3 from functools import partial
7 from cwltool.draft2tool import CommandLineTool
8 import cwltool.workflow
9 from cwltool.process import get_feature, scandeps, adjustFiles, UnsupportedRequirement
10 from cwltool.load_tool import fetch_document
12 import arvados.collection
14 from .arvdocker import arv_docker_get_image
15 from .pathmapper import ArvPathMapper
17 logger = logging.getLogger('arvados.cwl-runner')
20 def __init__(self, runner, tool, job_order, enable_reuse):
21 self.arvrunner = runner
23 self.job_order = job_order
25 self.enable_reuse = enable_reuse
28 def update_pipeline_component(self, record):
31 def upload_docker(self, tool):
32 if isinstance(tool, CommandLineTool):
33 (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
35 arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid)
36 elif isinstance(tool, cwltool.workflow.Workflow):
38 self.upload_docker(s.embedded_tool)
41 def arvados_job_spec(self, *args, **kwargs):
42 self.upload_docker(self.tool)
46 workflowfiles.add(self.tool.tool["id"])
48 self.name = os.path.basename(self.tool.tool["id"])
50 def visitFiles(files, path):
54 document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"])
57 joined = urlparse.urljoin(b, u)
58 if joined not in loaded:
60 return document_loader.fetch(urlparse.urljoin(b, u))
64 sc = scandeps(uri, workflowobj,
65 set(("$import", "run")),
66 set(("$include", "$schemas", "path")),
68 adjustFiles(sc, partial(visitFiles, workflowfiles))
69 adjustFiles(self.job_order, partial(visitFiles, jobfiles))
71 keepprefix = kwargs.get("keepprefix", "")
72 workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "",
78 jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "",
81 name=os.path.basename(self.job_order.get("id", "#")),
84 adjustFiles(self.job_order, lambda p: jobmapper.mapper(p)[1])
86 if "id" in self.job_order:
87 del self.job_order["id"]
92 def done(self, record):
93 if record["state"] == "Complete":
94 if record.get("exit_code") is not None:
95 if record["exit_code"] == 33:
96 processStatus = "UnsupportedRequirement"
97 elif record["exit_code"] == 0:
98 processStatus = "success"
100 processStatus = "permanentFail"
102 processStatus = "success"
104 processStatus = "permanentFail"
109 outc = arvados.collection.Collection(record["output"])
110 with outc.open("cwl.output.json") as f:
111 outputs = json.load(f)
113 if not path.startswith("keep:"):
114 return "keep:%s/%s" % (record["output"], path)
117 adjustFiles(outputs, keepify)
118 except Exception as e:
119 logger.error("While getting final output object: %s", e)
120 self.arvrunner.output_callback(outputs, processStatus)
122 del self.arvrunner.jobs[record["uuid"]]