Fix naming neuroncriteria

[floesche]

Adding backticks to names in the NeuronCriteria queries (similar and including the change from #41).

This part is not very well tested, but part of code basis that I am using.

[floesche]

With the high number of name changes in ROIs and neurons, it would be nice to have this "safety net" for the queries in neuprint-python.

[floesche]

For this minimal test:

from neuprint import Client, fetch_neurons, NeuronCriteria as NC
c = Client(<SERVER>, <DATASET>)
target_inst = 'ER4d_R'
n_target_all, _ = fetch_neurons(NC(instance= target_inst))

the connectome-neuprint:master branch produces the following error:

---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
~/srcs/neuprint-python/neuprint/client.py in wrapper(*args, **kwargs)
    227         try:
--> 228             return f(*args, **kwargs)
    229         except RequestException as ex:

~/srcs/neuprint-python/neuprint/client.py in _fetch(self, url, json, ispost)
    382             r = self.session.get(url, verify=self.verify)
--> 383         r.raise_for_status()
    384         return r

~/srcs/neuprint-python/.pixi/envs/default/lib/python3.9/site-packages/requests/models.py in raise_for_status(self)
    952         if http_error_msg:
--> 953             raise HTTPError(http_error_msg, response=self)
    954 

HTTPError: 400 Client Error: Bad Request for url: <SERVER>/api/custom/custom

The above exception was the direct cause of the following exception:

HTTPError                                 Traceback (most recent call last)
/tmp/ipykernel_12951/1932216900.py in <module>
      3 
      4 target_inst = 'ER4d_R'
----> 5 n_target_all, _ = fetch_neurons(NC(instance= target_inst))

~/srcs/neuprint-python/neuprint/client.py in wrapper(client, *args, **kwargs)
    211         if client is None:
    212             client = default_client()
--> 213         return f(*args, **kwargs, client=client)
    214 
    215     wrapper.__signature__ = inspect.signature(f)

~/srcs/neuprint-python/neuprint/queries/neuroncriteria.py in wrapper(*args, **kwargs)
     33             for name in argnames:
     34                 callargs[name] = copy_as_neuroncriteria(callargs[name], callargs.get('client', None))
---> 35             return f(**callargs)
     36 
     37         wrapper.__signature__ = inspect.signature(f)

~/srcs/neuprint-python/neuprint/queries/neurons.py in fetch_neurons(criteria, client)
    128         ORDER BY n.bodyId
    129     """
--> 130     neuron_df = client.fetch_custom(q)
    131     neuron_df, roi_counts_df = _process_neuron_df(neuron_df, client)
    132     return neuron_df, roi_counts_df

~/srcs/neuprint-python/neuprint/client.py in fetch_custom(self, cypher, dataset, format)
    420         """
    421         url = f"{self.server}/api/custom/custom"
--> 422         return self._fetch_cypher(url, cypher, dataset, format)
    423 
    424     def _fetch_cypher(self, url, cypher, dataset, format='pandas'):

~/srcs/neuprint-python/neuprint/client.py in _fetch_cypher(self, url, cypher, dataset, format)
    441         logger.debug(f"Performing cypher query against dataset '{dataset}':\n{cypher}")
    442 
--> 443         result = self._fetch_json(url,
    444                                   json={"cypher": cypher, "dataset": dataset},
    445                                   ispost=True)

~/srcs/neuprint-python/neuprint/client.py in _fetch_json(self, url, json, ispost)
    388 
    389     def _fetch_json(self, url, json=None, ispost=False):
--> 390         r = self._fetch(url, json=json, ispost=ispost)
    391         return ujson.loads(r.content)
    392 

~/srcs/neuprint-python/neuprint/client.py in wrapper(*args, **kwargs)
    269             # mark it as already modified it doesn't get modified twice.
    270             new_ex.response_content_appended = True
--> 271             raise new_ex from ex
    272     return wrapper
    273 

HTTPError: Error accessing POST <SERVER>/api/custom/custom

Cypher was:


    MATCH (n :Neuron)
    WHERE 
      // -- Basic conditions for segment 'n' --
      n.instance = 'ER4d_R'
    RETURN n.bodyId as bodyId,
           n.instance as instance,
           n.type as type,
           n.pre as pre,
           n.post as post,
           n.downstream as downstream,
           n.upstream as upstream,
           n.size as size,
           n.status as status,
           n.statusLabel as statusLabel,
           n.cellBodyFiber as cellBodyFiber,
           n.somaLocation as somaLocation,
           n.roiInfo as roiInfo,
           n.anteriorCervicalRootPosition as anteriorCervicalRootPosition,
           n.assignedOlHex1 as assignedOlHex1,
           n.assignedOlHex2 as assignedOlHex2,
           n.birthtime as birthtime,
           n.class as class,
           n.dimorphism as dimorphism,
           n.entryNerve as entryNerve,
           n.exitNerve as exitNerve,
           n.flywireId as flywireId,
           n.flywireType as flywireType,
           n.fru/dsx as fru/dsx,
           n.fruDsx as fruDsx,
           n.group as group,
           n.hemibrainBodyId as hemibrainBodyId,
           n.hemibrainType as hemibrainType,
           n.itoleeHl as itoleeHl,
           n.location as location,
           n.locationType as locationType,
           n.mancBodyid as mancBodyid,
           n.mancGroup as mancGroup,
           n.mancType as mancType,
           n.matchingNotes as matchingNotes,
           n.mcnsSerial as mcnsSerial,
           n.posteriorCervicalRootPosition as posteriorCervicalRootPosition,
           n.rootSide as rootSide,
           n.serialMotif as serialMotif,
           n.somaNeuromere as somaNeuromere,
           n.somaSide as somaSide,
           n.subclass as subclass,
           n.superclass as superclass,
           n.synonyms as synonyms,
           n.synweight as synweight,
           n.trumanHl as trumanHl
    ORDER BY n.bodyId


Returned Error (400):

Invalid input '/': expected
  ","
  "CALL"
  "CREATE"
  "DELETE"
  "DETACH"
  "FOREACH"
  "LIMIT"
  "LOAD"
  "MATCH"
  "MERGE"
  "OPTIONAL"
  "ORDER"
  "REMOVE"
  "RETURN"
  "SET"
  "SKIP"
  "UNION"
  "UNWIND"
  "USE"
  "WITH"
  <EOF> (line 29, column 28 (offset: 1010))
"           n.fru/dsx as fru/dsx,"
                            ^

while the floesche:fix-naming-neuroncriteria branch works (returning 13 rows in n_target_all.

[stuarteberg]

Yes, I was just rebasing this PR onto my local development branch. Thank you! (Will push soon...)

[floesche]

Looks like a similar solution was implemented in master. Closing this PR