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Code Issues Packages Projects Releases Wiki Activity

remove experimental reembedding support (#2301)

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* remove experimental reembedding support

* lint

* lint

* add prepare requirements to requirements-dev

* oops, revert accidental deletion of import

* more test modifications

* remove obsolete unit tests
This commit is contained in:
Bruce Martin
2021-07-15 13:55:26 -07:00
committed by GitHub
parent e334fbe96e
commit 0667ad0274
46 changed files with 12 additions and 661 deletions
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backend/czi_hosted/common/config/client_config.py
-1
View File
@@ -40,7 +40,6 @@ def get_client_config(app_config, data_adaptor):
"diffexp_lfc_cutoff": dataset_config.diffexp__lfc_cutoff,
"backed": server_config.adaptor__anndata_adaptor__backed,
"disable-diffexp": not dataset_config.diffexp__enable,
"enable-reembedding": dataset_config.embeddings__enable_reembedding,
"annotations": False,
"annotations_file": None,
"annotations_dir": None,
backend/czi_hosted/common/config/dataset_config.py
-21
View File
@@ -6,8 +6,6 @@ from backend.czi_hosted.common.annotations.hosted_tiledb import AnnotationsHoste
from backend.czi_hosted.common.annotations.local_file_csv import AnnotationsLocalFile
from backend.czi_hosted.common.config.base_config import BaseConfig
from backend.common.errors import ConfigurationError
from backend.czi_hosted.compute.scanpy import get_scanpy_module
from backend.czi_hosted.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
from backend.czi_hosted.db.db_utils import DbUtils
@@ -41,7 +39,6 @@ class DatasetConfig(BaseConfig):
]["hosted_file_directory"]
self.embeddings__names = default_config["embeddings"]["names"]
self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"]
self.diffexp__enable = default_config["diffexp"]["enable"]
self.diffexp__lfc_cutoff = default_config["diffexp"]["lfc_cutoff"]
@@ -186,24 +183,6 @@ class DatasetConfig(BaseConfig):
def handle_embeddings(self):
self.validate_correct_type_of_configuration_attribute("embeddings__names", list)
self.validate_correct_type_of_configuration_attribute("embeddings__enable_reembedding", bool)
server_config = self.app_config.server_config
if self.embeddings__enable_reembedding:
if server_config.single_dataset__datapath:
matrix_data_loader = MatrixDataLoader(
server_config.single_dataset__datapath, app_config=self.app_config
)
if matrix_data_loader.matrix_data_type != MatrixDataType.H5AD:
raise ConfigurationError("enable-reembedding is only supported with H5AD files.")
if server_config.adaptor__anndata_adaptor__backed:
raise ConfigurationError("enable-reembedding is not supported when run in --backed mode.")
try:
get_scanpy_module()
except NotImplementedError:
# Todo add scanpy to requirements.txt and remove this check once re-embeddings is fully supported
raise ConfigurationError("Please install scanpy to enable UMAP re-embedding")
def handle_diffexp(self, context):
self.validate_correct_type_of_configuration_attribute("diffexp__enable", bool)