def job(self,
joborder,
basedir,
output_callback,
use_container=True,
**kwargs):
builder = self._init_job(joborder, basedir, **kwargs)
if self.tool["baseCommand"]:
for n, b in enumerate(aslist(self.tool["baseCommand"])):
builder.bindings.append({
"position": [-1000000, n],
"valueFrom": b
})
if self.tool.get("arguments"):
for i, a in enumerate(self.tool["arguments"]):
if isinstance(a, dict):
a = copy.copy(a)
if a.get("position"):
a["position"] = [a["position"], i]
else:
a["position"] = [0, i]
a["do_eval"] = a["valueFrom"]
a["valueFrom"] = None
builder.bindings.append(a)
else:
builder.bindings.append({
"position": [0, i],
"valueFrom": a
})
builder.bindings.sort(key=lambda a: a["position"])
_logger.debug(pprint.pformat(builder.bindings))
_logger.debug(pprint.pformat(builder.files))
reffiles = [f["path"] for f in builder.files]
j = CommandLineJob()
j.joborder = builder.job
j.stdin = None
j.stdout = None
builder.pathmapper = None
if self.tool.get("stdin"):
j.stdin = self.tool["stdin"]
if isinstance(j.stdin, dict) and "ref" in j.stdin:
j.stdin = builder.job[j.stdin["ref"][1:]]["path"]
reffiles.append(j.stdin)
if self.tool.get("stdout"):
if isinstance(self.tool["stdout"],
dict) and "ref" in self.tool["stdout"]:
for out in self.tool.get("outputs", []):
if out["id"] == self.tool["stdout"]["ref"]:
filename = self.tool["stdout"]["ref"][1:]
j.stdout = filename
out["outputBinding"] = out.get("outputBinding", {})
out["outputBinding"]["glob"] = filename
if not j.stdout:
raise Exception("stdout refers to invalid output")
else:
j.stdout = self.tool["stdout"]
if os.path.isabs(j.stdout):
raise Exception("stdout must be a relative path")
j.requirements = self.requirements
j.hints = self.hints
for r in (j.requirements + j.hints):
if r["class"] == "DockerRequirement" and use_container:
builder.pathmapper = DockerPathMapper(reffiles, basedir)
if builder.pathmapper is None:
builder.pathmapper = PathMapper(reffiles, basedir)
for f in builder.files:
f["path"] = builder.pathmapper.mapper(f["path"])
builder.requirements = j.requirements
j.generatefiles = {}
for t in self.tool.get("fileDefs", []):
j.generatefiles[t["filename"]] = expression.do_eval(
t["value"], builder.job, j.requirements, self.docpath)
j.environment = {}
for t in self.tool.get("environmentDefs", []):
j.environment[t["env"]] = expression.do_eval(
t["value"], builder.job, j.requirements, self.docpath)
j.command_line = flatten(map(builder.generate_arg, builder.bindings))
if j.stdin:
j.stdin = j.stdin if os.path.isabs(j.stdin) else os.path.join(
basedir, j.stdin)
j.pathmapper = builder.pathmapper
j.collect_outputs = functools.partial(self.collect_output_ports,
self.tool["outputs"], builder)
j.output_callback = output_callback
yield j
def makeJobRunner(self):
return CommandLineJob()
def job(self, joborder, input_basedir, output_callback, use_container=True, **kwargs):
builder = self._init_job(joborder, input_basedir, **kwargs)
if self.tool["baseCommand"]:
for n, b in enumerate(aslist(self.tool["baseCommand"])):
builder.bindings.append({
"position": [-1000000, n],
"valueFrom": b
})
if self.tool.get("arguments"):
for i, a in enumerate(self.tool["arguments"]):
if isinstance(a, dict):
a = copy.copy(a)
if a.get("position"):
a["position"] = [a["position"], i]
else:
a["position"] = [0, i]
a["do_eval"] = a["valueFrom"]
a["valueFrom"] = None
builder.bindings.append(a)
else:
builder.bindings.append({
"position": [0, i],
"valueFrom": a
})
builder.bindings.sort(key=lambda a: a["position"])
reffiles = [f["path"] for f in builder.files]
j = CommandLineJob()
j.joborder = builder.job
j.stdin = None
j.stdout = None
j.successCodes = self.tool.get("successCodes")
j.temporaryFailCodes = self.tool.get("temporaryFailCodes")
j.permanentFailCodes = self.tool.get("permanentFailCodes")
j.requirements = self.requirements
j.hints = self.hints
builder.pathmapper = None
if self.tool.get("stdin"):
j.stdin = expression.do_eval(self.tool["stdin"], builder.job, self.requirements, self.docpath, j.stdin)
if isinstance(j.stdin, dict) and "ref" in j.stdin:
j.stdin = builder.job[j.stdin["ref"][1:]]["path"]
reffiles.append(j.stdin)
if self.tool.get("stdout"):
j.stdout = expression.do_eval(self.tool["stdout"], builder.job, j.requirements, self.docpath)
if os.path.isabs(j.stdout):
raise validate.ValidationException("stdout must be a relative path")
dockerReq, _ = get_feature("DockerRequirement", requirements=self.requirements, hints=self.hints)
if dockerReq and use_container:
builder.pathmapper = DockerPathMapper(reffiles, input_basedir)
if builder.pathmapper is None:
builder.pathmapper = PathMapper(reffiles, input_basedir)
for f in builder.files:
f["path"] = builder.pathmapper.mapper(f["path"])[1]
_logger.debug("Bindings is %s", pprint.pformat(builder.bindings))
_logger.debug("Files is %s", pprint.pformat({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}))
builder.requirements = j.requirements
j.generatefiles = {}
createFiles, _ = get_feature("CreateFileRequirement", requirements=self.requirements, hints=self.hints)
if createFiles:
for t in createFiles["fileDef"]:
j.generatefiles[t["filename"]] = expression.do_eval(t["fileContent"], builder.job, j.requirements, self.docpath)
j.environment = {}
evr, _ = get_feature("EnvVarRequirement", requirements=self.requirements, hints=self.hints)
if evr:
for t in evr["envDef"]:
j.environment[t["envName"]] = expression.do_eval(t["envValue"], builder.job, j.requirements, self.docpath)
j.command_line = flatten(map(builder.generate_arg, builder.bindings))
if j.stdin:
j.stdin = j.stdin if os.path.isabs(j.stdin) else os.path.join(input_basedir, j.stdin)
j.pathmapper = builder.pathmapper
j.collect_outputs = functools.partial(self.collect_output_ports, self.tool["outputs"], builder)
j.output_callback = output_callback
yield j