Merge pull request #360 from pepkit/dev

Release `v0.13.0`

environment/local.dev.env

@@ -15,4 +15,6 @@ export HF_MODEL="BAAI/bge-small-en-v1.5"
 
 export GH_CLIENT_ID=`pass databio/pephub/gh_client_id`
 export GH_CLIENT_SECRET=`pass databio/pephub/gh_client_secret`
-export BASE_URI=http://localhost:8000
+export BASE_URI=http://localhost:8000
+
+export PH_DEV_MODE=true

pephub/_version.py

@@ -1 +1 @@
-__version__ = "0.12.0"
+__version__ = "0.13.0"

pephub/const.py

@@ -132,7 +132,7 @@
 
 CALLBACK_ENDPOINT = "/auth/callback"
 
-DEFAULT_PEP_SCHEMA = "pep/2.1.0"
+DEFAULT_PEP_SCHEMA = "databio/pep-2.1.0"
 DEFAULT_TAG = "default"
 
 DEFAULT_QDRANT_SCORE_THRESHOLD = (

pephub/dependencies.py

@@ -13,7 +13,7 @@
 from fastapi import Depends, Header, Query
 from fastapi.exceptions import HTTPException
 from fastapi.security import HTTPBearer
-from fastembed.embedding import FlagEmbedding as Embedding
+from fastembed.embedding import TextEmbedding as Embedding
 from pepdbagent import PEPDatabaseAgent
 from pepdbagent.const import DEFAULT_TAG
 from pepdbagent.exceptions import ProjectNotFoundError

pephub/main.py

@@ -15,6 +15,8 @@
 from .routers.api.v1.project import project as api_project
 from .routers.api.v1.project import projects as api_projects
 from .routers.api.v1.search import search as api_search
+from .routers.api.v1.schemas import schemas as api_schemas
+from .routers.api.v1.schemas import groups as api_groups
 from .routers.auth.base import auth as auth_router
 from .routers.eido.eido import router as eido_router
 
@@ -82,6 +84,8 @@
 app.include_router(api_project)
 app.include_router(api_projects)
 app.include_router(api_search)
+app.include_router(api_schemas)
+app.include_router(api_groups)
 app.include_router(auth_router)
 app.include_router(eido_router)
 

pephub/routers/api/v1/namespace.py

@@ -1,11 +1,10 @@
-import json
 import shutil
 import tempfile
 from typing import List, Literal, Optional, Union
 
 import peppy
 from dotenv import load_dotenv
-from fastapi import APIRouter, Depends, File, Form, HTTPException, Request, UploadFile
+from fastapi import APIRouter, Depends, File, Form, HTTPException, UploadFile
 from fastapi.responses import JSONResponse
 from pepdbagent import PEPDatabaseAgent
 from pepdbagent.const import DEFAULT_LIMIT_INFO
@@ -27,17 +26,13 @@
 from typing_extensions import Annotated
 
 from ....const import (
-    BLANK_PEP_CONFIG,
-    BLANK_PEP_SAMPLE_TABLE,
-    DEFAULT_PEP_SCHEMA,
     DEFAULT_TAG,
 )
 from ....dependencies import (
     get_db,
     get_namespace_access_list,
     get_namespace_info,
     get_user_from_session_info,
-    read_authorization_header,
     verify_user_can_write_namespace,
     get_pepdb_namespace_info,
 )
@@ -148,7 +143,7 @@ async def create_pep(
     is_private: bool = Form(False),
     tag: str = Form(DEFAULT_TAG),
     description: Union[str, None] = Form(None),
-    pep_schema: str = Form(DEFAULT_PEP_SCHEMA),
+    pep_schema: str = Form(None),
     files: List[UploadFile] = File(
         None  # let the file upload be optional. dont send a file? We instantiate with blank
     ),
@@ -208,7 +203,7 @@ async def create_pep(
     # create a blank peppy.Project object with fake files
     else:
         raise HTTPException(
-            detail=f"Project files were not provided",
+            detail="Project files were not provided",
             status_code=400,
         )
 

pephub/routers/api/v1/project.py

@@ -729,7 +729,7 @@ async def create_view_of_the_project(
         _LOGGER.error(f"Could not create view. Error: {e}")
         raise HTTPException(
             status_code=409,
-            detail="Could not create view",
+            detail="A view with this name already exists in the project.",
         )
     return JSONResponse(
         content={