Virtual File Collection

BrainPortal/app/controllers/userfiles_controller.rb

@@ -40,7 +40,7 @@ class UserfilesController < ApplicationController
   around_action :permission_check, :only => [
       :download, :update_multiple, :delete_files,
       :create_collection, :change_provider, :quality_control,
-      :export_file_list
+      :export_file_list, :create_virtual_collection
   ]
 
   MAX_DOWNLOAD_MEGABYTES = 400
@@ -1001,6 +1001,15 @@ def create_collection #:nodoc:
       return
     end
 
+    virtual_files = FileCollection.where(id: filelist, type: ['CivetVirtualStudy', 'VirtualFileCollection']).to_a
+
+    if virtual_files.present?
+      virtual_files  = Userfile.find_accessible_by_user(virtual_files.pluck(:id), current_user, :access_requested  => :read)
+      flash[:error] = "Collections of Virtual Collection are not allowed. Exclude #{virtual_files.map(&:name).to_sentence} " if virtual_files
+      redirect_to :action => :index, :format =>  request.format.to_sym
+      return
+    end
+
     collection = FileCollection.new(
       :user_id          => current_user.id,
       :group_id         => file_group,
@@ -1040,6 +1049,84 @@ def create_collection #:nodoc:
 
   end
 
+  # Create a virtual 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:
 
@@ -1206,7 +1293,82 @@ def download #:nodoc:
     end
   end
 
-  #Extract a file from a collection and register it separately
+  # Extract files from a virtual collection and register them separately
+  # in the database.
+  def extract_from_virtual_collection #:nodoc:
+    success = failure = 0
+
+    unless params[:collection_files] && params[:collection_files].size > 0
+      flash[:notice] = "No files selected for extraction"
+      redirect_to :action  => :show
+      return
+    end
+
+    collection_ids_file_pairs = params[:collection_files].map {|x| x.split('#', 2)}
+    collections_file_names    = collection_ids_file_pairs.group_by { |first, _| first }
+    # add the object to hash and validate provider access, while keeping primitive keys
+
+    # todo - add option to specify target data_provider
+    collections_file_names.each do |collection_id, obj_file_list|
+      collection = FileCollection.find_accessible_by_user(collection_id, current_user, :access_requested  => :read)
+      obj_file_list.each { |pair| pair[0] = collection }
+      data_provider      = collection.data_provider
+      if data_provider.read_only?
+        flash[:error] = "Unfortunately file #{obj_filelist.second.first} of collection #{collection.name} is located on a not writable DataProvider #{data_provider.name}, so we can't extract its internal files."
+        redirect_to :action => :show
+        return
+      end
+    end
+
+    results = collections_file_names.map do |collection_id, collection_file_pairs|
+      collection      = collection_file_pairs.first.first
+      data_provider   = collection.data_provider
+      collection_path = collection.cache_full_path
+      collection_file_pairs.map do |_, file|       # Extract each file
+        # Validations; make sure "file" is a path inside the collection
+        rel_path = Pathname.new(file)
+        next :not_relative unless rel_path.relative?
+        full_path = collection_path.parent + rel_path
+        full_path = File.realpath(full_path.to_s) rescue nil
+        next :not_resolve unless full_path
+        next :is_symlink  if     File.symlink?(full_path.to_s)
+        next :not_file    unless File.file?(full_path.to_s)
+        next :outside_col unless full_path.start_with? collection_path.to_s
+        basename  = rel_path.basename.to_s
+        file_type = Userfile.suggested_file_type(basename) || SingleFile
+        userfile = file_type.new(
+          :name             => basename,
+          :user_id          => current_user.id,
+          :group_id         => collection.group_id,
+          :data_provider_id => data_provider.id
+        )
+        Dir.chdir(collection_path.parent) do
+          next :cannot_save_userfile unless userfile.save
+          userfile.addlog("Extracted from collection '#{collection.name}'.")
+          begin
+            userfile.cache_copy_from_local_file(full_path.to_s)
+            next :ok
+          rescue
+            userfile.data_provider_id = nil # nullifying will skip the provider_erase() in the destroy()
+            userfile.destroy
+            next :exception_copy
+          end
+        end
+      end
+    end
+    success = results.flatten.count { |x| x == :ok }
+    failure = results.flatten.size - success
+    if success > 0
+      flash[:notice] = "#{success} files were successfully extracted."
+    end
+    if failure > 0
+      flash[:error] =  "#{failure} files could not be extracted."
+    end
+    redirect_to :action  => :index
+  end
+
+
+  #Extract files from a collection and register it separately
   #in the database.
   def extract_from_collection #:nodoc:
     success = failure = 0

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/_cbrain_file_list.html.erb

@@ -0,0 +1,108 @@
+
+<%-
+#
+# 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/>.
+#
+-%>
+
+<% if @userfile.is_locally_synced? %>
+
+    <% @cbfl = @userfile.cached_cbrain_file_list %>
+
+    <p class="medium_paragraphs">
+    This Virtual File Collection consists of other CBRAIN files and collections
+    listed below. This simple view does allow you to explore sub-directories or
+     subfiles, for that you still can use Virtual File Collection view.
+     Note you only see files that you have assess too.
+    <p class="medium_paragraphs"> This is an experimental feature.
+    The files and collection could change name or content over time, potentially making collection unusable.
+    In the
+    table below, the names of the files are repeated: the first one is the name as
+    known within CBRAIN, and the second one is the original name of file when collection
+    was created.
+    </p>
+
+    <%
+      csv_array     = @cbfl.cached_csv_array
+      per_page      = 500
+      nb_row        = csv_array.size
+      page          = (params[:page] || 1).to_i
+      page          = 1 if page < 1
+      csv_array     = WillPaginate::Collection.create(page, per_page) do |pager|
+        pager.replace(csv_array[(page-1)*per_page, per_page] || [])
+        pager.total_entries = csv_array.size
+        pager
+      end
+    %>
+
+    <div class="no_ajax_pagination">
+      <span>
+        <%= will_paginate csv_array,
+          :params => { :controller => :userfiles, :action => :show, :sort_index => @sort_index },
+          :container => false
+        %>
+        (<%= pluralize nb_row, "file" %> in this list)
+      </span>
+    </div>
+
+    <table id="report_table">
+
+      <%
+        ################################
+        # Top headers of table
+        ################################
+      %>
+
+      <tr>
+        <% attlist = @cbfl.class.const_get('ATTRIBUTES_LIST') %>
+        <% attlist.each do |att| %>
+          <% att = :project if att == :group_id %>
+          <th><%= att.to_s.sub(/_id\z/,"").classify.gsub(/(.+)([A-Z])/, '\1 \2') %></th>
+        <% end %>
+      </tr>
+
+      <%
+        ################################
+        # Main body of table
+        ################################
+      %>
+
+      <% csv_array.each do |cvs_row| %>
+        <tr>
+          <% cur_file = nil %>
+          <% attlist.each_with_index do |att,idx|%>
+            <% val = cvs_row[idx] %>
+            <td class="left_align">
+              <% if att == :id %>
+                <% cur_file = Userfile.find_all_accessible_by_user(current_user, :access_requested => :read).where(:id => val).first %>
+                <%= val %> : <%= link_to_userfile_if_accessible(cur_file) %>
+              <% else %>
+                <%= val.nil? ? "-" : val %>
+              <% end %>
+            </td>
+          <% end %>
+        </tr>
+      <% end %>
+
+    </table>
+  <p></p>
+  <%= link_to 'Extract a file list', { :action => 'export_file_list', :file_ids => @userfile.get_userfiles.pluck(:id) }, :class  => "button", :method => :post  %>
+
+<% end %>