From a1337eff1420b5a47161814d89e68c2dbfc825bf Mon Sep 17 00:00:00 2001
From: will <theappdev@protonmail.com>
Date: Wed, 22 May 2019 14:47:04 -0400
Subject: [PATCH 1/7] Fix ellipses showing too soon

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index eb720d453b3..b8ebc1270a5 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -347,21 +347,18 @@ var View = Backbone.View.extend({
         return inputs;
     },
 
-    _templateRow: function(list, title, max = 3) {
-        var blurb = "";
-        list.sort(function(a, b) {
-            return b.hid - a.hid;
-        });
+    _templateRow: function(list, title) {
+        let blurb = "";
         if (list.length > 0) {
             blurb += `<p>${title}:</p>`;
-            for (const item of list) {
-                const rowString = max > 0 ? `${item.hid}: ${_.escape(item.name)}` : "...";
+            list.sort((a, b) => { b.hid - a.hid; });
+            const numRows = Math.min(list.length, 4);
+            for (let i = 0; i < numRows; i++) {
+                //use ellipses if it is the final row (last loop iteration) and the list length is larger than the number of rows
+                const rowString = (i === numRows - 1 && list.length > numRows) ? "..." : `${list[i].hid}: ${_.escape(list[i].name)}`;
                 blurb += `<p class="messagerow">
                             <b>${rowString}</b>
                           </p>`;
-                if (max-- <= 0) {
-                    break;
-                }
             }
         }
         return blurb;

From ed69f0053d9e28bb6e7d80b5718d72bbc8ebb430 Mon Sep 17 00:00:00 2001
From: will <theappdev@protonmail.com>
Date: Wed, 22 May 2019 14:48:02 -0400
Subject: [PATCH 2/7] Fix formatting

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index b8ebc1270a5..04a52ad1107 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -68,15 +68,15 @@ var View = Backbone.View.extend({
                                     );
                                 } else {
                                     Galaxy.modal &&
-                                        Galaxy.modal.show({
-                                            title: _l("Tool request failed"),
-                                            body: error_message,
-                                            buttons: {
-                                                Close: function() {
-                                                    Galaxy.modal.hide();
-                                                }
+                                    Galaxy.modal.show({
+                                        title: _l("Tool request failed"),
+                                        body: error_message,
+                                        buttons: {
+                                            Close: function() {
+                                                Galaxy.modal.hide();
                                             }
-                                        });
+                                        }
+                                    });
                                 }
                                 Galaxy.emit.debug(
                                     "tool-form-base::_buildModel()",
@@ -395,7 +395,7 @@ var View = Backbone.View.extend({
             .append(
                 $("<p/>").text(
                     `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${err_msg ||
-                        ""}`
+                    ""}`
                 )
             )
             .append($("<pre/>").text(JSON.stringify(response, null, 4)));

From f1158b9dcc233567adb6e5336e93f217669efd51 Mon Sep 17 00:00:00 2001
From: will <theappdev@protonmail.com>
Date: Wed, 22 May 2019 15:27:09 -0400
Subject: [PATCH 3/7] Use arrow functions and remove references to self = this

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 49 ++++++++++-----------
 1 file changed, 23 insertions(+), 26 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 04a52ad1107..b3f3b76539f 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -15,14 +15,13 @@ import Webhooks from "mvc/webhooks";
 var View = Backbone.View.extend({
     initialize: function(options) {
         const Galaxy = getGalaxyInstance();
-        const self = this;
         this.modal = Galaxy.modal || new Modal.View();
         this.form = new ToolFormBase(
             Utils.merge(
                 {
                     listen_to_history: true,
                     always_refresh: false,
-                    buildmodel: function(process, form) {
+                    buildmodel: (process, form) => {
                         var options = form.model.attributes;
 
                         // build request url
@@ -42,17 +41,17 @@ var View = Backbone.View.extend({
                         Utils.get({
                             url: build_url,
                             data: build_data,
-                            success: function(data) {
+                            success: data => {
                                 if (!data.display) {
                                     window.location = getAppRoot();
                                     return;
                                 }
                                 form.model.set(data);
-                                self._customize(form);
+                                this._customize(form);
                                 Galaxy.emit.debug("tool-form-base::_buildModel()", "Initial tool model ready.", data);
                                 process.resolve();
                             },
-                            error: function(response, status) {
+                            error: (response, status) => {
                                 var error_message = (response && response.err_msg) || "Uncaught error.";
                                 if (status == 401) {
                                     window.location = `${getAppRoot()}user/login?${$.param({
@@ -72,7 +71,7 @@ var View = Backbone.View.extend({
                                         title: _l("Tool request failed"),
                                         body: error_message,
                                         buttons: {
-                                            Close: function() {
+                                            Close: () => {
                                                 Galaxy.modal.hide();
                                             }
                                         }
@@ -87,7 +86,7 @@ var View = Backbone.View.extend({
                             }
                         });
                     },
-                    postchange: function(process, form) {
+                    postchange: (process, form) => {
                         var current_state = {
                             tool_id: form.model.get("id"),
                             tool_version: form.model.get("version"),
@@ -99,13 +98,13 @@ var View = Backbone.View.extend({
                             type: "POST",
                             url: `${getAppRoot()}api/tools/${form.model.get("id")}/build`,
                             data: current_state,
-                            success: function(data) {
+                            success: data => {
                                 form.update(data);
                                 form.wait(false);
                                 Galaxy.emit.debug("tool-form::postchange()", "Received new model.", data);
                                 process.resolve();
                             },
-                            error: function(response) {
+                            error: response => {
                                 Galaxy.emit.debug("tool-form::postchange()", "Refresh request failed.", response);
                                 process.reject();
                             }
@@ -121,7 +120,6 @@ var View = Backbone.View.extend({
     },
 
     _customize: function(form) {
-        var self = this;
         var options = form.model.attributes;
         // build execute button
         var execute_button = new Ui.Button({
@@ -130,10 +128,10 @@ var View = Backbone.View.extend({
             title: _l("Execute"),
             cls: "btn btn-primary",
             wait_cls: "btn btn-info",
-            onclick: function() {
+            onclick: () => {
                 execute_button.wait();
                 form.portlet.disable();
-                self.submit(options, () => {
+                this.submit(options, () => {
                     execute_button.unwait();
                     form.portlet.enable();
                 });
@@ -196,7 +194,6 @@ var View = Backbone.View.extend({
     submit: function(options, callback) {
         const Galaxy = getGalaxyInstance();
         const history_id = Galaxy.currHistoryPanel && Galaxy.currHistoryPanel.model.id;
-        const self = this;
         const job_def = {
             history_id: history_id,
             tool_id: options.id,
@@ -204,7 +201,7 @@ var View = Backbone.View.extend({
             inputs: this.form.data.create()
         };
         this.form.trigger("reset");
-        if (!self.validate(job_def)) {
+        if (!this.validate(job_def)) {
             Galaxy.emit.debug("tool-form::submit()", "Submission canceled. Validation failed.");
             callback && callback();
             return;
@@ -230,42 +227,42 @@ var View = Backbone.View.extend({
             type: "POST",
             url: `${getAppRoot()}api/tools`,
             data: job_def,
-            success: function(response) {
+            success: response => {
                 callback && callback();
-                self.$el.children().hide();
-                self.$el.append(self._templateSuccess(response, job_def));
+                this.$el.children().hide();
+                this.$el.append(this._templateSuccess(response, job_def));
                 // Show Webhook if job is running
                 if (response.jobs && response.jobs.length > 0) {
-                    self.$el.append($("<div/>", { id: "webhook-view" }));
+                    this.$el.append($("<div/>", { id: "webhook-view" }));
                     new Webhooks.WebhookView({
                         type: "tool",
                         toolId: job_def.tool_id
                     });
                 }
                 if (Galaxy.currHistoryPanel) {
-                    self.form.stopListening(Galaxy.currHistoryPanel.collection);
+                    this.form.stopListening(Galaxy.currHistoryPanel.collection);
                     Galaxy.currHistoryPanel.refreshContents();
                 }
             },
-            error: function(response) {
+            error: response => {
                 callback && callback();
                 Galaxy.emit.debug("tool-form::submit", "Submission failed.", response);
                 let input_found = false;
                 if (response && response.err_data) {
-                    const error_messages = self.form.data.matchResponse(response.err_data);
+                    const error_messages = this.form.data.matchResponse(response.err_data);
                     for (const input_id in error_messages) {
-                        self.form.highlight(input_id, error_messages[input_id]);
+                        this.form.highlight(input_id, error_messages[input_id]);
                         input_found = true;
                         break;
                     }
                 }
                 if (!input_found) {
-                    self.modal.show({
+                    this.modal.show({
                         title: _l("Job submission failed"),
-                        body: self._templateError(job_def, response && response.err_msg),
+                        body: this._templateError(job_def, response && response.err_msg),
                         buttons: {
-                            Close: function() {
-                                self.modal.hide();
+                            Close: () => {
+                                this.modal.hide();
                             }
                         }
                     });

From fc6a122545fc89723d5d7948d53a0936b52b9d5a Mon Sep 17 00:00:00 2001
From: will <theappdev@protonmail.com>
Date: Wed, 22 May 2019 15:40:07 -0400
Subject: [PATCH 4/7] prefer const and let over var

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 64 ++++++++++-----------
 1 file changed, 32 insertions(+), 32 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index b3f3b76539f..75f5a67f148 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -12,7 +12,7 @@ import Modal from "mvc/ui/ui-modal";
 import ToolFormBase from "mvc/tool/tool-form-base";
 import Webhooks from "mvc/webhooks";
 
-var View = Backbone.View.extend({
+const View = Backbone.View.extend({
     initialize: function(options) {
         const Galaxy = getGalaxyInstance();
         this.modal = Galaxy.modal || new Modal.View();
@@ -22,12 +22,12 @@ var View = Backbone.View.extend({
                     listen_to_history: true,
                     always_refresh: false,
                     buildmodel: (process, form) => {
-                        var options = form.model.attributes;
+                        const options = form.model.attributes;
 
                         // build request url
-                        var build_url = "";
-                        var build_data = {};
-                        var job_id = options.job_id;
+                        let build_url = "";
+                        let build_data = {};
+                        const job_id = options.job_id;
                         if (job_id) {
                             build_url = `${getAppRoot()}api/jobs/${job_id}/build_for_rerun`;
                         } else {
@@ -52,7 +52,7 @@ var View = Backbone.View.extend({
                                 process.resolve();
                             },
                             error: (response, status) => {
-                                var error_message = (response && response.err_msg) || "Uncaught error.";
+                                const error_message = (response && response.err_msg) || "Uncaught error.";
                                 if (status == 401) {
                                     window.location = `${getAppRoot()}user/login?${$.param({
                                         redirect: `${getAppRoot()}?tool_id=${options.id}`
@@ -87,7 +87,7 @@ var View = Backbone.View.extend({
                         });
                     },
                     postchange: (process, form) => {
-                        var current_state = {
+                        const current_state = {
                             tool_id: form.model.get("id"),
                             tool_version: form.model.get("version"),
                             inputs: $.extend(true, {}, form.data.create())
@@ -120,9 +120,9 @@ var View = Backbone.View.extend({
     },
 
     _customize: function(form) {
-        var options = form.model.attributes;
+        const options = form.model.attributes;
         // build execute button
-        var execute_button = new Ui.Button({
+        const execute_button = new Ui.Button({
             icon: "fa-check",
             tooltip: `Execute: ${options.name} (${options.version})`,
             title: _l("Execute"),
@@ -141,7 +141,7 @@ var View = Backbone.View.extend({
 
         // remap feature
         if (options.job_id && options.job_remap) {
-            var label, help;
+            let label, help;
             if (options.job_remap === "job_produced_collection_elements") {
                 label = "Replace elements in collection ?";
                 help =
@@ -165,11 +165,11 @@ var View = Backbone.View.extend({
 
         // Job Re-use Options
         const Galaxy = getGalaxyInstance();
-        var extra_user_preferences = {};
+        let extra_user_preferences = {};
         if (Galaxy.user.attributes.preferences && "extra_user_preferences" in Galaxy.user.attributes.preferences) {
             extra_user_preferences = JSON.parse(Galaxy.user.attributes.preferences.extra_user_preferences);
         }
-        var use_cached_job =
+        const use_cached_job =
             "use_cached_job|use_cached_job_checkbox" in extra_user_preferences
                 ? extra_user_preferences["use_cached_job|use_cached_job_checkbox"]
                 : false;
@@ -276,14 +276,14 @@ var View = Backbone.View.extend({
      */
     validate: function(job_def) {
         const Galaxy = getGalaxyInstance();
-        var job_inputs = job_def.inputs;
-        var batch_n = -1;
-        var batch_src = null;
-        for (var job_input_id in job_inputs) {
-            var input_value = job_inputs[job_input_id];
-            var input_id = this.form.data.match(job_input_id);
-            var input_field = this.form.field_list[input_id];
-            var input_def = this.form.input_list[input_id];
+        const job_inputs = job_def.inputs;
+        let batch_n = -1;
+        let batch_src = null;
+        for (const job_input_id in job_inputs) {
+            const input_value = job_inputs[job_input_id];
+            const input_id = this.form.data.match(job_input_id);
+            const input_field = this.form.field_list[input_id];
+            const input_def = this.form.input_list[input_id];
             if (!input_id || !input_def || !input_field) {
                 Galaxy.emit.debug("tool-form::validate()", "Retrieving input objects failed.");
                 continue;
@@ -300,8 +300,8 @@ var View = Backbone.View.extend({
                 }
             }
             if (input_value && input_value.batch) {
-                var n = input_value.values.length;
-                var src = n > 0 && input_value.values[0] && input_value.values[0].src;
+                const n = input_value.values.length;
+                const src = n > 0 && input_value.values[0] && input_value.values[0].src;
                 if (src) {
                     if (batch_src === null) {
                         batch_src = src;
@@ -328,8 +328,8 @@ var View = Backbone.View.extend({
     },
 
     _getInputs: function(job_def) {
-        var inputs = [];
-        var index = {};
+        const inputs = [];
+        const index = {};
         for (const i in job_def.inputs) {
             const input = job_def.inputs[i];
             if (input && $.isArray(input.values)) {
@@ -362,15 +362,15 @@ var View = Backbone.View.extend({
     },
 
     _templateSuccess: function(response, job_def) {
-        var njobs = response && response.jobs ? response.jobs.length : 0;
+        const njobs = response && response.jobs ? response.jobs.length : 0;
         if (njobs > 0) {
-            var inputs = this._getInputs(job_def);
-            var ninputs = inputs.length;
-            var noutputs = response.outputs.length;
-            var njobsText = njobs > 1 ? `${njobs} jobs` : `1 job`;
-            var ninputsText = ninputs > 1 ? `${ninputs} inputs` : `this input`;
-            var noutputsText = noutputs > 1 ? `${noutputs} outputs` : `this output`;
-            var tool_name = this.form.model.get("name");
+            const inputs = this._getInputs(job_def);
+            const ninputs = inputs.length;
+            const noutputs = response.outputs.length;
+            const njobsText = njobs > 1 ? `${njobs} jobs` : `1 job`;
+            const ninputsText = ninputs > 1 ? `${ninputs} inputs` : `this input`;
+            const noutputsText = noutputs > 1 ? `${noutputs} outputs` : `this output`;
+            const tool_name = this.form.model.get("name");
             return `<div class="donemessagelarge">
                         <p>
                             Executed <b>${tool_name}</b> and successfully added ${njobsText} to the queue.

From c4b31da7970f0d65f25d1257526bd6733122d5e2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 24 May 2019 13:43:14 -0400
Subject: [PATCH 5/7] Rerun prettier

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 25 ++++++++++++---------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 75f5a67f148..2ec48fbd648 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -67,15 +67,15 @@ const View = Backbone.View.extend({
                                     );
                                 } else {
                                     Galaxy.modal &&
-                                    Galaxy.modal.show({
-                                        title: _l("Tool request failed"),
-                                        body: error_message,
-                                        buttons: {
-                                            Close: () => {
-                                                Galaxy.modal.hide();
+                                        Galaxy.modal.show({
+                                            title: _l("Tool request failed"),
+                                            body: error_message,
+                                            buttons: {
+                                                Close: () => {
+                                                    Galaxy.modal.hide();
+                                                }
                                             }
-                                        }
-                                    });
+                                        });
                                 }
                                 Galaxy.emit.debug(
                                     "tool-form-base::_buildModel()",
@@ -348,11 +348,14 @@ const View = Backbone.View.extend({
         let blurb = "";
         if (list.length > 0) {
             blurb += `<p>${title}:</p>`;
-            list.sort((a, b) => { b.hid - a.hid; });
+            list.sort((a, b) => {
+                b.hid - a.hid;
+            });
             const numRows = Math.min(list.length, 4);
             for (let i = 0; i < numRows; i++) {
                 //use ellipses if it is the final row (last loop iteration) and the list length is larger than the number of rows
-                const rowString = (i === numRows - 1 && list.length > numRows) ? "..." : `${list[i].hid}: ${_.escape(list[i].name)}`;
+                const rowString =
+                    i === numRows - 1 && list.length > numRows ? "..." : `${list[i].hid}: ${_.escape(list[i].name)}`;
                 blurb += `<p class="messagerow">
                             <b>${rowString}</b>
                           </p>`;
@@ -392,7 +395,7 @@ const View = Backbone.View.extend({
             .append(
                 $("<p/>").text(
                     `The server could not complete the request. Please contact the Galaxy Team if this error persists. ${err_msg ||
-                    ""}`
+                        ""}`
                 )
             )
             .append($("<pre/>").text(JSON.stringify(response, null, 4)));

From f2a7f8c6bb39482104a0d29018b69f82d2fc1662 Mon Sep 17 00:00:00 2001
From: will <theappdev@protonmail.com>
Date: Thu, 6 Jun 2019 12:57:25 -0400
Subject: [PATCH 6/7] make tool form print all inputs/outputs and scroll to top

---
 client/galaxy/scripts/mvc/tool/tool-form.js | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index 2ec48fbd648..a015b004791 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -231,6 +231,7 @@ const View = Backbone.View.extend({
                 callback && callback();
                 this.$el.children().hide();
                 this.$el.append(this._templateSuccess(response, job_def));
+                this.$el.parent().scrollTop(0);
                 // Show Webhook if job is running
                 if (response.jobs && response.jobs.length > 0) {
                     this.$el.append($("<div/>", { id: "webhook-view" }));
@@ -351,11 +352,8 @@ const View = Backbone.View.extend({
             list.sort((a, b) => {
                 b.hid - a.hid;
             });
-            const numRows = Math.min(list.length, 4);
-            for (let i = 0; i < numRows; i++) {
-                //use ellipses if it is the final row (last loop iteration) and the list length is larger than the number of rows
-                const rowString =
-                    i === numRows - 1 && list.length > numRows ? "..." : `${list[i].hid}: ${_.escape(list[i].name)}`;
+            for (const item of list) {
+                const rowString = `${item.hid}: ${_.escape(item.name)}`;
                 blurb += `<p class="messagerow">
                             <b>${rowString}</b>
                           </p>`;

From 320655337b7f550ef8412c4c3cb30ea1720cda04 Mon Sep 17 00:00:00 2001
From: Martin Cech <marten@bx.psu.edu>
Date: Thu, 6 Jun 2019 13:40:25 -0400
Subject: [PATCH 7/7] improve styling of inpouts and outputs lists

on after-execution page
---
 client/galaxy/scripts/mvc/tool/tool-form.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/client/galaxy/scripts/mvc/tool/tool-form.js b/client/galaxy/scripts/mvc/tool/tool-form.js
index a015b004791..2eda949c313 100644
--- a/client/galaxy/scripts/mvc/tool/tool-form.js
+++ b/client/galaxy/scripts/mvc/tool/tool-form.js
@@ -352,12 +352,12 @@ const View = Backbone.View.extend({
             list.sort((a, b) => {
                 b.hid - a.hid;
             });
+            blurb += `<ul>`;
             for (const item of list) {
                 const rowString = `${item.hid}: ${_.escape(item.name)}`;
-                blurb += `<p class="messagerow">
-                            <b>${rowString}</b>
-                          </p>`;
+                blurb += `<li><b>${rowString}</b></li>`;
             }
+            blurb += `</ul>`;
         }
         return blurb;
     },