def set_project(self,project_config):
project_env=gb_m.loadEnv(project_config)
if project_env["DESIGN_FILE"]:
self.project_design_file=project_env["DESIGN_FILE"]
self.project_reads_base=dirname(project_env["DESIGN_FILE"])
if "ORIGINAL_READS_BASE" in project_env:
self.project_reads_base=project_env["ORIGINAL_READS_BASE"]
if project_env["PROJECT_TEAM_NAME"]: self.project_team_id=project_env["PROJECT_TEAM_NAME"]
if project_env["PROJECT_NAME"]: self.project_name=project_env["PROJECT_NAME"]
if project_env["LOG_BASE"]: self.biocore_log_base=project_env["LOG_BASE"]
if project_env["CWL_SCRIPT"]: self.project_cwl_script=project_env["CWL_SCRIPT"]
if project_env["RUN_ID"]: self.project_run_id=project_env["RUN_ID"]
if project_env["READS_BASE"]:self.scratch_reads_base=project_env["READS_BASE"]
if project_env["RESULTS_DIR"]:self.project_results_base=project_env["RESULTS_DIR"]
if project_env["PATH2_JSON_FILES"]:self.bicore_pipelinejson_dir=project_env["PATH2_JSON_FILES"]
if project_env["PIPELINE_META_BASE"]:self.bicore_pipelinemeta_dir=project_env["PIPELINE_META_BASE"]
if project_env["AWS_ACCOUNT_ID"]:self.aws_account_id=project_env["AWS_ACCOUNT_ID"]
if project_env["AWS_AGENT_ID"]:self.aws_onprem_agent_id=project_env["AWS_AGENT_ID"]
if project_env["AWS_AGENT_IP"]:self.aws_onprem_agent_ip=project_env["AWS_AGENT_IP"]
if project_env["JSON_TEMPLATE"]:
self.json_template=project_env["JSON_TEMPLATE"]
try:
with open(project_env["JSON_TEMPLATE"]) as f:
json_temp_obj=json.load(f)
for key in list(json_temp_obj.keys()):
data=json_temp_obj[key]
if isinstance(data,list):
for index,item in enumerate(data):
if isinstance(item,dict):
if "File" in item["class"]:
if isfile(str(item["path"])):self.json_template_files.append(item["path"])
elif "Directory" in item["class"]:
if isdir(str(item["location"])):self.json_template_directories.append(item["location"])
elif isinstance(data,dict):
if "File" in data["class"]:
if isfile(str(data["path"])):self.json_template_files.append(data["path"])
elif "Directory" in data["class"]:
if isdir(str(data["location"])):self.json_template_directories.append(data["location"])
else:
if isfile(str(data)):self.json_template_files.append(data)
except:pass
sys.exit()
if not isdir(source_dir):
print("ERROR: Bad source directory - see:%s " % (source_dir))
prog_usage()
sys.exit()
if not isdir(dest_dir):
print("ERROR: Bad destination directory - see:%s " % (dest_dir))
prog_usage()
sys.exit()
##reformat the input
if not source_dir.endswith("/"): source_dir += "/"
if not dest_dir.endswith("/"): dest_dir += "/"
target_dir = dest_dir
if target_dir.endswith("/"): target_dir = target_dir[:-1]
project_env = gb.loadEnv("~/.bashrc")
log_file = basename(__file__) + ".log"
if isinstance(project_env, dict) and "LOGS_BASE" in project_env:
if not isdir(project_env["LOGS_BASE"]):
gb.mkdir_p(project_env["LOGS_BASE"])
log_file = join(
project_env["LOGS_BASE"],
basename(target_dir) + "." + basename(__file__) + ".log")
## rsync the content between the source and destination directories
log = open(log_file, 'w')
log.write("**********************************\n")
log.write("**********************************\n")
log.write("Date:%s\n" % (date.today()))
print("Date:%s\n" % (date.today()))
log.write("\n")
log.write("Log file:%s\n" % (log_file))
assert False, "unhandled option"
if pipeline_config is None or not isfile(pipeline_config):
msg="ERROR: pipeline.cfg missing"
print("%s - Check %s"%(msg,pipeline_config))
prog_usage()
sys.exit()
#get project global environment variables
# variables of interest for this step:
# 1)LOG_BASE
# 2)JSON_TEMPLATE
# 3)PATH2_JSON_FILES
# 4)DESIGN_FILE
# 5)READS_BASE
# 6)RUN_ID
project_env=gb.loadEnv(pipeline_config)
if not project_env["LOG_BASE"]:
print("ERROR: Log directory missing - see:%s"%(project_env["LOG_BASE"]))
print("create the above directory and try again.")
sys.exit()
if not project_env["PATH2_JSON_FILES"]:
print("ERROR: Json files base directory missing - see:%s"%(project_env["PATH2_JSON_FILES"]))
print("create the above directory and try again.")
sys.exit()
if not project_env["ORIGINAL_READS_BASE"]:
print("ERROR: Path to Reads files is incorrect - see:%s"%(project_env["ORIGINAL_READS_BASE"]))
sys.exit()
if not isdir(project_env["LOG_BASE"]):
gb.mkdir_p(project_env["LOG_BASE"])
log_file=join(project_env["LOG_BASE"],basename(__file__)+".log")