Fixed #243

pephub/routers/api/v1/namespace.py

@@ -296,7 +296,7 @@ async def upload_raw_pep(
 
         # This configurations needed due to Issue #124 Should be removed in the future
         project_dict = ProjectRawModel(**project_from_json.pep_dict.dict())
-        ff = project_dict.dict(by_alias=True)
+        ff = project_dict.model_dump(by_alias=True)
         p_project = peppy.Project().from_dict(ff)
 
         p_project.name = name

pephub/routers/api/v1/project.py

@@ -65,7 +65,7 @@ async def get_a_pep(
             raw_project = ProjectRawModel(**proj)
         except Exception:
             raise HTTPException(500, "Unexpected project error!")
-        return raw_project.dict(by_alias=False)
+        return raw_project.model_dump(by_alias=False)
     samples = [s.to_dict() for s in proj.samples]
     sample_table_index = proj.sample_table_index
 
@@ -75,7 +75,7 @@ async def get_a_pep(
     sample_attributes = proj._samples[0]._attributes
 
     proj_dict = proj.to_dict()
-    proj_annotation_dict = proj_annotation.dict()
+    proj_annotation_dict = proj_annotation.model_dump()
 
     # default to name from annotation
     if hasattr(proj, "name") and hasattr(proj_annotation, "name"):
@@ -202,7 +202,7 @@ async def update_a_pep(
 
     # update "meta meta data"
     update_dict = {}  # dict used to pass to the `db.update_item` function
-    for k, v in updated_project.dict(exclude_unset=True).items():
+    for k, v in updated_project.model_dump(exclude_unset=True).items():
         # is the value an attribute of the peppy project?
         if k in new_raw_project:
             new_raw_project[k] = v
@@ -237,7 +237,7 @@ async def update_a_pep(
             # "project": raw_peppy_project,
             "registry": f"{namespace}/{project}:{tag}",
             "api_endpoint": f"/api/v1/namespaces/{namespace}/{project}",
-            "project": updated_project.dict(),
+            "project": updated_project.model_dump(),
         },
         status_code=202,
     )

pephub/routers/models.py

@@ -1,5 +1,5 @@
 from typing import Optional, List
-from pydantic import BaseModel, Field, Extra
+from pydantic import BaseModel, Field, ConfigDict
 from pepdbagent.models import UpdateItems
 from pepdbagent.const import DEFAULT_TAG
 
@@ -8,13 +8,12 @@
 
 class ProjectOptional(UpdateItems):
     # sample table is a list of JSON objects
-    sample_table: Optional[List[dict]]
-    project_config_yaml: Optional[str]
-    description: Optional[str]
-    subsample_tables: Optional[List[List[dict]]]
+    sample_table: Optional[List[dict]] = None
+    project_config_yaml: Optional[str] = None
+    description: Optional[str] = None
+    subsample_tables: Optional[List[List[dict]]] = None
 
-    class Config:
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True)
 
 
 class SearchQuery(BaseModel):
@@ -27,7 +26,7 @@ class SearchQuery(BaseModel):
 
 class RawValidationQuery(BaseModel):
     project_config: str
-    sample_table: Optional[str]
+    sample_table: Optional[str] = None
 
 
 class TokenExchange(BaseModel):
@@ -60,21 +59,18 @@ class JWTDeviceTokenResponse(BaseModel):
 
 class ProjectRawModel(BaseModel):
     config: dict = Field(alias="_config")
-    subsample_list: Optional[list] = Field(alias="_subsample_list")
+    subsample_list: Optional[list] = Field(alias="_subsample_list", default=None)
     sample_list: list[dict] = Field(alias="_sample_dict")
 
-    class Config:
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True)
 
 
 class ProjectRawRequest(BaseModel):
     config: dict
-    subsample_list: Optional[List[List[dict]]]
+    subsample_list: Optional[List[List[dict]]] = None
     sample_list: List[dict]
 
-    class Config:
-        allow_population_by_field_name = True
-        extra = Extra.allow
+    model_config = ConfigDict(populate_by_name=True, extra="allow")
 
 
 class ProjectJsonRequest(BaseModel):