From 2a827fa8ed7ad0989fe9ede1f7803fb410988fb8 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Thu, 4 Jun 2020 16:00:19 -0500
Subject: [PATCH 01/15] initial stub implementation of selection features

---
 app/views/datasets/filesAndFolders.scala.html | 163 +++++++++++++-----
 app/views/files/grid.scala.html               |   3 -
 app/views/files/listitem.scala.html           |   8 +-
 public/javascripts/deleteUtils.js             |  32 ++++
 4 files changed, 162 insertions(+), 44 deletions(-)

diff --git a/app/views/datasets/filesAndFolders.scala.html b/app/views/datasets/filesAndFolders.scala.html
index 3230dc605..07ceb09d9 100644
--- a/app/views/datasets/filesAndFolders.scala.html
+++ b/app/views/datasets/filesAndFolders.scala.html
@@ -1,4 +1,6 @@
-@(dataset: Dataset, currentFolder: Option[String], foldersList: List[Folder], folderHierarchy: List[Folder], filepage: Int, next: Boolean, fileList:List[File], fileComments: Map[UUID, Int], space: Option[String], filter: Option[String])(implicit user: Option[models.User])
+@(dataset: Dataset, currentFolder: Option[String], foldersList: List[Folder], folderHierarchy: List[Folder],
+        filepage: Int, next: Boolean, fileList:List[File], fileComments: Map[UUID, Int], space: Option[String],
+        filter: Option[String])(implicit user: Option[models.User])
 
 <!-- Breadcrumbs -->
 @if(folderHierarchy.length > 0 ) {
@@ -27,47 +29,126 @@
       });
     });
     </script>
-    <!--label class="sortchoice" for="filename-filter">Filter:-->
-        <table width=100%"">
-            <td width="40%">
-                <div class="input-group">
-                    <!-- TODO: Should the filter value reset when folder level changes? -->
-                    <input type="text" class="form-horizontal form-control" id="filename-filter" placeholder="Search folder and file names..."
-                    value="@filter.getOrElse("")"
-                    onchange="getUpdatedFilesAndFolders()">
-                    <div class="input-group-btn">
-                        <button class="btn btn-default" onclick="getUpdatedFilesAndFolders()">
-                            <span class="glyphicon glyphicon-search"></span></button>
-                    </div>
-                </div>
-            </td>
-            <td width="30%">
-                <div id="filter-box-value">
-                    &nbsp;
-                    @if(filter.getOrElse("")!="") {
-                        Filtering by <b>@filter.get</b>
-                    }
+
+    <table width=100%"">
+        <td width="30%">
+            <div class="input-group">
+                <!-- TODO: Should the filter value reset when folder level changes? -->
+                <input type="text" class="form-horizontal form-control" id="filename-filter" placeholder="Search folder and file names..."
+                value="@filter.getOrElse("")"
+                onchange="getUpdatedFilesAndFolders()">
+                <div class="input-group-btn">
+                    <button class="btn btn-default" onclick="getUpdatedFilesAndFolders()">
+                        <span class="glyphicon glyphicon-search"></span></button>
                 </div>
-            </td>
-            <td width="30%">
-                <label class="sortchoice" for="js-sort-single">Sort By:
-                    <select class="js-sort-single">
-                        <option value="dateN">Newest</option>
-                        <option value="dateO">Oldest</option>
-                        <option value="titleA">Title (A-Z)</option>
-                        <option value="titleZ">Title (Z-A)</option>
-                        <option value="sizeL">Size (L)</option>
-                        <option value="sizeS">Size (S)</option>
-                    </select>
-            </td>
-        </table>
+            </div>
+        </td>
+        <td width="20%">
+            <div id="filter-box-value">
+                &nbsp;
+                @if(filter.getOrElse("")!="") {
+                    Filtering by <b>@filter.get</b>
+                }
+            </div>
+        </td>
+        <td width="20%" >
+            <div id="selected-count-box"></div>
+        </td>
+        <td width="30%">
+            <label class="sortchoice" for="js-sort-single">Sort By:
+                <select class="js-sort-single">
+                    <option value="dateN">Newest</option>
+                    <option value="dateO">Oldest</option>
+                    <option value="titleA">Title (A-Z)</option>
+                    <option value="titleZ">Title (Z-A)</option>
+                    <option value="sizeL">Size (L)</option>
+                    <option value="sizeS">Size (S)</option>
+                </select>
+            </label>
+        </td>
+    </table>
 
+    </div>
+} else {
+    <!--Still want to show multiselect box even without sorting-->
+    <div id="selected-count-box"></div>
+}
 
+<script type="text/javascript">
+    function updateSelectedFileCount() {
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            var fileUUIDs = selected.split(',');
+            //$('#selected-count-box').html('Marked Files (<b>'+fileUUIDs.length+'</b>)')
+            $('#selected-count-box').html('<div class="dropdown"><a href="#" class="dropdown-toggle" ' +
+                    'data-toggle="dropdown" aria-expanded="false"> Marked Files (<b>'+fileUUIDs.length+'</b>)' +
+                    '<b class="caret"></b></a><ul class="dropdown-menu"><li>' +
+                    '<a onclick="deleteSelectedFiles();">Delete All</a></li></ul>' +
+                    '</div>')
+        } else {
+            $('#selected-count-box').html('Marked Files (<b>0</b>)')
+        }
+    }
 
+    function deleteSelectedFiles() {
+        console.log("Are you sure?");
+        confirmDeleteMarked('@dataset.id');
+    }
 
-    </label>
-    </div>
-}
+    $(document).ready(function() {
+        $('.fileselect').click(function() {
+            var file_id = $(this).data("id");
+
+            if ($("a[data-id='" + file_id + "'] span.glyphicon").hasClass('glyphicon-plus')) {
+                // SELECT THE FILE
+                // TODO: Add Clear All option
+                var selected = $.cookie('selected-files-@dataset.id');
+                if (selected) {
+                    if (selected.indexOf(file_id) == -1)
+                        selected += ","+file_id;
+                } else {
+                    selected = file_id;
+                }
+                $.cookie('selected-files-@dataset.id', selected);
+
+                $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-plus');
+                $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-ok');
+                updateSelectedFileCount();
+            } else {
+                // DESELECT THE FILE
+                var selected = $.cookie('selected-files-@dataset.id');
+                if (selected && selected.indexOf(file_id) > -1) {
+                    selected = selected.replace(file_id+',', '').replace(','+file_id, '').replace(file_id, '');
+                    $.cookie('selected-files-@dataset.id', selected, {expires: 14});
+                }
+
+                $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-ok');
+                $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-plus');
+                updateSelectedFileCount();
+                // TODO: plain jquery cookies? logout could still see them. play uses key
+                // TODO: show only marked files
+                // TODO: Downloading selected files as Zip - look at downloading folders tasks
+                // make separate tasks for my SIMPL task for a sprint with more granularity
+
+                // TODO: convert selection datasets to a collection
+                // TODO: Selections become Favorites
+                // TODO: recently viewed list?
+            }
+        });
+
+        // Check cookie for any selected files in this dataset and update icons + toolbar
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            var fileUUIDs = selected.split(',');
+            for (idx in fileUUIDs) {
+                file_id = fileUUIDs[idx];
+                $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-plus');
+                $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-ok');
+            }
+            updateSelectedFileCount();
+        }
+    });
+</script>
 
 <!-- Show message when the folder is empty -->
 <div style="display: none" id="empty-folder-div"><h4>
@@ -91,8 +172,12 @@
 
 <!-- Files list -->
 @currentFolder match {
-    case None => { @files.grid(fileList, fileComments, dataset.id, space, ResourceRef(ResourceRef.dataset, dataset.id), dataset.folders.length > 0) }
-    case Some(s) => { @files.grid(fileList, fileComments, dataset.id, space, ResourceRef(ResourceRef.folder, UUID(s)), dataset.folders.length > 0)}
+    case None => {
+        @files.grid(fileList, fileComments, dataset.id, space, ResourceRef(ResourceRef.dataset, dataset.id),
+            dataset.folders.length > 0) }
+    case Some(s) => {
+        @files.grid(fileList, fileComments, dataset.id, space, ResourceRef(ResourceRef.folder, UUID(s)),
+            dataset.folders.length > 0) }
 }
 
 <div class="row">
diff --git a/app/views/files/grid.scala.html b/app/views/files/grid.scala.html
index f66a4609e..58f19da71 100644
--- a/app/views/files/grid.scala.html
+++ b/app/views/files/grid.scala.html
@@ -4,15 +4,12 @@
 
 <div class="row" id="tile-view">
     <div class="col-md-12">
-
         @filesList.map { file =>
             @if(parent.resourceType == ResourceRef.folder) {
                 @files.listitem(file, (routes.Datasets.dataset(dsId)), Some(dsId.stringify), space, Some(parent.id.stringify), showMove)
             } else {
                 @files.listitem(file, (routes.Datasets.dataset(dsId)), Some(dsId.stringify), space, None,showMove)
             }
-
         }
-
     </div>
 </div>
diff --git a/app/views/files/listitem.scala.html b/app/views/files/listitem.scala.html
index 1524ec8ad..a4319413b 100644
--- a/app/views/files/listitem.scala.html
+++ b/app/views/files/listitem.scala.html
@@ -3,6 +3,12 @@
 @import _root_.util.Formatters.humanReadableByteCount
 <div class="panel panel-default file-panel" id="@file.id-listitem">
     <div class="panel-body">
+        @if(user.isDefined) {
+            <a href="javascript: void(0)" title="Click to mark file for bulk actions" class="pull-right fileselect" data-id="@file.id">
+                <span class="glyphicon glyphicon-plus"></span>
+            </a>
+        }
+
         <div class="row">
             <div class="col-md-2 col-sm-2 col-lg-2">
                 @if(!file.thumbnail_id.isEmpty){
@@ -87,8 +93,6 @@ <h3><a href="@(routes.Files.file(file.id, dataset, space, folder))">@file.filena
                                 }
                                 case None => {}
                             }
-
-
                         </ul>
                     </div>
                 </div>
diff --git a/public/javascripts/deleteUtils.js b/public/javascripts/deleteUtils.js
index eb903357b..655d9d830 100644
--- a/public/javascripts/deleteUtils.js
+++ b/public/javascripts/deleteUtils.js
@@ -48,6 +48,38 @@ function confirmDeleteSelected() {
     }
 }
 
+function confirmDeleteMarked(datasetId) {
+    console.log(datasetId);
+    var selected = $.cookie('selected-files-'+datasetId);
+    if (selected) {
+        var msg = "Are you sure you want to delete the selected files?";
+
+        var modalHTML = '<div id="confirm-delete" class="modal fade" role="dialog">';
+        modalHTML += '<div class="modal-dialog">';
+        modalHTML += '<div class="modal-content">';
+        modalHTML += '<div class="modal-header">';
+        modalHTML += '<button type="button" class="close" data-dismiss="modal">&times;</button>';
+        modalHTML += '<h4 class="modal-title">Confirm</h4>';
+        modalHTML += '</div>';
+        modalHTML += '<div class="modal-body">';
+        modalHTML += '<p>' + msg + '</p>';
+        modalHTML += '</div>';
+        modalHTML += '<div class="modal-footer">';
+        modalHTML += '<button type="button" class="btn btn-link" data-dismiss="modal"><span class="glyphicon glyphicon-remove"></span> Cancel</button>';
+        modalHTML += '<a type="button" class="btn btn-primary" id="OKModalButton" href="javascript:deleteAllSelections()"><span class="glyphicon glyphicon-ok"></span> OK</a>';
+        modalHTML += '</div>';
+        modalHTML += '</div>';
+        modalHTML += '</div>';
+        modalHTML += '</div>';
+
+        var confirmModal = $(modalHTML);
+        confirmModal.modal();
+        confirmModal.modal("show");
+    } else {
+        notify("No files currently selected", "warning")
+    }
+}
+
 function confirmDeleteTemplate(message, resourceType, resourceId, isreload, url) {
     var modalHTML = '<div id="confirm-delete" class="modal fade" role="dialog">';
     modalHTML += '<div class="modal-dialog">';

From 5f56c43386103d10c1cbb415d6f3132da16948a8 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Mon, 8 Jun 2020 10:18:21 -0500
Subject: [PATCH 02/15] implementation of bulk deletion, tagging of files

---
 app/views/datasets/filesAndFolders.scala.html | 233 +++++++++++++++---
 public/javascripts/deleteUtils.js             |  32 ---
 2 files changed, 197 insertions(+), 68 deletions(-)

diff --git a/app/views/datasets/filesAndFolders.scala.html b/app/views/datasets/filesAndFolders.scala.html
index 07ceb09d9..bffccfb44 100644
--- a/app/views/datasets/filesAndFolders.scala.html
+++ b/app/views/datasets/filesAndFolders.scala.html
@@ -2,6 +2,8 @@
         filepage: Int, next: Boolean, fileList:List[File], fileComments: Map[UUID, Int], space: Option[String],
         filter: Option[String])(implicit user: Option[models.User])
 
+@import play.api.Play.current
+
 <!-- Breadcrumbs -->
 @if(folderHierarchy.length > 0 ) {
     <div><h2 id='folderpath'>
@@ -52,7 +54,7 @@
             </div>
         </td>
         <td width="20%" >
-            <div id="selected-count-box"></div>
+            <div id="selected-count-box">Marked Files (<b>0</b>)</div>
         </td>
         <td width="30%">
             <label class="sortchoice" for="js-sort-single">Sort By:
@@ -82,57 +84,216 @@
             //$('#selected-count-box').html('Marked Files (<b>'+fileUUIDs.length+'</b>)')
             $('#selected-count-box').html('<div class="dropdown"><a href="#" class="dropdown-toggle" ' +
                     'data-toggle="dropdown" aria-expanded="false"> Marked Files (<b>'+fileUUIDs.length+'</b>)' +
-                    '<b class="caret"></b></a><ul class="dropdown-menu"><li>' +
-                    '<a onclick="deleteSelectedFiles();">Delete All</a></li></ul>' +
+                    '<b class="caret"></b></a><ul class="dropdown-menu">' +
+                    // TODO: Show All if only marked are shown
+                    '<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
+                    '<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
+                    '<li><a onclick="confirmTagMarked();"><span class="glyphicon glyphicon-tag"/>&nbsp;Tag All</a></li>' +
+                    '<li><a onclick="confirmDeleteMarked();"><span class="glyphicon glyphicon-trash"/>&nbsp;Delete All</a></li>' +
+                    '<li><a onclick="clearMarked();"><span class="glyphicon glyphicon-erase"/>&nbsp;Clear All</a></li></ul>' +
                     '</div>')
         } else {
             $('#selected-count-box').html('Marked Files (<b>0</b>)')
         }
     }
 
-    function deleteSelectedFiles() {
-        console.log("Are you sure?");
+    function confirmDeleteMarked() {
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            selected = selected.split(',');
+            if (selected.length > 0) {
+                var msg = "Are you sure you want to delete "+String(selected.length)+" marked files?";
+
+                var modalHTML = '<div id="confirm-delete" class="modal fade" role="dialog">';
+                modalHTML += '<div class="modal-dialog">';
+                modalHTML += '<div class="modal-content">';
+                modalHTML += '<div class="modal-header">';
+                modalHTML += '<button type="button" class="close" data-dismiss="modal">&times;</button>';
+                modalHTML += '<h4 class="modal-title">Confirm</h4>';
+                modalHTML += '</div>';
+                modalHTML += '<div class="modal-body">';
+                modalHTML += '<p>' + msg + '</p>';
+                modalHTML += '</div>';
+                modalHTML += '<div class="modal-footer">';
+                modalHTML += '<button type="button" class="btn btn-link" data-dismiss="modal"><span class="glyphicon glyphicon-remove"></span> Cancel</button>';
+                modalHTML += '<a type="button" class="btn btn-primary" id="OKModalButton" onclick="deleteAllMarked();" data-dismiss="modal"><span class="glyphicon glyphicon-ok"></span> OK</a>';
+                modalHTML += '</div>';
+                modalHTML += '</div>';
+                modalHTML += '</div>';
+                modalHTML += '</div>';
+
+                var confirmModal = $(modalHTML);
+                confirmModal.modal();
+                confirmModal.modal("show");
+            } else {
+                notify("No files currently marked", "warning")
+            }
+        } else {
+            notify("No files currently marked", "warning")
+        }
+    }
+
+    function deleteAllMarked() {
+        // TODO: Would be nice to have a bulk endpoint for this eventually that takes a string of comma-separated UUIDs
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            selected = selected.split(',');
+            for (entry in selected) {
+                var request = jsRoutes.api.Files.removeFile(selected[entry]).ajax({
+                    type: 'DELETE'
+                });
+                // If this is in request.done, only one ID gets removed in the for loop, so remove them all now
+                removeFileFromMarked(selected[entry]);
+                request.done(function (response, textStatus, jqXHR) {
+                    getUpdatedFilesAndFolders();
+                });
+                request.fail(function (jqXHR, textStatus, errorThrown){
+                    console.error("The following error occured: " + textStatus, errorThrown);
+                    notify("Could not delete marked file "+selected[entry]+": " + errorThrown, "error");
+                    // Add it back to selected list
+                    addFileToMarked(selected[entry]);
+                });
+            }
+        }
+    }
+
+    function showOnlyMarked() {
         confirmDeleteMarked('@dataset.id');
     }
 
+    function downloadMarked() {
+        // TODO: Downloading selected files as Zip - look at downloading folders tasks
+        console.log("Not implemented.")
+    }
+
+    function confirmTagMarked() {
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            var modalHTML = `
+            <div id="enter-tag" class="modal fade" role="dialog">
+                <div class="modal-dialog">
+                    <div class="modal-content">
+                        <div class="modal-header">
+                            <button type="button" class="close" data-dismiss="modal">&times;</button>
+                            <h4 class="modal-title">Tag All Marked Files</h4>
+                        </div>
+                        <div class="modal-body">
+                            <p>
+                                Multiple tags may be entered, separated by commas.
+                            </p>
+                            <input maxlength="@play.api.Play.configuration.getInt("clowder.tagLength").getOrElse(100)"
+                                type="text" id="bulk-tag-selector" class="form-control add-resource" placeholder="Enter a tag...">
+
+                        </div>
+                        <div class="modal-footer">
+                            <button type="button" class="btn btn-link" data-dismiss="modal"><span class="glyphicon glyphicon-remove"></span> Cancel</button>
+                            <a type="button" class="btn btn-primary" id="OKModalButton" onclick="tagMarked()"><span class="glyphicon glyphicon-ok"></span> OK</a>
+                        </div>
+                    </div>
+                </div>
+            </div>
+            `;
+
+            var confirmModal = $(modalHTML);
+            confirmModal.modal();
+            confirmModal.modal("show");
+        } else {
+            notify("No files currently marked", "warning")
+        }
+    }
+
+    function tagMarked() {
+        // TODO: Would be nice to have a bulk endpoint for this eventually that takes a string of comma-separated UUIDs
+        var tag = $('#bulk-tag-selector')[0].value;
+        if (tag.length > 0) {
+            var selected = $.cookie('selected-files-@dataset.id');
+            if (selected) {
+                selected = selected.split(',');
+                for (entry in selected) {
+                    var request = jsRoutes.api.Files.addTags(selected[entry]).ajax({
+                        type: 'POST',
+                        dataType: 'json',
+                        contentType: 'application/json',
+                        data: JSON.stringify({
+                            "tags": tag.split(',')
+                        })
+                    });
+                    request.done(function (response, textStatus, jqXHR) {
+                        getUpdatedFilesAndFolders();
+                    });
+                    request.fail(function (jqXHR, textStatus, errorThrown) {
+                        console.error("The following error occured: " + textStatus, errorThrown);
+                        notify("Could not tag marked file " + selected[entry] + ": " + errorThrown, "error");
+                    });
+                }
+            }
+        }
+
+
+
+
+
+        if (tag.length > 0) {
+            var request = jsRoutes.api.Selected.tagAll(tag.split(",")).ajax({
+                type: 'POST'
+            });
+            request.done(function (response, textStatus, jqXHR) {
+                notify("Tag(s) successfully added.", "success", false, 2000);
+            });
+            request.fail(function (jqXHR, textStatus, errorThrown){
+                console.error("The following error occured: " + textStatus, errorThrown);
+                notify("Could not tag selections: " + errorThrown, "error");
+            });
+
+        } else {
+            console.log("No tag was provided.")
+        }
+        $("#enter-tag").modal("hide")
+    }
+
+    function clearMarked() {
+        // Set cookie to empty, redraw the file list to get corrected display
+        $.cookie('selected-files-@dataset.id', "");
+        getUpdatedFilesAndFolders();
+    }
+
+    function addFileToMarked(file_id) {
+        // TODO: Use Play framework cookies instead of jquery flavor for better security
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            if (selected.indexOf(file_id) == -1)
+                selected += ","+file_id;
+        } else {
+            selected = file_id;
+        }
+        $.cookie('selected-files-@dataset.id', selected);
+
+        $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-plus');
+        $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-ok');
+        updateSelectedFileCount();
+    }
+
+    function removeFileFromMarked(file_id) {
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected && selected.indexOf(file_id) > -1) {
+            selected = selected.replace(file_id+',', '').replace(','+file_id, '').replace(file_id, '');
+            $.cookie('selected-files-@dataset.id', selected, {expires: 14});
+        }
+
+        $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-ok');
+        $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-plus');
+        updateSelectedFileCount();
+    }
+
     $(document).ready(function() {
         $('.fileselect').click(function() {
             var file_id = $(this).data("id");
 
             if ($("a[data-id='" + file_id + "'] span.glyphicon").hasClass('glyphicon-plus')) {
-                // SELECT THE FILE
-                // TODO: Add Clear All option
-                var selected = $.cookie('selected-files-@dataset.id');
-                if (selected) {
-                    if (selected.indexOf(file_id) == -1)
-                        selected += ","+file_id;
-                } else {
-                    selected = file_id;
-                }
-                $.cookie('selected-files-@dataset.id', selected);
-
-                $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-plus');
-                $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-ok');
-                updateSelectedFileCount();
+                addFileToMarked(file_id)
             } else {
-                // DESELECT THE FILE
-                var selected = $.cookie('selected-files-@dataset.id');
-                if (selected && selected.indexOf(file_id) > -1) {
-                    selected = selected.replace(file_id+',', '').replace(','+file_id, '').replace(file_id, '');
-                    $.cookie('selected-files-@dataset.id', selected, {expires: 14});
-                }
+                removeFileFromMarked(file_id);
 
-                $("a[data-id='"+file_id+"'] span.glyphicon").removeClass('glyphicon-ok');
-                $("a[data-id='"+file_id+"'] span.glyphicon").addClass('glyphicon-plus');
-                updateSelectedFileCount();
-                // TODO: plain jquery cookies? logout could still see them. play uses key
-                // TODO: show only marked files
-                // TODO: Downloading selected files as Zip - look at downloading folders tasks
-                // make separate tasks for my SIMPL task for a sprint with more granularity
-
-                // TODO: convert selection datasets to a collection
-                // TODO: Selections become Favorites
-                // TODO: recently viewed list?
             }
         });
 
diff --git a/public/javascripts/deleteUtils.js b/public/javascripts/deleteUtils.js
index 655d9d830..eb903357b 100644
--- a/public/javascripts/deleteUtils.js
+++ b/public/javascripts/deleteUtils.js
@@ -48,38 +48,6 @@ function confirmDeleteSelected() {
     }
 }
 
-function confirmDeleteMarked(datasetId) {
-    console.log(datasetId);
-    var selected = $.cookie('selected-files-'+datasetId);
-    if (selected) {
-        var msg = "Are you sure you want to delete the selected files?";
-
-        var modalHTML = '<div id="confirm-delete" class="modal fade" role="dialog">';
-        modalHTML += '<div class="modal-dialog">';
-        modalHTML += '<div class="modal-content">';
-        modalHTML += '<div class="modal-header">';
-        modalHTML += '<button type="button" class="close" data-dismiss="modal">&times;</button>';
-        modalHTML += '<h4 class="modal-title">Confirm</h4>';
-        modalHTML += '</div>';
-        modalHTML += '<div class="modal-body">';
-        modalHTML += '<p>' + msg + '</p>';
-        modalHTML += '</div>';
-        modalHTML += '<div class="modal-footer">';
-        modalHTML += '<button type="button" class="btn btn-link" data-dismiss="modal"><span class="glyphicon glyphicon-remove"></span> Cancel</button>';
-        modalHTML += '<a type="button" class="btn btn-primary" id="OKModalButton" href="javascript:deleteAllSelections()"><span class="glyphicon glyphicon-ok"></span> OK</a>';
-        modalHTML += '</div>';
-        modalHTML += '</div>';
-        modalHTML += '</div>';
-        modalHTML += '</div>';
-
-        var confirmModal = $(modalHTML);
-        confirmModal.modal();
-        confirmModal.modal("show");
-    } else {
-        notify("No files currently selected", "warning")
-    }
-}
-
 function confirmDeleteTemplate(message, resourceType, resourceId, isreload, url) {
     var modalHTML = '<div id="confirm-delete" class="modal fade" role="dialog">';
     modalHTML += '<div class="modal-dialog">';

From 6215e06aa8fbfa72fd463b71660284f1cf7c0e21 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Mon, 8 Jun 2020 10:24:30 -0500
Subject: [PATCH 03/15] hide non-implemented options

---
 app/views/datasets/filesAndFolders.scala.html | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/app/views/datasets/filesAndFolders.scala.html b/app/views/datasets/filesAndFolders.scala.html
index bffccfb44..8b01f790c 100644
--- a/app/views/datasets/filesAndFolders.scala.html
+++ b/app/views/datasets/filesAndFolders.scala.html
@@ -85,9 +85,11 @@
             $('#selected-count-box').html('<div class="dropdown"><a href="#" class="dropdown-toggle" ' +
                     'data-toggle="dropdown" aria-expanded="false"> Marked Files (<b>'+fileUUIDs.length+'</b>)' +
                     '<b class="caret"></b></a><ul class="dropdown-menu">' +
-                    // TODO: Show All if only marked are shown
-                    '<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
-                    '<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
+                    // TODO: Need better solution than cookies to support 'Show Only Marked' request
+                    //'<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
+                    //'<li><a onclick="showAllFiles();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show All Files</a></li>' +
+                    // TODO: Support for downloading by folder and marked list will be implemented in the future
+                    //'<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
                     '<li><a onclick="confirmTagMarked();"><span class="glyphicon glyphicon-tag"/>&nbsp;Tag All</a></li>' +
                     '<li><a onclick="confirmDeleteMarked();"><span class="glyphicon glyphicon-trash"/>&nbsp;Delete All</a></li>' +
                     '<li><a onclick="clearMarked();"><span class="glyphicon glyphicon-erase"/>&nbsp;Clear All</a></li></ul>' +

From 2e0a1c97f5439f24619649b30f5c71729ff2208c Mon Sep 17 00:00:00 2001
From: Mike Lambert <lambert8@illinois.edu>
Date: Tue, 9 Jun 2020 12:35:36 -0500
Subject: [PATCH 04/15] Fixed incorrect selector on imagesLoaded in the Space
 view

---
 app/views/datasets/tile.scala.html |  2 +-
 app/views/spaces/space.scala.html  | 25 ++++++++++++++-----------
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/app/views/datasets/tile.scala.html b/app/views/datasets/tile.scala.html
index de9ebd529..9dc94f066 100644
--- a/app/views/datasets/tile.scala.html
+++ b/app/views/datasets/tile.scala.html
@@ -17,7 +17,7 @@
         <div class="panel-body">
             @if(!dataset.thumbnail_id.isEmpty){
                 <a href="@(routes.Datasets.dataset(dataset.id,space))">
-                    <img class="img-responsive fit-in-space" src="@(routes.Files.thumbnail(UUID(dataset.thumbnail_id.toString().substring(5,dataset.thumbnail_id.toString().length-1))))" alt="Thumbnail of @Html(dataset.name)">
+                    <img class="img-responsive fit-in-space tiled-image" src="@(routes.Files.thumbnail(UUID(dataset.thumbnail_id.toString().substring(5,dataset.thumbnail_id.toString().length-1))))" alt="Thumbnail of @Html(dataset.name)">
                 </a>
             }
             <div class="caption break-word">
diff --git a/app/views/spaces/space.scala.html b/app/views/spaces/space.scala.html
index 21b2ca6b5..22c46ba42 100644
--- a/app/views/spaces/space.scala.html
+++ b/app/views/spaces/space.scala.html
@@ -128,18 +128,21 @@ <h3>@Messages("collections.title")</h3>
     <script>
         function activateOne(id) {
             // initialize Masonry
-            var items = $("#" + id); 
-            if(items.length) { 
-            	var $container = $("#" + id).masonry();
-	            // layout Masonry again after all images have loaded
-    	        imagesLoaded( '#masonry', function() {
-        	        $container.masonry({
-            	    itemSelector: '.post-box',
-                	columnWidth: '.post-box',
-                	transitionDuration: 4
-                	});
-            	});
+            var match = $("#" + id);
+            if (!match) {
+                return;
             }
+
+            match.masonry();
+
+            // layout Masonry again after all images have loaded
+            imagesLoaded( '.tiled-image', function() {
+                match.masonry({
+                    itemSelector: '.tiled-image',
+                    columnWidth: '.tiled-image',
+                    transitionDuration: 4
+                });
+            });
         }
 
         function activate(){

From e7d907ec79e8340f9422285daa7d371bf6337ad1 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Tue, 16 Jun 2020 18:30:29 -0500
Subject: [PATCH 05/15] return thumbnail (fixes #8)

---
 CHANGELOG.md        |  6 ++++++
 app/api/Files.scala | 27 +++++++--------------------
 public/swagger.yml  | 24 ++++++++++++++++++++----
 3 files changed, 33 insertions(+), 24 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3045d4581..4f2b1b2ca 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
+## [Unreleased]
+
+### Fixed
+- Return thumbnail as part of the file information.
+  [#8](https://github.com/clowder-framework/clowder/issues/8)
+
 ## 1.9.0 - 2020-06-01
 **_Warning:_ This update modifies information stored in Elasticsearch used for text based searching. To take advantage 
 of these changes a reindex of Elasticsearch is required. A reindex can be started by an admin from the Admin menu.**
diff --git a/app/api/Files.scala b/app/api/Files.scala
index 7aff652d7..a8c449f0c 100644
--- a/app/api/Files.scala
+++ b/app/api/Files.scala
@@ -728,6 +728,7 @@ class Files @Inject()(
       "content-type" -> file.contentType,
       "date-created" -> file.uploadDate.toString(),
       "size" -> file.length.toString,
+      "thumbnail" -> file.thumbnail_id.orNull,
       "authorId" -> file.author.id.stringify,
       "status" -> file.status)
 
@@ -735,16 +736,9 @@ class Files @Inject()(
     val jsonMap = file.loader match {
       case "services.filesystem.DiskByteStorageService" => {
         if (serverAdmin)
-          Map(
-            "id" -> file.id.toString,
-            "filename" -> file.filename,
-            "filepath" -> file.loader_id,
-            "filedescription" -> file.description,
-            "content-type" -> file.contentType,
-            "date-created" -> file.uploadDate.toString(),
-            "size" -> file.length.toString,
-            "authorId" -> file.author.id.stringify,
-            "status" -> file.status)
+          defaultMap ++ Map(
+            "filepath" -> file.loader_id
+          )
         else
           defaultMap
       }
@@ -752,18 +746,11 @@ class Files @Inject()(
         if (serverAdmin) {
           val bucketName = configuration.getString(S3ByteStorageService.BucketName).getOrElse("")
           val serviceEndpoint = configuration.getString(S3ByteStorageService.ServiceEndpoint).getOrElse("")
-          Map(
-            "id" -> file.id.toString,
-            "filename" -> file.filename,
+          defaultMap ++ Map(
             "service-endpoint" -> serviceEndpoint,
             "bucket-name" -> bucketName,
-            "object-key" -> file.loader_id,
-            "filedescription" -> file.description,
-            "content-type" -> file.contentType,
-            "date-created" -> file.uploadDate.toString(),
-            "size" -> file.length.toString,
-            "authorId" -> file.author.id.stringify,
-            "status" -> file.status)
+            "object-key" -> file.loader_id
+          )
         } else
           defaultMap
       }
diff --git a/public/swagger.yml b/public/swagger.yml
index 405b4bf03..c50c0108b 100644
--- a/public/swagger.yml
+++ b/public/swagger.yml
@@ -272,7 +272,7 @@ paths:
         - files
       summary: Retrieve physical file object metadata
       description: |
-        Get metadata of the file object (not the resource it describes) as JSON.
+        Get information of the file object (not the resource it describes) as JSON.
         For example, size of file, date created, content type, filename.
       parameters:
         - name: id
@@ -281,9 +281,16 @@ paths:
           schema:
             type: string
       responses:
-        200:
-          description: OK
-          content: {}
+        '200':
+          description: Successfully returns a list of files
+          content:
+            application/json:
+              schema:
+                $ref: '#/components/schemas/File'
+        '401':
+          $ref: '#/components/responses/Disabled'
+        '404':
+          $ref: '#/components/responses/NotFound'
     post:
       tags:
         - files
@@ -5363,13 +5370,16 @@ components:
       properties:
         id:
           type: string
+          example: "5b8e969d5e0e8690971ee23e"
         filename:
           type: string
+          example: "cat.jpg"
         filepath:
           type: string
           description: |
             only specified if user is serveradmin, and storage is
             DiskByteStorageService
+          example: "/home/clowder/data/uploads/41/e2/1e/5b8e969d5e0e8690971ee241"
         service-endpoint:
           type: string
           description: |
@@ -5387,18 +5397,24 @@ components:
             S3ByteStorageService
         filedescription:
           type: string
+          example: "Picture of a cat"
         content-type:
           type: string
+          example: "image/jpeg"
         date-created:
           type: string # should be date-time
+          example: "Tue Sep 04 09:28:45 CDT 2018"
         size:
           type: string # should be integer int64
           format: int64
+          example: "190497"
         authorId:
           type: string # should be miniuser
           #$ref: '#/components/schemas/MiniUser'
+          example: "5447f889fa429866bbd44dbd"
         status:
           type: string # should be enum
+          example: "PROCESSED"
     MiniUser:
       type: object
     Space:

From ec95e748d9f81b19a4a62d9f3011bdb167485bbc Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Wed, 17 Jun 2020 07:11:36 -0500
Subject: [PATCH 06/15] forgot to document thumbnail

---
 public/swagger.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/public/swagger.yml b/public/swagger.yml
index c50c0108b..3aa26e28c 100644
--- a/public/swagger.yml
+++ b/public/swagger.yml
@@ -5410,10 +5410,21 @@ components:
           example: "190497"
         authorId:
           type: string # should be miniuser
+          description: id of user who uploaded the file
           #$ref: '#/components/schemas/MiniUser'
           example: "5447f889fa429866bbd44dbd"
+        thumbnail:
+          type: string
+          description: |
+            optinal id of the thumbnail image of this file
+          example: "5bfd5a2640c6cd6147bb27e0"
         status:
           type: string # should be enum
+          description: |
+            status of the file, this can be one of the following:
+            - CREATED file is created, but blob is not in final place yes
+            - PROCESSING blob is in final place, final processing is done such as sending messagess to RabbitMQ
+            - PROCESSED file is fully procesed by clowder
           example: "PROCESSED"
     MiniUser:
       type: object

From fb1f2658fe46d7357a4bdb30b1374babfbc48a3c Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Tue, 23 Jun 2020 10:28:29 -0500
Subject: [PATCH 07/15] download selected files from within a dataset

For code simplicity, still includes bagit support, dataset metadata, etc.
---
 app/api/Datasets.scala                        | 45 ++++++++++++++++---
 app/controllers/Application.scala             |  1 +
 app/views/datasets/filesAndFolders.scala.html | 13 ++++--
 conf/routes                                   |  1 +
 4 files changed, 51 insertions(+), 9 deletions(-)

diff --git a/app/api/Datasets.scala b/app/api/Datasets.scala
index 0c758030b..acdb308d2 100644
--- a/app/api/Datasets.scala
+++ b/app/api/Datasets.scala
@@ -2068,7 +2068,9 @@ class  Datasets @Inject()(
     * @return Enumerator to produce array of bytes from a zipped stream containing the bytes of each file
     *         in the dataset
     */
-  def enumeratorFromDataset(dataset: Dataset, chunkSize: Int = 1024 * 8, compression: Int = Deflater.DEFAULT_COMPRESSION, bagit: Boolean, user : Option[User])
+  def enumeratorFromDataset(dataset: Dataset, chunkSize: Int = 1024 * 8,
+                            compression: Int = Deflater.DEFAULT_COMPRESSION, bagit: Boolean,
+                            user : Option[User], fileIDs: Option[List[UUID]])
                            (implicit ec: ExecutionContext): Enumerator[Array[Byte]] = {
     implicit val pec = ec.prepare()
     val dataFolder = if (bagit) "data/" else ""
@@ -2077,7 +2079,17 @@ class  Datasets @Inject()(
 
     // compute list of all files and folder in dataset. This will also make sure
     // that all files and folder names are unique.
-    listFilesInFolder(dataset.files, dataset.folders, dataFolder, filenameMap, inputFiles)
+    fileIDs match {
+      case Some(fids) => {
+        Logger.info("Downloading only some files")
+        Logger.info(fids.toString)
+        listFilesInFolder(fids, List.empty, dataFolder, filenameMap, inputFiles)
+      }
+      case None => {
+        // TODO: folderId match ...
+        listFilesInFolder(dataset.files, dataset.folders, dataFolder, filenameMap, inputFiles)
+      }
+    }
 
     val md5Files = scala.collection.mutable.HashMap.empty[String, MessageDigest] //for the files
     val md5Bag = scala.collection.mutable.HashMap.empty[String, MessageDigest] //for the bag files
@@ -2121,14 +2133,13 @@ class  Datasets @Inject()(
      * the enumerator is finished
      */
 
-    var is: Option[InputStream] = addDatasetInfoToZip(dataFolder,dataset,zip)
+    var is: Option[InputStream] = addDatasetInfoToZip(dataFolder, dataset, zip)
     //digest input stream
     val md5 = MessageDigest.getInstance("MD5")
     md5Files.put(dataFolder+"_info.json",md5)
     is = Some(new DigestInputStream(is.get,md5))
     file_type = 1 //next is metadata
 
-
     Enumerator.generateM({
       is match {
         case Some(inputStream) => {
@@ -2415,7 +2426,7 @@ class  Datasets @Inject()(
 
         // Use custom enumerator to create the zip file on the fly
         // Use a 1MB in memory byte array
-        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, compression,bagit,user)).withHeaders(
+        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, compression, bagit, user, None)).withHeaders(
           CONTENT_TYPE -> "application/zip",
           CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ ".zip", request.headers.get("user-agent").getOrElse("")))
         )
@@ -2427,6 +2438,30 @@ class  Datasets @Inject()(
     }
   }
 
+  def downloadPartial(id: UUID, fileList: String) = PermissionAction(Permission.DownloadFiles, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
+    implicit val user = request.user
+    datasets.get(id) match {
+      case Some(dataset) => {
+        val fileIDs = fileList.split(',').map(fid => new UUID(fid)).toList
+        val bagit = play.api.Play.configuration.getBoolean("downloadDatasetBagit").getOrElse(true)
+
+        // Increment download count for each file
+        fileIDs.foreach(fid => files.incrementDownloads(fid, user))
+
+        // Use custom enumerator to create the zip file on the fly
+        // Use a 1MB in memory byte array
+        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, -1, bagit, user, Some(fileIDs))).withHeaders(
+          CONTENT_TYPE -> "application/zip",
+          CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ " (Partial).zip", request.headers.get("user-agent").getOrElse("")))
+        )
+      }
+      // If the dataset wasn't found by ID
+      case None => {
+        NotFound
+      }
+    }
+  }
+
   def updateAccess(id:UUID, access:String) = PermissionAction(Permission.PublicDataset, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
     implicit val user = request.user
     user match {
diff --git a/app/controllers/Application.scala b/app/controllers/Application.scala
index b43a2251e..d6393aeb9 100644
--- a/app/controllers/Application.scala
+++ b/app/controllers/Application.scala
@@ -333,6 +333,7 @@ class Application @Inject() (files: FileService, collections: CollectionService,
         api.routes.javascript.Datasets.unfollow,
         api.routes.javascript.Datasets.detachFile,
         api.routes.javascript.Datasets.download,
+        api.routes.javascript.Datasets.downloadPartial,
         api.routes.javascript.Datasets.getPreviews,
         api.routes.javascript.Datasets.updateAccess,
         api.routes.javascript.Datasets.addFileEvent,
diff --git a/app/views/datasets/filesAndFolders.scala.html b/app/views/datasets/filesAndFolders.scala.html
index 8b01f790c..541dc560d 100644
--- a/app/views/datasets/filesAndFolders.scala.html
+++ b/app/views/datasets/filesAndFolders.scala.html
@@ -89,7 +89,7 @@
                     //'<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
                     //'<li><a onclick="showAllFiles();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show All Files</a></li>' +
                     // TODO: Support for downloading by folder and marked list will be implemented in the future
-                    //'<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
+                    '<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
                     '<li><a onclick="confirmTagMarked();"><span class="glyphicon glyphicon-tag"/>&nbsp;Tag All</a></li>' +
                     '<li><a onclick="confirmDeleteMarked();"><span class="glyphicon glyphicon-trash"/>&nbsp;Delete All</a></li>' +
                     '<li><a onclick="clearMarked();"><span class="glyphicon glyphicon-erase"/>&nbsp;Clear All</a></li></ul>' +
@@ -160,12 +160,17 @@
     }
 
     function showOnlyMarked() {
-        confirmDeleteMarked('@dataset.id');
+        console.log("Not implemented.")
     }
 
+    // Download selected files as Zip
     function downloadMarked() {
-        // TODO: Downloading selected files as Zip - look at downloading folders tasks
-        console.log("Not implemented.")
+        var selected = $.cookie('selected-files-@dataset.id');
+        if (selected) {
+            window.open(jsRoutes.api.Datasets.downloadPartial('@dataset.id', selected).url, '_blank');
+        } else {
+            notify("No files selected.")
+        }
     }
 
     function confirmTagMarked() {
diff --git a/conf/routes b/conf/routes
index dc3a343f8..a6dea7296 100644
--- a/conf/routes
+++ b/conf/routes
@@ -574,6 +574,7 @@ GET            /api/datasets/:id/files
 POST           /api/datasets/:id/files                                                  @api.Datasets.uploadToDatasetFile(id: UUID)
 POST           /api/datasets/:id/urls                                                   @api.Datasets.uploadToDatasetJSON(id: UUID)
 GET            /api/datasets/:id/download                                               @api.Datasets.download(id: UUID, compression: Int ?= -1, tracking: Boolean ?= true)
+GET            /api/datasets/:id/downloadPartial                                        @api.Datasets.downloadPartial(id: UUID, fileList: String)
 POST           /api/datasets/:id/comment                                                @api.Datasets.comment(id: UUID)
 POST           /api/datasets/:id/reindex                                                @api.Datasets.reindex(id:UUID, recursive: Boolean ?= true)
 POST           /api/datasets/:id/follow                                                 @api.Datasets.follow(id: UUID)

From 1eebfe22e853116acaeba49678d16f3da331a798 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Tue, 23 Jun 2020 10:50:11 -0500
Subject: [PATCH 08/15] add folder download support

---
 app/api/Datasets.scala                | 42 +++++++++++++++++++++++----
 app/controllers/Application.scala     |  1 +
 app/views/folders/listitem.scala.html | 17 ++++++++++-
 conf/routes                           |  1 +
 4 files changed, 55 insertions(+), 6 deletions(-)

diff --git a/app/api/Datasets.scala b/app/api/Datasets.scala
index acdb308d2..2eea193f0 100644
--- a/app/api/Datasets.scala
+++ b/app/api/Datasets.scala
@@ -2070,7 +2070,7 @@ class  Datasets @Inject()(
     */
   def enumeratorFromDataset(dataset: Dataset, chunkSize: Int = 1024 * 8,
                             compression: Int = Deflater.DEFAULT_COMPRESSION, bagit: Boolean,
-                            user : Option[User], fileIDs: Option[List[UUID]])
+                            user : Option[User], fileIDs: Option[List[UUID]], folderId: Option[UUID])
                            (implicit ec: ExecutionContext): Enumerator[Array[Byte]] = {
     implicit val pec = ec.prepare()
     val dataFolder = if (bagit) "data/" else ""
@@ -2086,8 +2086,10 @@ class  Datasets @Inject()(
         listFilesInFolder(fids, List.empty, dataFolder, filenameMap, inputFiles)
       }
       case None => {
-        // TODO: folderId match ...
-        listFilesInFolder(dataset.files, dataset.folders, dataFolder, filenameMap, inputFiles)
+        folderId match {
+          case Some(fid) => listFilesInFolder(List.empty, List(fid), dataFolder, filenameMap, inputFiles)
+          case None => listFilesInFolder(dataset.files, dataset.folders, dataFolder, filenameMap, inputFiles)
+        }
       }
     }
 
@@ -2426,7 +2428,7 @@ class  Datasets @Inject()(
 
         // Use custom enumerator to create the zip file on the fly
         // Use a 1MB in memory byte array
-        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, compression, bagit, user, None)).withHeaders(
+        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, compression, bagit, user, None, None)).withHeaders(
           CONTENT_TYPE -> "application/zip",
           CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ ".zip", request.headers.get("user-agent").getOrElse("")))
         )
@@ -2450,7 +2452,7 @@ class  Datasets @Inject()(
 
         // Use custom enumerator to create the zip file on the fly
         // Use a 1MB in memory byte array
-        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, -1, bagit, user, Some(fileIDs))).withHeaders(
+        Ok.chunked(enumeratorFromDataset(dataset,1024*1024, -1, bagit, user, Some(fileIDs), None)).withHeaders(
           CONTENT_TYPE -> "application/zip",
           CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ " (Partial).zip", request.headers.get("user-agent").getOrElse("")))
         )
@@ -2462,6 +2464,36 @@ class  Datasets @Inject()(
     }
   }
 
+  def downloadFolder(id: UUID, folderId: UUID) = PermissionAction(Permission.DownloadFiles, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
+    implicit val user = request.user
+    datasets.get(id) match {
+      case Some(dataset) => {
+        val bagit = play.api.Play.configuration.getBoolean("downloadDatasetBagit").getOrElse(true)
+
+        // Increment download count for each file in folder
+        folders.get(folderId) match {
+          case Some(fo) => {
+            fo.files.foreach(fid => files.incrementDownloads(fid, user))
+
+            // Use custom enumerator to create the zip file on the fly
+            // Use a 1MB in memory byte array
+            Ok.chunked(enumeratorFromDataset(dataset,1024*1024, -1, bagit, user, None, Some(folderId))).withHeaders(
+              CONTENT_TYPE -> "application/zip",
+              CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ " ( "+fo.name+" Folder).zip", request.headers.get("user-agent").getOrElse("")))
+            )
+          }
+          case None => NotFound
+        }
+
+
+      }
+      // If the dataset wasn't found by ID
+      case None => {
+        NotFound
+      }
+    }
+  }
+
   def updateAccess(id:UUID, access:String) = PermissionAction(Permission.PublicDataset, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
     implicit val user = request.user
     user match {
diff --git a/app/controllers/Application.scala b/app/controllers/Application.scala
index d6393aeb9..7433e186c 100644
--- a/app/controllers/Application.scala
+++ b/app/controllers/Application.scala
@@ -334,6 +334,7 @@ class Application @Inject() (files: FileService, collections: CollectionService,
         api.routes.javascript.Datasets.detachFile,
         api.routes.javascript.Datasets.download,
         api.routes.javascript.Datasets.downloadPartial,
+        api.routes.javascript.Datasets.downloadFolder,
         api.routes.javascript.Datasets.getPreviews,
         api.routes.javascript.Datasets.updateAccess,
         api.routes.javascript.Datasets.addFileEvent,
diff --git a/app/views/folders/listitem.scala.html b/app/views/folders/listitem.scala.html
index a114cded8..8262b8720 100644
--- a/app/views/folders/listitem.scala.html
+++ b/app/views/folders/listitem.scala.html
@@ -26,7 +26,7 @@ <h3 id="h-edit-@folder.id" class="hiddencomplete">
                 </div>
 
                 <div class="row">
-                    <div class="col-md-12 col-lg-12 col-sm-12">
+                    <div class="col-md-8 col-lg-8 col-sm-8">
                         <ul class="list-unstyled">
                             <li>
                                 <span class="glyphicon glyphicon-folder-close"></span> @folder.folders.length
@@ -44,6 +44,21 @@ <h3 id="h-edit-@folder.id" class="hiddencomplete">
                             </li>
                         </ul>
                     </div>
+                    <div class="col-md-4 col-lg-4 col-sm-4">
+                        <ul class="list-unstyled">
+                        @if(Permission.checkPermission(Permission.DownloadFiles, ResourceRef(ResourceRef.dataset, folder.parentDatasetId))) {
+                            <li>
+                                <button id="downloadButton" onclick="window.open(jsRoutes.api.Datasets.downloadFolder('@folder.parentDatasetId', '@folder.id').url, '_blank');" class="btn btn-link" title="Download and enjoy this file.">
+                                    <span class="glyphicon glyphicon-save"></span> Download
+                                </button>
+                            </li>
+                        } else {
+                            <li>
+                                <div class="inline" title="No permission to download the folder">
+                                    <button disabled class="btn btn-link"><span class="glyphicon glyphicon-save"></span> Download</button>
+                                </div>
+                            </li>
+                        }
                 </div>
             </div>
         </div>
diff --git a/conf/routes b/conf/routes
index a6dea7296..64530b9e2 100644
--- a/conf/routes
+++ b/conf/routes
@@ -575,6 +575,7 @@ POST           /api/datasets/:id/files
 POST           /api/datasets/:id/urls                                                   @api.Datasets.uploadToDatasetJSON(id: UUID)
 GET            /api/datasets/:id/download                                               @api.Datasets.download(id: UUID, compression: Int ?= -1, tracking: Boolean ?= true)
 GET            /api/datasets/:id/downloadPartial                                        @api.Datasets.downloadPartial(id: UUID, fileList: String)
+GET            /api/datasets/:id/downloadFolder                                         @api.Datasets.downloadFolder(id: UUID, folderId: UUID)
 POST           /api/datasets/:id/comment                                                @api.Datasets.comment(id: UUID)
 POST           /api/datasets/:id/reindex                                                @api.Datasets.reindex(id:UUID, recursive: Boolean ?= true)
 POST           /api/datasets/:id/follow                                                 @api.Datasets.follow(id: UUID)

From 4c35843c6f643ad0b5305dfd6fbc25254859e58d Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Fri, 26 Jun 2020 12:38:02 -0500
Subject: [PATCH 09/15] Improve comments and minor bugfix

---
 app/api/Datasets.scala                        |  7 ++++++-
 app/views/datasets/filesAndFolders.scala.html | 11 ++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/app/api/Datasets.scala b/app/api/Datasets.scala
index 2eea193f0..f2dfddf86 100644
--- a/app/api/Datasets.scala
+++ b/app/api/Datasets.scala
@@ -2065,6 +2065,10 @@ class  Datasets @Inject()(
     * @param dataset dataset from which to get teh files
     * @param chunkSize chunk size in memory in which to buffer the stream
     * @param compression java built in compression value. Use 0 for no compression.
+    * @param bagit whether or not to include bagit structures in zip
+    * @param user an optional user to include in metadata
+    * @param fileIDs a list of UUIDs of files in the dataset to include (i.e. marked file downloads)
+    * @param folderId a folder UUID in the dataset to include (i.e. folder download)
     * @return Enumerator to produce array of bytes from a zipped stream containing the bytes of each file
     *         in the dataset
     */
@@ -2440,6 +2444,7 @@ class  Datasets @Inject()(
     }
   }
 
+  // Takes dataset ID and a comma-separated string of file UUIDs in the dataset and streams just those files as a zip
   def downloadPartial(id: UUID, fileList: String) = PermissionAction(Permission.DownloadFiles, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
     implicit val user = request.user
     datasets.get(id) match {
@@ -2479,7 +2484,7 @@ class  Datasets @Inject()(
             // Use a 1MB in memory byte array
             Ok.chunked(enumeratorFromDataset(dataset,1024*1024, -1, bagit, user, None, Some(folderId))).withHeaders(
               CONTENT_TYPE -> "application/zip",
-              CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ " ( "+fo.name+" Folder).zip", request.headers.get("user-agent").getOrElse("")))
+              CONTENT_DISPOSITION -> (FileUtils.encodeAttachment(dataset.name+ " ("+fo.name+" Folder).zip", request.headers.get("user-agent").getOrElse("")))
             )
           }
           case None => NotFound
diff --git a/app/views/datasets/filesAndFolders.scala.html b/app/views/datasets/filesAndFolders.scala.html
index 541dc560d..88ae8262b 100644
--- a/app/views/datasets/filesAndFolders.scala.html
+++ b/app/views/datasets/filesAndFolders.scala.html
@@ -85,10 +85,10 @@
             $('#selected-count-box').html('<div class="dropdown"><a href="#" class="dropdown-toggle" ' +
                     'data-toggle="dropdown" aria-expanded="false"> Marked Files (<b>'+fileUUIDs.length+'</b>)' +
                     '<b class="caret"></b></a><ul class="dropdown-menu">' +
-                    // TODO: Need better solution than cookies to support 'Show Only Marked' request
-                    //'<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
-                    //'<li><a onclick="showAllFiles();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show All Files</a></li>' +
-                    // TODO: Support for downloading by folder and marked list will be implemented in the future
+                    @* TODO: Need better solution than cookies to support 'Show Only Marked' request
+                    '<li><a onclick="showOnlyMarked();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show Only Marked</a></li>' +
+                    '<li><a onclick="showAllFiles();"><span class="glyphicon glyphicon-ok"/>&nbsp;Show All Files</a></li>' +
+                    *@
                     '<li><a onclick="downloadMarked();"><span class="glyphicon glyphicon-download-alt"/>&nbsp;Download All</a></li>' +
                     '<li><a onclick="confirmTagMarked();"><span class="glyphicon glyphicon-tag"/>&nbsp;Tag All</a></li>' +
                     '<li><a onclick="confirmDeleteMarked();"><span class="glyphicon glyphicon-trash"/>&nbsp;Delete All</a></li>' +
@@ -136,7 +136,6 @@
     }
 
     function deleteAllMarked() {
-        // TODO: Would be nice to have a bulk endpoint for this eventually that takes a string of comma-separated UUIDs
         var selected = $.cookie('selected-files-@dataset.id');
         if (selected) {
             selected = selected.split(',');
@@ -210,7 +209,6 @@ <h4 class="modal-title">Tag All Marked Files</h4>
     }
 
     function tagMarked() {
-        // TODO: Would be nice to have a bulk endpoint for this eventually that takes a string of comma-separated UUIDs
         var tag = $('#bulk-tag-selector')[0].value;
         if (tag.length > 0) {
             var selected = $.cookie('selected-files-@dataset.id');
@@ -265,7 +263,6 @@ <h4 class="modal-title">Tag All Marked Files</h4>
     }
 
     function addFileToMarked(file_id) {
-        // TODO: Use Play framework cookies instead of jquery flavor for better security
         var selected = $.cookie('selected-files-@dataset.id');
         if (selected) {
             if (selected.indexOf(file_id) == -1)

From e10c7cbf77fbe85de10edcf4438677700d150732 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Fri, 26 Jun 2020 12:39:26 -0500
Subject: [PATCH 10/15] downloadfolder comment

---
 app/api/Datasets.scala | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/api/Datasets.scala b/app/api/Datasets.scala
index f2dfddf86..3cbaa0ecd 100644
--- a/app/api/Datasets.scala
+++ b/app/api/Datasets.scala
@@ -2469,6 +2469,7 @@ class  Datasets @Inject()(
     }
   }
 
+  // Takes dataset ID and a folder ID in that dataset and streams just that folder and sub-folders as a zip
   def downloadFolder(id: UUID, folderId: UUID) = PermissionAction(Permission.DownloadFiles, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>
     implicit val user = request.user
     datasets.get(id) match {

From a1e7cd01f7172b23101a544d81da9817c580bce5 Mon Sep 17 00:00:00 2001
From: Max Burnette <mburnet2@illinois.com>
Date: Fri, 26 Jun 2020 12:42:20 -0500
Subject: [PATCH 11/15] changelog

---
 CHANGELOG.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4f2b1b2ca..f1850bec9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+### Added
+- Ability to mark multiple files in a dataset and perform bulk operations (download, tag, delete) on them at once.
+
 ### Fixed
 - Return thumbnail as part of the file information.
   [#8](https://github.com/clowder-framework/clowder/issues/8)

From 686ccaaf651fb1f022905bcba1f669bd358c062d Mon Sep 17 00:00:00 2001
From: Mike Lambert <lambert8@illinois.edu>
Date: Mon, 29 Jun 2020 12:22:36 -0500
Subject: [PATCH 12/15] Revert invalid masonry selector to fix vertical
 stacking/overlap issues in Space view

---
 app/views/spaces/space.scala.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/spaces/space.scala.html b/app/views/spaces/space.scala.html
index 22c46ba42..419a443f6 100644
--- a/app/views/spaces/space.scala.html
+++ b/app/views/spaces/space.scala.html
@@ -139,7 +139,7 @@ <h3>@Messages("collections.title")</h3>
             imagesLoaded( '.tiled-image', function() {
                 match.masonry({
                     itemSelector: '.tiled-image',
-                    columnWidth: '.tiled-image',
+                    columnWidth: '.post-box',
                     transitionDuration: 4
                 });
             });

From 591bc0e1e7ece9c7bb5ae9a4282896c9ba0fe473 Mon Sep 17 00:00:00 2001
From: Luigi Marini <lmarini@illinois.edu>
Date: Mon, 29 Jun 2020 14:32:26 -0500
Subject: [PATCH 13/15] Updated version number to v1.10.0.

---
 CHANGELOG.md           | 3 ++-
 doc/src/sphinx/conf.py | 2 +-
 project/Build.scala    | 2 +-
 public/swagger.yml     | 2 +-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f1850bec9..5f9518ee5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## [Unreleased]
+## 1.10.0 - 2020-06-30
 
 ### Added
 - Ability to mark multiple files in a dataset and perform bulk operations (download, tag, delete) on them at once.
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ### Fixed
 - Return thumbnail as part of the file information.
   [#8](https://github.com/clowder-framework/clowder/issues/8)
+- Datasets layout on space page would sometimes have overlapping tiles.
 
 ## 1.9.0 - 2020-06-01
 **_Warning:_ This update modifies information stored in Elasticsearch used for text based searching. To take advantage 
diff --git a/doc/src/sphinx/conf.py b/doc/src/sphinx/conf.py
index 75778a7a8..8ec70ebda 100644
--- a/doc/src/sphinx/conf.py
+++ b/doc/src/sphinx/conf.py
@@ -20,7 +20,7 @@
 author = 'Luigi Marini'
 
 # The full version, including alpha/beta/rc tags
-release = '1.9.0'
+release = '1.10.0'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/project/Build.scala b/project/Build.scala
index d0124cf74..1ab9cf14a 100644
--- a/project/Build.scala
+++ b/project/Build.scala
@@ -13,7 +13,7 @@ import NativePackagerKeys._
 object ApplicationBuild extends Build {
 
   val appName = "clowder"
-  val version = "1.9.0"
+  val version = "1.10.0"
   val jvm = "1.7"
 
   def appVersion: String = {
diff --git a/public/swagger.yml b/public/swagger.yml
index 3aa26e28c..bb70f6135 100644
--- a/public/swagger.yml
+++ b/public/swagger.yml
@@ -9,7 +9,7 @@ info:
     Clowder is a customizable and scalable data management system to support any
     data format and multiple research domains. It is under active development
     and deployed for a variety of research projects.
-  version: 1.9.0
+  version: 1.10.0
   termsOfService: https://clowder.ncsa.illinois.edu/clowder/tos
   contact:
     name: Clowder

From 24c2c4b482287eea82bf14eb78a1d50e162b2bc7 Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Mon, 29 Jun 2020 23:01:49 -0500
Subject: [PATCH 14/15] exit with code 0

---
 CHANGELOG.md                     | 4 ++++
 scripts/mongo-init/mongo-init.py | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f9518ee5..28bb4100a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,7 +14,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
   [#8](https://github.com/clowder-framework/clowder/issues/8)
 - Datasets layout on space page would sometimes have overlapping tiles.
 
+### Changed
+- init script with users would return with exit code -1 if user exists, now returns exit code 0
+
 ## 1.9.0 - 2020-06-01
+
 **_Warning:_ This update modifies information stored in Elasticsearch used for text based searching. To take advantage 
 of these changes a reindex of Elasticsearch is required. A reindex can be started by an admin from the Admin menu.**
 
diff --git a/scripts/mongo-init/mongo-init.py b/scripts/mongo-init/mongo-init.py
index 4fe62260f..af513a874 100644
--- a/scripts/mongo-init/mongo-init.py
+++ b/scripts/mongo-init/mongo-init.py
@@ -62,7 +62,7 @@
 # check if user already exists
 if users.find_one({"identityId.userId": user_name, "identityId.providerId": "userpass"}):
     print("USER ALREADY EXISTS, will not create user")
-    sys.exit(-1)
+    sys.exit(0)
 
 # generate password if not specified
 encrypted_password = "$2a" + bcrypt.hash(user_password, rounds=10)[3:]

From 24d832a33884e60447ac2b37a42880df3a51c06d Mon Sep 17 00:00:00 2001
From: Rob Kooper <kooper@illinois.edu>
Date: Tue, 30 Jun 2020 16:44:38 -0500
Subject: [PATCH 15/15] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 28bb4100a..b3e5fffe3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,7 +15,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - Datasets layout on space page would sometimes have overlapping tiles.
 
 ### Changed
-- init script with users would return with exit code -1 if user exists, now returns exit code 0
+- mongo-init script with users would return with exit code -1 if user exists, now returns exit code 0.
 
 ## 1.9.0 - 2020-06-01