Remove old Boutiques integrator

.github/workflows/cbrain_ci.yaml

@@ -49,6 +49,16 @@ jobs:
         with:
           ruby-version: 2.7.2
 
+      ###########################################################
+      - name: Setup python
+        uses: actions/setup-python@v1
+
+      ###########################################################
+      - name: Setup python package Boutiques to install 'bosh'
+        uses: BSFishy/pip-action@v1
+        with:
+          packages: boutiques
+
       ###########################################################
       - name: Setup BrainPortal And Bourreau Names
         run: |

Bourreau/config/application.rb

@@ -32,15 +32,6 @@ class Application < Rails::Application
     # properly set up all tasks installed from plugins (and the defaults tasks).
     config.autoload_paths += Dir["#{config.root}/cbrain_plugins/installed-plugins/cbrain_task"]
 
-    # CBRAIN Plugins load paths: add directory for descriptor-based CbrainTask
-    # models. This directory, similarly to the one above, contains symbolic
-    # links to a special loader code which will call a task generator to
-    # generate the requested CbrainTask subclass on the fly.
-    #
-    # The rake task cbrain:plugins:install:all also takes care of creating the
-    # symlinks for this location.
-    config.autoload_paths += Dir["#{config.root}/cbrain_plugins/installed-plugins/cbrain_task_descriptors"]
-
     # Only load the plugins named here, in the order given (default is alphabetical).
     # :all can be used as a placeholder for all plugins not explicitly named.
     # config.plugins = [ :exception_notification, :ssl_requirement, :all ]

Bourreau/lib/boutiques.schema.json

@@ -0,0 +1 @@
+../../BrainPortal/lib/boutiques.schema.json

Bourreau/spec/rails_helper.rb

@@ -13,6 +13,7 @@
 # DATABASE_URL=mysql2://prioux:mypassword@localhost/prioux_test
 #
 require 'yaml'
+require 'uri'
 1.times do # a block to encapsulate local variables and not pollute anything
   env           = ENV['RAILS_ENV']
   dbconfig_file = "../BrainPortal/config/database.yml"

BrainPortal/app/models/boutiques_cluster_task.rb

@@ -118,22 +118,33 @@ def cluster_commands #:nodoc:
     descriptor    = self.descriptor_for_cluster_commands
     invoke_struct = self.invoke_params.dup # as it is in the task's params
 
+    # Used when building absolute paths
+    workdir = Pathname.new(self.full_cluster_workdir)
+
     # Replace userfile IDs for file basenames in the invoke struct
     descriptor.file_inputs.each do |input|
       userfile_id = invoke_params[input.id]
       next if userfile_id.blank? # that happens when it's an optional file
-      userfile    = Userfile.find(userfile_id)
+      userfiles   = Array(Userfile.find(userfile_id)) # can be one or many
+      jsonfnames  = userfiles.map(&:name) # by default, the basename
+      jsonfnames  = jsonfnames.map { |base| (workdir + base).to_s } if input.uses_absolute_path
 
       # Most common situation
-      if ! input.list || ! userfile.is_a?(CbrainFileList)
-        invoke_struct[input.id] = (input.list ? [ userfile.name ] : userfile.name)
+      if ! input.list || ! userfiles.first.is_a?(CbrainFileList)
+        invoke_struct[input.id] = (input.list ? jsonfnames : jsonfnames.first )
         next
       end
 
       # In case the input is a list and is assigned a CbrainFileList
+      userfile = userfiles.first
+      cb_error "Expected a CbrainFileList as a single entry for input '#{input.name}'" if
+        userfiles.size > 1 || ! userfile.is_a?(CbrainFileList)
       userfile.sync_to_cache
       userfile_list = userfile.userfiles_accessible_by_user!(user, nil, nil, file_access_symbol)
       subnames = userfile_list.compact.map(&:name)  # [ 'userfilename1', 'userfilename2' ... ]
+      if input.uses_absolute_path
+        subnames = subnames.map { |base| (workdir + base).to_s }
+      end
       invoke_struct[input.id] = subnames
     end
 
@@ -174,10 +185,25 @@ def cluster_commands #:nodoc:
       end
       simul_status = $? # a Process::Status object
       if ! simul_status.success?
-        cb_error "The 'bosh exec simulate' command failed with return code #{simul_status.exitstatus}"
+        bosh_message = simulout.split("\n").detect { |line| line =~ /ERROR/ }
+        bosh_message &&= ": #{bosh_message}"
+        cb_error "The 'bosh exec simulate' command failed with return code #{simul_status.exitstatus}#{bosh_message}"
       end
       simulout.sub!(/^Generated.*\n/,"") # header junk from simulate
-      commands = <<-COMMANDS
+
+      commands = ""
+      if descriptor.environment_variables.present?
+        commands = "# Environment variables defined by Boutiques descriptor\n"
+        descriptor.environment_variables.each do |struct|
+          ename  = (struct['name']  || struct[:name] ).to_s
+          evalue = (struct['value'] || struct[:value]).to_s
+          next if ename.blank? || ! ename.match(/\A[a-zA-Z]\w+\z/)
+          commands += "export #{ename.strip}=#{evalue.bash_escape}\n"
+        end
+        commands += "\n"
+      end
+
+      commands += <<-COMMANDS
         # Main tool command, generated with bosh exec simulate
         #{simulout.strip}
         status=$?

BrainPortal/app/models/boutiques_portal_task.rb

@@ -115,10 +115,12 @@ def before_form
 
     # return "Warning: you selected more files than this task requires, so you won't be able to assign them all."
     # Not available in case of descriptor qualified to launch multiple task
-    if !descriptor.qualified_to_launch_multiple_tasks? && (num_in_files < num_needed_inputs || num_in_files > num_needed_inputs+num_opt_inputs)
-      message = "This task requires #{num_needed_inputs} mandatory file(s) and #{num_opt_inputs} optional file(s)\n" +
-        input_infos
-      cb_error message
+    if num_in_files < num_needed_inputs || num_in_files > num_needed_inputs+num_opt_inputs
+      if (! descriptor.qualified_to_launch_multiple_tasks? || num_in_files == 0)
+        message = "This task requires #{num_needed_inputs} mandatory file(s) and #{num_opt_inputs} optional file(s)\n" +
+          input_infos
+        cb_error message
+      end
     end
 
     ""
@@ -299,6 +301,7 @@ def final_task_list #:nodoc:
     # --------------------------------------
     if descriptor.file_inputs.size == 1 || descriptor.qualified_to_launch_multiple_tasks?
       input = descriptor.file_inputs.first
+      input = descriptor.sole_mandatory_file_input if descriptor.qualified_to_launch_multiple_tasks?
 
       fillTask = lambda do |userfile,tsk,extra_params=nil|
         tsk.params[:interface_userfile_ids] |= [ userfile.id.to_s ]
@@ -445,6 +448,8 @@ def cbcsv_files(descriptor = self.descriptor_for_after_form)
         next if isInactive(input)
         userfile_id = invoke_params[input.id]
         next if userfile_id.blank?
+        next if userfile_id.is_a?(Array) && userfile_id.size > 1 # list = true
+        userfile_id = userfile_id.first if userfile_id.is_a?(Array)
         userfile = Userfile.find_accessible_by_user(userfile_id, self.user, :access_requested => file_access_symbol())
         next unless ( userfile.is_a?(CbrainFileList) || (userfile.suggested_file_type || Object) <= CbrainFileList )
         [ input, userfile ]
@@ -576,16 +581,18 @@ def sanitize_param(input)
 
       # Nothing special required for strings, bar for symbols being acceptable strings.
       when :string
-        value = value.to_s                                                 if value.is_a?(Symbol)
-        params_errors.add(invokename, " is not a string (#{value})")   unless value.is_a?(String)
-        value.strip!                                                       if value.is_a?(String)
-        params_errors.add(invokename, " is blank")                         if value.blank? && !empty_string_allowed
-        # The following three checks are to prevent cases when
-        # a string param is used as a path
-        params_errors.add(invokename, " cannot contain newlines")          if value =~ /[\n\r]/
-        params_errors.add(invokename, " cannot start with this character") if value =~ /^[\.\/]+/
-        params_errors.add(invokename, " cannot move up dirs")              if value.include? "/../"
-        if value.present? && input.value_choices.blank?
+        value = value.to_s                                                  if value.is_a?(Symbol)
+        params_errors.add(invokename, " is not a string")               unless value.is_a?(String)
+        value = value.to_s.strip # now force it
+        params_errors.add(invokename, " is blank")                           if value.blank? && !empty_string_allowed
+        # The following checks are to prevent cases when a string param is used as a path
+        if value.present?
+          params_errors.add(invokename, " cannot contain newlines")          if value =~ /[\n\r]/
+          params_errors.add(invokename, " cannot start with this character") if value =~ /^[\.\/]+/
+          params_errors.add(invokename, " cannot move up dirs")              if value.include? "/../"
+        end
+        # Finally, check allowed characters
+        if value.present? && input.value_choices.blank? # valid value choices are checked elsewhere
           params_errors.add(invokename, " contains invalid characters")  unless value.match?(charset_regex) # we can use a string in the match method
         end
 
@@ -628,7 +635,7 @@ def sanitize_param(input)
   end
 
   def check_enum_param(input)
-    value = invoke_params[input.id]
+    value = invoke_params[input.id] || input.default_value
     string_values  = Array(value).map(&:to_s)
     allowed_values = input.value_choices.map(&:to_s)
     return if (string_values - allowed_values).empty? # I hope that comparing the sets as strings is OK
@@ -714,7 +721,7 @@ def check_allornone_group(group, descriptor = self.descriptor_for_after_form)
   # MAYBE IN COMMON
 
   def invoke_params
-    self.params[:invoke] ||= {}
+    self.params[:invoke] ||= {}.with_indifferent_access
   end
 
   # In the case of a misconfiguration of the portal, or if the file for

BrainPortal/app/models/cbrain_task.rb

@@ -1109,12 +1109,9 @@ def struct_runtime_info(runtime_textfile=self.runtime_info) #:nodoc:
 
   # Patch: pre-load all model files for the subclasses
   def self.preload_subclasses
-    [ CBRAIN::TasksPlugins_Dir, CBRAIN::TaskDescriptorsPlugins_Dir ].each do |dir|
+    [ CBRAIN::TasksPlugins_Dir ].each do |dir|
       Dir.chdir(dir) do
         Dir.glob("*.rb").each do |rubyfile|
-          next if rubyfile == 'cbrain_task_class_loader.rb'      # skip that
-          next if rubyfile == 'cbrain_task_descriptor_loader.rb' # skip that
-
           model = rubyfile.sub(/.rb\z/, '')
           require_dependency "#{dir}/#{model}.rb" unless
             [ model.classify, model.camelize ].any? { |m| CbrainTask.const_defined?(m) rescue nil }

BrainPortal/app/views/tasks/_params.html.erb

@@ -24,17 +24,10 @@
 
 <%
   locals      = { :params  => @task.params, :form => form }
-  raw_partial = lambda do |partial|
-    @task.raw_partial(partial) if @task.respond_to?(:raw_partial)
-  end
 %>
 
 <h2>Task Parameters
-  <% if raw_partial.(:edit_help) %>
-    <%= overlay_content_link "(Help)", :class => "task_help_link", :enclosing_element => "span" do %>
-      <%= render :inline => raw_partial.(:edit_help), :locals => locals %>
-    <% end %>
-  <% elsif (public_path = @task.public_path("edit_params_help.html")) %>
+  <% if (public_path = @task.public_path("edit_params_help.html")) %>
     <%= overlay_ajax_link "(Help)", public_path.to_s, :class  => "task_help_link" %>
   <% elsif (edit_help_partial = task_partial(:edit_help) rescue nil) %>
     <%= overlay_content_link "(Help)", :class => "task_help_link", :enclosing_element => "span" do %>
@@ -46,9 +39,5 @@
 
 <div class="generalbox">
 <%= error_messages_for(@task) %>
-<% if raw_partial.(:task_params) %>
-  <%= render :inline => raw_partial.(:task_params), :locals => locals %>
-<% else %>
-  <%= render :partial => task_partial('task_params'), :locals => locals %>
-<% end %>
+<%= render :partial => task_partial('task_params'), :locals => locals %>
 </div>

BrainPortal/app/views/tasks/show.html.erb

@@ -203,15 +203,8 @@
          <% begin %>
            <%
              locals = { :task => @task, :params  => @task.params }
-             raw_partial = lambda do |partial|
-               @task.raw_partial(partial) if @task.respond_to?(:raw_partial)
-             end
            %>
-           <% if raw_partial.(:show_params) %>
-             <%= render :inline => raw_partial.(:show_params), :locals => locals %>
-           <% else %>
-             <%= render :partial => task_partial(:show_params), :locals => locals %>
-           <% end %>
+           <%= render :partial => task_partial(:show_params), :locals => locals %>
          <% rescue ActionView::MissingTemplate %>
            <pre>Problem loading summary view (no template provided by task author).</pre>
          <% rescue => ex %>