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Refactoring cxg utility classes in preparation for CXG conversion tooling (#1739)

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This commit is contained in:
maniarathi
2020-08-14 16:51:13 -07:00
committed by GitHub
parent b034055c35
commit 508889f74b
23 changed files with 607 additions and 177 deletions
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server/data_common/data_adaptor.py
+9 -8
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@@ -1,14 +1,15 @@
from abc import ABCMeta, abstractmethod
from server_timing import Timing as ServerTiming
import numpy as np
import pandas as pd
from os.path import basename, splitext
from server.data_common.fbs.matrix import encode_matrix_fbs
import numpy as np
import pandas as pd
from server_timing import Timing as ServerTiming
from server.common.app_config import AppFeature, AppConfig
from server.common.constants import Axis
from server.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError
from server.common.utils import jsonify_numpy
from server.common.app_config import AppFeature, AppConfig
from server.common.utils.utils import jsonify_numpy
from server.data_common.fbs.matrix import encode_matrix_fbs
class DataAdaptor(metaclass=ABCMeta):
@@ -172,7 +173,7 @@ class DataAdaptor(metaclass=ABCMeta):
mask = np.zeros((count,), dtype=np.bool)
for i in filter:
if type(i) == list:
mask[i[0] : i[1]] = True
mask[i[0]: i[1]] = True
else:
mask[i] = True
return mask
@@ -313,7 +314,7 @@ class DataAdaptor(metaclass=ABCMeta):
top_n = self.dataset_config.diffexp__top_n
if self.server_config.exceeds_limit(
"diffexp_cellcount_max", np.count_nonzero(obs_mask_A) + np.count_nonzero(obs_mask_B)
"diffexp_cellcount_max", np.count_nonzero(obs_mask_A) + np.count_nonzero(obs_mask_B)
):
raise ExceedsLimitError("Diffexp request exceeds max cell count limit")