Get minimal covering nodes (#274)

* fixing minimal covering nodes * adding version constraint * adding version constraint * add version 2 range constraint * adding test for new feature * fixing whitespace * ignoring notebooks in formatting * fixing formatting * updating uv.lock * including tests and docs in linting
CAVEconnectome · Dec 5, 2024 · bcc1c5b · bcc1c5b
1 parent c335026
commit bcc1c5b
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Showing 7 changed files with 143 additions and 3 deletions.
diff --git a/caveclient/chunkedgraph.py b/caveclient/chunkedgraph.py
@@ -261,6 +261,34 @@ def get_root_id(self, supervoxel_id, timestamp=None, level2=False) -> np.int64:
         response = self.session.get(url, params=query_d)
         return np.int64(handle_response(response, as_json=True)["root_id"])
 
+    @_check_version_compatibility(method_constraint="<3,>=2.18.0")
+    def get_minimal_covering_nodes(self, node_ids: Iterable[np.int64 or int]) -> dict:
+        """Get the minimal covering nodes for a list of root IDs.
+
+        Parameters
+        ----------
+        nodes_ids : Iterable of int or np.int64
+            List of root IDs to query.
+
+        Returns
+        -------
+        np.array of np.int64:
+            List of PCG node_ids that minimally and exactly cover the input nodes
+        """
+
+        endpoint_mapping = self.default_url_mapping
+        url = self._endpoints["minimal_covering_nodes"].format_map(endpoint_mapping)
+        query_d = {}
+        query_d["as_array"] = True
+        data = json.dumps({"node_ids": node_ids}, cls=BaseEncoder)
+        response = self.session.post(
+            url,
+            data=data,
+            params=query_d,
+            headers={"Content-Type": "application/json"},
+        )
+        return np.frombuffer(response.content, dtype=np.uint64)
+
     def get_merge_log(self, root_id) -> list:
         """Get the merge log (splits and merges) for an object.
 

diff --git a/caveclient/endpoints.py b/caveclient/endpoints.py
@@ -159,6 +159,7 @@
     "do_merge": pcg_v1 + "/table/{table_id}/merge",
     "get_roots": pcg_v1 + "/table/{table_id}/roots_binary",
     "leaves_many": pcg_v1 + "/table/{table_id}/node/leaves_many",
+    "minimal_covering_nodes": pcg_v1 + "/table/{table_id}/minimal_covering_nodes",
     "merge_log": pcg_v1 + "/table/{table_id}/root/{root_id}/merge_log",
     "change_log": pcg_v1 + "/table/{table_id}/root/{root_id}/change_log",
     "tabular_change_log": pcg_v1 + "/table/{table_id}/tabular_change_log_many",

diff --git a/caveclient/tools/testing.py b/caveclient/tools/testing.py
@@ -16,7 +16,7 @@
     warnings.warn("Must install responses to use CAVEclientMock for testing")
     imports_worked = False
 
-DEFAULT_CHUNKEDGRAPH_SERVER_VERSION = "2.15.0"
+DEFAULT_CHUNKEDGRAPH_SERVER_VERSION = "2.18.0"
 DEFAULT_MATERIALIZATION_SERVER_VERSON = "4.30.1"
 DEFAULT_SKELETON_SERVICE_SERVER_VERSION = "0.3.8"
 DEFAULT_JSON_SERVICE_SERVER_VERSION = "0.7.0"

diff --git a/pyproject.toml b/pyproject.toml
@@ -78,6 +78,9 @@ tag_name = "v{new_version}"
 [[tool.bumpversion.files]]
 filename = "pyproject.toml"
 
+[tool.ruff.lint]
+exclude = ['*.ipynb']
+
 [tool.poe.tasks]
 checks = ['doc-build', 'lint', 'test']
 doc-build = "mkdocs build"

diff --git a/tests/test_chunkedgraph.py b/tests/test_chunkedgraph.py
@@ -138,6 +138,114 @@ def test_get_leaves_many(self, myclient):
         for k, v in svids_ret.items():
             assert np.all(v == sv_dict[str(k)])
 
+    @responses.activate
+    def test_minimal_covering_nodes(self, myclient):
+        endpoint_mapping = self._default_endpoint_map
+        l2ids = [
+            151733086944494680,
+            151803455688671629,
+            151803524408148361,
+            151803524408148371,
+            151873824432849265,
+            151873893152326692,
+            151873961871802557,
+            151944261829395442,
+            151944261896503344,
+            151944330615980096,
+            152014630573572920,
+            152014630573573159,
+            152014699360157777,
+            152084999317750839,
+            152155368061928130,
+            152225736806105726,
+            152296105550283453,
+            152296174269760177,
+            152366543013938289,
+            152436911758115473,
+            152436980477592301,
+            152507349221769815,
+            152577717965948027,
+            152577786685424795,
+            152577786685424797,
+            152648155429602343,
+            152648155429602345,
+            152648224149078995,
+            152718524173779595,
+            152718592893256250,
+            152788961637433848,
+            152859330381611287,
+            152859399101088529,
+            152929767845266045,
+            152929767845266047,
+            152929836564742225,
+            153000136589443132,
+            153000205308919861,
+            153070574053098110,
+            153140942797275294,
+            153141011516751998,
+            153141080236228767,
+            153211311541453183,
+            153211380260929846,
+            153211448980406620,
+            153211448980406624,
+            153211517699883483,
+            153281817724584437,
+            153281886444061198,
+            153352186468762089,
+            153352255188238828,
+            153422623932416499,
+            153422692651893340,
+            153492992676594177,
+            153493061396070924,
+            153563430140248766,
+            153563498859725522,
+            153633798884426257,
+            153633867603903006,
+            153704236348080465,
+            153774605092258013,
+            153774673811734916,
+            153844973836435679,
+            153845042555912428,
+            153915342580613364,
+            153915411300090031,
+            153985711324791351,
+            154056080068969264,
+            154126448813146756,
+            154126448813146804,
+            154126517532623397,
+            154196817557324412,
+            154196886276800996,
+            154267186301502007,
+            154267255020978536,
+            154337623765156171,
+            154337692484633043,
+        ]
+
+        covering_nodes = [
+            226343819258366071,
+            298438259283864547,
+            441652105523081273,
+            441652105523071767,
+            441652105523184668,
+            441634513337085631,
+            650770146159222932,
+        ]
+
+        url = chunkedgraph_endpoints_v1["minimal_covering_nodes"].format_map(
+            endpoint_mapping
+        )
+        query_d = {"as_array": True}
+        urlq = url + "?" + urlencode(query_d)
+        responses.add(
+            responses.POST,
+            body=np.array(covering_nodes).tobytes(),
+            url=urlq,
+            match=[json_params_matcher({"node_ids": l2ids})],
+        )
+
+        node_ids = myclient.chunkedgraph.get_minimal_covering_nodes(l2ids)
+        assert np.all(node_ids == np.array(covering_nodes))
+
     @responses.activate
     def test_get_root(self, myclient):
         endpoint_mapping = self._default_endpoint_map

diff --git a/tests/test_framework.py b/tests/test_framework.py
@@ -91,7 +91,7 @@ def test_create_versioned_client(self):
         cg_version_url = endpoints.chunkedgraph_endpoints_common[
             "get_version"
         ].format_map(endpoint_mapping)
-        responses.add(responses.GET, cg_version_url, json="2.15.0", status=200)
+        responses.add(responses.GET, cg_version_url, json="2.18.0", status=200)
 
         mat_version_url = endpoints.materialization_common["get_version"].format_map(
             endpoint_mapping

diff --git a/uv.lock b/uv.lock