fix: add maps endpoint

Author: xgui3783

.helm/siibra-api-v4-worker/templates/_helpers.tpl

@@ -11,6 +11,7 @@ Expand the name of the chart.
 {{- else -}}
 {{- printf "%s:%s" .Values.image.repository .Values.image.spec }}
 {{- end -}}
+{{- end -}}
 
 
 {{/*

api/common/data_handlers/core/misc.py

@@ -1,7 +1,14 @@
 from api.common import data_decorator, get_filename, NotFound
 from api.models.volumes.volume import MapType
 from api.siibra_api_config import ROLE
-from typing import Union, Dict, Tuple
+from typing import Union, Dict, Tuple, List
+
+def parse_maptype(maptype: Union[MapType, str]):
+    if isinstance(maptype, MapType):
+        assert maptype.name == maptype.value, f"str enum, expecting .name and .value to equal"
+        return maptype.name
+    if isinstance(maptype, str):
+        return maptype
 
 @data_decorator(ROLE)
 def get_map(parcellation_id: str, space_id: str, maptype: Union[MapType, str]) -> Dict:
@@ -22,13 +29,7 @@ def get_map(parcellation_id: str, space_id: str, maptype: Union[MapType, str]) -
     import siibra
     from api.serialization.util import instance_to_model
 
-    maptype_string = None
-    # check maptype name and value both matches
-    if isinstance(maptype, MapType):
-        assert maptype.name == maptype.value, f"str enum, expecting .name and .value to equal"
-        maptype_string = maptype.name
-    if isinstance(maptype, str):
-        maptype_string = maptype
+    maptype_string = parse_maptype(maptype)
 
     assert maptype_string is not None, f"maptype is neither MapType nor str"
 
@@ -41,7 +42,7 @@ def get_map(parcellation_id: str, space_id: str, maptype: Union[MapType, str]) -
         raise NotFound
 
     return instance_to_model(
-        returned_map
+        returned_map, detail=True
     ).dict()
 
 
@@ -213,4 +214,42 @@ def get_resampled_map(parcellation_id: str, space_id: str):
             "parcellation_id": parcellation_id,
             "space_id": space_id,
         }, indent="\t", fp=fp)
-    return full_filename, False
+    return full_filename, False
+
+
+@data_decorator(ROLE)
+def get_filtered_maps(parcellation_id: str=None, space_id: str=None, maptype: Union[MapType, str, None]=None):
+    import siibra
+    from api.serialization.util import instance_to_model
+
+    return_arr: List[siibra._parcellationmap.Map] = []
+    for mp in siibra.maps:
+        mp: siibra._parcellationmap.Map = mp
+        if (
+            parcellation_id is not None
+            and mp.parcellation.id != parcellation_id
+        ):
+            continue
+        if (
+            space_id is not None
+            and mp.space.id != space_id
+        ):
+            continue
+        if (
+            maptype is not None
+            and mp.maptype != parse_maptype(maptype)
+        ):
+            continue
+        return_arr.append(mp)
+    return [ instance_to_model(m).dict() for m in return_arr]
+
+
+@data_decorator(ROLE)
+def get_single_map(map_id: str):
+    import siibra
+    from api.serialization.util import instance_to_model
+    for mp in siibra.maps:
+        mp: siibra._parcellationmap.Map = mp
+        if mp.id == map_id:
+            return instance_to_model(mp, detail=True).dict()
+    raise NotFound(f"map with id {map_id} not found.")

api/models/volumes/parcellationmap.py

@@ -9,5 +9,7 @@ class MapModel(_SiibraAtlasConcept):
     species: str
     indices: Dict[str, List[MapIndexModel]]
     volumes: List[VolumeModel]
+    parcellation: SiibraAtIdModel
+    space: SiibraAtIdModel
+    maptype: str
     # affine: List[float]
-    

api/serialization/core/_concept.py

@@ -3,7 +3,7 @@
 from api.models.core._concept import SiibraAtlasConcept, SiibraPublication
 
 @serialize(AtlasConcept)
-def atlasconcept_to_model(concept: AtlasConcept) -> SiibraAtlasConcept:
+def atlasconcept_to_model(concept: AtlasConcept, **kwargs) -> SiibraAtlasConcept:
     """Serialize base concept.
 
     Args:

api/serialization/volumes/parcellationmap.py

@@ -1,9 +1,10 @@
 from api.models.volumes.parcellationmap import MapModel
+from api.models._commons import SiibraAtIdModel
 from api.serialization.util import serialize, instance_to_model
 from api.serialization.util.siibra import Map
 
 @serialize(Map, pass_super_model=True)
-def map_to_model(map: Map, super_model_dict={}, **kwargs) -> MapModel:
+def map_to_model(map: Map, super_model_dict={}, detail=False, **kwargs) -> MapModel:
     """Serialize map instance
     
     Args:
@@ -15,10 +16,13 @@ def map_to_model(map: Map, super_model_dict={}, **kwargs) -> MapModel:
     return MapModel(
         **super_model_dict,
         species=str(map.species),
+        parcellation=SiibraAtIdModel(id=map.parcellation.id),
+        space=SiibraAtIdModel(id=map.space.id),
+        maptype=map.maptype.name,
         indices={
-            regionname: instance_to_model(mapindex, **kwargs)
+            regionname: instance_to_model(mapindex, detail=detail, **kwargs)
             for regionname, mapindex in map._indices.items()
-        },
-        volumes=[instance_to_model(v, **kwargs) for v in map.volumes],
+        } if detail else {},
+        volumes=[instance_to_model(v, detail=detail, **kwargs) for v in map.volumes] if detail else [],
         # affine=map.affine.tolist()
     )

api/server/volumes/__init__.py

@@ -1,6 +1,8 @@
 from . import parcellationmap
+from . import maps
 from ..const import PrefixedRouter
 
 prefixed_routers = (
     PrefixedRouter(prefix="/map", router=parcellationmap.router),
+    PrefixedRouter(prefix="/maps", router=maps.router),
 )

api/server/volumes/maps.py

@@ -0,0 +1,43 @@
+from typing import Union
+
+from pydantic import BaseModel
+from fastapi import APIRouter, HTTPException
+from fastapi.responses import FileResponse
+from fastapi_versioning import version
+from fastapi_pagination import Page, paginate
+
+from api.models.volumes.volume import MapType
+from api.siibra_api_config import ROLE
+from api.server import FASTAPI_VERSION, cache_header
+from api.server.util import SapiCustomRoute
+from api.models.volumes.parcellationmap import MapModel
+from api.common import router_decorator, get_filename, logger, NotFound
+from api.common.data_handlers.core.misc import (
+    get_filtered_maps,
+    get_single_map,
+)
+
+TAGS=["maps"]
+"""HTTP map tags"""
+
+router = APIRouter(route_class=SapiCustomRoute, tags=TAGS)
+"""HTTP map router"""
+
+@router.get("", response_model=Page[MapModel])
+@version(*FASTAPI_VERSION)
+@router_decorator(ROLE, func=get_filtered_maps)
+def filter_map(parcellation_id: str=None, space_id: str=None, map_type: Union[MapType, None]=None, *, func):
+    """Get a list of maps according to specification"""
+    if func is None:
+        raise HTTPException(500, f"func: None passsed")
+    return paginate(func(parcellation_id, space_id, map_type))
+
+
+@router.get("/{map_id:lazy_path}", response_model=MapModel)
+@version(*FASTAPI_VERSION)
+@router_decorator(ROLE, func=get_single_map)
+def single_map(map_id: str, *, func):
+    """Get a list of maps according to specification"""
+    if func is None:
+        raise HTTPException(500, f"func: None passsed")
+    return func(map_id)

api/server/volumes/parcellationmap.py

@@ -28,11 +28,13 @@
 """HTTP map router"""
 
 # still use the old worker. New worker not stable (?)
-@router.get("", response_model=MapModel)
+@router.get("", response_model=MapModel, deprecated=True)
 @version(*FASTAPI_VERSION)
 @router_decorator(ROLE, func=old_get_map)
 def get_siibra_map(parcellation_id: str, space_id: str, map_type: MapType,  name: str= "", *, func):
-    """Get map according to specification"""
+    """Get map according to specification.
+    
+    Deprecated. use /maps/{map_id} instead."""
     if func is None:
         raise HTTPException(500, f"func: None passsed")
     return func(parcellation_id, space_id, map_type)