John Chilton
d6f8620f62
More work on eliminating references to test_db_util.sa_session.
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... tweaked styling of several functional tests (the non-toolbox,datamanager,workflow,api functional tests) along the way - mostly PEP-8 fixes and eliminating * imports. Did not modify tests which do not pass - but did not in the source where they fail inside a TODO.
2014-01-11 22:40:18 -06:00
John Chilton
79c8f59341
Models: Introduce real class for app.model (ModelMapping).
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Shared across Tool Shed and Galaxy to reduce code duplication. Previously this was just a bunch, making it a real class allows placing some shared logic in there.
This refactoring also eliminates some global variables galaxy.model.mapping.Session, galaxy.model.mapping.context, and same for tool shed. This may break things, but these are things that should probably be fixed anyway.
In particular small changes to db_shell.py and a unit test that depended on these global variables have been updated. The functional test frameworks likewise needed to be updated to not depend on these - these changes were more substantial.
To fix these functional tests, I essentially replace old references to global variables in Galaxy with references to global variables just defined in the test framework in test/functional/database_contexts.py (a slight improvement).
2013-12-05 00:20:54 -06:00
Carl Eberhard
d777d8a4e9
Fixes to upload functional tests (test_get_data.py); TwillTestCase: add is_history_empty which checks the length of HDA JSON instead of relying on html, add check_hda_json_key_value which checks a specific HDA's JSON for a specific value
2012-12-11 17:29:35 -05:00
Carl Eberhard
4f83877e81
Fix sniff.py blastxml doc/unittest, removal of func.test_get_data.py 0140 (megablast xml upload), increased lines_diff in cuffmerge_wrapper.xml to handle inconsistent oId assignment (cuffmerge.test_tool_000000)
2012-09-04 13:28:25 -04:00
Greg Von Kuster
d8279f0e5c
Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.
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I've also added baseline support of the HDF5 data type in this change set, but it is currently required to be in the unsniffable_data_types list.
2011-07-27 16:14:15 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Nate Coraor
e1ea63eb9a
When comparing bam files in the test framework, convert them to sam for comparison.
2011-02-23 14:53:54 -05:00
Nate Coraor
7a87e6c6db
Fix for 3 of the 4 failing upload tests.
2011-02-18 16:21:11 -05:00
Nate Coraor
8e05ce7817
Add test for bz2 file upload
2010-09-10 14:17:05 -04:00
Greg Von Kuster
a7e30c4441
Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.
2010-08-19 13:58:10 -04:00
Nate Coraor
6e7427e8e2
Removed binseq.zip test and replace it with a zip test.
2010-07-01 08:59:26 -04:00
Daniel Blankenberg
183c2d3d13
Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
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Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes.
2010-06-07 15:34:20 -04:00
Kelly Vincent
710e9cfd07
Added new tabular/pileup join tool and associated test files. Also added pileup datatype.
2010-03-26 12:00:55 -04:00
Ross Lazarus
a6989261b7
Revert the twilltestcase upload_composite code needed for lped/pbed upload testing
2010-03-10 17:10:43 -05:00
Greg Von Kuster
bcd6751cdf
Fix for uploading a Bam file that has not yet been sorted, the call to samtools sort has been moved from the sam_to_bam tool to the Bam()set_meta() method to ensure all Bam datasets are sorted prior to indexing. Added new functional tests to cover uploaing unsorted Bam files. Also cleaned up code in the upload tool for uploaing various binary data formats.
2009-12-07 16:04:33 -05:00
Greg Von Kuster
0e807f13f5
Add support for uploading BAM files.
2009-12-02 20:02:05 -05:00
Greg Von Kuster
a722a2aa0a
Move line count processing from set_peek() methods to set_meta() methods for data types since set_meta can run externally and it does line by line processing in some cases. Added new MetadataElements to the Data, Text, Sequence and Maf classes to handle setting dataset.blurb from stored metadata. Cleaned up a lot of code in the process.
2009-11-20 11:03:41 -05:00
Greg Von Kuster
e38e78f5e4
Fixes, cleanup and new functional tests for data types and upload:
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- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
2009-11-13 14:13:03 -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
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
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
Greg Von Kuster
8d6652853a
Eliminate the encode data functional test.
2009-09-22 14:47:47 -04:00
Greg Von Kuster
ca6ba6e011
Many history-related feature enhancements, some fixes and enhanced functional tests:
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- history sharing is now modeled after workflow sharing - fixes ticket # 63.
- all history features pass encoded history ids between requests
- new, empty histories are no longer created when a user logs in, instead their last accessed history is displayed
- some other things I'm forgetting, I'm sure
This commit also includes a fix for remote user authentication where private roles and default permissions were not created for users ( Ross's and Assaf's issues ).
Many functional test enhancements.
2009-06-29 16:30:16 -04:00
Greg Von Kuster
5c1d1b1c78
Fixes for test_get_data functional test script.
2009-06-10 15:46:26 -04:00
Greg Von Kuster
8d8299a193
Fix for pasting data in the upload utility - no longer results in a UnicodeWarning, added new tests to cover case.
2009-05-01 10:11:00 -04:00
Greg Von Kuster
e94d18ad63
A better way to decompress UCSC gzipped files. Added functional tests for uploading binary, zipped and gzipped files. Added temp file removal to upload when exception thrown. Eliminated an unnecessary import in subtract_query.
2007-12-20 18:49:03 +00:00
Greg Von Kuster
5b4bc10b88
Functional test enhancements, history functions are now covered.
2007-10-09 18:19:44 +00:00
Greg Von Kuster
10152d8b27
Eliminating more unused test data.
2007-10-05 19:47:23 +00:00
Greg Von Kuster
43afaf3969
Added functional tests for sniffing and metadata settings on file upload. Fixed a test in the 'Filter Maf Blocks by size' tool. Added new test data. Commited the bug fix I really wanted in Axt.sniff().
2007-10-05 18:02:33 +00:00
Greg Von Kuster
48e9652241
More functional test code cleanup and first round of additional functional tests.
2007-10-04 19:43:24 +00:00
Greg Von Kuster
aa0dcc81d5
More functional test cleanup, eliminated redundant tests, unused test data, and renamed some test data files.
2007-10-04 14:14:15 +00:00
Greg Von Kuster
7f29b2b047
More functional test cleanup, renamed many functions to make it easier to undrstand what they do.
2007-10-03 20:50:16 +00:00
Greg Von Kuster
b3aa4efa6f
Cleaned up functional tests, eliminating some redundant tests and unused test data files. Next step, add many missing tests.
2007-10-03 14:17:41 +00:00
John Chilton