src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes 1.2
1.2 2010/03/15 23:34:11 krish
added flag to output lists of files and tables
Index: src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes 15 Mar 2010 22:58:29 -0000 1.1
+++ src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes 15 Mar 2010 23:34:11 -0000 1.2
@@ -96,8 +96,10 @@
parser.add_option("-t", "--track-name", dest="track_name",
help="the name of the composite track by default this is the name of the current directory", metavar="N")
parser.add_option("-n", "--name", dest="name",
help="the English name of track", metavar="N", default="Untitled")
+ parser.add_option("--files", dest="files_path", help="dump list of new files to F", metavar="F")
+ parser.add_option("--tables", dest="tables_path", help="dump list of new tablesto F", metavar="F")
global options
(options, args) = parser.parse_args()
@@ -159,9 +161,9 @@
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
unchanged_tables_list.append(name)
unchanged_files_list.append(f)
unchanged_wibs_list.append(wib_path)
- elif type == "narrowPeak":
+ elif type == "narrowPeak" or type.startswith("bedGraph"):
if not table_exists(database, name):
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
unchanged_tables_list.append(name)
unchanged_files_list.append(f)
@@ -183,9 +185,9 @@
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
removed_tables_list.append(name)
removed_files_list.append(f)
removed_wibs_list.append(wib_path)
- elif type == "narrowPeak":
+ elif type == "narrowPeak" or type.startswith("bedGraph"):
if not table_exists(database, name):
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
removed_tables_list.append(name)
removed_files_list.append(f)
@@ -207,9 +209,9 @@
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
new_tables_list.append(name)
new_files_list.append(os.path.join("/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC", options.track_name, current_release_dir, f))
new_wibs_list.append(wib_path)
- elif type == "narrowPeak":
+ elif type == "narrowPeak" or type.startswith("bedGraph"):
if not table_exists(database, name):
raise ValueError, "table %s does not exist, from filetype %s" % (name, type)
new_tables_list.append(name)
new_files_list.append(os.path.join("/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC", options.track_name, current_release_dir, f))
@@ -230,10 +232,31 @@
print >>sys.stderr, " new tables: %d" % len(new_tables_list)
print >>sys.stderr, " new files: %d" % len(new_files_list)
print >>sys.stderr, " new wibs: %d" % len(new_wibs_list)
+ # if asked, save the list of new files
+ if options.files_path:
+ new_files_file = open(options.files_path, "w")
+ new_files_list.sort()
+ for i in new_files_list:
+ print >>new_files_file, i
+ print >>new_files_file
+ new_wibs_list.sort()
+ for i in new_wibs_list:
+ print >>new_files_file, i
+ new_files_file.close()
+
+ # if asked, generate list of new tables
+ if options.tables_path:
+ new_tables_file = open(options.tables_path, "w")
+ new_tables_list.sort()
+ for i in new_tables_list:
+ print >>new_tables_file, i
+ print >>new_tables_file
+ new_tables_file.close()
+
# generate the header
- print "# Generated with %s %s" % (os.path.basename(sys.argv[0]), options.get_version())
+ print "# generated with %s" % parser.get_version()
print "This is a %s of the \"%s\"" % (current_release_dir, options.name)
print "The composite track is %s" % options.track_name
print """
Categories of tables and files('):
@@ -247,9 +270,10 @@
# untouched list
print "A) Untouched Tables (%d):" % len(unchanged_tables_list)
unchanged_tables_list.sort()
for i in unchanged_tables_list:
- print " %s" %i
+ print i
+ print
print "A') Untouched Files (%d downloadables, %d wibs):" % (len(unchanged_files_list),
len(unchanged_wibs_list))
print " current location on alpha:"
@@ -258,21 +282,22 @@
print " {...}/goldenPath/encodeDCC/%s/" % options.track_name
print
unchanged_files_list.sort()
for i in unchanged_files_list:
- print " %s" %i
+ print i
print
unchanged_wibs_list.sort()
for i in unchanged_wibs_list:
- print " %s" %i
+ print i
print
# eliminated list
print "B) Deprecated tables (%d):" % len(removed_tables_list)
removed_tables_list.sort()
for i in removed_tables_list:
- print " %s" %i
+ print i
+ print
print "B') Deprecated files (%d downloadables, %d wibs):" %(len(removed_files_list),
len(removed_wibs_list))
print " NOTE: NO FILES SHOULD BE REMOVED from the downloads directory on hgdownloads (RR)."
@@ -284,21 +309,22 @@
print
removed_files_list.sort()
for i in removed_files_list:
- print " %s" %i
+ print i
print
removed_wibs_list.sort()
for i in removed_wibs_list:
- print " %s" %i
+ print i
print
# new list
print "C) New tables (%d):" % len(new_tables_list)
new_tables_list.sort()
for i in new_tables_list:
- print " %s" %i
+ print i
+ print
print "C') New files (%d downloadables, %d wibs):" % (len(new_files_list),
len(new_wibs_list))
print " current location on alpha:"
@@ -308,13 +334,13 @@
print
new_files_list.sort()
for i in new_files_list:
- print " %s" %i
+ print i
print
new_wibs_list.sort()
for i in new_wibs_list:
- print " %s" %i
+ print i
print
print "D) Additional items:"
@@ -322,11 +348,11 @@
print " /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/%s/%s/" % (options.track_name, current_release_dir)
print " should be placed on the RR in (overwritting any existing copy):"
print " {...}/goldenPath/encodeDCC/%s/" % options.track_name
print
- print " index.html"
- print " files.txt"
- print " md5sum.txt"
+ print "index.html"
+ print "files.txt"
+ print "md5sum.txt"
#### Module ####################################################################
if __name__ == "__main__":