from cwltool.process import shortname, uniquename
from cwltool.workflow import Workflow, WorkflowException, WorkflowStep
from cwltool.utils import adjustFileObjs, adjustDirObjs, visit_class, normalizeFilesDirs
-from cwltool.context import LoadingContext
+from cwltool.context import LoadingContext, getdefault
from schema_salad.ref_resolver import file_uri, uri_file_path
from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
trim_anonymous_location, remove_redundant_fields, discover_secondary_files,
make_builder, arvados_jobs_image, FileUpdates)
+from .arvcontainer import RunnerContainer
from .pathmapper import ArvPathMapper, trim_listing
from .arvtool import ArvadosCommandTool, set_cluster_target
from ._version import __version__
from .util import common_prefix
+from .arvdocker import arv_docker_get_image
from .perf import Perf
def rel_ref(s, baseuri, urlexpander, merged_map, jobmapper):
- if s.startswith("keep:"):
+ if s.startswith("keep:") or s.startswith("arvwf:"):
return s
uri = urlexpander(s, baseuri)
def is_basetype(tp):
return _basetype_re.match(tp) is not None
-def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
+def update_refs(api, d, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix):
if isinstance(d, MutableSequence):
for i, s in enumerate(d):
if prefix and isinstance(s, str):
if s.startswith(prefix):
d[i] = replacePrefix+s[len(prefix):]
else:
- update_refs(s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+ update_refs(api, s, baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
elif isinstance(d, MutableMapping):
for field in ("id", "name"):
if isinstance(d.get(field), str) and d[field].startswith("_:"):
baseuri = urlexpander(d["name"], baseuri, scoped_id=True)
if d.get("class") == "DockerRequirement":
- dockerImageId = d.get("dockerImageId") or d.get("dockerPull")
- d["http://arvados.org/cwl#dockerCollectionPDH"] = runtimeContext.cached_docker_lookups.get(dockerImageId)
+ d["http://arvados.org/cwl#dockerCollectionPDH"] = arv_docker_get_image(api, d, False,
+ runtimeContext)
for field in d:
if field in ("location", "run", "name") and isinstance(d[field], str):
if isinstance(d["inputs"][inp], str) and not is_basetype(d["inputs"][inp]):
d["inputs"][inp] = rel_ref(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper)
if isinstance(d["inputs"][inp], MutableMapping):
- update_refs(d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+ update_refs(api, d["inputs"][inp], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
continue
+ if field in ("requirements", "hints") and isinstance(d[field], MutableMapping):
+ dr = d[field].get("DockerRequirement")
+ if dr:
+ dr["http://arvados.org/cwl#dockerCollectionPDH"] = arv_docker_get_image(api, dr, False,
+ runtimeContext)
+
if field == "$schemas":
for n, s in enumerate(d["$schemas"]):
d["$schemas"][n] = rel_ref(d["$schemas"][n], baseuri, urlexpander, merged_map, jobmapper)
continue
- update_refs(d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
+ update_refs(api, d[field], baseuri, urlexpander, merged_map, jobmapper, runtimeContext, prefix, replacePrefix)
def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh):
# Find the longest common prefix among all the file names. We'll
# use this to recreate the directory structure in a keep
# collection with correct relative references.
- prefix = common_prefix(firstfile, all_files)
+ prefix = common_prefix(firstfile, all_files) if firstfile else ""
+
col = arvados.collection.Collection(api_client=arvRunner.api)
# 2. find $import, $include, $schema, run, location
# 3. update field value
- update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
+ update_refs(arvRunner.api, result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
# Write the updated file to the collection.
with col.open(w[len(prefix):], "wt") as f:
wf_runner_resources = {"class": "http://arvados.org/cwl#WorkflowRunnerResources"}
hints.append(wf_runner_resources)
- wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner,
- submit_runner_image or "arvados/jobs:"+__version__,
- runtimeContext)
+ if "acrContainerImage" not in wf_runner_resources:
+ wf_runner_resources["acrContainerImage"] = arvados_jobs_image(arvRunner,
+ submit_runner_image or "arvados/jobs:"+__version__,
+ runtimeContext)
if submit_runner_ram:
wf_runner_resources["ramMin"] = submit_runner_ram
if r["class"] == "SchemaDefRequirement":
wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash())
- update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
+ update_refs(arvRunner.api, wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}
self.dynamic_resource_req = []
self.static_resource_req = []
self.wf_reffiles = []
- self.loadingContext = loadingContext
- super(ArvadosWorkflow, self).__init__(toolpath_object, loadingContext)
- self.cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
+ self.loadingContext = loadingContext.copy()
- def job(self, joborder, output_callback, runtimeContext):
+ self.requirements = copy.deepcopy(getdefault(loadingContext.requirements, []))
+ tool_requirements = toolpath_object.get("requirements", [])
+ self.hints = copy.deepcopy(getdefault(loadingContext.hints, []))
+ tool_hints = toolpath_object.get("hints", [])
- builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
- runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
+ workflow_runner_req, _ = self.get_requirement("http://arvados.org/cwl#WorkflowRunnerResources")
+ if workflow_runner_req and workflow_runner_req.get("acrContainerImage"):
+ self.loadingContext.default_docker_image = workflow_runner_req.get("acrContainerImage")
- req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
- if not req:
- return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
+ super(ArvadosWorkflow, self).__init__(toolpath_object, self.loadingContext)
+ self.cluster_target_req, _ = self.get_requirement("http://arvados.org/cwl#ClusterTarget")
- # RunInSingleContainer is true
+ def runInSingleContainer(self, joborder, output_callback, runtimeContext, builder):
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"]))
})
return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
+
+ def separateRunner(self, joborder, output_callback, runtimeContext, req, builder):
+
+ name = runtimeContext.name
+
+ rpn = req.get("runnerProcessName")
+ if rpn:
+ name = builder.do_eval(rpn)
+
+ return RunnerContainer(self.arvrunner,
+ self,
+ self.loadingContext,
+ runtimeContext.enable_reuse,
+ None,
+ None,
+ submit_runner_ram=runtimeContext.submit_runner_ram,
+ name=name,
+ on_error=runtimeContext.on_error,
+ submit_runner_image=runtimeContext.submit_runner_image,
+ intermediate_output_ttl=runtimeContext.intermediate_output_ttl,
+ merged_map=None,
+ priority=runtimeContext.priority,
+ secret_store=self.arvrunner.secret_store,
+ collection_cache_size=runtimeContext.collection_cache_size,
+ collection_cache_is_default=self.arvrunner.should_estimate_cache_size,
+ git_info=runtimeContext.git_info,
+ reuse_runner=True).job(joborder, output_callback, runtimeContext)
+
+
+ def job(self, joborder, output_callback, runtimeContext):
+
+ builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
+ runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
+
+ req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
+ if req:
+ return self.runInSingleContainer(joborder, output_callback, runtimeContext, builder)
+
+ req, _ = self.get_requirement("http://arvados.org/cwl#SeparateRunner")
+ if req:
+ return self.separateRunner(joborder, output_callback, runtimeContext, req, builder)
+
+ return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
+
+
def make_workflow_step(self,
toolpath_object, # type: Dict[Text, Any]
pos, # type: int
projects / arvados.git / blobdiff