def __init__(self, step):
self.step = step
self.tool = step.tool
self.id = step.id
self.submitted = False
self.completed = False
self.name = uniquename("step %s" % shortname(self.id))
def __init__(self, step):
self.step = step
self.tool = step.tool
self.id = step.id
self.submitted = False
self.completed = False
self.name = uniquename("step %s" % shortname(self.id))
def __init__(self, workflow, **kwargs):
self.workflow = workflow
self.tool = workflow.tool
self.steps = [WorkflowJobStep(s) for s in workflow.steps]
self.id = workflow.tool["id"]
if "outdir" in kwargs:
self.outdir = kwargs["outdir"]
elif "tmp_outdir_prefix" in kwargs:
self.outdir = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"])
else:
# tmp_outdir_prefix defaults to tmp, so this is unlikely to be used
self.outdir = tempfile.mkdtemp()
self.name = uniquename(kwargs.get("name", shortname(self.workflow.tool["id"])))
_logger.debug("[workflow %s] initialized from %s", self.name, self.tool["id"])
def job(self, joborder, input_basedir, output_callback, **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 = set((f["path"] for f in builder.files))
j = self.makeJobRunner()
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
j.name = uniquename(kwargs.get("name", str(id(j))))
_logger.debug("[job %s] initializing from %s%s",
j.name,
self.tool.get("id", ""),
" as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
_logger.debug("[job %s] %s", j.name, json.dumps(joborder, indent=4))
builder.pathmapper = None
if self.tool.get("stdin"):
j.stdin = builder.do_eval(self.tool["stdin"])
if isinstance(j.stdin, dict) and "ref" in j.stdin:
j.stdin = builder.job[j.stdin["ref"][1:]]["path"]
reffiles.add(j.stdin)
if self.tool.get("stdout"):
j.stdout = builder.do_eval(self.tool["stdout"])
if os.path.isabs(j.stdout) or ".." in j.stdout:
raise validate.ValidationException("stdout must be a relative path")
builder.pathmapper = self.makePathMapper(reffiles, input_basedir, **kwargs)
builder.requirements = j.requirements
for f in builder.files:
f["path"] = builder.pathmapper.mapper(f["path"])[1]
_logger.debug("[job %s] command line bindings is %s", j.name, json.dumps(builder.bindings, indent=4))
_logger.debug("[job %s] path mappings is %s", j.name, json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))
dockerReq, _ = self.get_requirement("DockerRequirement")
if dockerReq and kwargs.get("use_container"):
out_prefix = kwargs.get("tmp_outdir_prefix")
j.outdir = kwargs.get("outdir") or tempfile.mkdtemp(prefix=out_prefix)
tmpdir_prefix = kwargs.get('tmpdir_prefix')
j.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp(prefix=tmpdir_prefix)
else:
j.outdir = builder.outdir
j.tmpdir = builder.tmpdir
createFiles, _ = self.get_requirement("CreateFileRequirement")
j.generatefiles = {}
if createFiles:
for t in createFiles["fileDef"]:
j.generatefiles[builder.do_eval(t["filename"])] = copy.deepcopy(builder.do_eval(t["fileContent"]))
j.environment = {}
evr, _ = self.get_requirement("EnvVarRequirement")
if evr:
for t in evr["envDef"]:
j.environment[t["envName"]] = builder.do_eval(t["envValue"])
shellcmd, _ = self.get_requirement("ShellCommandRequirement")
if shellcmd:
cmd = []
for b in builder.bindings:
arg = builder.generate_arg(b)
if b.get("shellQuote", True):
arg = [shellescape.quote(a) for a in aslist(arg)]
cmd.extend(aslist(arg))
j.command_line = ["/bin/sh", "-c", " ".join(cmd)]
else:
j.command_line = flatten(map(builder.generate_arg, builder.bindings))
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 job(self, joborder, input_basedir, output_callback, **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 = set((f["path"] for f in builder.files))
j = self.makeJobRunner()
j.builder = builder
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
j.name = uniquename(kwargs.get("name", str(id(j))))
_logger.debug("[job %s] initializing from %s%s",
j.name,
self.tool.get("id", ""),
" as part of %s" % kwargs["part_of"] if "part_of" in kwargs else "")
_logger.debug("[job %s] %s", j.name, json.dumps(joborder, indent=4))
builder.pathmapper = None
if self.tool.get("stdin"):
j.stdin = builder.do_eval(self.tool["stdin"])
if isinstance(j.stdin, dict) and "ref" in j.stdin:
j.stdin = builder.job[j.stdin["ref"][1:]]["path"]
reffiles.add(j.stdin)
if self.tool.get("stdout"):
j.stdout = builder.do_eval(self.tool["stdout"])
if os.path.isabs(j.stdout) or ".." in j.stdout:
raise validate.ValidationException("stdout must be a relative path")
builder.pathmapper = self.makePathMapper(reffiles, input_basedir, **kwargs)
builder.requirements = j.requirements
# map files to assigned path inside a container. We need to also explicitly
# walk over input as implicit reassignment doesn't reach everything in builder.bindings
def _check_adjust(f):
if not f.get("containerfs"):
f["path"] = builder.pathmapper.mapper(f["path"])[1]
f["containerfs"] = True
return f
_logger.debug("[job %s] path mappings is %s", j.name, json.dumps({p: builder.pathmapper.mapper(p) for p in builder.pathmapper.files()}, indent=4))
adjustFileObjs(builder.files, _check_adjust)
adjustFileObjs(builder.bindings, _check_adjust)
_logger.debug("[job %s] command line bindings is %s", j.name, json.dumps(builder.bindings, indent=4))
dockerReq, _ = self.get_requirement("DockerRequirement")
if dockerReq and kwargs.get("use_container"):
out_prefix = kwargs.get("tmp_outdir_prefix")
j.outdir = kwargs.get("outdir") or tempfile.mkdtemp(prefix=out_prefix)
tmpdir_prefix = kwargs.get('tmpdir_prefix')
j.tmpdir = kwargs.get("tmpdir") or tempfile.mkdtemp(prefix=tmpdir_prefix)
else:
j.outdir = builder.outdir
j.tmpdir = builder.tmpdir
createFiles, _ = self.get_requirement("CreateFileRequirement")
j.generatefiles = {}
if createFiles:
for t in createFiles["fileDef"]:
j.generatefiles[builder.do_eval(t["filename"])] = copy.deepcopy(builder.do_eval(t["fileContent"]))
j.environment = {}
evr, _ = self.get_requirement("EnvVarRequirement")
if evr:
for t in evr["envDef"]:
j.environment[t["envName"]] = builder.do_eval(t["envValue"])
shellcmd, _ = self.get_requirement("ShellCommandRequirement")
if shellcmd:
cmd = []
for b in builder.bindings:
arg = builder.generate_arg(b)
if b.get("shellQuote", True):
arg = [shellescape.quote(a) for a in aslist(arg)]
cmd.extend(aslist(arg))
j.command_line = ["/bin/sh", "-c", " ".join(cmd)]
else:
j.command_line = flatten(map(builder.generate_arg, builder.bindings))
j.pathmapper = builder.pathmapper
j.collect_outputs = functools.partial(self.collect_output_ports, self.tool["outputs"], builder)
j.output_callback = output_callback
yield j
