Greg Von Kuster e38e78f5e4 Fixes, cleanup and new functional tests for data types and upload: ...

- 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

..

annotation_profiler

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

data_destination

merging from central

2008-10-28 11:28:15 -04:00

data_source

Fixes, cleanup and new functional tests for data types and upload:

2009-11-13 14:13:03 -05:00

emboss_5

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

encode

Completed an old FIXME in DefaultToolAction.execute() - metadata no longer added to "incoming". Tool config params changed from things like$input_chromCol to ${input.metadata.chromCol}.

2008-07-23 15:27:39 -04:00

evolution

Changing an 'and' to 'or' in SNP mutate codon tool error checking.

2009-09-22 11:40:41 -04:00

extract

Applied patch provided by Brad Chapman in the liftOver tool to support BED files that contain track or browser lines. Resolves bitbucket issue 201.

2009-11-12 13:20:19 -05:00

fasta_tools

Fixed for functional tests for new version of fasta_filter_by_length tool contributed by James Casbon.

2009-07-23 14:31:11 -04:00

fastx_toolkit

Modified test data and tool conf for fastq stats

2009-10-08 14:50:28 -04:00

filters

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

hyphy

typo fixes for tools in folders A-M

2009-09-27 23:11:43 -04:00

maf

Eliminate the _monkeypatch_session_method from assignmapper by cleaning up remaining object flushes. The _monkeypatch_query_method remains due to a single object query in ~/datatypes/metadata.py in the FileParameter.wrap() method. The sqlalchemy session is now also passed into the __init__ methods for both HistoryDatasetAssociation and LibraryDatasetDatasetAssociation when the create_dataset param is True to enable methods in the DatasetInstance class to correctly add the created dataset to the sqlalchemy session and flush it.

2009-11-12 15:25:48 -05:00

metag_tools

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -05:00

new_operations

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

next_gen_conversion

Updated solid_to_fastq so that -1 qualities are converted to 1 before conversion to FASTQ.

2009-10-21 16:04:24 -04:00

plotting

Fix bar chart output format.

2009-08-03 16:38:27 -04:00

regVariation

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

samtools

Changed sam-to-bam test by removing nonexistent dbkey from test input specification.

2009-11-11 13:53:48 -05:00

solid_tools

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

sr_mapping

Corrected sloppy temp file/directory cleanup in index creation for Bowtie and BWA

2009-11-12 13:02:04 -05:00

stats

Upgrade to Cheetah 2.2.2

2009-11-10 13:47:34 -05:00

taxonomy

fix some typos for tools in folders N-Z

2009-09-25 02:06:03 -04:00

validation

Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.

2008-03-28 15:24:50 +00:00

visualization

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