Allow rule based operations on existing collections.

client/galaxy/scripts/components/RulesDisplay.vue

@@ -0,0 +1,119 @@
+<template>
+    <div>
+        <ol class="rules">
+            <rule-display-preview
+              v-for="(rule, index) in rules"
+              v-bind:rule="rule"
+              v-bind:index="index"
+              v-bind:key="index"
+              :col-headers="columnData.colHeadersPerRule[index]" />
+            <identifier-display-preview v-for="(map, index) in mapping"
+                                        v-bind="map"
+                                        v-bind:index="index"
+                                        v-bind:key="map.type"
+                                        :col-headers="colHeaders" />
+        </ol>
+    </div>
+</template>
+<script>
+import RuleDefs from "mvc/rules/rule-definitions";
+import _l from "utils/localization";
+
+// read-only variants of the components for displaying these rules and mappings in builder widget.
+const RuleDisplayPreview = {
+    template: `
+        <li class="rule">
+            <span class="rule-display">{{ title }}
+            </span>
+            <span class="rule-warning" v-if="rule.warn">
+                {{ rule.warn }}
+            </span>
+            <span class="rule-error" v-if="rule.error">
+                <span class="alert-message">{{ rule.error }}</span>
+            </span>
+        </li>
+    `,
+    props: {
+        rule: {
+            required: true,
+            type: Object
+        },
+        colHeaders: {
+            type: Array,
+            required: false
+        }
+    },
+    computed: {
+        title() {
+            const ruleType = this.rule.type;
+            return RuleDefs.RULES[ruleType].display(this.rule, this.colHeaders);
+        }
+    },
+    methods: {}
+};
+
+const IdentifierDisplayPreview = {
+    template: `
+      <li class="rule" :title="help">
+        Set {{ columnsLabel }} as {{ typeDisplay }}
+      </li>
+    `,
+    props: {
+        type: {
+            type: String,
+            required: true
+        },
+        columns: {
+            required: true
+        },
+        colHeaders: {
+            type: Array,
+            required: true
+        }
+    },
+    computed: {
+        typeDisplay() {
+            return RuleDefs.MAPPING_TARGETS[this.type].label;
+        },
+        help() {
+            return RuleDefs.MAPPING_TARGETS[this.type].help || "";
+        },
+        columnsLabel() {
+            return RuleDefs.columnDisplay(this.columns, this.colHeaders);
+        }
+    }
+};
+
+export default {
+    data: function() {
+        return {};
+    },
+    computed: {
+        mapping: function() {
+            return this.inputRules ? this.inputRules.mapping : [];
+        },
+        rules: function() {
+            return this.inputRules ? this.inputRules.rules : [];
+        },
+        columnData: function() {
+            const colHeadersPerRule = [];
+            const hotData = RuleDefs.applyRules([], [], [], this.rules, colHeadersPerRule);
+            return { colHeadersPerRule: colHeadersPerRule, columns: hotData.columns };
+        },
+        colHeaders: function() {
+            const columns = this.columnData.columns;
+            return RuleDefs.colHeadersFor([], columns);
+        }
+    },
+    props: {
+        inputRules: {
+            required: false,
+            type: Object
+        }
+    },
+    components: {
+        RuleDisplayPreview,
+        IdentifierDisplayPreview
+    }
+};
+</script>

client/galaxy/scripts/mocha/tests/rules_tests.js

@@ -11,44 +11,29 @@ function applyRules(rules, data, sources) {
             columns.push("new");
         }
     }
-    for (var ruleIndex in rules) {
-        const rule = rules[ruleIndex];
-        rule.error = null;
-        rule.warn = null;
-
-        var ruleType = rule.type;
-        const ruleDef = RULES[ruleType];
-        const res = ruleDef.apply(rule, data, sources, columns);
-        if (res.error) {
-            throw res.error;
-        } else {
-            if (res.warn) {
-                rule.warn = res.warn;
-            }
-            data = res.data || data;
-            sources = res.sources || sources;
-            columns = res.columns || columns;
-        }
-    }
-    return { data, sources, columns };
+    return RuleDefs.applyRules(data, sources, columns, rules);
 }
 
 function itShouldConform(specTestCase, i) {
     it("should pass conformance test case " + i, function() {
         chai.assert.property(specTestCase, "rules");
-        chai.assert.property(specTestCase, "initial");
-        chai.assert.property(specTestCase, "final");
+        if (specTestCase.initial) {
+            chai.assert.property(specTestCase, "final");
 
-        const rules = specTestCase.rules;
-        const initial = specTestCase.initial;
-        const expectedFinal = specTestCase.final;
+            const rules = specTestCase.rules;
+            const initial = specTestCase.initial;
+            const expectedFinal = specTestCase.final;
 
-        const final = applyRules(rules, initial.data, initial.sources);
-        const finalData = final.data;
-        const finalSources = final.sources;
-        chai.assert.deepEqual(finalData, expectedFinal.data);
-        if (expectedFinal.sources !== undefined) {
-            chai.assert.deepEqual(finalSources, expectedFinal.sources);
+            const final = applyRules(rules, initial.data, initial.sources);
+            const finalData = final.data;
+            const finalSources = final.sources;
+            chai.assert.deepEqual(finalData, expectedFinal.data);
+            if (expectedFinal.sources !== undefined) {
+                chai.assert.deepEqual(finalSources, expectedFinal.sources);
+            }
+        } else {
+            chai.assert(specTestCase.error);
+            // TODO: test these...
         }
     });
 }

client/galaxy/scripts/mvc/collection/list-collection-creator.js

@@ -1069,6 +1069,8 @@ var ruleBasedCollectionCreatorModal = function _ruleBasedCollectionCreatorModal(
     let title;
     if (importType == "datasets") {
         title = _l("Build Rules for Uploading Datasets");
+    } else if (elementsType == "collection_contents") {
+        title = _l("Build Rules for Applying to Existing Collection");
     } else if (elementsType == "datasets" || elementsType == "library_datasets") {
         title = _l("Build Rules for Creating Collection(s)");
     } else {
@@ -1090,7 +1092,9 @@ var ruleBasedCollectionCreatorModal = function _ruleBasedCollectionCreatorModal(
             creationFn: options.creationFn,
             oncancel: options.oncancel,
             oncreate: options.oncreate,
-            defaultHideSourceItems: options.defaultHideSourceItems
+            defaultHideSourceItems: options.defaultHideSourceItems,
+            saveRulesFn: options.saveRulesFn,
+            initialRules: options.initialRules
         }
     }).$mount(vm);
     return deferred;
@@ -1128,7 +1132,8 @@ function createListCollection(contents, defaultHideSourceItems) {
 
 function createCollectionViaRules(selection, defaultHideSourceItems) {
     let elements, elementsType, importType;
-    if (!selection.selectionType) {
+    const selectionType = selection.selectionType;
+    if (!selectionType) {
         // Have HDAs from the history panel.
         elements = selection.toJSON();
         elementsType = "datasets";

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

@@ -85,11 +85,13 @@ export default Backbone.View.extend({
         // render visibility
         this.$el[this.model.get("hidden") ? "hide" : "show"]();
         // render preview view for collapsed fields
+        // allow at least newlines to render properly after escape
+        const html = _.escape(this.model.get("text_value")).replace(/\n/g, "<br />");
         this.$preview[
             (this.field.collapsed && this.model.get("collapsible_preview")) || this.model.get("disabled")
                 ? "show"
                 : "hide"
-        ]().html(_.escape(this.model.get("text_value")));
+        ]().html(html);
         // render error messages
         var error_text = this.model.get("error_text");
         this.$error[error_text ? "show" : "hide"]();
@@ -106,7 +108,14 @@ export default Backbone.View.extend({
                 style: this.model.get("style")
             });
         // render collapsible options
-        if (!this.model.get("disabled") && this.model.get("collapsible_value") !== undefined) {
+        const workflowRuntimeCompatible =
+            this.field.workflowRuntimeCompatible === undefined ? true : this.field.workflowRuntimeCompatible;
+        if (
+            workflowRuntimeCompatible &&
+            !this.model.get("disabled") &&
+            this.model.get("collapsible_value") !== undefined
+        ) {
+            console.log(this.field);
             var collapsible_state = this.field.collapsed ? "enable" : "disable";
             this.$title_text.hide();
             this.$collapsible.show();

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

@@ -7,6 +7,7 @@ import SelectContent from "mvc/ui/ui-select-content";
 import SelectLibrary from "mvc/ui/ui-select-library";
 import SelectFtp from "mvc/ui/ui-select-ftp";
 import SelectGenomeSpace from "mvc/ui/ui-select-genomespace";
+import RulesEdit from "mvc/ui/ui-rules-edit";
 import ColorPicker from "mvc/ui/ui-color-picker";
 // create form view
 export default Backbone.Model.extend({
@@ -30,6 +31,7 @@ export default Backbone.Model.extend({
         library_data: "_fieldLibrary",
         ftpfile: "_fieldFtp",
         upload: "_fieldUpload",
+        rules: "_fieldRulesEdit",
         genomespacefile: "_fieldGenomeSpace"
     },
 
@@ -215,13 +217,20 @@ export default Backbone.Model.extend({
     /** GenomeSpace file select field
      */
     _fieldGenomeSpace: function(input_def) {
-        var self = this;
         return new SelectGenomeSpace.View({
             id: `field-${input_def.id}`,
             onchange: input_def.onchange
         });
     },
 
+    _fieldRulesEdit: function(input_def) {
+        return new RulesEdit.View({
+            id: `field-${input_def.id}`,
+            onchange: input_def.onchange,
+            target: input_def.target
+        });
+    },
+
     /** Upload file field */
     _fieldUpload: function(input_def) {
         return new Ui.Upload({

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

@@ -25,10 +25,13 @@ export default Backbone.View.extend({
         var self = this;
         this.data.matchModel(new_model, (node, input_id) => {
             var input = self.input_list[input_id];
+            var field = self.field_list[input_id];
+            if (field.refreshDefinition) {
+                field.refreshDefinition(node);
+            }
             if (input && input.options) {
                 if (!_.isEqual(input.options, node.options)) {
                     input.options = node.options;
-                    var field = self.field_list[input_id];
                     if (field.update) {
                         var new_options = [];
                         if (["data", "data_collection", "drill_down"].indexOf(input.type) != -1) {