From 79745f40124ecfbd5dcf7cb23d9b6a9512f5a74c Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Thu, 29 Nov 2007 17:04:42 +0000 Subject: [PATCH] Modified all tools to use the new tag for dynamic select lists. Completely eliminated the tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py. --- lib/galaxy/tools/dynamic_options.py | 412 +++++++++--------- lib/galaxy/tools/parameters.py | 18 +- .../encode_import_all_latest_datasets.xml | 4 +- ...ncode_import_chromatin_and_chromosomes.xml | 4 +- tools/data_source/encode_import_gencode.xml | 4 +- .../encode_import_genes_and_transcripts.xml | 4 +- ...import_multi-species_sequence_analysis.xml | 4 +- ...encode_import_transcription_regulation.xml | 4 +- tools/data_source/microbial_import.xml | 78 ++-- tools/data_source/microbial_import_code.py | 80 ++++ tools/data_source/upload.xml | 7 +- tools/data_source/upload_code.py | 13 - tools/extract/interval2maf_pairwise.xml | 23 +- tools/extract/interval2maf_pairwise_code.py | 46 -- .../extract/interval_maf_to_merged_fasta.xml | 2 +- tools/filters/maf/maf_stats_code.py | 35 +- tools/filters/maf/maf_thread_for_species.xml | 3 +- .../maf/maf_thread_for_species_code.py | 38 -- tools/regVariation/windowSplitter.xml | 2 +- 19 files changed, 395 insertions(+), 386 deletions(-) delete mode 100644 tools/data_source/upload_code.py delete mode 100644 tools/extract/interval2maf_pairwise_code.py delete mode 100644 tools/filters/maf/maf_thread_for_species_code.py diff --git a/lib/galaxy/tools/dynamic_options.py b/lib/galaxy/tools/dynamic_options.py index 6ebee9e2362..0d847365f92 100644 --- a/lib/galaxy/tools/dynamic_options.py +++ b/lib/galaxy/tools/dynamic_options.py @@ -6,6 +6,7 @@ log = logging.getLogger(__name__) class DynamicOptions( object ): """Handles dynamically generated SelectToolParameter options""" def __init__( self, elem ): + self.from_file_data = None # FIXME: Pushing these things in as options ends up being pretty ugly. # We should find a way to make this work through the validation mechanism. self.no_data_option = [ ( 'No data available for this build', 'None', True ) ] @@ -23,28 +24,20 @@ class DynamicOptions( object ): except: self.data_file = self.from_file else: self.data_file = None - if elem.tag == 'select_options': - self.data_ref = elem.get( 'data_ref', None ) - self.param_ref = elem.get( 'param_ref', None ) - self.func = elem.get( 'func', None ) - assert self.func is not None, "Value for option generator function not found" - self.func_params = elem.findall( 'func_param' ) - else: #elem.tag =='options' - self.filters = elem.findall( 'filter' ) - self.data_ref = None - for filter in self.filters: - filter_type = filter.get( 'type', None ) - assert filter_type is not None, "Required 'type' attribute missing from filter" - if filter_type.strip() == 'data_meta': - self.data_ref = filter.get( 'data_ref', None ) - assert self.data_ref is not None, "Required 'data_ref' attribute missing from 'data_meta' filter" - self.data_ref = self.data_ref.strip() - elif filter_type.strip() == 'param_meta': - self.param_ref = filter.get( 'param_ref', None ) - assert self.param_ref is not None, "Required 'param_ref' attribute missing from 'param_meta' filter" - self.param_ref = self.param_ref.strip() - #FIXME: this attr is used only by microbial import, so shouldn't be at this level - self.microbe_info = None + self.tool_type = elem.get( 'tool_type', None ) + self.filters = elem.findall( 'filter' ) + self.data_ref = None + for filter in self.filters: + filter_type = filter.get( 'type', None ) + assert filter_type is not None, "Required 'type' attribute missing from filter" + if filter_type.strip() == 'data_meta': + self.data_ref = filter.get( 'data_ref', None ) + assert self.data_ref is not None, "Required 'data_ref' attribute missing from 'data_meta' filter" + self.data_ref = self.data_ref.strip() + elif filter_type.strip() == 'param_meta': + self.param_ref = filter.get( 'param_ref', None ) + assert self.param_ref is not None, "Required 'param_ref' attribute missing from 'param_meta' filter" + self.param_ref = self.param_ref.strip() def get_dataset( self, trans, other_values ): # No value indicates a configuration error, the named DataToolParameter must preceed this parameter in the tool config assert self.data_ref in other_values, "Value for associated DataToolParameter not found" @@ -56,14 +49,18 @@ class DynamicOptions( object ): # Currently dynamically generated select lists do not work well with optional datasets. return None return dataset - def get_param_value( self, trans, other_values ): + def get_param_value( self, param, trans, other_values ): + if param is None: return None + assert param in other_values, "Value for associated param_value %s not found" %param + return other_values[ param ] + def get_param_ref_value( self, trans, other_values ): if self.param_ref is None: return None - assert self.param_ref in other_values, "Value for associated parameter %s not found" %self.param_ref.name + assert self.param_ref in other_values, "Value for associated param_ref %s not found" %self.param_ref.name return other_values[ self.param_ref ] def get_unique_elems( self, elems ): seen = set() return [ x for x in elems if x not in seen and not seen.add( x ) ] - def get_options( self, trans, other_values, must_be_valid = False ): + def get_options( self, trans, other_values, must_be_valid=False ): filters = {} key = None # Check for filters and build a dictionary from them @@ -84,7 +81,6 @@ class DynamicOptions( object ): if key == 'build': value = dataset.get_dbkey() elif key == 'file_name': value = dataset.get_file_name() elif key == 'species': value = dataset.metadata.species - elif key == 'maf': pass # value does not need to be set, maf tools require special handling - see below filters[ 'data_meta' ][ 'value' ] = value if self.data_file == 'maf_index.loc' and key == 'build' and value == '?': if must_be_valid: return [] @@ -94,8 +90,20 @@ class DynamicOptions( object ): key = filter.get( 'key', None ) assert key is not None, "key attribute missing from param_meta filter" filters[ 'param_meta' ][ 'key' ] = key.strip() - value = self.get_param_value( trans, other_values ) + value = self.get_param_ref_value( trans, other_values ) filters[ 'param_meta' ][ 'value' ] = value + elif filter_type == 'param_value': + n = filter.get( 'name', None ) + assert n is not None, "param_value filters require a 'name' attribute" + n = n.strip() + v = self.get_param_value( n, trans, other_values ) + assert v is not None, "param_value filters require a 'value' attribute" + v = v.strip() + try: + filters[ 'param_values' ][ n ] = v + except: + filters[ 'param_values' ] = {} + filters[ 'param_values' ][ n ] = v elif filter_type == 'column': n = filter.get( 'name', None ) assert n is not None, "column filters require a 'name' attribute" @@ -109,7 +117,6 @@ class DynamicOptions( object ): filters[ 'columns' ] = {} filters[ 'columns' ][ n ] = v elif filter_type == 'param': - # TODO: I'm not sure I like the way 'param' filters are implemented, I may be rethinking this approach... n = filter.get( 'name', None ) assert n is not None, "param filters require a 'name' attribute" n = n.strip() @@ -121,14 +128,15 @@ class DynamicOptions( object ): except: filters[ 'params' ] = {} filters[ 'params' ][ n ] = v - # Now that we've parsed our filters, we need to see if the tool is a maf tool which requires special handling + # Now that we've parsed our filters, we need to see if the tool is a maf tool + # which requires special handling try: key = filters[ 'data_meta' ][ 'key' ] - except: key == None + except: key = None if key == 'maf': maf_source = filters[ 'params' ][ 'maf_source' ] if maf_source == 'cached': maf_uid = filters[ 'param_meta' ][ 'value' ] - if maf_uid in [None, 'None']: + if maf_uid in [ None, 'None' ]: if must_be_valid: return [] if maf_uid is None: return self.no_data_option if maf_uid == 'None': return self.build_not_set_option @@ -137,45 +145,62 @@ class DynamicOptions( object ): if dataset is None: return self.wait_for_maf_option filters[ 'data_meta' ][ 'key' ] = 'species' filters[ 'data_meta' ][ 'value' ] = dataset.metadata.species - return self.generate_options( filters, must_be_valid = must_be_valid ) - def generate_options( self, filters={}, sep='\t', must_be_valid = False ): - # Extract the info from the tool's options filters, if any - try: key = filters[ 'data_meta' ][ 'key' ] - except: key = None - try: value = filters[ 'data_meta' ][ 'value' ] - except: value = None - if key is None and value is None: - # Look for param_meta filter - try: key = filters[ 'param_meta' ][ 'key' ] - except: key = None - try: value = filters[ 'param_meta' ][ 'value' ] - except: value = None - try: name_col = int( filters[ 'columns' ][ 'name_col' ] ) - except: name_col = None - try: value_col = int( filters[ 'columns' ][ 'value_col' ] ) - except: value_col = None - try: encode_group = filters[ 'params' ][ 'encode_group' ] - except: encode_group = None - try: build = filters[ 'params' ][ 'build' ] - except: build = None - try: maf_source = filters[ 'params' ][ 'maf_source' ] - except: maf_source = None - - # Order of the following conditionals is critical - if encode_group is not None and build is not None: - return self.generate_from_file_for_encode( encode_group, build, must_be_valid = must_be_valid ) - elif key == 'species': - return self.generate_from_dataset_for_species( value ) - elif key == 'maf': - return self.generate_from_file_for_maf( maf_source, value, must_be_valid = must_be_valid ) - elif key == 'file_name': - return self.generate_from_dataset( value, value_col ) - elif key == 'build': - build_col = int( filters[ 'columns' ][ 'build_col' ].strip() ) - return self.generate_from_file_for_build( value, build_col, name_col, value_col, must_be_valid = must_be_valid ) - elif key is None: - return self.generate_from_file( name_col, value_col ) - def generate_from_file_for_encode( self, encode_group, build, sep='\t', must_be_valid = False ): + return self.generate_options( filters, must_be_valid=must_be_valid ) + def generate_options( self, filters={}, sep='\t', must_be_valid=False ): + if self.tool_type == 'upload': + return self.generate_from_datatypes_registry() + elif self.tool_type == 'encode': + encode_group = filters[ 'params' ][ 'encode_group' ] + build = filters[ 'params' ][ 'build' ] + return self.generate_from_file_for_encode( encode_group, build, must_be_valid=must_be_valid ) + elif self.tool_type == 'microbial': + if self.from_file_data is None: self.load_microbial_data() + try: kingdom = filters[ 'param_values' ][ 'kingdom' ] + except: kingdom = None + try: org = filters[ 'param_values' ][ 'org' ] + except: org = None + try: feature = filters[ 'params' ][ 'feature' ] + except: feature = None + return self.generate_from_file_for_microbial( kingdom, org, feature, must_be_valid=must_be_valid ) + else: # self.tool_type is None + try: key = filters[ 'data_meta' ][ 'key' ] + except: + try: key = filters[ 'param_meta' ][ 'key' ] + except: key = None + if key == 'species': + value = filters[ 'data_meta' ][ 'value' ] + return self.generate_from_dataset_for_species( value ) + elif key == 'maf': + maf_source = filters[ 'params' ][ 'maf_source' ] + try: value = filters[ 'data_meta' ][ 'value' ] + except: value = filters[ 'param_meta' ][ 'value' ] + return self.generate_from_file_for_maf( maf_source, value, must_be_valid=must_be_valid ) + elif key == 'file_name': + value = filters[ 'data_meta' ][ 'value' ] + value_col = int( filters[ 'columns' ][ 'value_col' ] ) + return self.generate_from_dataset( value, value_col ) + elif key == 'build': + value = filters[ 'data_meta' ][ 'value' ] + build_col = int( filters[ 'columns' ][ 'build_col' ].strip() ) + name_col = int( filters[ 'columns' ][ 'name_col' ] ) + value_col = int( filters[ 'columns' ][ 'value_col' ] ) + return self.generate_from_file_for_build( value, build_col, name_col, value_col, must_be_valid=must_be_valid ) + else: # key is None + name_col = int( filters[ 'columns' ][ 'name_col' ] ) + value_col = int( filters[ 'columns' ][ 'value_col' ] ) + return self.generate_from_file( name_col, value_col ) + def generate_from_datatypes_registry( self ): + from galaxy.datatypes import registry + datatypes_registry = registry.Registry() + options = [] + formats = datatypes_registry.datatypes_by_extension.keys() + formats.sort() + options.append( ( 'Auto-detect', 'auto', True ) ) + for format in formats: + label = format.capitalize() + options.append( ( label, format, False ) ) + return options + def generate_from_file_for_encode( self, encode_group, build, sep='\t', must_be_valid=False ): options = [] def generate(): encode_sets = {} @@ -253,12 +278,121 @@ class DynamicOptions( object ): if must_be_valid: return [] return self.no_data_option_not_selected return options + def generate_from_file_for_microbial( self, kingdom=None, org=None, feature=None, must_be_valid=False ): + options = [] + if not kingdom and not org and not feature: + kingdoms = self.from_file_data.keys() + kingdoms.sort() + for kingdom in kingdoms: + options.append( ( kingdom, kingdom, False ) ) + if options: + options[0] = ( options[0][0], options[0][1], True ) + elif kingdom and not org and not feature: + orgs = self.from_file_data[ kingdom ].keys() + #need to sort by name + swap_test = False + for i in range( 0, len( orgs ) - 1 ): + for j in range( 0, len( orgs ) - i - 1 ): + if self.from_file_data[ kingdom ][ orgs[ j ] ][ 'name' ] > self.from_file_data[ kingdom ][ orgs[ j + 1 ] ][ 'name' ]: + orgs[ j ], orgs[ j + 1 ] = orgs[ j + 1 ], orgs[ j ] + swap_test = True + if swap_test == False: break + for org in orgs: + if self.from_file_data[ kingdom ][ org ][ 'link_site' ] == "UCSC": + options.append( ( "" + self.from_file_data[ kingdom ][ org ][ 'name' ] + " (about)", org, False ) ) + else: + options.append( ( self.from_file_data[ kingdom ][ org ][ 'name' ] + " (about)", org, False ) ) + if options: + options[0] = ( options[0][0], options[0][1], True) + else: + chroms = self.from_file_data[ kingdom ][ org ][ 'chrs' ].keys() + chroms.sort() + for chr in chroms: + for data in self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'data' ]: + if self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'data' ][ data ][ 'feature' ] == feature: + options.append( ( self.from_file_data[ kingdom ][ org ][ 'chrs' ][ chr ][ 'name' ] + " (about)", data, False ) ) + return options + def load_microbial_data( self, sep='\t' ): + microbe_info= {} + orgs = {} + for line in open( self.from_file ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( sep ) + #read each line, if not enough fields, go to next line + try: + info_type = fields.pop(0) + if info_type.upper() == "ORG": + #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521 + org_num = fields.pop(0) + name = fields.pop(0) + kingdom = fields.pop(0) + group = fields.pop(0) + chromosomes = fields.pop(0) + info_url = fields.pop(0) + link_site = fields.pop(0) + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'name' ] = name + orgs[ org_num ][ 'kingdom' ] = kingdom + orgs[ org_num ][ 'group' ] = group + orgs[ org_num ][ 'chromosomes' ] = chromosomes + orgs[ org_num ][ 'info_url' ] = info_url + orgs[ org_num ][ 'link_site' ] = link_site + elif info_type.upper() == "CHR": + #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 + org_num = fields.pop(0) + chr_acc = fields.pop(0) + name = fields.pop(0) + length = fields.pop(0) + gi = fields.pop(0) + gb = fields.pop(0) + info_url = fields.pop(0) + chr = {} + chr[ 'name' ] = name + chr[ 'length' ] = length + chr[ 'gi' ] = gi + chr[ 'gb' ] = gb + chr[ 'info_url' ] = info_url + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr + elif info_type.upper() == "DATA": + #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed + uid = fields.pop(0) + org_num = fields.pop(0) + chr_acc = fields.pop(0) + feature = fields.pop(0) + filetype = fields.pop(0) + path = fields.pop(0) + data = {} + data[ 'filetype' ] = filetype + data[ 'path' ] = path + data[ 'feature' ] = feature + + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data + else: continue + except: continue + for org_num in orgs: + org = orgs[ org_num ] + if org[ 'kingdom' ] not in microbe_info: + microbe_info[ org[ 'kingdom' ] ] = {} + if org_num not in microbe_info[ org[ 'kingdom' ] ]: + microbe_info[ org[ 'kingdom' ] ][org_num] = org + self.from_file_data = microbe_info def generate_from_dataset_for_species( self, value ): options = [] for species in value: options.append( ( species, species, False ) ) return options - def generate_from_file_for_maf( self, maf_source, maf_uid, sep='\t', must_be_valid = False ): + def generate_from_file_for_maf( self, maf_source, maf_uid, sep='\t', must_be_valid=False ): options = [] d = {} # We will only reach here if the maf-source param value is 'cached' @@ -285,7 +419,7 @@ class DynamicOptions( object ): if must_be_valid: return [] return self.no_data_option return options - def generate_from_dataset( self, value, value_col, sep='\t', must_be_valid = False ): + def generate_from_dataset( self, value, value_col, sep='\t', must_be_valid=False ): options = [] elem_list = [] try: in_file = open( value, "r" ) @@ -307,7 +441,7 @@ class DynamicOptions( object ): for elem in elem_list: options.append( ( elem, elem, False ) ) return options - def generate_from_file_for_build( self, value, build_col, name_col, value_col, sep='\t', must_be_valid = False ): + def generate_from_file_for_build( self, value, build_col, name_col, value_col, sep='\t', must_be_valid=False ): options = [] d = {} for line in open( self.from_file ): @@ -330,7 +464,7 @@ class DynamicOptions( object ): if not fields[ build_col ] in d: d[ fields[ build_col ] ] = [] d[ fields[ build_col ] ].append( (fields[ name_col ], fields[ value_col ]) ) - elif self.data_file == 'maf_index.loc': + elif self.data_file == 'maf_index.loc' or self.data_file == 'maf_pairwise.loc': try: maf_desc = fields[ name_col ] # ENCODE TBA (hg17) maf_uid = fields[ value_col ] # ENCODE_TBA_hg17 @@ -359,7 +493,7 @@ class DynamicOptions( object ): if value in d: for (key, val) in d[ value ]: options.append( ( key, val, False ) ) - elif self.data_file == 'maf_index.loc': + elif self.data_file == 'maf_index.loc' or self.data_file == 'maf_pairwise.loc': for key in d: if value in d[ key ][ 'builds' ]: options.append( ( d[ key ][ 'description' ], key, False ) ) @@ -379,131 +513,3 @@ class DynamicOptions( object ): # TODO: this option list should be sorted options.append( ( fields[ name_col ], fields[ value_col ], False ) ) return options - def load_from_file_for_microbial( self ): - self.from_file = "/depot/data2/galaxy/microbes/microbial_data.loc" - microbe_info= {} - orgs = {} - for line in open( self.from_file ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( '\t' ) - #read each line, if not enough fields, go to next line - try: - info_type = fields.pop(0) - if info_type.upper() == "ORG": - #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521 - org_num = fields.pop(0) - name = fields.pop(0) - kingdom = fields.pop(0) - group = fields.pop(0) - chromosomes = fields.pop(0) - info_url = fields.pop(0) - link_site = fields.pop(0) - if org_num not in orgs: - orgs[org_num] = {} - orgs[org_num]['chrs'] = {} - orgs[org_num]['name'] = name - orgs[org_num]['kingdom'] = kingdom - orgs[org_num]['group'] = group - orgs[org_num]['chromosomes'] = chromosomes - orgs[org_num]['info_url'] = info_url - orgs[org_num]['link_site'] = link_site - elif info_type.upper() == "CHR": - #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 - org_num = fields.pop(0) - chr_acc = fields.pop(0) - name = fields.pop(0) - length = fields.pop(0) - gi = fields.pop(0) - gb = fields.pop(0) - info_url = fields.pop(0) - chr = {} - chr['name'] = name - chr['length'] = length - chr['gi'] = gi - chr['gb'] = gb - chr['info_url'] = info_url - if org_num not in orgs: - orgs[org_num] = {} - orgs[org_num]['chrs'] = {} - orgs[org_num]['chrs'][chr_acc] = chr - elif info_type.upper() == "DATA": - #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed - uid = fields.pop(0) - org_num = fields.pop(0) - chr_acc = fields.pop(0) - feature = fields.pop(0) - filetype = fields.pop(0) - path = fields.pop(0) - data = {} - data['filetype'] = filetype - data['path'] = path - data['feature'] = feature - - if org_num not in orgs: - orgs[org_num] = {} - orgs[org_num]['chrs'] = {} - if 'data' not in orgs[org_num]['chrs'][chr_acc]: - orgs[org_num]['chrs'][chr_acc]['data'] = {} - orgs[org_num]['chrs'][chr_acc]['data'][uid] = data - else: continue - except: continue - for org_num in orgs: - org = orgs[org_num] - if org['kingdom'] not in microbe_info: - microbe_info[org['kingdom']] = {} - if org_num not in microbe_info[org['kingdom']]: - microbe_info[org['kingdom']][org_num] = org - self.microbe_info = microbe_info - def get_options_for_kingdoms( self, trans, other_values ): - if self.microbe_info == None: self.load_from_file_for_microbial() - options = [] - kingdoms = self.microbe_info.keys() - kingdoms.sort() - for kingdom in kingdoms: - options.append( (kingdom, kingdom, False) ) - if options: - options[0] = ( options[0][0], options[0][1], True) - return options - def get_options_for_orgs_by_kingdom( self, trans, other_values ): - if self.microbe_info == None: self.load_from_file_for_microbial() - options = [] - for func_param in self.func_params: - if func_param.get( 'name' ) == 'kingdom': - kingdom = other_values[ func_param.get( 'value' ) ] - orgs = self.microbe_info[kingdom].keys() - #need to sort by name - swap_test = False - for i in range( 0, len(orgs) - 1 ): - for j in range( 0, len(orgs) - i - 1 ): - if self.microbe_info[kingdom][orgs[j]]['name'] > self.microbe_info[kingdom][orgs[j + 1]]['name']: - orgs[j], orgs[j + 1] = orgs[j + 1], orgs[j] - swap_test = True - if swap_test == False: break - for org in orgs: - if self.microbe_info[kingdom][org]['link_site'] == "UCSC": - options.append( ( "" + self.microbe_info[kingdom][org]['name'] + " (about)", org, False ) ) - else: - options.append( ( self.microbe_info[kingdom][org]['name'] + " (about)", org, False ) ) - if options: - options[0] = ( options[0][0], options[0][1], True) - return options - def get_options_for_kingdom_org_feature( self, trans, other_values ): - if self.microbe_info == None: self.load_from_file_for_microbial() - options = [] - for func_param in self.func_params: - if func_param.get( 'name' ) == 'kingdom': - kingdom = other_values[ func_param.get( 'value' ) ] - elif func_param.get( 'name' ) == 'org': - org = other_values[ func_param.get( 'value' ) ] - elif func_param.get( 'name' ) == 'feature': - feature = func_param.get( 'value' ) - log.debug("kingdom: %s, org: %s, feature: %s" %(kingdom, org, feature)) - chroms = self.microbe_info[kingdom][org]['chrs'].keys() - chroms.sort() - for chr in chroms: - for data in self.microbe_info[kingdom][org]['chrs'][chr]['data']: - if self.microbe_info[kingdom][org]['chrs'][chr]['data'][data]['feature'] == feature: - options.append( ( self.microbe_info[kingdom][org]['chrs'][chr]['name'] + " (about)", data, False ) ) - return options - diff --git a/lib/galaxy/tools/parameters.py b/lib/galaxy/tools/parameters.py index 865d9522fdd..721980e2de9 100644 --- a/lib/galaxy/tools/parameters.py +++ b/lib/galaxy/tools/parameters.py @@ -407,29 +407,22 @@ class SelectToolParameter( ToolParameter ): self.separator = elem.get( 'separator', ',' ) self.legal_values = set() self.dynamic_options = elem.get( "dynamic_options", None ) - select_options = elem.find( 'select_options' ) - if select_options is None: - self.select_options = None - else: - self.select_options = dynamic_options.DynamicOptions( select_options ) options = elem.find( 'options' ) if options is None: self.options = None else: self.options = dynamic_options.DynamicOptions( options ) - if self.dynamic_options is None and self.select_options is None and self.options is None: + if self.dynamic_options is None and self.options is None: self.static_options = list() for index, option in enumerate( elem.findall( "option" ) ): value = option.get( "value" ) self.legal_values.add( value ) selected = ( option.get( "selected", None ) == "true" ) self.static_options.append( ( option.text, value, selected ) ) - self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.select_options is not None ) or ( self.options is not None ) ) + self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) def get_options( self, trans, other_values ): if self.options: return self.options.get_options( trans, other_values ) - elif self.select_options: - return eval( '''self.select_options.%s( trans, other_values )''' %self.select_options.func ) elif self.dynamic_options: return eval( self.dynamic_options, self.tool.code_namespace, other_values ) else: @@ -437,8 +430,6 @@ class SelectToolParameter( ToolParameter ): def get_legal_values( self, trans, other_values ): if self.options: return set( v for _, v, _ in self.options.get_options( trans, other_values, must_be_valid = True ) ) - elif self.select_options: - return set( v for _, v, _ in eval( '''self.select_options.%s( trans, other_values )''' %self.select_options.func ) ) elif self.dynamic_options: return set( v for _, v, _ in eval( self.dynamic_options, self.tool.code_namespace, other_values ) ) else: @@ -519,11 +510,6 @@ class SelectToolParameter( ToolParameter ): except: pass try: param_ref = self.options.param_ref except: pass - elif self.select_options: - try: data_ref = self.select_options.data_ref - except: pass - try: param_ref = self.select_options.param_ref - except: pass if data_ref is None and param_ref is None: return [] elif data_ref is None: return [ param_ref ] elif param_ref is None: return [ data_ref ] diff --git a/tools/data_source/encode_import_all_latest_datasets.xml b/tools/data_source/encode_import_all_latest_datasets.xml index 03f47320780..61731cdeada 100644 --- a/tools/data_source/encode_import_all_latest_datasets.xml +++ b/tools/data_source/encode_import_all_latest_datasets.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/encode_import_chromatin_and_chromosomes.xml b/tools/data_source/encode_import_chromatin_and_chromosomes.xml index 9985f645c74..4712068e278 100644 --- a/tools/data_source/encode_import_chromatin_and_chromosomes.xml +++ b/tools/data_source/encode_import_chromatin_and_chromosomes.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/encode_import_gencode.xml b/tools/data_source/encode_import_gencode.xml index 9b64d3cc55b..f31b5617e48 100644 --- a/tools/data_source/encode_import_gencode.xml +++ b/tools/data_source/encode_import_gencode.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/encode_import_genes_and_transcripts.xml b/tools/data_source/encode_import_genes_and_transcripts.xml index d93740d1c71..a5a493fd898 100644 --- a/tools/data_source/encode_import_genes_and_transcripts.xml +++ b/tools/data_source/encode_import_genes_and_transcripts.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/encode_import_multi-species_sequence_analysis.xml b/tools/data_source/encode_import_multi-species_sequence_analysis.xml index d6cbed08adf..982fc564d3b 100644 --- a/tools/data_source/encode_import_multi-species_sequence_analysis.xml +++ b/tools/data_source/encode_import_multi-species_sequence_analysis.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/encode_import_transcription_regulation.xml b/tools/data_source/encode_import_transcription_regulation.xml index 83dceedd494..26db457e369 100644 --- a/tools/data_source/encode_import_transcription_regulation.xml +++ b/tools/data_source/encode_import_transcription_regulation.xml @@ -6,13 +6,13 @@

hg16 (most recent datasets in bold)
$hg16

- + - + diff --git a/tools/data_source/microbial_import.xml b/tools/data_source/microbial_import.xml index 4dc76e95c54..9b67a4b7f74 100644 --- a/tools/data_source/microbial_import.xml +++ b/tools/data_source/microbial_import.xml @@ -6,7 +6,7 @@

Select the Desired Kingdom
$kingdom

- + @@ -14,9 +14,9 @@

Select the Desired Organism
$org

- - - + + + @@ -30,53 +30,53 @@

Select Desired Glimmer3 Annotations
$Glimmer3

- - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + - - - - - + + + + + diff --git a/tools/data_source/microbial_import_code.py b/tools/data_source/microbial_import_code.py index bbdd0b878a5..f5a211dd9be 100644 --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -1,7 +1,86 @@ +def load_microbial_data( sep='\t' ): + # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to + # set data.name in exec_after_process(). + microbe_info= {} + orgs = {} + for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( sep ) + #read each line, if not enough fields, go to next line + try: + info_type = fields.pop(0) + if info_type.upper() == "ORG": + #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=12521 + org_num = fields.pop(0) + name = fields.pop(0) + kingdom = fields.pop(0) + group = fields.pop(0) + chromosomes = fields.pop(0) + info_url = fields.pop(0) + link_site = fields.pop(0) + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'name' ] = name + orgs[ org_num ][ 'kingdom' ] = kingdom + orgs[ org_num ][ 'group' ] = group + orgs[ org_num ][ 'chromosomes' ] = chromosomes + orgs[ org_num ][ 'info_url' ] = info_url + orgs[ org_num ][ 'link_site' ] = link_site + elif info_type.upper() == "CHR": + #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 + org_num = fields.pop(0) + chr_acc = fields.pop(0) + name = fields.pop(0) + length = fields.pop(0) + gi = fields.pop(0) + gb = fields.pop(0) + info_url = fields.pop(0) + chr = {} + chr[ 'name' ] = name + chr[ 'length' ] = length + chr[ 'gi' ] = gi + chr[ 'gb' ] = gb + chr[ 'info_url' ] = info_url + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr + elif info_type.upper() == "DATA": + #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed + uid = fields.pop(0) + org_num = fields.pop(0) + chr_acc = fields.pop(0) + feature = fields.pop(0) + filetype = fields.pop(0) + path = fields.pop(0) + data = {} + data[ 'filetype' ] = filetype + data[ 'path' ] = path + data[ 'feature' ] = feature + + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data + else: continue + except: continue + for org_num in orgs: + org = orgs[ org_num ] + if org[ 'kingdom' ] not in microbe_info: + microbe_info[ org[ 'kingdom' ] ] = {} + if org_num not in microbe_info[ org[ 'kingdom' ] ]: + microbe_info[ org[ 'kingdom' ] ][org_num] = org + return microbe_info + #post processing, set build for data and add additional data to history from galaxy import datatypes, config, jobs from shutil import copyfile + def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): history = out_data.items()[0][1].history if history == None: @@ -15,6 +94,7 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr if not (kingdom or org): print "Parameters are not available." + microbe_info = load_microbial_data() new_stdout = "" split_stdout = stdout.split("\n") basic_name = "" diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml index e8d46194c12..55f3b5d6d2f 100644 --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -11,8 +11,10 @@ - - + + + + **Auto-detect** @@ -128,5 +130,4 @@ Any data in tab delimited format (tabular) Any text file - diff --git a/tools/data_source/upload_code.py b/tools/data_source/upload_code.py deleted file mode 100644 index 245ec44c92e..00000000000 --- a/tools/data_source/upload_code.py +++ /dev/null @@ -1,13 +0,0 @@ -from galaxy.datatypes import registry - -def get_formats(): - datatypes_registry = registry.Registry() - options = [] - formats = datatypes_registry.datatypes_by_extension.keys() - formats.sort() - - options.append(('Auto-detect','auto',True)) - for format in formats: - label = format.capitalize() - options.append((label,format,False)) - return options \ No newline at end of file diff --git a/tools/extract/interval2maf_pairwise.xml b/tools/extract/interval2maf_pairwise.xml index 38ca12c326f..0f0fb52dd9e 100644 --- a/tools/extract/interval2maf_pairwise.xml +++ b/tools/extract/interval2maf_pairwise.xml @@ -2,16 +2,26 @@ given a set of genomic intervals interval2maf_pairwise.py --dbkey=$dbkey --chromCol=$input1_chromCol --startCol=$input1_startCol --endCol=$input1_endCol --strandCol=$input1_strandCol --mafType=$mafType --interval_file=$input1 --output_file=$out_file1 - - - - - - + + + + + + + + + + + + + + + + **What it does** @@ -26,5 +36,4 @@ Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are t .. image:: ../static/images/maf_icons/interval2maf.png - diff --git a/tools/extract/interval2maf_pairwise_code.py b/tools/extract/interval2maf_pairwise_code.py deleted file mode 100644 index c02b3944e96..00000000000 --- a/tools/extract/interval2maf_pairwise_code.py +++ /dev/null @@ -1,46 +0,0 @@ -#build list of available data -import os, sys -maf_sets = {} - -try: - for line in open( "/depot/data2/galaxy/maf_pairwise.loc" ): - if line[0:1] == "#" : continue - - fields = line.split('\t') - #read each line, if not enough fields, go to next line - try: - maf_desc = fields[0] - maf_uid = fields[1] - builds = fields[2] - build_list =[] - split_builds = builds.split(",") - for build in split_builds: - this_build = build.split("=")[0] - build_list.append(this_build) - paths = fields[3].replace("\n","").replace("\r","") - maf_sets[maf_uid]={} - maf_sets[maf_uid]['description']=maf_desc - maf_sets[maf_uid]['builds']=build_list - except: - continue - -except Exception, exc: - print >>sys.stdout, 'interval2maf_pairwise_code.py initialization error -> %s' % exc - -#return available datasets for group and build, set None option as selected for hg16 -def get_available_data( build ): - available_sets = [] - for key in maf_sets: - if build in maf_sets[key]['builds']: - available_sets.append((maf_sets[key]['description'],key,False)) - if len(available_sets) < 1: - available_sets.append(('No data available for this build','None',True)) - return available_sets - - -def exec_before_job(app,inp_data, out_data, param_dict, tool): - for name, data in out_data.items(): - try: - data.name = data.name + " [" + maf_sets[param_dict['mafType']]['description'] + "]" - except KeyError: - data.name = data.name + " [unknown MAF source specified]" diff --git a/tools/extract/interval_maf_to_merged_fasta.xml b/tools/extract/interval_maf_to_merged_fasta.xml index e33ac1fc30b..1ebf27489fb 100644 --- a/tools/extract/interval_maf_to_merged_fasta.xml +++ b/tools/extract/interval_maf_to_merged_fasta.xml @@ -23,7 +23,7 @@ - + diff --git a/tools/filters/maf/maf_stats_code.py b/tools/filters/maf/maf_stats_code.py index 46ae78996fb..2a6c233d322 100644 --- a/tools/filters/maf/maf_stats_code.py +++ b/tools/filters/maf/maf_stats_code.py @@ -1,12 +1,37 @@ -def exec_before_job(app, inp_data, out_data, param_dict, tool): +def load_maf_data( sep='\t' ): + # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to + # set data.name in exec_before_job(). maf_sets = {} - if param_dict['maf_source_type']['maf_source'] == "cached": + for line in open( "/depot/data2/galaxy/maf_index.loc" ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( sep ) + #read each line, if not enough fields, go to next line + try: + maf_desc = fields[0] + maf_uid = fields[1] + builds = fields[2] + build_list =[] + split_builds = builds.split( "," ) + for build in split_builds: + this_build = build.split( "=" )[0] + build_list.append( this_build ) + paths = fields[3] + maf_sets[ maf_uid ] = {} + maf_sets[ maf_uid ][ 'description' ] = maf_desc + maf_sets[ maf_uid ][ 'builds' ] = build_list + except: + continue + return maf_sets +def exec_before_job(app, inp_data, out_data, param_dict, tool): + maf_sets = load_maf_data() + if param_dict[ 'maf_source_type' ][ 'maf_source' ] == "cached": for name, data in out_data.items(): try: - data.name = data.name + " [" + maf_sets[str(param_dict['maf_source_type']['mafType'])]['description'] + "]" + data.name = data.name + " [" + maf_sets[ str( param_dict[ 'maf_source_type' ][ 'mafType' ] ) ][ 'description' ] + "]" except KeyError: data.name = data.name + " [unknown MAF source specified]" - if param_dict['summary'].lower() == "true": + if param_dict[ 'summary' ].lower() == "true": for name, data in out_data.items(): - data.change_datatype('tabular') + data.change_datatype( 'tabular' ) diff --git a/tools/filters/maf/maf_thread_for_species.xml b/tools/filters/maf/maf_thread_for_species.xml index dc31122722b..3b39038156c 100644 --- a/tools/filters/maf/maf_thread_for_species.xml +++ b/tools/filters/maf/maf_thread_for_species.xml @@ -50,7 +50,6 @@ results in:: - - + diff --git a/tools/filters/maf/maf_thread_for_species_code.py b/tools/filters/maf/maf_thread_for_species_code.py deleted file mode 100644 index fe414c098ce..00000000000 --- a/tools/filters/maf/maf_thread_for_species_code.py +++ /dev/null @@ -1,38 +0,0 @@ -import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.align import maf -# No initialization required. - -#return lists of species available, showing gapped and ungapped base counts -def get_available_species( input_filename ): - try: - rval = [] - species={} - - file_in = open(input_filename, 'r') - try: - maf_reader = maf.Reader( file_in ) - - for i, m in enumerate( maf_reader ): - l = m.components - for c in l: - spec,chrom = maf.src_split( c.src ) - if not spec or not chrom: - spec = chrom = c.src - if spec not in species: - species[spec]={"bases":0,"nongaps":0} - species[spec]["bases"] = species[spec]["bases"] + c.size + c.text.count("-") - species[spec]["nongaps"] = species[spec]["nongaps"] + c.size - - file_in.close() - except: - return [("There is a problem with your MAF file",'None',True)] - species_names = species.keys() - species_names.sort() - - for spec in species_names: - display = "%s: %i nongap, %i total bases" % (spec, species[spec]["nongaps"], species[spec]["bases"] ) - rval.append( ( display,spec,True) ) - - return rval - except: - return [("You must wait for the MAF file to be created before you can merge MAF blocks by species.",'None',True)] diff --git a/tools/regVariation/windowSplitter.xml b/tools/regVariation/windowSplitter.xml index f9322a23ce8..60aa7a51024 100644 --- a/tools/regVariation/windowSplitter.xml +++ b/tools/regVariation/windowSplitter.xml @@ -2,7 +2,7 @@ windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l $input_chromCol,$input_startCol,$input_endCol,$input_strandCol - +