Server error when calling pcg_skel.coord_space_meshwork #28
Description
Dear Allen Institute team,
(I am aware that I should not expect active support for this, but I just document the issue in case that would be useful)
I would like to create skeletons for a few interneurons of the EM dataset and I get a server error when calling pcg_skel.coord_space_meshwork.
The minimal working example to reproduce the error is the following:
from meshparty import meshwork
import pcg_skel
from caveclient import CAVEclient
datastack_name = 'minnie65_public_v343'
client = CAVEclient(datastack_name)
client.materialize.version = 343
bpc_mw = pcg_skel.coord_space_meshwork(
root_id=864691136008567724, # the bipolar cell of the tutorial
client=client
)
The output/error is the following:
/home/yann.zerlaut/miniconda3/envs/allen/lib/python3.8/site-packages/caveclient/l2cache.py:78: UserWarning: L2Cache is in an experimental stage
warnings.warn("L2Cache is in an experimental stage", UserWarning)
---------------------------------------------------------------------------
HTTPError Traceback (most recent call last)
Cell In [1], line 9
6 client = CAVEclient(datastack_name)
7 client.materialize.version = 343
----> 9 bpc_mw = pcg_skel.coord_space_meshwork(
10 root_id=864691136008567724, # the bipolar cell of the tutorial
11 client=client
12 )
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/pcg_skel.py:665, in coord_space_meshwork(root_id, datastack_name, client, cv, root_point, root_point_resolution, collapse_soma, collapse_radius, synapses, synapse_table, remove_self_synapse, live_query, timestamp, invalidation_d, require_complete)
662 if root_point_resolution is None:
663 root_point_resolution = cv.mip_resolution(0)
--> 665 sk, mesh, (l2dict_mesh, l2dict_mesh_r) = coord_space_skeleton(
666 root_id,
667 client=client,
668 cv=cv,
669 root_point=root_point,
670 root_point_resolution=root_point_resolution,
671 collapse_soma=collapse_soma,
672 collapse_radius=collapse_radius,
673 invalidation_d=invalidation_d,
674 return_mesh=True,
675 return_l2dict_mesh=True,
676 require_complete=require_complete,
677 )
679 nrn = meshwork.Meshwork(mesh, seg_id=root_id, skeleton=sk)
681 pre, post = False, False
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/pcg_skel.py:125, in coord_space_skeleton(root_id, client, datastack_name, cv, invalidation_d, return_mesh, return_l2dict, return_l2dict_mesh, root_point, root_point_resolution, collapse_soma, collapse_radius, nan_rounds, require_complete)
122 if root_point is not None:
123 root_point = np.array(root_point) * root_point_resolution
--> 125 mesh, l2dict_mesh, l2dict_r_mesh = coord_space_mesh(
126 root_id,
127 client=client,
128 return_l2dict=True,
129 nan_rounds=nan_rounds,
130 require_complete=require_complete,
131 )
133 metameta = {"space": "l2cache", "datastack": client.datastack_name}
134 sk = skeletonize.skeletonize_mesh(
135 mesh,
136 invalidation_d=invalidation_d,
(...)
147 },
148 )
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/pcg_skel.py:78, in coord_space_mesh(root_id, client, cv, return_l2dict, nan_rounds, require_complete)
75 cv = client.info.segmentation_cloudvolume(progress=False)
77 lvl2_eg = client.chunkedgraph.level2_chunk_graph(root_id)
---> 78 eg, l2dict_mesh, l2dict_r_mesh, x_ch = build_spatial_graph(
79 lvl2_eg,
80 cv,
81 client=client,
82 method="service",
83 require_complete=require_complete,
84 )
85 mesh_loc = trimesh_io.Mesh(
86 vertices=x_ch,
87 faces=[[0, 0, 0]], # Some functions fail if no faces are set.
88 link_edges=eg,
89 )
91 sk_utils.fix_nan_verts_mesh(mesh_loc, nan_rounds)
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/pcg_skel.py:57, in build_spatial_graph(lvl2_edge_graph, cv, client, method, require_complete)
55 x_ch = [np.array(cv.mesh.meta.meta.decode_chunk_position(l)) for l in lvl2_ids]
56 elif method == "service":
---> 57 x_ch = chunk_tools.dense_spatial_lookup(
58 lvl2_ids,
59 eg_arr_rm,
60 client,
61 require_complete=require_complete,
62 )
63 return eg_arr_rm, l2dict, l2dict_reversed, x_ch
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/chunk_tools.py:23, in dense_spatial_lookup(l2ids, eg, client, require_complete)
21 def dense_spatial_lookup(l2ids, eg, client, require_complete=False):
22 l2means = np.full((len(l2ids), 3), np.nan)
---> 23 locs, inds_found = chunk_cache.get_locs_remote(l2ids, client)
24 if require_complete:
25 if not np.all(inds_found):
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/pcg_skel/chunk_cache.py:10, in get_locs_remote(l2_ids, client)
8 def get_locs_remote(l2_ids, client):
9 """Retrieve ids from the l2 cache service"""
---> 10 l2_info = client.l2cache.get_l2data(list(l2_ids), attributes=[POSITION_ATTRIBUTE])
11 l2loc = [l2_info[str(l2id)].get(POSITION_ATTRIBUTE, None) for l2id in l2_ids]
13 l2means = np.array([x for x in l2loc if x is not None])
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/caveclient/l2cache.py:111, in L2CacheClientLegacy.get_l2data(self, l2_ids, attributes)
101 url = self._endpoints["l2cache_data"].format_map(endpoint_mapping)
103 response = self.session.post(
104 url,
105 data=json.dumps(
(...)
109 params=query_d,
110 )
--> 111 return handle_response(response)
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/caveclient/base.py:78, in handle_response(response, as_json)
76 def handle_response(response, as_json=True):
77 """Deal with potential errors in endpoint response and return json for default case"""
---> 78 _raise_for_status(response)
79 _check_authorization_redirect(response)
80 if as_json:
File ~/miniconda3/envs/allen/lib/python3.8/site-packages/caveclient/base.py:70, in _raise_for_status(r)
62 http_error_msg = "%s Server Error: %s for url: %s content:%s" % (
63 r.status_code,
64 reason,
65 r.url,
66 r.content,
67 )
69 if http_error_msg:
---> 70 raise requests.HTTPError(http_error_msg, response=r)
71 warning = r.headers.get("Warning")
72 if warning:
HTTPError: 500 Server Error: INTERNAL SERVER ERROR for url: https://minnie.microns-daf.com/l2cache/api/v1/table/minnie65_public_v343/attributes?int64_as_str=False&attribute_names=rep_coord_nm content:b'{\n "code": 500,\n "duration": 1.9135475158691406,\n "message": "Dataset minnie65_public_v343 does not have an L2 Cache.",\n "timestamp": "2022-10-07 14:35:56.882805",\n "traceback": [\n "Traceback (most recent call last):\\n",\n " File \\"/usr/local/lib/python3.7/site-packages/flask/app.py\\", line 1820, in full_dispatch_request\\n rv = self.dispatch_request()\\n",\n " File \\"/usr/local/lib/python3.7/site-packages/flask/app.py\\", line 1796, in dispatch_request\\n return self.ensure_sync(self.view_functions[rule.endpoint])(**view_args)\\n",\n " File \\"/usr/local/lib/python3.7/site-packages/middle_auth_client/decorators.py\\", line 265, in decorated_function\\n return f(*args, **kwargs)\\n",\n " File \\"/usr/local/lib/python3.7/site-packages/middle_auth_client/decorators.py\\", line 397, in decorated_function\\n return f(*args, **kwargs)\\n",\n " File \\"./pcgl2cache/app/v1/routes.py\\", line 27, in decorated_function\\n return f(*args, **kwargs)\\n",\n " File \\"./pcgl2cache/app/v1/routes.py\\", line 94, in attributes\\n common.handle_attributes(table_id), int64_as_str=int64_as_str\\n",\n " File \\"./pcgl2cache/app/common.py\\", line 162, in handle_attributes\\n cache_client = get_l2cache_client(graph_id)\\n",\n " File \\"./pcgl2cache/app/utils.py\\", line 47, in get_l2cache_client\\n assert graph_id in l2cache_config, f\\"Dataset {graph_id} does not have an L2 Cache.\\"\\n",\n "AssertionError: Dataset minnie65_public_v343 does not have an L2 Cache.\\n"\n ]\n}\n'