From cef03056926a73ec7dfd4ee569bfdc14b3538bd0 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 5 Jul 2015 16:25:08 +0200 Subject: [PATCH] indentation fixes --- lib/galaxy/datatypes/binary.py | 6 +-- .../converters/pbed_ldreduced_converter.py | 6 +-- lib/galaxy/datatypes/data.py | 4 +- lib/galaxy/datatypes/dataproviders/column.py | 4 +- lib/galaxy/datatypes/dataproviders/dataset.py | 4 +- .../datatypes/dataproviders/hierarchy.py | 2 +- .../display_applications/parameters.py | 2 +- lib/galaxy/datatypes/genetics.py | 52 +++++++++---------- lib/galaxy/datatypes/interval.py | 10 ++-- lib/galaxy/datatypes/metadata.py | 6 +-- lib/galaxy/datatypes/tabular.py | 14 ++--- 11 files changed, 55 insertions(+), 55 deletions(-) diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index fc0944f5a28..3ba39bed2c6 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -323,7 +323,7 @@ class Bam( Binary ): if exit_code == -6: # SIGABRT, most likely samtools 1.0+ which does not accept the index name parameter. dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), - '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) os.symlink( dataset.file_name, dataset_symlink ) try: command = [ 'samtools', 'index', dataset_symlink ] @@ -494,7 +494,7 @@ class Bcf( Binary): # Usage: bcftools index dataset_symlink = os.path.join( os.path.dirname( index_file.file_name ), - '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) + '__dataset_%d_%s' % ( dataset.id, os.path.basename( index_file.file_name ) ) ) os.symlink( dataset.file_name, dataset_symlink ) stderr_name = tempfile.NamedTemporaryFile( prefix="bcf_index_stderr" ).name @@ -799,7 +799,7 @@ class GeminiSQLite( SQlite ): def sniff( self, filename ): if super( GeminiSQLite, self ).sniff( filename ): gemini_table_names = [ "gene_detailed", "gene_summary", "resources", "sample_genotype_counts", "sample_genotypes", "samples", - "variant_impacts", "variants", "version" ] + "variant_impacts", "variants", "version" ] try: conn = sqlite.connect( filename ) c = conn.cursor() diff --git a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py index 0491ae7ee88..15b4f2eeaed 100644 --- a/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py +++ b/lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py @@ -54,7 +54,7 @@ def pruneLD(plinktasks=[], cd='./', vclbase=[]): def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcerebuild=False, returnFname=False, - winsize="60", winmove="40", r2thresh="0.1" ): + winsize="60", winmove="40", r2thresh="0.1" ): """ not there so make and leave in output dir for post job hook to copy back into input extra files path for next time """ ldr = basename # we store ld reduced and thinned data @@ -70,7 +70,7 @@ def makeLDreduced(basename, infpath=None, outfpath=None, plinke='plink', forcere plinktasks = [] vclbase = [plinke, '--noweb'] plinktasks += [['--bfile', inbase, '--indep-pairwise %s %s %s' % (winsize, winmove, r2thresh), '--out %s' % outbase], - ['--bfile', inbase, '--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]] + ['--bfile', inbase, '--extract %s.prune.in --make-bed --out %s' % (outbase, outbase)]] vclbase = [plinke, '--noweb'] loglines = pruneLD(plinktasks=plinktasks, cd=outfpath, vclbase=vclbase) @@ -105,7 +105,7 @@ def main(): pass plink = sys.argv[7] makeLDreduced(base_name, infpath=inpedfilepath, outfpath=outfilepath, plinke=plink, forcerebuild=False, returnFname=False, - winsize=winsize, winmove=winmove, r2thresh=r2thresh) + winsize=winsize, winmove=winmove, r2thresh=r2thresh) f = file(outhtmlname, 'w') f.write(galhtmlprefix % prog) flist = os.listdir(outfilepath) diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index f5e96baa55f..0432a451dad 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -376,8 +376,8 @@ class Data( object ): else: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data=open( data.file_name ).read(max_peek_size), - data=data) + truncated_data=open( data.file_name ).read(max_peek_size), + data=data) def display_name(self, dataset): """Returns formatted html of dataset name""" diff --git a/lib/galaxy/datatypes/dataproviders/column.py b/lib/galaxy/datatypes/dataproviders/column.py index 7f7a39fbe0c..08ee29e9e40 100644 --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -42,8 +42,8 @@ class ColumnarDataProvider( line.RegexLineDataProvider ): } def __init__( self, source, indeces=None, - column_count=None, column_types=None, parsers=None, parse_columns=True, - deliminator='\t', filters=None, **kwargs ): + column_count=None, column_types=None, parsers=None, parse_columns=True, + deliminator='\t', filters=None, **kwargs ): """ :param indeces: a list of indeces of columns to gather from each row Optional: will default to `None`. diff --git a/lib/galaxy/datatypes/dataproviders/dataset.py b/lib/galaxy/datatypes/dataproviders/dataset.py index b225675e6cd..b692f271ef8 100644 --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -119,7 +119,7 @@ class DatasetDataProvider( base.DataProvider ): getattr( self.dataset.datatype, 'column_names', None ) or None ) if not metadata_column_names: raise KeyError( 'No column_names found for ' + - 'datatype: %s, dataset: %s' % ( str( self.dataset.datatype ), str( self.dataset ) ) ) + 'datatype: %s, dataset: %s' % ( str( self.dataset.datatype ), str( self.dataset ) ) ) indeces = [] # if indeces and column_names: # pull using indeces and re-name with given names - no need to alter (does as super would) # pass @@ -295,7 +295,7 @@ class GenomicRegionDataProvider( column.ColumnarDataProvider ): indeces = [ chrom_column, start_column, end_column ] if not all( map( lambda i: i is not None, indeces ) ): raise ValueError( "Could not determine proper column indeces for" + - " chrom, start, end: %s" % ( str( indeces ) ) ) + " chrom, start, end: %s" % ( str( indeces ) ) ) kwargs.update({ 'indeces' : indeces }) if not kwargs.get( 'column_types', None ): diff --git a/lib/galaxy/datatypes/dataproviders/hierarchy.py b/lib/galaxy/datatypes/dataproviders/hierarchy.py index 8306d84d26d..3d75f17f9d4 100644 --- a/lib/galaxy/datatypes/dataproviders/hierarchy.py +++ b/lib/galaxy/datatypes/dataproviders/hierarchy.py @@ -64,7 +64,7 @@ class XMLDataProvider( HierarchalDataProvider ): # TODO: fails with '#' - browser thinks it's an anchor - use urlencode # TODO: need removal/replacement of etree namespacing here - then move to string match return bool( ( selector is None ) or - ( isinstance( element, Element ) and selector in element.tag ) ) + ( isinstance( element, Element ) and selector in element.tag ) ) def element_as_dict( self, element ): """ diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py index 63dada77199..715dc4ba79c 100644 --- a/lib/galaxy/datatypes/display_applications/parameters.py +++ b/lib/galaxy/datatypes/display_applications/parameters.py @@ -153,7 +153,7 @@ class DisplayApplicationTemplateParameter( DisplayApplicationParameter ): return DisplayParameterValueWrapper( value, self, other_values, dataset_hash, user_hash, trans ) parameter_type_to_class = { DisplayApplicationDataParameter.type: DisplayApplicationDataParameter, - DisplayApplicationTemplateParameter.type: DisplayApplicationTemplateParameter } + DisplayApplicationTemplateParameter.type: DisplayApplicationTemplateParameter } class DisplayParameterValueWrapper( object ): diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py index d9aff1c5f0d..fa80e1d9f2c 100644 --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -253,7 +253,7 @@ class Rgenetics(Html): """ MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='RgeneticsData', - readonly=True, set_in_upload=True) + readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' allow_datatype_change = False @@ -365,13 +365,13 @@ class Lped(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.ped', - description='Pedigree File', - substitute_name_with_metadata='base_name', - is_binary=False ) + description='Pedigree File', + substitute_name_with_metadata='base_name', + is_binary=False ) self.add_composite_file( '%s.map', - description='Map File', - substitute_name_with_metadata='base_name', - is_binary=False ) + description='Map File', + substitute_name_with_metadata='base_name', + is_binary=False ) class Pphe(Rgenetics): @@ -383,9 +383,9 @@ class Pphe(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.pphe', - description='Plink Phenotype File', - substitute_name_with_metadata='base_name', - is_binary=False ) + description='Plink Phenotype File', + substitute_name_with_metadata='base_name', + is_binary=False ) class Fphe(Rgenetics): @@ -398,8 +398,8 @@ class Fphe(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.fphe', - description='FBAT Phenotype File', - substitute_name_with_metadata='base_name' ) + description='FBAT Phenotype File', + substitute_name_with_metadata='base_name' ) class Phe(Rgenetics): @@ -411,9 +411,9 @@ class Phe(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.phe', - description='Phenotype File', - substitute_name_with_metadata='base_name', - is_binary=False ) + description='Phenotype File', + substitute_name_with_metadata='base_name', + is_binary=False ) class Fped(Rgenetics): @@ -426,8 +426,8 @@ class Fped(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.fped', description='FBAT format pedfile', - substitute_name_with_metadata='base_name', - is_binary=False ) + substitute_name_with_metadata='base_name', + is_binary=False ) class Pbed(Rgenetics): @@ -483,7 +483,7 @@ class Eigenstratpca(Rgenetics): def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.eigenstratpca', - description='Eigenstrat PCA file', substitute_name_with_metadata='base_name' ) + description='Eigenstrat PCA file', substitute_name_with_metadata='base_name' ) class Snptest(Rgenetics): @@ -510,7 +510,7 @@ class RexpBase( Html ): MetadataElement( name="column_names", default=[], desc="Column names", visible=True ) MetadataElement(name="pheCols", default=[], desc="Select list for potentially interesting variables", visible=True) MetadataElement( name="base_name", - desc="base name for all transformed versions of this expression dataset", default='rexpression', set_in_upload=True) + desc="base name for all transformed versions of this expression dataset", default='rexpression', set_in_upload=True) MetadataElement( name="pheno_path", desc="Path to phenotype data for this experiment", default="rexpression.pheno", visible=True) file_ext = 'rexpbase' html_table = None @@ -521,7 +521,7 @@ class RexpBase( Html ): def __init__( self, **kwd ): Html.__init__(self, **kwd) self.add_composite_file( '%s.pheno', description='Phenodata tab text file', - substitute_name_with_metadata='base_name', is_binary=False) + substitute_name_with_metadata='base_name', is_binary=False) def generate_primary_file( self, dataset=None ): """ @@ -776,8 +776,8 @@ class Affybatch( RexpBase ): def __init__( self, **kwd ): RexpBase.__init__(self, **kwd) self.add_composite_file( '%s.affybatch', - description='AffyBatch R object saved to file', - substitute_name_with_metadata='base_name', is_binary=True ) + description='AffyBatch R object saved to file', + substitute_name_with_metadata='base_name', is_binary=True ) class Eset( RexpBase ): @@ -789,8 +789,8 @@ class Eset( RexpBase ): def __init__( self, **kwd ): RexpBase.__init__(self, **kwd) self.add_composite_file( '%s.eset', - description='ESet R object saved to file', - substitute_name_with_metadata='base_name', is_binary=True ) + description='ESet R object saved to file', + substitute_name_with_metadata='base_name', is_binary=True ) class MAlist( RexpBase ): @@ -802,8 +802,8 @@ class MAlist( RexpBase ): def __init__( self, **kwd ): RexpBase.__init__(self, **kwd) self.add_composite_file( '%s.malist', - description='MAlist R object saved to file', - substitute_name_with_metadata='base_name', is_binary=True ) + description='MAlist R object saved to file', + substitute_name_with_metadata='base_name', is_binary=True ) if __name__ == '__main__': diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index c55029a846b..24b8c039891 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -263,9 +263,9 @@ class Interval( Tabular ): internal_url = url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" - % (base_url, url_for( controller='root' ), dataset.id, type) ) + % (base_url, url_for( controller='root' ), dataset.id, type) ) redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" - % (site_url, dataset.dbkey, chrom, start, stop ) ) + % (site_url, dataset.dbkey, chrom, start, stop ) ) link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) ret_val.append( ( site_name, link ) ) return ret_val @@ -650,7 +650,7 @@ class Gff( Tabular, _RemoteCallMixin ): """Add metadata elements""" MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str', 'str', 'str', 'int', 'int', 'int', 'str', 'str', 'str'], - param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) + param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) MetadataElement( name="attributes", default=0, desc="Number of attributes", readonly=True, visible=False, no_value=0 ) MetadataElement( name="attribute_types", default={}, desc="Attribute types", param=metadata.DictParameter, readonly=True, visible=False, no_value=[] ) @@ -902,7 +902,7 @@ class Gff3( Gff ): """Add metadata elements""" MetadataElement( name="column_types", default=['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list'], - param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) + param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) def __init__(self, **kwd): """Initialize datatype, by adding GBrowse display app""" @@ -1014,7 +1014,7 @@ class Gtf( Gff ): """Add metadata elements""" MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str', 'str', 'str', 'int', 'int', 'float', 'str', 'int', 'list'], - param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) + param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) def sniff( self, filename ): """ diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py index ead8cc68ed9..9385ad987c8 100644 --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -827,9 +827,9 @@ class JobExternalOutputMetadataWrapper( object ): sa_session.flush() metadata_files_list.append( metadata_files ) args = "%s %s %s %s" % ( datatypes_config, - job_metadata, - " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ), - max_metadata_value_size) + job_metadata, + " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ), + max_metadata_value_size) if include_command: # return command required to build fd, fp = tempfile.mkstemp( suffix='.py', dir=tmp_dir, prefix="set_metadata_" ) diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py index 3327f9888a8..f96bb0508c5 100644 --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -83,8 +83,8 @@ class TabularData( data.Text ): else: trans.response.set_content_type( "text/html" ) return trans.stream_template_mako( "/dataset/large_file.mako", - truncated_data=open( dataset.file_name ).read(max_peek_size), - data=dataset) + truncated_data=open( dataset.file_name ).read(max_peek_size), + data=dataset) else: column_names = 'null' if dataset.metadata.column_names: @@ -98,11 +98,11 @@ class TabularData( data.Text ): if column_number is None: column_number = 'null' return trans.fill_template( "/dataset/tabular_chunked.mako", - dataset=dataset, - chunk=self.get_chunk(trans, dataset, 0), - column_number=column_number, - column_names=column_names, - column_types=column_types ) + dataset=dataset, + chunk=self.get_chunk(trans, dataset, 0), + column_number=column_number, + column_names=column_names, + column_types=column_types ) def make_html_table( self, dataset, **kwargs ): """Create HTML table, used for displaying peek"""