Several fixes all bundled together.

1- The controls channel for Bourreau has a new 'StopYourself'
   command, which is much more efficient than the old way
   of stopping the rails app using an external script.
   Fixes #55 .
2- The 'ibc' utility provides access to it with the 'J' command
3- Tooltips in the interface could never be positioned
   at offset_x set to 0 because 0 is falsy in javascript. Fixed.
4- We no longer ever keep a backup of database.yml on remote sites.
5- Userfiles viewers that have conditions which crash no
   longer prevent the 'show' page from rendering; instead the
   viewer is ignored and removed from the available list.
   Fixes #25
6- Task forms for boutiques tasks will present list
   inputs in proper order.
   Fixes #830
7- Support for lists for File inputs in boutiques
   Fixes #831

Bourreau/script/cbrain_remote_ctl

@@ -47,13 +47,7 @@
 # script/rails server thin -d -e <environment> -p <port> -b 127.0.0.1 -P pidfile
 #
 # and finally removing the database.yml file. Any database.yml file
-# already present before doing all this will be backed up in
-#
-# database.yml.cbrain_remote_bak.
-#
-# Note that if stdin contains nothing (zero bytes) the current
-# database.yml file will be used, or the script will restore and use
-# the backup file 'database.yml.cbrain_remote_bak'.
+# already present before doing all this will be erased.
 #
 #
 # To stop the Rails app:
@@ -197,25 +191,16 @@ fatal("Port argument must be a number greater than 1024 and less than 65530") un
 
 db_yml_text = mode == "start" ? (STDIN.read || "") : ""
 db_file = rails_home + "/config/database.yml"
-db_file_bak = rails_home + "/config/database.yml.cbrain_remote_bak"
 
 # Install or restore database.yml if necessary
 db_exists = File.exist?(db_file)
-bak_exists = File.exist?(db_file_bak)
 blank_yml = db_yml_text !~ /\S/
 
 if blank_yml # blank? use what db.yml is already here
- if db_exists
- # nothing to do
- elsif bak_exists
- File.rename(db_file_bak,db_file)
- else
+ if ! db_exists
  fatal("Could not find a database.yml file for the Rails application!")
  end
 else # db text is provided to us
- if db_exists
- File.rename(db_file,db_file_bak) # will crush existing bak file
- end
  # Optional: change stuff in it, depending on the environment
  unless ENV['CBRAIN_FRONTEND_HOSTNAME'].nil? || ENV['CBRAIN_FRONTEND_HOSTNAME'] =~ /^\s*$/
  db_yml_text.sub!(/hostname:\s*\S+/,"hostname: #{ENV['CBRAIN_FRONTEND_HOSTNAME']}")

BrainPortal/app/helpers/resource_link_helper.rb

@@ -255,7 +255,7 @@ def link_to_user_with_tooltip(user, cur_user = current_user, options = {})
  return "(None)" if user.blank?
  cb_error "This method requires the first argument to be a User object." unless user.is_a?(User)
  capture do
- html_tool_tip(link_to_user_if_accessible(user,current_user,options), :offset_x => 60 ) do
+ html_tool_tip(link_to_user_if_accessible(user,current_user,options), :offset_x => 0, :offset_y => 20 ) do
  (
  "<div class=\"left_align\">\n" +
  "#{h(user.full_name)}<br>\n" +

BrainPortal/app/models/bourreau.rb

@@ -353,6 +353,15 @@ def build_db_yml_for_tunnel(railsenv) #:nodoc:
 
  public
 
+ # Utility method to sends a +stop_yourself+ command to a
+ # Bourreau RemoteResource, whether local or not.
+ def send_command_stop_yourself
+ command = RemoteCommand.new(
+ :command => 'stop_yourself',
+ )
+ send_command(command)
+ end
+
  # Utility method to send a +get_task_outputs+ command to a
  # Bourreau RemoteResource, whether local or not.
  def send_command_get_task_outputs(task_id,run_number=nil,stdout_lim=nil,stderr_lim=nil)
@@ -393,6 +402,18 @@ def send_command_alter_tasks(tasks,new_task_status,extra_remote_commands = {})
 
  protected
 
+ # This comaand is a bit dangerous: it will first trigger a +stop_workers+
+ # command to be sent locally, and then the rails app will kill itself with
+ # a TERM signal, thus exiting right after the current request. The user should
+ # really make sure the workers are inactive and there is no other background
+ # activity.
+ def self.process_command_stop_yourself(command)
+ process_command_stop_workers(
+ command.dup.tap { |com| com.command = "stop_workers" }
+ )
+ Process.kill('TERM',Process.pid) # the rails server will shut down after the current request
+ end
+
  # Starts Bourreau worker processes.
  # This also triggers a 'wakeup' command if they are already
  # started.

BrainPortal/app/models/cbrain_task.rb

@@ -47,7 +47,7 @@ class CbrainTask < ApplicationRecord
  validates_presence_of :tool_config_id
 
  # Rails5 make belongs_to association required by default
- # Task presets have bourreau id set to 0, 
+ # Task presets have bourreau id set to 0,
  # that's why the :bourreau assocition should be optionnal
  belongs_to :bourreau, optional: true
  belongs_to :user
@@ -889,8 +889,24 @@ def remove_workdir_archive #:nodoc:
  archive.destroy
  true
  rescue
+ if archive
+ archive.tag_ids |= [ self.class.destroyed_archived_tag.id ]
+ end
  true
  end
 
+ # This returns (and if necessary creates the first time)
+ # a Tag object named 'TaskDestroyed', belonging to the main
+ # admin, that is used to mark any TaskWorkdirArchive that
+ # a user tried to delete but couldn't (e.g on unaccessible
+ # or read-only DPs etc). The admin can later find and delete them
+ # himself.
+ def self.destroyed_archived_tag #:nodoc:
+ @_destroyed_task_tag_ ||=
+ Tag.find_or_create_by( :name => 'TaskDestroyed',
+ :user_id => User.admin.id,
+ :group_id => User.admin.own_group.id )
+ end
+
 end
 

BrainPortal/app/models/userfile.rb

@@ -720,6 +720,8 @@ def initialize_from_hash(atts = {}) #:nodoc:
  def valid_for?(userfile) #:nodoc:
  return true if @conditions.empty?
  @conditions.all? { |condition| condition.call(userfile) }
+ rescue
+ false
  end
 
  def ==(other) #:nodoc:

BrainPortal/config/console_rc/lib/interactive_bourreau_control.rb

@@ -52,8 +52,8 @@ def initialize(bourreaux_list = Bourreau.order(:id).all, term_width = nil)
  @bourreaux = bourreaux_list
  @width = term_width
  if term_width.blank? || term_width.to_i < 1
- numrows,numcols = Readline.get_screen_size rescue [25,120]
- @width  = numcols
+ _,numcols = Readline.get_screen_size rescue [25,120]
+ @width = numcols
  end
  @selected = {}
  end
@@ -138,7 +138,7 @@ def interactive_control(initial_command = nil)
  def process_user_letter(letter) #:nodoc:
 
  # Validate the user input
- if letter !~ /^([haombwitukygsrczqx]|\d+|exit|quit)$/
+ if letter !~ /^([haombwitukygsrczqxj]|\d+|exit|quit)$/
  puts "Unknown command: #{letter} (ignored)"
  return false
  end
@@ -157,7 +157,10 @@ def process_user_letter(letter) #:nodoc:
  W = starts workers
  T = stops workers
  U = stops workers and waits to make sure
- K = stops bourreaux
+ K = stops bourreaux (using shell commands)
+ J = stops workers and bourreaux (using command control
+ messages; use this only if you're sure no workers
+ are active and the SSH masters are opened)
  Y = cycle: stop workers and bourreaux then
  start bourreaux and workers (replace operation queue)
 
@@ -226,13 +229,14 @@ def process_user_letter(letter) #:nodoc:
  end
 
  # Operation queue commands
- if letter =~ /^[bwtku]$/
+ if letter =~ /^[bwtkuj]$/
  @operations += " " if @operations.present?
  @operations += "StartBourreaux" if letter == "b"
  @operations += "StartWorkers" if letter == "w"
  @operations += "StopBourreaux" if letter == "k"
  @operations += "StopWorkers" if letter == "t"
  @operations += "StopWorkersAndWait" if letter == "u"
+ @operations += "StopAllByCommand" if letter == "j"
  return false
  end
 
@@ -341,11 +345,12 @@ def process_user_letter(letter) #:nodoc:
  def apply_operation(op, bou) #:nodoc:
  printf "... %18s %-15s : ", op, bou.name
  res,mess = [ false, "Unknown Operation #{op}" ]
- res,mess = start_bourreaux(bou) if op == "StartBourreaux"
+ res,mess = start_bourreau(bou)  if op == "StartBourreaux"
  res,mess = start_workers(bou) if op == "StartWorkers"
- res,mess = stop_bourreaux(bou) if op == "StopBourreaux"
+ res,mess = stop_bourreau(bou)  if op == "StopBourreaux"
  res,mess = stop_workers(bou) if op == "StopWorkers"
  res,mess = stop_workers_and_wait(bou) if op == "StopWorkersAndWait"
+ res,mess = stop_all_by_command(bou) if op == "StopAllByCommand"
  printf "%s\n", mess == nil ? "(nil)" : mess
  [ res, mess ]
  rescue IRB::Abort => ex
@@ -381,14 +386,22 @@ def stop_workers_and_wait(b) #:nodoc:
  [ output.blank? , output.blank? ? "OK" : "Workers still active" ] # message text used to abort sequence, see earlier in code
  end
 
- def stop_bourreaux(b) #:nodoc:
+ def stop_bourreau(b) #:nodoc:
  r1=b.stop rescue nil
  r2=b.stop_tunnels rescue nil
  b.update_attribute(:online, false)
  [ !!(r1 && r2) , "App: #{r1 or false}\tSSH Master: #{r2 or false}" ]
  end
 
- def start_bourreaux(b) #:nodoc:
+ def stop_all_by_command(b)
+ r1=b.send_command_stop_yourself rescue "(Exc)"
+ r1=r1.command_execution_status if r1.is_a?(RemoteCommand)
+ r2=b.stop_tunnels rescue nil
+ b.update_attribute(:online, false)
+ [ ((r1 == "OK") && r2.present?), "App: #{r1 or false}\tSSH Master: #{r2 or false}" ]
+ end
+
+ def start_bourreau(b) #:nodoc:
  r = b.start rescue nil
  rev = "???"
  if (r == true)

BrainPortal/lib/cbrain_task_generators/templates/task_params.html.erb.erb

@@ -130,7 +130,7 @@
  <%%
  values = @task.params[name.to_sym] if name && values.nil?
  values = values.is_a?(Enumerable) ? values.compact : [values].compact
- first = values.pop
+ first  = values.shift
  %>
  <ul class="tsk-prm-list">
  <li>
@@ -343,7 +343,8 @@
  )
  <%- else -%>
  # File input dropdown
- dropdown.(id, id,
+ name = id <%= list ? '+ "[]"' : '' %>
+ dropdown.(id, name,
  input_files.map { |f| [ f.id.to_s, f.name ] },
  optional: <%= opt %>
  )

BrainPortal/public/javascripts/cbrain.js

@@ -674,8 +674,11 @@
  var trigger = $(this);
  var tool_tip_id = trigger.data("tool-tip-id");
  var tool_tip = $("#" + tool_tip_id);
- var offset_x = trigger.data("offset-x") || '30';
+ var offset_x = trigger.data("offset-x");
  var offset_y = trigger.data("offset-y") || '0';
+ if (typeof offset_x == 'undefined') {
+ offset_x = '30';
+ }
 
  var x = trigger.position().left + parseInt(offset_x, 10);
  var y = trigger.position().top + parseInt(offset_y, 10);