def validate(upload_id, base_path, meta, bed_file, bed_type):
print("Validating %s file: %s" % (bed_type,bed_file))
print
path_end = '/'+meta["reference"]+"/unmerged/detail/"+bed_file
data, response, raw = api.get("content", publisher_name='BED', format='json', path__endswith=path_end)
if int(data['meta']['total_count']) > 0:
if meta['is_ampliseq']:
return data['objects'][0]['file']
#api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id),
# text='Error: The file %s already exists. Please rename your file.'%bed_file)
print 'ERROR: The file %s already exists. Please rename your file.' % bed_file
sys.exit(1)
result_UD_dir = os.path.join(base_path,meta['reference'],'unmerged','detail')
result_UP_dir = os.path.join(base_path,meta['reference'],'unmerged','plain')
result_MD_dir = os.path.join(base_path,meta['reference'],'merged','detail')
result_MP_dir = os.path.join(base_path,meta['reference'],'merged','plain')
if not os.path.exists(result_UD_dir):
os.makedirs(result_UD_dir)
if not os.path.exists(result_UP_dir):
os.makedirs(result_UP_dir)
if not os.path.exists(result_MD_dir):
os.makedirs(result_MD_dir)
if not os.path.exists(result_MP_dir):
os.makedirs(result_MP_dir)
#output_log = os.path.join(base_path, bed_file+'.log')
output_json = os.path.join(base_path, bed_file+'.json')
cmd = '/usr/local/bin/tvcutils validate_bed'
cmd += ' --reference /results/referenceLibrary/tmap-f3/%s/%s.fasta' % (meta['reference'],meta['reference'])
if bed_type == 'target regions BED':
cmd += ' --target-regions-bed "%s"' % os.path.join(base_path, bed_file)
elif bed_type == 'hotspots BED':
cmd += ' --hotspots-bed "%s"' % os.path.join(base_path, bed_file)
cmd += ' --unmerged-detail-bed "%s"' % os.path.join(result_UD_dir, bed_file)
cmd += ' --unmerged-plain-bed "%s"' % os.path.join(result_UP_dir, bed_file)
cmd += ' --merged-detail-bed "%s"' % os.path.join(result_MD_dir, bed_file)
cmd += ' --merged-plain-bed "%s"' % os.path.join(result_MP_dir, bed_file)
#cmd += ' --validation-log "%s"' % output_log
cmd += ' --meta-json "%s"' % output_json
#print cmd
p = subprocess.Popen(cmd, stderr=subprocess.STDOUT, stdout=subprocess.PIPE, shell=True)
print p.communicate()[0]
#sys.stderr.write("=== -.- ===\n")
#print stdout
#print stderr
#if os.path.exists(output_log):
# for line in open(output_log):
# api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id), text=line.strip())
if os.path.exists(output_json):
with open(output_json) as json_file:
meta.update(json.load(json_file))
if p.returncode != 0:
sys.exit(p.returncode)
return None
def get(self, endpoint, data=None):
return get(VentataAPI.BASE_URL + endpoint, self.api_key, data)
def validate(upload_id, base_path, meta, bed_file, bed_type):
print("Validating %s file: %s" % (bed_type, bed_file))
print
path_end = '/' + meta["reference"] + "/unmerged/detail/" + bed_file
data, response, raw = api.get("content",
publisher_name='BED',
format='json',
path__endswith=path_end)
if int(data['meta']['total_count']) > 0:
if meta['is_ampliseq']:
return data['objects'][0]['file']
#api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id),
# text='Error: The file %s already exists. Please rename your file.'%bed_file)
print 'ERROR: The file %s already exists. Please rename your file.' % bed_file
sys.exit(1)
result_UD_dir = os.path.join(base_path, meta['reference'], 'unmerged',
'detail')
result_UP_dir = os.path.join(base_path, meta['reference'], 'unmerged',
'plain')
result_MD_dir = os.path.join(base_path, meta['reference'], 'merged',
'detail')
result_MP_dir = os.path.join(base_path, meta['reference'], 'merged',
'plain')
if not os.path.exists(result_UD_dir):
os.makedirs(result_UD_dir)
if not os.path.exists(result_UP_dir):
os.makedirs(result_UP_dir)
if not os.path.exists(result_MD_dir):
os.makedirs(result_MD_dir)
if not os.path.exists(result_MP_dir):
os.makedirs(result_MP_dir)
#output_log = os.path.join(base_path, bed_file+'.log')
output_json = os.path.join(base_path, bed_file + '.json')
cmd = '/usr/local/bin/tvcutils validate_bed'
cmd += ' --reference /results/referenceLibrary/tmap-f3/%s/%s.fasta' % (
meta['reference'], meta['reference'])
if bed_type == 'target regions BED':
cmd += ' --target-regions-bed "%s"' % os.path.join(
base_path, bed_file)
elif bed_type == 'hotspots BED':
cmd += ' --hotspots-bed "%s"' % os.path.join(base_path, bed_file)
cmd += ' --unmerged-detail-bed "%s"' % os.path.join(
result_UD_dir, bed_file)
cmd += ' --unmerged-plain-bed "%s"' % os.path.join(
result_UP_dir, bed_file)
cmd += ' --merged-detail-bed "%s"' % os.path.join(result_MD_dir, bed_file)
cmd += ' --merged-plain-bed "%s"' % os.path.join(result_MP_dir, bed_file)
#cmd += ' --validation-log "%s"' % output_log
cmd += ' --meta-json "%s"' % output_json
#print cmd
p = subprocess.Popen(cmd,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE,
shell=True)
print p.communicate()[0]
#sys.stderr.write("=== -.- ===\n")
#print stdout
#print stderr
#if os.path.exists(output_log):
# for line in open(output_log):
# api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id), text=line.strip())
if os.path.exists(output_json):
with open(output_json) as json_file:
meta.update(json.load(json_file))
if p.returncode != 0:
sys.exit(p.returncode)
return None
def get(self, endpoint, data=None): return get(VentataAPI.BASE_URL + endpoint, self.api_key, data)
def validate(upload_id, base_path, meta, bed_file, bed_type):
print("Validating %s file: %s" % (bed_type, bed_file))
print()
if meta["is_ampliseq"] and bed_file and not meta["reference"]:
print(
"ERROR: The Bed file (%s) exists without reference. Please check your ampliseq bundle "
"or contact Technical Support." % bed_file)
sys.exit(1)
path_end = "/" + meta["reference"] + "/unmerged/detail/" + bed_file
data, response, raw = api.get("content",
publisher_name="BED",
format="json",
path__endswith=path_end)
if int(data["meta"]["total_count"]) > 0:
if meta["is_ampliseq"]:
return data["objects"][0]["file"]
# api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id),
# text='Error: The file %s already exists. Please rename your file.'%bed_file)
print("ERROR: The file %s already exists. Please rename your file." %
bed_file)
sys.exit(1)
result_UD_dir = os.path.join(base_path, meta["reference"], "unmerged",
"detail")
result_UP_dir = os.path.join(base_path, meta["reference"], "unmerged",
"plain")
result_MD_dir = os.path.join(base_path, meta["reference"], "merged",
"detail")
result_MP_dir = os.path.join(base_path, meta["reference"], "merged",
"plain")
if not os.path.exists(result_UD_dir):
os.makedirs(result_UD_dir)
if not os.path.exists(result_UP_dir):
os.makedirs(result_UP_dir)
if not os.path.exists(result_MD_dir):
os.makedirs(result_MD_dir)
if not os.path.exists(result_MP_dir):
os.makedirs(result_MP_dir)
# output_log = os.path.join(base_path, bed_file+'.log')
output_json = os.path.join(base_path, bed_file + ".json")
cmd = "/usr/local/bin/tvcutils validate_bed"
cmd += " --reference /results/referenceLibrary/tmap-f3/%s/%s.fasta" % (
meta["reference"],
meta["reference"],
)
if bed_type == publisher_types.TARGET:
cmd += ' --target-regions-bed "%s"' % os.path.join(
base_path, bed_file)
elif bed_type == publisher_types.HOTSPOT:
cmd += ' --hotspots-bed "%s"' % os.path.join(base_path, bed_file)
elif bed_type == publisher_types.SSE:
cmd += ' --hotspots-bed "%s"' % os.path.join(base_path, bed_file)
cmd += ' --unmerged-detail-bed "%s"' % os.path.join(
result_UD_dir, bed_file)
cmd += ' --unmerged-plain-bed "%s"' % os.path.join(
result_UP_dir, bed_file)
cmd += ' --merged-detail-bed "%s"' % os.path.join(result_MD_dir, bed_file)
cmd += ' --merged-plain-bed "%s"' % os.path.join(result_MP_dir, bed_file)
# cmd += ' --validation-log "%s"' % output_log
cmd += ' --meta-json "%s"' % output_json
# print cmd
p = subprocess.Popen(cmd,
stderr=subprocess.STDOUT,
stdout=subprocess.PIPE,
shell=True)
print(p.communicate()[0])
# sys.stderr.write("=== -.- ===\n")
# print stdout
# print stderr
# if os.path.exists(output_log):
# for line in open(output_log):
# api.post('log', upload='/rundb/api/v1/contentupload/%s/' % str(upload_id), text=line.strip())
if os.path.exists(output_json):
with open(output_json) as json_file:
meta.update(json.load(json_file))
if p.returncode != 0:
sys.exit(p.returncode)
return None
