Revert to the OpenApiGenNoneType for tests

metamist/parser/generic_parser.py

@@ -320,8 +320,8 @@ def __init__(
     def to_sm(self) -> AssayUpsert:
         """Convert to SM upsert model"""
         return AssayUpsert(
-            type=self.assay_type,
             id=self.internal_id,
+            type=self.assay_type,
             external_ids=self.external_ids,
             # sample_id=self.s,
             meta=self.meta,

models/base.py

@@ -2,7 +2,7 @@
 
 # annotate any external objects that must be instantiated with this
 # type to force openapi generator to allow for Nones (it will actually allow Any)
-OpenApiGenNoneType = bytes
+OpenApiGenNoneType = bytes | None
 
 
 class SMBase(BaseModel):

models/models/assay.py

@@ -1,7 +1,7 @@
 import json
 from typing import Any
 
-from models.base import SMBase
+from models.base import OpenApiGenNoneType, SMBase
 from models.utils.sample_id_format import sample_id_format, sample_id_transform_to_raw
 
 
@@ -88,11 +88,11 @@ def to_internal(self):
 class AssayUpsert(SMBase):
     """Assay upsert model for external use"""
 
-    id: int | None = None
-    type: str | None = None
-    external_ids: dict[str, str] | None = None
-    sample_id: str | None = None
-    meta: dict[str, Any] | None = None
+    id: int | OpenApiGenNoneType = None
+    type: str | OpenApiGenNoneType = None
+    external_ids: dict[str, str] | OpenApiGenNoneType = None
+    sample_id: str | OpenApiGenNoneType = None
+    meta: dict[str, Any] | OpenApiGenNoneType = None
 
     def to_internal(self):
         """Convert to internal model"""
@@ -101,12 +101,12 @@ def to_internal(self):
         _sample_id = None
         if self.sample_id:
             # but may be provided directly when inserting directly
-            _sample_id = sample_id_transform_to_raw(self.sample_id)
+            _sample_id = sample_id_transform_to_raw(self.sample_id)  # type: ignore
 
         return AssayUpsertInternal(
-            id=self.id,
-            type=self.type,
-            external_ids=self.external_ids,
-            sample_id=_sample_id,
-            meta=self.meta,
+            id=self.id,  # type: ignore
+            type=self.type,  # type: ignore
+            external_ids=self.external_ids,  # type: ignore
+            sample_id=_sample_id,  # type: ignore
+            meta=self.meta,  # type: ignore
         )

models/models/participant.py

@@ -1,7 +1,7 @@
 import json
 
 from db.python.utils import ProjectId
-from models.base import SMBase
+from models.base import OpenApiGenNoneType, SMBase
 from models.models.family import FamilySimple, FamilySimpleInternal
 from models.models.sample import (
     NestedSample,
@@ -123,24 +123,24 @@ class NestedParticipant(SMBase):
 class ParticipantUpsert(SMBase):
     """External upsert model for participant"""
 
-    id: int | None = None
-    external_id: str | None = None
-    reported_sex: int | None = None
-    reported_gender: str | None = None
-    karyotype: str | None = None
-    meta: dict | None = None
+    id: int | OpenApiGenNoneType = None
+    external_id: str | OpenApiGenNoneType = None
+    reported_sex: int | OpenApiGenNoneType = None
+    reported_gender: str | OpenApiGenNoneType = None
+    karyotype: str | OpenApiGenNoneType = None
+    meta: dict | OpenApiGenNoneType = None
 
     samples: list[SampleUpsert] | None = None
 
     def to_internal(self):
         """Convert to internal model, doesn't really do much"""
         p = ParticipantUpsertInternal(
-            id=self.id,
-            external_id=self.external_id,
-            reported_sex=self.reported_sex,
-            reported_gender=self.reported_gender,
-            karyotype=self.karyotype,
-            meta=self.meta,
+            id=self.id,  # type: ignore
+            external_id=self.external_id,  # type: ignore
+            reported_sex=self.reported_sex,  # type: ignore
+            reported_gender=self.reported_gender,  # type: ignore
+            karyotype=self.karyotype,  # type: ignore
+            meta=self.meta,  # type: ignore
         )
 
         if self.samples:

models/models/sample.py

@@ -1,6 +1,6 @@
 import json
 
-from models.base import SMBase
+from models.base import OpenApiGenNoneType, SMBase
 from models.models.assay import Assay, AssayInternal, AssayUpsert, AssayUpsertInternal
 from models.models.sequencing_group import (
     NestedSequencingGroup,
@@ -159,13 +159,13 @@ class NestedSample(SMBase):
 class SampleUpsert(SMBase):
     """Upsert model for a Sample"""
 
-    id: str | None = None
-    external_id: str | None = None
-    meta: dict | None = None
-    project: int | None = None
-    type: str | None = None
-    participant_id: int | None = None
-    active: bool | None = None
+    id: str | OpenApiGenNoneType = None
+    external_id: str | OpenApiGenNoneType = None
+    meta: dict | OpenApiGenNoneType = None
+    project: int | OpenApiGenNoneType = None
+    type: str | OpenApiGenNoneType = None
+    participant_id: int | OpenApiGenNoneType = None
+    active: bool | OpenApiGenNoneType = None
 
     sequencing_groups: list[SequencingGroupUpsert] | None = None
     non_sequencing_assays: list[AssayUpsert] | None = None
@@ -178,12 +178,12 @@ def to_internal(self) -> SampleUpsertInternal:
 
         sample_upsert = SampleUpsertInternal(
             id=_id,
-            external_id=self.external_id,
-            meta=self.meta,
-            project=self.project,
-            type=self.type,
-            participant_id=self.participant_id,
-            active=self.active,
+            external_id=self.external_id,  # type: ignore
+            meta=self.meta,  # type: ignore
+            project=self.project,  # type: ignore
+            type=self.type,  # type: ignore
+            participant_id=self.participant_id,  # type: ignore
+            active=self.active,  # type: ignore
         )
 
         if self.sequencing_groups:

models/models/sequencing_group.py

@@ -1,6 +1,6 @@
 import json
 
-from models.base import SMBase
+from models.base import OpenApiGenNoneType, SMBase
 from models.models.assay import Assay, AssayInternal, AssayUpsert, AssayUpsertInternal
 from models.utils.sample_id_format import sample_id_format, sample_id_transform_to_raw
 from models.utils.sequencing_group_id_format import (
@@ -163,15 +163,15 @@ class SequencingGroupUpsert(SMBase):
     Upsert model for sequence group
     """
 
-    id: int | str | None = None
-    type: str | None = None
-    technology: str | None = None
-    platform: str | None = None
-    meta: dict[str, str] | None = None
-    sample_id: str | None = None
-    external_ids: dict[str, str] | None = None
+    id: int | str | OpenApiGenNoneType = None
+    type: str | OpenApiGenNoneType = None
+    technology: str | OpenApiGenNoneType = None
+    platform: str | OpenApiGenNoneType = None
+    meta: dict[str, str] | OpenApiGenNoneType = None
+    sample_id: str | OpenApiGenNoneType = None
+    external_ids: dict[str, str] | OpenApiGenNoneType = None
 
-    assays: list[AssayUpsert] | None = None
+    assays: list[AssayUpsert] | OpenApiGenNoneType = None
 
     def to_internal(self) -> SequencingGroupUpsertInternal:
         """
@@ -187,15 +187,15 @@ def to_internal(self) -> SequencingGroupUpsertInternal:
 
         sg_internal = SequencingGroupUpsertInternal(
             id=_id,
-            type=self.type,
-            technology=self.technology,
-            platform=self.platform.lower() if self.platform else None,
-            meta=self.meta,
+            type=self.type,  # type: ignore
+            technology=self.technology,  # type: ignore
+            platform=self.platform.lower() if self.platform else None,  # type: ignore
+            meta=self.meta,  # type: ignore
             sample_id=_sample_id,
-            external_ids=self.external_ids or {},
+            external_ids=self.external_ids or {},  # type: ignore
         )
 
         if self.assays is not None:
-            sg_internal.assays = [a.to_internal() for a in self.assays]
+            sg_internal.assays = [a.to_internal() for a in self.assays]  # type: ignore
 
         return sg_internal