From 9ae00c3adc083b7ea9689e786ca63fbaaa4092ad Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 31 Jan 2025 12:50:25 -0500
Subject: [PATCH 1/2] featremove unsafe uses of assert

---
 src/ga4gh/core/enderef.py  | 4 +++-
 src/ga4gh/vrs/dataproxy.py | 3 ++-
 src/ga4gh/vrs/normalize.py | 4 +++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/ga4gh/core/enderef.py b/src/ga4gh/core/enderef.py
index 7808d2b0..17319107 100644
--- a/src/ga4gh/core/enderef.py
+++ b/src/ga4gh/core/enderef.py
@@ -48,7 +48,9 @@ def _enref(o):
             elif isinstance(v, str):
                 pass
             elif is_curie_type(v):    # already a reference
-                assert is_ga4gh_identifier(v), "Identifiable attribute CURIE is contains an invalid identifier"
+                if not is_ga4gh_identifier(v):
+                    msg = "Identifiable attribute CURIE is contains an invalid identifier"
+                    raise TypeError(msg)
             elif v is not None:
                 _id = _id_and_store(v)
                 if _id:
diff --git a/src/ga4gh/vrs/dataproxy.py b/src/ga4gh/vrs/dataproxy.py
index 0fd4d73b..53cb1e9a 100644
--- a/src/ga4gh/vrs/dataproxy.py
+++ b/src/ga4gh/vrs/dataproxy.py
@@ -308,7 +308,8 @@ def _isoformat(o):
     """
 
     # stolen from connexion flask_app.py
-    assert isinstance(o, datetime.datetime)
+    if not isinstance(o, datetime.datetime):
+        raise TypeError
     if o.tzinfo:
         # eg: '2015-09-25T23:14:42.588601+00:00'
         return o.isoformat("T")
diff --git a/src/ga4gh/vrs/normalize.py b/src/ga4gh/vrs/normalize.py
index 2e37bf60..744390a2 100644
--- a/src/ga4gh/vrs/normalize.py
+++ b/src/ga4gh/vrs/normalize.py
@@ -277,7 +277,9 @@ def normalize(vo, data_proxy=None, **kwargs):
             of the `sequence`. To exclude `state.sequence`, set to 0.
     """
 
-    assert is_pydantic_instance(vo)
+    if not is_pydantic_instance(vo):
+        msg = f"Object is of class {vo.__class__} (with parents {vo.__class__.__mro__}), but normalize requires objects that inherit from pydantic.BaseModel."
+        raise TypeError(msg)
     vo_type = vo.type
 
     if vo_type in handlers:

From 70d1420086b75a53e4298618ff8d95f0744c120b Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 31 Jan 2025 14:05:23 -0500
Subject: [PATCH 2/2] update docstrngs

---
 src/ga4gh/core/enderef.py  | 14 +++++++-------
 src/ga4gh/vrs/dataproxy.py |  3 +++
 src/ga4gh/vrs/normalize.py |  9 ++++++---
 3 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/src/ga4gh/core/enderef.py b/src/ga4gh/core/enderef.py
index 49b75027..ed6af244 100644
--- a/src/ga4gh/core/enderef.py
+++ b/src/ga4gh/core/enderef.py
@@ -26,13 +26,13 @@ def ga4gh_enref(o, cra_map, object_store=None, return_id_obj_tuple=False) -> tup
     """Recursively convert "referable attributes" from inlined to
     referenced form.  Returns a new object.
 
-    cra_map: class referrable-attribute map; { o.type: [attr, attr, ...] }
-
-    If `object_store` is provided, it must be an
-    collections.abc.MutableMapping subclass and will be used to store
-    objects as they are referenced.  If `object_store` is not provided
-    (or None), referenced objects will not be stored.
-
+    :param o: VRS object
+    :param cra_map: class referrable-attribute map; { o.type: [attr, attr, ...] }
+    :param object_store: `collections.abc.MutableMapping` subclass that stores
+        objects as they are referenced. If not given, referenced objects are not stored.
+    :param return_id_obj_tuple: include ID with return value or not
+    :return: new, enref'd object, as well as object ID if param set
+    :raise TypeError: if any object IDs are non-GA4GH CURIEs
     """
 
     def _id_and_store(o):  # noqa: ANN202 ANN001
diff --git a/src/ga4gh/vrs/dataproxy.py b/src/ga4gh/vrs/dataproxy.py
index e3d44d5f..ba2b5e2e 100644
--- a/src/ga4gh/vrs/dataproxy.py
+++ b/src/ga4gh/vrs/dataproxy.py
@@ -320,6 +320,9 @@ def _isoformat(o: datetime.datetime) -> str:
     >>> _isoformat(dt)
     '2019-10-15T10:23:41.115927Z'
 
+    :param o: date object to format
+    :return: ISO8601-formatted string equivalent
+    :raise TypeError: if object given isn't a Python datetime instance
     """
     # stolen from connexion flask_app.py
     if not isinstance(o, datetime.datetime):
diff --git a/src/ga4gh/vrs/normalize.py b/src/ga4gh/vrs/normalize.py
index 349e28e2..cc929a4f 100644
--- a/src/ga4gh/vrs/normalize.py
+++ b/src/ga4gh/vrs/normalize.py
@@ -273,9 +273,12 @@ def _normalize_cis_phased_block(o, data_proxy: _DataProxy | None = None):  # noq
 def normalize(vo, data_proxy: _DataProxy | None = None, **kwargs):
     """Normalize given vrs object, regardless of type
 
-    kwargs:
-        rle_seq_limit: If RLE is set as the new state, set the limit for the length
-            of the `sequence`. To exclude `state.sequence`, set to 0.
+    :param vo:
+    :param data_proxy: GA4GH sequence dataproxy instance, if needed
+    :keyword rle_seq_limit: If RLE is set as the new state, set the limit for the length
+        of the `sequence`. To exclude `state.sequence`, set to 0.
+    :return: normalized object
+    :raise TypeError: if given object isn't a pydantic.BaseModel
     """
     if not is_pydantic_instance(vo):
         msg = f"Object is of class {vo.__class__} (with parents {vo.__class__.__mro__}), but normalize requires objects that inherit from pydantic.BaseModel."