workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
- self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"])[1]
+ self.job_order["cwl:tool"] = workflowmapper.mapper(self.tool.tool["id"]).target[5:]
return {
"script": "cwl-runner",
"script_version": "master",
cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
def upload_dependencies(arvrunner, name, document_loader,
- workflowobj, uri, keepprefix, loadref_run):
+ workflowobj, uri, loadref_run):
loaded = set()
def loadref(b, u):
joined = urlparse.urljoin(b, u)
files.append({"class": "File", "location": workflowobj["id"]})
mapper = ArvPathMapper(arvrunner, files, "",
- keepprefix+"%s",
- keepprefix+"%s/%s",
+ "keep:%s",
+ "keep:%s/%s",
name=name)
def setloc(p):
self.tool.doc_loader,
self.tool.tool,
self.tool.tool["id"],
- kwargs.get("keepprefix", ""),
True)
jobmapper = upload_dependencies(self.arvrunner,
self.tool.doc_loader,
self.job_order,
self.job_order.get("id", "#"),
- kwargs.get("keepprefix", ""),
False)
if "id" in self.job_order: