Allow specification of multiple data manager configuration files...

... use this to create API functional tests for data managers.

lib/galaxy/tools/data_manager/manager.py

@@ -25,7 +25,10 @@ class DataManagers( object ):
         self.managed_data_tables = odict()
         self.tool_path = None
         self.filename = xml_filename or self.app.config.data_manager_config_file
-        self.load_from_xml( self.filename )
+        for filename in util.listify( self.filename ):
+            if not filename:
+                continue
+            self.load_from_xml( filename )
         if self.app.config.shed_data_manager_config_file:
             self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True )
 

scripts/functional_tests.py

@@ -241,6 +241,12 @@ def main():
             if os.path.exists( tool_data_config ):
                 default_tool_data_config = tool_data_config
         tool_data_table_config_path = '%s,test/functional/tool-data/sample_tool_data_tables.xml' % default_tool_data_config
+
+    default_data_manager_config = 'config/data_manager_conf.xml.sample'
+    for data_manager_config in ['config/data_manager_conf.xml', 'data_manager_conf.xml' ]:
+        if os.path.exists( data_manager_config ):
+            default_data_manager_config = data_manager_config
+    data_manager_config_file = "%s,test/functional/tools/sample_data_manager_conf.xml" % default_data_manager_config
     shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml'
     tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None )
     use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False )
@@ -329,6 +335,7 @@ def main():
                        master_api_key=master_api_key,
                        use_tasked_jobs=True,
                        enable_beta_tool_formats=True,
+                       data_manager_config_file=data_manager_config_file,
         )
         if install_database_connection is not None:
             kwargs[ 'install_database_connection' ] = install_database_connection

test/api/test_tool_data.py

@@ -1,6 +1,9 @@
 """ Tests for the tool data API.
 """
+import json
+
 from base import api
+from .helpers import DatasetPopulator
 
 import operator
 
@@ -42,3 +45,19 @@ class ToolDataApiTestCase( api.ApiTestCase ):
         self._assert_status_code_is( show_field_response, 200 )
         content = show_field_response.content
         assert content == "This is data 1.", content
+
+    def test_create_data_with_manager(self):
+        dataset_populator = DatasetPopulator( self.galaxy_interactor )
+        history_id = dataset_populator.new_history()
+        payload = dataset_populator.run_tool_payload(
+            tool_id="data_manager",
+            inputs={"ignored_value": "moo"},
+            history_id=history_id,
+        )
+        create_response = self._post( "tools", data=payload )
+        self._assert_status_code_is( create_response, 200 )
+        dataset_populator.wait_for_history( history_id, assert_ok=True )
+        show_response = self._get( "tool_data/testbeta", admin=True )
+        print show_response.content
+        assert False
+

test/functional/tool-data/sample_tool_data_tables.xml

@@ -3,10 +3,8 @@
     <columns>value, name, path</columns>
     <file path="${__HERE__}/testalpha.loc" />
   </table>
-  <!--
   <table name="testbeta" comment_char="#">
-    <columns>value, foo, bar, path</columns>
+    <columns>value, path</columns>
     <file path="${__HERE__}/testbeta.loc" />
   </table>
-  -->
 </tables>

test/functional/tools/data_manager.xml

@@ -0,0 +1,16 @@
+<tool id="data_manager" name="Test Data Manager" tool_type="manage_data" version="0.0.1">
+    <configfiles>
+        <configfile name="static_test_data">{"data_tables": {"testbeta": [{"value": "newvalue", "path": "newvalue.txt"}]}}</configfile>
+    </configfiles>
+    <command>
+        mkdir $out_file.files_path ;
+        echo "A new value" > $out_file.files_path/newvalue.txt;
+        cp $static_test_data $out_file
+    </command>
+    <inputs>
+        <param type="text" name="ignored_value" value="" label="Ignored" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>    
+</tool>

test/functional/tools/sample_data_manager_conf.xml

@@ -0,0 +1,16 @@
+<data_managers tool_path="test/functional/tools">
+  <data_manager tool_file="data_manager.xml" id="test_data_manager" version="1.0">
+    <data_table name="testbeta">
+      <output>
+        <column name="value" />
+        <column name="path" output_ref="out_file" >
+		  <move type="directory" relativize_symlinks="True">
+		  	<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">testbeta/${value}</target>
+		  </move>
+ 		  <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/testbeta/${value}/${path}</value_translation>
+		  <value_translation type="function">abspath</value_translation>
+		</column>
+      </output>
+    </data_table>
+  </data_manager>
+</data_managers>