Added validators to nanopub model

bel/schemas/nanopubs.py

@@ -4,7 +4,7 @@
 
 # Third Party
 import pydantic
-from pydantic import AnyUrl, BaseModel, Field, HttpUrl, validator
+from pydantic import AnyUrl, BaseModel, Field, HttpUrl, root_validator, validator
 
 # Local
 from bel.schemas.bel import ValidationErrors
@@ -27,6 +27,13 @@ class Annotation(BaseModel):
     class Config:
         extra = "allow"
 
+    @validator("type")
+    def clean_type(cls, v):
+        """Clean types which are merged together - taking first instance"""
+        if ";" in v:
+            v = v.split(";")[0]
+        return v
+
 
 class Assertion(BaseModel):
     subject: str
@@ -37,6 +44,11 @@ class Assertion(BaseModel):
     class Config:
         extra = "allow"
 
+    @validator("subject", "object")
+    def clean_assertion(cls, v):
+        v = v.replace("“", '"').replace("”", '"').strip()
+        return v
+
 
 class CitationDatabase(BaseModel):
     name: str
@@ -59,6 +71,33 @@ class Citation(BaseModel):
     class Config:
         extra = "allow"
 
+    @root_validator
+    def create_id(cls, values):
+        """Generate citation id from database, uri or reference string"""
+        citation_id, database, uri, reference = (
+            values.get("id", None),
+            values.get("database", None),
+            values.get("uri"),
+            values.get("reference", None),
+        )
+        if not citation_id:
+            citation_id = ""
+            if database:
+                citation_id = f"{database.name}:{database.id}"
+            elif uri:
+                citation_id = uri
+            elif reference:
+                citation_id = reference
+
+            values.id = citation_id
+
+        return values
+
+
+class Metadata(BaseModel):
+    class Config:
+        extra = "allow"
+
 
 class NanopubBody(BaseModel):
     """Nanopub content"""