WIP: implement field parameter type for CWL.

Author: jmchilton

client/galaxy/scripts/mvc/form/form-parameters.js

@@ -4,6 +4,7 @@
 import { getGalaxyInstance } from "app";
 import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
+import UiField from "mvc/ui/ui-field";
 import SelectContent from "mvc/ui/ui-select-content";
 import SelectLibrary from "mvc/ui/ui-select-library";
 import SelectFtp from "mvc/ui/ui-select-ftp";
@@ -34,6 +35,7 @@ export default Backbone.Model.extend({
         ftpfile: "_fieldFtp",
         upload: "_fieldUpload",
         rules: "_fieldRulesEdit",
+        field: "_fieldField",
         genomespacefile: "_fieldGenomeSpace"
     },
 
@@ -233,5 +235,13 @@ export default Backbone.Model.extend({
             id: `field-${input_def.id}`,
             onchange: input_def.onchange
         });
+    },
+
+    _fieldField: function(input_def) {
+        return new UiField({
+            id: `field-${input_def.id}`,
+            onchange: input_def.onchange
+        });
     }
+
 });

client/galaxy/scripts/mvc/ui/ui-field.js

@@ -0,0 +1,96 @@
+/** Renders the color picker used e.g. in the tool form **/
+import Utils from "utils/utils";
+import Ui from "mvc/ui/ui-misc";
+
+/** Renders an input element used e.g. in the tool form */
+export default Backbone.View.extend({
+    initialize: function(options) {
+        this.model =
+            (options && options.model) ||
+            new Backbone.Model({
+                value: {"src": "json", "value": null, "representation": "null"},
+            }).set(options);
+        this.$el = $("<div><p>moo cow</p></div>").addClass("ui-field");
+        console.log(this.model.get("value"));
+        var menuButton = new Ui.ButtonMenu({
+            id: "options",
+            icon: "fa-caret-down",
+            title: "Input Type",
+            tooltip: "View available input type options"
+        });
+        menuButton.addMenu({
+            title: "Integer",
+            onclick: () => {
+                this._changeType("integer")
+            }
+        });
+        menuButton.addMenu({
+            title: "Leave Unselected",
+            onclick: () => {
+                this._changeType("null")
+            }
+        });
+        this.$menuButton = menuButton;
+        this.$inputDiv = $("<div/>").addClass("select-input");
+
+        this.$el.append(menuButton.$el);
+        this.$el.append(this.$inputDiv);
+        this.setElement(this.$el);
+        this.listenTo(this.model, "change", this.render, this);
+        this.render();
+    },
+    value: function(new_val) {
+        var options = this.model.attributes;
+        if (new_val) {
+            this.model.set("value", new_val);
+            this.model.trigger("change");
+            options.onchange(new_val);
+        }
+        return this.model.get("value");
+    },
+    render: function() {
+        const value = this.model.get("value");
+        const rep = value.representation;
+        if ( rep == "null" ) {
+            this.$inputDiv.html($("<p>No value selected (null)</p>"));
+        } else if ( rep == "integer" ) {
+            const tagName = this.model.get("area") ? "textarea" : "input";
+            this.$inputDiv.html($(`<${tagName} value="${value.value}"/>`));
+            console.log(this.$inputDiv.find("input"));
+            this.$inputDiv.find("input").on("change", () => { this._onchange() });
+        }
+        return this;
+    },
+    _changeType: function(representation) {
+        const previousValue = this.model.get("value");
+        const previousRawValue = previousValue.value;
+        if ( representation == "null" ) {
+            this.model.set("value", {"src": "json", "value": null, "representation": "null"});
+        } else if ( representation == "integer" ) {
+            var value = parseInt(previousRawValue);
+            if ( isNaN( value ) ) {
+                value = 0;
+            }
+            this.model.set("value", {"src": "json", "value": 0, "representation": "integer"});
+        }
+    },
+    _rawValue: function(previousValue) {
+        const rep = previousValue.representation;
+        let rawVal;
+        if ( rep == "null" ) {
+            rawVal = null;
+        } else if ( rep == "integer" ) {
+            rawVal = parseInt(this.$inputDiv.find("input").val());
+        }
+        console.log("_rawValue returning " + rawVal);
+        return rawVal;
+
+    },
+    _onchange: function() {
+        const previousValue = this.model.get("value");
+        const newValue = this._rawValue(previousValue);
+        previousValue["value"] = newValue;
+        this.value(previousValue);
+        this.model.get("onchange") && this.model.get("onchange")(this.model.get("value"));
+    }
+});

lib/galaxy/workflow/run_request.py

@@ -277,13 +277,17 @@ def build_workflow_run_configs(trans, workflow, payload):
                 if step.type == "parameter_input":
                     if normalized_key in param_map:
                         value = param_map.pop(normalized_key)
-                        normalized_inputs[normalized_key] = value["input"]
+                        input_value = value["input"]
+                        if isinstance(input_value, dict) and input_value.get("src") == "json":
+                            input_value = input_value.get("value")
+                        normalized_inputs[normalized_key] = input_value
+
 
         steps_by_id = workflow.steps_by_id
         # Set workflow inputs.
         for key, input_dict in normalized_inputs.items():
             step = steps_by_id[key]
-            if step.type == 'parameter_input' and (step.tool_inputs["parameter_type"] != "field" or not isinstance(input_dict, dict)):
+            if step.type == 'parameter_input' and (step.tool_inputs["parameter_type"] != "field" or not isinstance(input_dict, dict) or "id" not in input_dict):
                 continue
             if 'src' not in input_dict:
                 raise exceptions.RequestParameterInvalidException("Not input source type defined for input '%s'." % input_dict)