def make_builder(joborder, hints, requirements, runtimeContext, metadata):
return Builder(
job=joborder,
files=[], # type: List[Dict[Text, Text]]
bindings=[], # type: List[Dict[Text, Any]]
schemaDefs={}, # type: Dict[Text, Dict[Text, Any]]
names=None, # type: Names
requirements=requirements, # type: List[Dict[Text, Any]]
hints=hints, # type: List[Dict[Text, Any]]
resources={}, # type: Dict[str, int]
mutation_manager=None, # type: Optional[MutationManager]
formatgraph=None, # type: Optional[Graph]
make_fs_access=None, # type: Type[StdFsAccess]
fs_access=None, # type: StdFsAccess
job_script_provider=runtimeContext.
job_script_provider, # type: Optional[Any]
timeout=runtimeContext.eval_timeout, # type: float
debug=runtimeContext.debug, # type: bool
js_console=runtimeContext.js_console, # type: bool
force_docker_pull=runtimeContext.force_docker_pull, # type: bool
loadListing="", # type: Text
outdir="", # type: Text
tmpdir="", # type: Text
stagedir="", # type: Text
cwlVersion=metadata.get(
"http://commonwl.org/cwltool#original_cwlVersion")
or metadata.get("cwlVersion"),
container_engine="docker")
def _makebuilder(cudaReq: CWLObjectType) -> Builder:
return Builder(
{},
[],
[],
{},
schema.Names(),
[cudaReq],
[],
{"cudaDeviceCount": 1},
None,
None,
StdFsAccess,
StdFsAccess(""),
None,
0.1,
False,
False,
False,
"",
"",
"",
"",
INTERNAL_VERSION,
"docker",
)
def job(self, joborder, output_callback, runtimeContext):
req, _ = self.get_requirement(
"http://arvados.org/cwl#RunInSingleContainer")
if req:
with SourceLine(self.tool, None, WorkflowException,
logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" %
(self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader,
self.doc_loader.fetch(
self.tool["id"]),
self.tool["id"])
discover_secondary_files(self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
document_loader, joborder,
joborder.get("id", "#"), False)
if self.wf_pdh is None:
workflowobj["requirements"] = dedup_reqs(self.requirements)
workflowobj["hints"] = dedup_reqs(self.hints)
packed = pack(document_loader, workflowobj, uri,
self.metadata)
builder = Builder(joborder,
requirements=workflowobj["requirements"],
hints=workflowobj["hints"],
resources={})
def visit(item):
for t in ("hints", "requirements"):
if t not in item:
continue
for req in item[t]:
if req["class"] == "ResourceRequirement":
dyn = False
for k in max_res_pars + sum_res_pars:
if k in req:
if isinstance(req[k], basestring):
if item["id"] == "#main":
# only the top-level requirements/hints may contain expressions
self.dynamic_resource_req.append(
req)
dyn = True
break
else:
with SourceLine(
req, k,
WorkflowException):
raise WorkflowException(
"Non-top-level ResourceRequirement in single container cannot have expressions"
)
if not dyn:
self.static_resource_req.append(req)
visit_class(packed["$graph"],
("Workflow", "CommandLineTool"), visit)
if self.static_resource_req:
self.static_resource_req = [
get_overall_res_req(self.static_resource_req)
]
upload_dependencies(self.arvrunner, runtimeContext.name,
document_loader, packed, uri, False)
# Discover files/directories referenced by the
# workflow (mainly "default" values)
visit_class(packed, ("File", "Directory"),
self.wf_reffiles.append)
if self.dynamic_resource_req:
builder = Builder(joborder,
requirements=self.requirements,
hints=self.hints,
resources={})
# Evaluate dynamic resource requirements using current builder
rs = copy.copy(self.static_resource_req)
for dyn_rs in self.dynamic_resource_req:
eval_req = {"class": "ResourceRequirement"}
for a in max_res_pars + sum_res_pars:
if a in dyn_rs:
eval_req[a] = builder.do_eval(dyn_rs[a])
rs.append(eval_req)
job_res_reqs = [get_overall_res_req(rs)]
else:
job_res_reqs = self.static_resource_req
with Perf(metrics, "subworkflow adjust"):
joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
reffiles = []
visit_class(joborder_keepmount, ("File", "Directory"),
reffiles.append)
mapper = ArvPathMapper(self.arvrunner,
reffiles + self.wf_reffiles,
runtimeContext.basedir, "/keep/%s",
"/keep/%s/%s")
# For containers API, we need to make sure any extra
# referenced files (ie referenced by the workflow but
# not in the inputs) are included in the mounts.
if self.wf_reffiles:
runtimeContext = runtimeContext.copy()
runtimeContext.extra_reffiles = copy.deepcopy(
self.wf_reffiles)
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException,
logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException(
"%s object is missing required 'location' field: %s"
% (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException,
logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(
obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException(
"Location is not a keep reference or a literal: '%s'"
% obj["location"])
visit_class(joborder_keepmount, ("File", "Directory"),
keepmount)
def resolved(obj):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(
obj["location"]).resolved
visit_class(joborder_resolved, ("File", "Directory"), resolved)
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
adjustDirObjs(packed, keepmount)
self.wf_pdh = upload_workflow_collection(
self.arvrunner, shortname(self.tool["id"]), packed)
wf_runner = cmap({
"class":
"CommandLineTool",
"baseCommand":
"cwltool",
"inputs":
self.tool["inputs"],
"outputs":
self.tool["outputs"],
"stdout":
"cwl.output.json",
"requirements":
self.requirements + job_res_reqs +
[{
"class": "InlineJavascriptRequirement"
}, {
"class":
"InitialWorkDirRequirement",
"listing": [{
"entryname":
"workflow.cwl",
"entry":
'$({"class": "File", "location": "keep:%s/workflow.cwl"})'
% self.wf_pdh
}, {
"entryname":
"cwl.input.yml",
"entry":
json.dumps(joborder_keepmount,
indent=2,
sort_keys=True,
separators=(',', ': ')).replace(
"\\", "\\\\").replace(
'$(', '\$(').replace('${', '\${')
}]
}],
"hints":
self.hints,
"arguments": [
"--no-container", "--move-outputs",
"--preserve-entire-environment", "workflow.cwl#main",
"cwl.input.yml"
],
"id":
"#"
})
return ArvadosCommandTool(self.arvrunner, wf_runner,
self.loadingContext).job(
joborder_resolved, output_callback,
runtimeContext)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback,
runtimeContext)
def test_docker_tmpdir_prefix(tmp_path: Path) -> None:
"""Test that DockerCommandLineJob respects temp directory directives."""
(tmp_path / "3").mkdir()
tmpdir_prefix = str(tmp_path / "3" / "ttmp")
runtime_context = RuntimeContext({
"tmpdir_prefix": tmpdir_prefix,
"user_space_docker_cmd": None
})
builder = Builder(
{},
[],
[],
{},
schema.Names(),
[],
[],
{},
None,
None,
StdFsAccess,
StdFsAccess(""),
None,
0.1,
False,
False,
False,
"",
runtime_context.get_outdir(),
runtime_context.get_tmpdir(),
runtime_context.get_stagedir(),
INTERNAL_VERSION,
)
job = DockerCommandLineJob(builder, {}, PathMapper, [], [], "")
runtime: List[str] = []
volume_writable_file = MapperEnt(resolved=get_data("tests/2.fastq"),
target="foo",
type=None,
staged=None)
(tmp_path / "1").mkdir()
job.add_writable_file_volume(runtime, volume_writable_file, None,
str(tmp_path / "1" / "writable_file"))
children = sorted((tmp_path / "1").glob("*"))
assert len(children) == 1
subdir = tmp_path / children[0]
assert subdir.name.startswith("writable_file")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "2.fastq").exists()
resolved_writable_dir = tmp_path / "data_orig"
resolved_writable_dir.mkdir(parents=True)
volume_dir = MapperEnt(resolved=str(resolved_writable_dir),
target="bar",
type=None,
staged=None)
(tmp_path / "2").mkdir()
job.add_writable_directory_volume(runtime, volume_dir, None,
str(tmp_path / "2" / "dir"))
children = sorted((tmp_path / "2").glob("*"))
assert len(children) == 1
subdir = tmp_path / "2" / children[0]
assert subdir.name.startswith("dir")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "data_orig").exists()
cidfile = job.create_runtime({}, runtime_context)[1]
assert cidfile and cidfile.startswith(tmpdir_prefix)
volume_file = MapperEnt(resolved="Hoopla!",
target="baz",
type=None,
staged=None)
(tmp_path / "4").mkdir()
job.create_file_and_add_volume(runtime, volume_file, None, None,
str(tmp_path / "4" / "file"))
children = sorted((tmp_path / "4").glob("*"))
assert len(children) == 1
subdir = tmp_path / "4" / children[0]
assert subdir.name.startswith("file")
assert len(sorted(subdir.glob("*"))) == 1
assert (subdir / "baz").exists()
def job(self, joborder, output_callback, runtimeContext):
req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
if req:
with SourceLine(self.tool, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "id" not in self.tool:
raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
discover_secondary_files(self.tool["inputs"], joborder)
with Perf(metrics, "subworkflow upload_deps"):
upload_dependencies(self.arvrunner,
os.path.basename(joborder.get("id", "#")),
document_loader,
joborder,
joborder.get("id", "#"),
False)
if self.wf_pdh is None:
workflowobj["requirements"] = dedup_reqs(self.requirements)
workflowobj["hints"] = dedup_reqs(self.hints)
packed = pack(document_loader, workflowobj, uri, self.metadata)
builder = Builder(joborder,
requirements=workflowobj["requirements"],
hints=workflowobj["hints"],
resources={})
def visit(item):
for t in ("hints", "requirements"):
if t not in item:
continue
for req in item[t]:
if req["class"] == "ResourceRequirement":
dyn = False
for k in max_res_pars + sum_res_pars:
if k in req:
if isinstance(req[k], basestring):
if item["id"] == "#main":
# only the top-level requirements/hints may contain expressions
self.dynamic_resource_req.append(req)
dyn = True
break
else:
with SourceLine(req, k, WorkflowException):
raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions")
if not dyn:
self.static_resource_req.append(req)
visit_class(packed["$graph"], ("Workflow", "CommandLineTool"), visit)
if self.static_resource_req:
self.static_resource_req = [get_overall_res_req(self.static_resource_req)]
upload_dependencies(self.arvrunner,
runtimeContext.name,
document_loader,
packed,
uri,
False)
# Discover files/directories referenced by the
# workflow (mainly "default" values)
visit_class(packed, ("File", "Directory"), self.wf_reffiles.append)
if self.dynamic_resource_req:
builder = Builder(joborder,
requirements=self.requirements,
hints=self.hints,
resources={})
# Evaluate dynamic resource requirements using current builder
rs = copy.copy(self.static_resource_req)
for dyn_rs in self.dynamic_resource_req:
eval_req = {"class": "ResourceRequirement"}
for a in max_res_pars + sum_res_pars:
if a in dyn_rs:
eval_req[a] = builder.do_eval(dyn_rs[a])
rs.append(eval_req)
job_res_reqs = [get_overall_res_req(rs)]
else:
job_res_reqs = self.static_resource_req
with Perf(metrics, "subworkflow adjust"):
joborder_resolved = copy.deepcopy(joborder)
joborder_keepmount = copy.deepcopy(joborder)
reffiles = []
visit_class(joborder_keepmount, ("File", "Directory"), reffiles.append)
mapper = ArvPathMapper(self.arvrunner, reffiles+self.wf_reffiles, runtimeContext.basedir,
"/keep/%s",
"/keep/%s/%s")
# For containers API, we need to make sure any extra
# referenced files (ie referenced by the workflow but
# not in the inputs) are included in the mounts.
if self.wf_reffiles:
runtimeContext = runtimeContext.copy()
runtimeContext.extra_reffiles = copy.deepcopy(self.wf_reffiles)
def keepmount(obj):
remove_redundant_fields(obj)
with SourceLine(obj, None, WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if "location" not in obj:
raise WorkflowException("%s object is missing required 'location' field: %s" % (obj["class"], obj))
with SourceLine(obj, "location", WorkflowException, logger.isEnabledFor(logging.DEBUG)):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).target
if "listing" in obj:
del obj["listing"]
elif obj["location"].startswith("_:"):
del obj["location"]
else:
raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
visit_class(joborder_keepmount, ("File", "Directory"), keepmount)
def resolved(obj):
if obj["location"].startswith("keep:"):
obj["location"] = mapper.mapper(obj["location"]).resolved
visit_class(joborder_resolved, ("File", "Directory"), resolved)
if self.wf_pdh is None:
adjustFileObjs(packed, keepmount)
adjustDirObjs(packed, keepmount)
self.wf_pdh = upload_workflow_collection(self.arvrunner, shortname(self.tool["id"]), packed)
wf_runner = cmap({
"class": "CommandLineTool",
"baseCommand": "cwltool",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"requirements": self.requirements+job_res_reqs+[
{"class": "InlineJavascriptRequirement"},
{
"class": "InitialWorkDirRequirement",
"listing": [{
"entryname": "workflow.cwl",
"entry": '$({"class": "File", "location": "keep:%s/workflow.cwl"})' % self.wf_pdh
}, {
"entryname": "cwl.input.yml",
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"hints": self.hints,
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})
return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
else:
return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
