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: