Update prov jsonld representation

clinica/engine/prov_model.py

@@ -28,12 +28,15 @@ class Identifier:
         validator=attr.validators.optional(attr.validators.instance_of(str)),
     )
 
+    def __repr__(self):
+        return "%s" % self.label
+
 
 class ProvElement(ABC):
     @property
     @classmethod
     @abstractmethod
-    def id(cls):
+    def uid(cls):
         """id is required for ProvElements"""
         return NotImplementedError
 
@@ -61,67 +64,33 @@ class ProvRelation(ABC):
 class ProvEntity(ProvElement):
     """Provenance Entity element"""
 
-    id: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
+    uid: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
     attributes: dict = field(default=attr.Factory(dict))
 
+    def unstrct(self):
+        return {"id": str(self.uid), **self.attributes}
+
 
 @define
 class ProvActivity(ProvElement):
     """Provenance Activity element"""
 
-    id: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
+    uid: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
     attributes: dict = field(default=attr.Factory(dict))
 
+    def unstrct(self):
+        return {"id": str(self.uid), **self.attributes}
+
 
 @define
 class ProvAgent(ProvElement):
     """Provenance Agent element"""
 
-    id: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
-    attributes: dict = field(
-        default=attr.Factory(dict),
-        validator=attr.validators.optional(attr.validators.instance_of(dict)),
-    )
-
-
-# Define PROV Relations
-
-
-@define
-class ProvGeneration(ProvRelation):
-    id: Identifier = field(
-        init=False,
-        validator=attr.validators.optional(attr.validators.instance_of(Identifier)),
-    )
-
-    src: ProvActivity = field(
-        init=False,
-        validator=attr.validators.optional(attr.validators.instance_of(ProvActivity)),
-    )
-    dest: ProvEntity = field(
-        init=False,
-        validator=attr.validators.optional(attr.validators.instance_of(ProvEntity)),
-    )
-
-    def __attrs_post_init__(self):
-        self.id = Identifier(label="")
-        self.src = ProvActivity()
-        self.dest = ProvEntity()
-
-    # entity: an identifier (e) for a created entity;
-    # activity: an OPTIONAL identifier (a) for the activity that creates the entity;
-    # time: an OPTIONAL "generation time" (t), the time at which the entity was completely created;
-    # attributes: an OPTIONALa
-
-
-@define
-class ProvUsage(ProvRelation):
-    pass
-
+    uid: Identifier = field(validator=[attr.validators.instance_of(Identifier)])
+    attributes: dict = field(default=attr.Factory(dict))
 
-@define
-class ProvAssociation(ProvRelation):
-    pass
+    def unstrct(self):
+        return {"id": str(self.uid), **self.attributes}
 
 
 @define
@@ -146,18 +115,18 @@ class ProvRecord:
 
     def __getitem__(self, idx):
         for element in self.elements:
-            if element.id == idx:
+            if element.uid == idx:
                 return element
 
     def json(self):
         json_dict = {}
         json_dict["prov:Agent"] = [
-            cattr.unstructure(x) for x in self.elements if isinstance(x, ProvAgent)
+            x.unstrct() for x in self.elements if isinstance(x, ProvAgent)
         ]
         json_dict["prov:Activity"] = [
-            cattr.unstructure(x) for x in self.elements if isinstance(x, ProvActivity)
+            x.unstrct() for x in self.elements if isinstance(x, ProvActivity)
         ]
         json_dict["prov:Entity"] = [
-            cattr.unstructure(x) for x in self.elements if isinstance(x, ProvEntity)
+            x.unstrct() for x in self.elements if isinstance(x, ProvEntity)
         ]
         return json_dict

clinica/engine/prov_utils.py

@@ -75,7 +75,7 @@ def get_last_activity(path_entity: Path) -> Optional[ProvActivity]:
         last_activity = [
             x for x in prov_record.elements if isinstance(x, ProvActivity)
         ][-1]
-        return last_activity.id.label
+        return str(last_activity.uid)
     return None
 
 
@@ -99,6 +99,7 @@ def create_prov_file(prov_command, prov_path):
 
     with open(prov_path, "w") as fp:
         json.dump(prov_command.json(), fp, indent=4)
+
     return
 
 

clinica/engine/provenance.py

@@ -105,7 +105,7 @@ def write_prov_file(
     entity_path: path of the prov-associated element
     """
 
-    from .prov_utils import read_prov_jsonld, get_path_prov
+    from .prov_utils import get_path_prov
 
     prov_path = get_path_prov(path_entity)
 
@@ -130,7 +130,7 @@ def get_agent() -> ProvAgent:
     import clinica
     from .prov_utils import generate_agent_id
 
-    new_agent = ProvAgent(id=generate_agent_id())
+    new_agent = ProvAgent(uid=generate_agent_id())
 
     new_agent.attributes["version"] = clinica.__version__
     new_agent.attributes["label"] = clinica.__name__
@@ -146,13 +146,13 @@ def get_activity(self, agent: Identifier, entities: List[ProvEntity]) -> ProvAct
     import sys
     from .prov_utils import generate_activity_id
 
-    new_activity = ProvActivity(id=generate_activity_id(self.fullname))
+    new_activity = ProvActivity(uid=generate_activity_id(self.fullname))
 
     new_activity.attributes["parameters"] = self.parameters
     new_activity.attributes["label"] = self.fullname
     new_activity.attributes["command"] = (sys.argv[1:],)
-    new_activity.attributes["used"] = [x.id for x in entities]
-    new_activity.attributes["wasAssociatedWith"] = agent.id
+    new_activity.attributes["used"] = [str(x.uid) for x in entities]
+    new_activity.attributes["wasAssociatedWith"] = str(agent.uid)
 
     return new_activity
 
@@ -164,7 +164,7 @@ def get_entity(path_curr: Path) -> ProvEntity:
 
     from clinica.engine.prov_utils import generate_entity_id, get_last_activity
 
-    new_entity = ProvEntity(id=generate_entity_id(path_curr))
+    new_entity = ProvEntity(uid=generate_entity_id(path_curr))
     new_entity.attributes["label"] = path_curr.name
     new_entity.attributes["path"] = str(path_curr)