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fix typos
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@bdpedigo
bdpedigo committed Feb 22, 2024
1 parent d54c8a0 commit e819d7c
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Showing 2 changed files with 36 additions and 33 deletions.
51 changes: 27 additions & 24 deletions caveclient/materializationengine.py
View file
Original file line number Diff line number Diff line change
@@ -1,27 +1,29 @@
import itertools
import json
import logging
import re
from urllib.error import HTTPError
import warnings
import pytz
import pandas as pd
from IPython.display import HTML
from .mytimer import MyTimeIt
from typing import Union, Iterable
import itertools
import pyarrow as pa
from datetime import datetime, timezone
from typing import Iterable, Union
from urllib.error import HTTPError

import numpy as np
import json
from .endpoints import materialization_api_versions, materialization_common
import pandas as pd
import pyarrow as pa
import pytz
from cachetools import TTLCache, cached
from IPython.display import HTML

from .auth import AuthClient
from .base import (
ClientBase,
BaseEncoder,
ClientBase,
_api_endpoints,
handle_response,
)
from cachetools import cached, TTLCache
from .endpoints import materialization_api_versions, materialization_common
from .mytimer import MyTimeIt
from .tools.table_manager import TableManager, ViewManager
import logging

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -213,7 +215,7 @@ def MaterializationClient(
)


class MaterializatonClientV2(ClientBase):
class MaterializationClientV2(ClientBase):
def __init__(
self,
server_address,
Expand All @@ -232,7 +234,7 @@ def __init__(
over_client=None,
desired_resolution=None,
):
super(MaterializatonClientV2, self).__init__(
super(MaterializationClientV2, self).__init__(
server_address,
auth_header,
api_version,
Expand Down Expand Up @@ -747,7 +749,6 @@ def query_table(
df = deserialize_query_response(response)
if desired_resolution is not None:
if not response.headers.get("dataframe_resolution", None):

if len(desired_resolution) != 3:
raise ValueError(
"desired resolution needs to be of length 3, for xyz"
Expand Down Expand Up @@ -1287,7 +1288,6 @@ def live_live_query(
warnings.simplefilter(action="ignore", category=DeprecationWarning)
df = deserialize_query_response(response)
if desired_resolution is not None:

if len(desired_resolution) != 3:
raise ValueError(
"desired resolution needs to be of length 3, for xyz"
Expand Down Expand Up @@ -1528,7 +1528,6 @@ def live_query(
df = deserialize_query_response(response)
if desired_resolution is not None:
if not response.headers.get("dataframe_resolution", None):

if len(desired_resolution) != 3:
raise ValueError(
"desired resolution needs to be of length 3, for xyz"
Expand Down Expand Up @@ -1761,9 +1760,9 @@ def _assemble_attributes(
return attrs


class MaterializatonClientV3(MaterializatonClientV2):
class MaterializationClientV3(MaterializationClientV2):
def __init__(self, *args, **kwargs):
super(MaterializatonClientV3, self).__init__(*args, **kwargs)
super(MaterializationClientV3, self).__init__(*args, **kwargs)

@cached(cache=TTLCache(maxsize=100, ttl=60 * 60 * 12))
def get_tables_metadata(
Expand Down Expand Up @@ -1962,7 +1961,6 @@ def live_live_query(
df = deserialize_query_response(response)
if desired_resolution is not None:
if not response.headers.get("dataframe_resolution", None):

if len(desired_resolution) != 3:
raise ValueError(
"desired resolution needs to be of length 3, for xyz"
Expand Down Expand Up @@ -2291,8 +2289,13 @@ def get_unique_string_values(self, table: str, datastack_name: str = None):
return response.json()


# included for historical reasons, there was a typo in the class name
MaterializatonClientV2 = MaterializationClientV2

MaterializatonClientV3 = MaterializationClientV3

client_mapping = {
2: MaterializatonClientV2,
3: MaterializatonClientV3,
"latest": MaterializatonClientV2,
2: MaterializationClientV2,
3: MaterializationClientV3,
"latest": MaterializationClientV2,
}
18 changes: 9 additions & 9 deletions docs/guide/materialization.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ The Materialization client allows one to interact with the materialized
annotation tables, that were posted to the annotation service (see
:doc:`annotation`).

To see the entire class visit the API doc :class:`~caveclient.materializationengine.MaterializatonClientV2`
To see the entire class visit the API doc :class:`~caveclient.materializationengine.MaterializationClientV2`

The service regularly looks up all annotations and the segids underneath
all the boundspatialpoints. You can then query these tables to find out
Expand All @@ -30,17 +30,17 @@ materialization version available. This may or may not be desirable depending o
use case. If your code involves using specific IDs then you should be using a
specific version that is tied to a timepoint where those IDs are valid.

To see what versions are available, use the :func:`~caveclient.materializationengine.MaterializatonClientV2.get_versions`
To see what versions are available, use the :func:`~caveclient.materializationengine.MaterializationClientV2.get_versions`

.. code:: python
client.materialize.get_versions()
Each version has a timestamp it was run on as well as a date when it will expire.
You can query all this metadata for a specific version using
:func:`~caveclient.materializationengine.MaterializatonClientV2.get_version_metadata`
:func:`~caveclient.materializationengine.MaterializationClientV2.get_version_metadata`
or all versions using
:func:`~caveclient.materializationengine.MaterializatonClientV2.get_versions_metadata`
:func:`~caveclient.materializationengine.MaterializationClientV2.get_versions_metadata`


To change the default version, alter the .version property of the materialization client.
Expand All @@ -54,7 +54,7 @@ or specify the version when making a particular call.
Browsing versions
^^^^^^^^^^^^^^^^^
To see what tables are available in a version you can use
:func:`~caveclient.materializationengine.MaterializatonClientV2.get_tables`
:func:`~caveclient.materializationengine.MaterializationClientV2.get_tables`

If you want to read about the description of what that table is, use the annotationengine client
:func:`~caveclient.annotationengine.AnnotationClientV2.get_table_metadata`
Expand All @@ -79,7 +79,7 @@ To see how many annotations are in a particular table use
Querying tables
^^^^^^^^^^^^^^^
To query a small table, you can just download the whole thing using
:func:`~caveclient.materializationengine.MaterializatonClientV2.query_table`
:func:`~caveclient.materializationengine.MaterializationClientV2.query_table`
which will return a dataframe of the table.

Note however, some tables, such as the synapse table might be very large 200-300 million rows
Expand Down Expand Up @@ -149,7 +149,7 @@ You can also filter columns that are associated with spatial locations based upo

This is done by adding a filter_spatial_dict argument to query_table.
The units of the bounding box should be in the units of the voxel_resolution of the table
(which can be obtained from :func:`~caveclient.materializationengine.MaterializatonClientV2.get_table_metadata`).
(which can be obtained from :func:`~caveclient.materializationengine.MaterializationClientV2.get_table_metadata`).


.. code:: python
Expand All @@ -164,7 +164,7 @@ The units of the bounding box should be in the units of the voxel_resolution of
Synapse Query
^^^^^^^^^^^^^
For synapses in particular, we have a simplified method for querying them with a reduced syntax.
:func:`~caveclient.materializationengine.MaterializatonClientV2.synapse_query`
:func:`~caveclient.materializationengine.MaterializationClientV2.synapse_query`
lets you specify pre and post synaptic partners as keyword arguments and bounding boxes.
The defaults make reasonable assumptions about what you want to query, namely that the synapse_table is
the table that the info service advertises, and that if you specify a bounding box, that you want the post_pt_position.
Expand Down Expand Up @@ -208,7 +208,7 @@ object in the most recent materialization.

However, sometimes you might be browsing and proofreadding the data and get an ID
that is more recent that the most recent version available. For convience, you can use
:func:`~caveclient.materializationengine.MaterializatonClientV2.live_query`.
:func:`~caveclient.materializationengine.MaterializationClientV2.live_query`.


to automatically update the results of your query to a time in the future, such as now.
Expand Down

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