add logs to debug broken ORCID login

backend/app/api/nanopub.py

@@ -77,7 +77,8 @@ def get_np_config(user_id: str) -> NanopubConf:
 @router.post(
     "/assertion",
     name="Publish an Assertion",
-    description="""Post an RDF assertion as JSON-LD (only triples, no graph) that will be published in a Nanopublication using the key previously stored with your ORCID user""",
+    description="""Post an RDF assertion as JSON-LD that will be published in a Nanopublication using the key previously stored with your ORCID user.
+You can also provide additional provenance using the special `@provenance` key.""",
     response_description="Operation result",
     response_model={},
 )
@@ -91,6 +92,7 @@ async def publish_assertion(
 ) -> Response:
     nanopub_rdf = jsonable_encoder(nanopub_rdf)
 
+    print(current_user)
     if not current_user or "id" not in current_user.keys():
         raise HTTPException(
             status_code=403,

backend/app/config.py

@@ -2,7 +2,9 @@
 import secrets
 from typing import Optional, Union
 
-from pydantic import BaseSettings, validator
+from pydantic import validator, BaseSettings
+# from pydantic_settings import BaseSettings
+# from pydantic_settings import BaseSettings, SettingsConfigDict
 
 
 class Settings(BaseSettings):
@@ -11,7 +13,7 @@ class Settings(BaseSettings):
     STAGING_URL: str = "https://collaboratory-api.ci.transltr.io"
     DEV_URL: str = "https://api.collaboratory.semanticscience.org"
 
-    VIRTUAL_HOST: str = None
+    VIRTUAL_HOST: Optional[str] = None
 
     BIOLINK_VERSION: str = "3.1.0"
     TRAPI_VERSION: str = "1.4.0"
@@ -23,8 +25,8 @@ class Settings(BaseSettings):
     # The settings used by Docker deployment are in the .env file
     PROJECT_NAME: str = "Knowledge Collaboratory API"
     DATA_PATH: str = "/data"
-    KEYSTORE_PATH: Optional[str]
-    NER_MODELS_PATH: Optional[str]
+    KEYSTORE_PATH: str = "./nanopub-keystore"
+    NER_MODELS_PATH: str = "./ner-models"
 
     NANOPUB_GRLC_URL: str = "https://grlc.np.dumontierlab.com/api/local/local"
     NANOPUB_SPARQL_URL: str = "https://virtuoso.nps.petapico.org/sparql"
@@ -72,6 +74,7 @@ def assemble_cors_origins(cls, v: Union[str, list[str]]) -> Union[list[str], str
     class Config:
         case_sensitive = True
         env_file = ".env"
+    # model_config = SettingsConfigDict(env_file=".env", env_file_encoding='utf-8')
 
     def __init__(
         self,

backend/pyproject.toml

@@ -28,14 +28,14 @@ dependencies = [
     "python-multipart >=0.0.5",
     "requests >=2.23.0",
     "httpx >=0.21.1",
-    "pydantic[dotenv] >=1.9",
+    "pydantic[dotenv] <2.0.0", # reasoner-pydantic not updated to v2 https://github.com/TranslatorSRI/reasoner-pydantic/issues/63
+    # "pydantic-settings",
     "fastapi >=0.68.1",
     "uvicorn >=0.15.0",
     "gunicorn >=20.0.4",
     "Authlib >=0.15.4",
     "itsdangerous >=2.0.1",
     "reasoner-pydantic >=2.2.3",
-    # "reasoner-pydantic ==3.0.1",
     # TODO: we can remove kgx once poetry finally manage to find 3.1.5
     # "kgx >=1.6.0",
     "rdflib >=6.1.1",

frontend/src/components/PublishNanopubButtons.tsx

@@ -126,6 +126,7 @@ const PublishNanopubButtons = ({
         requestParams['source'] = inputSource
       }
       const access_token = user['access_token']
+      console.log(user)
       axios
         .post(`${$userSettings.api}/assertion`, stmtJsonld, {
           headers: {Authorization: `Bearer ${access_token}`},

frontend/src/pages/about.tsx

@@ -8,6 +8,7 @@ import ApiIcon from '@mui/icons-material/Storage'
 import SearchIcon from '@mui/icons-material/Search'
 import PublishIcon from '@mui/icons-material/Outbox'
 
+
 export default function About() {
   const theme = useTheme()
   const [state, setState] = React.useState({