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Fix misake in arvados-cwl-runner upload_dependencies refactor. refs #9766
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
runner.py
diff --git
a/sdk/cwl/arvados_cwl/runner.py
b/sdk/cwl/arvados_cwl/runner.py
index 9f7b84a73a012027528d39d1a77ca21d678a5018..72f347e439ab61b9b3f77d2fc6ac4f98bd08bd8e 100644
(file)
--- a/
sdk/cwl/arvados_cwl/runner.py
+++ b/
sdk/cwl/arvados_cwl/runner.py
@@
-22,7
+22,7
@@
logger = logging.getLogger('arvados.cwl-runner')
cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
def upload_dependencies(arvrunner, name, document_loader,
cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
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)
loaded = set()
def loadref(b, u):
joined = urlparse.urljoin(b, u)
@@
-55,8
+55,8
@@
def upload_dependencies(arvrunner, name, document_loader,
files.append({"class": "File", "location": workflowobj["id"]})
mapper = ArvPathMapper(arvrunner, files, "",
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):
name=name)
def setloc(p):
@@
-99,7
+99,6
@@
class Runner(object):
self.tool.doc_loader,
self.tool.tool,
self.tool.tool["id"],
self.tool.doc_loader,
self.tool.tool,
self.tool.tool["id"],
- kwargs.get("keepprefix", ""),
True)
jobmapper = upload_dependencies(self.arvrunner,
True)
jobmapper = upload_dependencies(self.arvrunner,
@@
-107,7
+106,6
@@
class Runner(object):
self.tool.doc_loader,
self.job_order,
self.job_order.get("id", "#"),
self.tool.doc_loader,
self.job_order,
self.job_order.get("id", "#"),
- kwargs.get("keepprefix", ""),
False)
if "id" in self.job_order:
False)
if "id" in self.job_order: