Merge pull request #1808 from jmchilton/empty_dataset

Implement dataset empty input validator.

lib/galaxy/tools/parameters/validation.py

@@ -229,6 +229,23 @@ class DatasetOkValidator( Validator ):
             raise ValueError( self.message )
 
 
+class DatasetEmptyValidator( Validator ):
+    """Validator that checks if a dataset has a positive file size."""
+    def __init__( self, message=None ):
+        self.message = message
+
+    @classmethod
+    def from_element( cls, param, elem ):
+        return cls( elem.get( 'message', None ) )
+
+    def validate( self, value, trans=None ):
+        if value:
+            if value.get_size() == 0:
+                if self.message is None:
+                    self.message = "The selected dataset is empty, this tool expects non-empty files."
+                raise ValueError( self.message )
+
+
 class MetadataValidator( Validator ):
     """
     Validator that checks for missing metadata
@@ -416,9 +433,10 @@ validator_types = dict( expression=ExpressionValidator,
                         unspecified_build=UnspecifiedBuildValidator,
                         no_options=NoOptionsValidator,
                         empty_field=EmptyTextfieldValidator,
+                        empty_dataset=DatasetEmptyValidator,
                         dataset_metadata_in_file=MetadataInFileColumnValidator,
                         dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
-                        dataset_ok_validator=DatasetOkValidator )
+                        dataset_ok_validator=DatasetOkValidator, )
 
 
 def get_suite():

test/api/test_tools.py

@@ -237,6 +237,20 @@ class ToolsTestCase( api.ApiTestCase ):
         response = self._run( "validation_default", history_id, inputs )
         self._assert_status_code_is( response, 400 )
 
+    @skip_without_tool( "validation_empty_dataset" )
+    def test_validation_empty_dataset( self ):
+        history_id = self.dataset_populator.new_history()
+        inputs = {
+        }
+        outputs = self._run_and_get_outputs( 'empty_output', history_id, inputs )
+        empty_dataset = outputs[0]
+        inputs = {
+            'input1': dataset_to_param(empty_dataset),
+        }
+        self.dataset_populator.wait_for_history( history_id, assert_ok=True )
+        response = self._run( "validation_empty_dataset", history_id, inputs )
+        self._assert_status_code_is( response, 400 )
+
     @skip_without_tool( "validation_repeat" )
     def test_validation_in_repeat( self ):
         history_id = self.dataset_populator.new_history()

test/functional/tools/empty_output.xml

@@ -0,0 +1,12 @@
+<tool id="empty_output" name="empty_output" version="1.0.0">
+    <command>
+        touch $out_file1;
+    </command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+    <tests>
+    </tests>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -55,6 +55,8 @@
   <tool file="validation_default.xml" />
   <tool file="validation_sanitizer.xml" />
   <tool file="validation_repeat.xml" />
+  <tool file="empty_output.xml" />
+  <tool file="validation_empty_dataset.xml" />
   <tool file="identifier_single.xml" />
   <tool file="identifier_multiple.xml" />
   <tool file="tool_directory.xml" />

test/functional/tools/validation_empty_dataset.xml

@@ -0,0 +1,17 @@
+<tool id="validation_empty_dataset" name="validation_empty_dataset">
+  <command>
+    echo "Hello World" > out1;
+  </command>
+  <inputs>
+    <param name="input1" type="data" label="non-empty input">
+      <validator type="empty_dataset" />
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" from_work_dir="out1" />
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+  </help>
+</tool>