def check_module(config, modname, indent=''):
""" Check module """
cnts = [0] * NUMCNTS
print "%sChecking module %s..." % (indent, modname)
moddict = config[pfwdefs.SW_MODULESECT][modname]
dataobjs = {pfwdefs.SW_INPUTS: {}, pfwdefs.SW_OUTPUTS: {}}
# check that have wrappername (required)
if pfwdefs.SW_WRAPPERNAME not in moddict and \
not miscutils.convertBool(moddict[pfwdefs.PF_NOOP]):
error(indent+' ', "module %s - missing %s value" % (modname, pfwdefs.SW_WRAPPERNAME))
cnts[ERRCNT_POS] += 1
# check that have at least 1 exec section (required)
execsects = intgmisc.get_exec_sections(moddict, pfwdefs.SW_EXECPREFIX)
if not execsects and not miscutils.convertBool(moddict[pfwdefs.PF_NOOP]):
error(indent+' ', "module %s - 0 exec sections (%s*)" % (modname, pfwdefs.SW_EXECPREFIX))
cnts[ERRCNT_POS] += 1
else:
# check exec sections
for xsectname in execsects:
xsectdict = moddict[xsectname]
cnts2 = check_exec(config, modname, dataobjs, xsectname, xsectdict, indent+" ")
cnts = [x + y for x, y in zip(cnts, cnts2)] # increment counts
# check file/list sections
cnts2 = check_dataobjs(config, modname, moddict, dataobjs, indent+" ")
cnts = [x + y for x, y in zip(cnts, cnts2)] # increment counts
return cnts
def determine_status(self):
""" Check all task status to determine wrapper status """
status = 0
execs = intgmisc.get_exec_sections(self.inputwcl,
intgdefs.IW_EXEC_PREFIX)
if miscutils.fwdebug_check(6, 'BASICWRAP_DEBUG'):
miscutils.fwdebug_print(f"INFO: exec sections = {execs}",
WRAPPER_OUTPUT_PREFIX)
for ekey in sorted(execs.keys()):
if ekey in self.outputwcl:
if 'task_info' in self.outputwcl[ekey]:
for taskd in self.outputwcl[ekey]['task_info'].values():
if 'status' in taskd:
if taskd['status'] != 0:
status = taskd['status']
else:
if miscutils.fwdebug_check(3, "BASICWRAP_DEBUG"):
miscutils.fwdebug_print(
f"WARN: Missing status in outputwcl task_info for {ekey}",
WRAPPER_OUTPUT_PREFIX)
status = 1
else:
if miscutils.fwdebug_check(3, "BASICWRAP_DEBUG"):
miscutils.fwdebug_print(
f"WARN: Missing task_info in outputwcl for {ekey}",
WRAPPER_OUTPUT_PREFIX)
status = 1
else:
status = 1
return status
def run_wrapper(self):
""" Workflow for this wrapper """
if miscutils.fwdebug_check(3, 'BASICWRAP_DEBUG'):
miscutils.fwdebug_print("INFO: Begin", WRAPPER_OUTPUT_PREFIX)
self.outputwcl['wrapper']['start_time'] = time.time()
try:
execs = intgmisc.get_exec_sections(self.inputwcl,
intgdefs.IW_EXEC_PREFIX)
if miscutils.fwdebug_check(6, 'BASICWRAP_DEBUG'):
miscutils.fwdebug_print(f"INFO: exec sections = {execs}",
WRAPPER_OUTPUT_PREFIX)
for ekey, iw_exec in sorted(execs.items()):
ow_exec = {'task_info': {}}
self.outputwcl[ekey] = ow_exec
self.curr_exec = ow_exec
self.transform_inputs(iw_exec)
inputs = self.check_inputs(ekey)
self.check_command_line(ekey, iw_exec)
self.save_exec_version(iw_exec)
self.create_command_line(ekey, iw_exec)
self.create_output_dirs(iw_exec)
self.run_exec()
self.transform_outputs(iw_exec)
outexist = self.check_outputs(ekey, ow_exec['status'])
self.save_outputs_by_section(ekey, outexist)
self.save_provenance(ekey, iw_exec, inputs, outexist,
ow_exec['status'])
ow_exec['status'] = 0
self.cleanup()
self.outputwcl['wrapper']['status'] = self.determine_status()
except SystemExit as e:
miscutils.fwdebug_print(
f"INFO: wrapper called sys.exit ({str(e)}). Halting.",
WRAPPER_OUTPUT_PREFIX)
self.outputwcl['wrapper']['status'] = int(str(e))
self.end_all_tasks(1)
except Exception:
(exc_type, exc_value, exc_trback) = sys.exc_info()
traceback.print_exception(exc_type,
exc_value,
exc_trback,
file=sys.stdout)
self.outputwcl['wrapper']['status'] = 1
self.end_all_tasks(1)
if miscutils.fwdebug_check(6, 'BASICWRAP_DEBUG'):
miscutils.fwdebug_print(
f"INFO: outputwcl[intgdefs.OW_OUTPUTS_BY_SECT]={self.outputwcl[intgdefs.OW_OUTPUTS_BY_SECT]}",
WRAPPER_OUTPUT_PREFIX)
for fsname, fssect in self.outputwcl[
intgdefs.OW_OUTPUTS_BY_SECT].items():
if miscutils.fwdebug_check(6, 'BASICWRAP_DEBUG'):
miscutils.fwdebug_print(
f"INFO: making string for sect {fsname}: {fssect}",
WRAPPER_OUTPUT_PREFIX)
for exname, exlist in fssect.items():
self.outputwcl[intgdefs.OW_OUTPUTS_BY_SECT][fsname][
exname] = provdefs.PROV_DELIM.join(exlist)
self.outputwcl['wrapper']['end_time'] = time.time()
miscutils.fwdebug_print(
f"INFO: end - exit status = {self.get_status()}",
WRAPPER_OUTPUT_PREFIX)