE library_folder ADD COLUMN purged BOOLEAN DEFAULT FALSE;
CREATE INDEX ix_library_folder_purged ON library_folder USING btree (purged);
- Deleting a library will mark all folders and contents ( LibraryFolderDatasetAssociations ) deleted in the db (weakness is that state is not saved for undeleting )
- Undeleting a library will mark all folders and contents as undeleted in the db
- Purging a library will mark the library, all folders, and LibraryFolderDatasetAssociations as purged, datasets will only be marked as deleted - marking as purged and removing the file from disk will be handled by the cleanup_datasets script.
2008-11-12 14:35:07 -05:00
Greg Von Kuster
124a811f4b
merging from central
2008-11-10 14:23:38 -05:00
Greg Von Kuster
5331dee076
Add functioal test baseline support for the repeat construct, more work needed ( e.g., multiple repeat elements, refresh_on_change when the input to be refreshed is within a repeat construct ). Added functional tests for some tools that use this construct.
2008-11-10 14:22:01 -05:00
Nate Coraor
235864e3d5
Merging heads
2008-11-10 12:42:40 -05:00
Daniel Blankenberg
b853633200
Add a test for the sample analysis of retrieving genes flanked by DNAse HSS.
2008-11-07 16:27:07 -05:00
Daniel Blankenberg
8ff58ac96f
Fixes for testing framework to allow it to be run against an external server.
2008-11-07 15:39:47 -05:00
Daniel Blankenberg
1c6a2b993d
Fix for library tests.
2008-10-31 14:42:02 -04:00
Greg Von Kuster
15d4ce552b
User mako templates for library pages for easier testing / maintenance, add baseline functional tests for libraries.
2008-10-30 14:05:42 -04:00
Greg Von Kuster
57fe5145f0
More functional tests for admin controller.
2008-10-24 16:06:13 -04:00
Greg Von Kuster
187a7f555e
Bug fixes in the admin controller and a few functional tests for security and libraries.
2008-10-23 16:57:52 -04:00
Greg Von Kuster
952a9238ff
Code cleanup and feature fixes in admin controller - groups interface is fairly close, next I'll get users and roles up to par.
2008-10-17 16:11:32 -04:00
Nate Coraor
dfdbef9d36
Reintroduce roles. Unfinished stuff: setting default user and history
...
permissions, user-side permissions settings on datasets, viewing
associated datasets under the role page in the admin controler (is this
even necessary?), filtering out roles by type. I haven't addressed
tests, so the security-related functional tests will fail. I haven't
looked at history sharing yet either. Cleanup to remove unused methods
is needed in the admin controller. And the admin templates are a
bit messy.
2008-10-09 17:05:57 -04:00
Greg Von Kuster
5b75630cae
Migrate sqlalchemy queries to 0.4 by eliminating deprecated queries ( select_by, selectone_by, get_by all replaced by filter_by ).
2008-09-25 16:14:26 -04:00
Greg Von Kuster
8e17384a79
Upgrade to SQLAlchemy 0.4.7 and correct conflicts in ~/model/__init__.py.
2008-09-18 15:18:12 -04:00
James Taylor
8266801ea0
Fix for admin interface functional test.
2008-09-08 14:27:56 -04:00
Greg Von Kuster
d5da21bb5b
my message
2008-09-05 16:39:38 -04:00
Greg Von Kuster
2da6139199
More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.
2008-09-05 16:36:51 -04:00
Greg Von Kuster
ec39cc7a41
this is just me
2008-08-27 15:37:10 -04:00
Greg Von Kuster
4d4663c144
More fixes for twill 0.9.
2008-08-27 15:35:14 -04:00
Greg Von Kuster
3210ad4284
Fix for new twill version 0.9
2008-08-26 17:09:49 -04:00
Greg Von Kuster
a613587d7f
Fix for new twill version 0.9.
2008-08-26 17:07:44 -04:00
Greg Von Kuster
1df6382c09
Retrieved lost deleted_groups.mako template due to corrupted repo, polished several templates, fixed twilltestcase so new version of twill will work, add some functional tests.
2008-08-26 15:36:39 -04:00
Greg Von Kuster
b8882ce7c6
A few functional tests ( not even close to being enough to test everything ) for dataset security and libraries. Also a better fix for ensuring a group named public exists in mapping.py.
2008-08-25 14:04:42 -04:00
Greg Von Kuster