details: http://www.bx.psu.edu/hg/galaxy/rev/f5b051c51295 changeset: 1558:f5b051c51295 user: Greg Von Kuster greg@bx.psu.edu date: Fri Oct 17 10:46:29 2008 -0400 description: Fixes for data_source tools, data.name, data.info, data.dbkey, and data.extension should now be properly set. Eliminated fastq data type from datatypes_conf.xml.sample since it is not a supported data type.
6 file(s) affected in this change:
datatypes_conf.xml.sample lib/galaxy/tools/__init__.py tools/data_source/flymine.xml tools/data_source/ucsc_tablebrowser.xml tools/data_source/ucsc_tablebrowser_archaea.xml tools/data_source/ucsc_tablebrowser_test.xml
diffs (119 lines):
diff -r a5831435c654 -r f5b051c51295 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Oct 16 14:12:37 2008 -0400 +++ b/datatypes_conf.xml.sample Fri Oct 17 10:46:29 2008 -0400 @@ -150,7 +150,6 @@ <sniffer order="05" type="galaxy.datatypes.sequence:Maf"/> <sniffer order="10" type="galaxy.datatypes.sequence:Lav"/> <sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/> - <sniffer order="20" type="galaxy.datatypes.sequence:Fastq"/> <sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/> <sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/> <sniffer order="35" type="galaxy.datatypes.images:Html"/> diff -r a5831435c654 -r f5b051c51295 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Thu Oct 16 14:12:37 2008 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Oct 17 10:46:29 2008 -0400 @@ -23,6 +23,7 @@ from galaxy.tools.actions import DefaultToolAction from galaxy.model import directory_hash_id from galaxy.util.none_like import NoneDataset +from galaxy.datatypes import sniff
log = logging.getLogger( __name__ )
@@ -1143,22 +1144,21 @@ description = param_dict.get( 'position', '' ) if not description: description = 'unknown position' - data_type = param_dict.get( 'data_type ') + data_type = param_dict.get( 'data_type' ) items = out_data.items() for name, data in items: if organism and table and description: data.name = '%s on %s: %s (%s)' % ( data.name, organism, table, description ) data.info = info data.dbkey = dbkey - ext = data_type - try: - ext = data_type_to_ext[ data_type ] + try: + data_type = data_type_to_ext[ data_type ] except: pass - if ext not in app.datatypes_registry.datatypes_by_extension: - ext = 'interval' - data = app.datatypes_registry.change_datatype( data, ext ) - # store external data source's request parameters temporarily in output file + if data_type not in app.datatypes_registry.datatypes_by_extension: + data_type = 'interval' + data = app.datatypes_registry.change_datatype( data, data_type ) + # Store external data source's request parameters temporarily in output file out = open( data.file_name, 'w' ) for key, value in param_dict.items(): print >> out, '%s\t%s' % ( key, value ) @@ -1171,9 +1171,15 @@ # tag set in the tool config. if self.tool_type == 'data_source': name, data = out_data.items()[0] - if data.state == data.states.OK and not data.info: - data.info = data.name - if not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ): + if data.state == data.states.OK: + data.name = param_dict.get( 'name', data.name ) + data.info = param_dict.get( 'info', data.name ) + data.dbkey = param_dict.get( 'dbkey', data.dbkey ) + data.extension = param_dict.get( 'data_type', data.extension ) + if data.extension == 'txt': + data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) + data = app.datatypes_registry.change_datatype( data, data_type ) + elif not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ): data.set_meta() if data.missing_meta(): data = app.datatypes_registry.change_datatype( data, 'tabular' ) diff -r a5831435c654 -r f5b051c51295 tools/data_source/flymine.xml --- a/tools/data_source/flymine.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/flymine.xml Fri Oct 17 10:46:29 2008 -0400 @@ -14,7 +14,7 @@ <request_param galaxy_name="description" remote_name="description" missing="" /> <request_param galaxy_name="name" remote_name="name" missing="FlyMine query" /> <request_param galaxy_name="info" remote_name="info" missing="" /> - <request_param galaxy_name="data_type" remote_name="data_type" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser.xml --- a/tools/data_source/ucsc_tablebrowser.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser_archaea.xml --- a/tools/data_source/ucsc_tablebrowser_archaea.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser_archaea.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs> diff -r a5831435c654 -r f5b051c51295 tools/data_source/ucsc_tablebrowser_test.xml --- a/tools/data_source/ucsc_tablebrowser_test.xml Thu Oct 16 14:12:37 2008 -0400 +++ b/tools/data_source/ucsc_tablebrowser_test.xml Fri Oct 17 10:46:29 2008 -0400 @@ -16,7 +16,7 @@ <request_param galaxy_name="organism" remote_name="org" missing="unknown species" /> <request_param galaxy_name="table" remote_name="hgta_track" missing="" /> <request_param galaxy_name="description" remote_name="hgta_regionType" missing="" /> - <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" /> </request_param_translation> <uihints minwidth="800"/> <outputs>