diff --git a/client/galaxy/scripts/components/User/UserPreferences.vue b/client/galaxy/scripts/components/User/UserPreferences.vue
index 6bc0e467dd5..2d7453652f1 100644
--- a/client/galaxy/scripts/components/User/UserPreferences.vue
+++ b/client/galaxy/scripts/components/User/UserPreferences.vue
@@ -5,16 +5,16 @@
             {{ message }}
         </b-alert>
         <p>
-            You are logged in as <strong>{{ email }}</strong
+            You are logged in as <strong id="user-preferences-current-email">{{ email }}</strong
             >.
         </p>
         <b-row class="ml-3 mb-1" v-for="(link, index) in activeLinks" :key="index">
             <i :class="['pref-icon pt-1 fa fa-lg', link.icon]" />
             <div class="pref-content pr-1">
-                <a v-if="link.onclick" @click="link.onclick" href="javascript:void(0)"
+                <a :id="link.id" v-if="link.onclick" @click="link.onclick" href="javascript:void(0)"
                     ><b>{{ link.title }}</b></a
                 >
-                <a v-else :href="`${baseUrl}/${link.action}`"
+                <a :id="link.id" v-else :href="`${baseUrl}/${link.action}`"
                     ><b>{{ link.title }}</b></a
                 >
                 <div class="form-text text-muted">
@@ -22,6 +22,16 @@
                 </div>
             </div>
         </b-row>
+        <b-row class="ml-3 mb-1">
+            <i class="pref-icon pt-1 fa fa-lg fa-plus-square-o" />
+            <div class="pref-content pr-1">
+                <a @click="toggleNotifications" href="javascript:void(0)"><b>Enable notifications</b></a>
+                <div class="form-text text-muted">
+                    Allow push and tab notifcations on job completion. To disable, revoke the site notification
+                    privilege in your browser.
+                </div>
+            </div>
+        </b-row>
         <p class="mt-2">
             You are using <strong>{{ diskUsage }}</strong> of disk space in this Galaxy instance.
             <span v-html="quotaUsageString"></span>
@@ -107,6 +117,18 @@ export default {
         }
     },
     methods: {
+        toggleNotifications() {
+            Notification.requestPermission().then(function(permission) {
+                //If the user accepts, let's create a notification
+                if (permission === "granted") {
+                    new Notification("Notifications enabled", {
+                        icon: "static/favicon.ico"
+                    });
+                } else {
+                    alert("Notifications disabled, please re-enable through browser settings.");
+                }
+            });
+        },
         openManageCustomBuilds() {
             const Galaxy = getGalaxyInstance();
             Galaxy.page.router.push(`${getAppRoot()}custom_builds`);
diff --git a/client/galaxy/scripts/components/User/UserPreferencesModel.js b/client/galaxy/scripts/components/User/UserPreferencesModel.js
index 58660c8549e..702d038ae39 100644
--- a/client/galaxy/scripts/components/User/UserPreferencesModel.js
+++ b/client/galaxy/scripts/components/User/UserPreferencesModel.js
@@ -7,6 +7,7 @@ export const getUserPreferencesModel = () => {
     return {
         information: {
             title: _l("Manage Information"),
+            id: "edit-preferences-information",
             description: "Edit your email, addresses and custom parameters or change your public name.",
             url: `api/users/${Galaxy.user.id}/information/inputs`,
             icon: "fa-user",
@@ -15,6 +16,7 @@ export const getUserPreferencesModel = () => {
         },
         password: {
             title: _l("Change Password"),
+            id: "edit-preferences-password",
             description: _l("Allows you to change your login credentials."),
             icon: "fa-unlock-alt",
             url: `api/users/${Galaxy.user.id}/password/inputs`,
@@ -24,6 +26,7 @@ export const getUserPreferencesModel = () => {
         },
         communication: {
             title: _l("Change Communication Settings"),
+            id: "edit-preferences-communication",
             description: _l("Enable or disable the communication feature to chat with other users."),
             url: `api/users/${Galaxy.user.id}/communication/inputs`,
             icon: "fa-comments-o",
@@ -32,6 +35,7 @@ export const getUserPreferencesModel = () => {
         },
         permissions: {
             title: _l("Set Dataset Permissions for new Histories"),
+            id: "edit-preferences-permissions",
             description:
                 "Grant others default access to newly created histories. Changes made here will only affect histories created after these settings have been stored.",
             url: `api/users/${Galaxy.user.id}/permissions/inputs`,
@@ -41,11 +45,13 @@ export const getUserPreferencesModel = () => {
         },
         make_data_private: {
             title: _l("Make all Data Private"),
+            id: "edit-preferences-make-data-private",
             description: _l("Click here to make all data private."),
             icon: "fa-lock"
         },
         api_key: {
             title: _l("Manage API Key"),
+            id: "edit-preferences-api-key",
             description: _l("Access your current API key or create a new one."),
             url: `api/users/${Galaxy.user.id}/api_key/inputs`,
             icon: "fa-key",
@@ -53,6 +59,7 @@ export const getUserPreferencesModel = () => {
             submit_icon: "fa-check"
         },
         cloud_auth: {
+            id: "edit-preferences-cloud-auth",
             title: _l("Manage Cloud Authorization"),
             description: _l("Add or modify the configuration that grants Galaxy to access your cloud-based resources."),
             icon: "fa-cloud",
@@ -61,6 +68,7 @@ export const getUserPreferencesModel = () => {
         },
         toolbox_filters: {
             title: _l("Manage Toolbox Filters"),
+            id: "edit-preferences-toolbox-filters",
             description: _l("Customize your Toolbox by displaying or omitting sets of Tools."),
             url: `api/users/${Galaxy.user.id}/toolbox_filters/inputs`,
             icon: "fa-filter",
@@ -75,6 +83,7 @@ export const getUserPreferencesModel = () => {
         },
         logout: {
             title: _l("Sign Out"),
+            id: "edit-preferences-custom-builds",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
             shouldRender: !!Galaxy.session_csrf_token
diff --git a/client/galaxy/scripts/components/Workflow/Editor/Node.vue b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
index 444443f16c2..5de4895e817 100644
--- a/client/galaxy/scripts/components/Workflow/Editor/Node.vue
+++ b/client/galaxy/scripts/components/Workflow/Editor/Node.vue
@@ -1,9 +1,10 @@
 <template>
     <div>
-        <div class="toolFormTitle unselectable clearfix">
-            <i :class="iconClass" />
-            <span class="node-title">{{ title }}</span>
-            <span class="sr-only">&nbsp;Node</span>
+        <div class="node-header unselectable clearfix">
+            <div class="header float-left">
+                <i :class="iconClass" />
+                <span class="node-title">{{ title }}</span>
+            </div>
             <div class="buttons float-right">
                 <a
                     v-if="canClone"
@@ -22,7 +23,7 @@
                 />
             </div>
         </div>
-        <div class="toolFormBody">
+        <div class="node-body">
             <div>
                 <loading-span message="Loading details" />
             </div>
diff --git a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
index fa1139df378..972612a8116 100644
--- a/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
+++ b/client/galaxy/scripts/components/admin/DataManager/DataManagerTable.vue
@@ -13,22 +13,20 @@
             <b-row>
                 <b-col>
                     <b-card id="data-table-card" flush>
-                        <b-container v-slot:header>
-                            <b-row align-v="center">
-                                <b-col cols="auto">
-                                    <b-button
-                                        @click="reload()"
-                                        v-b-tooltip.hover
-                                        :title="'Reload ' + this.dataTable['name'] + ' tool data table'"
-                                    >
-                                        <span class="fa fa-refresh" />
-                                    </b-button>
-                                </b-col>
-                                <b-col>
-                                    <b>{{ this.dataTable["name"] }}</b>
-                                </b-col>
-                            </b-row>
-                        </b-container>
+                        <template v-slot:header>
+                            <b-container>
+                                <b-row align-v="center">
+                                    <b-col cols="auto">
+                                        <b-button @click="reload()" v-b-tooltip.hover :title="buttonLabel">
+                                            <span class="fa fa-refresh" />
+                                        </b-button>
+                                    </b-col>
+                                    <b-col>
+                                        <b>{{ dataTableName }}</b>
+                                    </b-col>
+                                </b-row>
+                            </b-container>
+                        </template>
                         <b-table
                             :fields="fields(this.dataTable['columns'])"
                             :items="dataTable['data']"
@@ -68,6 +66,12 @@ export default {
         };
     },
     computed: {
+        dataTableName() {
+            return this.dataTable && this.dataTable.name ? this.dataTable.name : "null";
+        },
+        buttonLabel() {
+            return `Reload ${this.dataTableName} tool data table`;
+        },
         breadcrumbItems() {
             return [
                 {
@@ -75,7 +79,7 @@ export default {
                     to: "/"
                 },
                 {
-                    text: this.dataTable["name"]
+                    text: this.dataTableName
                 }
             ];
         }
@@ -88,7 +92,7 @@ export default {
         },
         reload() {
             axios
-                .get(`${getAppRoot()}data_manager/reload_tool_data_tables?table_name=${this.dataTable["name"]}`)
+                .get(`${getAppRoot()}data_manager/reload_tool_data_tables?table_name=${this.dataTableName}`)
                 .then(response => {
                     if (response.data.dataTable) {
                         this.dataTable = response.data.dataTable;
diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index f41788705e9..9cd4fd36ecf 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -267,7 +267,6 @@ const Collection = Backbone.Collection.extend({
                     cls: "loggedout-only",
                     tooltip: _l("Login"),
                     url: "login",
-                    target: "galaxy_main",
                     noscratchbook: true
                 };
             }
diff --git a/client/galaxy/scripts/mvc/dataset/dataset-model.js b/client/galaxy/scripts/mvc/dataset/dataset-model.js
index 69f18aa6ce0..85a8559bea5 100644
--- a/client/galaxy/scripts/mvc/dataset/dataset-model.js
+++ b/client/galaxy/scripts/mvc/dataset/dataset-model.js
@@ -5,8 +5,10 @@ import { getAppRoot } from "onload/loadConfig";
 import STATES from "mvc/dataset/states";
 import BASE_MVC from "mvc/base-mvc";
 import _l from "utils/localization";
+import TAB_UPDATES from "mvc/user/tab-updates";
 
 var logNamespace = "dataset";
+var hiddenupdates = 1;
 //==============================================================================
 var searchableMixin = BASE_MVC.SearchableModelMixin;
 /** @class base model for any DatasetAssociation (HDAs, LDDAs, DatasetCollectionDAs).
@@ -99,6 +101,24 @@ var DatasetAssociation = Backbone.Model.extend(BASE_MVC.LoggableMixin).extend(
                     this.log(`${this} has changed state:`, currModel, newState);
                     if (this.inReadyState()) {
                         this.trigger("state:ready", currModel, newState, this.previous("state"));
+                        if (newState != "discarded") {
+                            if (newState === "ok") {
+                                new Notification(`Job complete: ${this.get("name")}`, {
+                                    icon: "static/favicon.ico"
+                                });
+                                if (TAB_UPDATES.is_hidden()) {
+                                    TAB_UPDATES.hidden_count(hiddenupdates);
+                                    hiddenupdates++;
+                                }
+                            } else if (newState == "error") {
+                                new Notification(`Job failure: ${this.get("name")}`, {
+                                    icon: "static/erricon.ico"
+                                });
+                                if (TAB_UPDATES.is_hidden() && Notification.permission == "granted") {
+                                    TAB_UPDATES.change_favicon("static/erricon.ico");
+                                }
+                            }
+                        }
                     }
                 });
                 // the download url (currently) relies on having a correct file extension
@@ -349,6 +369,14 @@ var DatasetAssociationCollection = Backbone.Collection.extend(BASE_MVC.LoggableM
     }
 );
 
+window.addEventListener("focus", function() {
+    const testing = document.getElementById("tabicon");
+    if (testing && testing.href.search("erricon") != -1) {
+        TAB_UPDATES.change_favicon("static/favicon.ico");
+    }
+    document.title = "Galaxy";
+    hiddenupdates = 1;
+});
 //==============================================================================
 export default {
     DatasetAssociation: DatasetAssociation,
diff --git a/client/galaxy/scripts/mvc/form/form-input.js b/client/galaxy/scripts/mvc/form/form-input.js
index 89ecd872df1..2f1c2274e07 100644
--- a/client/galaxy/scripts/mvc/form/form-input.js
+++ b/client/galaxy/scripts/mvc/form/form-input.js
@@ -177,6 +177,7 @@ export default Backbone.View.extend({
             this.$title_text.show().text(this.model.get("label"));
             this.$collapsible.hide();
         }
+        this.$field.attr("data-label", this.model.get("label"));
     },
 
     _template: function() {
diff --git a/client/galaxy/scripts/mvc/user/tab-updates.js b/client/galaxy/scripts/mvc/user/tab-updates.js
new file mode 100644
index 00000000000..5b32f63d7ea
--- /dev/null
+++ b/client/galaxy/scripts/mvc/user/tab-updates.js
@@ -0,0 +1,51 @@
+//Allow change tab on event=====================================================
+function change_favicon(img) {
+    var favicon = document.createElement("link");
+    favicon.id = "tabicon";
+    favicon.setAttribute("rel", "shortcut icon");
+    var head = document.querySelector("head");
+    head.appendChild(favicon);
+    favicon.setAttribute("type", "image/png");
+    favicon.setAttribute("href", img);
+}
+
+//Check if browser is hidden-aware==============================================
+function hidden_permit() {
+    var browsers = ["webkit", "moz", "ms", "o"];
+    if ("hidden" in document) {
+        return "hidden";
+    }
+    for (var i = 0; i < browsers.length; i++) {
+        if (browsers[i] + "Hidden" in document) {
+            return browsers[i] + "Hidden";
+        }
+    }
+    return null;
+}
+
+//Find out if browser tab is hidden=============================================
+function is_hidden() {
+    var state = hidden_permit();
+    if (!state) {
+        return false;
+    }
+    return document[state];
+}
+
+//Generate new tab message to display on update in window=======================
+function hidden_count(current) {
+    if (is_hidden()) {
+        if (current === 1) {
+            document.title = "Galaxy (1 job completed)";
+        } else {
+            document.title = "Galaxy (" + current + " jobs completed)";
+        }
+    }
+}
+
+export default {
+    change_favicon: change_favicon,
+    hidden_permit: hidden_permit,
+    is_hidden: is_hidden,
+    hidden_count: hidden_count
+};
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-connector.js b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
index 7201d9162e2..eeb2735d7de 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-connector.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-connector.js
@@ -1,19 +1,35 @@
 import $ from "jquery";
-
+import * as d3 from "d3";
 import { Toast } from "ui/toast";
 
-function Connector(manager, handle1, handle2) {
-    this.manager = manager;
-    this.canvas = null;
-    this.dragging = false;
-    this.inner_color = "#FFFFFF";
-    this.outer_color = "#25537b";
-    if (handle1 && handle2) {
-        this.connect(handle1, handle2);
+// Rendering parameters
+const zIndex = 1000;
+const cpFactor = 10;
+const canvasExtra = 100;
+const handleMarginX = 8;
+const handleMarginY = 5;
+const ribbonMargin = 4;
+const ribbonInnerSingle = 4;
+const ribbonOuterSingle = 6;
+const ribbonInnerMultiple = 1;
+const ribbonOuterMultiple = 3;
+
+class Connector {
+    constructor(manager = {}, handle1 = null, handle2 = null) {
+        this.manager = manager;
+        this.dragging = false;
+        this.innerClass = "ribbon-inner";
+        this.canvas = document.createElement("div");
+        this.canvas.style.position = "absolute";
+        const container = document.getElementById("canvas-container");
+        container.appendChild(this.canvas);
+        this.svg = d3.select(this.canvas).append("svg");
+        this.svg.attr("class", "ribbon");
+        if (handle1 && handle2) {
+            this.connect(handle1, handle2);
+        }
     }
-}
-$.extend(Connector.prototype, {
-    connect: function(t1, t2) {
+    connect(t1, t2) {
         this.handle1 = t1;
         if (this.handle1) {
             this.handle1.connect(this);
@@ -22,38 +38,42 @@ $.extend(Connector.prototype, {
         if (this.handle2) {
             this.handle2.connect(this);
         }
-    },
-    destroy: function() {
+    }
+    destroy() {
         if (this.handle1) {
             this.handle1.disconnect(this);
         }
         if (this.handle2) {
             this.handle2.disconnect(this);
         }
-        $(this.canvas).remove();
-    },
-    destroyIfInvalid: function(warn) {
+        this.canvas.remove();
+    }
+    destroyIfInvalid(warn) {
         if (this.handle1 && this.handle2 && !this.handle2.attachable(this.handle1).canAccept) {
             if (warn) {
                 Toast.warning("Destroying a connection because collection type has changed.");
             }
             this.destroy();
         }
-    },
-    redraw: function() {
+    }
+    dropStart(canAccept) {
+        if (canAccept) {
+            this.innerClass = "ribbon-inner-valid";
+        } else {
+            this.innerClass = "ribbon-inner-invalid";
+        }
+    }
+    dropEnd() {
+        this.innerClass = "ribbon-inner";
+    }
+    redraw() {
+        // Identify handles
         const handle1 = this.handle1;
         const handle2 = this.handle2;
-        const startRibbon = handle1 && handle1.isMappedOver();
-        const endRibbon = handle2 && handle2.isMappedOver();
-        const canvasClass = `${startRibbon ? "start-ribbon" : ""} ${endRibbon ? "end-ribbon" : ""}`;
-        var canvas_container = $("#canvas-container");
-        var canvasZoom = this.manager.canvasZoom;
-        if (!this.canvas) {
-            this.canvas = document.createElement("canvas");
-            canvas_container.append($(this.canvas));
-            if (this.dragging) {
-                this.canvas.style.zIndex = "300";
-            }
+        const canvas_container = $("#canvas-container");
+        const canvasZoom = this.manager.canvasZoom;
+        if (this.dragging) {
+            this.canvas.style.zIndex = zIndex;
         }
         this.canvas.setAttribute(
             "handle1-id",
@@ -63,66 +83,75 @@ $.extend(Connector.prototype, {
             "handle2-id",
             handle2 && handle2.element.getAttribute ? handle2.element.getAttribute("id") : ""
         );
-        var relativeLeft = e => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
-        var relativeTop = e => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
+        const relativeLeft = e => ($(e).offset().left - canvas_container.offset().left) / canvasZoom;
+        const relativeTop = e => ($(e).offset().top - canvas_container.offset().top) / canvasZoom;
         if (!handle1 || !handle2) {
             return;
         }
+
         // Find the position of each handle
-        var start_x = relativeLeft(handle1.element) + 5;
-        var start_y = relativeTop(handle1.element) + 5;
-        var end_x = relativeLeft(handle2.element) + 5;
-        var end_y = relativeTop(handle2.element) + 5;
+        let start_x = relativeLeft(handle1.element) + handleMarginX;
+        let start_y = relativeTop(handle1.element) + handleMarginY;
+        let end_x = relativeLeft(handle2.element) + handleMarginX;
+        let end_y = relativeTop(handle2.element) + handleMarginY;
+
         // Calculate canvas area
-        var canvas_extra = 100;
-        var canvas_min_x = Math.min(start_x, end_x);
-        var canvas_max_x = Math.max(start_x, end_x);
-        var canvas_min_y = Math.min(start_y, end_y);
-        var canvas_max_y = Math.max(start_y, end_y);
-        var cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, 100), 300);
-        var canvas_left = canvas_min_x - canvas_extra;
-        var canvas_top = canvas_min_y - canvas_extra;
-        var canvas_width = canvas_max_x - canvas_min_x + 2 * canvas_extra;
-        var canvas_height = canvas_max_y - canvas_min_y + 2 * canvas_extra;
+        const canvas_min_x = Math.min(start_x, end_x);
+        const canvas_max_x = Math.max(start_x, end_x);
+        const canvas_min_y = Math.min(start_y, end_y);
+        const canvas_max_y = Math.max(start_y, end_y);
+        const canvas_left = canvas_min_x - canvasExtra;
+        const canvas_top = canvas_min_y - canvasExtra;
+        const canvas_width = canvas_max_x - canvas_min_x + 2 * canvasExtra;
+        const canvas_height = canvas_max_y - canvas_min_y + 2 * canvasExtra;
+
         // Place the canvas
         this.canvas.style.left = `${canvas_left}px`;
         this.canvas.style.top = `${canvas_top}px`;
-        this.canvas.setAttribute("width", canvas_width);
-        this.canvas.setAttribute("height", canvas_height);
-        this.canvas.setAttribute("class", canvasClass);
+
+        // Resize the svg
+        this.svg.style("width", `${canvas_width}px`);
+        this.svg.style("height", `${canvas_height}px`);
+
         // Adjust points to be relative to the canvas
         start_x -= canvas_left;
         start_y -= canvas_top;
         end_x -= canvas_left;
         end_y -= canvas_top;
 
-        // Draw the line
+        // Determine line shift
+        const cp_shift = Math.min(Math.max(Math.abs(canvas_max_y - canvas_min_y) / 2, cpFactor), 3 * cpFactor);
 
-        var start_offsets = null;
-        var end_offsets = null;
-        var num_offsets = 1;
+        // Draw ribbons
+        this.drawRibbon(handle1, handle2, cp_shift, start_x, start_y, end_x, end_y);
+    }
+    drawRibbon(handle1, handle2, cp_shift, start_x, start_y, end_x, end_y) {
+        // Check ribbon type
+        const startRibbon = handle1 && handle1.isMappedOver();
+        const endRibbon = handle2 && handle2.isMappedOver();
+
+        // Draw the line
+        let start_offsets = [0];
+        let end_offsets = [0];
+        const offsets = [-2 * ribbonMargin, -ribbonMargin, 0, ribbonMargin, 2 * ribbonMargin];
+        let num_offsets = 1;
         if (startRibbon) {
-            start_offsets = [-6, -3, 0, 3, 6];
-            num_offsets = 5;
-        } else {
-            start_offsets = [0];
+            start_offsets = offsets;
+            num_offsets = offsets.length;
         }
         if (endRibbon) {
-            end_offsets = [-6, -3, 0, 3, 6];
-            num_offsets = 5;
-        } else {
-            end_offsets = [0];
+            end_offsets = offsets;
+            num_offsets = offsets.length;
         }
-        var connector = this;
-        for (var i = 0; i < num_offsets; i++) {
-            var inner_width = 5;
-            var outer_width = 7;
+        this.svg.selectAll("*").remove();
+        for (let i = 0; i < num_offsets; i++) {
+            let inner_width = ribbonInnerSingle;
+            let outer_width = ribbonOuterSingle;
             if (start_offsets.length > 1 || end_offsets.length > 1) {
-                // We have a multi-run, using many lines, make them small.
-                inner_width = 1;
-                outer_width = 3;
+                inner_width = ribbonInnerMultiple;
+                outer_width = ribbonOuterMultiple;
             }
-            connector.draw_outlined_curve(
+            this.drawCurve(
                 start_x,
                 start_y,
                 end_x,
@@ -134,49 +163,37 @@ $.extend(Connector.prototype, {
                 end_offsets[i % end_offsets.length]
             );
         }
-    },
-    draw_outlined_curve: function(
-        start_x,
-        start_y,
-        end_x,
-        end_y,
-        cp_shift,
-        inner_width,
-        outer_width,
-        offset_start,
-        offset_end
-    ) {
-        var c = this.canvas.getContext("2d");
+    }
+    drawCurve(start_x, start_y, end_x, end_y, cp_shift, inner_width, outer_width, offset_start, offset_end) {
         offset_start = offset_start || 0;
         offset_end = offset_end || 0;
-        c.lineCap = "round";
-        c.strokeStyle = this.outer_color;
-        c.lineWidth = outer_width;
-        c.beginPath();
-        c.moveTo(start_x, start_y + offset_start);
-        c.bezierCurveTo(
-            start_x + cp_shift,
-            start_y + offset_start,
-            end_x - cp_shift,
-            end_y + offset_end,
-            end_x,
-            end_y + offset_end
-        );
-        c.stroke();
-        // Inner line
-        c.strokeStyle = this.inner_color;
-        c.lineWidth = inner_width;
-        c.beginPath();
-        c.moveTo(start_x, start_y + offset_start);
-        c.bezierCurveTo(
-            start_x + cp_shift,
-            start_y + offset_start,
-            end_x - cp_shift,
-            end_y + offset_end,
-            end_x,
-            end_y + offset_end
-        );
-        c.stroke();
+        const lineData = [
+            { x: start_x, y: start_y + offset_start },
+            { x: start_x + cp_shift, y: start_y + offset_start },
+            { x: end_x - cp_shift, y: end_y + offset_end },
+            { x: end_x, y: end_y + offset_end }
+        ];
+        const lineFunction = d3.svg
+            .line()
+            .x(function(d) {
+                return d.x;
+            })
+            .y(function(d) {
+                return d.y;
+            })
+            .interpolate("basis");
+        this.svg
+            .append("path")
+            .attr("class", "ribbon-outer")
+            .attr("d", lineFunction(lineData))
+            .attr("stroke-width", outer_width)
+            .attr("fill", "none");
+        this.svg
+            .append("path")
+            .attr("class", this.innerClass)
+            .attr("d", lineFunction(lineData))
+            .attr("stroke-width", inner_width)
+            .attr("fill", "none");
     }
-});
+}
 export default Connector;
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
index 16ffd2c7156..ada79e2c245 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js
@@ -134,7 +134,7 @@ class Workflow extends EventEmitter {
 
         // Create node wrapper
         const container = document.createElement("div");
-        container.className = "toolForm toolFormInCanvas";
+        container.className = "workflow-node";
         document.getElementById("canvas-container").appendChild(container);
         var $f = $(container);
 
@@ -380,15 +380,15 @@ class Workflow extends EventEmitter {
         wf.id_counter = max_id + 1;
         // Second pass, connections
         $.each(data.steps, (id, step) => {
-            var node = wf.nodes[parseInt(id) + offset];
+            const node = wf.nodes[parseInt(id) + offset];
             $.each(step.input_connections, (k, v) => {
                 if (v) {
                     if (!$.isArray(v)) {
                         v = [v];
                     }
                     $.each(v, (l, x) => {
-                        var other_node = wf.nodes[parseInt(x.id) + offset];
-                        var c = new Connector(this.canvas_manager);
+                        const other_node = wf.nodes[parseInt(x.id) + offset];
+                        const c = new Connector(this.canvas_manager);
                         c.connect(other_node.output_terminals[x.output_name], node.input_terminals[k]);
                         c.redraw();
                     });
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js
index 2952b9b04be..94938aff0f2 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js
@@ -10,7 +10,7 @@ export class Node {
         this.element = attr.element;
         this.input_terminals = {};
         this.output_terminals = {};
-        this.errors = {};
+        this.errors = null;
         this.workflow_outputs = [];
     }
     getWorkflowOutput(outputName) {
@@ -191,7 +191,7 @@ export class Node {
         $(this.element).remove();
     }
     make_active() {
-        $(this.element).addClass("toolForm-active");
+        $(this.element).addClass("node-active");
     }
     make_inactive() {
         // Keep inactive nodes stacked from most to least recently active
@@ -202,7 +202,7 @@ export class Node {
             p.appendChild(element);
         })(element.parentNode);
         // Remove active class
-        $(element).removeClass("toolForm-active");
+        $(element).removeClass("node-active");
     }
     set_tool_version() {
         if (this.type === "tool" && this.config_form) {
@@ -309,7 +309,7 @@ export class Node {
             var pja_in = data.post_job_actions;
             this.post_job_actions = pja_in ? pja_in : {};
         }
-        node.nodeView.renderToolErrors();
+        node.nodeView.renderErrors();
         // Update input rows
         var old_body = nodeView.$el.find("div.inputs");
         var new_body = nodeView.newInputsDiv();
@@ -340,14 +340,6 @@ export class Node {
         this.markChanged();
         this.redraw();
     }
-    error(text) {
-        var b = $(this.element).find(".toolFormBody");
-        b.find("div").remove();
-        var tmp = `<div style='color: red; text-style: italic;'>${text}</div>`;
-        this.config_form = tmp;
-        b.html(tmp);
-        this.app.node_changed(this);
-    }
     markChanged() {
         this.app.node_changed(this);
     }
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
index c18207dd113..0686f57ff94 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js
@@ -9,26 +9,31 @@ export class NodeView {
         this.$el = options.$el;
         this.node = options.node;
         this.output_width = Math.max(150, this.$el.width());
-        this.tool_body = this.$el.find(".toolFormBody");
-        this.tool_body.find("div").remove();
-        this.newInputsDiv().appendTo(this.tool_body);
+        this.node_body = this.$el.find(".node-body");
+        this.node_body.find("div").remove();
+        this.newInputsDiv().appendTo(this.node_body);
         this.terminalViews = {};
         this.outputViews = {};
     }
 
     render() {
-        this.renderToolLabel();
-        this.renderToolErrors();
+        this.renderLabel();
+        this.renderErrors();
         this.$el.css("width", Math.min(250, Math.max(this.$el.width(), this.output_width)));
     }
 
-    renderToolLabel() {
+    renderLabel() {
         this.$el.find(".node-title").text(this.node.label || this.node.name);
         this.$el.attr("node-label", this.node.label);
     }
 
-    renderToolErrors() {
-        this.node.errors ? this.$el.addClass("tool-node-error") : this.$el.removeClass("tool-node-error");
+    renderErrors() {
+        if (this.node.errors) {
+            this.$el.addClass("node-error");
+            this.node_body.text(this.node.errors);
+        } else {
+            this.$el.removeClass("node-error");
+        }
     }
 
     newInputsDiv() {
@@ -40,7 +45,7 @@ export class NodeView {
     }
 
     addRule() {
-        this.tool_body.append($("<div/>").addClass("rule"));
+        this.node_body.append($("<div/>").addClass("rule"));
     }
 
     addDataInput(input, body) {
@@ -111,7 +116,7 @@ export class NodeView {
         const terminalView = this.terminalViewForOutput(output);
         const outputView = this.outputViewforOutput(output, terminalView);
         this.outputViews[output.name] = outputView;
-        this.tool_body.append(outputView.$el.append(terminalView.terminalElements()));
+        this.node_body.append(outputView.$el.append(terminalView.terminalElements()));
     }
 
     redrawWorkflowOutputs() {
diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
index 546fead9497..c481940b653 100644
--- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
+++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
@@ -91,10 +91,10 @@ class BaseInputTerminalView extends TerminalView {
     onDropStart(e, d = {}) {
         if (d.proxy.terminal) {
             if (this.$el.hasClass("can-accept")) {
-                d.proxy.terminal.connectors[0].inner_color = "#BBFFBB";
+                d.proxy.terminal.connectors[0].dropStart(true);
                 d.proxy.dropTooltip = "";
             } else {
-                d.proxy.terminal.connectors[0].inner_color = "#fe7f02";
+                d.proxy.terminal.connectors[0].dropStart(false);
                 if (this.reason) {
                     d.proxy.dropTooltip = this.reason;
                     $(d.proxy).tooltip("show");
@@ -107,14 +107,15 @@ class BaseInputTerminalView extends TerminalView {
     onDropEnd(e, d = {}) {
         d.proxy.dropTooltip = "";
         if (d.proxy.terminal) {
-            d.proxy.terminal.connectors[0].inner_color = "#FFFFFF";
+            d.proxy.terminal.connectors[0].dropEnd();
         }
     }
     onDrop(e, d = {}) {
         d.proxy.dropTooltip = "";
         if (this.$el.hasClass("can-accept")) {
             const terminal = this.el.terminal;
-            new Connector(this.app.canvas_manager, d.drag.terminal, terminal).redraw();
+            const c = new Connector(this.app.canvas_manager, d.drag.terminal, terminal);
+            c.redraw();
         }
     }
     onHover() {
@@ -357,7 +358,7 @@ export class BaseOutputTerminalView extends TerminalView {
             }
         });
         h.terminal = new Terminals.OutputTerminal({ element: h });
-        var c = new Connector(this.app.canvas_manager);
+        const c = new Connector(this.app.canvas_manager);
         c.dragging = true;
         c.connect(this.el.terminal, h.terminal);
         return h;
diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
index 116ecb708d2..449ab170409 100644
--- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
+++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js
@@ -242,9 +242,7 @@ QUnit.test("default attributes", function(assert) {
     const output = { connect: sinon.spy() };
     const connector = new Connector({}, input, output);
     assert.equal(connector.dragging, false);
-    assert.equal(connector.canvas, null);
-    assert.equal(connector.inner_color, "#FFFFFF");
-    assert.equal(connector.outer_color, "#25537b");
+    assert.equal(connector.svg.attr("class"), "ribbon");
 });
 
 QUnit.test("destroy", function(assert) {
@@ -271,13 +269,12 @@ QUnit.test("initial redraw", function(assert) {
             return false;
         }
     };
+    const n = $("#canvas-container").find("svg").length;
     const connector = new Connector({}, input, output);
-    const n = $("#canvas-container").find("canvas").length;
-    connector.redraw();
     // Ensure canvas gets set
     assert.ok(connector.canvas);
     // Ensure it got added to canvas container
-    assert.equal(n + 1, $("#canvas-container").find("canvas").length);
+    assert.equal(n + 1, $("#canvas-container").find("svg").length);
 });
 
 QUnit.module("Input collection terminal model test", {
@@ -366,9 +363,9 @@ QUnit.module("Node unit test", {
 });
 
 QUnit.test("make active", function(assert) {
-    assert.ok(!this.element.hasClass("toolForm-active"));
+    assert.ok(!this.element.hasClass("node-active"));
     this.node.make_active();
-    assert.ok(this.element.hasClass("toolForm-active"));
+    assert.ok(this.element.hasClass("node-active"));
 });
 
 QUnit.test("destroy", function(assert) {
@@ -380,11 +377,11 @@ QUnit.test("destroy", function(assert) {
 });
 
 QUnit.test("error", function(assert) {
-    // Test body of toolFormBody div updated and workflow notified of change.
+    // Test body of div updated and workflow notified of change.
     var test = this;
     this.expect_workflow_node_changed(assert, function() {
-        test.node.error("TOOL ERROR");
-        assert.equal($(test.$(".toolFormBody").children()[0]).html(), "TOOL ERROR");
+        test.node.init_field_data({ errors: "NODE ERROR", inputs: [], outputs: [] });
+        assert.equal(test.$(".node-body").html(), "NODE ERROR");
     });
 });
 
@@ -428,10 +425,10 @@ QUnit.test("init_field_data data", function(assert) {
         assert.equal(this.$(".output-terminal").length, 1);
         assert.equal(this.$(".input-terminal").length, 1);
         assert.equal(this.$(".rule").length, 1);
-        assert.equal(this.$(".toolFormBody").children().length, 3);
+        assert.equal(this.$(".node-body").children().length, 3);
         assert.equal(this.$(".node-title").text(), "newnode");
         assert.ok(
-            this.$(".toolFormTitle")
+            this.$(".node-header")
                 .find("i")
                 .hasClass("fa-wrench")
         );
@@ -607,10 +604,10 @@ QUnit.module("Node view ", {
 QUnit.test("tool error styling", function(assert) {
     this.set_for_node({ errors: false });
     this.view.render();
-    assert.ok(!this.view.$el.hasClass("tool-node-error"));
+    assert.ok(!this.view.$el.hasClass("node-error"));
     this.set_for_node({ errors: true });
     this.view.render();
-    assert.ok(this.view.$el.hasClass("tool-node-error"));
+    assert.ok(this.view.$el.hasClass("node-error"));
 });
 
 QUnit.test("rendering correct width", function(assert) {
diff --git a/client/galaxy/style/scss/workflow.scss b/client/galaxy/style/scss/workflow.scss
index 30e5e950d05..b34decf2b3b 100644
--- a/client/galaxy/style/scss/workflow.scss
+++ b/client/galaxy/style/scss/workflow.scss
@@ -7,40 +7,44 @@
         display: flex;
         flex-direction: column;
         flex-grow: 1;
-        .toolForm.toolFormInCanvas {
+        .workflow-node {
             @extend .card;
+            @extend .position-absolute;
             z-index: 100;
             width: $worfklow-node-width;
-            position: absolute;
-            border-color: $brand-primary;
-            &.toolForm-active {
+            border: solid $brand-primary 1px;
+            &.node-active {
                 z-index: 1001;
+                border: solid $white 1px;
                 box-shadow: 0 0 0 2px $brand-primary;
             }
-            .toolFormTitle {
+            .node-header {
                 @extend .card-header;
                 @extend .py-1;
                 @extend .px-2;
                 cursor: move;
                 background: $brand-secondary;
+                .header {
+                    width: $worfklow-node-width - 2rem;
+                }
             }
-            .toolFormBody {
+            .node-body {
                 @extend .card-body;
                 @extend .p-0;
                 @extend .mx-2;
                 .rule {
                     height: 0;
                     border: none;
-                    border-bottom: dotted black 1px;
+                    border-bottom: dotted $brand-primary 1px;
                     margin: 0 5px;
                 }
             }
         }
-        .toolForm.toolFormInCanvas.tool-node-error {
-            border-color: $state-danger-border;
-            .toolFormTitle {
-                background: $state-danger-bg;
-                border-color: $state-danger-border;
+        .workflow-node.node-error {
+            border-color: $brand-danger;
+            .node-header {
+                background: $brand-danger;
+                border-color: $brand-danger;
             }
         }
         .workflow-canvas {
@@ -55,6 +59,20 @@
                 position: relative;
                 overflow: hidden;
             }
+            .ribbon {
+                .ribbon-outer {
+                    stroke: $brand-primary;
+                }
+                .ribbon-inner {
+                    stroke: $white;
+                }
+                .ribbon-inner-valid {
+                    stroke: $brand-success;
+                }
+                .ribbon-inner-invalid {
+                    stroke: $brand-warning;
+                }
+            }
             .base-terminal {
                 @extend .fa;
                 @extend .fa-circle;
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index ac2f2193d4b..41abe433853 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -711,19 +711,6 @@
 :Type: int
 
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``manage_dependency_relationships``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    Enable use of an in-memory registry with bi-directional
-    relationships between repositories (i.e., in addition to lists of
-    dependencies for a repository, keep an in-memory registry of
-    dependent items for each repository.
-:Default: ``false``
-:Type: bool
-
-
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``tool_data_table_config_path``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1234,6 +1221,21 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~
+``whitelist_file``
+~~~~~~~~~~~~~~~~~~
+
+:Description:
+    E-mail domains whitelist is used to specify allowed email address
+    domains. If the list is non-empty and a user attempts registration
+    using an email address belonging to a domain that is not on the
+    list, registration will be enied. This is a more restrictive
+    option than <blacklist_file>, and therefore, in case
+    <whitelist_file> is defined, <blacklist_file> will be ignored.
+:Default: ``disposable_email_whitelist.conf``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``registration_warning_message``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3271,6 +3273,19 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``job_metrics_config_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    XML config file that contains the job metric collection
+    configuration.
+    The value of this option will be resolved with respect to
+    <config_dir>.
+:Default: ``job_metrics_conf.xml``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``expose_potentially_sensitive_job_metrics``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -3673,7 +3688,7 @@
 
 :Description:
     CSS file to apply to "Galaxy Page" exports to PDF. Generally
-    prefer  markdown_export_css, but this is here for deployments that
+    prefer markdown_export_css, but this is here for deployments that
     would like to tailor different kinds of exports.
 :Default: ``markdown_export_pages.css``
 :Type: str
@@ -3685,7 +3700,7 @@
 
 :Description:
     CSS file to apply to invocation report exports to PDF. Generally
-    prefer  markdown_export_css, but this is here for deployments that
+    prefer markdown_export_css, but this is here for deployments that
     would like to tailor different kinds of exports.
 :Default: ``markdown_export_invocation_reports.css``
 :Type: str
diff --git a/lib/galaxy/actions/admin.py b/lib/galaxy/actions/admin.py
index e6d622bdb6d..e6666986ca3 100644
--- a/lib/galaxy/actions/admin.py
+++ b/lib/galaxy/actions/admin.py
@@ -45,7 +45,7 @@ class AdminActions(object):
             # If this is a default quota, create the DefaultQuotaAssociation
             if params.default != 'no':
                 self.app.quota_agent.set_default_quota(params.default, quota)
-                message = "Default quota '%s' has been created."
+                message = "Default quota '%s' has been created." % quota.name
             else:
                 # Create the UserQuotaAssociations
                 in_users = [self.sa_session.query(self.app.model.User).get(decode_id(x) if decode_id else x) for x in util.listify(params.in_users)]
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
index 7cc31f01f08..5b13f02a54b 100644
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -91,9 +91,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
         check_migrate_tools = self.config.check_migrate_tools
         self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
 
-        # Manage installed tool shed repositories.
         self.installed_repository_manager = InstalledRepositoryManager(self)
-
         self._configure_datatypes_registry(self.installed_repository_manager)
         galaxy.model.set_datatypes_registry(self.datatypes_registry)
 
diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 3fdc7f9af3a..6595236349d 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -100,11 +100,24 @@ LOGGING_CONFIG_DEFAULT = {
 
 
 def find_root(kwargs):
-    root = os.path.abspath(kwargs.get('root_dir', '.'))
-    return root
+    return os.path.abspath(kwargs.get('root_dir', '.'))
 
 
 class BaseAppConfiguration(object):
+    # Override in subclasses (optional): {KEY: config option, VALUE: deprecated directory name}
+    # If VALUE == first directory in a user-supplied path that resolves to KEY, it will be stripped from that path
+    deprecated_dirs = None
+
+    def __init__(self, **kwargs):
+        self.config_dict = kwargs
+        self.root = find_root(kwargs)
+        self._set_config_base(kwargs)
+        self.schema = self._load_schema()  # Load schema from schema definition file
+        self._raw_config = self.schema.defaults.copy()  # Save schema defaults as initial config values (raw_config)
+        self._update_raw_config_from_kwargs(kwargs)  # Overwrite raw_config with values passed in kwargs
+        self._create_attributes_from_raw_config()  # Create attributes based on raw_config
+        self._resolve_paths()  # Overwrite attribute values with resolved paths
+
     def _set_config_base(self, config_kwargs):
 
         def _set_global_conf():
@@ -163,6 +176,75 @@ class BaseAppConfiguration(object):
         _set_global_conf()
         _set_config_directories()
 
+    def _load_schema(self):
+        # Override in subclasses
+        raise Exception('Not implemented')
+
+    def _update_raw_config_from_kwargs(self, kwargs):
+
+        def convert_datatype(key, value):
+            datatype = self.schema.app_schema[key].get('type')
+            # check for `not None` explicitly (value can be falsy)
+            if value is not None and datatype in type_converters:
+                return type_converters[datatype](value)
+            return value
+
+        def strip_deprecated_dir(key, value):
+            resolves_to = self.schema.paths_to_resolve.get(key)
+            if resolves_to:  # value is a path that will be resolved
+                first_dir = value.split(os.sep)[0]  # get first directory component
+                if first_dir == self.deprecated_dirs.get(resolves_to):  # first_dir is deprecated for this option
+                    ignore = first_dir + os.sep
+                    log.warning(
+                        "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
+                        "to suppress this warning: %s", key, resolves_to, ignore, value
+                    )
+                    return value[len(ignore):]
+            return value
+
+        type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
+
+        for key, value in kwargs.items():
+            if key in self.schema.app_schema:
+                value = convert_datatype(key, value)
+                if value and self.deprecated_dirs:
+                    value = strip_deprecated_dir(key, value)
+                self._raw_config[key] = value
+
+    def _create_attributes_from_raw_config(self):
+        # `base_configs` are a special case: these attributes have been created and will be ignored
+        # by the code below. Trying to overwrite any other existing attributes will raise an error.
+        base_configs = {'config_dir', 'data_dir', 'managed_config_dir'}
+        for key, value in self._raw_config.items():
+            if not hasattr(self, key):
+                setattr(self, key, value)
+            elif key not in base_configs:
+                raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
+
+    def _resolve_paths(self):
+
+        def resolve(key):
+            if key in _cache:  # resolve each path only once
+                return _cache[key]
+
+            path = getattr(self, key)  # path prior to being resolved
+            parent = self.schema.paths_to_resolve.get(key)
+            if not parent:  # base case: nothing else needs resolving
+                return path
+            parent_path = resolve(parent)  # recursively resolve parent path
+            if path is not None:
+                path = os.path.join(parent_path, path)  # resolve path
+            else:
+                path = parent_path  # or use parent path
+
+            setattr(self, key, path)  # update property
+            _cache[key] = path  # cache it!
+            return path
+
+        _cache = {}
+        for key in self.schema.paths_to_resolve:
+            resolve(key)
+
     def _in_managed_config_dir(self, path):
         return os.path.join(self.managed_config_dir, path)
 
@@ -212,133 +294,14 @@ class BaseAppConfiguration(object):
 class GalaxyAppConfiguration(BaseAppConfiguration):
     deprecated_options = ('database_file', 'track_jobs_in_database')
     default_config_file_name = 'galaxy.yml'
-    # {key: config option, value: deprecated directory name}
-    # If value == first dir in a user path that resolves to key, it will be stripped from the path
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
 
     def __init__(self, **kwargs):
-        self._load_schema()  # Load schema from schema definition file
-        self._load_config_from_schema()  # Load default propery values from schema
-        self._validate_schema_paths()  # check that paths can be resolved
-        self._update_raw_config_from_kwargs(kwargs)  # Overwrite default values passed as kwargs
-        self._create_attributes_from_raw_config()  # Create attributes for LOADED properties
-
-        self.config_dict = kwargs
-        self.root = find_root(kwargs)
-        self._set_config_base(kwargs)  # must be called prior to _resolve_paths()
-
-        self._resolve_paths(kwargs)  # Overwrite attributes (not _raw_config) w/resolved paths
-        self._process_config(kwargs)  # Finish processing configuration
+        super(GalaxyAppConfiguration, self).__init__(**kwargs)
+        self._process_config(kwargs)
 
     def _load_schema(self):
-        self.schema = AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
-        self.appschema = self.schema.app_schema
-
-    def _load_config_from_schema(self):
-        self._raw_config = {}  # keeps track of startup values (kwargs or schema default)
-        self.reloadable_options = set()  # config options we can reload at runtime
-        self._paths_to_resolve = {}  # {config option: referenced config option}
-        for key, data in self.appschema.items():
-            self._raw_config[key] = data.get('default')
-            if data.get('reloadable'):
-                self.reloadable_options.add(key)
-            if data.get('path_resolves_to'):
-                self._paths_to_resolve[key] = data.get('path_resolves_to')
-
-    def _validate_schema_paths(self):
-
-        def check_exists(option, key):
-            if not option:
-                message = "Invalid schema: property '{}' listed as path resolution target " \
-                    "for '{}' does not exist".format(resolves_to, key)
-                raise_error(message)
-
-        def check_type_is_str(option, key):
-            if option.get('type') != 'str':
-                message = "Invalid schema: property '{}' should have type 'str'".format(key)
-                raise_error(message)
-
-        def check_is_dag():
-            visited = set()
-            for key in self._paths_to_resolve:
-                visited.clear()
-                while key:
-                    visited.add(key)
-                    key = self.appschema[key].get('path_resolves_to')
-                    if key and key in visited:
-                        raise_error('Invalid schema: cycle detected')
-
-        def raise_error(message):
-            log.error(message)
-            raise ConfigurationError(message)
-
-        for key, resolves_to in self._paths_to_resolve.items():
-            parent = self.appschema.get(resolves_to)
-            check_exists(parent, key)
-            check_type_is_str(parent, key)
-            check_type_is_str(self.appschema[key], key)
-        check_is_dag()  # must be called last: walks entire graph
-
-    def _update_raw_config_from_kwargs(self, kwargs):
-
-        def convert_datatype(key, value):
-            datatype = self.appschema[key].get('type')
-            # check for `not None` explicitly (value can be falsy)
-            if value is not None and datatype in type_converters:
-                return type_converters[datatype](value)
-            return value
-
-        def strip_deprecated_dir(key, value):
-            resolves_to = self.appschema[key].get('path_resolves_to')
-            if resolves_to:  # value is a path that will be resolved
-                first_dir = value.split(os.sep)[0]  # get first directory component
-                if first_dir == self.deprecated_dirs[resolves_to]:  # first_dir is deprecated for this option
-                    ignore = first_dir + os.sep
-                    log.warning(
-                        "Paths for the '%s' option are now relative to '%s', remove the leading '%s' "
-                        "to suppress this warning: %s", key, resolves_to, ignore, value
-                    )
-                    return value[len(ignore):]
-            return value
-
-        type_converters = {'bool': string_as_bool, 'int': int, 'float': float, 'str': str}
-
-        for key, value in kwargs.items():
-            if key in self.appschema:
-                value = convert_datatype(key, value)
-                if value:
-                    value = strip_deprecated_dir(key, value)
-                self._raw_config[key] = value
-
-    def _create_attributes_from_raw_config(self):
-        for key, value in self._raw_config.items():
-            if hasattr(self, key):
-                raise ConfigurationError("Attempting to override existing attribute '%s'" % key)
-            setattr(self, key, value)
-
-    def _resolve_paths(self, kwargs):
-
-        def resolve(key):
-            if key in _cache:  # resolve each path only once
-                return _cache[key]
-
-            path = getattr(self, key)  # path prior to being resolved
-            parent = self.appschema[key].get('path_resolves_to')
-            if not parent:  # base case: nothing else needs resolving
-                return path
-            parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
-                path = os.path.join(parent_path, path)  # resolve path
-            else:
-                path = parent_path  # or use parent path
-
-            setattr(self, key, path)  # update property
-            _cache[key] = path  # cache it!
-            return path
-
-        _cache = {}
-        for key in self._paths_to_resolve:
-            resolve(key)
+        return AppSchema(GALAXY_CONFIG_SCHEMA_PATH, GALAXY_APP_NAME)
 
     def _process_config(self, kwargs):
         # Resolve paths of other config files
@@ -465,6 +428,15 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             except IOError:
                 log.error("CONFIGURATION ERROR: Can't open supplied blacklist file from path: %s", self.blacklist_file)
 
+        #  Create whitelist file to accept only certain email domains
+        self.whitelist_content = None
+        if self.whitelist_file:
+            try:
+                with open(self.whitelist_file) as f:
+                    self.whitelist_content = [line.rstrip() for line in f]
+            except IOError:
+                log.error("CONFIGURATION ERROR: Can't open supplied whitelist file from path: %s", self.whitelist_file)
+
         self.persistent_communication_rooms = listify(self.persistent_communication_rooms, do_strip=True)
         # The transfer manager and deferred job queue
         self.enable_beta_job_managers = string_as_bool(kwargs.get('enable_beta_job_managers', 'False'))
@@ -526,7 +498,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
             self.tool_dependency_dir = None
         if self.involucro_path is None:
-            target_dir = self.tool_dependency_dir or self.appschema['tool_dependency_dir'].get('default')
+            target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
             self.involucro_path = os.path.join(self.data_dir, target_dir, "involucro")
         self.involucro_path = os.path.join(self.root, self.involucro_path)
         if self.mulled_channels:
@@ -897,7 +869,7 @@ Configuration = GalaxyAppConfiguration
 def reload_config_options(current_config):
     """ Reload modified reloadable config options """
     modified_config = read_properties_from_file(current_config.config_file)
-    for option in current_config.reloadable_options:
+    for option in current_config.schema.reloadable_options:
         if option in modified_config:
             # compare to raw value, as that one is set only on load and reload
             if current_config._raw_config[option] != modified_config[option]:
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index 8ae4035bc63..9588d2d9c15 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -30,12 +30,12 @@ if __name__ == '__main__':
 from galaxy.config import GALAXY_CONFIG_SCHEMA_PATH
 from galaxy.config.schema import (
     AppSchema,
+    OPTION_DEFAULTS,
     Schema,
 )
 from galaxy.util import safe_makedirs
 from galaxy.util.properties import nice_config_parser
 from galaxy.util.yaml_util import (
-    OPTION_DEFAULTS,
     ordered_dump,
     ordered_load,
 )
diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index b5301b9a427..433b799404b 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -561,8 +561,17 @@
     <datatype extension="cel" type="galaxy.datatypes.microarrays:Cel" display_in_upload="true"/>
     <datatype extension="gpr" type="galaxy.datatypes.microarrays:Gpr" display_in_upload="true"/>
     <datatype extension="gal" type="galaxy.datatypes.microarrays:Gal" display_in_upload="true"/>
-    <datatype extension="rdata" type="galaxy.datatypes.binary:RData" display_in_upload="true" description="Stored data from an R session"/>
-    <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" description="Stored RDS from a SingleCellObject" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" display_in_upload="true" description="Stored data from an R session"/>
+    <datatype extension="rdata.sce" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true" description="Stored RDS from a SingleCellObject"/>
+    <datatype extension="rdata.xcms.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.group" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.xcms.fillpeaks" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.positive" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.negative" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
+    <datatype extension="rdata.camera.quick" type="galaxy.datatypes.binary:RData" mimetype="application/x-gzip" subclass="true" display_in_upload="true"/>
     <datatype extension="rdock_as" type="galaxy.datatypes.binary:Binary" description="rDock active site format" subclass="true" display_in_upload="true"/>
     <datatype extension="oxlicg" type="galaxy.datatypes.binary:OxliCountGraph" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="oxling" type="galaxy.datatypes.binary:OxliNodeGraph" mimetype="application/octet-stream" display_in_upload="true"/>
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index d8368867158..dc1e81c10ed 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -451,12 +451,6 @@ galaxy:
   # between 1 and 24.
   #hours_between_check: 12
 
-  # Enable use of an in-memory registry with bi-directional
-  # relationships between repositories (i.e., in addition to lists of
-  # dependencies for a repository, keep an in-memory registry of
-  # dependent items for each repository.
-  #manage_dependency_relationships: false
-
   # XML config file that contains data table entries for the
   # ToolDataTableManager.  This file is manually # maintained by the
   # Galaxy administrator (.sample used if default does not exist).
@@ -693,6 +687,14 @@ galaxy:
   # Example value 'config/disposable_email_blacklist.conf'
   #blacklist_file: null
 
+  # E-mail domains whitelist is used to specify allowed email address
+  # domains. If the list is non-empty and a user attempts registration
+  # using an email address belonging to a domain that is not on the
+  # list, registration will be enied. This is a more restrictive option
+  # than <blacklist_file>, and therefore, in case <whitelist_file> is
+  # defined, <blacklist_file> will be ignored.
+  #whitelist_file: disposable_email_whitelist.conf
+
   # Registration warning message is used to discourage people from
   # registering multiple accounts.  Applies mostly for the main Galaxy
   # instance. If no message specified the warning box will not be shown.
@@ -1611,6 +1613,12 @@ galaxy:
   # see dataset paths.
   #expose_dataset_path: false
 
+  # XML config file that contains the job metric collection
+  # configuration.
+  # The value of this option will be resolved with respect to
+  # <config_dir>.
+  #job_metrics_config_file: job_metrics_conf.xml
+
   # This option allows users to see the job metrics (except for
   # environment variables).
   #expose_potentially_sensitive_job_metrics: false
@@ -1815,7 +1823,7 @@ galaxy:
   #markdown_export_css_pages: markdown_export_pages.css
 
   # CSS file to apply to invocation report exports to PDF. Generally
-  # prefer  markdown_export_css, but this is here for deployments that
+  # prefer markdown_export_css, but this is here for deployments that
   # would like to tailor different kinds of exports.
   #markdown_export_css_invocation_reports: markdown_export_invocation_reports.css
 
diff --git a/lib/galaxy/config/sample/tool_shed.yml.sample b/lib/galaxy/config/sample/tool_shed.yml.sample
index 2e1934d55fa..0c4c9907021 100644
--- a/lib/galaxy/config/sample/tool_shed.yml.sample
+++ b/lib/galaxy/config/sample/tool_shed.yml.sample
@@ -344,6 +344,14 @@ tool_shed:
   # the registration.
   #blacklist_file: config/disposable_email_blacklist.conf
 
+  # E-mail domains whitelist is used to specify allowed email address
+  # domains. If the list is non-empty and a user attempts registration
+  # using an email address belonging to a domain that is not on the
+  # list, registration will be enied. This is a more restrictive option
+  # than <blacklist_file>, and therefore, in case <whitelist_file> is
+  # defined, <blacklist_file> will be ignored.
+  #whitelist_file: disposable_email_whitelist.conf
+
   # Append "/{brand}" to the "Galaxy" text in the masthead.
   #brand: null
 
diff --git a/lib/galaxy/config/schema.py b/lib/galaxy/config/schema.py
index 780f6763ac5..66e3905881f 100644
--- a/lib/galaxy/config/schema.py
+++ b/lib/galaxy/config/schema.py
@@ -1,8 +1,16 @@
-from galaxy.util.yaml_util import (
-    OPTION_DEFAULTS,
-    ordered_load,
-)
+import logging
 
+from galaxy.exceptions import ConfigurationError
+from galaxy.util.yaml_util import ordered_load
+
+log = logging.getLogger(__name__)
+
+OPTION_DEFAULTS = {
+    "type": "str",
+    "unknown_option": False,
+    "default": None,
+    "desc": None,
+}
 
 UNKNOWN_OPTION = {
     "type": "str",
@@ -33,8 +41,70 @@ class AppSchema(Schema):
         self.raw_schema = self._read_schema(schema_path)
         self.description = self.raw_schema.get("desc", None)
         app_schema = self.raw_schema['mapping'][app_name]['mapping']
+        self._preprocess(app_schema)
         super(AppSchema, self).__init__(app_schema)
 
     def _read_schema(self, path):
         with open(path, "r") as f:
             return ordered_load(f)
+
+    def _preprocess(self, app_schema):
+        """Populate schema collections used for app configuration."""
+        self._defaults = {}  # {config option: default value or null}
+        self._reloadable_options = set()  # config options we can reload at runtime
+        self._paths_to_resolve = {}  # {config option: referenced config option}
+        for key, data in app_schema.items():
+            self._defaults[key] = data.get('default')
+            if data.get('reloadable'):
+                self._reloadable_options.add(key)
+            if data.get('path_resolves_to'):
+                self._paths_to_resolve[key] = data.get('path_resolves_to')
+
+    @property
+    def defaults(self):
+        return self._defaults
+
+    @property
+    def paths_to_resolve(self):
+        return self._paths_to_resolve
+
+    @property
+    def reloadable_options(self):
+        return self._reloadable_options
+
+    def validate_path_resolution_graph(self):
+        """This method is for tests only: we SHOULD validate the schema's path resolution graph
+           as part of automated testing; but we should NOT validate it at runtime.
+        """
+        def check_exists(option, key):
+            if not option:
+                message = "Invalid schema: property '{}' listed as path resolution target " \
+                    "for '{}' does not exist".format(resolves_to, key)
+                raise_error(message)
+
+        def check_type_is_str(option, key):
+            if option.get('type') != 'str':
+                message = "Invalid schema: property '{}' should have type 'str'".format(key)
+                raise_error(message)
+
+        def check_is_dag():
+            visited = set()
+            for key in self.paths_to_resolve:
+                visited.clear()
+                while key:
+                    visited.add(key)
+                    key = self.app_schema[key].get('path_resolves_to')
+                    if key and key in visited:
+                        raise_error('Invalid schema: cycle detected')
+
+        def raise_error(message):
+            log.error(message)
+            raise ConfigurationError(message)
+
+        for key, resolves_to in self.paths_to_resolve.items():
+            print(key)
+            parent = self.app_schema.get(resolves_to)
+            check_exists(parent, key)
+            check_type_is_str(parent, key)
+            check_type_is_str(self.app_schema[key], key)
+        check_is_dag()  # must be called last: walks entire graph
diff --git a/lib/galaxy/model/migrate/check.py b/lib/galaxy/model/migrate/check.py
index 0feaaefa789..a5c9388dd54 100644
--- a/lib/galaxy/model/migrate/check.py
+++ b/lib/galaxy/model/migrate/check.py
@@ -61,8 +61,7 @@ def create_or_verify_database(url, galaxy_config_file, engine_options={}, app=No
         # Apply all scripts to get to current version
         migrate_to_current_version(engine, db_schema)
 
-    meta = MetaData(bind=engine)
-    if new_database:
+    def migrate_from_scratch():
         log.info("Creating new database from scratch, skipping migrations")
         current_version = migrate_repository.version().version
         mapping.init(file_path='/tmp', url=url, map_install_models=map_install_models, create_tables=True)
@@ -70,6 +69,13 @@ def create_or_verify_database(url, galaxy_config_file, engine_options={}, app=No
         db_schema = schema.ControlledSchema(engine, migrate_repository)
         assert db_schema.version == current_version
         migrate()
+        if app:
+            # skips the tool migration process.
+            app.new_installation = True
+
+    meta = MetaData(bind=engine)
+    if new_database:
+        migrate_from_scratch()
         return
     elif app and getattr(app.config, 'database_auto_migrate', False):
         migrate()
@@ -79,12 +85,9 @@ def create_or_verify_database(url, galaxy_config_file, engine_options={}, app=No
     try:
         Table("dataset", meta, autoload=True)
     except NoSuchTableError:
-        # No 'dataset' table means a completely uninitialized database.  If we have an app, we'll
-        # set its new_installation setting to True so the tool migration process will be skipped.
-        if app:
-            app.new_installation = True
+        # No 'dataset' table means a completely uninitialized database.
         log.info("No database, initializing")
-        migrate()
+        migrate_from_scratch()
         return
     try:
         hda_table = Table("history_dataset_association", meta, autoload=True)
diff --git a/lib/galaxy/model/security.py b/lib/galaxy/model/security.py
index ec728dc6143..a73e4967f51 100644
--- a/lib/galaxy/model/security.py
+++ b/lib/galaxy/model/security.py
@@ -658,8 +658,7 @@ class GalaxyRBACAgent(RBACAgent):
 
     def create_user_role(self, user, app):
         # Create private user role if necessary
-        if not self.get_private_user_role(user):
-            self.create_private_user_role(user)
+        self.get_private_user_role(user, auto_create=True)
         # Create default user permissions if necessary
         if not user.default_permissions:
             if hasattr(app.config, "new_user_dataset_access_role_default_private"):
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index 82d4878eb14..b1dccf8b249 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -82,7 +82,7 @@ class ObjectStore(object):
         000/obj.id)
     """
 
-    def __init__(self, config, config_dict={}, **kwargs):
+    def __init__(self, config, config_dict=None, **kwargs):
         """
         :type config: object
         :param config: An object, most likely populated from
@@ -95,6 +95,8 @@ class ObjectStore(object):
               parent directory those directories will be created.
             * new_file_path -- Used to set the 'temp' extra_dir.
         """
+        if config_dict is None:
+            config_dict = {}
         self.running = True
         self.config = config
         self.check_old_style = config.object_store_check_old_style
diff --git a/lib/galaxy/objectstore/s3.py b/lib/galaxy/objectstore/s3.py
index 0ecd8891447..a1729498391 100644
--- a/lib/galaxy/objectstore/s3.py
+++ b/lib/galaxy/objectstore/s3.py
@@ -125,7 +125,8 @@ class CloudConfigMixin(object):
             'cache': {
                 'size': self.cache_size,
                 'path': self.staging_path,
-            }
+            },
+            'enable_cache_monitor': False,
         }
 
 
@@ -138,7 +139,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
     store_type = 's3'
 
     def __init__(self, config, config_dict):
-        super(S3ObjectStore, self).__init__(config)
+        super(S3ObjectStore, self).__init__(config, config_dict)
 
         self.transfer_progress = 0
 
@@ -146,6 +147,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         bucket_dict = config_dict['bucket']
         connection_dict = config_dict.get('connection', {})
         cache_dict = config_dict['cache']
+        self.enable_cache_monitor = config_dict.get('enable_cache_monitor', True)
 
         self.access_key = auth_dict.get('access_key')
         self.secret_key = auth_dict.get('secret_key')
@@ -167,9 +169,6 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             (e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
         self.extra_dirs.update(extra_dirs)
 
-        log.debug("Object cache dir:    %s", self.staging_path)
-        log.debug("       job work dir: %s", self.extra_dirs['job_work'])
-
         self._initialize()
 
     def _initialize(self):
@@ -187,9 +186,17 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                          'conn_path': self.conn_path}
 
         self._configure_connection()
-        self.bucket = self._get_bucket(self.bucket)
+        self._bucket = self._get_bucket(self.bucket)
+        self.start_cache_monitor()
+        # Test if 'axel' is available for parallel download and pull the key into cache
+        if which('axel'):
+            self.use_axel = True
+        else:
+            self.use_axel = False
+
+    def start_cache_monitor(self):
         # Clean cache only if value is set in galaxy.ini
-        if self.cache_size != -1:
+        if self.cache_size != -1 and self.enable_cache_monitor:
             # Convert GBs to bytes for comparison
             self.cache_size = self.cache_size * 1073741824
             # Helper for interruptable sleep
@@ -197,11 +204,6 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             self.cache_monitor_thread = threading.Thread(target=self.__cache_monitor)
             self.cache_monitor_thread.start()
             log.info("Cache cleaner manager started")
-        # Test if 'axel' is available for parallel download and pull the key into cache
-        if which('axel'):
-            self.use_axel = True
-        else:
-            self.use_axel = False
 
     def _configure_connection(self):
         log.debug("Configuring S3 Connection")
@@ -325,7 +327,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # alt_name can contain parent directory references, but S3 will not
             # follow them, so if they are valid we normalize them out
             alt_name = os.path.normpath(alt_name)
-        rel_path = os.path.join(*directory_hash_id(obj.id))
+        rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
         if extra_dir is not None:
             if extra_dir_at_root:
                 rel_path = os.path.join(extra_dir, rel_path)
@@ -334,7 +336,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
 
         # for JOB_WORK directory
         if obj_dir:
-            rel_path = os.path.join(rel_path, str(obj.id))
+            rel_path = os.path.join(rel_path, str(self._get_object_id(obj)))
         if base_dir:
             base = self.extra_dirs.get(base_dir)
             return os.path.join(base, rel_path)
@@ -343,7 +345,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         rel_path = '%s/' % rel_path
 
         if not dir_only:
-            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % self._get_object_id(obj))
         return rel_path
 
     def _get_cache_path(self, rel_path):
@@ -354,7 +356,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
 
     def _get_size_in_s3(self, rel_path):
         try:
-            key = self.bucket.get_key(rel_path)
+            key = self._bucket.get_key(rel_path)
             if key:
                 return key.size
         except S3ResponseError:
@@ -367,19 +369,17 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # A hackish way of testing if the rel_path is a folder vs a file
             is_dir = rel_path[-1] == '/'
             if is_dir:
-                keyresult = self.bucket.get_all_keys(prefix=rel_path)
+                keyresult = self._bucket.get_all_keys(prefix=rel_path)
                 if len(keyresult) > 0:
                     exists = True
                 else:
                     exists = False
             else:
-                key = Key(self.bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 exists = key.exists()
         except S3ResponseError:
             log.exception("Trouble checking existence of S3 key '%s'", rel_path)
             return False
-        if rel_path[0] == '/':
-            raise
         return exists
 
     def _in_cache(self, rel_path):
@@ -427,7 +427,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
     def _download(self, rel_path):
         try:
             log.debug("Pulling key '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
-            key = self.bucket.get_key(rel_path)
+            key = self._bucket.get_key(rel_path)
             # Test if cache is large enough to hold the new file
             if self.cache_size > 0 and key.size > self.cache_size:
                 log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
@@ -446,7 +446,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 key.get_contents_to_filename(self._get_cache_path(rel_path), cb=self._transfer_cb, num_cb=10)
                 return True
         except S3ResponseError:
-            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self.bucket.name)
+            log.exception("Problem downloading key '%s' from S3 bucket '%s'", rel_path, self._bucket.name)
         return False
 
     def _push_to_os(self, rel_path, source_file=None, from_string=None):
@@ -460,7 +460,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         try:
             source_file = source_file if source_file else self._get_cache_path(rel_path)
             if os.path.exists(source_file):
-                key = Key(self.bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 if os.path.getsize(source_file) == 0 and key.exists():
                     log.debug("Wanted to push file '%s' to S3 key '%s' but its size is 0; skipping.", source_file, rel_path)
                     return True
@@ -478,7 +478,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                                                        cb=self._transfer_cb,
                                                        num_cb=10)
                     else:
-                        multipart_upload(self.s3server, self.bucket, key.name, source_file, mb_size)
+                        multipart_upload(self.s3server, self._bucket, key.name, source_file, mb_size)
                     end_time = datetime.now()
                     log.debug("Pushed cache file '%s' to key '%s' (%s bytes transfered in %s sec)",
                               source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
@@ -547,7 +547,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             alt_name = kwargs.get('alt_name', None)
 
             # Construct hashed path
-            rel_path = os.path.join(*directory_hash_id(obj.id))
+            rel_path = os.path.join(*directory_hash_id(self._get_object_id(obj)))
 
             # Optionally append extra_dir
             if extra_dir is not None:
@@ -568,7 +568,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # self._push_to_os(s3_dir, from_string='')
             # If instructed, create the dataset in cache & in S3
             if not dir_only:
-                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % self._get_object_id(obj))
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
@@ -609,7 +609,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             # but requires iterating through each individual key in S3 and deleing it.
             if entire_dir and extra_dir:
                 shutil.rmtree(self._get_cache_path(rel_path))
-                results = self.bucket.get_all_keys(prefix=rel_path)
+                results = self._bucket.get_all_keys(prefix=rel_path)
                 for key in results:
                     log.debug("Deleting key %s", key.name)
                     key.delete()
@@ -619,7 +619,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 os.unlink(self._get_cache_path(rel_path))
                 # Delete from S3 as well
                 if self._key_exists(rel_path):
-                    key = Key(self.bucket, rel_path)
+                    key = Key(self._bucket, rel_path)
                     log.debug("Deleting key %s", key.name)
                     key.delete()
                     return True
@@ -707,7 +707,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         if self.exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
-                key = Key(self.bucket, rel_path)
+                key = Key(self._bucket, rel_path)
                 return key.generate_url(expires_in=86400)  # 24hrs
             except S3ResponseError:
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
@@ -716,6 +716,14 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
     def get_store_usage_percent(self):
         return 0.0
 
+    def shutdown(self):
+        self.running = False
+        thread = getattr(self, 'cache_monitor_thread', None)
+        if thread:
+            log.debug("Shutting down thread")
+            self.sleeper.wake()
+            thread.join(5)
+
 
 class SwiftObjectStore(S3ObjectStore):
     """
diff --git a/lib/galaxy/security/validate_user_input.py b/lib/galaxy/security/validate_user_input.py
index ae5dc840910..d81f7ef5398 100644
--- a/lib/galaxy/security/validate_user_input.py
+++ b/lib/galaxy/security/validate_user_input.py
@@ -39,6 +39,13 @@ def validate_email(trans, email, user=None, check_dup=True, allow_empty=False):
         message = "Email address cannot be more than %d characters in length." % EMAIL_MAX_LEN
     elif check_dup and trans.sa_session.query(trans.app.model.User).filter(func.lower(trans.app.model.User.table.c.email) == email.lower()).first():
         message = "User with email '%s' already exists." % email
+    #  If the whitelist is not empty filter out any domain not in the list and ignore blacklist.
+    elif trans.app.config.whitelist_content is not None:
+        domain = email.split('@')[1]
+        if len(domain.split('.')) > 2:
+            domain = ('.').join(domain.split('.')[-2:])
+        if domain not in trans.app.config.whitelist_content:
+            message = "Please enter an allowed domain email address for this server."
     #  If the blacklist is not empty filter out the disposable domains.
     elif trans.app.config.blacklist_content is not None:
         domain = email.split('@')[1]
diff --git a/lib/galaxy/selenium/navigation.yml b/lib/galaxy/selenium/navigation.yml
index ae2678deb0f..bb2960f278f 100644
--- a/lib/galaxy/selenium/navigation.yml
+++ b/lib/galaxy/selenium/navigation.yml
@@ -60,6 +60,7 @@ masthead:
     # user menu
     logout: 'Logout'
     custom_builds: 'Custom Builds'
+    preferences: 'Preferences'
     histories: 'Histories'
     pages: 'Pages'
 
@@ -67,6 +68,21 @@ masthead:
     libraries: 'Data Libraries'
     published_histories: 'Histories'
 
+preferences:
+  selectors:
+    manage_information: '#edit-preferences-information'
+    current_email: "#user-preferences-current-email"
+
+change_user_email:
+  selectors:
+    submit: '#submit'
+
+change_user_address:
+  selectors:
+    address_button:
+      type: xpath
+      selector: '//span[contains(text(), "Insert Address")]'
+
 history_panel:
   menu:
     labels:
@@ -294,7 +310,7 @@ workflow_editor:
     label_input: "[tour_id='__label'] input"
     annotation_input: "[tour_id='__annotation'] textarea"
 
-    connector_for: "canvas[handle1-id='${source_id}'][handle2-id='${sink_id}']"
+    connector_for: "div[handle1-id='${source_id}'][handle2-id='${sink_id}']"
 
     connector_destroy_callout: '.delete-terminal'
 
diff --git a/lib/galaxy/tool_shed/galaxy_install/install_manager.py b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
index db53e270cec..f8091aa5631 100644
--- a/lib/galaxy/tool_shed/galaxy_install/install_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/install_manager.py
@@ -215,10 +215,6 @@ class InstallToolDependencyManager(object):
                         if tool_dependency and tool_dependency.status in [self.install_model.ToolDependency.installation_status.INSTALLED,
                                                                           self.install_model.ToolDependency.installation_status.ERROR]:
                             installed_packages.append(tool_dependency)
-                            if self.app.config.manage_dependency_relationships:
-                                # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager.
-                                self.app.installed_repository_manager.handle_tool_dependency_install(tool_shed_repository,
-                                                                                                     tool_dependency)
         return installed_packages
 
     def install_via_fabric(self, tool_shed_repository, tool_dependency, install_dir, package_name=None, custom_fabfile_path=None,
@@ -946,10 +942,6 @@ class InstallRepositoryManager(object):
                 basic_util.remove_dir(work_dir)
             self.update_tool_shed_repository_status(tool_shed_repository,
                                                     self.install_model.ToolShedRepository.installation_status.INSTALLED)
-            if self.app.config.manage_dependency_relationships:
-                # Add the installed repository and any tool dependencies to the in-memory dictionaries
-                # in the installed_repository_manager.
-                self.app.installed_repository_manager.handle_repository_install(tool_shed_repository)
         else:
             # An error occurred while cloning the repository, so reset everything necessary to enable another attempt.
             repository_util.set_repository_attributes(self.app,
diff --git a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
index 58f3ba686d6..3ccd62febb7 100644
--- a/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
+++ b/lib/galaxy/tool_shed/galaxy_install/installed_repository_manager.py
@@ -79,9 +79,6 @@ class InstalledRepositoryManager(object):
         # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key
         # at runtime.  The value defines the entire tool dependency tree.
         self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
-        if app.config.manage_dependency_relationships:
-            # Load defined dependency relationships for installed tool shed repositories and their contents.
-            self.load_dependency_relationships()
 
     def activate_repository(self, repository):
         """Activate an installed tool shed repository that has been marked as deactivated."""
@@ -651,90 +648,6 @@ class InstalledRepositoryManager(object):
                     deleted_tool_dependency_names.append(original_dependency_val_dict['name'])
         return updated_tool_dependency_names, deleted_tool_dependency_names
 
-    def handle_repository_install(self, repository):
-        """Load the dependency relationships for a repository that was just installed or reinstalled."""
-        # Populate self.repository_dependencies_of_installed_repositories.
-        self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_repository_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-        # Populate self.tool_dependencies_of_installed_repositories.
-        self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-        # Populate self.installed_tool_dependencies_of_installed_repositories.
-        self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        for tool_dependency in repository.tool_dependencies:
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
-    def handle_repository_uninstall(self, repository):
-        """Remove the dependency relationships for a repository that was just uninstalled."""
-        for tool_dependency in repository.tool_dependencies:
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            # Remove this tool_dependency from all values in
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {}
-            for (td_tup, installed_runtime_dependent_tool_dependency_tups) in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items():
-                if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups:
-                    # Remove the tool_dependency from the list.
-                    installed_runtime_dependent_tool_dependency_tups.remove(tool_dependency_tup)
-                # Add the possibly altered list to the altered dictionary.
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[td_tup] = \
-                    installed_runtime_dependent_tool_dependency_tups
-            self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \
-                altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies
-            # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Remove the entry for this tool_dependency from
-            # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-        # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.tool_dependencies_of_installed_repositories
-        self.remove_entry_from_tool_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_installed_repository_dependencies_of_installed_repositories(repository)
-        # Remove this repository's entry from self.repository_dependencies_of_installed_repositories.
-        self.remove_entry_from_repository_dependencies_of_installed_repositories(repository)
-
-    def handle_tool_dependency_install(self, repository, tool_dependency):
-        """Load the dependency relationships for a tool dependency that was just installed independently of its containing repository."""
-        # The received repository must have a status of 'Installed'.  The value of tool_dependency.status will either be
-        # 'Installed' or 'Error', but we only need to change the in-memory dictionaries if it is 'Installed'.
-        if tool_dependency.is_installed:
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            repository_tup = self.get_repository_tuple_for_installed_repository_manager(repository)
-            tool_dependency_tup = self.get_tool_dependency_tuple_for_installed_repository_manager(tool_dependency)
-            if repository_tup in self.installed_tool_dependencies_of_installed_repositories:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup].append(tool_dependency_tup)
-            else:
-                self.installed_tool_dependencies_of_installed_repositories[repository_tup] = [tool_dependency_tup]
-
-    def load_dependency_relationships(self):
-        """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries."""
-        # Get the list of installed tool shed repositories.
-        for repository in self.context.query(self.app.install_model.ToolShedRepository) \
-                                      .filter(self.app.install_model.ToolShedRepository.table.c.status ==
-                                              self.app.install_model.ToolShedRepository.installation_status.INSTALLED):
-            # Populate self.repository_dependencies_of_installed_repositories.
-            self.add_entry_to_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_repository_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_repository_dependencies_of_installed_repositories(repository)
-            # Populate self.tool_dependencies_of_installed_repositories.
-            self.add_entry_to_tool_dependencies_of_installed_repositories(repository)
-            # Populate self.installed_tool_dependencies_of_installed_repositories.
-            self.add_entry_to_installed_tool_dependencies_of_installed_repositories(repository)
-        # Get the list of installed tool dependencies.
-        for tool_dependency in self.context.query(self.app.install_model.ToolDependency) \
-                                           .filter(self.app.install_model.ToolDependency.table.c.status ==
-                                                   self.app.install_model.ToolDependency.installation_status.INSTALLED):
-            # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-            # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.
-            self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies(tool_dependency)
-
     def load_proprietary_datatypes(self):
         cdl = custom_datatype_manager.CustomDatatypeLoader(self.app)
         for tool_shed_repository in self.context.query(self.install_model.ToolShedRepository) \
@@ -814,10 +727,6 @@ class InstalledRepositoryManager(object):
         if remove_from_disk:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.UNINSTALLED
             repository.error_message = None
-            if self.app.config.manage_dependency_relationships:
-                # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the
-                # installed_repository_manager.
-                self.handle_repository_uninstall(repository)
         else:
             repository.status = self.app.install_model.ToolShedRepository.installation_status.DEACTIVATED
         self.app.install_model.context.current.add(repository)
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
index a6f830e746a..8f64a80c050 100644
--- a/lib/galaxy/tools/parameters/basic.py
+++ b/lib/galaxy/tools/parameters/basic.py
@@ -1913,7 +1913,7 @@ class DataToolParameter(BaseDataToolParameter):
             ref = getattr(ref, attribute)
         if call_attribute:
             ref = ref()
-        return ref
+        return str(ref)
 
     def to_dict(self, trans, other_values={}):
         # create dictionary and fill default parameters
diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py
index 129dd3909b2..070791cf08f 100644
--- a/lib/galaxy/tools/toolbox/base.py
+++ b/lib/galaxy/tools/toolbox/base.py
@@ -1217,9 +1217,10 @@ class BaseGalaxyToolBox(AbstractToolBox):
             return
         app_config_dict = self.app.config.config_dict
         conf_file = app_config_dict.get("dependency_resolvers_config_file")
-        default_tool_dependency_dir = os.path.join(self.app.config.data_dir, self.app.config.appschema['tool_dependency_dir'].get('default'))
-        self.dependency_manager = build_dependency_manager(app_config_dict=app_config_dict, conf_file=conf_file,
-                                                           default_tool_dependency_dir=default_tool_dependency_dir)
+        default_tool_dependency_dir = os.path.join(
+            self.app.config.data_dir, self.app.config.schema.defaults['tool_dependency_dir'])
+        self.dependency_manager = build_dependency_manager(
+            app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir=default_tool_dependency_dir)
 
     def reload_dependency_manager(self):
         self._init_dependency_manager()
diff --git a/lib/galaxy/util/yaml_util.py b/lib/galaxy/util/yaml_util.py
index 70f4683359d..bb466a96981 100644
--- a/lib/galaxy/util/yaml_util.py
+++ b/lib/galaxy/util/yaml_util.py
@@ -10,13 +10,6 @@ from yaml.constructor import ConstructorError
 
 log = logging.getLogger(__name__)
 
-OPTION_DEFAULTS = {
-    "type": "str",
-    "unknown_option": False,
-    "default": None,
-    "desc": None,
-}
-
 
 class OrderedLoader(yaml.SafeLoader):
     # This class was pulled out of ordered_load() for the sake of
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index 692a0e4a3b4..d8529ef43fd 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -537,15 +537,6 @@ mapping:
           server process should be able to check for repository updates.  The
           setting for hours_between_check should be an integer between 1 and 24.
 
-      manage_dependency_relationships:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          Enable use of an in-memory registry with bi-directional relationships between
-          repositories (i.e., in addition to lists of dependencies for a repository,
-          keep an in-memory registry of dependent items for each repository.
-
       tool_data_table_config_path:
         type: str
         default: config/tool_data_table_conf.xml
@@ -911,6 +902,18 @@ mapping:
 
           Example value 'config/disposable_email_blacklist.conf'
 
+      whitelist_file:
+        type: str
+        default: disposable_email_whitelist.conf
+        path_resolves_to: config_dir
+        required: false
+        desc: |
+          E-mail domains whitelist is used to specify allowed email address domains.
+          If the list is non-empty and a user attempts registration using an email
+          address belonging to a domain that is not on the list, registration will be
+          enied. This is a more restrictive option than <blacklist_file>, and therefore,
+          in case <whitelist_file> is defined, <blacklist_file> will be ignored.
+
       registration_warning_message:
         type: str
         default: >-
@@ -2417,6 +2420,15 @@ mapping:
           Details" option in the history. This option also exposes the command line to
           non-administrative users. Administrators can always see dataset paths.
 
+      job_metrics_config_file:
+        type: str
+        default: job_metrics_conf.xml
+        required: false
+        desc: |
+          XML config file that contains the job metric collection configuration.
+
+          The value of this option will be resolved with respect to <config_dir>.
+
       expose_potentially_sensitive_job_metrics:
         type: bool
         default: false
@@ -2728,7 +2740,7 @@ mapping:
         default: markdown_export_pages.css
         required: false
         desc: |
-          CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer 
+          CSS file to apply to "Galaxy Page" exports to PDF. Generally prefer
           markdown_export_css, but this is here for deployments that
           would like to tailor different kinds of exports.
 
@@ -2737,7 +2749,7 @@ mapping:
         default: markdown_export_invocation_reports.css
         required: false
         desc: |
-          CSS file to apply to invocation report exports to PDF. Generally prefer 
+          CSS file to apply to invocation report exports to PDF. Generally prefer
           markdown_export_css, but this is here for deployments that
           would like to tailor different kinds of exports.
 
diff --git a/lib/galaxy_test/selenium/test_personal_information.py b/lib/galaxy_test/selenium/test_personal_information.py
new file mode 100644
index 00000000000..4de0dd03060
--- /dev/null
+++ b/lib/galaxy_test/selenium/test_personal_information.py
@@ -0,0 +1,111 @@
+from .framework import (
+    selenium_test,
+    SeleniumTestCase,
+)
+
+
+class ManageInformationTestCase(SeleniumTestCase):
+
+    @selenium_test
+    def test_change_email(self):
+        def assert_email(email_to_check):
+            self.assertTrue(email_to_check == self.driver.find_element_by_id("user-preferences-current-email").text)
+
+        email = self._get_random_email()
+        self.register(email)
+        self.navigate_to_user_preferences()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # rendered email should be equal
+        assert_email(email)
+
+        self.components.preferences.manage_information.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        new_email = self._get_random_email()
+        # new email should be different from initially registered
+        self.assertTrue(email != new_email)
+        email_input_field = self.driver.find_element_by_css_selector("[tour_id='email'] input")
+
+        self.clear_input_field_and_write(email_input_field, new_email)
+        self.components.change_user_email.submit.wait_for_and_click()
+
+        # UX_RENDER time sometimes is not enough
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        # email should be changed
+        assert_email(new_email)
+
+    @selenium_test
+    def test_public_name(self):
+        def get_name_input_field():
+            return self.driver.find_element_by_css_selector("[tour_id='username'] input")
+
+        def assert_public_name(expected_name):
+            self.assertTrue(expected_name == get_name_input_field().get_attribute('value'))
+
+        public_name = "user-public-name"
+        self.register(username=public_name)
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # make sure that public name is the same as registered
+        assert_public_name(public_name)
+        new_public_name = "new-public-name"
+        # change public name
+        self.clear_input_field_and_write(get_name_input_field(), new_public_name)
+        self.components.change_user_email.submit.wait_for_and_click()
+
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+        # public name field should render new public name
+        assert_public_name(new_public_name)
+
+    @selenium_test
+    def test_user_address(self):
+        def get_address_form():
+            return self.driver.find_element_by_css_selector("div.ui-portlet-section > div.portlet-content")
+
+        self.register(self._get_random_email())
+        self.navigate_to_manage_information()
+        self.components.change_user_address.address_button.wait_for_and_click()
+
+        address_field_labels = ["Short address description", "Name", "Institution", "Address", "City",
+                                "State/Province/Region", "Postal Code", "Country", "Phone"]
+
+        address_fields = {}
+        # fill address fields with random data
+        for input_field_label in address_field_labels:
+            input_value = self._get_random_name(prefix=input_field_label)
+            address_fields[input_field_label] = input_value
+            input_field = self.get_address_input_field(get_address_form(), input_field_label)
+            self.clear_input_field_and_write(input_field, input_value)
+        # save new address
+        self.components.change_user_email.submit.wait_for_and_click()
+        self.sleep_for(self.wait_types.UX_TRANSITION)
+
+        self.navigate_to_manage_information()
+        self.sleep_for(self.wait_types.UX_RENDER)
+
+        # check if address was saved correctly
+        for input_field_label in address_fields.keys():
+            input_field = self.get_address_input_field(get_address_form(), input_field_label)
+            self.assertTrue(input_field.get_attribute('value') == address_fields[input_field_label])
+
+    def navigate_to_user_preferences(self):
+        self.home()
+        self.click_masthead_user()
+        self.components.masthead.preferences.wait_for_and_click()
+
+    def navigate_to_manage_information(self):
+        self.navigate_to_user_preferences()
+        self.components.preferences.manage_information.wait_for_and_click()
+
+    def clear_input_field_and_write(self, element, new_input_text):
+        element.clear()
+        element.send_keys(new_input_text)
+
+    def get_address_input_field(self, address_form, input_field_label):
+        return address_form.find_element_by_css_selector("[data-label='" + input_field_label + "'] > input")
diff --git a/lib/tool_shed/webapp/config.py b/lib/tool_shed/webapp/config.py
index 424207d353f..df627d91643 100644
--- a/lib/tool_shed/webapp/config.py
+++ b/lib/tool_shed/webapp/config.py
@@ -10,6 +10,7 @@ from datetime import timedelta
 from six.moves import configparser
 
 from galaxy.config import BaseAppConfiguration
+from galaxy.config.schema import AppSchema
 from galaxy.util import string_as_bool
 from galaxy.version import VERSION, VERSION_MAJOR
 from galaxy.web.formatting import expand_pretty_datetime_format
@@ -19,6 +20,9 @@ log = logging.getLogger(__name__)
 ts_webapp_path = os.path.abspath(os.path.dirname(__file__))
 templates_path = os.path.join(ts_webapp_path, "templates")
 
+TOOLSHED_APP_NAME = 'tool_shed'
+TOOLSHED_CONFIG_SCHEMA_PATH = 'lib/tool_shed/webapp/config_schema.yml'
+
 
 def resolve_path(path, root):
     """If 'path' is relative make absolute by prepending 'root'"""
@@ -34,6 +38,18 @@ class ConfigurationError(Exception):
 class ToolShedAppConfiguration(BaseAppConfiguration):
     default_config_file_name = 'tool_shed.yml'
 
+    def _load_schema(self):
+        return AppSchema(TOOLSHED_CONFIG_SCHEMA_PATH, TOOLSHED_APP_NAME)
+
+    def _update_raw_config_from_kwargs(self, kwargs):
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
+
+    def _create_attributes_from_raw_config(self):
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
+
+    def _resolve_paths(self, paths_to_resolve):
+        pass  # Intentionally does nothing. To enable, remove + call base __init__().
+
     def __init__(self, **kwargs):
         self.config_dict = kwargs
         self.root = kwargs.get('root_dir', '.')
diff --git a/lib/tool_shed/webapp/config_schema.yml b/lib/tool_shed/webapp/config_schema.yml
index cc014e2c630..9de65d6ef68 100644
--- a/lib/tool_shed/webapp/config_schema.yml
+++ b/lib/tool_shed/webapp/config_schema.yml
@@ -482,6 +482,18 @@ mapping:
           disposable email address during the registration.  If their address domain
           matches any domain in the blacklist, they are refused the registration.
 
+      whitelist_file:
+        type: str
+        default: disposable_email_whitelist.conf
+        path_resolves_to: config_dir
+        required: false
+        desc: |
+          E-mail domains whitelist is used to specify allowed email address domains.
+          If the list is non-empty and a user attempts registration using an email
+          address belonging to a domain that is not on the list, registration will be
+          enied. This is a more restrictive option than <blacklist_file>, and therefore,
+          in case <whitelist_file> is defined, <blacklist_file> will be ignored.
+
       brand:
         type: str
         default: null
diff --git a/static/erricon.ico b/static/erricon.ico
new file mode 100644
index 00000000000..c5ee4d32e54
Binary files /dev/null and b/static/erricon.ico differ
diff --git a/test/integration/objectstore/test_swift_objectstore.py b/test/integration/objectstore/test_swift_objectstore.py
new file mode 100644
index 00000000000..c3e90af1506
--- /dev/null
+++ b/test/integration/objectstore/test_swift_objectstore.py
@@ -0,0 +1,113 @@
+
+import os
+import string
+import subprocess
+
+from galaxy_test.driver import integration_util
+
+OBJECT_STORE_HOST = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_HOST', '127.0.0.1')
+OBJECT_STORE_PORT = int(os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_PORT', 9000))
+OBJECT_STORE_ACCESS_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_ACCESS_KEY', 'minioadmin')
+OBJECT_STORE_SECRET_KEY = os.environ.get('GALAXY_INTEGRATION_OBJECT_STORE_SECRET_KEY', 'minioadmin')
+OBJECT_STORE_CONFIG = string.Template("""
+<object_store type="hierarchical" id="primary">
+    <backends>
+        <object_store id="swifty" type="swift" weight="1" order="0">
+            <auth access_key="${access_key}" secret_key="${secret_key}" />
+            <bucket name="galaxy" use_reduced_redundancy="False" max_chunk_size="250"/>
+            <connection host="${host}" port="${port}" is_secure="False" conn_path="" multipart="True"/>
+            <cache path="${temp_directory}/object_store_cache" size="1000" />
+            <extra_dir type="job_work" path="${temp_directory}/job_working_directory_swift"/>
+            <extra_dir type="temp" path="${temp_directory}/tmp_swift"/>
+        </object_store>
+    </backends>
+</object_store>
+""")
+TEST_TOOL_IDS = [
+    "multi_output",
+    "multi_output_configured",
+    "multi_output_assign_primary",
+    "multi_output_recurse",
+    "tool_provided_metadata_1",
+    "tool_provided_metadata_2",
+    "tool_provided_metadata_3",
+    "tool_provided_metadata_4",
+    "tool_provided_metadata_5",
+    "tool_provided_metadata_6",
+    "tool_provided_metadata_7",
+    "tool_provided_metadata_8",
+    "tool_provided_metadata_9",
+    "tool_provided_metadata_10",
+    "tool_provided_metadata_11",
+    "tool_provided_metadata_12",
+    "composite_output",
+    "composite_output_tests",
+    "metadata",
+    "metadata_bam",
+    "output_format",
+    "output_auto_format",
+]
+
+
+def start_minio(container_name):
+    minio_start_args = [
+        'docker',
+        'run',
+        '-p',
+        '{port}:9000'.format(port=OBJECT_STORE_PORT),
+        '-d',
+        '--name',
+        container_name,
+        # '--rm',
+        'minio/minio:latest',
+        'server',
+        '/tmp/data']
+    subprocess.check_call(minio_start_args)
+
+
+def stop_minio(container_name):
+    subprocess.check_call(['docker', 'rm', '-f', container_name])
+
+
+@integration_util.skip_unless_docker()
+class SwiftObjectStoreIntegrationTestCase(integration_util.IntegrationTestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.container_name = "%s_container" % cls.__name__
+        start_minio(cls.container_name)
+        super(SwiftObjectStoreIntegrationTestCase, cls).setUpClass()
+
+    @classmethod
+    def tearDownClass(cls):
+        stop_minio(cls.container_name)
+        super(SwiftObjectStoreIntegrationTestCase, cls).tearDownClass()
+
+    @classmethod
+    def handle_galaxy_config_kwds(cls, config):
+        temp_directory = cls._test_driver.mkdtemp()
+        cls.object_stores_parent = temp_directory
+        config_path = os.path.join(temp_directory, "object_store_conf.xml")
+        config["object_store_store_by"] = "uuid"
+        # This doesn't quite work yet, fails with extra_files_path
+        # config["metadata_strategy"] = "extended"
+        config["outpus_to_working_dir"] = True
+        config["retry_metadata_internally"] = False
+        with open(config_path, "w") as f:
+            f.write(
+                OBJECT_STORE_CONFIG.safe_substitute(
+                    {
+                        "temp_directory": temp_directory,
+                        "host": OBJECT_STORE_HOST,
+                        "port": OBJECT_STORE_PORT,
+                        "access_key": OBJECT_STORE_ACCESS_KEY,
+                        "secret_key": OBJECT_STORE_SECRET_KEY,
+                    }
+                )
+            )
+        config["object_store_config_file"] = config_path
+
+
+instance = integration_util.integration_module_instance(SwiftObjectStoreIntegrationTestCase)
+
+test_tools = integration_util.integration_tool_runner(TEST_TOOL_IDS)
diff --git a/test/integration/test_config_defaults.py b/test/integration/test_config_defaults.py
index c8d2ff5f26e..8c970a11c29 100644
--- a/test/integration/test_config_defaults.py
+++ b/test/integration/test_config_defaults.py
@@ -178,6 +178,7 @@ DO_NOT_TEST = [
     'id_secret',  # broken: default overridden
     'job_config',  # no obvious testable defaults
     'job_config_file',  # broken: remove 'config/' prefix from schema
+    'job_metrics_config_file',
     'job_working_directory',  # broken; may or may not be able to test
     'library_import_dir',  # broken: default overridden
     'logging',  # mapping loaded in config/
@@ -253,7 +254,7 @@ def get_config_data():
 
     create_driver()  # create + setup DRIVER
     parent_dirs = load_parent_dirs()  # called after DRIVER is setup
-    items = ((k, v) for k, v in DRIVER.app.config.appschema.items() if k not in DO_NOT_TEST)
+    items = ((k, v) for k, v in DRIVER.app.config.schema.app_schema.items() if k not in DO_NOT_TEST)
     for key, data in items:
         expected_value = get_expected(key, data, parent_dirs)
         loaded_value = getattr(DRIVER.app.config, key)
diff --git a/test/integration/test_config_schema.py b/test/integration/test_config_schema.py
new file mode 100644
index 00000000000..8766c91f660
--- /dev/null
+++ b/test/integration/test_config_schema.py
@@ -0,0 +1,9 @@
+from galaxy_test.driver import integration_util
+
+
+class ConfigSchemaTestCase(integration_util.IntegrationTestCase):
+
+    def test_schema_path_resolution_graph(self):
+        # Run schema's validation method; throws error if schema invalid
+        schema = self._app.config.schema
+        schema.validate_path_resolution_graph()
diff --git a/test/unit/config/test_load_config.py b/test/unit/config/test_load_config.py
index e6c9f36a370..f7deb4a49cf 100644
--- a/test/unit/config/test_load_config.py
+++ b/test/unit/config/test_load_config.py
@@ -1,9 +1,10 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.config.schema import AppSchema
 
 
-MOCK_PROPERTIES = {
+MOCK_SCHEMA = {
     'property1': {'default': 'a', 'type': 'str'},  # str
     'property2': {'default': 1, 'type': 'int'},  # int
     'property3': {'default': 1.0, 'type': 'float'},  # float
@@ -13,17 +14,14 @@ MOCK_PROPERTIES = {
 }
 
 
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
+
+
 @pytest.fixture
 def mock_init(monkeypatch):
-
-    def mock_load_schema(self):
-        self.appschema = MOCK_PROPERTIES
-
-    def mock_process_config(self, kwargs):
-        pass
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
 
 def test_load_config_from_schema(mock_init):
diff --git a/test/unit/config/test_path_graph.py b/test/unit/config/test_path_graph.py
index 7d3a3626653..73c719594ea 100644
--- a/test/unit/config/test_path_graph.py
+++ b/test/unit/config/test_path_graph.py
@@ -1,6 +1,7 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.config.schema import AppSchema
 from galaxy.exceptions import ConfigurationError
 
 
@@ -15,14 +16,11 @@ from galaxy.exceptions import ConfigurationError
 # whereas an invalid configuration raises an error.
 
 
-@pytest.fixture
-def mock_config(monkeypatch):
-    def mock_process_config(self, kwargs):
-        pass
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
 
 
-def test_basecase(mock_config, monkeypatch):
+def test_basecase(monkeypatch):
     # Check that a valid graph is loaded correctly (this graph has 2 components)
     mock_schema = {
         'component1_path0': {
@@ -48,12 +46,9 @@ def test_basecase(mock_config, monkeypatch):
             'default': 'value4',
             'path_resolves_to': 'component2_path0',
         },
-
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.component1_path0 == 'value0'
@@ -63,7 +58,7 @@ def test_basecase(mock_config, monkeypatch):
     assert config.component2_path1 == 'value3/value4'
 
 
-def test_resolves_to_invalid_property(mock_config, monkeypatch):
+def test_resolves_to_invalid_property(monkeypatch):
     # 'path_resolves_to' should point to an existing property in the schema
     mock_schema = {
         'path0': {
@@ -76,17 +71,13 @@ def test_resolves_to_invalid_property(mock_config, monkeypatch):
             'path_resolves_to': 'invalid',  # invalid
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_path_resolution_cycle(mock_config, monkeypatch):
+def test_path_resolution_cycle(monkeypatch):
     # Must be a DAG, but this one has a cycle
     mock_schema = {
         'path0': {
@@ -105,17 +96,13 @@ def test_path_resolution_cycle(mock_config, monkeypatch):
             'path_resolves_to': 'path1',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_path_invalid_type(mock_config, monkeypatch):
+def test_path_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
         'path0': {
@@ -128,17 +115,13 @@ def test_path_invalid_type(mock_config, monkeypatch):
             'path_resolves_to': 'path0',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_resolves_to_invalid_type(mock_config, monkeypatch):
+def test_resolves_to_invalid_type(monkeypatch):
     # Paths should be strings
     mock_schema = {
         'path0': {
@@ -151,17 +134,13 @@ def test_resolves_to_invalid_type(mock_config, monkeypatch):
             'path_resolves_to': 'path0',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
 
     with pytest.raises(ConfigurationError):
-        GalaxyAppConfiguration()
+        AppSchema(None, 'galaxy').validate_path_resolution_graph()
 
 
-def test_resolves_with_empty_component(mock_config, monkeypatch):
+def test_resolves_with_empty_component(monkeypatch):
     # A path can be None (root path is never None; may be asigned elsewhere)
     mock_schema = {
         'path0': {
@@ -178,11 +157,8 @@ def test_resolves_with_empty_component(mock_config, monkeypatch):
             'path_resolves_to': 'path1',
         },
     }
-
-    def mock_load_schema(self):
-        self.appschema = mock_schema
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(mock_schema))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
     assert config.path0 == 'value0'
diff --git a/test/unit/config/test_path_resolves_to.py b/test/unit/config/test_path_resolves_to.py
index 83b5c3198d1..439d2c6c001 100644
--- a/test/unit/config/test_path_resolves_to.py
+++ b/test/unit/config/test_path_resolves_to.py
@@ -1,6 +1,7 @@
 import pytest
 
 from galaxy.config import GalaxyAppConfiguration
+from galaxy.config.schema import AppSchema
 
 
 MOCK_DEPRECATED_DIRS = {
@@ -35,34 +36,23 @@ MOCK_SCHEMA = {
 }
 
 
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
+
+
 def test_deprecated_prefixes_set_correctly(monkeypatch):
     # Before we mock them, check that correct values are assigned
-    def mock_load_schema(self):
-        self.appschema = {}
-
-    def mock_process_config(self, kwargs):
-        pass
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
 
     config = GalaxyAppConfiguration()
-    expected_deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
-
-    assert config.deprecated_dirs == expected_deprecated_dirs
+    assert config.deprecated_dirs == {'config_dir': 'config', 'data_dir': 'database'}
 
 
 @pytest.fixture
 def mock_init(monkeypatch):
-
-    def mock_load_schema(self):
-        self.appschema = MOCK_SCHEMA
-
-    def mock_process_config(self, kwargs):
-        pass  # because we're done before this is called
-
-    monkeypatch.setattr(GalaxyAppConfiguration, '_load_schema', mock_load_schema)
-    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', mock_process_config)
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
     monkeypatch.setattr(GalaxyAppConfiguration, 'deprecated_dirs', MOCK_DEPRECATED_DIRS)
 
 
diff --git a/test/unit/config/test_reload_config.py b/test/unit/config/test_reload_config.py
index e63cdcbce0a..3064b0475ad 100644
--- a/test/unit/config/test_reload_config.py
+++ b/test/unit/config/test_reload_config.py
@@ -1,33 +1,41 @@
+import pytest
+
 from galaxy import config
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.config import reload_config_options
+from galaxy.config.schema import AppSchema
 
 
 R1, R2, N1, N2 = 'reloadable1', 'reloadable2', 'nonrelodable1', 'nonreloadable2'  # config options
 
-
-class MockGalaxyAppConfiguration():
-    def __init__(self, properties):
-        self.config_file = None
-        self.reloadable_options = {R1, R2}
-        self._raw_config = {}
-        for key, value in properties.items():
-            setattr(self, key, value)
-            self._raw_config[key] = value
-
-    def update_reloadable_property(self, key, value):
-        setattr(self, key, value)
+MOCK_SCHEMA = {
+    R1: {'reloadable': True, 'default': 1},
+    R2: {'reloadable': True, 'default': 2},
+    N1: {'default': 3},
+    N2: {'default': 4},
+}
 
 
-def test_update_property(monkeypatch):
+def get_schema(app_mapping):
+    return {'mapping': {'galaxy': {'mapping': app_mapping}}}
+
+
+@pytest.fixture
+def mock_init(monkeypatch):
+
+    monkeypatch.setattr(AppSchema, '_read_schema', lambda a, b: get_schema(MOCK_SCHEMA))
+    monkeypatch.setattr(GalaxyAppConfiguration, '_process_config', lambda a, b: None)
+
+
+def test_update_property(mock_init, monkeypatch):
     # This also covers adding a property. When a config file does not set a property,
     # that property is set to its default value. Thus, if we add a reloadable property
     # to the config file, it's the same as modifying that property's value.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, R2: 42, N1: 99}  # edits: R2, N1 modified
+    # edits to config file: R2, N1 modified
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42, N1: 99})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2
@@ -40,7 +48,7 @@ def test_update_property(monkeypatch):
     assert getattr(appconfig, N1) == 3  # no change: option modified but is non-relodable
 
 
-def test_overwrite_reloadable_attribute(monkeypatch):
+def test_overwrite_reloadable_attribute(mock_init, monkeypatch):
     # This is similar to test_update_property, but here we overwrite the attribute before reloading.
     # This can happen if a config property is modified AFTER it has been loaded from schema or kwargs.
     # For example: load `foo` (from schema or kwargs), but then, in a # subsequent step while initializing
@@ -48,12 +56,11 @@ def test_overwrite_reloadable_attribute(monkeypatch):
     # is not what was initially loaded, and if `foo` is reloadable, it will be reset to its default as soon
     # as the config file is modified. To prevent this, we compare the values read from the modified file
     # to the `_raw_config` dict. This test ensures this works correctly.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, R2: 42}  # edits: R2 modified
+    # edits to config file: R2 modified
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, R2: 42})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2
@@ -67,16 +74,15 @@ def test_overwrite_reloadable_attribute(monkeypatch):
     assert getattr(appconfig, R2) == 42  # change: reloadable option modified
 
 
-def test_cant_delete_property(monkeypatch):
+def test_cant_delete_property(mock_init, monkeypatch):
     # A property should not be deleted: we don't know whether it was initially
     # set to a default, loaded from a config file, env var, etc. Therefore, if a property
     # is removed from the config file, it will not be modified or deleted.
-    appconfig = MockGalaxyAppConfiguration({R1: 1, R2: 2, N1: 3, N2: 4})
 
-    def mock_read_properties_from_file(values):
-        return {R1: 1, N1: 3}  # edits: R2, N2 deleted
+    # edits to config file: R2, N2 deleted
+    monkeypatch.setattr(config, 'read_properties_from_file', lambda _: {R1: 1, N1: 3})
 
-    monkeypatch.setattr(config, 'read_properties_from_file', mock_read_properties_from_file)
+    appconfig = GalaxyAppConfiguration()
 
     assert getattr(appconfig, R1) == 1
     assert getattr(appconfig, R2) == 2
diff --git a/test/unit/config/test_schema.py b/test/unit/config/test_schema.py
index 6569627f2e2..c727d0e4a00 100644
--- a/test/unit/config/test_schema.py
+++ b/test/unit/config/test_schema.py
@@ -12,9 +12,27 @@ MOCK_YAML = '''
       mockgalaxy:
         type: map
         mapping:
-          option:
-            attr1: a
-            attr2: b
+          property1:
+            default: a
+            type: str
+            path_resolves_to: foo
+          property2:
+            default: 1
+            type: int
+            reloadable: true
+          property3:
+            default: 1.0
+            type: float
+            reloadable: true
+          property4:
+            default: true
+            type: bool
+            path_resolves_to: foo
+          property5:
+            something_else: b
+            type: invalid
+          property6:
+            something_else: b
     '''
 
 
@@ -29,10 +47,29 @@ def test_schema_is_loaded(monkeypatch):
     monkeypatch.setattr(AppSchema, '_read_schema', mock_read_schema)
     monkeypatch.setattr(OrderedLoader, '__init__', mock_init)
 
-    loaded_schema = AppSchema('no path', 'mockgalaxy')
+    schema = AppSchema('no path', 'mockgalaxy')
     data = ordered_load(MOCK_YAML)
 
-    assert loaded_schema.description == data['desc']
-    assert loaded_schema.raw_schema['foo'] == 'bar'
-    assert loaded_schema.app_schema['option']['attr1'] == 'a'
-    assert loaded_schema.get_app_option('option')['attr2'] == 'b'
+    assert schema.description == data['desc']
+    assert schema.raw_schema['foo'] == 'bar'
+
+    assert len(schema.defaults) == 6
+    assert schema.defaults['property1'] == 'a'
+    assert schema.defaults['property2'] == 1
+    assert schema.defaults['property3'] == 1.0
+    assert schema.defaults['property4'] is True
+    assert schema.defaults['property5'] is None
+    assert schema.defaults['property6'] is None
+
+    assert type(schema.defaults['property1']) is str
+    assert type(schema.defaults['property2']) is int
+    assert type(schema.defaults['property3']) is float
+    assert type(schema.defaults['property4']) is bool
+
+    assert len(schema.reloadable_options) == 2
+    assert 'property2' in schema.reloadable_options
+    assert 'property3' in schema.reloadable_options
+
+    assert len(schema.paths_to_resolve) == 2
+    assert 'property1' in schema.paths_to_resolve
+    assert 'property4' in schema.paths_to_resolve
diff --git a/test/unit/tools/test_toolbox.py b/test/unit/tools/test_toolbox.py
index c5695c4ef78..974b30bfb41 100644
--- a/test/unit/tools/test_toolbox.py
+++ b/test/unit/tools/test_toolbox.py
@@ -564,11 +564,7 @@ class SimplifiedToolBox(ToolBox):
         app.tool_cache = ToolCache() if not hasattr(app, 'tool_cache') else app.tool_cache
         app.job_config.get_tool_resource_parameters = lambda tool_id: None
         app.config.update_integrated_tool_panel = True
-        app.config.appschema = {
-            'tool_dependency_dir': {
-                'default': 'dependencies',
-            }
-        }
+        app.config.schema.defaults = {'tool_dependency_dir': 'dependencies'}
         config_files = test_case.config_files
         tool_root_dir = test_case.test_directory
         super(SimplifiedToolBox, self).__init__(
diff --git a/test/unit/unittest_utils/galaxy_mock.py b/test/unit/unittest_utils/galaxy_mock.py
index 5b9d06978fc..3cde0eaa3e3 100644
--- a/test/unit/unittest_utils/galaxy_mock.py
+++ b/test/unit/unittest_utils/galaxy_mock.py
@@ -111,6 +111,9 @@ class MockLock(object):
 
 class MockAppConfig(Bunch):
 
+    class MockSchema(Bunch):
+        pass
+
     def __init__(self, root=None, **kwargs):
         Bunch.__init__(self, **kwargs)
         if not root:
@@ -118,6 +121,7 @@ class MockAppConfig(Bunch):
             self._remove_root = True
         else:
             self._remove_root = False
+        self.schema = self.MockSchema()
         self.security = idencoding.IdEncodingHelper(id_secret='6e46ed6483a833c100e68cc3f1d0dd76')
         self.database_connection = kwargs.get('database_connection', "sqlite:///:memory:")
         self.use_remote_user = kwargs.get('use_remote_user', False)