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

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

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" ) )

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 )

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()

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

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>

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">

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">