galaxy

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Greg Von Kuster 98f8c9df29 Enhance lastz tool, enhance functional test framework, and fix a bug in¬†editing permissions on a folder:

- until now,¬†lastz will (mostly) ignore alignments in masked regions since¬†soft-masking has been enabled. ¬†Now the default has changed to disable soft masking, and an option has been added to the tool to enable it if desired.
- the functional test framework now allows for a new "sort" attribute in the output tag for functional tests. ¬†For example: ¬†<output name="output1" file="lastz_wrapper_out4.tabular" sort="True" />
If set to True, the output dataset will be sorted prior to comparing. ¬†This is needed for the lastz tool since multiple threads generate output randomly if the input file has more than 1 sequence. ¬†The default is False.
- Decode the id of a folder prior when retrieving from the database - fixes the bug reported by Guru.

2010-01-11 13:26:00 -05:00

__init__.py

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.

2009-10-20 13:08:29 -04:00

test_DNAse_flanked_genes.py

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

test_forms_and_requests.py

Data library cleanup

2009-12-23 20:26:01 -05:00

test_get_data.py

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.