add customized fields and fix typos

Author: yibeichan

pydra/engine/audit.py

@@ -62,8 +62,7 @@ def start_audit(self, odir):
             start_message = {
                 "@id": self.aid,
                 "@type": "task",
-                "startedAtTime": now(),
-                "executedBy": user_id,
+                "StartedAtTime": now(),
             }
 
         os.chdir(self.odir)
@@ -84,7 +83,7 @@ def monitor(self):
                     {
                         "@id": self.mid,
                         "@type": "monitor",
-                        "startedAtTime": now(),
+                        "StartedAtTime": now(),
                         "wasStartedBy": self.aid,
                     },
                     AuditFlag.PROV,
@@ -97,7 +96,7 @@ 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
@@ -107,14 +106,14 @@ 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,
@@ -123,7 +122,7 @@ 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,
             )
 
@@ -181,6 +180,8 @@ def audit_task(self, task):
 
         label = task.name
 
+        # YC: currently command only support shellcommand task
+        # we can make function itself a command too
         command = task.cmdline if hasattr(task.inputs, "executable") else None
         attr_list = attr_fields(task.inputs)
         for attrs in attr_list:
@@ -224,7 +225,15 @@ def audit_task(self, task):
             "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)

pydra/schema/context.jsonld

@@ -36,6 +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"