utility module make folders #1343

Bourreau/lib/boutiques_dir_maker.rb

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+../../BrainPortal/lib/boutiques_dir_maker.rb

BrainPortal/lib/boutiques_dir_maker.rb

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+
+#
+# CBRAIN Project
+#
+# Copyright (C) 2008-2023
+# 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/>.
+#
+
+require 'fileutils'
+
+# Some tools expect that a directory e.g. results, etc exists in the working directory
+#
+# While traditionally we add to the boutiques command line prefix akin to 'mkdir -p [OUTPUT];'
+# external collaborators might dislike polluting the command line with technical details
+# and prefer a clean boutiques descriptor which does not create any new folders
+# The the `cbrain:integrator_modules` section look like:
+#
+#     "BoutiquesDirMaker":
+#          [ "[OUTDIR]", "[OUTDIR]/[THRESHOLD]_res", "tmp" ]
+#
+# Please avoid special characters save underscore and hyphen, and
+# use relative paths. Boutiques templates (hereafter called patterns) are supported
+#
+module BoutiquesDirMaker
+
+  # Note: to access the revision info of the module,
+  # you need to access the constant directly, the
+  # object method revision_info() won't work.
+  Revision_info=CbrainFileRevision[__FILE__] #:nodoc:
+
+  ############################################
+  # Bourreau (Cluster) Side Modifications
+  ############################################
+
+  # create few sub directories in the work folder
+  def cluster_commands #:nodoc:
+
+    # Log revision information
+    self.addlog("Creating directories with BoutiquesDirMaker.")
+    basename = Revision_info.basename
+    commit   = Revision_info.short_commit
+    self.addlog("#{basename} rev. #{commit}")
+
+    descriptor = self.descriptor_for_setup
+    patterns   = descriptor.custom_module_info('BoutiquesDirMaker')
+
+    # invoke overridden method
+    commands = super
+    return false if ! commands # early return
+
+    substitutions_by_token  = descriptor.build_substitutions_by_tokens_hash(
+      JSON.parse(File.read(self.invoke_json_basename))
+    )
+
+    # Process each directory pattern
+    paths = patterns.map do |pattern|
+      # Replace tokens
+      path = descriptor.apply_substitutions(pattern, substitutions_by_token)
+
+      if Pathname(path).absolute?
+        self.addlog("BoutiquesDirMaker skips '#{pattern}', dir '#{path}', absolute paths are not supported")
+        next
+      end
+
+      # replacing weird and special characters
+      if path.gsub!(/[^0-9A-Za-z.\/\-_ ]+|(\.\.+)/, '_')
+        self.addlog("Note that in '#{path}', underscore is used instead of special symbol(s)")
+      end
+      path
+    end
+    FileUtils.mkdir_p paths.compact
+    commands
+  end
+end