Merge branch 'release_19.01' into dev

lib/galaxy/model/__init__.py

@@ -3521,14 +3521,13 @@ class DatasetCollection(Dictifiable, UsesAnnotations, RepresentById):
         self.populated_state = DatasetCollection.populated_states.FAILED
         self.populated_state_message = message
 
-    def finalize(self):
+    def finalize(self, collection_type_description):
         # All jobs have written out their elements - everything should be populated
         # but might not be - check that second case! (TODO)
         self.mark_as_populated()
-        if self.has_subcollections:
-            # THIS IS WRONG - SHOULD ONLY BE TO THE DEPTH OF THE MAP OVER.
+        if self.has_subcollections and collection_type_description.has_subcollections():
             for element in self.elements:
-                element.child_collection.finalize()
+                element.child_collection.finalize(collection_type_description.child_collection_type_description())
 
     @property
     def dataset_instances(self):

lib/galaxy/tools/execute.py

@@ -314,7 +314,9 @@ class ExecutionTracker(object):
                     implicit_collection_jobs = implicit_collection.implicit_collection_jobs
                     implicit_collection_jobs.populated_state = "ok"
                     trans.sa_session.add(implicit_collection_jobs)
-                implicit_collection.collection.finalize()
+                implicit_collection.collection.finalize(
+                    collection_type_description=self.collection_info.structure.collection_type_description
+                )
                 trans.sa_session.add(implicit_collection.collection)
         trans.sa_session.flush()
 

lib/galaxy/tools/wrappers.py

@@ -108,7 +108,7 @@ class InputValueWrapper(ToolParameterValueWrapper):
         return getattr(self.value, key)
 
     def __int__(self):
-        return int(str(self))
+        return int(float(self))
 
     def __float__(self):
         return float(str(self))

test/api/test_workflows.py

@@ -1165,6 +1165,41 @@ steps:
             assert len(identifiers) == 6
             assert "oe1-ie1" in identifiers
 
+    @skip_without_tool("collection_paired_test")
+    def test_workflow_flatten_with_mapped_over_execution(self):
+        with self.dataset_populator.test_history() as history_id:
+            self._run_jobs(r"""
+class: GalaxyWorkflow
+inputs:
+  input_fastqs: collection
+steps:
+  split_up:
+    tool_id: collection_split_on_column
+    in:
+      input1: input_fastqs
+  flatten:
+    tool_id: '__FLATTEN__'
+    in:
+      input: split_up/split_output
+    join_identifier: '-'
+test_data:
+  input_fastqs:
+    type: list
+    elements:
+      - identifier: samp1
+        content: "0\n1"
+""", history_id=history_id)
+            history = self._get('histories/%s/contents' % history_id).json()
+            flattened_collection = history[-1]
+            assert flattened_collection['history_content_type'] == 'dataset_collection'
+            assert flattened_collection['collection_type'] == 'list'
+            assert flattened_collection['element_count'] == 2
+            nested_collection = self.dataset_populator.get_history_collection_details(history_id, hid=3)
+            assert nested_collection['collection_type'] == 'list:list'
+            assert nested_collection['element_count'] == 1
+            assert nested_collection['elements'][0]['object']['populated']
+            assert nested_collection['elements'][0]['object']['element_count'] == 2
+
     @skip_without_tool("__APPLY_RULES__")
     def test_workflow_run_apply_rules(self):
         with self.dataset_populator.test_history() as history_id:

test/functional/tools/cheetah_casting.xml

@@ -1,9 +1,11 @@
 <tool id="cheetah_casting" name="cheetah_casting" version="1.0.0">
     <command>
         #set $int_val_inc = int($inttest) + 1
+        #set $int_flot_val_inc = int($floattest) + 1
         #set $float_val_inc = float($floattest) + 1
-        echo $int_val_inc   >> $out_file1;
-        echo $float_val_inc >> $out_file1;
+        echo $int_val_inc   >> '$out_file1';
+        echo $int_flot_val_inc >> '$out_file1';
+        echo $float_val_inc >> '$out_file1';
     </command>
     <inputs>
         <param name="inttest" value="1" type="integer" />
@@ -19,6 +21,7 @@
             <output name="out_file1">
                 <assert_contents>
                     <has_line line="2" />
+                    <has_line line="3" />
                     <has_line line="3.5" />
                 </assert_contents>
             </output>