Aysam Guerler
edd8892a4a
UI: Fix iconbar css
2013-12-05 00:05:20 -05:00
Aysam Guerler
894ec4a475
Grids: Fix tag click event
2013-12-04 19:59:07 -05:00
Aysam Guerler
250dd672bd
Grids: Refactoring and fixes
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iG: removed templates/grid_common.mako
2013-12-04 18:51:44 -05:00
Greg Von Kuster
6d55496418
Fixes for rendering tools and invalid tools in the tools container.
2013-12-04 15:48:16 -05:00
Greg Von Kuster
340762bbf1
Correctly use the initialized test_environment dict when running the tool shed's install and test framework and additional code cleanup for the framework.
2013-12-04 15:07:39 -05:00
Greg Von Kuster
24ee75b05c
Actually skip inspection of repository revisions that have the skip_tool_test set in the Tool Shed instead of just stating we're going to...
2013-12-04 11:01:32 -05:00
Greg Von Kuster
59e949f353
Final fixes for rendering installation errors in the tool test results container in the tool shed.
2013-12-04 10:29:59 -05:00
Greg Von Kuster
22df2c0db9
More fixes for rendering tests that resulted in installation errors within the tool test results container in the tool shed.
2013-12-04 09:49:17 -05:00
Dave Bouvier
88ec4149d2
Update test 0450 to also verify the list of testable revisions returned by the repository_revisions tool shed API controller.
2013-12-04 08:41:23 -05:00
Greg Von Kuster
ea8d67499d
Fix for displaying installation errors in the Tool Shed's tool test results container.
2013-12-03 16:15:03 -05:00
Greg Von Kuster
2f56fc479e
Fix tool shed unit test I broke with a recent commit.
2013-12-03 15:52:46 -05:00
Greg Von Kuster
00857760f0
Fixes for filtering repository revision to be tested by the Tool Shed's install and test framework, and a new Tool Shed API script to enable analyzing the the Tool Shed's install and test framework.
2013-12-03 15:16:14 -05:00
Carl Eberhard
1a766e25a1
History panel: allow anon use of dataset search
2013-12-03 15:13:17 -05:00
Carl Eberhard
e377fbcfc7
History panel: allow searching datasets: name, tags, annotation, dbkey, file_ext, blurb, and info will be searched when enter is pressed in the search field, include whitespace by enclosing search term in double quotes, allow specifying which field to search by using the idiom 'field=term' where field is any of the previous field names (or more user-centric aliases: database for dbkey, etc.), (GUI filters as an alternate means to accomplish field specifiers to be added soon); Allow showing and hiding search input; Tweak style on panel-header buttons; pack scripts
2013-12-03 15:03:32 -05:00
John Chilton
188dcb17e8
Another attempt to fix nosetests' handling of rods.py.
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Further dirtying @dannon's code :(, sorry.
2013-12-03 12:59:35 -06:00
John Chilton
209243aa67
Remove unused get_missing_tool_dependencies in install_and_test_tool_shed_repositories/base/test_db_util.py.
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Looks to have been replaced by method with same name in install_and_test_tool_shed_repositories/functional_tests.py and would throw a NameError on repository_id if ever used.
2013-12-03 11:54:56 -06:00
John Chilton
ae34c75c7b
Merged in jmchilton/galaxy-central-fork-1 (pull request #270 )
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Delay potential problems with fluent logger dependencies until fluent logger used.
2013-12-03 10:39:21 -06:00
Greg Von Kuster
28d2c1bb38
Code cleanup for rendering the tool test results container in the tool shed.
2013-12-03 11:32:00 -05:00
Dannon Baker
8bb209cae3
Merged in jmchilton/galaxy-central-fork-1 (pull request #269 )
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Object Store dependency refactoring, testing, and added LWR implementation.
2013-12-03 11:12:57 -05:00
Greg Von Kuster
8192156632
Refactoring code cleanup for installing tool dependencies from the tool shed into Galaxy.
2013-12-03 11:01:20 -05:00
Greg Von Kuster
a91ccbf8fb
Fix for determining if a required tool dependency is in an error state.
2013-12-03 09:35:05 -05:00
Aysam Guerler
8a3ff9163a
UI: Improve masthead, simplify code
2013-12-03 01:42:58 -05:00
Greg Von Kuster
b2c873bc1e
Fix type in my last commit - thanks John!
2013-12-02 21:35:00 -05:00
Greg Von Kuster
93953d0a75
Tweak changeset 5b8c91e4183664c90f4d95699ab971e674ffd67d which created symlinks to a required tool dep endncy env.sh file for dependent tool dependencies being installed. This approach was better than the previous approach which parsed the requried repository's tool_dependencies.xml file to create the env.sh file. This changeset uses a slightly different approach: it creates an env.sh file for the dependent tool dependency whose first line "sources" the required tool dende pendcy's env.sh file. This allows for the dependent env.sh file to be managed by its tool dependency (e.g., its tool dependency may require additional env.sh paths beyond those contained in the requyired tool dependency's env.sh file). This changeset also handles sysncing the database with the file system when tool dependencies are being installed when handling a complex repository dependency definition. This process used to be handled only when not dealing with a complex repository dependency definition. This fix should correct problems encounted by the Tool Shed's install and test framework which were introduced in 5b8c91e4183664c90f4d95699ab971e674ffd67d.
2013-12-02 20:36:59 -05:00
John Chilton
32d5ef1820
Delay problems with fluent logger dependencies until fluent logger used.
2013-12-02 15:15:16 -06:00
John Chilton
4bc289707a
Fix test case in test/unit/test_tool_deps.py which fails if modulecmd is unavailable.
2013-12-02 14:57:00 -06:00
John Chilton
258f5b36b3
Tell nose functions in lib/galaxy/tools/test.py are not unit tests.
2013-12-02 14:57:00 -06:00
Daniel Blankenberg
422ea67297
Fix for missing eggs.require in lib/galaxy/exceptions/__init__.py.
2013-12-02 14:48:30 -05:00
John Chilton
58dd0fde13
Fix default behavior of composite archival broken with previous changeset.
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Other small tweaks this implementation.
2013-12-02 12:40:43 -06:00
John Chilton
159adbbd19
Add an LWR object store implementation.
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This changeset implements an object store implementation that delegates to a concrete remote object store instance via an LWR server. Can utilize existing LWR security mechanisms and multiple transport options.
Updates the Galaxy LWR client through LWR changeset 2333f57.
This changeset contains no tests for this new implementation, but the LWR contains the same code along with an integration test that spins up a temp LWR to test against - this test case demonstrating the lwr object store client and server can be found here : https://bitbucket.org/jmchilton/lwr/src/default/test/lwr_objectstore_test.py .
2013-12-01 19:07:04 -06:00
John Chilton
a4c38261d1
Add test cases for some basic object store types.
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Namely tests for disk, hierarchical, and distributed stores - as well parsing.
2013-12-01 19:07:04 -06:00
John Chilton
f745c44f28
Update objectstore XML parsing to stdlib's ElementTree implementation.
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Eliminates dependency on older elementtree egg.
2013-12-01 19:07:04 -06:00
John Chilton
7b053cee87
Make sqlalchemy dependency in object store optional unless create is used.
2013-12-01 19:07:04 -06:00
John Chilton
622e3ae0a4
Use relative imports in objectstore code.
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Goal is to enable the whole module to be placed in lwr.objectstore.
2013-12-01 19:07:04 -06:00
John Chilton
32db70a2a7
More work on objectstore dependencies.
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Be explicit about what in galaxy.util is being used, don't fail if galaxy.eggs is unavailable - assume the actual dependencies will be there (boto and rods) if not fail just a little later. If nothing else, this should fix some failing buildbot tests (nosetests records a failure if it cannot import a file and it cannot import the s3 or irods object store files because of these imports).
2013-12-01 19:07:04 -06:00
John Chilton
d02bba0567
Refactor jobs.Sleeper into its own module.
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This eliminates explicit dependency between galaxy.objectstore and galaxy.job - with the ultimate goal of being able to utilize all object store functionality except dataset creation from a remote LWR instance with minimal dependencies.
2013-12-01 19:07:04 -06:00
John Chilton
09bf7116ea
PEP-8 fixes for object store module.
2013-12-01 19:07:04 -06:00
John Chilton
cda736de98
Refactor directory_hash_id into its own module.
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Also add PEP-8 cleanup and unit tests. This eliminates explicit dependency between galaxy.objectstore and galaxy.model - with the ultimate goal of being able to utilize all object store functionality except dataset creation from a remote LWR instance without a database connection.
2013-12-01 19:07:03 -06:00
John Chilton
226f468b40
Update LWR client through LWR revision acecc74f7016.
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Mostly small modifications related Python 3 compat. (no iteritems, diff. StringIO, exception syntax, urllib diffs,) and improved handling of unicode data.
2013-12-01 06:14:32 -06:00
Jeremy Goecks
82467b0b96
Automated merge of local changesets with default branch.
2013-11-30 17:00:44 -05:00
Jeremy Goecks
da0967233d
Trackster: (a) use colors to denote track state and (b) add and use function to show messages.
2013-11-30 17:00:01 -05:00
Nate Coraor
cc0a59eb9e
merge stable.
2013-11-30 12:47:19 -05:00
Nate Coraor
e197bc6742
Remove broken GeneTrack tools.
2013-11-30 12:46:53 -05:00
John Chilton
bd02a77c13
Merge latest stable.
2013-11-30 08:29:06 -06:00
John Chilton
3591c00e3c
Fix from Jim Johnson for optional input handling in provenance API.
2013-11-30 08:28:38 -06:00
Greg Von Kuster
3b33ebf130
Tool shed api fix for filtering tools that should not be tested via the tool shed's install and test framework.
2013-11-29 17:06:02 -05:00
Greg Von Kuster
1b2c3b67cd
Attempt to display the results of the tool shed's install and test framework test run even if the preparation script was not executed before the test run.
2013-11-29 16:28:25 -05:00
Greg Von Kuster
d6b6ea9d8b
Minor fix for the tool shed's install and test framework.
2013-11-29 15:18:22 -05:00
Greg Von Kuster
b5e5b5bb69
Additional code cleanup, better logging and more minor fixes for the tool shed's install and test framework.
2013-11-29 14:34:35 -05:00
Jeremy Goecks
224071102c
Trackster: move static CSS settings out of JavaScript and into CSS file.
2013-11-29 11:41:26 -05:00
Aysam Guerler