Merge pull request #274 from dpryan79/dev

Add usage information to python cleanup scripts

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -74,7 +74,8 @@ def main():
     contains the specified text will be marked as deleted in user's history and
     the user will be notified by email using the specified template file.
     """
-    parser = OptionParser()
+    usage = "usage: %prog [options] galaxy.ini"
+    parser = OptionParser(usage=usage)
     parser.add_option("-d", "--days", dest="days", action="store",
                       type="int", help="number of days (60)", default=60)
     parser.add_option("--tool_id", default=None,
@@ -100,6 +101,9 @@ def main():
                       help="From address to use to send email. "
                       "Default: [read from galaxy ini file]")
     (options, args) = parser.parse_args()
+    if len(args) != 1 :
+        parser.print_help()
+        sys.exit()
     ini_file = args[0]
 
     config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})

scripts/cleanup_datasets/cleanup_datasets.py

@@ -66,7 +66,8 @@ def main():
     Another way of stating it is: LibraryDatasetDatasetAssociation objects map LibraryDataset objects to Dataset objects,
     and Dataset objects may be mapped to History objects via HistoryDatasetAssociation objects.  
     """
-    parser = OptionParser()
+    usage = "usage: %prog [options] galaxy.ini"
+    parser = OptionParser(usage=usage)
     parser.add_option( "-d", "--days", dest="days", action="store", type="int", help="number of days (60)", default=60 )
     parser.add_option( "-r", "--remove_from_disk", action="store_true", dest="remove_from_disk", help="remove datasets from disk when purged", default=False )
     parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False )
@@ -79,6 +80,9 @@ def main():
     parser.add_option( "-6", "--delete_datasets", action="store_true", dest="delete_datasets", default=False, help="mark deletable datasets as deleted and purge associated dataset instances" )
 
     ( options, args ) = parser.parse_args()
+    if len(args) != 1 :
+        parser.print_help()
+        sys.exit()
     ini_file = args[0]
     
     if not ( options.purge_folders ^ options.delete_userless_histories ^ \

scripts/cleanup_datasets/populate_uuid.py

@@ -22,7 +22,19 @@ from sqlalchemy import *
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+def usage(prog) :
+    print "usage: %s galaxy.ini" % prog
+    print """
+Populates blank uuid fields in datasets with randomly generated values.
+            
+Going forward, these ids will be generated for all new datasets. This
+script fixes datasets that were generated before the change.
+    """
+
 def main():
+    if len(sys.argv) != 2 or sys.argv == "-h" or sys.argv == "--help" :
+        usage(sys.argv[0])
+        sys.exit()
     ini_file = sys.argv.pop(1)
     config = get_config(ini_file)
 

scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py

@@ -8,7 +8,21 @@ import sys, os
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+def usage(prog) :
+    print "usage: %s file" % prog
+    print """
+Removes a set of files from disk. The input file should contain a list of files
+to be deleted, one per line. The full path must be specified and must begin
+with /var/opt/galaxy.
+
+A log of files deleted is created in a file with the same name as that input but
+with .removed.log appended.
+    """
+
 def main():
+    if len(sys.argv) != 2 or sys.argv == "-h" or sys.argv == "--help" :
+        usage(sys.argv[0])
+        sys.exit()
     infile = sys.argv[1]
     outfile = infile + ".removed.log"
     out = open( outfile, 'w' )

scripts/cleanup_datasets/rename_purged_datasets.py

@@ -8,7 +8,22 @@ import sys, os
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+def usage(prog) :
+    print "usage: %s file" % prog
+    print """
+Marks a set of files as purged and renames them. The input file should contain a
+list of files to be purged, one per line. The full path must be specified and
+must begin with /var/opt/galaxy.
+A log of files marked as purged is created in a file with the same name as that
+input but with _purged appended. The resulting files can finally be removed from
+disk with remove_renamed_datasets_from_disk.py, by supplying it with a list of
+them.
+    """
+
 def main():
+    if len(sys.argv) != 2 or sys.argv == "-h" or sys.argv == "--help" :
+        usage(sys.argv[0])
+        sys.exit()
     infile = sys.argv[1]
     outfile = infile + ".renamed.log"
     out = open( outfile, 'w' )

scripts/cleanup_datasets/update_dataset_size.py

@@ -9,7 +9,17 @@ import galaxy.app
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+def usage(prog) :
+    print "usage: %s galaxy.ini" % prog
+    print """
+Updates the dataset.size column. Users are advised to backup the database before
+running.
+    """
+
 def main():
+    if len(sys.argv) != 1 or sys.argv[1] == "-h" or sys.argv[1] == "--help" :
+        usage(sys.argv[0])
+        sys.exit()
     ini_file = sys.argv.pop(1)
     conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
     conf_parser.read( ini_file )

scripts/cleanup_datasets/update_metadata.py

@@ -13,7 +13,18 @@ import galaxy.datatypes.tabular
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+def usage(prog) :
+    print "usage: %s galaxy.ini" % prog
+    print """
+Updates the metadata in the database to match rev 1981.
+
+Remember to backup your database before running.
+    """
+
 def main():
+    if len(sys.argv) != 1 or sys.argv[1] == "-h" or sys.argv[1] == "--help" :
+        usage(sys.argv[0])
+        sys.exit()
     ini_file = sys.argv.pop(1)
     conf_parser = ConfigParser.ConfigParser({'here':os.getcwd()})
     conf_parser.read(ini_file)