indentation fixes

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 <in.bcf>
 
         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()

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)

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"""

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`.

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 ):

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 ):
         """

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 ):

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__':

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 ):
         """

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_" )

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"""