Hack in support for int parameters in Galaxy.

Author: jmchilton

lib/galaxy/tools/cwl/parser.py

@@ -600,7 +600,9 @@ def cwl_input_to_galaxy_step(self, input, i):
             input_as_dict["type"] = "data_collection_input"
             input_as_dict["collection_type"] = "record"
         else:
-            input_as_dict["type"] = "parameter_input"
+            # input_as_dict["type"] = "parameter_input"
+            input_as_dict["type"] = "data_input"
+            # TODO: format = expression.json
 
         return input_as_dict
 

lib/galaxy/workflow/modules.py

@@ -913,7 +913,7 @@ def from_cwl(value):
             as_cwl_value = do_eval(
                 value_from,
                 step_state,
-                [],
+                [{"class": "InlineJavascriptRequirement"}],
                 None,
                 None,
                 {},
@@ -1290,6 +1290,8 @@ def populate_module_and_state( trans, workflow, param_map, allow_tool_state_corr
     for step in workflow.steps:
         step_args = param_map.get( step.id, {} )
         step_errors = module_injector.inject( step, step_args=step_args )
+        # RESTRICT TO THIS JUST TO CONNECTIONS
+        step.upgrade_messages = []
         if step_errors:
             raise exceptions.MessageException( step_errors, err_data={ step.order_index: step_errors } )
         if step.upgrade_messages:

lib/galaxy/workflow/run.py

@@ -311,21 +311,23 @@ def replacement_for_tool_input( self, step, input, prefixed_name ):
                     input_collection_type = None
                     for i, c in enumerate(connection):
                         input_from_connection = self.replacement_for_connection( c, is_data=is_data )
-                        input_history_content_type = input_from_connection.history_content_type
-                        if i == 0:
-                            if input_history_content_type == "dataset_collection":
-                                input_collection_type = input_from_connection.collection.collection_type
+                        is_data = hasattr(input_from_connection, "history_content_type")
+                        if is_data:
+                            input_history_content_type = input_from_connection.history_content_type
+                            if i == 0:
+                                if input_history_content_type == "dataset_collection":
+                                    input_collection_type = input_from_connection.collection.collection_type
+                                else:
+                                    input_collection_type = None
                             else:
-                                input_collection_type = None
-                        else:
-                            if input_collection_type is None:
-                                if input_history_content_type != "dataset":
-                                    raise Exception("Cannot map over a combination of datasets and collections.")
-                            else:
-                                if input_history_content_type != "dataset_collection":
-                                    raise Exception("Cannot merge over combinations of datasets and collections.")
-                                elif input_from_connection.collection.collection_type != input_collection_type:
-                                    raise Exception("Cannot merge collections of different collection types.")
+                                if input_collection_type is None:
+                                    if input_history_content_type != "dataset":
+                                        raise Exception("Cannot map over a combination of datasets and collections.")
+                                else:
+                                    if input_history_content_type != "dataset_collection":
+                                        raise Exception("Cannot merge over combinations of datasets and collections.")
+                                    elif input_from_connection.collection.collection_type != input_collection_type:
+                                        raise Exception("Cannot merge collections of different collection types.")
 
                         inputs.append(input_from_connection)
 

test/api/test_workflows_cwl.py

@@ -137,6 +137,9 @@ def test_scatter_wf1_v1(self):
     def test_record_io(self):
         self.run_conformance_test("v1.0_custom", "Test record type inputs to and outputs from workflows.")
 
+    def test_workflow_int_io(self):
+        self.run_conformance_test("v1.0_custom", "Test integer workflow input and outputs")
+
     def _run_count_lines_wf(self, wf_path):
         workflow_id = self._load_workflow(wf_path)
         hda1 = self.dataset_populator.new_dataset(self.history_id, content="hello world\nhello all\nhello all in world\nhello")

test/base/populators.py

@@ -92,7 +92,7 @@ def replacement_item(value, force_to_file=False):
         if isinstance(value, list):
             return replacement_list(value)
         elif not isinstance(value, dict):
-            return value
+            return upload_object(value)
 
         if is_file:
             return replacement_file(value)

test/unit/tools/cwl_tools/v1.0_custom/conformance_tests.yaml

@@ -17,3 +17,8 @@
     }
   tool: v1.0_custom/record-output-wf.cwl
   doc: Test record type inputs to and outputs from workflows.
+
+- job: v1.0_custom/int-io-job.json
+  output: {"o": 10}
+  tool: v1.0_custom/int-io-wf.cwl
+  doc: Test integer workflow input and outputs

test/unit/tools/cwl_tools/v1.0_custom/int-io-job.json

@@ -0,0 +1 @@
+{"i": 5}

test/unit/tools/cwl_tools/v1.0_custom/int-io-wf.cwl

@@ -0,0 +1,31 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.0
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+inputs:
+  i:
+    type: int
+
+outputs:
+  o:
+    type: int
+    outputSource: step1/o
+
+steps:
+  step1:
+    in:
+      i: i
+    out: [o]
+    run:
+      class: ExpressionTool
+      inputs:
+        i:
+          type: int
+      outputs:
+        o:
+          type: int
+      expression: >
+        ${return {'o': inputs.i * 2};}