X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0f53d219c91812baeac4cff3387196c6501ec0c0..e68177bfa8de36bd54f705e16e5c4854eafb29a2:/sdk/cwl/arvados_cwl/arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 0e1ad9fbaa..8eb8fe6fee 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -1,36 +1,128 @@
 import os
 import json
+import copy
+import logging
 
 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
 
-from .runner import upload_docker, upload_dependencies
+import ruamel.yaml as yaml
 
-def make_workflow(arvRunner, tool, job_order, project_uuid, update_uuid):
+from .runner import upload_docker, upload_dependencies, trim_listing
+from .arvtool import ArvadosCommandTool
+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, update_uuid):
     upload_docker(arvRunner, tool)
 
     document_loader, workflowobj, uri = (tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]), tool.tool["id"])
-    for inp in workflowobj["inputs"]:
+
+    packed = pack(document_loader, workflowobj, uri, tool.metadata)
+
+    adjustDirObjs(job_order, trim_listing)
+
+    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]
 
-    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)
+                        packed, uri, 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)
+            "definition":yaml.safe_dump(packed)
         }}
 
     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"]
+
+class ArvadosWorkflow(Workflow):
+    """Wrap cwltool Workflow to override selected methods."""
+
+    def __init__(self, arvrunner, toolpath_object, **kwargs):
+        super(ArvadosWorkflow, self).__init__(toolpath_object, **kwargs)
+        self.arvrunner = arvrunner
+        self.work_api = kwargs["work_api"]
+
+    def job(self, joborder, output_callback, **kwargs):
+        kwargs["work_api"] = self.work_api
+        req, _ = self.get_requirement("http://arvados.org/cwl#RunInSingleContainer")
+        if req:
+            document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
+
+            with Perf(metrics, "subworkflow upload_deps"):
+                workflowobj["requirements"] = self.requirements + workflowobj.get("requirements", [])
+                workflowobj["hints"] = self.hints + workflowobj.get("hints", [])
+                packed = pack(document_loader, workflowobj, uri, self.metadata)
+
+                upload_dependencies(self.arvrunner,
+                                    kwargs.get("name", ""),
+                                    document_loader,
+                                    packed,
+                                    uri,
+                                    False)
+
+                upload_dependencies(self.arvrunner,
+                                    os.path.basename(joborder.get("id", "#")),
+                                    document_loader,
+                                    joborder,
+                                    joborder.get("id", "#"),
+                                    False)
+
+            with Perf(metrics, "subworkflow adjust"):
+                joborder_keepmount = copy.deepcopy(joborder)
+
+                def keepmount(obj):
+                    if obj["location"].startswith("keep:"):
+                        obj["location"] = "/keep/" + obj["location"][5:]
+                        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"])
+
+                adjustFileObjs(joborder_keepmount, keepmount)
+                adjustDirObjs(joborder_keepmount, keepmount)
+                adjustFileObjs(packed, keepmount)
+                adjustDirObjs(packed, keepmount)
+
+            wf_runner = {
+                "class": "CommandLineTool",
+                "baseCommand": "cwltool",
+                "inputs": self.tool["inputs"],
+                "outputs": self.tool["outputs"],
+                "stdout": "cwl.output.json",
+                "requirements": workflowobj["requirements"]+[
+                    {
+                    "class": "InitialWorkDirRequirement",
+                    "listing": [{
+                            "entryname": "workflow.cwl",
+                            "entry": yaml.safe_dump(packed).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+                        }, {
+                            "entryname": "cwl.input.yml",
+                            "entry": yaml.safe_dump(joborder_keepmount).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
+                        }]
+                }],
+                "hints": workflowobj["hints"],
+                "arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"]
+            }
+            kwargs["loader"] = self.doc_loader
+            kwargs["avsc_names"] = self.doc_schema
+            return ArvadosCommandTool(self.arvrunner, wf_runner, **kwargs).job(joborder, output_callback, **kwargs)
+        else:
+            return super(ArvadosWorkflow, self).job(joborder, output_callback, **kwargs)