def deal_with_upload(meta, args):
print("Dealing with the upload file")
is_zip = zipfile.is_zipfile(args.upload_file)
if is_zip:
files = file_utils.unzip_archive(args.path, args.upload_file)
print "Compressed: Yes (zip)"
elif args.upload_file.endswith('.gz'):
print "Compressed: Yes (gzip)"
files = [os.path.basename(args.upload_file[:-3])]
cmd = 'gzip -dc %s > %s ' % (args.upload_file,
os.path.join(args.path, files[0]))
p = subprocess.Popen(cmd,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE,
shell=True)
print p.communicate()[0]
if p.returncode != 0:
sys.exit(p.returncode)
subprocess.call(cmd, shell=True)
else:
print "Compressed: No"
files = [args.upload_file]
meta['pre_process_files'] = files
api.update_meta(meta, args)
return files
def deal_with_upload(meta, args):
print("Dealing with the upload file")
is_zip = zipfile.is_zipfile(args.upload_file)
if is_zip:
files = file_utils.unzip_archive(args.path, args.upload_file)
print "Compressed: Yes (zip)"
elif args.upload_file.endswith('.gz'):
print "Compressed: Yes (gzip)"
files = [os.path.basename(args.upload_file[:-3])]
cmd = 'gzip -dc %s > %s ' % (args.upload_file, os.path.join(args.path,files[0]))
p = subprocess.Popen(cmd, stderr=subprocess.STDOUT, stdout=subprocess.PIPE, shell=True)
print p.communicate()[0]
if p.returncode != 0:
sys.exit(p.returncode)
subprocess.call(cmd, shell=True)
else:
print "Compressed: No"
files = [args.upload_file]
meta['pre_process_files'] = files
api.update_meta(meta, args)
return files
def main():
parse = argparse.ArgumentParser()
parse.add_argument('upload_id', type=int)
parse.add_argument('path')
parse.add_argument('upload_file')
parse.add_argument('meta_file')
try:
args = parse.parse_args()
except IOError as err:
print("Input file error: %s" % err)
parse.print_help()
sys.exit(1)
meta_file_handle = open(args.meta_file,'r')
meta = json.load(meta_file_handle, parse_float=Decimal)
meta_file_handle.close()
is_zip = zipfile.is_zipfile(args.upload_file)
if is_zip:
files = file_utils.unzip_archive(args.path, args.upload_file)
elif args.upload_file.endswith('.gz'):
files = [os.path.basename(args.upload_file[:-3])]
cmd = 'gzip -dc %s > %s ' % (args.upload_file, os.path.join(args.path,files[0]))
subprocess.call(cmd, shell=True)
else:
files = [args.upload_file]
''' Establish the upload type '''
target_regions_bed = None
hotspots_bed = None
meta['is_ampliseq'] = False
if len(files) == 1 and files[0].endswith('.bed') and meta.get('hotspot',False) == False:
target_regions_bed = os.path.basename(files[0])
meta['is_ampliseq'] = False
elif len(files) == 1 and files[0].endswith('.bed') and meta.get('hotspot',False) == True:
hotspots_bed = os.path.basename(files[0])
meta['is_ampliseq'] = False
elif len(files) == 1 and files[0].endswith('.vcf') and meta.get('hotspot',False) == True:
hotspots_bed = os.path.basename(files[0]) + '.bed'
convert_command = '/usr/local/bin/tvcutils prepare_hotspots'
convert_command += ' --input-vcf %s' % os.path.join(args.path,os.path.basename(files[0]))
convert_command += ' --output-bed %s' % os.path.join(args.path,hotspots_bed)
convert_command += ' --reference /results/referenceLibrary/tmap-f3/%s/%s.fasta' % (meta["reference"],meta["reference"]) #TODO: is this just name or full path??
convert_command += ' --filter-bypass on'
process = subprocess.Popen(convert_command, stderr=subprocess.STDOUT, stdout=subprocess.PIPE, shell=True)
for line in process.communicate()[0].splitlines():
api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id), text=line.strip())
meta['is_ampliseq'] = False
elif "plan.json" in files:
meta['is_ampliseq'] = True
plan_data = json.load(open(os.path.join(args.path, "plan.json")))
version, design = ampliseq.handle_versioned_plans(plan_data, meta)
meta['design'] = design
try:
target_regions_bed = design['plan']['designed_bed']
hotspots_bed = design['plan']['hotspot_bed']
if not meta.get("reference", None):
meta['reference'] = design['genome'].lower()
if 'design_name' in plan_data:
meta['description'] = design['design_name']
meta_file_handle = open(args.meta_file,'w')
json.dump(meta, meta_file_handle, cls=JSONEncoder)
meta_file_handle.close()
api.patch("contentupload", args.upload_id, meta=meta)
except KeyError as err:
api.patch("contentupload", args.upload_id, status="Error: malformed AmpliSeq archive")
api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id), text="Malformed AmpliSeq archive: missing json key "+str(err))
raise
if target_regions_bed and target_regions_bed not in files:
api.patch("contentupload", args.upload_id, status="Error: malformed AmpliSeq archive")
api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id),
text="Malformed AmpliSeq archive: Target region file %s not present in AmpliSeq archive" % target_regions_bed)
raise ValueError("Target region file %s not present in AmpliSeq archive" % target_regions_bed)
if hotspots_bed and hotspots_bed not in files:
api.patch("contentupload", args.upload_id, status="Error: malformed AmpliSeq archive")
api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id),
text="Malformed AmpliSeq archive: Hotspots file %s not present in AmpliSeq archive" % target_regions_bed)
raise ValueError("Hotspots file %s not present in AmpliSeq archive" % target_regions_bed)
else:
api.patch("contentupload", args.upload_id, status="Error: Upload must be either valid Ampliseq export or contain a single BED or VCF file.")
raise ValueError("Upload must be either valid Ampliseq export or contain a single BED or VCF file.")
''' === Validate and Register === '''
primary_path = None
secondary_path = None
if target_regions_bed:
primary_path = validate(args.upload_id, args.path, meta, target_regions_bed, 'target regions BED')
if hotspots_bed:
secondary_path = validate(args.upload_id, args.path, meta, hotspots_bed, 'hotspots BED')
meta["hotspot"] = False
if target_regions_bed and not primary_path:
register_bed_file(args.upload_id, args.path, meta, target_regions_bed)
if hotspots_bed:
meta["hotspot"] = True
if not secondary_path:
register_bed_file(args.upload_id, args.path, meta, hotspots_bed)
if meta['is_ampliseq']:
try:
if target_regions_bed and not primary_path:
primary_path = os.path.join(args.path, meta["reference"]+"/unmerged/detail/"+target_regions_bed)
if hotspots_bed and not secondary_path:
secondary_path = os.path.join(args.path, meta["reference"]+"/unmerged/detail/"+hotspots_bed)
plan_prototype = plan_json(meta, primary_path, secondary_path)
api.post("plannedexperiment", **plan_prototype)
except Exception as err:
print("Could not create plan from this zip: %s" % err)
meta_file_handle = open(args.meta_file,'w')
json.dump(meta, meta_file_handle, cls=JSONEncoder)
meta_file_handle.close()
api.patch("contentupload", args.upload_id, meta=meta)
def main():
parse = argparse.ArgumentParser()
parse.add_argument('upload_id', type=int)
parse.add_argument('path')
parse.add_argument('upload_file')
parse.add_argument('meta_file')
try:
args = parse.parse_args()
except IOError as err:
print("ERROR: Input file error: %s" % err)
parse.print_help()
sys.exit(1)
meta_file_handle = open(args.meta_file, 'r')
meta = json.load(meta_file_handle, parse_float=Decimal)
meta_file_handle.close()
print "Uploaded file: " + os.path.basename(args.upload_file)
is_zip = zipfile.is_zipfile(args.upload_file)
if is_zip:
files = file_utils.unzip_archive(args.path, args.upload_file)
print "Compressed: Yes (zip)"
elif args.upload_file.endswith('.gz'):
print "Compressed: Yes (gzip)"
files = [os.path.basename(args.upload_file[:-3])]
cmd = 'gzip -dc %s > %s ' % (args.upload_file,
os.path.join(args.path, files[0]))
p = subprocess.Popen(cmd,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE,
shell=True)
print p.communicate()[0]
if p.returncode != 0:
sys.exit(p.returncode)
subprocess.call(cmd, shell=True)
else:
print "Compressed: No"
files = [args.upload_file]
''' Establish the upload type '''
target_regions_bed = None
hotspots_bed = None
meta['is_ampliseq'] = False
if len(files) == 1 and files[0].endswith('.bed') and meta.get(
'hotspot', False) == False:
target_regions_bed = os.path.basename(files[0])
meta['is_ampliseq'] = False
print "Content: Target regions file in BED format"
print
elif len(files) == 1 and files[0].endswith('.bed') and meta.get(
'hotspot', False) == True:
hotspots_bed = os.path.basename(files[0])
meta['is_ampliseq'] = False
print "Content: Hotspots file in BED format"
print
elif len(files) == 1 and files[0].endswith('.vcf') and meta.get(
'hotspot', False) == True:
print "Content: Hotspots file in VCF format"
print
print "Converting hotspot VCF file to BED: %s" % files[0]
print
hotspots_bed = os.path.basename(files[0]) + '.bed'
convert_command = '/usr/local/bin/tvcutils prepare_hotspots'
convert_command += ' --input-vcf %s' % os.path.join(
args.path, os.path.basename(files[0]))
convert_command += ' --output-bed %s' % os.path.join(
args.path, hotspots_bed)
convert_command += ' --reference /results/referenceLibrary/tmap-f3/%s/%s.fasta' % (
meta["reference"], meta["reference"])
convert_command += ' --filter-bypass on'
p = subprocess.Popen(convert_command,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE,
shell=True)
print p.communicate()[0]
if p.returncode != 0:
sys.exit(p.returncode)
#process = subprocess.Popen(convert_command, stderr=subprocess.STDOUT, stdout=subprocess.PIPE, shell=True)
#for line in process.communicate()[0].splitlines():
# api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id), text=line.strip())
meta['is_ampliseq'] = False
elif "plan.json" in files:
print "Content: AmpliSeq ZIP"
print
meta['is_ampliseq'] = True
plan_data = json.load(open(os.path.join(args.path, "plan.json")))
version, design, meta = ampliseq.handle_versioned_plans(
plan_data, meta)
meta['design'] = design
try:
target_regions_bed = design['plan']['designed_bed']
hotspots_bed = design['plan']['hotspot_bed']
if not meta.get("reference", None):
meta['reference'] = design['genome'].lower()
if 'design_name' in plan_data:
meta['description'] = design['design_name']
meta_file_handle = open(args.meta_file, 'w')
json.dump(meta, meta_file_handle, cls=JSONEncoder)
meta_file_handle.close()
api.patch("contentupload", args.upload_id, meta=meta)
except KeyError as err:
api.patch("contentupload",
args.upload_id,
status="Error: malformed AmpliSeq archive")
print "ERROR: Malformed AmpliSeq archive: missing json key " + str(
err)
sys.exit(1)
#api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id), text="Malformed AmpliSeq archive: missing json key "+str(err))
#raise
if target_regions_bed and target_regions_bed not in files:
api.patch("contentupload",
args.upload_id,
status="Error: malformed AmpliSeq archive")
print "ERROR: Target region file %s not present in AmpliSeq archive" % target_regions_bed
sys.exit(1)
#api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id),
# text="Malformed AmpliSeq archive: Target region file %s not present in AmpliSeq archive" % target_regions_bed)
#raise ValueError("Target region file %s not present in AmpliSeq archive" % target_regions_bed)
if hotspots_bed and hotspots_bed not in files:
api.patch("contentupload",
args.upload_id,
status="Error: malformed AmpliSeq archive")
print "ERROR: Hotspots file %s not present in AmpliSeq archive" % target_regions_bed
sys.exit(1)
#api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(args.upload_id),
# text="Malformed AmpliSeq archive: Hotspots file %s not present in AmpliSeq archive" % target_regions_bed)
#raise ValueError("Hotspots file %s not present in AmpliSeq archive" % target_regions_bed)
else:
api.patch("contentupload",
args.upload_id,
status="Error: Unrecognized upload type.")
print
print "ERROR: Unrecognized upload type. Upload must be either a valid Ampliseq ZIP or contain a single BED or VCF file."
sys.exit(1)
''' === Validate and Register === '''
primary_path = None
secondary_path = None
if target_regions_bed:
primary_path = validate(args.upload_id, args.path, meta,
target_regions_bed, 'target regions BED')
if hotspots_bed:
secondary_path = validate(args.upload_id, args.path, meta,
hotspots_bed, 'hotspots BED')
meta["hotspot"] = False
if target_regions_bed and not primary_path:
register_bed_file(args.upload_id, args.path, meta, target_regions_bed)
if hotspots_bed:
meta["hotspot"] = True
if not secondary_path:
register_bed_file(args.upload_id, args.path, meta, hotspots_bed)
if meta['is_ampliseq']:
try:
if target_regions_bed and not primary_path:
primary_path = os.path.join(
args.path, meta["reference"] + "/unmerged/detail/" +
target_regions_bed)
if hotspots_bed and not secondary_path:
secondary_path = os.path.join(
args.path,
meta["reference"] + "/unmerged/detail/" + hotspots_bed)
plan_prototype = plan_json(meta, args.upload_id, primary_path,
secondary_path)
success, response, content = api.post("plannedexperiment",
**plan_prototype)
if not success:
api.patch("contentupload",
args.upload_id,
status="Error: unable to create TS Plan")
raise Exception("Plan creation API request failed.")
except Exception as err:
print("ERROR: Could not create plan from this zip: %s" % err)
raise
meta_file_handle = open(args.meta_file, 'w')
json.dump(meta, meta_file_handle, cls=JSONEncoder)
meta_file_handle.close()
api.patch("contentupload", args.upload_id, meta=meta)
