Adjusted a bunch of Boutiques modules

The adjustements here are meant to make sure
each of the modules do nothing if they happen to be
including in a task class, but the associated
ToolConfig's boutiques descriptor doesn't contain
any configuration for them. See github issue aces#1462

BrainPortal/lib/boutiques_allowed_exit_codes.rb

@@ -48,7 +48,7 @@ def exit_status_means_failure?(status)
 
     # Get the acceptable status codes.
     descriptor = self.descriptor_for_save_results
-    ok_codes   = descriptor.custom_module_info('BoutiquesAllowedExitCodes')
+    ok_codes   = descriptor.custom_module_info('BoutiquesAllowedExitCodes') || [ 0 ]
 
     addlog("BoutiquesAllowedExitCodes rev. #{Revision_info.short_commit}, status=#{status}, allowed=#{ok_codes}")
 

BrainPortal/lib/boutiques_collection_basenames_list_maker.rb

@@ -54,6 +54,7 @@ module BoutiquesCollectionBasenamesListMaker
     def descriptor_for_form #:nodoc:
         descriptor             = super.dup()
         input_id, type, regex_string,  = descriptor.custom_module_info('BoutiquesCollectionBasenamesListMaker')
+        return descriptor if input_id.nil? # no config at all
 
         # Get the userfile_ids from the params
         # Return immediately if there is no exactly one file.
@@ -81,6 +82,7 @@ def descriptor_for_form #:nodoc:
     def final_task_list #:nodoc:
       descriptor     = self.descriptor_for_final_task_list
       input_id, _, _ = descriptor.custom_module_info('BoutiquesCollectionBasenamesListMaker')
+      return super if input_id.nil? # no config at all
 
       params_values = self.invoke_params[input_id]
       return super if params_values.blank? || params_values.size == 1
@@ -95,4 +97,5 @@ def final_task_list #:nodoc:
       end
 
     end
-  end
+
+end

BrainPortal/lib/boutiques_ext3_capturer.rb

@@ -54,7 +54,7 @@ def ext3capture_basenames
 
     # Get values in descriptor, as a hash
     descriptor = self.descriptor_for_cluster_commands
-    ext3_specs = descriptor.custom_module_info('BoutiquesExt3Capturer')
+    ext3_specs = descriptor.custom_module_info('BoutiquesExt3Capturer') || {}
 
     # Append our own entries; note that duplications of basenames
     # will mean only the first entry is used!

BrainPortal/lib/boutiques_file_name_matcher.rb

@@ -47,7 +47,7 @@ module BoutiquesFileNameMatcher
 
   def after_form #:nodoc:
     descriptor = self.descriptor_for_after_form
-    verifs     = descriptor.custom_module_info('BoutiquesFileNameMatcher')
+    verifs     = descriptor.custom_module_info('BoutiquesFileNameMatcher') || []
 
     verifs.each do |inputid,regexstring| # 'myinput' => "^sub-[a-zA-Z0-9]*$"
       input = descriptor.input_by_id(inputid)

BrainPortal/lib/boutiques_file_type_verifier.rb

@@ -47,7 +47,7 @@ module BoutiquesFileTypeVerifier
 
   def after_form #:nodoc:
     descriptor = self.descriptor_for_after_form
-    verifs     = descriptor.custom_module_info('BoutiquesFileTypeVerifier')
+    verifs     = descriptor.custom_module_info('BoutiquesFileTypeVerifier') || {}
 
     verifs.each do |inputid,typenames| # 'myinput' => [ 'TextFile', 'MincFile' ]
       input = descriptor.input_by_id(inputid)

BrainPortal/lib/boutiques_forced_output_browse_path.rb

@@ -20,6 +20,28 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
+# This module will attempt to force an output file
+# created by the boutiques integrator to be stored
+# with a "browse_path" under the target destination
+# DataProvider, if possible. e.g.
+#
+#    "custom": {
+#        "cbrain:integrator_modules": {
+#            "BoutiquesForcedOutputBrowsePath" : {
+#              "supertool_output_dir":  "derivatives/supertool",
+#              "supertool_html_report": "reports/[VERSION]/supertool",
+#            },
+#        }
+#    }
+#
+# The keys are IDs of the output-files section of the descriptor,
+# and the values are relative paths on the target result DP.
+# The relative paths can contain templated values that will be
+# substituted when the results are saved.
+#
+# If the target DP doesn't have browse_path capabilities, the
+# browse path will be set to nil and a warning will be added
+# to the task's log.
 module BoutiquesForcedOutputBrowsePath
 
   # Note: to access the revision info of the module,
@@ -72,7 +94,7 @@ def name_and_type_for_output_file(output, pathname)
     end
     name, type  = super # the standard names and types; the name will be replaced
     descriptor  = descriptor_for_save_results
-    config      = descriptor.custom_module_info('BoutiquesForcedOutputBrowsePath')
+    config      = descriptor.custom_module_info('BoutiquesForcedOutputBrowsePath') || {}
     browse_path = config[output.id]  # "a/b/c"
     return [ name, type ] if browse_path.blank? # no configured browse_path for this output
     browse_path = apply_value_keys(browse_path) # replaces [XYZ] strings with values from params

BrainPortal/lib/boutiques_input_cache_cleaner.rb

@@ -108,7 +108,7 @@ def save_results #:nodoc:
   # module's config.
   def to_clean_userfile_ids #:nodoc:
     descriptor = self.descriptor_for_save_results
-    input_ids  = descriptor.custom_module_info('BoutiquesInputCacheCleaner')
+    input_ids  = descriptor.custom_module_info('BoutiquesInputCacheCleaner') || []
     input_ids # 'my_input1', 'my_input2'
       .map { |inputid| invoke_params[inputid] } # the userfile ID(s) in the params; scalar or array
       .flatten                                  # flatten them all

BrainPortal/lib/boutiques_input_copier.rb

@@ -203,7 +203,7 @@ def finalize_bosh_invoke_struct(invoke_struct) #:nodoc:
     override_invoke_params = super.dup
 
     descriptor    = self.descriptor_for_cluster_commands
-    module_config = descriptor.custom_module_info('BoutiquesInputCopier')
+    module_config = descriptor.custom_module_info('BoutiquesInputCopier') || {}
 
     # For each input in BoutiquesInputCopier override the input with the copy
     # if the checkbox is selected

BrainPortal/lib/boutiques_input_regex_checker.rb

@@ -49,7 +49,7 @@ def after_form
 
     # Find the configured info
     descriptor = self.boutiques_descriptor
-    checkers   = descriptor.custom_module_info('BoutiquesInputRegexChecker') || {} # the raw struct in the decriptor
+    checkers   = descriptor.custom_module_info('BoutiquesInputRegexChecker') || {} # the raw struct in the descriptor
 
     # Run the checks
     checkers.each do |input_id,regex_message|

BrainPortal/lib/boutiques_input_subdir_maker.rb

@@ -103,7 +103,7 @@ module BoutiquesInputSubdirMaker
   # the fake parent directory information
   def descriptor_for_form #:nodoc:
     descriptor                = super.dup
-    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker')
+    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker') || {}
 
     parent_dirname_by_inputid.each do |inputid,subdir_config|
       # Adjust the description
@@ -126,6 +126,10 @@ def descriptor_for_form #:nodoc:
   # create a fake parent directory that will contains a symlink
   # to the orginal selected Userfile.
   def setup #:nodoc:
+    descriptor = self.descriptor_for_setup
+    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker') || {}
+    return super if parent_dirname_by_inputid.blank? # no config means nothing to do
+
     original_userfile_ids = {}
 
     # Log revision information
@@ -134,10 +138,7 @@ def setup #:nodoc:
     self.addlog("Creating parent directories in BoutiquesInputSubdirMaker.")
     self.addlog("#{basename} rev. #{commit}")
 
-    descriptor = self.descriptor_for_setup
-
     # Remove IDs from invoke_params
-    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker')
     parent_dirname_by_inputid.each_key do |inputid|
       original_userfile_ids[inputid]  = invoke_params[inputid]
       invoke_params[inputid]          = nil
@@ -187,7 +188,7 @@ def finalize_bosh_invoke_struct(invoke_struct) #:nodoc:
     override_invoke_params = super.dup
 
     descriptor = self.descriptor_for_cluster_commands
-    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker')
+    parent_dirname_by_inputid = descriptor.custom_module_info('BoutiquesInputSubdirMaker') || {}
     parent_dirname_by_inputid.each do |inputid,subdir_config|
       if override_invoke_params[inputid].blank?
         override_invoke_params.delete(inputid)

BrainPortal/lib/boutiques_input_value_fixer.rb

@@ -20,9 +20,9 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-# This module allows one to fix some of input parameters to specific constand values
+# This module allows one to fix some of input parameters to specific constant values
 # The fixed input(s) would no longer be shown to the user in the form.
-# The optional inputs assigned null value will be removed 
+# The optional inputs assigned null value will be removed
 # (do not use with mandatory input parameters)
 #
 # In the descriptor, the spec would look like:
@@ -52,9 +52,9 @@ module BoutiquesInputValueFixer
   Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
 
 
-  # the hash of input parameter values to be fixed or, if value is null, to be omited  
+  # the hash of input parameter values to be fixed or, if value is null, to be omitted
   def fixed_values
-    self.boutiques_descriptor.custom_module_info('BoutiquesInputValueFixer')
+    self.boutiques_descriptor.custom_module_info('BoutiquesInputValueFixer') || {}
   end
 
   # deletes fixed inputs listed in the custom 'integrator_modules'
@@ -63,6 +63,7 @@ def descriptor_without_fixed_inputs(descriptor)
     # other will be given fixed values during execution; neither should appear in web form UI
 
     fixed_input_ids = fixed_values.keys
+    return descriptor if fixed_input_ids.blank? # no config means nothing to do
     descriptor_dup  = descriptor.dup
     fully_removed   = fixed_input_ids.select do |i_id|  # this variables are flagged to be removed rather than assigned value
                                                    # in the spec, so they will be treated slightly different

BrainPortal/lib/boutiques_output_cache_cleaner.rb

@@ -52,6 +52,8 @@ module BoutiquesOutputCacheCleaner
   # user to disable this module's core function.
   def descriptor_with_special_input(descriptor)
     descriptor = descriptor.dup
+    output_ids = descriptor.custom_module_info('BoutiquesOutputCacheCleaner') || []
+    return descriptor if output_ids.blank? # no config means no changes.
 
     # Add new input
     new_input = BoutiquesSupport::Input.new(
@@ -108,7 +110,7 @@ def after_form #:nodoc:
     message = super
     return message if params_errors.present? || errors.present?
     enabled = self.invoke_params.delete :cbrain_enable_output_cache_cleaner
-    self.params[:cbrain_enable_output_cache_cleaner] = (enabled.to_s.match? /^(1|true)$/)
+    self.params[:cbrain_enable_output_cache_cleaner] = (enabled.to_s.match?(/^(1|true)$/))
     message
   end
 
@@ -126,7 +128,7 @@ def save_results #:nodoc:
 
     # Get the list of outputs to clean from the descriptor
     descriptor = self.descriptor_for_save_results
-    output_ids = descriptor.custom_module_info('BoutiquesOutputCacheCleaner')
+    output_ids = descriptor.custom_module_info('BoutiquesOutputCacheCleaner') || []
 
     # Get the userfile IDs of all outputs.
     # The Boutiques integrator create arrays of userfile

BrainPortal/lib/boutiques_output_file_type_setter.rb

@@ -49,7 +49,7 @@ def name_and_type_for_output_file(output, pathname) #:nodoc:
 
     # Get the suggestion from the descriptor
     descriptor           = self.descriptor_for_save_results
-    out_classes          = descriptor.custom_module_info('BoutiquesOutputFileTypeSetter')
+    out_classes          = descriptor.custom_module_info('BoutiquesOutputFileTypeSetter') || {}
     suggested_class_name = out_classes[output.id]
     return [ name, userfile_class ] if suggested_class_name.blank?
 

BrainPortal/lib/boutiques_output_filename_renamer.rb

@@ -109,7 +109,8 @@ module BoutiquesOutputFilenameRenamer
   # each configured String input fields.
   def descriptor_with_renaming_explanations(descriptor)
     descriptor = descriptor.dup
-    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer')
+    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer') || {}
+    return descriptor if config_map.blank? # no config means nothing to do
 
     uniq_outnames = {}
 
@@ -170,7 +171,7 @@ def descriptor_for_show_params #:nodoc:
   def after_form
     message    = super
     descriptor = descriptor_for_after_form
-    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer')
+    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer') || {}
     config_map.each do |_, pair|  # pair = [ boutiques ID of input, filename for output ]
       _, outnameinputid = *pair
       outname_pattern = invoke_params[outnameinputid].presence || ""
@@ -195,7 +196,7 @@ def after_form
   # as the new effective value for the name.
   def setup
     descriptor = descriptor_for_setup
-    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer')
+    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer') || {}
     config_map.each do |_, pair|
       fileinputid, outnameinputid = *pair
       input_userfile_id = invoke_params[fileinputid]
@@ -220,7 +221,7 @@ def setup
   def name_and_type_for_output_file(output, pathname)
     name, type = super # the standard names and types; the name will be replaced outright
     descriptor = descriptor_for_save_results
-    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer')
+    config_map = descriptor.custom_module_info('BoutiquesOutputFilenameRenamer') || {}
     config_map.each do |outputid, pair| # boutiques ID of outfile-files entry, pair
       next unless outputid == output.id
       _, outnameinputid = *pair

BrainPortal/lib/boutiques_post_processing_cleaner.rb

@@ -63,7 +63,8 @@ def save_results
 
     # Get the cleaning paths patterns from the descriptor
     descriptor = self.descriptor_for_save_results
-    patterns   = descriptor.custom_module_info('BoutiquesPostProcessingCleaner')
+    patterns   = descriptor.custom_module_info('BoutiquesPostProcessingCleaner') || []
+    return true if patterns.blank? # nothing else to do and super already worked fine
 
     # Prepare the substitution hash
     substitutions_by_token  = descriptor.build_substitutions_by_tokens_hash(

BrainPortal/lib/boutiques_save_std_out_std_err.rb

@@ -51,7 +51,8 @@ module BoutiquesSaveStdOutStdErr
   def save_results
     # Get the folder where to save the log files from the descriptor
     descriptor  = self.descriptor_for_save_results
-    module_info = descriptor.custom_module_info('BoutiquesSaveStdOutStdErr')
+    module_info = descriptor.custom_module_info('BoutiquesSaveStdOutStdErr') || {}
+    return super if module_info.blank? # nothing special to do
 
     # Get parent file to set stderr and stdout as children of first input file
     main_input_id = descriptor.file_inputs.first.id
@@ -81,6 +82,8 @@ def save_results
   # for the show page of the task.
   def descriptor_for_show_params  #:nodoc:
     descriptor = super.dup
+    module_info = descriptor.custom_module_info('BoutiquesSaveStdOutStdErr') || {}
+    return descriptor if module_info.blank? # nothing special to do
 
     stdout_file = BoutiquesSupport::OutputFile.new({
       "id"   => "cbrain_stdout",

BrainPortal/lib/boutiques_task_logs_copier.rb

@@ -90,7 +90,7 @@ def save_results
 
     # Get the cleaning paths patterns from the descriptor
     descriptor = self.descriptor_for_save_results
-    destpaths  = descriptor.custom_module_info('BoutiquesTaskLogsCopier')
+    destpaths  = descriptor.custom_module_info('BoutiquesTaskLogsCopier') || {}
 
     # Copy STDOUT and STDERR, if possible
     install_std_log_file(science_stdout_basename, destpaths[:stdout],     "stdout")
@@ -189,6 +189,3 @@ def install_std_log_file(stdlogfile, destpath, typeinfo)
 
 end
 
-
-
-