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/>.
+#
+
+# 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 staff
+# or need a clean boutiques descriptor which does not create any new folders
+# For example :
+#
+#
+# and in the `cbrain:integrator_modules` section look like:
+#
+#     "BoutiquesDirMaker":
+#          [ "[OUTDIR]", "[OUTDIR]/[THRESHOLD]_res", "tmp" ]
+#
+# Absolute paths and special symbols are not supported, please use only alphanumericals,
+# underscores, hyphens, spaces, and square brackets
+#
+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
+  ############################################
+
+  # Add mkdir to json descriptor
+  def descriptor_for_cluster_commands
+    descriptor = super.dup()
+    dir_names  = descriptor.custom_module_info('BoutiquesDirMaker')
+
+    # Log revision information
+    basename = Revision_info.basename
+    commit   = Revision_info.short_commit
+    self.addlog("Creating directories with BoutiquesDirMaker.")
+    self.addlog("#{basename} rev. #{commit}")
+
+    dir_names.each do |x|
+      if Pathname(x).absolute?
+         raise CbrainError("#{x} is absolute paths, which are presently not supported")
+      end
+      x.gsub!(/[^0-9A-Za-z.\/\-_\[\]]|(\.\.+)/, '_')  # silent sanitizing and quotes
+    end
+
+    # adds folder creation, the quotation is used to allow for spaces
+    descriptor.command_line = "mkdir -p '" + dir_names.join("' '") + "'; " + descriptor.command_line
+
+    descriptor
+  end
+end