refactor: remove unused code + small cleanup (#432)

* Only focused on ga4gh.core + Pydantic models

src/ga4gh/core/__init__.py

@@ -8,12 +8,12 @@
 from .enderef import ga4gh_enref, ga4gh_deref
 from .identifiers import (
     ga4gh_digest, ga4gh_identify, ga4gh_serialize, is_ga4gh_identifier,
-    parse_ga4gh_identifier, VrsObjectIdentifierIs, use_ga4gh_compute_identifier_when,
+    VrsObjectIdentifierIs, use_ga4gh_compute_identifier_when,
     CURIE_NAMESPACE, CURIE_SEP, GA4GH_PREFIX_SEP, GA4GH_IR_REGEXP, GA4GH_DIGEST_REGEXP,
     PrevVrsVersion
 )
 from .pydantic import (
-    is_pydantic_instance, is_curie_type, is_ga4gh_identifiable, is_literal, pydantic_copy
+    is_pydantic_instance, is_curie_type, pydantic_copy
 )
 from . import entity_models, domain_models
 
@@ -25,7 +25,6 @@
     "ga4gh_identify",
     "ga4gh_serialize",
     "is_ga4gh_identifier",
-    "parse_ga4gh_identifier",
     "VrsObjectIdentifierIs",
     "use_ga4gh_compute_identifier_when",
     "CURIE_NAMESPACE",
@@ -36,8 +35,6 @@
     "PrevVrsVersion",
     "is_pydantic_instance",
     "is_curie_type",
-    "is_ga4gh_identifiable",
-    "is_literal",
     "pydantic_copy",
     "entity_models",
     "domain_models"

src/ga4gh/core/enderef.py

@@ -13,9 +13,7 @@
 from .identifiers import ga4gh_identify, is_ga4gh_identifier
 from .pydantic import (
     is_pydantic_instance,
-    is_list,
     is_curie_type,
-    is_ga4gh_identifiable,
     get_pydantic_root,
     pydantic_copy)
 
@@ -45,7 +43,7 @@ def _enref(o):
         ref_att_names = cra_map.get(o.type, [])
         for ran in ref_att_names:
             v = getattr(o, ran)
-            if is_list(v):
+            if isinstance(v, list):
                 setattr(o, ran, [_enref(o2) for o2 in v])
             elif isinstance(v, str):
                 pass
@@ -60,7 +58,7 @@ def _enref(o):
 
     if not is_pydantic_instance(o):
         raise ValueError("Called ga4gh_enref() with non-pydantic instance")
-    if not is_ga4gh_identifiable(o):
+    if not o.is_ga4gh_identifiable():
         raise ValueError("Called ga4gh_enref() with non-identifiable object")
 
     # in-place replacement on object copy
@@ -88,7 +86,7 @@ def _deref(o):
         ref_att_names = cra_map[o.type]
         for ran in ref_att_names:
             v = getattr(o, ran)
-            if is_list(v):
+            if isinstance(v, list):
                 setattr(o, ran, [_deref(object_store[str(curie)]) for curie in v])
             elif is_ga4gh_identifier(v):
                 v = get_pydantic_root(v)
@@ -101,7 +99,7 @@ def _deref(o):
 
     if not is_pydantic_instance(o):
         raise ValueError("Called ga4gh_deref() with non-pydantic instance")
-    if not is_ga4gh_identifiable(o):
+    if not o.is_ga4gh_identifiable():
         raise ValueError("Called ga4gh_deref() with non-identifiable object")
 
     # in-place replacement on object copy

src/ga4gh/core/identifiers.py

@@ -16,18 +16,15 @@
 """
 
 import contextvars
-import logging
 import re
 from contextlib import ContextDecorator
 from enum import Enum, IntEnum
-from typing import Union, Optional
-from pydantic import BaseModel, RootModel
+from typing import Optional
+from pydantic import BaseModel
 
-from .pydantic import get_pydantic_root
+from ga4gh.core.pydantic import get_pydantic_root
 
-__all__ = "ga4gh_digest ga4gh_identify ga4gh_serialize is_ga4gh_identifier parse_ga4gh_identifier".split()
-
-_logger = logging.getLogger(__name__)
+__all__ = "ga4gh_digest ga4gh_identify ga4gh_serialize is_ga4gh_identifier".split()
 
 CURIE_NAMESPACE = "ga4gh"
 CURIE_SEP = ":"
@@ -36,7 +33,7 @@
 GA4GH_IR_REGEXP = re.compile(r"^ga4gh:(?P<type>[^.]+)\.(?P<digest>[0-9A-Za-z_\-]{32})$")
 GA4GH_DIGEST_REGEXP = re.compile(r"^[0-9A-Za-z_\-]{32}$")
 
-ns_w_sep = CURIE_NAMESPACE + CURIE_SEP
+NS_W_SEP = f"{CURIE_NAMESPACE}{CURIE_SEP}"
 
 
 class VrsObjectIdentifierIs(IntEnum):
@@ -47,9 +44,9 @@ class VrsObjectIdentifierIs(IntEnum):
       GA4GH_INVALID - Compute the identifier if it is missing or is present but syntactically invalid
       MISSING - Only compute the identifier if missing
 
-    The default behavior is safe and ensures that the identifiers are correct, 
-    but at a performance cost. Where the source of inputs to `ga4gh_identify` 
-    are well controlled, for example when annotating a VCF file with VRS IDs, 
+    The default behavior is safe and ensures that the identifiers are correct,
+    but at a performance cost. Where the source of inputs to `ga4gh_identify`
+    are well controlled, for example when annotating a VCF file with VRS IDs,
     using `MISSING` can improve performance.
     """
 
@@ -113,27 +110,7 @@ def is_ga4gh_identifier(ir):
     False
 
     """
-    return str(get_pydantic_root(ir)).startswith(ns_w_sep)
-
-
-def parse_ga4gh_identifier(ir):
-    """
-    Parses a GA4GH identifier, returning a dict with type and digest components
-
-    >>> parse_ga4gh_identifier("ga4gh:SQ.0123abcd")
-    {'type': 'SQ', 'digest': '0123abcd'}
-
-    >>> parse_ga4gh_identifier("notga4gh:SQ.0123abcd")
-    Traceback (most recent call last):
-    ...
-    ValueError: notga4gh:SQ.0123abcd
-
-    """
-
-    try:
-        return GA4GH_IR_REGEXP.match(str(ir)).groupdict()
-    except AttributeError as e:
-        raise ValueError(ir) from e
+    return str(get_pydantic_root(ir)).startswith(NS_W_SEP)
 
 
 def ga4gh_identify(vro, in_place: str = 'default', as_version: PrevVrsVersion | None = None) -> str | None:
@@ -171,7 +148,7 @@ def ga4gh_identify(vro, in_place: str = 'default', as_version: PrevVrsVersion |
             obj_id = getattr(vro, "id", None)
             if when_rule == VrsObjectIdentifierIs.MISSING:
                 do_compute = obj_id is None or obj_id == ""
-            else:  # GA4GHComputeIdentifierIs.GA4GH_INVALID
+            else:  # VrsObjectIdentifierIs.GA4GH_INVALID
                 do_compute = not vro.has_valid_ga4gh_id()
 
         if do_compute:
@@ -182,9 +159,11 @@ def ga4gh_identify(vro, in_place: str = 'default', as_version: PrevVrsVersion |
     return None
 
 
-def ga4gh_digest(vro: BaseModel, overwrite: bool = False, as_version: PrevVrsVersion | None = None) -> str:
+def ga4gh_digest(vro: BaseModel, overwrite: bool = False, as_version: PrevVrsVersion | None = None) -> str | None:
     """Return the GA4GH digest for the object.
 
+    Only GA4GH identifiable objects are GA4GH digestible.
+
     If ``as_version`` is provided, other parameters are ignored and a digest is returned
     following the conventions of the VRS version indicated by ``as_version_``.
     Raises ``ValueError`` if ``as_version`` is not a ``PrevVrsVersion``.
@@ -197,7 +176,7 @@ def ga4gh_digest(vro: BaseModel, overwrite: bool = False, as_version: PrevVrsVer
     """
     PrevVrsVersion.validate(as_version)
 
-    if vro.is_ga4gh_identifiable():  # Only GA4GH identifiable objects are GA4GH digestible
+    if vro.is_ga4gh_identifiable():
         if as_version is None:
             return vro.get_or_create_digest(overwrite)
         else:
@@ -206,30 +185,6 @@ def ga4gh_digest(vro: BaseModel, overwrite: bool = False, as_version: PrevVrsVer
         return None
 
 
-def replace_with_digest(val: dict) -> Union[str, dict]:
-    """
-    If val has a digest computed, return it, else return val
-    """
-    if isinstance(val, dict) and val.get("digest", None) is not None:
-        return val["digest"]
-    return val
-
-
-def collapse_identifiable_values(obj: dict) -> dict:
-    """
-    Replaces dict values with their digests if they are defined.
-    Does not collapse the top level object, only objects it contains.
-    """
-    if isinstance(obj, dict):
-        obj = {
-            k: replace_with_digest(collapse_identifiable_values(obj[k]))
-            for k in obj.keys()
-        }
-    elif isinstance(obj, list) or isinstance(obj, set):
-        obj = [replace_with_digest(collapse_identifiable_values(elem)) for elem in obj]
-    return obj
-
-
 def ga4gh_serialize(obj: BaseModel, as_version: PrevVrsVersion | None = None) -> Optional[bytes]:
     """Serializes an object for use in computed digest computation.
 

src/ga4gh/core/pydantic.py

@@ -21,24 +21,6 @@ def getattr_in(obj, names) -> Any:
     return v
 
 
-def is_ga4gh_identifiable(o: Any) -> bool:
-    """
-    Determine if object is a GA4GH identifiable type.
-
-    :param o: Object
-    :return: `True` if `o` is a GA4GH Identifiable Object. `False` otherwise.
-    """
-    return o.is_ga4gh_identifiable()
-
-
-def is_literal(o: Any) -> bool:
-    return isinstance(o, (str, int, float, complex, bool))
-
-
-def is_list(o: Any) -> bool:
-    return isinstance(o, list)
-
-
 def is_curie_type(o: Any) -> bool:
     """
     Returns true if the object is a str-like matching the CURIE pattern.

src/ga4gh/vrs/models.py

@@ -29,7 +29,6 @@
 from pydantic import BaseModel, Field, RootModel, StringConstraints, model_serializer
 
 from ga4gh.core.pydantic import (
-    is_ga4gh_identifiable,
     getattr_in
 )
 from ga4gh.core.entity_models import IRI, Expression, DomainEntity
@@ -44,7 +43,6 @@ def is_coll(thing):
         Return True if the thing looks like a collection.
         This is not exhaustive, do not use in general.
         """
-        # return hasattr(thing, '__iter__') and not isinstance(thing, str) and not inspect.isclass(thing)
         return type(thing) in [list, set]
     if is_coll(vals):
         for x in vals:
@@ -94,7 +92,7 @@ def pydantic_class_refatt_map():
     # Types directly reffable
     reffable_classes = list(filter(
         lambda c: ('id' in c.model_fields
-                   and is_ga4gh_identifiable(c)),
+                   and c.is_ga4gh_identifiable()),
         model_classes
     ))
     # Types reffable because they are a union of reffable types
@@ -235,9 +233,6 @@ def is_ga4gh_identifiable():
     def has_valid_ga4gh_id(self):
         return self.id and GA4GH_IR_REGEXP.match(self.id) is not None
 
-    def has_valid_digest(self):
-        return bool(self.digest)  # Pydantic constraint ensures digest field value is valid
-
     def compute_digest(self, store=True, as_version: PrevVrsVersion | None = None) -> str:
         """A sha512t24u digest created using the VRS Computed Identifier algorithm.