pyobo 0.11.2__py3-none-any.whl → 0.12.0__py3-none-any.whl

pyobo/identifier_utils/model.py

@@ -0,0 +1,130 @@
+"""Reusable configuration."""
+
+from typing import TypeVar
+
+import curies
+from pydantic import BaseModel, Field
+
+__all__ = ["Blacklist", "Rewrites", "Rules"]
+
+X = TypeVar("X", bound=curies.Reference)
+
+
+class Blacklist(BaseModel):
+    """A model for prefix and full blacklists."""
+
+    full: list[str]
+    resource_full: dict[str, list[str]]
+    prefix: list[str]
+    resource_prefix: dict[str, list[str]]
+    suffix: list[str]
+
+    def _sort(self) -> None:
+        self.full.sort()
+        self.prefix.sort()
+        self.suffix.sort()
+        for v in self.resource_full.values():
+            v.sort()
+        for v in self.resource_prefix.values():
+            v.sort()
+
+    def str_has_blacklisted_prefix(
+        self, str_or_curie_or_uri: str, *, ontology_prefix: str | None = None
+    ) -> bool:
+        """Check if the CURIE string has a blacklisted prefix."""
+        if ontology_prefix:
+            prefixes: list[str] = self.resource_prefix.get(ontology_prefix, [])
+            if prefixes and any(str_or_curie_or_uri.startswith(prefix) for prefix in prefixes):
+                return True
+        return any(str_or_curie_or_uri.startswith(prefix) for prefix in self.prefix)
+
+    def str_has_blacklisted_suffix(self, str_or_curie_or_uri: str) -> bool:
+        """Check if the CURIE string has a blacklisted suffix."""
+        return any(str_or_curie_or_uri.endswith(suffix) for suffix in self.suffix)
+
+    def str_is_blacklisted_full(
+        self, str_or_curie_or_uri: str, *, ontology_prefix: str | None = None
+    ) -> bool:
+        """Check if the full CURIE string is blacklisted."""
+        if ontology_prefix and str_or_curie_or_uri in self.resource_full.get(
+            ontology_prefix, set()
+        ):
+            return True
+        return str_or_curie_or_uri in self.full
+
+
+class Rewrites(BaseModel):
+    """A model for prefix and full rewrites."""
+
+    full: dict[str, str] = Field(..., description="Global remappings for an entire string")
+    resource_full: dict[str, dict[str, str]] = Field(
+        ..., description="Resource-keyed remappings for an entire string"
+    )
+    prefix: dict[str, str] = Field(..., description="Global remappings of just the prefix")
+    resource_prefix: dict[str, dict[str, str]] = Field(
+        ..., description="Resource-keyed remappings for just a prefix"
+    )
+
+    def remap_full(
+        self, str_or_curie_or_uri: str, cls: type[X], *, ontology_prefix: str | None = None
+    ) -> X | None:
+        """Remap the string if possible otherwise return it."""
+        if ontology_prefix:
+            resource_rewrites: dict[str, str] = self.resource_full.get(ontology_prefix, {})
+            if resource_rewrites and str_or_curie_or_uri in resource_rewrites:
+                return cls.from_curie(resource_rewrites[str_or_curie_or_uri])
+
+        if str_or_curie_or_uri in self.full:
+            return cls.from_curie(self.full[str_or_curie_or_uri])
+
+        return None
+
+    def remap_prefix(self, str_or_curie_or_uri: str, ontology_prefix: str | None = None) -> str:
+        """Remap a prefix."""
+        if ontology_prefix is not None:
+            for old_prefix, new_prefix in self.resource_prefix.get(ontology_prefix, {}).items():
+                if str_or_curie_or_uri.startswith(old_prefix):
+                    return new_prefix + str_or_curie_or_uri[len(old_prefix) :]
+        for old_prefix, new_prefix in self.prefix.items():
+            if str_or_curie_or_uri.startswith(old_prefix):
+                return new_prefix + str_or_curie_or_uri[len(old_prefix) :]
+        return str_or_curie_or_uri
+
+
+class Rules(BaseModel):
+    """A model for blacklists and rewrites."""
+
+    blacklists: Blacklist
+    rewrites: Rewrites
+
+    def str_has_blacklisted_prefix(
+        self, str_or_curie_or_uri: str, *, ontology_prefix: str | None = None
+    ) -> bool:
+        """Check if the CURIE string has a blacklisted prefix."""
+        return self.blacklists.str_has_blacklisted_prefix(
+            str_or_curie_or_uri, ontology_prefix=ontology_prefix
+        )
+
+    def str_has_blacklisted_suffix(self, str_or_curie_or_uri: str) -> bool:
+        """Check if the CURIE string has a blacklisted suffix."""
+        return self.blacklists.str_has_blacklisted_suffix(str_or_curie_or_uri)
+
+    def str_is_blacklisted_full(
+        self, str_or_curie_or_uri: str, *, ontology_prefix: str | None = None
+    ) -> bool:
+        """Check if the full CURIE string is blacklisted."""
+        return self.blacklists.str_is_blacklisted_full(
+            str_or_curie_or_uri, ontology_prefix=ontology_prefix
+        )
+
+    def remap_full(
+        self, str_or_curie_or_uri: str, cls: type[X], *, ontology_prefix: str | None = None
+    ) -> X | None:
+        """Remap the string if possible otherwise return it."""
+        return self.rewrites.remap_full(
+            str_or_curie_or_uri, cls=cls, ontology_prefix=ontology_prefix
+        )
+
+    def remap_prefix(self, str_or_curie_or_uri: str, ontology_prefix: str | None = None) -> str:
+        """Remap a prefix."""
+        return self.rewrites.remap_prefix(str_or_curie_or_uri, ontology_prefix=ontology_prefix)