6 from cwltool.pack import pack
7 from cwltool.load_tool import fetch_document
8 from cwltool.process import shortname
9 from cwltool.workflow import Workflow, WorkflowException
10 from cwltool.pathmapper import adjustFileObjs, adjustDirObjs
12 import ruamel.yaml as yaml
14 from .runner import upload_docker, upload_dependencies
15 from .arvtool import ArvadosCommandTool
17 logger = logging.getLogger('arvados.cwl-runner')
19 def upload_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
20 upload_docker(arvRunner, tool)
22 document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
24 packed = pack(document_loader, workflowobj, uri, tool.metadata)
26 main = [p for p in packed["$graph"] if p["id"] == "#main"][0]
27 for inp in main["inputs"]:
28 sn = shortname(inp["id"])
30 inp["default"] = job_order[sn]
32 name = os.path.basename(tool.tool["id"])
33 upload_dependencies(arvRunner, name, document_loader,
38 "owner_uuid": project_uuid,
39 "name": tool.tool.get("label", name),
40 "description": tool.tool.get("doc", ""),
41 "definition":yaml.safe_dump(packed)
45 return arvRunner.api.workflows().update(uuid=update_uuid, body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
47 return arvRunner.api.workflows().create(body=body).execute(num_retries=arvRunner.num_retries)["uuid"]
49 class ArvadosWorkflow(Workflow):
50 """Wrap cwltool Workflow to override selected methods."""
52 def __init__(self, arvrunner, toolpath_object, **kwargs):
53 super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
54 self.arvrunner = arvrunner
55 self.work_api = kwargs["work_api"]
57 def job(self, joborder, output_callback, **kwargs):
58 kwargs["work_api"] = self.work_api
59 req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
61 document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
63 workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
64 workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
65 packed = pack(document_loader, workflowobj, uri, self.metadata)
67 upload_dependencies(self.arvrunner,
68 kwargs.get("name", ""),
74 upload_dependencies(self.arvrunner,
75 os.path.basename(joborder.get("id", "#")),
78 joborder.get("id", "#"),
81 joborder_keepmount = copy.deepcopy(joborder)
84 if obj["location"].startswith("keep:"):
85 obj["location"] = "/keep/" + obj["location"][5:]
86 elif obj["location"].startswith("_:"):
89 raise WorkflowException("Location is not a keep reference or a literal: '%s'" % obj["location"])
92 adjustFileObjs(joborder_keepmount, keepmount)
93 adjustDirObjs(joborder_keepmount, keepmount)
94 adjustFileObjs(packed, keepmount)
95 adjustDirObjs(packed, keepmount)
98 "class": "CommandLineTool",
99 "baseCommand": "cwltool",
100 "inputs": self.tool["inputs"],
101 "outputs": self.tool["outputs"],
102 "stdout": "cwl.output.json",
103 "requirements": workflowobj["requirements"]+[
104 {"class": "InlineJavascriptRequirement"},
106 "class": "InitialWorkDirRequirement",
108 "entryname": "workflow.cwl",
109 "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
111 "entryname": "cwl.input.yml",
112 "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
115 "hints": workflowobj["hints"],
116 "arguments": ["--no-container", "--move-outputs", "workflow.cwl#main", "cwl.input.yml"]
118 kwargs["loader"] = self.doc_loader
119 kwargs["avsc_names"] = self.doc_schema
120 return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
122 return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)