galaxy-dist commit 37f4420ba3fc: Bug fix for handling 'spaces to tab' for non-binary composite datatype files.
# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dan Blankenberg <dan@bx.psu.edu> # Date 1275939260 14400 # Node ID 37f4420ba3fcf9eb0fd097cf812ad91cc2824f99 # Parent 7de1adaf5628e04e2da0d948f03d08cb5ce5d7f3 Bug fix for handling 'spaces to tab' for non-binary composite datatype files. Add upload tests for testing 'space to tab' when uploading composite and non-composite datatypes. --- a/test/functional/test_get_data.py +++ b/test/functional/test_get_data.py @@ -4,14 +4,16 @@ from galaxy.model.mapping import context from base.twilltestcase import TwillTestCase class UploadData( TwillTestCase ): - def test_0005_upload_file( self ): - """Test uploading 1.bed, NOT setting the file format""" + def test_0000_setup_upload_tests( self ): + """Configuring upload tests, setting admin_user""" self.logout() self.login( email='test@bx.psu.edu' ) global admin_user admin_user = sa_session.query( galaxy.model.User ) \ .filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ) \ .one() + def test_0005_upload_file( self ): + """Test uploading 1.bed, NOT setting the file format""" history = sa_session.query( galaxy.model.History ) \ .filter( and_( galaxy.model.History.table.c.deleted==False, galaxy.model.History.table.c.user_id==admin_user.id ) ) \ @@ -25,6 +27,21 @@ class UploadData( TwillTestCase ): self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0006_upload_file( self ): + """Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format""" + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + self.upload_file( '1.bed.spaces', space_to_tab = True ) + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) ) + self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" ) + self.delete_history( id=self.security.encode_id( history.id ) ) def test_0010_upload_file( self ): """Test uploading 4.bed.gz, manually setting the file format""" self.check_history_for_string( 'Your history is empty' ) @@ -174,15 +191,36 @@ class UploadData( TwillTestCase ): .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() # lped data types include a ped_file and a map_file ( which is binary ) - self.upload_composite_datatype_file( 'lped', ped_file='tinywga.ped', map_file='tinywga.map', base_name='rgenetics' ) + self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] ) # Get the latest hid for testing hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda.id ) ) + self.verify_composite_datatype_file_content( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) + self.check_history_for_string( "rgenetics" ) + self.delete_history( id=self.security.encode_id( history.id ) ) + def test_0056_upload_file( self ): + """Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped)""" + # Logged in as admin_user + self.check_history_for_string( 'Your history is empty' ) + history = sa_session.query( galaxy.model.History ) \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.user_id==admin_user.id ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + # lped data types include a ped_file and a map_file ( which is binary ) + self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] ) + # Get the latest hid for testing + hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ + .first() + assert hda is not None, "Problem retrieving hda from database" + # We'll test against the resulting ped file and map file for correctness + self.verify_composite_datatype_file_content( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' ) + self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' ) self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0060_upload_file( self ): @@ -195,16 +233,16 @@ class UploadData( TwillTestCase ): .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ .first() # pbed data types include a bim_file, a bed_file and a fam_file - self.upload_composite_datatype_file( 'pbed', bim_file='tinywga.bim', bed_file='tinywga.bed', fam_file='tinywga.fam', base_name='rgenetics' ) + self.upload_file( None, ftype='pbed', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'bim_file', 'value':'tinywga.bim' }, { 'name':'bed_file', 'value':'tinywga.bed'}, { 'name':'fam_file', 'value':'tinywga.fam' } ] ) # Get the latest hid for testing hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \ .first() assert hda is not None, "Problem retrieving hda from database" # We'll test against the resulting ped file and map file for correctness - self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda.id ) ) - self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda.id ) ) + self.verify_composite_datatype_file_content( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' ) + self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' ) + self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' ) self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0065_upload_file( self ): --- /dev/null +++ b/test-data/tinywga.ped.space_to_tab @@ -0,0 +1,40 @@ +101 1 3 2 2 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CCDS14736.1_cds_0_0_chrX_152694030_r 0 - --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -295,7 +295,7 @@ class Data( object ): def after_setting_metadata( self, dataset ): """This function is called on the dataset after metadata is set.""" dataset.clear_associated_files( metadata_safe = True ) - def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = True, **kwds ): + def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = False, **kwds ): kwds[ 'name' ] = name kwds[ 'optional' ] = optional kwds[ 'mimetype' ] = mimetype --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -143,7 +143,7 @@ class TwillTestCase( unittest.TestCase ) filename = os.path.join( *path ) file(filename, 'wt').write(buffer.getvalue()) - def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', metadata = None, composite_data = None ): + def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', space_to_tab = False, metadata = None, composite_data = None ): """Uploads a file""" self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: @@ -156,9 +156,11 @@ class TwillTestCase( unittest.TestCase ) for i, composite_file in enumerate( composite_data ): filename = self.get_filename( composite_file.get( 'value' ) ) tc.formfile( "1", "files_%i|file_data" % i, filename ) + tc.fv( "1", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) else: filename = self.get_filename( filename ) tc.formfile( "1", "file_data", filename ) + tc.fv( "1", "space_to_tab", space_to_tab ) tc.submit("runtool_btn") self.home() except AssertionError, err: @@ -196,60 +198,6 @@ class TwillTestCase( unittest.TestCase ) # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait() - def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', - fped_file='',fphe_file='',pphe_file='',fam_file='',pheno_file='',eset_file='',malist_file='', - affybatch_file='', dbkey='unspecified (?)', base_name='rgenetics' ): - """Tests uploading either of 2 different composite data types ( lped and pbed )""" - self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url ) - # Handle refresh_on_change - self.refresh_form( "file_type", ftype ) - tc.fv( "1", "dbkey", dbkey ) - tc.fv( "1", "files_metadata|base_name", base_name ) - if ftype == 'lped': - # lped data types include a ped_file and a map_file - ped_file = self.get_filename( ped_file ) - tc.formfile( "1", "files_0|file_data", ped_file ) - map_file = self.get_filename( map_file ) - tc.formfile( "1", "files_1|file_data", map_file ) - elif ftype == 'pbed': - # pbed data types include a bim_file, a bed_file and a fam_file - bim_file = self.get_filename( bim_file ) - tc.formfile( "1", "files_0|file_data", bim_file ) - bed_file = self.get_filename( bed_file ) - tc.formfile( "1", "files_1|file_data", bed_file ) - fam_file = self.get_filename( fam_file ) - tc.formfile( "1", "files_2|file_data", fam_file ) - elif ftype == 'pphe': - # pphe data types include a phe_file - pphe_file = self.get_filename( pphe_file ) - tc.formfile( "1", "files_0|file_data", pphe_file ) - elif ftype == 'fped': - # fped data types include an fped_file only - fped_file = self.get_filename( fped_file ) - tc.formfile( "1", "files_0|file_data", fped_file ) - elif ftype == 'eset': - # eset data types include a eset_file, a pheno_file - eset_file = self.get_filename( eset_file ) - tc.formfile( "1", "files_0|file_data", eset_file ) - pheno_file = self.get_filename( pheno_file ) - tc.formfile( "1", "files_1|file_data", pheno_file ) - elif ftype == 'affybatch': - # affybatch data types include an affybatch_file, and a pheno_file - affybatch_file = self.get_filename( affybatch_file ) - tc.formfile( "1", "files_0|file_data", affybatch_file ) - pheno_file = self.get_filename( pheno_file ) - tc.formfile( "1", "files_1|file_data", pheno_file ) - else: - raise AssertionError, "Unsupported composite data type (%s) received, currently only %s data types are supported."\ - % (ftype,','.join(self.composite_extensions)) - tc.submit( "runtool_btn" ) - self.check_page_for_string( 'The following job has been succesfully added to the queue:' ) - check_str = base_name #'Uploaded Composite Dataset (%s)' % ftype - self.check_page_for_string( check_str ) - # Wait for upload processing to finish (TODO: this should be done in each test case instead) - self.wait() - self.check_history_for_string( check_str ) - # Functions associated with histories def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -241,8 +241,8 @@ class UploadDataset( Group ): name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) warnings = [] - space_to_tab = False - if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = False + if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) if file_bunch.path and url_paste: @@ -261,7 +261,7 @@ class UploadDataset( Group ): name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) space_to_tab = False - if context.get( 'space_to_tab', None ) not in ["None", None]: + if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True warnings = [] file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -299,7 +299,7 @@ def add_composite_file( dataset, json_fi break elif dataset.composite_file_paths[value.name] is not None: if not value.is_binary: - if value.space_to_tab: + if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ): sniff.convert_newlines_sep2tabs( dataset.composite_file_paths[ value.name ][ 'path' ] ) else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] )
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