from glob import glob
import json
import logging
+import netrc
from optparse import OptionParser
import os
from pprint import pprint, pformat
import shlex
from StringIO import StringIO
-import time
+import stat
+from subprocess import Popen, PIPE
import sys
+import time
import types
import urllib
import urllib2
if opts.host is None or opts.apiid is None or opts.apikey is None:
parser.error("Please specify host url, apiid, apikey")
+ if opts.makeddf and opts.daf is None:
+ parser.error("Please specify your daf when making ddf files")
+
if len(args) == 0:
parser.error("I need at least one library submission-dir input file")
base_daf = os.path.basename(daf_path)
for lib_id, result_dir in library_result_map:
+ if not os.path.exists(result_dir):
+ raise RuntimeError("Couldn't find target directory %s" %(result_dir,))
submission_daf = os.path.join(result_dir, base_daf)
if not os.path.exists(submission_daf):
+ if not os.path.exists(daf_path):
+ raise RuntimeError("Couldn't find daf: %s" %(daf_path,))
os.link(daf_path, submission_daf)
for lib_id, result_dir in library_result_map:
order_by = ['order_by=files', 'view', 'replicate', 'cell',
- 'readType', 'mapAlgorithm', 'insertLength' ]
+ 'readType', 'mapAlgorithm', 'insertLength', 'md5sum' ]
inifile = ['[config]']
inifile += [" ".join(order_by)]
inifile += ['']
attributes = view_map.find_attributes(f, lib_id)
if attributes is None:
raise ValueError("Unrecognized file: %s" % (f,))
+ attributes['md5sum'] = "None"
ext = attributes["extension"]
if attributes['view'] is None:
fastqs.setdefault(ext, set()).add(f)
fastq_attributes[ext] = attributes
else:
+ md5sum = make_md5sum(os.path.join(result_dir,f))
+ if md5sum is not None:
+ attributes['md5sum']=md5sum
inifile.extend(
make_submission_section(line_counter,
[f],
output = open(ddf_name,'w')
file_list = read_ddf_ini(ininame, output)
+ logging.info(
+ "Read config {0}, found files: {1}".format(
+ ininame, ", ".join(file_list)))
file_list.append(daf_name)
if ddf_name is not None:
script = """Universe = vanilla
Executable = /usr/bin/lftp
-arguments = -c put ../%(archivename)s -o ftp://detrout@encodeftp.cse.ucsc.edu/%(archivename)s
+arguments = -c put ../%(archivename)s -o ftp://%(ftpuser)s:%(ftppassword)s@%(ftphost)s/%(archivename)s
Error = upload.err.$(Process).log
Output = upload.out.$(Process).log
queue
"""
+ auth = netrc.netrc(os.path.expanduser("~diane/.netrc"))
+
+ encodeftp = 'encodeftp.cse.ucsc.edu'
+ ftpuser = auth.hosts[encodeftp][0]
+ ftppassword = auth.hosts[encodeftp][2]
context = {'archivename': make_submission_name(ininame),
'initialdir': os.getcwd(),
- 'user': os.getlogin()}
+ 'user': os.getlogin(),
+ 'ftpuser': ftpuser,
+ 'ftppassword': ftppassword,
+ 'ftphost': encodeftp}
condor_script = make_condor_name(ininame, 'upload')
condor_stream = open(condor_script,'w')
condor_stream.write(script % context)
condor_stream.close()
+ os.chmod(condor_script, stat.S_IREAD|stat.S_IWRITE)
+
return condor_script
('*.bam', self._guess_bam_view),
('junctions.bed', 'Junctions'),
('*.jnct', 'Junctions'),
- ('*.unique.bigwig', None),
- ('*.plus.bigwig', 'PlusSignal'),
- ('*.minus.bigwig', 'MinusSignal'),
+ ('*unique.bigwig', None),
+ ('*plus.bigwig', 'PlusSignal'),
+ ('*minus.bigwig', 'MinusSignal'),
('*.bigwig', 'Signal'),
('*.tar.bz2', None),
('*.condor', None),
('*.gtf', 'GeneModel'),
('*.ini', None),
('*.log', None),
+ ('*.md5', None),
('paired-end-distribution*', 'InsLength'),
('*.stats.txt', 'InsLength'),
('*.srf', None),
if not os.path.exists(f):
raise RuntimeError("%s does not exist" % (f,))
+def make_md5sum(filename):
+ """Quickly find the md5sum of a file
+ """
+ md5_cache = os.path.join(filename+".md5")
+ print md5_cache
+ if os.path.exists(md5_cache):
+ logging.debug("Found md5sum in {0}".format(md5_cache))
+ stream = open(md5_cache,'r')
+ lines = stream.readlines()
+ md5sum = parse_md5sum_line(lines, filename)
+ else:
+ md5sum = make_md5sum_unix(filename, md5_cache)
+ return md5sum
+
+def make_md5sum_unix(filename, md5_cache):
+ cmd = ["md5sum", filename]
+ logging.debug("Running {0}".format(" ".join(cmd)))
+ p = Popen(cmd, stdout=PIPE)
+ stdin, stdout = p.communicate()
+ retcode = p.wait()
+ logging.debug("Finished {0} retcode {1}".format(" ".join(cmd), retcode))
+ if retcode != 0:
+ logging.error("Trouble with md5sum for {0}".format(filename))
+ return None
+ lines = stdin.split(os.linesep)
+ md5sum = parse_md5sum_line(lines, filename)
+ if md5sum is not None:
+ logging.debug("Caching sum in {0}".format(md5_cache))
+ stream = open(md5_cache, "w")
+ stream.write(stdin)
+ stream.close()
+ return md5sum
+
+def parse_md5sum_line(lines, filename):
+ md5sum, md5sum_filename = lines[0].split()
+ if md5sum_filename != filename:
+ errmsg = "MD5sum and I disagre about filename. {0} != {1}"
+ logging.error(errmsg.format(filename, md5sum_filename))
+ return None
+ return md5sum
if __name__ == "__main__":
main()