Merged in abretaud/galaxy-central (pull request #577)

Add an API to remove items from tool data tables

lib/galaxy/tools/data/__init__.py

@@ -211,6 +211,13 @@ class ToolDataTable( object ):
                 self.add_entry( entry, allow_duplicates=allow_duplicates, persist=persist, persist_on_error=persist_on_error, entry_source=entry_source, **kwd )
         return self._loaded_content_version
 
+    def _remove_entry(self, values):
+        raise NotImplementedError( "Abstract method" )
+
+    def remove_entry(self, values):
+        self._remove_entry( values )
+        return self._update_version()
+
     def is_current_version( self, other_version ):
         return self._loaded_content_version == other_version
 
@@ -506,6 +513,42 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
                 data_table_fh.write( "%s\n" % ( self.separator.join( fields ) ) )
         return not is_error
 
+    def _remove_entry( self, values):
+
+        # update every file
+        for filename in self.filenames:
+
+            if os.path.exists( filename ):
+                values = self._replace_field_separators( values )
+                self.filter_file_fields( filename, values )
+            else:
+                log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) )
+        
+        self.reload_from_files()
+
+    def filter_file_fields( self, loc_file, values ):
+        """
+        Reads separated lines from file and print back only the lines that pass a filter.
+        """
+        separator_char = (lambda c: '<TAB>' if c == '\t' else c)(self.separator)
+
+        with open(loc_file) as reader:
+            rval = ""
+            for i, line in enumerate( reader ):
+                if line.lstrip().startswith( self.comment_char ):
+                    rval += line
+                else:
+                    line_s = line.rstrip( "\n\r" )
+                    if line_s:
+                        fields = line_s.split( self.separator )
+                        if fields != values:
+                            rval += line
+        
+        with open(loc_file, 'wb') as writer:
+            writer.write(rval)
+        
+        return rval
+
     def _replace_field_separators( self, fields, separator=None, replace=None, comment_char=None ):
         #make sure none of the fields contain separator
         #make sure separator replace is different from comment_char,

lib/galaxy/webapps/galaxy/api/tool_data.py

@@ -20,3 +20,44 @@ class ToolData( BaseAPIController ):
     @web.expose_api
     def show( self, trans, id, **kwds ):
         return trans.app.tool_data_tables.data_tables[id].to_dict(view='element')
+
+    @web.require_admin
+    @web.expose_api
+    def delete( self, trans, id, **kwd ):
+        """
+        DELETE /api/tool_data/{id}
+        Removes an item from a data table
+
+        :type   id:     str
+        :param  id:     the id of the data table containing the item to delete
+        :type   kwd:    dict
+        :param  kwd:    (required) dictionary structure containing:
+
+            * payload:     a dictionary itself containing:
+                * values:   <TAB> separated list of column contents, there must be a value for all the columns of the data table
+        """
+        decoded_tool_data_id = id
+        
+        try:
+            data_table = trans.app.tool_data_tables.data_tables.get(decoded_tool_data_id)
+        except:
+            data_table = None
+        if not data_table:
+            trans.response.status = 400
+            return "Invalid data table id ( %s ) specified." % str( decoded_tool_data_id )
+        
+        values = None
+        if kwd.get( 'payload', None ):
+            values = kwd['payload'].get( 'values', '' )
+
+        if not values:
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified." % str( values )
+        
+        split_values = values.split("\t")
+        
+        if len(split_values) != len(data_table.get_column_name_list()):
+            trans.response.status = 400
+            return "Invalid data table item ( %s ) specified. Wrong number of columns (%s given, %s required)." % ( str( values ), str(len(split_values)), str(len(data_table.get_column_name_list())))
+
+        return data_table.remove_entry(split_values)