From 0a3682804f9acf39cff12826eea04905a211e45d Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Tue, 24 Apr 2018 11:01:55 -0400
Subject: [PATCH 1/3] Revert "Fix links in rule builder to not interfere with
 the library router."

This reverts commit d4a890f2fc46c4dd82a77e3a5772546d88a6b95d.
---
 .../scripts/components/RuleCollectionBuilder.vue     | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index dcf3ebd682db..589446199449 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -204,6 +204,7 @@
                                         v-bind:index="target"
                                         v-bind:key="target"
                                         class="dropdown-item"
+                                        href="#"
                                         :class="'rule-add-mapping-' + target.replace(/_/g, '-')"
                                         @click="addIdentifier(target)">
                                       {{ mappingTargets()[target].label }}
@@ -240,7 +241,7 @@
                                                     v-on:mouseout.native="map.columns.forEach((col) => unhighlightColumn(col))"
                                                     :col-headers="colHeaders" />
                                 <div v-if="mapping.length == 0">
-                                    One or more column definitions must be specified. These are required to specify how to build collections and datasets from rows and columns of the table. <a class="force-link-style" @click="displayRuleType = 'mapping'">Click here</a> to manage column definitions.
+                                    One or more column definitions must be specified. These are required to specify how to build collections and datasets from rows and columns of the table. <a href="#" @click="displayRuleType = 'mapping'">Click here</a> to manage column definitions.
                                 </div>
                             </ol>
                             <div class="rules-buttons">
@@ -253,7 +254,7 @@
                                     <rule-target-component :builder="this" rule-type="remove_columns" />
                                     <rule-target-component :builder="this" rule-type="split_columns" />
                                     <rule-target-component :builder="this" rule-type="swap_columns" />
-                                    <a class="dropdown-item rule-link rule-link-mapping" @click="displayRuleType = 'mapping'">Add / Modify Column Definitions</a>
+                                    <a href="#" class="dropdown-item rule-link rule-link-mapping" @click="displayRuleType = 'mapping'">Add / Modify Column Definitions</a>
                                   </div>
                                 </div>
                                 <div class="btn-group dropup">
@@ -707,7 +708,7 @@ const IdentifierDisplay = {
 };
 
 const RuleTargetComponent = {
-    template: `<a class="rule-link dropdown-item" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
+    template: `<a class="rule-link dropdown-item" href="#" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
     props: {
         ruleType: {
             type: String,
@@ -1784,9 +1785,4 @@ export default {
 .fa-wrench {
     cursor: pointer;
 }
-/* Galaxy's drops underline on a without href, but I cannot use href="#" in this component
-   because it interferes with the library router. */
-a.force-link-style {
-    text-decoration: underline !important;
-}
 </style>

From 4f4cb148b748aa5ca3b1f27d978565728f7df7d8 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Tue, 24 Apr 2018 11:36:01 -0400
Subject: [PATCH 2/3] better fix for href containing hashes

removing href messes with styles and also with bs4
(e.g. active highlighting of dropdowns was broken)
---
 .../scripts/components/RuleCollectionBuilder.vue       | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 589446199449..6153c7ee238e 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -204,7 +204,7 @@
                                         v-bind:index="target"
                                         v-bind:key="target"
                                         class="dropdown-item"
-                                        href="#"
+                                        href="javascript:void(0)"
                                         :class="'rule-add-mapping-' + target.replace(/_/g, '-')"
                                         @click="addIdentifier(target)">
                                       {{ mappingTargets()[target].label }}
@@ -241,7 +241,7 @@
                                                     v-on:mouseout.native="map.columns.forEach((col) => unhighlightColumn(col))"
                                                     :col-headers="colHeaders" />
                                 <div v-if="mapping.length == 0">
-                                    One or more column definitions must be specified. These are required to specify how to build collections and datasets from rows and columns of the table. <a href="#" @click="displayRuleType = 'mapping'">Click here</a> to manage column definitions.
+                                    One or more column definitions must be specified. These are required to specify how to build collections and datasets from rows and columns of the table. <a href="javascript:void(0)" @click="displayRuleType = 'mapping'">Click here</a> to manage column definitions.
                                 </div>
                             </ol>
                             <div class="rules-buttons">
@@ -254,7 +254,7 @@
                                     <rule-target-component :builder="this" rule-type="remove_columns" />
                                     <rule-target-component :builder="this" rule-type="split_columns" />
                                     <rule-target-component :builder="this" rule-type="swap_columns" />
-                                    <a href="#" class="dropdown-item rule-link rule-link-mapping" @click="displayRuleType = 'mapping'">Add / Modify Column Definitions</a>
+                                    <a href="javascript:void(0)" class="dropdown-item rule-link rule-link-mapping" @click="displayRuleType = 'mapping'">Add / Modify Column Definitions</a>
                                   </div>
                                 </div>
                                 <div class="btn-group dropup">
@@ -708,7 +708,7 @@ const IdentifierDisplay = {
 };
 
 const RuleTargetComponent = {
-    template: `<a class="rule-link dropdown-item" href="#" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
+    template: `<a class="rule-link dropdown-item" href="javascript:void(0)" :class="linkClassName" @click="builder.addNewRule(ruleType)">{{title}}</a>`,
     props: {
         ruleType: {
             type: String,
@@ -787,7 +787,7 @@ const RuleModalMiddle = {
 }
 
 const RuleModalFooter = {
-    template: `   
+    template: `
         <div class="rule-footer footer flex-row no-flex">
             <slot name="inputs"></slot>
             <div class="actions clear vertically-spaced">

From 2fcfec1bd3b8b31e39c2ae67816c723d96ebf177 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 24 Apr 2018 11:26:31 -0400
Subject: [PATCH 3/3] Data Libary -> Rule Builder fixes.

- Missed allowing collection name in library mode - I told Martin this possible because I thought it was and the library collection type text states it is possible but I didn't fix the switch in rule-definitions.js and notice the problems in createCollection associated with that.
- Fix to drop file type and genome selector when coming from libraries because this targets existing datasets - think this might have slipped back in a bad merge.
- Fix modal title when coming from data library folders.
- Improve text instructions when coming from a library.

Fixes #5967.
---
 .../components/RuleCollectionBuilder.vue      | 25 ++++++++-----------
 .../mvc/collection/list-collection-creator.js |  4 +--
 .../scripts/mvc/rules/rule-definitions.js     |  1 -
 3 files changed, 13 insertions(+), 17 deletions(-)

diff --git a/client/galaxy/scripts/components/RuleCollectionBuilder.vue b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
index 6153c7ee238e..cac85f619f20 100644
--- a/client/galaxy/scripts/components/RuleCollectionBuilder.vue
+++ b/client/galaxy/scripts/components/RuleCollectionBuilder.vue
@@ -6,7 +6,7 @@
             Below is a raw JSON description of the rules to apply to the tabular data. This is an advanced setting.
         </rule-modal-header>
         <rule-modal-header v-else-if="elementsType == 'datasets' || elementsType == 'library_datasets'">
-            Use this form to describe rules for building a collection from the specified datasets.
+            Use this form to describe rules for building collection(s) from the specified datasets. <b>Be sure to specify at least one column as a list identifier</b> - specify more to created nested list structures. Specify a column to serve as "collection name" to group datasets into multiple collections.
         </rule-modal-header>
         <!-- This modality allows importing individual datasets, multiple collections,
              and requires a data source - note that. -->
@@ -381,6 +381,7 @@
     </state-div>
 </template>
 <script>
+import AjaxQueue from "utils/ajax-queue";
 import axios from "axios";
 import _l from "utils/localization";
 import HotTable from "@handsontable/vue";
@@ -930,7 +931,7 @@ export default {
     computed: {
         exisistingDatasets() {
             const elementsType = this.elementsType;
-            return elementsType === "datasets";
+            return elementsType === "datasets" || elementsType === "library_datasets";
         },
         showFileTypeSelector() {
             return !this.exisistingDatasets && !this.mappingAsDict.file_type;
@@ -1312,11 +1313,13 @@ export default {
             const collectionType = this.collectionType;
             if (this.elementsType == "datasets" || this.elementsType == "library_datasets") {
                 const elements = this.creationElementsFromDatasets();
-                if (this.state !== "error") {
-                    const response = this.creationFn(elements, collectionType, name, this.hideSourceItems);
-                    response.done(this.oncreate);
-                    response.error(this.renderFetchError);
-                }
+                new AjaxQueue.AjaxQueue(
+                    _.map(elements, (elements, name) => {
+                        return () => {
+                           const response = this.creationFn(elements, collectionType, name, this.hideSourceItems);
+                           return response;
+                        };
+                })).done(this.oncreate).fail(this.renderFetchError);
             } else {
                 const historyId = Galaxy.currHistoryPanel.model.id;
                 let elements, targets;
@@ -1483,13 +1486,7 @@ export default {
                 },
                 "element_identifiers"
             );
-            // This modality only allows a single collection to be created currently.
-            if (elementsByCollectionName) {
-                return elementsByCollectionName[this.collectionName];
-            } else {
-                // state was set to error...
-                return;
-            }
+            return elementsByCollectionName;
         },
         creationElementsForFetch() {
             // fetch elements for HDCA
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
index 351bebe99efd..3657cd773568 100644
--- a/client/galaxy/scripts/mvc/collection/list-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -1069,8 +1069,8 @@ var ruleBasedCollectionCreatorModal = function _ruleBasedCollectionCreatorModal(
     let title;
     if (importType == "datasets") {
         title = _l("Build Rules for Uploading Datasets");
-    } else if (elementsType == "datasets") {
-        title = _l("Build Rules for Creating Collection");
+    } else if (elementsType == "datasets" || elementsType == "library_datasets") {
+        title = _l("Build Rules for Creating Collection(s)");
     } else {
         title = _l("Build Rules for Uploading Collections");
     }
diff --git a/client/galaxy/scripts/mvc/rules/rule-definitions.js b/client/galaxy/scripts/mvc/rules/rule-definitions.js
index e233547ee903..7071d674af28 100644
--- a/client/galaxy/scripts/mvc/rules/rule-definitions.js
+++ b/client/galaxy/scripts/mvc/rules/rule-definitions.js
@@ -659,7 +659,6 @@ const MAPPING_TARGETS = {
         help: _l(
             "If this is set, all rows with the same collection name will be joined into a collection and it is possible to create multiple collections at once."
         ),
-        modes: ["raw", "ftp"], // TODO: allow this in datasets mode.
         importType: "collections"
     },
     name: {