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
27 def update_pipeline_component(self, record):
30 def upload_docker(self, tool):
31 if isinstance(tool, CommandLineTool):
32 (docker_req, docker_is_req) = get_feature(tool, "DockerRequirement")
34 arv_docker_get_image(self.arvrunner.api, docker_req, True, self.arvrunner.project_uuid)
35 elif isinstance(tool, cwltool.workflow.Workflow):
37 self.upload_docker(s.embedded_tool)
40 def arvados_job_spec(self, *args, **kwargs):
41 self.upload_docker(self.tool)
45 workflowfiles.add(self.tool.tool["id"])
47 self.name = os.path.basename(self.tool.tool["id"])
49 def visitFiles(files, path):
53 document_loader, workflowobj, uri = fetch_document(self.tool.tool["id"])
55 return document_loader.fetch(urlparse.urljoin(b, u))
57 sc = scandeps(uri, workflowobj,
58 set(("$import", "run")),
59 set(("$include", "$schemas", "path")),
61 adjustFiles(sc, partial(visitFiles, workflowfiles))
62 adjustFiles(self.job_order, partial(visitFiles, jobfiles))
64 keepprefix = kwargs.get("keepprefix", "")
65 workflowmapper = ArvPathMapper(self.arvrunner, workflowfiles, "",
71 jobmapper = ArvPathMapper(self.arvrunner, jobfiles, "",
74 name=os.path.basename(self.job_order.get("id", "#")),
77 adjustFiles(self.job_order, lambda p: jobmapper.mapper(p)[1])
79 if "id" in self.job_order:
80 del self.job_order["id"]
85 def done(self, record):
86 if record["state"] == "Complete":
87 if record.get("exit_code") is not None:
88 if record["exit_code"] == 33:
89 processStatus = "UnsupportedRequirement"
90 elif record["exit_code"] == 0:
91 processStatus = "success"
93 processStatus = "permanentFail"
95 processStatus = "success"
97 processStatus = "permanentFail"
102 outc = arvados.collection.Collection(record["output"])
103 with outc.open("cwl.output.json") as f:
104 outputs = json.load(f)
106 if not path.startswith("keep:"):
107 return "keep:%s/%s" % (record["output"], path)
110 adjustFiles(outputs, keepify)
111 except Exception as e:
112 logger.error("While getting final output object: %s", e)
113 self.arvrunner.output_callback(outputs, processStatus)
115 del self.arvrunner.jobs[record["uuid"]]