deploy: reverse volume mapping

deploy: more efficient service meta
fix: tests/remapping url

.helm/adhoc/configmaps-siibra-api-common.yml

@@ -8,7 +8,6 @@ data:
   # when prod migrates to 0.3.18, remove prepend
   _MONITOR_FIRSTLVL_DIR: /siibra-api-volume
   SIIBRA_API_REMAP_PROVIDERS: |-
-    https://neuroglancer.humanbrainproject.eu::https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data
     https://object.cscs.ch/v1/AUTH_08c08f9f119744cbbf77e216988da3eb::https://data-proxy.ebrains.eu/api/v1/buckets/reference-atlas-data/imgsvc
 kind: ConfigMap
 metadata:

api/serialization/volumes/volume.py

@@ -24,12 +24,12 @@ def remap_provider(obj: Dict[str, Union[dict, str]]) -> None:
     """
     if len(SIIBRA_API_REMAP_PROVIDERS) == 0:
         return obj
-    for key, value in obj.items():
-        if isinstance(value, str):
+    for key in obj:
+        if isinstance(obj[key], str):
             for from_host, to_host in SIIBRA_API_REMAP_PROVIDERS.items():
-                obj[key] = value.replace(from_host, to_host)
-        if isinstance(value, dict):
-            remap_provider(value)
+                obj[key] = obj[key].replace(from_host, to_host)
+        if isinstance(obj[key], dict):
+            remap_provider(obj[key])
 
 
 @serialize(Volume)

api/server/api.py

@@ -70,18 +70,23 @@ def get_ready():
     TODO: implement me"""
     return "ready"
 
+_code_meta = None
 @siibra_api.get("/about", include_in_schema=False)
 def servicemeta():
-    with open(Path(__file__).parent.parent.parent / "codemeta.json", "r") as fp:
-        code_meta = json.load(fp=fp)
+    global _code_meta
+    if _code_meta is None:
+        with open(Path(__file__).parent.parent.parent / "codemeta.json", "r") as fp:
+            _code_meta = json.load(fp=fp)
+    if _code_meta is None:
+        raise Exception("code meta is not found, cannot populate servicemeta")
     return {
         "@context": "https://gitlab.ebrains.eu/lauramble/servicemeta/-/raw/main/data/contexts/servicemeta.jsonld",
         "type": "WebApplication",
-        "author": code_meta["author"],
-        "dateModified": code_meta["dateModified"],
+        "author": _code_meta["author"],
+        "dateModified": _code_meta["dateModified"],
         "documentation": DOCUMENTATION_URL,
-        "name": code_meta["name"],
-        "version": code_meta["version"],
+        "name": _code_meta["name"],
+        "version": _code_meta["version"],
         "inputFormat": INPUT_FORMAT,
         "outputFormat": OUTPUT_FORMAT
     }
@@ -113,7 +118,7 @@ async def read_bytes(generator) -> bytes:
     "metrics",
     "openapi.json",
     "atlas_download",
-    "servicemeta",
+    "/about",
 ]
 
 do_no_cache_query_list = [
@@ -124,7 +129,7 @@ async def read_bytes(generator) -> bytes:
 do_not_logs = (
     "/ready",
     "/metrics",
-    "servicemeta"
+    "/about"
 )
 
 

test/serialization/features/molecular/test_receptor_density_fingerprint.py

@@ -10,7 +10,7 @@
     instance_to_model
 )
 
-receptor_fp_feats = ReceptorDensityFingerprint._get_instances()
+receptor_fp_feats = ReceptorDensityFingerprint.get_instances()
 
 def test_length():
     assert len(receptor_fp_feats) > 0

test/serialization/features/test_connectivity.py

@@ -6,9 +6,9 @@
 
 jba29 = parcellations['2.9']
 
-streamline_counts = [f for f in StreamlineCounts._get_instances()]
-streamline_lengths = [f for f in StreamlineLengths._get_instances()]
-functional_conn = [f for f in FunctionalConnectivity._get_instances()]
+streamline_counts = [f for f in StreamlineCounts.get_instances()]
+streamline_lengths = [f for f in StreamlineLengths.get_instances()]
+functional_conn = [f for f in FunctionalConnectivity.get_instances()]
 
 all_connectivity: list[RegionalConnectivity] = [
     *streamline_counts,
@@ -25,14 +25,15 @@ def test_conn(conn: RegionalConnectivity):
 
 if not os.getenv("FAST_RUN"):
     @pytest.mark.parametrize("conn,subject",
-                            [(f, f.subject)
+                            [(f, subject)
                                 for f in all_connectivity
+                                for subject in f.subjects
                                 if jba29 in f.anchor.parcellations],
                             ids=lambda arg: f"name: {arg.name!r} paradigm: {arg.paradigm if hasattr(arg, 'paradigmn') else ''}"
                                 if isinstance(arg, RegionalConnectivity)
                                 else f"subject: {arg!r}")
     def test_conn_subject(conn: RegionalConnectivity, subject: str):
         model = instance_to_model(conn, subject=subject, detail=True)
         assert isinstance(model, SiibraRegionalConnectivityModel)
-        assert model.matrix is not None
+        assert model.matrices is not None
         model.dict()

test/serialization/features/test_tabular.py

@@ -24,9 +24,9 @@ def get_random_n(n: int, lls: List[List[Any]]):
         for ls in lls
     ]
 
-celldensity = LayerwiseCellDensity._get_instances()
-bb_intensities = LayerwiseBigBrainIntensities._get_instances()
-receptor_fp_features = ReceptorDensityFingerprint._get_instances()
+celldensity = LayerwiseCellDensity.get_instances()
+bb_intensities = LayerwiseBigBrainIntensities.get_instances()
+receptor_fp_features = ReceptorDensityFingerprint.get_instances()
 
 all_fp_features = [
     *bb_intensities[10:],

test/serialization/features/test_voi.py

@@ -6,8 +6,8 @@
 )
 
 features = [feat 
-            for Cls in Feature._SUBCLASSES[Image]
-            for feat in Cls._get_instances()]
+            for Cls in Feature.SUBCLASSES[Image]
+            for feat in Cls.get_instances()]
 
 def test_len():
     assert len(features) > 0