Re-implemented the hook for database directories

bob/bio/base/database/DatabaseBob.py

 from .Database import Database, DatabaseZT
+import os
 
 class DatabaseBob (Database):
   """This class can be used whenever you have a database that follows the default Bob database interface."""
@@ -51,6 +52,10 @@ class DatabaseBob (Database):
 
     self.database = database
     self.original_directory = database.original_directory
+    try:
+      self.annotation_directory = database.annotation_directory
+    except AttributeError:
+      pass
 
     self.all_files_options = all_files_options
     self.extractor_training_options = extractor_training_options
@@ -73,6 +78,36 @@ class DatabaseBob (Database):
     return "%s(%s)" % (str(self.__class__), params)
 
 
+  def replace_directories(self, replacements = None):
+    """This function replaces the original_directory and the annotation_directory with the directories read from the given replacement file."""
+    if replacements is None:
+      return
+    if isinstance(replacements, str):
+      if not os.path.exists(replacements):
+        return
+      # Open the database replacement file and reads its content
+      with open(replacements) as f:
+        replacements = {}
+        for line in f:
+          if line.strip() and not line.startswith("#"):
+            splits = line.split("=")
+            assert len(splits) == 2
+            replacements[splits[0].strip()] = splits[1].strip()
+
+    assert isinstance(replacements, dict)
+
+    if self.original_directory in replacements:
+      self.original_directory = replacements[self.original_directory]
+      self.database.original_directory = replacements[self.database.original_directory]
+
+    try:
+      if self.annotation_directory in replacements:
+        self.annotation_directory = replacements[self.annotation_directory]
+        self.database.annotation_directory = replacements[self.database.annotation_directory]
+    except AttributeError:
+      pass
+
+
   def uses_probe_file_sets(self):
     """Defines if, for the current protocol, the database uses several probe files to generate a score."""
     return self.protocol != 'None' and self.database.provides_file_set_for_protocol(self.protocol)

bob/bio/base/script/resources.py

@@ -2,8 +2,9 @@
 
 from __future__ import print_function
 import bob.bio.base
+import os
 
-def main():
+def resources():
 
   import argparse
   parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -35,3 +36,23 @@ def main():
     print (bob.bio.base.list_resources('grid'))
 
   print()
+
+def databases():
+  import argparse
+  database_replacement = "/idiap/home/%s/.bob_bio_databases.txt" % os.environ["USER"] if os.path.isdir("/idiap") else "/home/%s/.bob_bio_databases.txt" % os.environ["USER"]
+
+  parser = argparse.ArgumentParser(description="Prints a list of directories for registered databases", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+  parser.add_argument('-D', '--database-directories-file', metavar = 'FILE', default = database_replacement, help = 'The file, where database directories are stored (to avoid changing the database configurations)')
+
+  args = parser.parse_args()
+
+  # get registered databases
+  databases = bob.bio.base.utils.resources.database_directories(replacements=args.database_directories_file)
+
+  # print directories for all databases
+  for d in sorted(databases):
+    print ("\n%s:" % d)
+
+    print ("Original data: %s" % databases[d][0])
+    if len(databases[d]) > 1:
+      print ("Annotations: %s" % databases[d][1])

bob/bio/base/tools/command_line.py

@@ -67,7 +67,7 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
       help = 'The database file in which the submitted jobs will be written; relative to the current directory (only valid with the --grid option).')
   file_group.add_argument('--experiment-info-file', metavar = 'FILE', default = 'Experiment.info',
       help = 'The file where the configuration of all parts of the experiments are written; relative to te --result-directory.')
-  file_group.add_argument('--database-directories-file', metavar = 'FILE', default = database_replacement,
+  file_group.add_argument('-D', '--database-directories-file', metavar = 'FILE', default = database_replacement,
       help = 'An optional file, where database directories are stored (to avoid changing the database configurations)')
 
   sub_dir_group = parser.add_argument_group('\nSubdirectories of certain parts of the tool chain. You can specify directories in case you want to reuse parts of the experiments (e.g. extracted features) in other experiments. Please note that these directories are relative to the --temp-directory, but you can also specify absolute paths')
@@ -98,7 +98,7 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
       help = 'Try to recursively stop the dependent jobs from the SGE grid queue, when a job failed')
   flag_group.add_argument('-X', '--external-dependencies', type=int, default = [], nargs='+',
       help = 'The jobs submitted to the grid have dependencies on the given job ids.')
-  flag_group.add_argument('-D', '--timer', choices=('real', 'system', 'user'), nargs = '*',
+  flag_group.add_argument('-B', '--timer', choices=('real', 'system', 'user'), nargs = '*',
       help = 'Measure and report the time required by the execution of the tool chain (only on local machine)')
   flag_group.add_argument('-L', '--run-local-scheduler', action='store_true',
       help = 'Starts the local scheduler after submitting the jobs to the local queue (by default, local jobs must be started by hand, e.g., using ./bin/jman --local -vv run-scheduler -x)')
@@ -169,7 +169,6 @@ def initialize(parsers, command_line_parameters = None, skips = []):
   args.grid_log_directory = os.path.join(args.temp_directory, args.grid_log_directory)
 
 
-
   # protocol command line override
   if args.protocol is not None:
     args.database.protocol = args.protocol
@@ -185,34 +184,8 @@ def initialize(parsers, command_line_parameters = None, skips = []):
   enroller_sub_dir = protocol if args.database.training_depends_on_protocol and args.algorithm.requires_enroller_training else projector_sub_dir
   model_sub_dir = protocol if args.database.models_depend_on_protocol else enroller_sub_dir
 
-
   # Database directories, which should be automatically replaced
-  if os.path.exists(args.database_directories_file):
-    #
-    replacements = {}
-    with open(args.database_directories_file) as f:
-      for line in f:
-        if line.strip() and not line.startswith("#"):
-          splits = line.split("=")
-          assert len(splits) == 2
-          replacements[splits[0].strip()] = splits[1].strip()
-
-    try:
-      for d in replacements:
-        if args.database.original_directory == d:
-          args.database.original_directory = replacements[d]
-          args.database.database.original_directory = replacements[d]
-    except AttributeError:
-      pass
-
-    try:
-      for d in replacements:
-        if args.database.annotation_directory == d:
-          args.database.annotation_directory = replacements[d]
-          args.database.database.annotation_directory = replacements[d]
-    except AttributeError:
-      pass
-
+  args.database.replace_directories(args.database_directories_file)
 
   # initialize the file selector
   FileSelector.create(

bob/bio/base/utils/resources.py

@@ -186,3 +186,22 @@ def list_resources(keyword, strip=['dummy']):
     else:
       retval += "  + %s --> %s\n" % (entry_point.name + " "*(length - len(entry_point.name)), entry_point.module_name)
   return retval
+
+
+def database_directories(strip=['dummy'], replacements = None):
+  """Returns a dictionary of original directories for all registered databases."""
+  entry_points = _get_entry_points('database', strip)
+
+  dirs = {}
+  for entry_point in sorted(entry_points):
+    try:
+      db = load_resource(entry_point.name, 'database')
+      db.replace_directories(replacements)
+      dirs[entry_point.name] = [db.original_directory]
+#      import ipdb; ipdb.set_trace()
+      if db.annotation_directory is not None:
+        dirs[entry_point.name].append(db.annotation_directory)
+    except (AttributeError, ValueError):
+      pass
+
+  return dirs

setup.py

@@ -104,7 +104,8 @@ setup(
       # scripts should be declared using this entry:
       'console_scripts' : [
         'verify.py         = bob.bio.base.script.verify:main',
-        'resources.py      = bob.bio.base.script.resources:main',
+        'resources.py      = bob.bio.base.script.resources:resources',
+        'databases.py      = bob.bio.base.script.resources:databases',
         'evaluate.py       = bob.bio.base.script.evaluate:main',
         'collect_results.py = bob.bio.base.script.collect_results:main',
         'grid_search.py    = bob.bio.base.script.grid_search:main',