debug: access log middleware

.helm/adhoc/copy-cache.yaml

@@ -12,7 +12,7 @@ spec:
     - /bin/ash
     args:
     - -c
-    - "echo FROM_DIR: $FROM_DIR TO_DIR: $TO_DIR && mkdir $TO_DIR && cp -r $FROM_DIR/* $TO_DIR/"
+    - "echo FROM_DIR: $FROM_DIR TO_DIR: $TO_DIR && mkdir -p $TO_DIR && cp -r $FROM_DIR/* $TO_DIR/"
     resources:
       limits:
         cpu: 1000m

VERSION

@@ -1 +1 @@
-0.3.18
+0.3.19

api/server/api.py

@@ -298,6 +298,8 @@ async def middleware_add_version_header(request: Request, call_next):
 @siibra_api.middleware("http")
 async def middleware_access_log(request: Request, call_next):
     """Access log middleware"""
+
+    print("AccessLog middleware called")
 
     if request.url.path in do_not_logs:
         return await call_next(request)
@@ -324,6 +326,7 @@ async def middleware_access_log(request: Request, call_next):
             "hit_cache": "cache_miss"
         })
     except Exception as e:
+        print("Exception at logging:", type(e), str(e))
         general_logger.critical(e)
 
 # some plugins may strip origin header for privacy reasons

api/server/volumes/parcellationmap.py

@@ -38,7 +38,6 @@ def get_resampled_map(parcellation_id: str, space_id: str, *, func):
     """Get resampled map according to specification"""
     if func is None:
         raise HTTPException(500, f"func: None passsed")
-    raise HTTPException(501, "Not yet implemented. If you are using this endpoint, please contact us.")
     headers={
         "content-type": "application/octet-stream",
         "content-disposition": f'attachment; filename="labelled_map.nii.gz"'

api/siibra_api_config.py

@@ -70,6 +70,7 @@ def get_config_dir_short_hash(path_to_config: str):
     "features",
     "volumes",
     "compounds",
+    "vocabularies",
 ]
 
 class CELERY_CONFIG:

new_api/data_handlers/maps.py

@@ -106,13 +106,15 @@ def cache_resampled_map(parcellation_id: str, space_id: str, *, no_cache: bool):
 
     import nibabel as nib
     import siibra
-    from siibra.commons.maps import resample_img_to_img
+    from siibra.operations.volume_fetcher.nifti import ResampleNifti
 
     mp = siibra.get_map(parcellation_id, space_id, "labelled")
-    nii = mp.fetch()
+    src_dp = mp.extract_full_map()
+    nii = src_dp.get_data()
     space = siibra.get_space(space_id)
-    tmpl_nii = space.fetch_template()
-    resampled = resample_img_to_img(nii, tmpl_nii)
+    target_dp = space.get_dataprovider(index=0)
+    tmpl_nii = target_dp.get_data()
+    resampled = ResampleNifti.resample_img_to_img(nii, tmpl_nii)
 
     nib.save(resampled, full_filename)
     with open(f"{full_filename}.{str(int(time.time()))}.json", "w") as fp:

requirements/v4-siibra.txt

@@ -1,2 +1,2 @@
 # refactor_attr is... borked since dataops are being introduced
-git+https://github.com/xgui3783/siibra-python.git@aeffb478a1c98f3bec276ab820f5e50355c598a4
+git+https://github.com/xgui3783/siibra-python.git@90ba8150f4d3b01c36176b03ffa906f8090907cd