SkeletonService docs update. SkeletonService default versions clean-u…

…p on cache-query and exists entry points. (#268)
CAVEconnectome · Nov 21, 2024 · c80ee4d · c80ee4d
1 parent 6434662
commit c80ee4d
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Showing 3 changed files with 25 additions and 34 deletions.
diff --git a/caveclient/endpoints.py b/caveclient/endpoints.py
@@ -304,12 +304,8 @@
     "bulk_skeleton_info": skeleton_v1 + "/{datastack_name}/bulk/skeleton/info",
     "skeleton_info_versioned": skeleton_v1
     + "/{datastack_name}/precomputed/skeleton/{skvn}/info",
-    "get_cache_contents_via_ridprefixes": skeleton_v1
-    + "/{datastack_name}/precomputed/skeleton/query_cache/{root_id_prefixes}/{limit}",
     "get_cache_contents_via_skvn_ridprefixes": skeleton_v1
     + "/{datastack_name}/precomputed/skeleton/query_cache/{skeleton_version}/{root_id_prefixes}/{limit}",
-    "skeletons_exist_via_rids": skeleton_v1
-    + "/{datastack_name}/precomputed/skeleton/exists/{root_ids}",
     "skeletons_exist_via_skvn_rids": skeleton_v1
     + "/{datastack_name}/precomputed/skeleton/exists/{skeleton_version}/{root_ids}",
     "get_skeleton_via_rid": skeleton_v1

diff --git a/caveclient/skeletonservice.py b/caveclient/skeletonservice.py
@@ -316,7 +316,7 @@ def _build_bulk_async_endpoint(
     def get_cache_contents(
         self,
         datastack_name: Optional[str] = None,
-        skeleton_version: Optional[int] = 0,
+        skeleton_version: Optional[int] = 3,
         root_id_prefixes: Union[int, str, List] = 0,
         limit: Optional[int] = 0,
         log_warning: bool = True,
@@ -328,6 +328,12 @@ def get_cache_contents(
             datastack_name = self._datastack_name
         assert datastack_name is not None
 
+        valid_skeleton_versions = [-1, 0, 1, 2, 3]
+        if skeleton_version not in valid_skeleton_versions:
+            raise ValueError(
+                f"Unknown skeleton version: {skeleton_version}. Valid options: {valid_skeleton_versions}"
+            )
+
         if isinstance(root_id_prefixes, int):
             root_id_prefixes = str(root_id_prefixes)
         elif isinstance(root_id_prefixes, List):
@@ -338,15 +344,10 @@ def get_cache_contents(
         endpoint_mapping["root_id_prefixes"] = root_id_prefixes
         endpoint_mapping["limit"] = limit
 
-        if not skeleton_version:
-            url = self._endpoints["get_cache_contents_via_ridprefixes"].format_map(
-                endpoint_mapping
-            )
-        else:
-            endpoint_mapping["skeleton_version"] = skeleton_version
-            url = self._endpoints["get_cache_contents_via_skvn_ridprefixes"].format_map(
-                endpoint_mapping
-            )
+        endpoint_mapping["skeleton_version"] = skeleton_version
+        url = self._endpoints["get_cache_contents_via_skvn_ridprefixes"].format_map(
+            endpoint_mapping
+        )
 
         response = self.session.get(url)
         self.raise_for_status(response, log_warning=log_warning)
@@ -357,7 +358,7 @@ def get_cache_contents(
     def skeletons_exist(
         self,
         datastack_name: Optional[str] = None,
-        skeleton_version: Optional[int] = 0,
+        skeleton_version: Optional[int] = 3,
         root_ids: Union[int, str, List] = 0,
         log_warning: bool = True,
     ):
@@ -368,6 +369,12 @@ def skeletons_exist(
             datastack_name = self._datastack_name
         assert datastack_name is not None
 
+        valid_skeleton_versions = [-1, 0, 1, 2, 3]
+        if skeleton_version not in valid_skeleton_versions:
+            raise ValueError(
+                f"Unknown skeleton version: {skeleton_version}. Valid options: {valid_skeleton_versions}"
+            )
+
         if isinstance(root_ids, int):
             root_ids = str(root_ids)
         elif isinstance(root_ids, List):
@@ -377,15 +384,10 @@ def skeletons_exist(
         endpoint_mapping["datastack_name"] = datastack_name
         endpoint_mapping["root_ids"] = root_ids
 
-        if not skeleton_version:
-            url = self._endpoints["skeletons_exist_via_rids"].format_map(
-                endpoint_mapping
-            )
-        else:
-            endpoint_mapping["skeleton_version"] = skeleton_version
-            url = self._endpoints["skeletons_exist_via_skvn_rids"].format_map(
-                endpoint_mapping
-            )
+        endpoint_mapping["skeleton_version"] = skeleton_version
+        url = self._endpoints["skeletons_exist_via_skvn_rids"].format_map(
+            endpoint_mapping
+        )
 
         response = self.session.get(url)
         self.raise_for_status(response, log_warning=log_warning)

diff --git a/docs/tutorials/skeletonization.md b/docs/tutorials/skeletonization.md
@@ -39,15 +39,8 @@ sk = client.skeleton.get_skeleton(
 
 where the availale output_formats (described below) are:
 
-* none (default if unspecified)
-* h5
-* swc
-* swccompressed
-* json
-* jsoncompressed
-* arrays
-* arrayscompressed
-* precomputed
+* ```'dict'``` (default if unspecified)
+* ```'swc'``` (a Pandas Dataframe)
 
 If the skeleton doesn't exist in the server cache, it may take 20-60 seconds to generate the skeleton before it is returned. This function will block during that time. Any subsequent retrieval of the same skeleton should go very quickly however.
 
@@ -82,7 +75,7 @@ get_cache_contents(
 )
 ```
 
-You can also add addiional parameters as needed:
+You can also add additional parameters as needed:
 
 ```python
 get_cache_contents(