# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor james@jamestaylor.org # Date 1278614219 14400 # Node ID 2447b9a4dae30b17df089290a6471f3401fa5f78 # Parent e683c6995fb5d032660d1c28cff2e1bc578d1298 Make "loc files" more flexible by adding "tool data tables". These are configured at the application level. Specific tabular data files are specified in a application config file and bound to names, the tools then refer to these names. Thus users can configure where location files are located without modifying tool configs.

Also:

- Simpler column name configuration - Columns can be referred to by name in addition to index in all dynamic option filters - A data table can merge multiple files - Design can support other types of data files

--- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -46,9 +46,9 @@ class StaticValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.value = elem.get( "value", None ) assert self.value is not None, "Required 'value' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter, when loading from file" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter, when loading from file" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def filter_options( self, options, trans, other_values ): rval = [] @@ -81,11 +81,11 @@ class DataMetaFilter( Filter ): d_option.has_dataset_dependencies = True self.key = elem.get( "key", None ) assert self.key is not None, "Required 'key' attribute missing from filter" - self.column = elem.get( "column", None ) - if self.column is None: + column = elem.get( "column", None ) + if column is None: assert self.dynamic_option.file_fields is None and self.dynamic_option.dataset_ref_name is None, "Required 'column' attribute missing from filter, when loading from file" else: - self.column = int ( self.column ) + self.column = d_option.column_spec_to_index( column ) self.multiple = string_as_bool( elem.get( "multiple", "False" ) ) self.separator = elem.get( "separator", "," ) def get_dependency_name( self ): @@ -141,9 +141,9 @@ class ParamValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.ref_name = elem.get( "ref", None ) assert self.ref_name is not None, "Required 'ref' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def get_dependency_name( self ): return self.ref_name @@ -168,9 +168,9 @@ class UniqueValueFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def get_dependency_name( self ): return self.dynamic_option.dataset_ref_name def filter_options( self, options, trans, other_values ): @@ -196,9 +196,9 @@ class MultipleSplitterFilter( Filter ): def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) self.separator = elem.get( "separator", "," ) - self.columns = elem.get( "column", None ) - assert self.columns is not None, "Required 'columns' attribute missing from filter" - self.columns = [ int ( column ) for column in self.columns.split( "," ) ] + columns = elem.get( "column", None ) + assert columns is not None, "Required 'columns' attribute missing from filter" + self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] def filter_options( self, options, trans, other_values ): rval = [] for fields in options: @@ -302,9 +302,9 @@ class SortByColumnFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def filter_options( self, options, trans, other_values ): rval = [] for i, fields in enumerate( options ): @@ -354,20 +354,25 @@ class DynamicOptions( object ): data_file = elem.get( 'from_file', None ) dataset_file = elem.get( 'from_dataset', None ) from_parameter = elem.get( 'from_parameter', None ) - if data_file is not None or dataset_file is not None or from_parameter is not None: - for column_elem in elem.findall( 'column' ): - name = column_elem.get( 'name', None ) - assert name is not None, "Required 'name' attribute missing from column def" - index = column_elem.get( 'index', None ) - assert index is not None, "Required 'index' attribute missing from column def" - index = int( index ) - self.columns[name] = index - if index > self.largest_index: - self.largest_index = index - assert 'value' in self.columns, "Required 'value' column missing from column def" - if 'name' not in self.columns: - self.columns['name'] = self.columns['value'] + tool_data_table_name = elem.get( 'from_data_table', None ) + + # Options are defined from a data table loaded by the app + self.tool_data_table = None + if tool_data_table_name: + app = tool_param.tool.app + assert tool_data_table_name in app.tool_data_tables, \ + "Data table named '%s' is required by tool but not configured" % tool_data_table_name + self.tool_data_table = app.tool_data_tables[ tool_data_table_name ] + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns

+ # Options are defined by parsing tabular text data from an data file + # on disk, a dataset, or the value of another parameter + elif data_file is not None or dataset_file is not None or from_parameter is not None: + self.parse_column_definitions( elem ) if data_file is not None: data_file = data_file.strip() if not os.path.isabs( data_file ): @@ -388,6 +393,20 @@ class DynamicOptions( object ): # Load Validators for validator in elem.findall( 'validator' ): self.validators.append( validation.Validator.from_element( self.tool_param, validator ) ) + + def parse_column_definitions( self, elem ): + for column_elem in elem.findall( 'column' ): + name = column_elem.get( 'name', None ) + assert name is not None, "Required 'name' attribute missing from column def" + index = column_elem.get( 'index', None ) + assert index is not None, "Required 'index' attribute missing from column def" + index = int( index ) + self.columns[name] = index + if index > self.largest_index: + self.largest_index = index + assert 'value' in self.columns, "Required 'value' column missing from column def" + if 'name' not in self.columns: + self.columns['name'] = self.columns['value']

def parse_file_fields( self, reader ): rval = [] @@ -421,6 +440,8 @@ class DynamicOptions( object ): assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name if not dataset: return [] #no valid dataset in history options = self.parse_file_fields( open( dataset.file_name ) ) + elif self.tool_data_table: + options = self.tool_data_table.get_fields() else: options = list( self.file_fields ) for filter in self.filters: @@ -429,7 +450,7 @@ class DynamicOptions( object ):

def get_options( self, trans, other_values ): rval = [] - if self.file_fields is not None or self.dataset_ref_name is not None: + if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None: options = self.get_fields( trans, other_values ) for fields in options: rval.append( ( fields[self.columns['name']], fields[self.columns['value']], False ) ) @@ -437,3 +458,15 @@ class DynamicOptions( object ): for filter in self.filters: rval = filter.filter_options( rval, trans, other_values ) return rval + + def column_spec_to_index( self, column_spec ): + """ + Convert a column specification (as read from the config file), to an + index. A column specification can just be a number, a column name, or + a column alias. + """ + # Name? + if column_spec in self.columns: + return self.columns[column_spec] + # Int? + return int( column_spec )

--- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -192,10 +192,13 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_data_table="bowtie_indexes"/> + <!-- <options from_file="bowtie_indices.loc"><column name="value" index="1" /><column name="name" index="0" /></options> + --></param></when><when value="history">

--- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -231,13 +231,17 @@ def rst_to_html( s ): log.warn( str ) return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) )

-def xml_text(root, name): +def xml_text(root, name=None): """Returns the text inside an element""" - # Try attribute first - val = root.get(name) - if val: return val - # Then try as element - elem = root.find(name) + if name is not None: + # Try attribute first + val = root.get(name) + if val: + return val + # Then try as element + elem = root.find(name) + else: + elem = root if elem is not None and elem.text: text = ''.join(elem.text.splitlines()) return text.strip()

--- a/setup.sh +++ b/setup.sh @@ -7,6 +7,7 @@ SAMPLES=" datatypes_conf.xml.sample reports_wsgi.ini.sample tool_conf.xml.sample +tool_data_table_conf.xml.sample universe_wsgi.ini.sample tool-data/alignseq.loc.sample tool-data/annotation_profiler_options.xml.sample

--- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -34,10 +34,13 @@ </param><when value="indexed"><param name="indices" type="select" label="Select a reference genome"> + <options from_data_table="bwa_indexes"/> + <!-- <options from_file="bwa_index.loc"><column name="value" index="1" /><column name="name" index="0" /></options> + --></param></when><when value="history">

--- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys, os, atexit

from galaxy import config, jobs, util, tools, web import galaxy.tools.search +import galaxy.tools.data from galaxy.web import security import galaxy.model import galaxy.datatypes.registry @@ -36,6 +37,8 @@ class UniverseApplication( object ): self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = GalaxyTagHandler() + # Tool data tables + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) # Initialize the tools self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self ) # Search support for tools

--- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -48,6 +48,7 @@ class Configuration( object ): self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) + self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )

--- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -32,22 +32,24 @@ </when><when value="cached"><param name="mafType" type="select" label="Choose alignments"> - <options from_file="maf_index.loc"> + <options from_data_table="indexed_maf_files"> + <!-- <column name="name" index="0"/><column name="value" index="1"/><column name="dbkey" index="2"/><column name="species" index="3"/> - <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> + --> + <filter type="data_meta" ref="input1" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/></options></param><param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> - <options from_file="maf_index.loc"> + <options from_data_table="indexed_maf_files"><column name="uid" index="1"/><column name="value" index="3"/><column name="name" index="3"/> - <filter type="param_value" ref="mafType" name="uid" column="1"/> - <filter type="multiple_splitter" column="3" separator=","/> + <filter type="param_value" ref="mafType" column="uid"/> + <filter type="multiple_splitter" column="name" separator=","/></options></param></when>