[ARVADOS] created: 58cf00ded1d8210a2a27257f5ec828551e66fb67
Git user
git at public.curoverse.com
Mon Aug 29 15:17:54 EDT 2016
at 58cf00ded1d8210a2a27257f5ec828551e66fb67 (commit)
commit 58cf00ded1d8210a2a27257f5ec828551e66fb67
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Fri Aug 26 17:11:50 2016 -0400
9766: Supports packing workflow, setting defaults, uploading dependent
files/docker images, creating/updating workflow record.
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 0d0d416..80734d2 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -23,6 +23,7 @@ from .arvcontainer import ArvadosContainer, RunnerContainer
from .arvjob import ArvadosJob, RunnerJob, RunnerTemplate
from .arvtool import ArvadosCommandTool
from .fsaccess import CollectionFsAccess
+from .arvworkflow import make_workflow
from cwltool.process import shortname, UnsupportedRequirement
from cwltool.pathmapper import adjustFileObjs
@@ -172,6 +173,9 @@ class ArvCwlRunner(object):
# cwltool.main will write our return value to stdout.
return tmpl.uuid
+ if kwargs.get("create_workflow") or kwargs.get("update_workflow"):
+ return make_workflow(self, tool, job_order, self.project_uuid, kwargs.get("update_workflow"))
+
self.debug = kwargs.get("debug")
self.ignore_docker_for_reuse = kwargs.get("ignore_docker_for_reuse")
@@ -335,6 +339,8 @@ def arg_parser(): # type: () -> argparse.ArgumentParser
exgroup.add_argument("--local", action="store_false", help="Run workflow on local host (submits jobs to Arvados).",
default=True, dest="submit")
exgroup.add_argument("--create-template", action="store_true", help="Create an Arvados pipeline template.")
+ exgroup.add_argument("--create-workflow", action="store_true", help="Create an Arvados workflow.")
+ exgroup.add_argument("--update-workflow", type=str, help="Update Arvados workflow.")
exgroup = parser.add_mutually_exclusive_group()
exgroup.add_argument("--wait", action="store_true", help="After submitting workflow runner job, wait for completion.",
@@ -361,7 +367,7 @@ def main(args, stdout, stderr, api_client=None):
job_order_object = None
arvargs = parser.parse_args(args)
- if arvargs.create_template and not arvargs.job_order:
+ if (arvargs.create_template or arvargs.create_workflow or arvargs.update_workflow) and not arvargs.job_order:
job_order_object = ({}, "")
try:
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
new file mode 100644
index 0000000..9a649eb
--- /dev/null
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -0,0 +1,37 @@
+import os
+import json
+
+from cwltool.pack import pack
+from cwltool.load_tool import fetch_document
+from cwltool.process import shortname
+
+from .runner import upload_docker, upload_dependencies
+
+def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
+ upload_docker(arvRunner, tool)
+
+ document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
+ print workflowobj["steps"]
+ for inp in workflowobj["inputs"]:
+ sn = shortname(inp["id"])
+ if sn in job_order:
+ inp["default"] = job_order[sn]
+
+ packed = pack(document_loader, workflowobj, uri, tool.metadata)
+
+ name = os.path.basename(tool.tool["id"])
+ upload_dependencies(arvRunner, name, document_loader,
+ packed, uri, "keep:", False)
+
+ body = {
+ "workflow": {
+ "owner_uuid": project_uuid,
+ "name": tool.tool.get("label", name),
+ "description": tool.tool.get("doc", ""),
+ "workflow":json.dumps(packed, sort_keys=True, indent=4)
+ }}
+
+ if update_uuid:
+ return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
+ else:
+ return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d7d5d2b..315be0c 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -21,6 +21,59 @@ logger = logging.getLogger('arvados.cwl-runner')
cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
+def upload_dependencies(arvrunner, name, document_loader,
+ workflowobj, uri, keepprefix, loadref_run):
+ loaded = set()
+ def loadref(b, u):
+ joined = urlparse.urljoin(b, u)
+ if joined not in loaded:
+ loaded.add(joined)
+ return document_loader.fetch(urlparse.urljoin(b, u))
+ else:
+ return {}
+
+ if loadref_run:
+ loadref_fields = set(("$import", "run"))
+ else:
+ loadref_fields = set(("$import",))
+
+ sc = scandeps(uri, workflowobj,
+ loadref_fields,
+ set(("$include", "$schemas", "path", "location")),
+ loadref)
+
+ files = []
+ def visitFiles(path):
+ files.append(path)
+
+ adjustFileObjs(sc, visitFiles)
+ adjustDirObjs(sc, visitFiles)
+
+ normalizeFilesDirs(files)
+
+ mapper = ArvPathMapper(arvrunner, files, "",
+ keepprefix+"%s",
+ keepprefix+"%s/%s",
+ name=name)
+
+ def setloc(p):
+ p["location"] = mapper.mapper(p["location"]).target
+ adjustFileObjs(workflowobj, setloc)
+ adjustDirObjs(workflowobj, setloc)
+
+ return mapper
+
+
+def upload_docker(arvrunner, tool):
+ if isinstance(tool, CommandLineTool):
+ (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
+ if docker_req:
+ arv_docker_get_image(arvrunner.api, docker_req, True, arvrunner.project_uuid)
+ elif isinstance(tool, cwltool.workflow.Workflow):
+ for s in tool.steps:
+ upload_docker(arvrunner, s.embedded_tool)
+
+
class Runner(object):
def __init__(self, runner, tool, job_order, enable_reuse):
self.arvrunner = runner
@@ -33,67 +86,26 @@ class Runner(object):
def update_pipeline_component(self, record):
pass
- def upload_docker(self, tool):
- if isinstance(tool, CommandLineTool):
- (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
- if docker_req:
- arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid)
- elif isinstance(tool, cwltool.workflow.Workflow):
- for s in tool.steps:
- self.upload_docker(s.embedded_tool)
-
-
def arvados_job_spec(self, *args, **kwargs):
- self.upload_docker(self.tool)
-
- workflowfiles = []
- jobfiles = []
- workflowfiles.append({"class":"File", "location": self.tool.tool["id"]})
+ upload_docker(self.arvrunner, self.tool)
self.name = os.path.basename(self.tool.tool["id"])
- def visitFiles(files, path):
- files.append(path)
-
- document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"])
- loaded = set()
- def loadref(b, u):
- joined = urlparse.urljoin(b, u)
- if joined not in loaded:
- loaded.add(joined)
- return document_loader.fetch(urlparse.urljoin(b, u))
- else:
- return {}
-
- sc = scandeps(uri, workflowobj,
- set(("$import", "run")),
- set(("$include", "$schemas", "path", "location")),
- loadref)
- adjustFileObjs(sc, partial(visitFiles, workflowfiles))
- adjustFileObjs(self.job_order, partial(visitFiles, jobfiles))
- adjustDirObjs(sc, partial(visitFiles, workflowfiles))
- adjustDirObjs(self.job_order, partial(visitFiles, jobfiles))
-
- normalizeFilesDirs(jobfiles)
- normalizeFilesDirs(workflowfiles)
-
- keepprefix = kwargs.get("keepprefix", "")
- workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "",
- keepprefix+"%s",
- keepprefix+"%s/%s",
- name=self.name,
- **kwargs)
-
- jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "",
- keepprefix+"%s",
- keepprefix+"%s/%s",
- name=os.path.basename(self.job_order.get("id", "#")),
- **kwargs)
-
- def setloc(p):
- p["location"] = jobmapper.mapper(p["location"])[1]
- adjustFileObjs(self.job_order, setloc)
- adjustDirObjs(self.job_order, setloc)
+ workflowmapper = upload_dependencies(self.arvrunner,
+ self.name,
+ self.tool.doc_loader,
+ self.tool.tool,
+ self.tool.tool["id"],
+ kwargs.get("keepprefix", ""),
+ True)
+
+ jobmapper = upload_dependencies(self.arvrunner,
+ os.path.basename(self.job_order.get("id", "#")),
+ self.tool.doc_loader,
+ self.job_order,
+ self.job_order.get("id", "#"),
+ kwargs.get("keepprefix", ""),
+ False)
if "id" in self.job_order:
del self.job_order["id"]
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index e22a74f..14fa045 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
# Make sure to update arvados/build/run-build-packages.sh as well
# when updating the cwltool version pin.
install_requires=[
- 'cwltool==1.0.20160811184335',
+ 'cwltool==1.0.20160826210233',
'arvados-python-client>=0.1.20160714204738',
],
data_files=[
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