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13200:test to remove prefix on python
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
arvworkflow.py
diff --git
a/sdk/cwl/arvados_cwl/arvworkflow.py
b/sdk/cwl/arvados_cwl/arvworkflow.py
index 15704dba66884e512d10afa5b87cfcfa2f40d78d..5aed871a12bc58d1a747efd2035dbf9d2a23b5a4 100644
(file)
--- a/
sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/
sdk/cwl/arvados_cwl/arvworkflow.py
@@
-27,6
+27,9
@@
from .perf import Perf
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
logger = logging.getLogger('arvados.cwl-runner')
metrics = logging.getLogger('arvados.cwl-runner.metrics')
+max_res_pars = ("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax")
+sum_res_pars = ("outdirMin", "outdirMax")
+
def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
submit_runner_ram=0, name=None, merged_map=None):
def upload_workflow(arvRunner, tool, job_order, project_uuid, uuid=None,
submit_runner_ram=0, name=None, merged_map=None):
@@
-72,17
+75,19
@@
def dedup_reqs(reqs):
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
dedup[r["class"]] = r
return [dedup[r] for r in sorted(dedup.keys())]
-def get_max_res_req(res_reqs):
- """Take the max of a list of ResourceRequirement."""
+def get_overall_res_req(res_reqs):
+ """Take the overall of a list of ResourceRequirement,
+ i.e., the max of coresMin, coresMax, ramMin, ramMax, tmpdirMin, tmpdirMax
+ and the sum of outdirMin, outdirMax."""
-
tota
l_res_req = {}
+
al
l_res_req = {}
exception_msgs = []
exception_msgs = []
- for a in
("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax")
:
-
tota
l_res_req[a] = []
+ for a in
max_res_pars + sum_res_pars
:
+
al
l_res_req[a] = []
for res_req in res_reqs:
if a in res_req:
if isinstance(res_req[a], int): # integer check
for res_req in res_reqs:
if a in res_req:
if isinstance(res_req[a], int): # integer check
-
tota
l_res_req[a].append(res_req[a])
+
al
l_res_req[a].append(res_req[a])
else:
msg = SourceLine(res_req).makeError(
"Non-top-level ResourceRequirement in single container cannot have expressions")
else:
msg = SourceLine(res_req).makeError(
"Non-top-level ResourceRequirement in single container cannot have expressions")
@@
-90,13
+95,16
@@
def get_max_res_req(res_reqs):
if exception_msgs:
raise WorkflowException("\n".join(exception_msgs))
else:
if exception_msgs:
raise WorkflowException("\n".join(exception_msgs))
else:
- max_res_req = {}
- for a in total_res_req:
- if total_res_req[a]:
- max_res_req[a] = max(total_res_req[a])
- if max_res_req:
- max_res_req["class"] = "ResourceRequirement"
- return cmap(max_res_req)
+ overall_res_req = {}
+ for a in all_res_req:
+ if all_res_req[a]:
+ if a in max_res_pars:
+ overall_res_req[a] = max(all_res_req[a])
+ elif a in sum_res_pars:
+ overall_res_req[a] = sum(all_res_req[a])
+ if overall_res_req:
+ overall_res_req["class"] = "ResourceRequirement"
+ return cmap(overall_res_req)
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
class ArvadosWorkflow(Workflow):
"""Wrap cwltool Workflow to override selected methods."""
@@
-134,8
+142,8
@@
class ArvadosWorkflow(Workflow):
builder = Builder()
builder.job = joborder
builder = Builder()
builder.job = joborder
- builder.requirements =
self.requirements
- builder.hints =
self.hints
+ builder.requirements =
workflowobj["requirements"]
+ builder.hints =
workflowobj["hints"]
builder.resources = {}
res_reqs = {"requirements": [], "hints": []}
builder.resources = {}
res_reqs = {"requirements": [], "hints": []}
@@
-146,7
+154,7
@@
class ArvadosWorkflow(Workflow):
for req in item[t]:
if req["class"] == "ResourceRequirement":
eval_req = {"class": "ResourceRequirement"}
for req in item[t]:
if req["class"] == "ResourceRequirement":
eval_req = {"class": "ResourceRequirement"}
- for a in
("coresMin", "coresMax", "ramMin", "ramMax", "tmpdirMin", "tmpdirMax", "outdirMin", "outdirMax")
:
+ for a in
max_res_pars + sum_res_pars
:
if a in req:
eval_req[a] = builder.do_eval(req[a])
res_reqs[t].append(eval_req)
if a in req:
eval_req[a] = builder.do_eval(req[a])
res_reqs[t].append(eval_req)
@@
-154,16
+162,16
@@
class ArvadosWorkflow(Workflow):
for req in item[t]:
if req["class"] == "ResourceRequirement":
res_reqs[t].append(req)
for req in item[t]:
if req["class"] == "ResourceRequirement":
res_reqs[t].append(req)
-
max_res_req = {"requirements": get_max
_res_req(res_reqs["requirements"]),
-
"hints": get_max
_res_req(res_reqs["hints"])}
+
overall_res_req = {"requirements": get_overall
_res_req(res_reqs["requirements"]),
+
"hints": get_overall
_res_req(res_reqs["hints"])}
new_spec = {"requirements": self.requirements, "hints": self.hints}
for t in ("requirements", "hints"):
for req in new_spec[t]:
if req["class"] == "ResourceRequirement":
new_spec[t].remove(req)
new_spec = {"requirements": self.requirements, "hints": self.hints}
for t in ("requirements", "hints"):
for req in new_spec[t]:
if req["class"] == "ResourceRequirement":
new_spec[t].remove(req)
- if
max
_res_req[t]:
- new_spec[t].append(
max
_res_req[t])
+ if
overall
_res_req[t]:
+ new_spec[t].append(
overall
_res_req[t])
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
upload_dependencies(self.arvrunner,
kwargs.get("name", ""),
@@
-218,7
+226,7
@@
class ArvadosWorkflow(Workflow):
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
"inputs": self.tool["inputs"],
"outputs": self.tool["outputs"],
"stdout": "cwl.output.json",
- "requirements":
new_spec["requirements"]
+[
+ "requirements":
self.requirements
+[
{
"class": "InitialWorkDirRequirement",
"listing": [{
{
"class": "InitialWorkDirRequirement",
"listing": [{
@@
-232,7
+240,7
@@
class ArvadosWorkflow(Workflow):
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
"entry": json.dumps(joborder_keepmount, indent=2, sort_keys=True, separators=(',',': ')).replace("\\", "\\\\").replace('$(', '\$(').replace('${', '\${')
}]
}],
- "hints":
new_spec["hints"]
,
+ "hints":
self.hints
,
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})
"arguments": ["--no-container", "--move-outputs", "--preserve-entire-environment", "workflow.cwl#main", "cwl.input.yml"],
"id": "#"
})