Virtual collection

BrainPortal/app/controllers/userfiles_controller.rb

@@ -39,7 +39,7 @@ class UserfilesController < ApplicationController
 
   around_action :permission_check, :only => [
       :download, :update_multiple, :delete_files,
-      :create_collection, :change_provider, :quality_control,
+      :create_collection, :create_virtual_collection, :change_provider, :quality_control,
       :export_file_list
   ]
 
@@ -1040,6 +1040,84 @@ def create_collection #:nodoc:
 
   end
 
+  #Create a collection from the selected files.
+  def create_virtual_collection #:nodoc:
+    filelist         = params[:file_ids].uniq || []
+    data_provider_id = params[:data_provider_id_for_collection]
+    collection_name  = params[:collection_name]
+    file_group       = current_assignable_group.id
+
+    if data_provider_id.blank?
+      flash[:error] = "No data provider selected.\n"
+      redirect_to :action => :index
+      return
+    end
+
+    # Handle collection name
+    if collection_name.blank?
+      suffix = Time.now.to_i
+      while Userfile.where(:user_id => current_user.id, :name => "VirtualCollection-#{suffix}").first.present?
+        suffix += 1
+      end
+      collection_name = "VirtualCollection-#{suffix}"
+    end
+
+    if ! Userfile.is_legal_filename?(collection_name)
+      flash[:error] = "Error: collection name '#{collection_name}' is not acceptable (illegal characters?)."
+      redirect_to :action => :index, :format =>  request.format.to_sym
+      return
+    end
+
+    # Check if the collection name chosen by the user already exists for this user on the data_provider
+    if current_user.userfiles.exists?(:name => collection_name, :data_provider_id => data_provider_id)
+      flash[:error] = "Error: collection with name '#{collection_name}' already exists."
+      redirect_to :action => :index, :format =>  request.format.to_sym
+      return
+    end
+
+    userfiles = Userfile.find_accessible_by_user(filelist, current_user, :access_requested  => :read)
+
+    # todo double check how 0 is possible, bad files should cause exception
+    if userfiles.count == 0
+      flash[:error] = "Error: Inaccessible files selected."
+      redirect_to :action => :index, :format =>  request.format.to_sym
+      return
+    end
+
+    collection = VirtualFileCollection.new(
+      :user_id          => current_user.id,
+      :group_id         => file_group,
+      :data_provider_id => data_provider_id,
+      :name             => collection_name
+    )
+
+    collection.save!
+    collection.cache_prepare
+    coldir = collection.cache_full_path
+    Dir.mkdir(coldir)
+
+    collection.set_virtual_file_collection(userfiles)
+
+    # Save the content and DB model
+
+    collection.sync_to_provider
+    collection.save
+    collection.set_size
+
+    # Find the files
+    userfiles = Userfile
+                  .find_all_accessible_by_user(current_user, :access_requested => :read)
+                  .where(:id => filelist).all.to_a
+
+    if userfiles.empty?
+      flash[:error] = "You need to select some files first."
+      redirect_to(:action => :index)
+      return
+    end
+    redirect_to(:controller => :userfiles, :action => :show, :id => collection.id)
+
+  end
+
   # Copy or move files to a new provider.
   def change_provider #:nodoc:
 

BrainPortal/app/helpers/userfiles_helper.rb

@@ -110,11 +110,11 @@ def data_link(file_name, userfile, replace_div_id="sub_viewer_filecollection_cbr
       end
     elsif display_name =~ /\.html$/i # TODO: this will never happen if we ever create a HtmlFile model with at least one viewer
       link_to "#{display_name}",
-        stream_userfile_path(@userfile, :file_path => file_name, :disposition => 'inline'),
+        stream_userfile_path(userfile, :file_path => file_name, :disposition => 'inline'),
         :target => '_BLANK'
     else
       link_to h(display_name),
-              url_for(:action  => :content, :content_loader => :collection_file, :arguments => file_name)
+              url_for(:action  => :content, :id => userfile.id, :content_loader => :collection_file, :arguments => file_name)
     end
   end
 

BrainPortal/app/views/userfiles/_dialogs.html.erb

@@ -349,6 +349,36 @@
   </form>
 </div>
 
+<div id="virtual-collection-dialog" class="dlg-dialog" title="New virtual collection">
+  <form action="<%= create_virtual_collection_userfiles_path %>" method="post">
+    <label for="co-name" class="dlg-fld-lbl">Name</label>
+    <input id="co-name"
+           class="dlg-fld"
+           type="text"
+           name="collection_name"
+           value="NewVirtualCollection"
+      />
+    <span id="co-invalid-name" class="dlg-msg-err">
+      &#9888; Invalid!
+    </span>
+    <br />
+
+    <label for="co-dp" class="dlg-fld-lbl">Provider</label>
+    <%=
+      data_provider_select('data_provider_id_for_collection',
+                           { :data_providers => writable_dps },
+                           {
+                             :id    => 'co-dp',
+                             :class => 'dlg-fld',
+                             :'data-placeholder' => "A data provider..."
+                           }
+      )
+    %>
+    <br /><br />
+  </form>
+</div>
+
+
 <div id="delete-confirm"
   class="dlg-dialog dlg-cfrm"
   title="Delete"

BrainPortal/app/views/userfiles/_file_menu.html.erb

@@ -162,6 +162,17 @@
     </li>
     <li class="menu-separator dyn-item">-</li>
 
+    <li id="col-item"
+        class="act-item dyn-item"
+        data-dialog="virtual-collection-dialog"
+    >
+      <div>
+        New virtual collection
+        <span class="ui-icon ui-icon-folder-collapsed"></span>
+      </div>
+    </li>
+    <li class="menu-separator dyn-item">-</li>
+
     <li id="exp-item"
       class="act-item"
       data-url="<%= userfiles_path(:format => :csv) %>"

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/virtual_file_collection/views/_directory_contents.html.erb

@@ -0,0 +1,113 @@
+
+<%-
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2012
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<% limit = 500 %>
+<% base_dir = base_directory rescue params[:base_directory] %>
+<% base_dir = base_dir.presence || "." %>
+
+<% file_list ||= ( @userfile.list_linked_files(base_dir, [:regular, :directory, :link]) rescue [] ) %>
+
+<% if file_list.blank? %>
+
+ <tr class="<%= cycle("list-odd", "list-even") %>">
+    <td></td>
+    <td colspan="2"> (<span class="warning">Empty</span>) </td>
+    <td></td>
+ </tr>
+
+<% else %>
+
+  <% for file in file_list[0,limit] %>
+     <% fname = file.name %>
+     <% fname = fname.delete_prefix(@userfile.name + '/') unless @userfile.id == file.userfile.id %>
+     <% if file.symbolic_type == :directory %>
+       <%= on_click_ajax_replace( { :element  => "tr",
+                                    :url      => url_for(
+                                                         :id                    => file.userfile.id,
+                                                         :action                => :display,
+                                                         :viewer                => "directory_contents",
+                                                         :viewer_userfile_class => "FileCollection",
+                                                         :base_directory        => ".",
+                                                         :apply_div             => "false"
+                                                        ),
+                                         :position => "after",
+                                    :before   => "<td colspan='4' class='loading_message'>Loading...</td>"
+                                  },
+                                  { :class  => "#{cycle("list-odd", "list-even")}",
+                                    :id     => file.name.gsub(/\W+/, "_")
+                                  }
+                                ) do %>
+         <%= render :file => @viewer.partial_path(:plain_file_list_row), :locals  => {:file  => file} %>
+       <% end %>
+     <% else %>
+       <tr class="<%= cycle("list-odd", "list-even") %>">
+         <%= render :file => @viewer.partial_path(:plain_file_list_row), :locals  => {:file  => file} %>
+       </tr>
+     <% end %>
+  <% end %>
+
+  <% if file_list.size > limit %>
+    <tr class="<%= cycle("list-odd", "list-even") %>">
+      <td></td>
+      <td colspan="2" class="left"> <%= ("&nbsp;" * 6 * file_list.first.depth).html_safe %> ... <%= image_tag "/images/lotsa_files_icon.png" %> <%= pluralize(file_list.size-limit, "more entry") %></td>
+      <td></td>
+    </tr>
+  <% end %>
+
+<% end %>
+
+
+<script>
+$(document).ready(function() {
+    // removes first column (checkboxes)
+    // there is no point to extract constituents userfiles of they already exist as separate entity
+    // and if user need sub-files of constituents, he or she can go below
+
+    // Function to delete the first column with checkbox
+    function deleteFirstColumn() {
+        $('.plain_file_list tr').each(function() {
+            firstCell = $(this).find('td:first, th:first'); // Select the first cell
+            cellContent = firstCell.text().trim(); // Get trimmed content of the first cell
+
+            // Check if the first cell contains a checkbox or is empty/whitespace
+            if (firstCell.find('input[type="checkbox"]').length || cellContent === '') {
+                firstCell.remove(); // Remove the cell
+            }
+        });
+        alarm('done');
+    }
+
+    // Create a mutation observer to address newly added rows
+    const observer = new MutationObserver(deleteFirstColumn);
+
+    // Start observing the table body for changes
+    observer.observe(document.getElementsByClassName('plain_file_list')[0].querySelector('tbody'), {
+        childList: true,
+        subtree: true
+    });
+
+    // Initial call to remove the first column
+    deleteFirstColumn();
+});
+</script>

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/virtual_file_collection/views/_file_collection.html.erb

@@ -0,0 +1,36 @@
+
+<%-
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2012
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<%
+  # This partial can be invoked directly as a viewer from the display action,
+  # or rendered as part of another piece of view code. As such it will
+  # accept a "base_directory" either as a params[] or as a local variable
+  base_dir = base_directory rescue params[:base_directory]
+%>
+
+<%= render :file   => VirtualFileCollection.view_path(:file_collection_form),
+           :locals => { :base_directory => base_dir } %>
+
+<div id="sub_viewer_filecollection_cbrain"></div>
+

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/virtual_file_collection/views/_file_collection.json.erb

@@ -0,0 +1,2 @@
+<%= @userfile.list_linked_files.to_json %>
+

BrainPortal/cbrain_plugins/cbrain-plugins-base/userfiles/virtual_file_collection/views/_file_collection_form.html.erb

@@ -0,0 +1,57 @@
+
+<%-
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2012
+# The Royal Institution for the Advancement of Learning
+# McGill University
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+-%>
+
+<%
+  # This partial requires one local variable:
+  #
+  #    base_directory : the subdirectory inside the userfile where we start to render the directory content
+%>
+
+<% if @userfile.num_files && @userfile.num_files > 0 %>
+
+
+  <%= form_for @userfile, :as   => :userfile,
+                          :url  => { :controller => :userfiles,
+                                     :action => :extract_from_collection
+                                   },
+                          :html => { :method => :post,
+                                     :id     => "userfile_edit_#{@userfile.id}_#{base_directory}"
+                                   } do |f| %>
+
+    <%= ajax_element(display_userfile_path(@userfile,
+            :viewer                => :file_collection_top_table,
+            :viewer_userfile_class => :VirtualFileCollection,
+            :base_directory        => base_directory,
+        ), :class => "loading_message") do %>
+      <br>
+      Loading...
+      <br>
+    <% end %>
+
+
+
+  <% end %>
+
+<% end %>
+