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Add some logging code to report what the program is doing
author
Diane Trout
<diane@caltech.edu>
Mon, 30 Mar 2009 18:52:26 +0000
(18:52 +0000)
committer
Diane Trout
<diane@caltech.edu>
Mon, 30 Mar 2009 18:52:26 +0000
(18:52 +0000)
scripts/make-library-tree
patch
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diff --git
a/scripts/make-library-tree
b/scripts/make-library-tree
index 67a9282b60557cf875a57a8cda17e37ac3c62749..1c3772efb9f6050086f79138dfae8e4c03ebb967 100644
(file)
--- a/
scripts/make-library-tree
+++ b/
scripts/make-library-tree
@@
-1,3
+1,4
@@
+#!/usr/bin/python
"""
Make a tree of symlinks organized by library id.
"""
"""
Make a tree of symlinks organized by library id.
"""
@@
-5,15
+6,15
@@
from ConfigParser import SafeConfigParser
from glob import glob
import logging
from optparse import OptionParser
from glob import glob
import logging
from optparse import OptionParser
+import logging
import os
import stat
import sys
from htsworkflow.util import fctracker
import os
import stat
import sys
from htsworkflow.util import fctracker
-
def find_lanes(flowcell_dir, flowcell_id, lane):
def find_lanes(flowcell_dir, flowcell_id, lane):
- lane_name = "s_%s_eland_
result
*" %(lane)
+ lane_name = "s_%s_eland_*" %(lane)
pattern = os.path.join(flowcell_dir, flowcell_id, "*", lane_name)
lanes = glob(pattern)
return lanes
pattern = os.path.join(flowcell_dir, flowcell_id, "*", lane_name)
lanes = glob(pattern)
return lanes
@@
-75,6
+76,7
@@
def carefully_make_hardlink(source, destination, dry_run=False):
else:
raise IOError('%s and %s are different files' % \
(source, destination))
else:
raise IOError('%s and %s are different files' % \
(source, destination))
+ logging.info('Linking: %s -> %s' % (source, destination))
if dry_run: return
if dry_run: return
@@
-152,7
+154,7
@@
def make_parser():
help='path to a configuration file containing a '
'sequence archive section')
help='path to a configuration file containing a '
'sequence archive section')
- parser.add_option("-
d", "-
-database", dest="database",
+ parser.add_option("--database", dest="database",
help="path to the fctracker.db",
default=None)
parser.add_option('-a', '--sequence-archive', default=None,
help="path to the fctracker.db",
default=None)
parser.add_option('-a', '--sequence-archive', default=None,
@@
-161,14
+163,17
@@
def make_parser():
help="add a where clause",
default=None)
help="add a where clause",
default=None)
+ parser.add_option('-v', '--verbose', action='store_true', default=False,
+ help='be more verbose')
+ parser.add_option('-d', '--debug', action='store_true', default=False,
+ help='report everything')
+
parser.add_option("--dry-run", dest="dry_run", action="store_true",
default=False,
help="Don't modify the filesystem")
return parser
def main(argv=None):
parser.add_option("--dry-run", dest="dry_run", action="store_true",
default=False,
help="Don't modify the filesystem")
return parser
def main(argv=None):
- logging.basicConfig(level=logging.INFO)
-
FRONTEND_NAME = 'frontend'
SECTION_NAME = 'sequence_archive'
DATABASE_OPT = 'database_name'
FRONTEND_NAME = 'frontend'
SECTION_NAME = 'sequence_archive'
DATABASE_OPT = 'database_name'
@@
-181,6
+186,14
@@
def main(argv=None):
# parse command line arguments
opt, args = parser.parse_args(argv)
# parse command line arguments
opt, args = parser.parse_args(argv)
+ # setup logging
+ level = logging.WARN
+ if opt.verbose:
+ level = logging.INFO
+ if opt.debug:
+ level = logging.DEBUG
+ logging.basicConfig(level=level)
+
# figure out what config file to read
config_path = [os.path.expanduser('~/.htsworkflow.ini'),
'/etc/htsworkflow.ini']
# figure out what config file to read
config_path = [os.path.expanduser('~/.htsworkflow.ini'),
'/etc/htsworkflow.ini']