fix: logger -> general_logger

fix: move origin header middleware
fix: ebrains ds person default None value
feat: cache retrieved dsv

api/server/api.py

@@ -21,7 +21,7 @@
 from .metrics import prom_metrics_resp, on_startup as metrics_on_startup, on_terminate as metrics_on_terminate
 from .code_snippet import get_sourcecode
 
-from ..common import logger, access_logger, NotFound, SapiBaseException, name_to_fns_map
+from ..common import logger, general_logger, access_logger, NotFound, SapiBaseException, name_to_fns_map
 from ..siibra_api_config import GIT_HASH
 
 siibra_version_header = "x-siibra-api-version"
@@ -55,18 +55,6 @@
     expose_headers=[siibra_version_header]
 )
 
-# some plugins may strip origin header for privacy reasons
-# so if origin is unavailable, append it to trick corsmiddleware to activate
-@siibra_api.middleware("http")
-async def append_origin_header(request: Request, call_next):
-    headers = dict(request.scope["headers"])
-    origin = request.headers.get("origin")
-    new_headers = [(k, v) for k, v in headers.items()]
-    if not origin:
-        new_headers.append((b"origin", b"unknownorigin.dev"))
-    request.scope["headers"] = new_headers
-    return await call_next(request)
-
 @siibra_api.get("/metrics", include_in_schema=False)
 def get_metrics():
     """Get prometheus metrics"""
@@ -295,15 +283,27 @@ async def middleware_access_log(request: Request, call_next):
             "hit_cache": "cache_miss"
         })
     except Exception as e:
-        logger.critical(e)
+        general_logger.critical(e)
+
+# some plugins may strip origin header for privacy reasons
+# so if origin is unavailable, append it to trick corsmiddleware to activate
+@siibra_api.middleware("http")
+async def append_origin_header(request: Request, call_next):
+    headers = dict(request.scope["headers"])
+    origin = request.headers.get("origin")
+    new_headers = [(k, v) for k, v in headers.items()]
+    if not origin:
+        new_headers.append((b"origin", b"unknownorigin.dev"))
+    request.scope["headers"] = new_headers
+    return await call_next(request)
 
 @siibra_api.exception_handler(RuntimeError)
 async def exception_runtime(request: Request, exc: RuntimeError) -> JSONResponse:
     """Handling RuntimeErrors.
     Most of the RuntimeErrors are thrown by the siibra-python library when other Services are not responding.
     To be more resilient and not throw a simple and unplanned HTTP 500 response, this handler will return an HTTP 503
     status."""
-    logger.warning(f"Error handler: exception_runtime: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_runtime: {str(exc)}")
     return JSONResponse(
         status_code=503,
         content={
@@ -312,16 +312,17 @@ async def exception_runtime(request: Request, exc: RuntimeError) -> JSONResponse
         },
     )
 
+
 @siibra_api.exception_handler(SapiBaseException)
 def exception_sapi(request: Request, exc: SapiBaseException):
     """Handle sapi errors"""
-    logger.warning(f"Error handler: exception_sapi: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_sapi: {str(exc)}")
     raise HTTPException(400, str(exc))
 
 @siibra_api.exception_handler(Exception)
 async def exception_other(request: Request, exc: Exception):
     """Catch all exception handler"""
-    logger.warning(f"Error handler: exception_other: {str(exc)}")
+    general_logger.warning(f"Error handler: exception_other: {str(exc)}")
     return JSONResponse(
         status_code=500,
         content={

new_api/v3/models/_retrieval/datasets.py

@@ -11,7 +11,7 @@ class EbrainsDsUrl(ConfigBaseModel):
 class EbrainsDsPerson(ConfigBaseModel):
     """EbrainsDsPerson"""
     id: str = Field(..., alias="@id")
-    schema_shortname: Optional[str] = Field(..., alias="schema.org/shortName")
+    schema_shortname: Optional[str] = Field(None, alias="schema.org/shortName")
     identifier: str
     shortName: str
     name: str

new_api/v3/serialization/map.py

@@ -8,6 +8,7 @@
 from new_api.v3.models.core._concept import SiibraPublication
 from new_api.v3.models._retrieval.datasets import EbrainsDatasetModel, EbrainsDsPerson
 
+from siibra.cache import fn_call_cache
 from siibra.atlases.parcellationmap import Map
 from siibra.atlases.sparsemap import SparseMap
 from siibra.attributes.descriptions import Name, EbrainsRef
@@ -44,6 +45,13 @@ def clear_name(name: str):
         result = result.replace(search, repl)
     return " ".join(w for w in result.split(" ") if len(w))
 
+@fn_call_cache
+def retrieve_dsv(mp: Map):
+    got_dsv = [ EbrainsQuery.get_dsv(dsv)
+                for ref in mp._find(EbrainsRef)
+                for dsv in ref._dataset_verion_ids]
+    return got_dsv
+
 @serialize(SparseMap)
 @serialize(Map)
 def map_to_model(mp: Map, **kwargs):
@@ -57,20 +65,17 @@ def map_to_model(mp: Map, **kwargs):
     publications = [SiibraPublication(citation=pub.text, url=pub.value)
                     for pub in mp.publications]
 
-    got_dsv = [ EbrainsQuery.get_dsv(dsv)
-                for ref in mp._find(EbrainsRef)
-                for dsv in ref._dataset_verion_ids]
-
+    got_dsv = retrieve_dsv(mp)
     # TODO check for any non empty entry of custodian and transform properly
     datasets = [EbrainsDatasetModel(id=dsv["id"],
-                                   name=dsv["fullName"] or "",
-                                   urls=[{"url": dsv["homepage"]}] if dsv["homepage"] else [],
-                                   description=dsv["description"],
-                                   contributors=[EbrainsDsPerson(id=author["id"],
-                                                                 identifier=author["id"],
-                                                                 shortName=author["shortName"],
-                                                                 name=author["fullName"]) for author in dsv["author"]],
-                                   custodians=[]) for dsv in got_dsv]
+                                    name=dsv["fullName"] or "",
+                                    urls=[{"url": dsv["homepage"]}] if dsv["homepage"] else [],
+                                    description=dsv["description"],
+                                    contributors=[EbrainsDsPerson(id=author["id"],
+                                                                  identifier=author["id"],
+                                                                  shortName=author["shortName"] or f"{author['givenName']} {author['familyName']}",
+                                                                  name=author["fullName"] or f"{author['givenName']} {author['familyName']}") for author in dsv["author"]],
+                                    custodians=[]) for dsv in got_dsv]
 
     # specific to map model
     species = mp.species