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WIP - BEP 028 prov #750

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WIP - BEP 028 prov #750

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6b3a556
update context using bep028 context
Apr 12, 2024
e00a61a
add customized fields and fix typos
Apr 12, 2024
2c0f6aa
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 12, 2024
b1f347a
Merge branch 'main' into bep028_prov
tclose Apr 2, 2025
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26 changes: 17 additions & 9 deletions pydra/engine/audit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -66,8 +66,7 @@ def start_audit(self, odir):
start_message = {
"@id": self.aid,
"@type": "job",
"startedAtTime": now(),
"executedBy": user_id,
"StartedAtTime": now(),
}

os.chdir(self.odir)
Expand All @@ -88,7 +87,7 @@ def monitor(self):
{
"@id": self.mid,
"@type": "monitor",
"startedAtTime": now(),
"StartedAtTime": now(),
"wasStartedBy": self.aid,
},
AuditFlag.PROV,
Expand All @@ -103,7 +102,7 @@ def finalize_audit(self, result):
result.runtime = gather_runtime_info(self.resource_monitor.fname)
if self.audit_check(AuditFlag.PROV):
self.audit_message(
{"@id": self.mid, "endedAtTime": now(), "wasEndedBy": self.aid},
{"@id": self.mid, "EndedAtTime": now(), "wasEndedBy": self.aid},
AuditFlag.PROV,
)
# audit resources/runtime information
Expand All @@ -113,14 +112,14 @@ def finalize_audit(self, result):
**{
"@id": self.eid,
"@type": "runtime",
"prov:wasGeneratedBy": self.aid,
"GeneratedBy": self.aid,
}
)
self.audit_message(entity, AuditFlag.PROV)
self.audit_message(
{
"@type": "prov:Generation",
"entity_generated": self.eid,
"runtime": self.eid,
"hadActivity": self.mid,
},
AuditFlag.PROV,
Expand All @@ -129,7 +128,7 @@ def finalize_audit(self, result):
if self.audit_check(AuditFlag.PROV):
# audit outputs
self.audit_message(
{"@id": self.aid, "endedAtTime": now(), "errored": result.errored},
{"@id": self.aid, "EndedAtTime": now(), "errored": result.errored},
AuditFlag.PROV,
)

Expand Down Expand Up @@ -188,8 +187,10 @@ def audit_task(self, job: "Job"):

label = job.name

# YC: currently command only support shellcommand task
# we can make function itself a command too
command = job.task.cmdline if hasattr(job.task, "executable") else None
attr_list = task_fields(job.task)
attr_list = attr_fields(task.inputs)
for attrs in attr_list:
input_name = attrs.name
value = job.inputs[input_name]
Expand Down Expand Up @@ -231,7 +232,14 @@ def audit_task(self, job: "Job"):
"Label": label,
"Command": command,
"StartedAtTime": now(),
"AssociatedWith": version_cmd,
"AssociatedWith": {
"@id": self.aid,
# YC: need to add Label, which should be
# the software name in a shellcommand task
# the function's package in a function task
# else be python
"Version": version_cmd,
},
}

self.audit_message(start_message, AuditFlag.PROV)
15 changes: 10 additions & 5 deletions pydra/schema/context.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"@container": "@type"
}
},
"https://raw.githubusercontent.com/openprov/prov-jsonld/69964ed16818f78dc5f71bdf97add026288291d4/context.json",
"https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
{
"pydra": "http://s.pydra.org/",
"uid": "pydra:id/",
Expand All @@ -24,10 +24,6 @@
"@id": "pydra:runtimeInformation",
"@type": "@vocab"
},
"prov:wasGeneratedBy": {
"@id": "prov:wasGeneratedBy",
"@type": "@vocab"
},
"rss_peak_gb": {
"@id": "pydra:rss_peak_gb",
"@type": "xsd:float"
Expand All @@ -40,6 +36,15 @@
"@id": "pydra:cpu_peak_percent",
"@type": "xsd:float"
},
"wasStartedBy": {
"@id": "uid"
},
"wasEndedBy": {
"@id": "uid"
},
"hadActivity": {
"@id": "uid"
},
"errored": {
"@id": "pydra:errored",
"@type": "xsd:boolean"
Expand Down