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- def parseSubJob(subjobopt,clusterjob):
- #subjobvars={};
- commasplit=subjobopt.split(",");
- for commaItem in commasplit:
- eqsplit=commaItem.split("=")
- print("split on equal sign: %s" % eqsplit)
- if (len(eqsplit)!=2):
- raise PipelineError("[PipelineTemplateGenerator.parseVars] invalid argument syntax! should have 2 elements separated by '=', have: %d" % len(eqsplit));
- attrib_name=eqsplit[0]
- attrib_val=eqsplit[1]
- print("attrib_name:")
- print(attrib_name)
- print("attrib_val:")
- print(attrib_val)
- if attrib_name is "order_after":
- print("found order_after!!!");
- print("parsing: %s" % attrib_val);
- if ':' in attrib_val:
- arr=attrib_val.split(":");
- print("split order after: %s" % arr);
- clusterjob.order_after.append(arr);
- else:
- print("order after: %s" % attrib_val);
- clusterjob.order_after.append(attrib_val);
- elif attrib_name is "cmd":
- print("found cmd!!!");
- print("split cmd: %s" % attrib_val);
- clusterjob.cmd.append(attrib_val);
- else:
- print("found %s!!!" % attrib_name)
- setattr(clusterjob, attrib_name, attrib_val)
- if clusterjob.module is None:
- clusterjob.module=BiotoolsSettings.getValue("MODULEFILE")
- if clusterjob.directory is None:
- clusterjob.directory=BiotoolsSettings.getValue("CURDIR")
- if clusterjob.queue is None:
- clusterjob.queue=BiotoolsSettings.getValue("JOBQUEUE")
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