fetch_synapse_connections time out: markdown render found here https://github.com/connectome-neuprint/neuprint-python/issues/27

[Markus Pleijzier]

I'm running the function neuprint.fetch_synapse_connections for 7 neurons but this returns a 400 timeout error. This was always the case, and shouldn't be timing out for 7 neurons. Seems like a cypher error contained within neuprint.fetch_synapse_connections

• Running neuprint version: 0.4.15 with revision id c5c01a0f4c78a8716d2040b190e5a81b97edc298

The code to run:

import neuprint as neu neu.fetch_synapse_connections(source_criteria = [328861282, 360284300, 327499164, 487144598, 511271574, 517506265, 579912201])

Full error:

HTTPError Traceback (most recent call last) ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in wrapper(*args, **kwargs) 225 try: --> 226 return f(*args, **kwargs) 227 except RequestException as ex: ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in _fetch(self, url, json, ispost) 379 r = self.session.get(url, verify=self.verify) --> 380 r.raise_for_status() 381 return r ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/requests/models.py in raise_for_status(self) 942 if http_error_msg: --> 943 raise HTTPError(http_error_msg, response=self) 944 HTTPError: 400 Client Error: Bad Request for url: https://neuprint.janelia.org/api/custom/custom The above exception was the direct cause of the following exception: HTTPError Traceback (most recent call last) <ipython-input-24-71b141a19cc7> in <module> ----> 1 lhcent_presyn = neu.fetch_synapse_connections(source_criteria=list(fib_cent_ca_whole.id)) 2 lhcent_presyn ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in wrapper(client, *args, **kwargs) 209 if client is None: 210 client = default_client() --> 211 return f(*args, **kwargs, client=client) 212 213 wrapper.__signature__ = inspect.signature(f) ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/neuroncriteria.py in wrapper(*args, **kwargs) 31 for name in argnames: 32 callargs[name] = copy_as_neuroncriteria(callargs[name], callargs.get('client', None)) ---> 33 return f(**callargs) 34 35 wrapper.__signature__ = inspect.signature(f) ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/queries.py in fetch_synapse_connections(source_criteria, target_criteria, synapse_criteria, min_total_weight, batch_size, client) 2131 synapse_criteria, 2132 min_total_weight, -> 2133 client ) 2134 syn_dfs.append(batch_syn_df) 2135 ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/queries.py in _fetch_synapse_connections(source_criteria, target_criteria, synapse_criteria, min_total_weight, client) 2189 apoc.map.removeKeys(ms, ['location', 'confidence', 'type']) as info_post 2190 """) -> 2191 data = client.fetch_custom(cypher, format='json')['data'] 2192 2193 # Assemble DataFrame ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in fetch_custom(self, cypher, dataset, format) 417 """ 418 url = f"{self.server}/api/custom/custom" --> 419 return self._fetch_cypher(url, cypher, dataset, format) 420 421 def _fetch_cypher(self, url, cypher, dataset, format='pandas'): ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in _fetch_cypher(self, url, cypher, dataset, format) 440 result = self._fetch_json(url, 441 json={"cypher": cypher, "dataset": dataset}, --> 442 ispost=True) 443 444 if format == 'json': ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in _fetch_json(self, url, json, ispost) 385 386 def _fetch_json(self, url, json=None, ispost=False): --> 387 r = self._fetch(url, json=json, ispost=ispost) 388 return ujson.loads(r.content) 389 ~/miniconda3/envs/venv_3_7/lib/python3.7/site-packages/neuprint/client.py in wrapper(*args, **kwargs) 267 # mark it as already modified it doesn't get modified twice. 268 new_ex.response_content_appended = True --> 269 raise new_ex from ex 270 return wrapper 271 HTTPError: Error accessing POST https://neuprint.janelia.org/api/custom/custom Cypher was: WITH [327499164, 328861282, 360284300, 487144598, 511271574, 517506265, 579912201] as n_search_bodyIds, [263674097, 264783939, 264822904, 265120324, 266187477, 266187559, 266528069, 266528086, 266873389, 268237554, 294424196, 294436967, 294445804, 294445931, 294450004, 294756576, 294786630, 294787849, 294792184, 295107330, 295111672, 295120620, 295124412, 295434457, 295461871, 295473400, 295779879, 295785459, 295814565, 296139882, 296199149, 296203324, 296203623, 296535619, 296543992, 296544262, 296837846, 296841676, 297179343, 297230760, 297251714, 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5813022453, 5813026589, 5813035183, 5813049045, 5813053821, 5813053888, 5813053935, 5813056355, 5813057162, 5813062645, 5813068801, 5813077616, 5813083723, 5813083780, 5813087837, 5813094364, 5813123585, 5901208687] as m_search_bodyIds MATCH (n:Segment)-[e:ConnectsTo]->(m:Neuron), (n)-[:Contains]->(nss:SynapseSet)-[:ConnectsTo]->(mss:SynapseSet)<-[:Contains]-(m), (nss)-[:Contains]->(ns:Synapse)-[:SynapsesTo]->(ms:Synapse)<-[:Contains]-(mss) WHERE // -- Basic conditions for segment 'n' -- n.bodyId in n_search_bodyIds AND // -- Basic conditions for segment 'm' -- m.bodyId in m_search_bodyIds WITH n, m, ns, ms, e WHERE e.weight >= 1 // -- Filter synapse 'ns' -- WITH n, m, ns, ms WHERE (ns.type = 'pre') // -- Filter synapse 'ms' -- WITH n, m, ns, ms WHERE (ms.type = 'post') RETURN n.bodyId as bodyId_pre, m.bodyId as bodyId_post, ns.location.x as ux, ns.location.y as uy, ns.location.z as uz, ms.location.x as dx, ms.location.y as dy, ms.location.z as dz, ns.confidence as confidence_pre, ms.confidence as confidence_post, apoc.map.removeKeys(ns, ['location', 'confidence', 'type']) as info_pre, apoc.map.removeKeys(ms, ['location', 'confidence', 'type']) as info_post Returned Error (400): Timeout experienced. This could be due to database traffic or to non-optimal database queries. If the latter, please consult neuPrint documentation or post a question at https://groups.google.com/forum/#!forum/neuprint to understand other options.```

[Chris Liu]

I have the same problem. And it's just searching for connections between two neurons

[Stuart Berg]

Hi Chris,

I have the same problem. And it's just searching for connections between two neurons

Sorry to hear that.  Can you please give some more details, such as the version of neuprint-python you're using, and the exact Python code (with body IDs) that triggers the problem?

You can reply here, or (preferably) on github: https://github.com/connectome-neuprint/neuprint-python/issues/27

Best regards,

Stuart