def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_single:
if is_thumbnail:
blocks.append({'id_str': 'thumbnail', 'datasubdir': 'thumbnail', 'jobid': None, 'status': None})
elif is_single:
blocks.append({'id_str': 'wholechip', 'datasubdir': '', 'jobid': None, 'status': None})
else:
explogblocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True)
for block in explogblocks:
rawDirectory = os.path.join(env['pathToRaw'], block['datasubdir'])
toProcess = (block['autoanalyze'] and block['analyzeearly']) or os.path.isdir(rawDirectory)
if env.get('chipBlocksOverride') and toProcess:
if env['chipBlocksOverride'] == '510':
toProcess = block['id_str'].endswith('Y0')
if toProcess:
print "block: " + str(block)
blocks.append(block)
else:
print "skip block: " + str(block)
print blocks
return blocks
def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_wholechip:
if is_thumbnail:
blocks.append({"id_str": "thumbnail", "datasubdir": "thumbnail", "jobid": None, "status": None})
elif is_wholechip:
blocks.append({"id_str": "wholechip", "datasubdir": "", "jobid": None, "status": None})
else:
explogblocks = explogparser.getBlocksFromExpLogJson(env["exp_json"], excludeThumbnail=True)
for block in explogblocks:
rawDirectory = block["datasubdir"]
print "expblock: " + str(block)
if (
(block["autoanalyze"] and block["analyzeearly"])
or os.path.isdir(os.path.join(env["pathToRaw"], rawDirectory))
or env["blockArgs"] == "fromWells"
):
print "block: " + str(block)
blocks.append(block)
print blocks
return blocks
def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_wholechip:
block = {'id_str':'',
'datasubdir':'',
'jobid':None,
'status':None}
if is_thumbnail:
block['id_str'] = 'thumbnail'
elif is_wholechip:
block['id_str'] = 'wholechip'
print block
blocks.append(block)
else:
explogblocks = explogparser.getBlocksFromExpLogJson(env['exp_json'],excludeThumbnail=True)
for block in explogblocks:
rawDirectory = block['datasubdir']
print "expblock: " + str(block)
if (block['autoanalyze'] and block['analyzeearly']) or os.path.isdir(os.path.join(env['pathToRaw'],rawDirectory)) or env['blockArgs'] == "fromWells":
print "block: " + str(block)
blocks.append(block)
return blocks
def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_wholechip:
block = {'id_str': '', 'datasubdir': '', 'jobid': None, 'status': None}
if is_thumbnail:
block['id_str'] = 'thumbnail'
elif is_wholechip:
block['id_str'] = 'wholechip'
print block
blocks.append(block)
else:
explogblocks = explogparser.getBlocksFromExpLogJson(
env['exp_json'], excludeThumbnail=True)
for block in explogblocks:
rawDirectory = block['datasubdir']
print "expblock: " + str(block)
if (block['autoanalyze']
and block['analyzeearly']) or os.path.isdir(
os.path.join(
env['pathToRaw'],
rawDirectory)) or env['blockArgs'] == "fromWells":
print "block: " + str(block)
blocks.append(block)
return blocks
def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_single:
if is_thumbnail:
blocks.append({
'id_str': 'thumbnail',
'datasubdir': 'thumbnail',
'jobid': None,
'status': None
})
elif is_single:
blocks.append({
'id_str': 'wholechip',
'datasubdir': '',
'jobid': None,
'status': None
})
else:
explogblocks = explogparser.getBlocksFromExpLogJson(
env['exp_json'], excludeThumbnail=True)
for block in explogblocks:
rawDirectory = os.path.join(env['pathToRaw'], block['datasubdir'])
toProcess = (block['autoanalyze'] and
block['analyzeearly']) or os.path.isdir(rawDirectory)
if env.get('chipBlocksOverride') and toProcess:
if env['chipBlocksOverride'] == '510':
toProcess = block['id_str'].endswith('Y0')
if toProcess:
print "block: " + str(block)
blocks.append(block)
else:
print "skip block: " + str(block)
print blocks
return blocks
def GetBlocksToAnalyze(env):
blocks = []
if is_thumbnail or is_single:
if is_thumbnail:
blocks.append({
"id_str": "thumbnail",
"datasubdir": "thumbnail",
"jobid": None,
"status": None,
})
elif is_single:
blocks.append({
"id_str": "wholechip",
"datasubdir": "",
"jobid": None,
"status": None
})
else:
explogblocks = explogparser.getBlocksFromExpLogJson(
env["exp_json"], excludeThumbnail=True)
for block in explogblocks:
rawDirectory = os.path.join(env["pathToRaw"], block["datasubdir"])
toProcess = (block["autoanalyze"] and
block["analyzeearly"]) or os.path.isdir(rawDirectory)
if env.get("chipBlocksOverride") and toProcess:
if env["chipBlocksOverride"] == "510":
toProcess = block["id_str"].endswith("Y0")
if toProcess:
print("block: " + str(block))
blocks.append(block)
else:
print("skip block: " + str(block))
print(blocks)
return blocks
graph_max_x = int(50 * math.ceil(0.014 * int(env['flows'])))
except:
traceback.print_exc()
graph_max_x = 400
def set_result_status(status):
try:
if os.path.exists(primary_key_file):
jobserver.updatestatus(primary_key_file, status, True)
printtime("MergeTLStatus %s\tpid %d\tpk file %s started" %
(status, os.getpid(), primary_key_file))
except:
traceback.print_exc()
blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True)
dirs = ['block_%s' % block['id_str'] for block in blocks]
if not is_composite:
dirs=[]
if args.do_sigproc:
set_result_status('Merge Heatmaps')
exclusionMaskFile = 'exclusionMask_%s.txt' % env.get('chipType','').lower()
sigproc.mergeSigProcResults(
dirs,
env['SIGPROC_RESULTS'],
env['shortRunName'],
exclusionMaskFile)
try:
graph_max_x = int(50 * math.ceil(0.014 * int(env["flows"])))
except Exception:
traceback.print_exc()
graph_max_x = 400
def set_result_status(status):
try:
if os.path.exists(primary_key_file):
jobserver.updatestatus(primary_key_file, status, True)
printtime("MergeTLStatus %s\tpid %d\tpk file %s started" %
(status, os.getpid(), primary_key_file))
except Exception:
traceback.print_exc()
explogblocks = explogparser.getBlocksFromExpLogJson(env["exp_json"],
excludeThumbnail=True)
blocks_to_process = []
for block in explogblocks:
toProcess = block["autoanalyze"] and block["analyzeearly"]
if env.get("chipBlocksOverride") and toProcess:
if env["chipBlocksOverride"] == "510":
toProcess = block["id_str"].endswith("Y0")
if toProcess:
blocks_to_process.append(block)
number_of_total_blocks = len(blocks_to_process)
dirs = ["block_%s" % block["id_str"] for block in blocks_to_process]
if not is_composite:
dirs = []
if args.do_sigproc: