Merge pull request #11 from geneontology/issue-8-activity-input-output

Add `has_direct_output` slot to `Activity` class

project/gocam.py

@@ -1,5 +1,5 @@
 # Auto generated from gocam.yaml by pythongen.py version: 0.0.1
-# Generation date: 2024-08-28T17:21:26
+# Generation date: 2024-09-13T15:30:52
 # Schema: gocam
 #
 # id: https://w3id.org/gocam
@@ -211,7 +211,10 @@ class Activity(YAMLRoot):
     molecular_function: Optional[Union[dict, "MolecularFunctionAssociation"]] = None
     occurs_in: Optional[Union[dict, "CellularAnatomicalEntityAssociation"]] = None
     part_of: Optional[Union[dict, "BiologicalProcessAssociation"]] = None
-    has_direct_input: Optional[Union[dict, "MoleculeAssociation"]] = None
+    has_input: Optional[Union[Union[dict, "MoleculeAssociation"], List[Union[dict, "MoleculeAssociation"]]]] = empty_list()
+    has_primary_input: Optional[Union[dict, "MoleculeAssociation"]] = None
+    has_output: Optional[Union[Union[dict, "MoleculeAssociation"], List[Union[dict, "MoleculeAssociation"]]]] = empty_list()
+    has_primary_output: Optional[Union[dict, "MoleculeAssociation"]] = None
     causal_associations: Optional[Union[Union[dict, "CausalAssociation"], List[Union[dict, "CausalAssociation"]]]] = empty_list()
     provenances: Optional[Union[Union[dict, "ProvenanceInfo"], List[Union[dict, "ProvenanceInfo"]]]] = empty_list()
 
@@ -233,8 +236,19 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         if self.part_of is not None and not isinstance(self.part_of, BiologicalProcessAssociation):
             self.part_of = BiologicalProcessAssociation(**as_dict(self.part_of))
 
-        if self.has_direct_input is not None and not isinstance(self.has_direct_input, MoleculeAssociation):
-            self.has_direct_input = MoleculeAssociation(**as_dict(self.has_direct_input))
+        if not isinstance(self.has_input, list):
+            self.has_input = [self.has_input] if self.has_input is not None else []
+        self.has_input = [v if isinstance(v, MoleculeAssociation) else MoleculeAssociation(**as_dict(v)) for v in self.has_input]
+
+        if self.has_primary_input is not None and not isinstance(self.has_primary_input, MoleculeAssociation):
+            self.has_primary_input = MoleculeAssociation(**as_dict(self.has_primary_input))
+
+        if not isinstance(self.has_output, list):
+            self.has_output = [self.has_output] if self.has_output is not None else []
+        self.has_output = [v if isinstance(v, MoleculeAssociation) else MoleculeAssociation(**as_dict(v)) for v in self.has_output]
+
+        if self.has_primary_output is not None and not isinstance(self.has_primary_output, MoleculeAssociation):
+            self.has_primary_output = MoleculeAssociation(**as_dict(self.has_primary_output))
 
         if not isinstance(self.causal_associations, list):
             self.causal_associations = [self.causal_associations] if self.causal_associations is not None else []
@@ -1172,8 +1186,17 @@ class slots:
 slots.activity__part_of = Slot(uri=GOCAM.part_of, name="activity__part_of", curie=GOCAM.curie('part_of'),
                    model_uri=GOCAM.activity__part_of, domain=None, range=Optional[Union[dict, BiologicalProcessAssociation]])
 
-slots.activity__has_direct_input = Slot(uri=GOCAM.has_direct_input, name="activity__has_direct_input", curie=GOCAM.curie('has_direct_input'),
-                   model_uri=GOCAM.activity__has_direct_input, domain=None, range=Optional[Union[dict, MoleculeAssociation]])
+slots.activity__has_input = Slot(uri=GOCAM.has_input, name="activity__has_input", curie=GOCAM.curie('has_input'),
+                   model_uri=GOCAM.activity__has_input, domain=None, range=Optional[Union[Union[dict, MoleculeAssociation], List[Union[dict, MoleculeAssociation]]]])
+
+slots.activity__has_primary_input = Slot(uri=GOCAM.has_primary_input, name="activity__has_primary_input", curie=GOCAM.curie('has_primary_input'),
+                   model_uri=GOCAM.activity__has_primary_input, domain=None, range=Optional[Union[dict, MoleculeAssociation]])
+
+slots.activity__has_output = Slot(uri=GOCAM.has_output, name="activity__has_output", curie=GOCAM.curie('has_output'),
+                   model_uri=GOCAM.activity__has_output, domain=None, range=Optional[Union[Union[dict, MoleculeAssociation], List[Union[dict, MoleculeAssociation]]]])
+
+slots.activity__has_primary_output = Slot(uri=GOCAM.has_primary_output, name="activity__has_primary_output", curie=GOCAM.curie('has_primary_output'),
+                   model_uri=GOCAM.activity__has_primary_output, domain=None, range=Optional[Union[dict, MoleculeAssociation]])
 
 slots.activity__causal_associations = Slot(uri=GOCAM.causal_associations, name="activity__causal_associations", curie=GOCAM.curie('causal_associations'),
                    model_uri=GOCAM.activity__causal_associations, domain=None, range=Optional[Union[Union[dict, CausalAssociation], List[Union[dict, CausalAssociation]]]])

project/graphql/gocam.graphql

@@ -6,7 +6,10 @@ type Activity
     molecularFunction: MolecularFunctionAssociation
     occursIn: CellularAnatomicalEntityAssociation
     partOf: BiologicalProcessAssociation
-    hasDirectInput: MoleculeAssociation
+    hasInput: [MoleculeAssociation]
+    hasPrimaryInput: MoleculeAssociation
+    hasOutput: [MoleculeAssociation]
+    hasPrimaryOutput: MoleculeAssociation
     causalAssociations: [CausalAssociation]
     provenances: [ProvenanceInfo]
   }

project/jsonld/gocam.context.jsonld

@@ -1,7 +1,7 @@
 {
    "comments": {
       "description": "Auto generated by LinkML jsonld context generator",
-      "generation_date": "2024-08-28T17:21:26",
+      "generation_date": "2024-09-13T15:30:51",
       "source": "gocam.yaml"
    },
    "@context": {
@@ -59,9 +59,21 @@
          "@type": "@id",
          "@id": "enabled_by"
       },
-      "has_direct_input": {
+      "has_input": {
          "@type": "@id",
-         "@id": "has_direct_input"
+         "@id": "has_input"
+      },
+      "has_output": {
+         "@type": "@id",
+         "@id": "has_output"
+      },
+      "has_primary_input": {
+         "@type": "@id",
+         "@id": "has_primary_input"
+      },
+      "has_primary_output": {
+         "@type": "@id",
+         "@id": "has_primary_output"
       },
       "id": "@id",
       "molecular_function": {

project/jsonld/gocam.jsonld

@@ -690,11 +690,57 @@
       "@type": "SlotDefinition"
     },
     {
-      "name": "activity__has_direct_input",
+      "name": "activity__has_input",
       "description": "The input molecules that are directly consumed by the activity",
       "from_schema": "https://w3id.org/gocam",
-      "slot_uri": "https://w3id.org/gocam/has_direct_input",
-      "alias": "has_direct_input",
+      "slot_uri": "https://w3id.org/gocam/has_input",
+      "multivalued": true,
+      "alias": "has_input",
+      "owner": "Activity",
+      "domain_of": [
+        "Activity"
+      ],
+      "range": "MoleculeAssociation",
+      "inlined": true,
+      "inlined_as_list": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "activity__has_primary_input",
+      "description": "The primary input molecule that is directly consumed by the activity",
+      "from_schema": "https://w3id.org/gocam",
+      "slot_uri": "https://w3id.org/gocam/has_primary_input",
+      "alias": "has_primary_input",
+      "owner": "Activity",
+      "domain_of": [
+        "Activity"
+      ],
+      "range": "MoleculeAssociation",
+      "inlined": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "activity__has_output",
+      "description": "The output molecules that are directly produced by the activity",
+      "from_schema": "https://w3id.org/gocam",
+      "slot_uri": "https://w3id.org/gocam/has_output",
+      "multivalued": true,
+      "alias": "has_output",
+      "owner": "Activity",
+      "domain_of": [
+        "Activity"
+      ],
+      "range": "MoleculeAssociation",
+      "inlined": true,
+      "inlined_as_list": true,
+      "@type": "SlotDefinition"
+    },
+    {
+      "name": "activity__has_primary_output",
+      "description": "The primary output molecule that is directly produced by the activity",
+      "from_schema": "https://w3id.org/gocam",
+      "slot_uri": "https://w3id.org/gocam/has_primary_output",
+      "alias": "has_primary_output",
       "owner": "Activity",
       "domain_of": [
         "Activity"
@@ -1373,7 +1419,10 @@
         "activity__molecular_function",
         "activity__occurs_in",
         "activity__part_of",
-        "activity__has_direct_input",
+        "activity__has_input",
+        "activity__has_primary_input",
+        "activity__has_output",
+        "activity__has_primary_output",
         "activity__causal_associations",
         "activity__provenances"
       ],
@@ -1421,8 +1470,31 @@
           "@type": "SlotDefinition"
         },
         {
-          "name": "has_direct_input",
+          "name": "has_input",
           "description": "The input molecules that are directly consumed by the activity",
+          "multivalued": true,
+          "range": "MoleculeAssociation",
+          "inlined_as_list": true,
+          "@type": "SlotDefinition"
+        },
+        {
+          "name": "has_primary_input",
+          "description": "The primary input molecule that is directly consumed by the activity",
+          "range": "MoleculeAssociation",
+          "inlined": true,
+          "@type": "SlotDefinition"
+        },
+        {
+          "name": "has_output",
+          "description": "The output molecules that are directly produced by the activity",
+          "multivalued": true,
+          "range": "MoleculeAssociation",
+          "inlined_as_list": true,
+          "@type": "SlotDefinition"
+        },
+        {
+          "name": "has_primary_output",
+          "description": "The primary output molecule that is directly produced by the activity",
           "range": "MoleculeAssociation",
           "inlined": true,
           "@type": "SlotDefinition"
@@ -2138,9 +2210,9 @@
   ],
   "metamodel_version": "1.7.0",
   "source_file": "gocam.yaml",
-  "source_file_date": "2024-08-28T16:22:21",
-  "source_file_size": 13188,
-  "generation_date": "2024-08-28T17:21:26",
+  "source_file_date": "2024-09-13T14:36:24",
+  "source_file_size": 13755,
+  "generation_date": "2024-09-13T15:30:51",
   "@type": "SchemaDefinition",
   "@context": [
     "project/jsonld/gocam.context.jsonld",

project/jsonschema/gocam.schema.json

@@ -22,9 +22,27 @@
                     ],
                     "description": "The gene product or complex that carries out the activity"
                 },
-                "has_direct_input": {
+                "has_input": {
+                    "description": "The input molecules that are directly consumed by the activity",
+                    "items": {
+                        "$ref": "#/$defs/MoleculeAssociation"
+                    },
+                    "type": "array"
+                },
+                "has_output": {
+                    "description": "The output molecules that are directly produced by the activity",
+                    "items": {
+                        "$ref": "#/$defs/MoleculeAssociation"
+                    },
+                    "type": "array"
+                },
+                "has_primary_input": {
+                    "$ref": "#/$defs/MoleculeAssociation",
+                    "description": "The primary input molecule that is directly consumed by the activity"
+                },
+                "has_primary_output": {
                     "$ref": "#/$defs/MoleculeAssociation",
-                    "description": "The input molecules that are directly consumed by the activity"
+                    "description": "The primary output molecule that is directly produced by the activity"
                 },
                 "id": {
                     "description": "Identifier of the activity unit. Should be in gocam namespace.",