def write_result_yaml(self):
self.parameters["processed"] = "true"
with open(os.path.join(self.LOCAL_RES_DIR, 'data.yml'), 'w') as outfile:
outfile.write(yaml.dump(self.parameters, default_flow_style=True))
path_to_zip = os.path.dirname(self.OUT_ZIP)
if not os.path.exists(path_to_zip):
os.makedirs(path_to_zip)
BiblioSpecLib.zip_dir(self.LOCAL_RES_DIR, self.OUT_ZIP)
def set_up(self, assay_library_yaml):
with open(assay_library_yaml, 'r') as stream:
self.parameters = yaml.load(stream)
self.JOB_ID = int(self.parameters["bfabric_external_job_id"])
self.LOCAL_WORK_DIR = "{}.{}".format(self.LOCAL_WORK_DIR, self.JOB_ID)
if not os.path.exists(self.LOCAL_WORK_DIR):
os.makedirs(self.LOCAL_WORK_DIR)
self.LOCAL_RES_DIR = "{}.{}".format(self.LOCAL_RES_DIR, self.JOB_ID)
if not os.path.exists(self.LOCAL_RES_DIR):
os.makedirs(self.LOCAL_RES_DIR)
self.logger = BiblioSpecLib.setUpLogging(os.path.join(self.LOCAL_RES_DIR, "fgcz_test_yaml.log"))
self.OUT_ZIP = replaceUriHeader(self.parameters["output_zip"])
self.LIST_OF_DAT_FILES = self.parameters["input_mascot_dat_file"]
self.MASCOT_DATABASE_LOCATION = self.parameters['mascot_database_location']
self.MIN_N = self.parameters['minN']
self.MAX_N = self.parameters['maxN']
self.check_dat_files()
