From a1b7105b389e8a7b8f9ed9aab630c8b543825da4 Mon Sep 17 00:00:00 2001
From: Saskia Hiltemann <zazkia@gmail.com>
Date: Tue, 30 Oct 2018 13:21:59 +0100
Subject: [PATCH 1/2] add option to strip url prefix from pair names

---
 .../list-of-pairs-collection-creator.js       | 39 ++++++++++++++++++-
 1 file changed, 37 insertions(+), 2 deletions(-)

diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
index b79e7c39883..2111fc20374 100644
--- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -256,6 +256,9 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             this.removeExtensions = true;
             //this.removeExtensions = false;
 
+             /** remove file extensions (\.*) from created pair names? */
+            this.removeUrlPrefix = true;
+
             /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */
             this.oncancel = attributes.oncancel;
             /** fn to call when the collection is created (scoped to this) */
@@ -544,8 +547,9 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** try to find a good pair name for the given fwd and rev datasets */
-        _guessNameForPair: function(fwd, rev, removeExtensions) {
+        _guessNameForPair: function(fwd, rev, removeExtensions, removeUrlPrefix) {
             removeExtensions = removeExtensions !== undefined ? removeExtensions : this.removeExtensions;
+            removeUrlPrefix = removeUrlPrefix !== undefined ? removeUrlPrefix : this.removeUrlPrefix;
             var fwdName = fwd.name;
             var revName = rev.name;
 
@@ -563,6 +567,15 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     revName = revName.replace(extension, "");
                 }
             }
+            if (removeUrlPrefix) {
+                var lastSlashIndex = lcs.lastIndexOf("/");
+                if (lastSlashIndex > 0) {
+                    var urlprefix = lcs.slice(0, lastSlashIndex + 1);
+                    lcs = lcs.replace(urlprefix, "");
+                    fwdName = fwdName.replace(extension, "");
+                    revName = revName.replace(extension, "");
+                }
+            }
             return lcs || `${fwdName} & ${revName}`;
         },
 
@@ -891,7 +904,8 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         footerSettings: {
             ".hide-originals": "hideOriginals",
-            ".remove-extensions": "removeExtensions"
+            ".remove-extensions": "removeExtensions",
+            ".remove-urlprefix": "removeUrlPrefix"
         },
 
         /** add any jQuery/bootstrap/custom plugins to elements rendered */
@@ -1082,6 +1096,9 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             "change .remove-extensions": function(ev) {
                 this.toggleExtensions();
             },
+            "change .remove-urlprefix": function(ev) {
+                this.toggleUrlPrefix();
+            },
             "change .collection-name": "_changeName",
             "keydown .collection-name": "_nameCheckForEnter",
             "change .hide-originals": "_changeHideOriginals",
@@ -1492,7 +1509,20 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         toggleExtensions: function(force) {
             var self = this;
             self.removeExtensions = force !== undefined ? force : !self.removeExtensions;
+            _.each(self.paired, pair => {
+                // don't overwrite custom names
+                if (pair.customizedName) {
+                    return;
+                }
+                pair.name = self._guessNameForPair(pair.forward, pair.reverse);
+            });
 
+            self._renderPaired();
+            self._renderFooter();
+        },
+        toggleUrlPrefix: function(force) {
+            var self = this;
+            self.removeUrlPrefix = force !== undefined ? force : !self.removeUrlPrefix;
             _.each(self.paired, pair => {
                 // don't overwrite custom names
                 if (pair.customizedName) {
@@ -1640,6 +1670,11 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     '<input class="hide-originals float-right" type="checkbox" />',
                     "</label>",
                     '<label class="setting-prompt float-right">',
+                    _l("Remove url prefix from pair names"),
+                    "?",
+                    '<input class="remove-urlprefix float-right" type="checkbox" />',
+                    "</label>",
+                    '<label class="setting-prompt float-right">',
                     _l("Remove file extensions from pair names"),
                     "?",
                     '<input class="remove-extensions float-right" type="checkbox" />',

From 41d60f576122a74a87ca060a6813d0e6ca903c05 Mon Sep 17 00:00:00 2001
From: Saskia Hiltemann <zazkia@gmail.com>
Date: Tue, 30 Oct 2018 14:24:31 +0100
Subject: [PATCH 2/2] always strip url prefix

---
 .../list-of-pairs-collection-creator.js       | 48 +++++--------------
 1 file changed, 11 insertions(+), 37 deletions(-)

diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
index 2111fc20374..671b55544fd 100644
--- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -256,9 +256,6 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             this.removeExtensions = true;
             //this.removeExtensions = false;
 
-             /** remove file extensions (\.*) from created pair names? */
-            this.removeUrlPrefix = true;
-
             /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */
             this.oncancel = attributes.oncancel;
             /** fn to call when the collection is created (scoped to this) */
@@ -547,9 +544,8 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         },
 
         /** try to find a good pair name for the given fwd and rev datasets */
-        _guessNameForPair: function(fwd, rev, removeExtensions, removeUrlPrefix) {
+        _guessNameForPair: function(fwd, rev, removeExtensions) {
             removeExtensions = removeExtensions !== undefined ? removeExtensions : this.removeExtensions;
-            removeUrlPrefix = removeUrlPrefix !== undefined ? removeUrlPrefix : this.removeUrlPrefix;
             var fwdName = fwd.name;
             var revName = rev.name;
 
@@ -558,6 +554,15 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                 revName.replace(new RegExp(this.filters[1]), "")
             );
 
+            /** remove url prefix if files were uploaded by url */
+            var lastSlashIndex = lcs.lastIndexOf("/");
+            if (lastSlashIndex > 0) {
+                var urlprefix = lcs.slice(0, lastSlashIndex + 1);
+                lcs = lcs.replace(urlprefix, "");
+                fwdName = fwdName.replace(extension, "");
+                revName = revName.replace(extension, "");
+            }
+
             if (removeExtensions) {
                 var lastDotIndex = lcs.lastIndexOf(".");
                 if (lastDotIndex > 0) {
@@ -567,15 +572,6 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     revName = revName.replace(extension, "");
                 }
             }
-            if (removeUrlPrefix) {
-                var lastSlashIndex = lcs.lastIndexOf("/");
-                if (lastSlashIndex > 0) {
-                    var urlprefix = lcs.slice(0, lastSlashIndex + 1);
-                    lcs = lcs.replace(urlprefix, "");
-                    fwdName = fwdName.replace(extension, "");
-                    revName = revName.replace(extension, "");
-                }
-            }
             return lcs || `${fwdName} & ${revName}`;
         },
 
@@ -904,8 +900,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
 
         footerSettings: {
             ".hide-originals": "hideOriginals",
-            ".remove-extensions": "removeExtensions",
-            ".remove-urlprefix": "removeUrlPrefix"
+            ".remove-extensions": "removeExtensions"
         },
 
         /** add any jQuery/bootstrap/custom plugins to elements rendered */
@@ -1096,9 +1091,6 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
             "change .remove-extensions": function(ev) {
                 this.toggleExtensions();
             },
-            "change .remove-urlprefix": function(ev) {
-                this.toggleUrlPrefix();
-            },
             "change .collection-name": "_changeName",
             "keydown .collection-name": "_nameCheckForEnter",
             "change .hide-originals": "_changeHideOriginals",
@@ -1509,20 +1501,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
         toggleExtensions: function(force) {
             var self = this;
             self.removeExtensions = force !== undefined ? force : !self.removeExtensions;
-            _.each(self.paired, pair => {
-                // don't overwrite custom names
-                if (pair.customizedName) {
-                    return;
-                }
-                pair.name = self._guessNameForPair(pair.forward, pair.reverse);
-            });
 
-            self._renderPaired();
-            self._renderFooter();
-        },
-        toggleUrlPrefix: function(force) {
-            var self = this;
-            self.removeUrlPrefix = force !== undefined ? force : !self.removeUrlPrefix;
             _.each(self.paired, pair => {
                 // don't overwrite custom names
                 if (pair.customizedName) {
@@ -1670,11 +1649,6 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin)
                     '<input class="hide-originals float-right" type="checkbox" />',
                     "</label>",
                     '<label class="setting-prompt float-right">',
-                    _l("Remove url prefix from pair names"),
-                    "?",
-                    '<input class="remove-urlprefix float-right" type="checkbox" />',
-                    "</label>",
-                    '<label class="setting-prompt float-right">',
                     _l("Remove file extensions from pair names"),
                     "?",
                     '<input class="remove-extensions float-right" type="checkbox" />',