#
# SPDX-License-Identifier: Apache-2.0
+from past.builtins import basestring
+from future.utils import viewitems
+
import os
import json
import copy
import logging
+import urllib
+from io import StringIO
+import sys
+import re
+
+from typing import (MutableSequence, MutableMapping)
+
+from ruamel.yaml import YAML
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
from schema_salad.sourceline import SourceLine, cmap
+import schema_salad.ref_resolver
+
+import arvados.collection
from cwltool.pack import pack
-from cwltool.load_tool import fetch_document
-from cwltool.process import shortname
-from cwltool.workflow import Workflow, WorkflowException
-from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, visit_class
-from cwltool.builder import Builder
+from cwltool.load_tool import fetch_document, resolve_and_validate_document
+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 schema_salad.ref_resolver import file_uri, uri_file_path
import ruamel.yaml as yaml
from .runner import (upload_dependencies, packed_workflow, upload_workflow_collection,
- trim_anonymous_location, remove_redundant_fields, discover_secondary_files)
+ trim_anonymous_location, remove_redundant_fields, discover_secondary_files,
+ make_builder, arvados_jobs_image, FileUpdates)
from .pathmapper import ArvPathMapper, trim_listing
-from .arvtool import ArvadosCommandTool
+from .arvtool import ArvadosCommandTool, set_cluster_target
+from ._version import __version__
+
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
-def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
- submit_runner_ram=0, name=None, merged_map=None):
+max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
+sum_res_pars = ("outdirMin", "outdirMax")
+
+def make_wrapper_workflow(arvRunner, main, packed, project_uuid, name, git_info, tool):
+ col = arvados.collection.Collection(api_client=arvRunner.api,
+ keep_client=arvRunner.keep_client)
+
+ with col.open("workflow.json", "wt") as f:
+ json.dump(packed, f, sort_keys=True, indent=4, separators=(',',': '))
+
+ pdh = col.portable_data_hash()
+
+ toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+ if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):
+ toolname = "%s (%s)" % (toolname, git_info.get("http://arvados.org/cwl#gitDescribe"))
+
+ existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", pdh], ["owner_uuid", "=", project_uuid]]).execute(num_retries=arvRunner.num_retries)
+ if len(existing["items"]) == 0:
+ col.save_new(name=toolname, owner_uuid=project_uuid, ensure_unique_name=True)
- packed = packed_workflow(arvRunner, tool, merged_map)
+ # now construct the wrapper
+ step = {
+ "id": "#main/" + toolname,
+ "in": [],
+ "out": [],
+ "run": "keep:%s/workflow.json#main" % pdh,
+ "label": name
+ }
+
+ newinputs = []
+ for i in main["inputs"]:
+ inp = {}
+ # Make sure to only copy known fields that are meaningful at
+ # the workflow level. In practice this ensures that if we're
+ # wrapping a CommandLineTool we don't grab inputBinding.
+ # Right now also excludes extension fields, which is fine,
+ # Arvados doesn't currently look for any extension fields on
+ # input parameters.
+ for f in ("type", "label", "secondaryFiles", "streamable",
+ "doc", "id", "format", "loadContents",
+ "loadListing", "default"):
+ if f in i:
+ inp[f] = i[f]
+ newinputs.append(inp)
+
+ wrapper = {
+ "class": "Workflow",
+ "id": "#main",
+ "inputs": newinputs,
+ "outputs": [],
+ "steps": [step]
+ }
+
+ for i in main["inputs"]:
+ step["in"].append({
+ "id": "#main/step/%s" % shortname(i["id"]),
+ "source": i["id"]
+ })
+
+ for i in main["outputs"]:
+ step["out"].append({"id": "#main/step/%s" % shortname(i["id"])})
+ wrapper["outputs"].append({"outputSource": "#main/step/%s" % shortname(i["id"]),
+ "type": i["type"],
+ "id": i["id"]})
+
+ wrapper["requirements"] = [{"class": "SubworkflowFeatureRequirement"}]
+
+ if main.get("requirements"):
+ wrapper["requirements"].extend(main["requirements"])
+ if main.get("hints"):
+ wrapper["hints"] = main["hints"]
+
+ doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}
+
+ if git_info:
+ for g in git_info:
+ doc[g] = git_info[g]
+
+ return json.dumps(doc, sort_keys=True, indent=4, separators=(',',': '))
+
+
+def rel_ref(s, baseuri, urlexpander, merged_map, jobmapper):
+ if s.startswith("keep:"):
+ return s
+
+ uri = urlexpander(s, baseuri)
+
+ if uri.startswith("keep:"):
+ return uri
+
+ fileuri = urllib.parse.urldefrag(baseuri)[0]
+
+ for u in (baseuri, fileuri):
+ if u in merged_map:
+ replacements = merged_map[u].resolved
+ if uri in replacements:
+ return replacements[uri]
+
+ if uri in jobmapper:
+ return jobmapper.mapper(uri).target
+
+ p1 = os.path.dirname(uri_file_path(fileuri))
+ p2 = os.path.dirname(uri_file_path(uri))
+ p3 = os.path.basename(uri_file_path(uri))
+
+ r = os.path.relpath(p2, p1)
+ if r == ".":
+ r = ""
+
+ return os.path.join(r, p3)
+
+def is_basetype(tp):
+ basetypes = ("null", "boolean", "int", "long", "float", "double", "string", "File", "Directory", "record", "array", "enum")
+ for b in basetypes:
+ if re.match(b+"(\[\])?\??", tp):
+ return True
+ return False
+
+
+def update_refs(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)
+ elif isinstance(d, MutableMapping):
+ for field in ("id", "name"):
+ if isinstance(d.get(field), str) and d[field].startswith("_:"):
+ # blank node reference, was added in automatically, can get rid of it.
+ del d[field]
+
+ if "id" in d:
+ baseuri = urlexpander(d["id"], baseuri, scoped_id=True)
+ elif "name" in d and isinstance(d["name"], str):
+ 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)
+
+ for field in d:
+ if field in ("location", "run", "name") and isinstance(d[field], str):
+ d[field] = rel_ref(d[field], baseuri, urlexpander, merged_map, jobmapper)
+ continue
+
+ if field in ("$include", "$import") and isinstance(d[field], str):
+ d[field] = rel_ref(d[field], baseuri, urlexpander, {}, jobmapper)
+ continue
+
+ for t in ("type", "items"):
+ if (field == t and
+ isinstance(d[t], str) and
+ not is_basetype(d[t])):
+ d[t] = rel_ref(d[t], baseuri, urlexpander, merged_map, jobmapper)
+ continue
+
+ if field == "inputs" and isinstance(d["inputs"], MutableMapping):
+ for inp in d["inputs"]:
+ 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)
+ continue
+
+ 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)
+
+
+def fix_schemadef(req, baseuri, urlexpander, merged_map, jobmapper, pdh):
+ req = copy.deepcopy(req)
+
+ for f in req["types"]:
+ r = f["name"]
+ path, frag = urllib.parse.urldefrag(r)
+ rel = rel_ref(r, baseuri, urlexpander, merged_map, jobmapper)
+ merged_map.setdefault(path, FileUpdates({}, {}))
+ rename = "keep:%s/%s" %(pdh, rel)
+ for mm in merged_map:
+ merged_map[mm].resolved[r] = rename
+ return req
+
+def drop_ids(d):
+ if isinstance(d, MutableSequence):
+ for i, s in enumerate(d):
+ drop_ids(s)
+ elif isinstance(d, MutableMapping):
+ if "id" in d and d["id"].startswith("file:"):
+ del d["id"]
+
+ for field in d:
+ drop_ids(d[field])
+
+
+def upload_workflow(arvRunner, tool, job_order, project_uuid,
+ runtimeContext,
+ uuid=None,
+ submit_runner_ram=0, name=None, merged_map=None,
+ submit_runner_image=None,
+ git_info=None,
+ set_defaults=False,
+ jobmapper=None):
+
+ firstfile = None
+ workflow_files = set()
+ import_files = set()
+ include_files = set()
+
+ # The document loader index will have entries for all the files
+ # that were loaded in the process of parsing the entire workflow
+ # (including subworkflows, tools, imports, etc). We use this to
+ # get compose a list of the workflow file dependencies.
+ for w in tool.doc_loader.idx:
+ if w.startswith("file://"):
+ workflow_files.add(urllib.parse.urldefrag(w)[0])
+ if firstfile is None:
+ firstfile = urllib.parse.urldefrag(w)[0]
+ if w.startswith("import:file://"):
+ import_files.add(urllib.parse.urldefrag(w[7:])[0])
+ if w.startswith("include:file://"):
+ include_files.add(urllib.parse.urldefrag(w[8:])[0])
+
+ all_files = workflow_files | import_files | include_files
+
+ # 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.
+ n = 7
+ allmatch = True
+ if firstfile:
+ while allmatch:
+ n += 1
+ for f in all_files:
+ if len(f)-1 < n:
+ n -= 1
+ allmatch = False
+ break
+ if f[n] != firstfile[n]:
+ allmatch = False
+ break
+
+ while firstfile[n] != "/":
+ n -= 1
+
+ col = arvados.collection.Collection(api_client=arvRunner.api)
+
+ # Now go through all the files and update references to other
+ # files. We previously scanned for file dependencies, these are
+ # are passed in as merged_map.
+ #
+ # note about merged_map: we upload dependencies of each process
+ # object (CommandLineTool/Workflow) to a separate collection.
+ # That way, when the user edits something, this limits collection
+ # PDH changes to just that tool, and minimizes situations where
+ # small changes break container reuse for the whole workflow.
+ #
+ for w in workflow_files | import_files:
+ # 1. load the YAML file
+
+ text = tool.doc_loader.fetch_text(w)
+ if isinstance(text, bytes):
+ textIO = StringIO(text.decode('utf-8'))
+ else:
+ textIO = StringIO(text)
+
+ yamlloader = schema_salad.utils.yaml_no_ts()
+ result = yamlloader.load(textIO)
+
+ # If the whole document is in "flow style" it is probably JSON
+ # formatted. We'll re-export it as JSON because the
+ # ruamel.yaml round-trip mode is a lie and only preserves
+ # "block style" formatting and not "flow style" formatting.
+ export_as_json = result.fa.flow_style()
+
+ # 2. find $import, $include, $schema, run, location
+ # 3. update field value
+ update_refs(result, w, tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, "", "")
+
+ # Write the updated file to the collection.
+ with col.open(w[n+1:], "wt") as f:
+ if export_as_json:
+ json.dump(result, f, indent=4, separators=(',',': '))
+ else:
+ yamlloader.dump(result, stream=f)
+
+ # Also store a verbatim copy of the original files
+ with col.open(os.path.join("original", w[n+1:]), "wt") as f:
+ f.write(text)
+
+
+ # Upload files referenced by $include directives, these are used
+ # unchanged and don't need to be updated.
+ for w in include_files:
+ with col.open(w[n+1:], "wb") as f1:
+ with col.open(os.path.join("original", w[n+1:]), "wb") as f3:
+ with open(uri_file_path(w), "rb") as f2:
+ dat = f2.read(65536)
+ while dat:
+ f1.write(dat)
+ f3.write(dat)
+ dat = f2.read(65536)
+
+ # Now collect metadata: the collection name and git properties.
+
+ toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
+ if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):
+ toolname = "%s (%s)" % (toolname, git_info.get("http://arvados.org/cwl#gitDescribe"))
+
+ toolfile = tool.tool["id"][n+1:]
+
+ properties = {
+ "type": "workflow",
+ "arv:workflowMain": toolfile,
+ }
+
+ if git_info:
+ for g in git_info:
+ p = g.split("#", 1)[1]
+ properties["arv:"+p] = git_info[g]
+
+ # Check if a collection with the same content already exists in the target project. If so, just use that one.
+ existing = arvRunner.api.collections().list(filters=[["portable_data_hash", "=", col.portable_data_hash()],
+ ["owner_uuid", "=", arvRunner.project_uuid]]).execute(num_retries=arvRunner.num_retries)
+
+ if len(existing["items"]) == 0:
+ toolname = toolname.replace("/", " ")
+ col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties)
+ logger.info("Workflow uploaded to %s", col.manifest_locator())
+ else:
+ logger.info("Workflow uploaded to %s", existing["items"][0]["uuid"])
+
+ # Now that we've updated the workflow and saved it to a
+ # collection, we're going to construct a minimal "wrapper"
+ # workflow which consists of only of input and output parameters
+ # connected to a single step that runs the real workflow.
+
+ runfile = "keep:%s/%s" % (col.portable_data_hash(), toolfile)
+
+ step = {
+ "id": "#main/" + toolname,
+ "in": [],
+ "out": [],
+ "run": runfile,
+ "label": name
+ }
+
+ main = tool.tool
+
+ wf_runner_resources = None
+
+ hints = main.get("hints", [])
+ found = False
+ for h in hints:
+ if h["class"] == "http://arvados.org/cwl#WorkflowRunnerResources":
+ wf_runner_resources = h
+ found = True
+ break
+ if not found:
+ 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 submit_runner_ram:
+ wf_runner_resources["ramMin"] = submit_runner_ram
+
+ # Remove a few redundant fields from the "job order" (aka input
+ # object or input parameters). In the situation where we're
+ # creating or updating a workflow record, any values in the job
+ # order get copied over as default values for input parameters.
adjustDirObjs(job_order, trim_listing)
adjustFileObjs(job_order, trim_anonymous_location)
adjustDirObjs(job_order, trim_anonymous_location)
- main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
- for inp in main["inputs"]:
- sn = shortname(inp["id"])
- if sn in job_order:
- inp["default"] = job_order[sn]
+ newinputs = []
+ for i in main["inputs"]:
+ inp = {}
+ # Make sure to only copy known fields that are meaningful at
+ # the workflow level. In practice this ensures that if we're
+ # wrapping a CommandLineTool we don't grab inputBinding.
+ # Right now also excludes extension fields, which is fine,
+ # Arvados doesn't currently look for any extension fields on
+ # input parameters.
+ for f in ("type", "label", "secondaryFiles", "streamable",
+ "doc", "format", "loadContents",
+ "loadListing", "default"):
+ if f in i:
+ inp[f] = i[f]
+
+ if set_defaults:
+ sn = shortname(i["id"])
+ if sn in job_order:
+ inp["default"] = job_order[sn]
+
+ inp["id"] = "#main/%s" % shortname(i["id"])
+ newinputs.append(inp)
+
+ wrapper = {
+ "class": "Workflow",
+ "id": "#main",
+ "inputs": newinputs,
+ "outputs": [],
+ "steps": [step]
+ }
+
+ for i in main["inputs"]:
+ step["in"].append({
+ "id": "#main/step/%s" % shortname(i["id"]),
+ "source": "#main/%s" % shortname(i["id"])
+ })
+
+ for i in main["outputs"]:
+ step["out"].append({"id": "#main/step/%s" % shortname(i["id"])})
+ wrapper["outputs"].append({"outputSource": "#main/step/%s" % shortname(i["id"]),
+ "type": i["type"],
+ "id": "#main/%s" % shortname(i["id"])})
+
+ wrapper["requirements"] = [{"class": "SubworkflowFeatureRequirement"}]
+
+ if main.get("requirements"):
+ wrapper["requirements"].extend(main["requirements"])
+ if hints:
+ wrapper["hints"] = hints
+
+ # Schema definitions (this lets you define things like record
+ # types) require a special handling.
+
+ for i, r in enumerate(wrapper["requirements"]):
+ if r["class"] == "SchemaDefRequirement":
+ wrapper["requirements"][i] = fix_schemadef(r, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, col.portable_data_hash())
- if not name:
- name = tool.tool.get("label", os.path.basename(tool.tool["id"]))
+ update_refs(wrapper, main["id"], tool.doc_loader.expand_url, merged_map, jobmapper, runtimeContext, main["id"]+"#", "#main/")
- upload_dependencies(arvRunner, name, tool.doc_loader,
- packed, tool.tool["id"], False)
+ doc = {"cwlVersion": "v1.2", "$graph": [wrapper]}
- # TODO nowhere for submit_runner_ram to go.
+ if git_info:
+ for g in git_info:
+ doc[g] = git_info[g]
+
+ # Remove any lingering file references.
+ drop_ids(wrapper)
+
+ return doc
+
+
+def make_workflow_record(arvRunner, doc, name, tool, project_uuid, update_uuid):
+
+ wrappertext = json.dumps(doc, sort_keys=True, indent=4, separators=(',',': '))
body = {
"workflow": {
"name": name,
"description": tool.tool.get("doc", ""),
- "definition":yaml.round_trip_dump(packed)
+ "definition": wrappertext
}}
if project_uuid:
body["workflow"]["owner_uuid"] = project_uuid
- if uuid:
- call = arvRunner.api.workflows().update(uuid=uuid, body=body)
+ if update_uuid:
+ call = arvRunner.api.workflows().update(uuid=update_uuid, body=body)
else:
call = arvRunner.api.workflows().create(body=body)
return call.execute(num_retries=arvRunner.num_retries)["uuid"]
+
def dedup_reqs(reqs):
dedup = {}
for r in reversed(reqs):
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
-def get_max_res_req(res_reqs):
- """Take the max of a list of ResourceRequirement."""
+def get_overall_res_req(res_reqs):
+ """Take the overall of a list of ResourceRequirement,
+ i.e., the max of coresMin, coresMax, ramMin, ramMax, tmpdirMin, tmpdirMax
+ and the sum of outdirMin, outdirMax."""
- total_res_req = {}
+ all_res_req = {}
exception_msgs = []
- for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
- total_res_req[a] = []
+ for a in max_res_pars + sum_res_pars:
+ all_res_req[a] = []
for res_req in res_reqs:
if a in res_req:
if isinstance(res_req[a], int): # integer check
- total_res_req[a].append(res_req[a])
+ all_res_req[a].append(res_req[a])
else:
- msg = SourceLine(res_req).makeError(
+ msg = SourceLine(res_req, a).makeError(
"Non-top-level ResourceRequirement in single container cannot have expressions")
exception_msgs.append(msg)
if exception_msgs:
raise WorkflowException("\n".join(exception_msgs))
else:
- max_res_req = {}
- for a in total_res_req:
- if total_res_req[a]:
- max_res_req[a] = max(total_res_req[a])
- if max_res_req:
- max_res_req["class"] = "ResourceRequirement"
- return cmap(max_res_req)
+ overall_res_req = {}
+ for a in all_res_req:
+ if all_res_req[a]:
+ if a in max_res_pars:
+ overall_res_req[a] = max(all_res_req[a])
+ elif a in sum_res_pars:
+ overall_res_req[a] = sum(all_res_req[a])
+ if overall_res_req:
+ overall_res_req["class"] = "ResourceRequirement"
+ return cmap(overall_res_req)
+
+class ArvadosWorkflowStep(WorkflowStep):
+ def __init__(self,
+ toolpath_object, # type: Dict[Text, Any]
+ pos, # type: int
+ loadingContext, # type: LoadingContext
+ arvrunner,
+ *argc,
+ **argv
+ ): # type: (...) -> None
+
+ if arvrunner.fast_submit:
+ self.tool = toolpath_object
+ self.tool["inputs"] = []
+ self.tool["outputs"] = []
+ else:
+ super(ArvadosWorkflowStep, self).__init__(toolpath_object, pos, loadingContext, *argc, **argv)
+ self.tool["class"] = "WorkflowStep"
+ self.arvrunner = arvrunner
+
+ def job(self, joborder, output_callback, runtimeContext):
+ runtimeContext = runtimeContext.copy()
+ runtimeContext.toplevel = True # Preserve behavior for #13365
+
+ builder = make_builder({shortname(k): v for k,v in viewitems(joborder)}, self.hints, self.requirements,
+ runtimeContext, self.metadata)
+ runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
+ return super(ArvadosWorkflowStep, self).job(joborder, output_callback, runtimeContext)
+
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
- def __init__(self, arvrunner, toolpath_object, **kwargs):
- super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
+ def __init__(self, arvrunner, toolpath_object, loadingContext):
self.arvrunner = arvrunner
- self.work_api = kwargs["work_api"]
self.wf_pdh = None
+ 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")
- def job(self, joborder, output_callback, **kwargs):
- kwargs["work_api"] = self.work_api
- 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"])
+ def job(self, joborder, output_callback, runtimeContext):
- discover_secondary_files(self.tool["inputs"], joborder)
+ builder = make_builder(joborder, self.hints, self.requirements, runtimeContext, self.metadata)
+ runtimeContext = set_cluster_target(self.tool, self.arvrunner, builder, runtimeContext)
- 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()
- builder.job = joborder
- builder.requirements = self.requirements
- builder.hints = self.hints
- builder.resources = {}
-
- res_reqs = {"requirements": [], "hints": []}
- for t in ("requirements", "hints"):
- for item in packed["$graph"]:
- if t in item:
- if item["id"] == "#main": # evaluate potential expressions in the top-level requirements/hints
- for req in item[t]:
- if req["class"] == "ResourceRequirement":
- eval_req = {"class": "ResourceRequirement"}
- for a in ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax"):
- if a in req:
- eval_req[a] = builder.do_eval(req[a])
- res_reqs[t].append(eval_req)
- else:
- for req in item[t]:
- if req["class"] == "ResourceRequirement":
- res_reqs[t].append(req)
- max_res_req = {"requirements": get_max_res_req(res_reqs["requirements"]),
- "hints": get_max_res_req(res_reqs["hints"])}
-
- new_spec = {"requirements": self.requirements, "hints": self.hints}
- for t in ("requirements", "hints"):
- for req in new_spec[t]:
+ req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
+ if not req:
+ return super(ArvadosWorkflow, self).job(joborder, output_callback, runtimeContext)
+
+ # RunInSingleContainer is true
+
+ 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"]))
+
+ discover_secondary_files(self.arvrunner.fs_access, builder,
+ self.tool["inputs"], joborder)
+
+ normalizeFilesDirs(joborder)
+
+ with Perf(metrics, "subworkflow upload_deps"):
+ upload_dependencies(self.arvrunner,
+ os.path.basename(joborder.get("id", "#")),
+ self.doc_loader,
+ joborder,
+ joborder.get("id", "#"),
+ runtimeContext)
+
+ if self.wf_pdh is None:
+ packed = pack(self.loadingContext, self.tool["id"], loader=self.doc_loader)
+
+ for p in packed["$graph"]:
+ if p["id"] == "#main":
+ p["requirements"] = dedup_reqs(self.requirements)
+ p["hints"] = dedup_reqs(self.hints)
+
+ def visit(item):
+ if "requirements" in item:
+ item["requirements"] = [i for i in item["requirements"] if i["class"] != "DockerRequirement"]
+ for t in ("hints", "requirements"):
+ if t not in item:
+ continue
+ for req in item[t]:
if req["class"] == "ResourceRequirement":
- new_spec[t].remove(req)
- if max_res_req[t]:
- new_spec[t].append(max_res_req[t])
-
- upload_dependencies(self.arvrunner,
- kwargs.get("name", ""),
- document_loader,
- packed,
- uri,
- False)
-
- with Perf(metrics, "subworkflow adjust"):
- joborder_resolved = copy.deepcopy(joborder)
- joborder_keepmount = copy.deepcopy(joborder)
-
- reffiles = []
- visit_class(joborder_keepmount, ("File", "Directory"), lambda x: reffiles.append(x))
-
- mapper = ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
- "/keep/%s",
- "/keep/%s/%s",
- **kwargs)
-
- 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": new_spec["requirements"]+[
- {
- "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('${', '\${')
- }]
- }],
- "hints": new_spec["hints"],
- "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
- "id": "#"
- })
- kwargs["loader"] = self.doc_loader
- kwargs["avsc_names"] = self.doc_schema
- return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder_resolved, output_callback, **kwargs)
+ dyn = False
+ for k in max_res_pars + sum_res_pars:
+ if k in req:
+ if isinstance(req[k], basestring):
+ if item["id"] == "#main":
+ # only the top-level requirements/hints may contain expressions
+ self.dynamic_resource_req.append(req)
+ dyn = True
+ break
+ else:
+ with SourceLine(req, k, WorkflowException):
+ raise WorkflowException("Non-top-level ResourceRequirement in single container cannot have expressions")
+ if not dyn:
+ self.static_resource_req.append(req)
+
+ visit_class(packed["$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,
+ self.doc_loader,
+ packed,
+ self.tool["id"],
+ runtimeContext)
+
+ # Discover files/directories referenced by the
+ # workflow (mainly "default" values)
+ visit_class(packed, ("File", "Directory"), self.wf_reffiles.append)
+
+
+ if self.dynamic_resource_req:
+ # 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:
- return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)
+ 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, runtimeContext)
+
+ self.loadingContext = self.loadingContext.copy()
+ self.loadingContext.metadata = self.loadingContext.metadata.copy()
+ self.loadingContext.metadata["http://commonwl.org/cwltool#original_cwlVersion"] = "v1.0"
+
+ if len(job_res_reqs) == 1:
+ # RAM request needs to be at least 128 MiB or the workflow
+ # runner itself won't run reliably.
+ if job_res_reqs[0].get("ramMin", 1024) < 128:
+ job_res_reqs[0]["ramMin"] = 128
+
+ arguments = ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl", "cwl.input.yml"]
+ if runtimeContext.debug:
+ arguments.insert(0, '--debug')
+
+ 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": arguments,
+ "id": "#"
+ })
+ return ArvadosCommandTool(self.arvrunner, wf_runner, self.loadingContext).job(joborder_resolved, output_callback, runtimeContext)
+
+ def make_workflow_step(self,
+ toolpath_object, # type: Dict[Text, Any]
+ pos, # type: int
+ loadingContext, # type: LoadingContext
+ *argc,
+ **argv
+ ):
+ # (...) -> WorkflowStep
+ return ArvadosWorkflowStep(toolpath_object, pos, loadingContext, self.arvrunner, *argc, **argv)
projects / arvados.git / blobdiff