better error with lack of l2 service

docs/changelog.md

@@ -4,6 +4,12 @@ title: Changelog
 
 `pcg_skel` aims to follow semantic versioning, such that major versions are potentially backward-incompatible, minor versions add new features, and patch versions are bug fixes. This changelog is a summary of the changes in each version.
 
+## [1.0.4]
+
+### Fixes
+
+* Raise a clear error when a level 2 cache service, which is needed, is not available.
+
 ## [1.0.3]
 
 ### Fixes

pcg_skel/chunk_cache.py

@@ -1,12 +1,31 @@
 import numpy as np
 import orjson
 from sqlitedict import SqliteDict
+from cachetools import LRUCache, cached
+from cachetools.keys import hashkey
 
 POSITION_ATTRIBUTE = "rep_coord_nm"
 
 
+class NoL2CacheException(Exception):
+    pass
+
+
+def cachekey(client):
+    return hashkey(client.datastack_name)
+
+
+@cached(LRUCache(16), key=cachekey)
+def check_l2cache(client):
+    return client.l2cache.has_cache()
+
+
 def get_locs_remote(l2_ids, client):
     """Retrieve ids from the l2 cache service"""
+    if check_l2cache(client) is False:
+        raise NoL2CacheException(
+            f"No L2 Cache service is running for datastack {client.datastack_name} and you cannot use PCGSkel without an L2 Cache. Contact your admin for more information."
+        )
     l2_info = client.l2cache.get_l2data(list(l2_ids), attributes=[POSITION_ATTRIBUTE])
     l2loc = [l2_info[str(l2id)].get(POSITION_ATTRIBUTE, None) for l2id in l2_ids]
 
@@ -59,7 +78,6 @@ def save_ids_to_cache(l2_ids, l2_locs, cache_file):
     cache_file : str
 
     """
-    ii = 0
     with SqliteDict(cache_file, encode=orjson.dumps, flag="c") as cache_dict:
         for k, v in zip(l2_ids, l2_locs):
             if not np.any(np.isnan(v)):

tests/conftest.py

@@ -10,10 +10,11 @@
 base_path = pathlib.Path(__file__).parent.resolve()
 
 TEST_DATASTACK = "minnie65_public"
+TEST_DATASTACK_NOCACHE = "minnie65_public_nocache"
 MAT_VERSION = 795
 
 INFO_CACHE = {
-    "minnie65_public": {
+    TEST_DATASTACK: {
         "proofreading_review_table": None,
         "description": "This is the publicly released version of the minnie65 volume and segmentation. ",
         "proofreading_status_table": None,
@@ -34,7 +35,29 @@
         "viewer_resolution_x": 4.0,
         "viewer_resolution_y": 4.0,
         "viewer_resolution_z": 40.0,
-    }
+    },
+    TEST_DATASTACK_NOCACHE: {
+        "proofreading_review_table": None,
+        "description": "This is the publicly released version of the minnie65 volume and segmentation. ",
+        "proofreading_status_table": None,
+        "cell_identification_table": None,
+        "local_server": "https://minnie.microns-daf.com",
+        "aligned_volume": {
+            "description": "This is the second alignment of the IARPA 'minnie65' dataset, completed in the spring of 2020 that used the seamless approach.",
+            "name": "minnie65_phase3",
+            "id": 1,
+            "image_source": "precomputed://https://bossdb-open-data.s3.amazonaws.com/iarpa_microns/minnie/minnie65/em",
+            "display_name": "Minnie65",
+        },
+        "synapse_table": "synapses_pni_2",
+        "viewer_site": "https://neuroglancer.neuvue.io",
+        "analysis_database": None,
+        "segmentation_source": "graphene://https://minnie.microns-daf.com/segmentation/table/minnie65_public",
+        "soma_table": "nucleus_detection_v0",
+        "viewer_resolution_x": 4.0,
+        "viewer_resolution_y": 4.0,
+        "viewer_resolution_z": 40.0,
+    },
 }
 
 
@@ -75,14 +98,27 @@ def test_client(mocker):
     client = CAVEclient(TEST_DATASTACK, info_cache=INFO_CACHE)
     mocker.patch.object(client.info, "segmentation_cloudvolume", return_value=test_cv)
     mocker.patch.object(client.l2cache, "get_l2data", return_value=test_l2ids)
+    mocker.patch.object(client.l2cache, "has_cache", return_value=True)
     mocker.patch.object(
         client.chunkedgraph, "level2_chunk_graph", return_value=test_l2graph
     )
     synapse_table = mocker.PropertyMock(return_value="synapses_pni_2")
     type(client.materialize).synapse_table = synapse_table
+    mocker.patch.object(client.materialize, "get_versions", return_value=[1])
     mocker.patch.object(client.materialize, "get_timestamp", return_value="1234")
     mocker.patch(
         "pcg_skel.pcg_anno.get_level2_synapses",
         return_value=(test_pre_synapses, test_post_synapses),
     )
     return client
+
+
+@pytest.fixture()
+def test_client_nol2cache(mocker):
+    client = CAVEclient(TEST_DATASTACK_NOCACHE, info_cache=INFO_CACHE)
+    mocker.patch.object(client.info, "segmentation_cloudvolume", return_value=test_cv)
+    mocker.patch.object(client.l2cache, "has_cache", return_value=False)
+    mocker.patch.object(
+        client.chunkedgraph, "level2_chunk_graph", return_value=test_l2graph
+    )
+    return client

tests/test_pcg_skel.py

@@ -1,8 +1,9 @@
 import pytest
 import pcg_skel
+from pcg_skel.chunk_cache import NoL2CacheException
 import numpy as np
 
-from conftest import test_client
+from conftest import test_client, test_client_nol2cache
 from conftest import root_id, center_pt
 
 
@@ -74,3 +75,14 @@ def test_defunct_meshwork(test_client, root_id, center_pt):
     )
     assert len(nrn2.anno.table_names) > 0
     assert nrn2.mesh.vertices.shape[0] > 0
+
+
+def test_pcg_meshwork_noclient(test_client_nol2cache, root_id, center_pt):
+    with pytest.raises(NoL2CacheException):
+        pcg_skel.pcg_skeleton(
+            root_id,
+            test_client_nol2cache,
+            collapse_radius=True,
+            root_point=center_pt,
+            root_point_resolution=[4, 4, 40],
+        )