Workflow replacement parameters polish.

- Selenium test case demonstrating their use in simple workflows.
- API test demonstrating they work with nested workflows from the run perspective.
- Update run variant of workflow to_dict to parse out replacement parameters to display on the backend and tweak the client to just accept these.
- Parse out replacement parameters for subworkflows recursively, include in new run output attribute - nested workflow replacement parameters work now.
- Selenium test case demosntrating subworkflow replacement parameters are rendered and used when submitted.

client/galaxy/scripts/mvc/tool/tool-form-composite.js

@@ -127,21 +127,24 @@ var View = Backbone.View.extend({
         // identify and configure workflow parameters
         var wp_count = 0;
         this.wp_inputs = {};
+
+        function _ensureWorkflowParameter(wp_name) {
+            return self.wp_inputs[wp_name] = self.wp_inputs[wp_name] || {
+                label: wp_name,
+                name: wp_name,
+                type: "text",
+                color: `hsl( ${++wp_count * 100}, 70%, 30% )`,
+                style: "ui-form-wp-source",
+                links: []
+            };
+        }
+
         function _handleWorkflowParameter(value, callback) {
             var re = /\$\{(.+?)\}/g;
             var match;
             while ((match = re.exec(String(value)))) {
                 var wp_name = match[1];
-                callback(
-                    (self.wp_inputs[wp_name] = self.wp_inputs[wp_name] || {
-                        label: wp_name,
-                        name: wp_name,
-                        type: "text",
-                        color: `hsl( ${++wp_count * 100}, 70%, 30% )`,
-                        style: "ui-form-wp-source",
-                        links: []
-                    })
-                );
+                callback(_ensureWorkflowParameter(wp_name));
             }
         }
         _.each(this.steps, (step, i) => {
@@ -154,10 +157,8 @@ var View = Backbone.View.extend({
                     input.style = "ui-form-wp-target";
                 });
             });
-            _.each(step.post_job_actions, pja => {
-                _.each(pja.action_arguments, arg => {
-                    _handleWorkflowParameter(arg, () => {});
-                });
+            _.each(step.replacement_parameters, wp_name => {
+                _ensureWorkflowParameter(wp_name);
             });
         });
 

lib/galaxy/managers/workflows.py

@@ -444,6 +444,7 @@ class WorkflowContentsManager(UsesAnnotations):
                 step_model = {
                     'inputs' : [input.to_dict(trans) for input in inputs.values()]
                 }
+            step_model['replacement_parameters'] = step.module.get_replacement_parameters(step)
             step_model['step_type'] = step.type
             step_model['step_label'] = step.label
             step_model['step_name'] = step.module.get_name()

lib/galaxy/workflow/modules.py

@@ -2,6 +2,7 @@
 Modules used in building workflows
 """
 import logging
+import re
 from json import loads
 from xml.etree.ElementTree import (
     Element,
@@ -259,6 +260,11 @@ class WorkflowModule(object):
 
         progress.set_step_outputs(invocation_step, outputs, already_persisted=True)
 
+    def get_replacement_parameters(self, step):
+        """Return a list of replacement parameters."""
+
+        return []
+
 
 class SubWorkflowModule(WorkflowModule):
     # Two step improvements to build runtime inputs for subworkflow modules
@@ -403,6 +409,16 @@ class SubWorkflowModule(WorkflowModule):
 
         return inputs
 
+    def get_replacement_parameters(self, step):
+        """Return a list of replacement parameters."""
+        replacement_parameters = set()
+        for subworkflow_step in self.subworkflow.steps:
+            module = subworkflow_step.module
+            for replacement_parameter in module.get_replacement_parameters(subworkflow_step):
+                replacement_parameters.add(replacement_parameter)
+
+        return list(replacement_parameters)
+
 
 class InputProxy(object):
     """Provide InputParameter-interfaces over inputs but renamed for workflow context."""
@@ -1088,6 +1104,16 @@ class ToolModule(WorkflowModule):
             action_arguments = None
         return PostJobAction(value['action_type'], step, output_name, action_arguments)
 
+    def get_replacement_parameters(self, step):
+        """Return a list of replacement parameters."""
+        replacement_parameters = set()
+        for pja in step.post_job_actions:
+            for argument in pja.action_arguments.values():
+                for match in re.findall(r'\$\{(.+?)\}', argument):
+                    replacement_parameters.add(match)
+
+        return list(replacement_parameters)
+
 
 class WorkflowModuleFactory(object):
 

test/api/test_workflows.py

@@ -20,8 +20,10 @@ from base.populators import (  # noqa: I100
     WorkflowPopulator
 )
 from base.workflow_fixtures import (  # noqa: I100
+    WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
     WORKFLOW_NESTED_RUNTIME_PARAMETER,
     WORKFLOW_NESTED_SIMPLE,
+    WORKFLOW_RENAME_ON_INPUT,
     WORKFLOW_RUNTIME_PARAMETER_AFTER_PAUSE,
     WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
     WORKFLOW_WITH_OUTPUT_COLLECTION,
@@ -224,6 +226,7 @@ class BaseWorkflowsApiTestCase(api.ApiTestCase):
 
         test_data = jobs_descriptions.get("test_data", {})
         parameters = test_data.pop('step_parameters', {})
+        replacement_parameters = test_data.pop("replacement_parameters", {})
         inputs, label_map, has_uploads = load_data_dict(history_id, test_data, self.dataset_populator, self.dataset_collection_populator)
         workflow_request = dict(
             history="hist_id=%s" % history_id,
@@ -234,6 +237,8 @@ class BaseWorkflowsApiTestCase(api.ApiTestCase):
         if parameters:
             workflow_request["parameters"] = dumps(parameters)
             workflow_request["parameters_normalized"] = True
+        if replacement_parameters:
+            workflow_request["replacement_params"] = dumps(replacement_parameters)
         if has_uploads:
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
         url = "workflows/%s/usage" % (workflow_id)
@@ -980,6 +985,23 @@ test_data:
             content = self.dataset_populator.get_history_dataset_content(history_id)
             assert len([x for x in content.split("\n") if x]) == 2
 
+    @skip_without_tool("cat")
+    def test_run_subworkflow_replacment_parameters(self):
+        with self.dataset_populator.test_history() as history_id:
+            workflow_run_description = """%s
+
+test_data:
+  replacement_parameters:
+    replaceme: moocow
+  outer_input:
+    value: 1.bed
+    type: File
+""" % WORKFLOW_NESTED_REPLACEMENT_PARAMETER
+            self._run_jobs(workflow_run_description, history_id=history_id)
+
+            details = self.dataset_populator.get_history_dataset_details(history_id)
+            assert details["name"] == "moocow suffix"
+
     @skip_without_tool("random_lines1")
     def test_run_runtime_parameters_after_pause(self):
         with self.dataset_populator.test_history() as history_id:
@@ -2247,25 +2269,7 @@ test_data: {}
     @skip_without_tool("cat")
     def test_run_rename_based_on_input(self):
         with self.dataset_populator.test_history() as history_id:
-            self._run_jobs("""
-class: GalaxyWorkflow
-inputs:
-  - id: input1
-steps:
-  - tool_id: cat
-    label: first_cat
-    state:
-      input1:
-        $link: input1
-    outputs:
-      out_file1:
-        rename: "#{input1 | basename} suffix"
-test_data:
-  input1:
-    value: 1.fasta
-    type: File
-    name: fasta1
-""", history_id=history_id)
+            self._run_jobs(WORKFLOW_RENAME_ON_INPUT, history_id=history_id)
             content = self.dataset_populator.get_history_dataset_details(history_id, wait=True, assert_ok=True)
             name = content["name"]
             assert name == "fasta1 suffix", name

test/base/workflow_fixtures.py

@@ -319,3 +319,67 @@ steps:
         seed_source_selector: set_seed
         seed: asdf
 """
+
+WORKFLOW_RENAME_ON_INPUT = """
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        rename: "#{input1 | basename} suffix"
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+"""
+
+WORKFLOW_RENAME_ON_REPLACEMENT_PARAM = """
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        rename: "${replaceme} suffix"
+"""
+
+WORKFLOW_NESTED_REPLACEMENT_PARAMETER = """
+class: GalaxyWorkflow
+inputs:
+  - id: outer_input
+outputs:
+  - id: outer_output
+    source: nested_workflow#workflow_output
+steps:
+  - run:
+      class: GalaxyWorkflow
+      inputs:
+        - id: inner_input
+      outputs:
+        - id: workflow_output
+          source: first_cat#out_file1
+      steps:
+        - tool_id: cat
+          label: first_cat
+          state:
+            input1:
+              $link: inner_input
+          outputs:
+            out_file1:
+              rename: "${replaceme} suffix"
+    label: nested_workflow
+    connect:
+      inner_input: outer_input
+"""

test/selenium_tests/test_workflow_run.py

@@ -2,8 +2,10 @@ import yaml
 from base import rules_test_data
 from base.populators import load_data_dict
 from base.workflow_fixtures import (
+    WORKFLOW_NESTED_REPLACEMENT_PARAMETER,
     WORKFLOW_NESTED_RUNTIME_PARAMETER,
     WORKFLOW_NESTED_SIMPLE,
+    WORKFLOW_RENAME_ON_REPLACEMENT_PARAM,
     WORKFLOW_RUNTIME_PARAMETER_SIMPLE,
     WORKFLOW_SIMPLE_CAT_TWICE,
     WORKFLOW_WITH_DYNAMIC_OUTPUT_COLLECTION,
@@ -78,6 +80,38 @@ class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
 
         self._assert_has_3_lines_after_run(hid=2)
 
+    @selenium_test
+    @managed_history
+    def test_replacement_parameters(self):
+        self.perform_upload(self.get_filename("1.txt"))
+        self.wait_for_history()
+        self.open_in_workflow_run(WORKFLOW_RENAME_ON_REPLACEMENT_PARAM)
+        self.screenshot("workflow_run_rename_simple_empty")
+        self._set_replacement_parameter("replaceme", "moocow")
+        self.screenshot("workflow_run_rename_simple_input")
+        self.workflow_run_submit()
+        output_hid = 2
+        self.history_panel_wait_for_hid_ok(output_hid, allowed_force_refreshes=1)
+        history_id = self.current_history_id()
+        details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
+        assert details["name"] == "moocow suffix", details
+
+    @selenium_test
+    @managed_history
+    def test_replacement_parameters_on_subworkflows(self):
+        self.perform_upload(self.get_filename("1.txt"))
+        self.wait_for_history()
+        self.open_in_workflow_run(WORKFLOW_NESTED_REPLACEMENT_PARAMETER)
+        self.screenshot("workflow_run_rename_subworkflow_empty")
+        self._set_replacement_parameter("replaceme", "moocow")
+        self.screenshot("workflow_run_rename_subworkflow_input")
+        self.workflow_run_submit()
+        output_hid = 2
+        self.history_panel_wait_for_hid_ok(output_hid, allowed_force_refreshes=1)
+        history_id = self.current_history_id()
+        details = self.dataset_populator.get_history_dataset_details(history_id, hid=output_hid)
+        assert details["name"] == "moocow suffix", details
+
     @selenium_test
     def test_execution_with_tool_upgrade(self):
         name = self.workflow_upload_yaml_with_random_name(WORKFLOW_WITH_OLD_TOOL_VERSION, exact_tools=True)
@@ -148,3 +182,12 @@ class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
         assert initial_value == "1", initial_value
         input_element.clear()
         input_element.send_keys("3")
+
+    def _set_replacement_parameter(self, tour_id, value):
+        # for random_lines num_lines parameter as runtime parameter in workflow form.
+        div = self.tool_parameter_div(tour_id)
+        input_element = div.find_element_by_css_selector("input")
+        initial_value = input_element.get_attribute("value")
+        assert initial_value == "", initial_value
+        input_element.clear()
+        input_element.send_keys(value)