Tool config data immutability flag resolves #1054

BrainPortal/app/controllers/tasks_controller.rb

@@ -201,11 +201,15 @@ def new #:nodoc:
       @task.tool_config  = lastest_toolconfig if lastest_toolconfig
     end
 
-    @tool_config = @task.tool_config # for acces in view
+    @tool_config = @task.tool_config # for access in view
 
     # Filter list of files as provided by the get request
     file_ids = params[:file_ids] || []
-    access   = @task.class.properties[:readonly_input_files] ? :read : :write
+    if @tool_config.inputs_readonly || @task.class.properties[:readonly_input_files]
+      access = :read
+    else
+      access = :write
+    end
     @files   = Userfile.find_accessible_by_user(file_ids, current_user, :access_requested => access) rescue []
     if @files.empty?
       flash[:error] = "You must select at least one file to which you have write access."

BrainPortal/app/controllers/tool_configs_controller.rb

@@ -200,6 +200,7 @@ def update #:nodoc:
            @tool_config.version_name                = other_tc.version_name
            @tool_config.group                       = other_tc.group
            @tool_config.ncpus                       = other_tc.ncpus
+           @tool_config.inputs_readonly             = other_tc.inputs_readonly
            @tool_config.container_engine            = other_tc.container_engine
            @tool_config.containerhub_image_name     = other_tc.containerhub_image_name
            @tool_config.container_image_userfile_id = other_tc.container_image_userfile_id
@@ -283,6 +284,7 @@ def tool_config_params #:nodoc:
     params.require(:tool_config).permit(
       :version_name, :description, :tool_id, :bourreau_id, :env_array, :script_prologue, :script_epilogue,
       :group_id, :ncpus, :container_image_userfile_id, :containerhub_image_name, :container_index_location,
+      :inputs_readonly,
       :container_engine, :extra_qsub_args, :singularity_overlays_specs, :container_exec_args,
       # The configuration of a tool in a VM managed by a
       # ScirCloud Bourreau is defined by the following

BrainPortal/app/views/tool_configs/_form_fields.html.erb

@@ -67,6 +67,14 @@
         </div>
       <% end %>
 
+      <% t.edit_cell(:inputs_readonly, :header => "Does not modify its inputs files", :show_width => 2) do |f| %>
+        <%= f.check_box :inputs_readonly %>
+        <div class="wide_field_explanation">
+          Check this if the tool is known <strong>not to modify its input files </strong>.
+          This will allow a user to launch the tool on files that are not marked as group-writable in the file manager.
+        </div>
+      <% end %>
+
     <% end %>
 
   <% end %>

BrainPortal/db/migrate/20201123133913_add_inputs_readonly_to_tool_config.rb

@@ -0,0 +1,28 @@
+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2020
+# 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/>.
+#
+
+
+class AddInputsReadonlyToToolConfig < ActiveRecord::Migration[5.0]
+  def change
+    add_column :tool_configs, :inputs_readonly, :boolean, default: false
+  end
+end

BrainPortal/db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 20201119174821) do
+ActiveRecord::Schema.define(version: 20201123133913) do
 
   create_table "access_profiles", force: :cascade, options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci" do |t|
     t.string   "name",        null: false
@@ -437,6 +437,7 @@
     t.string   "container_index_location"
     t.text     "singularity_overlays_specs",  limit: 65535
     t.string   "container_exec_args"
+    t.boolean  "inputs_readonly",                                 default: false
     t.index ["bourreau_id"], name: "index_tool_configs_on_bourreau_id", using: :btree
     t.index ["tool_id"], name: "index_tool_configs_on_tool_id", using: :btree
   end

BrainPortal/lib/cbrain_task_generators/templates/portal.rb.erb

@@ -117,7 +117,7 @@ class CbrainTask::<%= name %> < <%= (descriptor['custom'] || {})['cbrain:inherit
   # The symbol can be passed to methods such as Userfile.find_accessible_by_user().
   # Depending on the value, more or less files are allowed to be processed.
   def file_access
-    @_file_access ||= (self.class.properties[:readonly_input_files].present? ? :read : :write)
+    @_file_access ||= (self.class.properties[:readonly_input_files].present? || self.tool_config.inputs_readonly ? :read : :write)
   end
 
 % unless defaults.empty?

BrainPortal/spec/boutiques/boutiques_tester_spec.rb

@@ -158,6 +158,7 @@
       # Instantiate a task object
       @task          = CbrainTask::BoutiquesTest.new
       @task.bourreau = execer
+      @task.tool_config = FactoryBot.create(:tool_config)
       @task.user_id, @task.group_id, @task.params = @user.id, @group.id, {}
       # Setup for holding the files the user had selected in the UI
       @task.params[:interface_userfile_ids] = []
@@ -443,6 +444,7 @@
         @task.bourreau = FactoryBot.create(:bourreau)
         @task.user_id, @task.group_id, @task.params = @user.id, @group.id, {}
         @task.params[:interface_userfile_ids] = []
+        @task.tool_config = FactoryBot.create(:tool_config)
         # Generate some userfiles for testing
         @f1, @f2, @f3 = @addUserFile.('f1.cpp',@task,false), @addUserFile.('f2.java',@task,false), @addUserFile.('f3.j',@task,false)
       end