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Merged
fcollman merged 2 commits into from
Mar 14, 2026
Merged

Address PR #335 review feedback: version compat, validation, error handling, tests #336

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f33afc3
Initial plan
Copilot Mar 14, 2026
13247eb
Address all 6 review comments from PR #335
Copilot Mar 14, 2026
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76 changes: 46 additions & 30 deletions caveclient/skeletonservice.py
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Original file line number Diff line number Diff line change
Expand Up @@ -959,6 +959,7 @@ def generate_bulk_skeletons_async(

return estimated_async_time_secs_upper_bound_sum

@_check_version_compatibility(method_constraint=">=0.22.51")
def get_cached_skeletons_bulk(
self,
root_ids: List,
Expand Down Expand Up @@ -1003,6 +1004,12 @@ def get_cached_skeletons_bulk(
assert datastack_name is not None
assert skeleton_version is not None

skeleton_versions = self.get_versions()
if skeleton_version not in skeleton_versions:
raise ValueError(
f"Unknown skeleton version: {skeleton_version}. Valid options: {skeleton_versions}"
)

if len(root_ids) > MAX_BULK_CACHED_SKELETONS:
logging.warning(
f"The number of root_ids exceeds MAX_BULK_CACHED_SKELETONS ({MAX_BULK_CACHED_SKELETONS}). "
Expand All @@ -1022,7 +1029,6 @@ def get_cached_skeletons_bulk(
endpoint_mapping["skeleton_version"] = skeleton_version
endpoint_mapping["output_format"] = server_format
url = self._endpoints["get_cached_skeletons_bulk_as_post"].format_map(endpoint_mapping)
url += f"?verbose_level={verbose_level}"

data = {
"root_ids": root_ids,
Expand Down Expand Up @@ -1055,6 +1061,7 @@ def get_cached_skeletons_bulk(

return {"skeletons": skeletons, "missing": missing, "async_queued": async_queued}

@_check_version_compatibility(method_constraint=">=0.22.51")
def get_skeleton_access_token(
self,
root_ids: List,
Expand Down Expand Up @@ -1109,15 +1116,21 @@ def get_skeleton_access_token(
assert datastack_name is not None
assert skeleton_version is not None

skeleton_versions = self.get_versions()
if skeleton_version not in skeleton_versions:
raise ValueError(
f"Unknown skeleton version: {skeleton_version}. Valid options: {skeleton_versions}"
)

endpoint_mapping = self.default_url_mapping
endpoint_mapping["datastack_name"] = datastack_name
endpoint_mapping["skeleton_version"] = skeleton_version
url = self._endpoints["get_skeleton_token_as_post"].format_map(endpoint_mapping)
url += f"?verbose_level={verbose_level}"

data = {
"root_ids": root_ids,
"expiration_minutes": expiration_minutes,
"verbose_level": verbose_level,
}
response = self.session.post(url, json=data)
return handle_response(response)
Expand Down Expand Up @@ -1156,33 +1169,36 @@ def download_skeletons_with_token(
skeletons = {}

for rid, obj_path in object_paths.items():
encoded_path = urllib.parse.quote(obj_path, safe="")
url = f"https://storage.googleapis.com/download/storage/v1/b/{bucket}/o/{encoded_path}?alt=media"

# Use a direct get with the GCS token (overrides any session auth headers)
resp = self.session.get(url, headers=gcs_headers)
resp.raise_for_status()

# Stored files are gzip-compressed H5
h5_bytes = gzip.decompress(resp.content)

with h5py.File(io.BytesIO(h5_bytes), "r") as f:
sk = {
"vertices": np.array(f["vertices"][()]),
"edges": np.array(f["edges"][()]),
}
if "mesh_to_skel_map" in f:
sk["mesh_to_skel_map"] = np.array(f["mesh_to_skel_map"][()])
if "lvl2_ids" in f:
sk["lvl2_ids"] = np.array(f["lvl2_ids"][()])
if "vertex_properties" in f:
for vp_key in f["vertex_properties"].keys():
sk[vp_key] = np.array(
json.loads(f["vertex_properties"][vp_key][()])
)
if "meta" in f:
sk["meta"] = json.loads(f["meta"][()].tobytes())

skeletons[rid] = sk
try:
encoded_path = urllib.parse.quote(obj_path, safe="")
url = f"https://storage.googleapis.com/download/storage/v1/b/{bucket}/o/{encoded_path}?alt=media"

# Use a direct get with the GCS token (overrides any session auth headers)
resp = self.session.get(url, headers=gcs_headers)
resp.raise_for_status()

# Stored files are gzip-compressed H5
h5_bytes = gzip.decompress(resp.content)

with h5py.File(io.BytesIO(h5_bytes), "r") as f:
sk = {
"vertices": np.array(f["vertices"][()]),
"edges": np.array(f["edges"][()]),
}
if "mesh_to_skel_map" in f:
sk["mesh_to_skel_map"] = np.array(f["mesh_to_skel_map"][()])
if "lvl2_ids" in f:
sk["lvl2_ids"] = np.array(f["lvl2_ids"][()])
if "vertex_properties" in f:
for vp_key in f["vertex_properties"].keys():
sk[vp_key] = np.array(
json.loads(f["vertex_properties"][vp_key][()])
)
if "meta" in f:
sk["meta"] = json.loads(f["meta"][()].tobytes())

skeletons[rid] = sk
except Exception as e:
logging.error(f"Error downloading skeleton for root_id {rid}: {e}")

return skeletons
4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ maintainers = [{ name = "CAVE Developers" }]
name = "caveclient"
readme = "README.md"
requires-python = ">=3.9"
version = "8.0.0"
version = "8.1.0"

[project.urls]
Documentation = "https://caveconnectome.github.io/CAVEclient/"
Expand Down Expand Up @@ -73,7 +73,7 @@ test = [
allow_dirty = false
commit = true
commit_args = ""
current_version = "8.0.0"
current_version = "8.1.0"
ignore_missing_version = false
message = "Bump version: {current_version} → {new_version}"
parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
Expand Down
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