def makePathMapper(self, reffiles, input_basedir, **kwargs):
dockerReq, _ = self.get_requirement("DockerRequirement")
try:
if dockerReq and kwargs.get("use_container"):
return DockerPathMapper(reffiles, input_basedir)
else:
return PathMapper(reffiles, input_basedir)
except OSError as e:
if e.errno == errno.ENOENT:
raise WorkflowException("Missing input file %s" % e)
def makePathMapper(self, reffiles, input_basedir, **kwargs):
dockerReq, _ = self.get_requirement("DockerRequirement")
if dockerReq and kwargs.get("use_container"):
return DockerPathMapper(reffiles, input_basedir)
else:
return PathMapper(reffiles, input_basedir)
def job(self, joborder, basedir, output_callback, use_container=True):
inputs = joborder['inputs']
Draft4Validator(self.tool['inputs']).validate(inputs)
adapter = self.tool["adapter"]
adapters = [{
"order": [-1000000],
"schema":
tool_schema_doc["properties"]["adapter"]["properties"]["baseCmd"],
"value":
adapter['baseCmd']
}]
builder = Builder()
builder.base_url = "file:" + os.path.abspath(basedir) + "/"
builder.ref_base_url = "file:" + toolpath
requirements = self.tool.get("requirements")
builder.jslib = ''
if requirements and 'expressionlib' in requirements:
for ex in requirements['expressionlib']:
builder.jslib += builder.resolve_eval(joborder, ex) + "\n"
if "args" in adapter:
for i, a in enumerate(adapter["args"]):
a = copy.copy(a)
if "order" in a:
a["order"] = [a["order"]]
else:
a["order"] = [0]
a["schema"] = tool_schema_doc["definitions"]["strOrExpr"]
adapters.append(a)
adapters.extend(
builder.adapt_inputs(self.tool['inputs'], inputs, inputs, ""))
adapters.sort(key=lambda a: a["order"])
referenced_files = filter(
lambda a: a is not None,
flatten(map(lambda a: builder.find_files(a, joborder), adapters)))
j = CommandLineProcess()
j.joborder = joborder
j.container = None
if 'stdin' in adapter:
j.stdin = flatten(
builder.adapt(
{
"value":
adapter['stdin'],
"schema":
tool_schema_doc["properties"]["adapter"]["properties"]
["stdin"]
}, joborder, None))[0]
referenced_files.append(j.stdin)
else:
j.stdin = None
if 'stdout' in adapter:
j.stdout = flatten(
builder.adapt(
{
"value":
adapter['stdout'],
"schema":
tool_schema_doc["properties"]["adapter"]["properties"]
["stdout"]
}, joborder, None))[0]
if os.path.isabs(j.stdout):
raise Exception("stdout must be a relative path")
else:
j.stdout = None
j.generatefiles = {}
for t in adapter.get("generatefiles", []):
j.generatefiles[builder.resolve_eval(
inputs, t["name"])] = builder.resolve_eval(inputs, t["value"])
d = None
if requirements:
b = requirements.get("environment")
if b:
c = b.get("container")
if use_container and c:
if c.get("type") == "docker":
d = DockerPathMapper(referenced_files, basedir)
j.container = c
if d is None:
d = PathMapper(referenced_files, basedir)
if j.stdin:
j.stdin = j.stdin if os.path.isabs(j.stdin) else os.path.join(
basedir, j.stdin)
j.command_line = flatten(
map(lambda a: builder.adapt(a, joborder, d.mapper), adapters))
j.pathmapper = d
j.collect_outputs = functools.partial(self.collect_outputs,
self.tool.get("outputs", {}),
joborder)
j.output_callback = output_callback
yield j
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