fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-04 00:18:11 +08:00
Code Issues Packages Projects Releases Wiki Activity

refactor config to support different config options for datasets in different dataroots. (#1596)

Browse Source 
This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.
This commit is contained in:
bmccandless
2020-07-10 16:21:40 -07:00
committed by GitHub
parent 13246cb6d1
commit f69d141336
21 changed files with 1021 additions and 710 deletions
Download Patch File Download Diff File Expand all files Collapse all files
server/test/__init__.py
+20 -23
View File
@@ -27,21 +27,18 @@ def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
annotations_file = path.join(tmp_dir, "test_annotations.csv")
if annotations_fixture:
shutil.copyfile(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k-annotations.csv", annotations_file)
args = {
"embeddings__names": ["umap"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
}
fname = {
MatrixDataType.H5AD: f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad",
MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
}[ext]
data_locator = DataLocator(fname)
config = AppConfig()
config.update(**args)
config.update(single_dataset__datapath=data_locator.path)
config.update_server_config(
single_dataset__obs_names=None, single_dataset__var_names=None, single_dataset__datapath=data_locator.path
)
config.update_default_dataset_config(
embeddings__names=["umap"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01,
)
config.complete_config()
data = MatrixDataLoader(data_locator.abspath()).open(config)
annotations = AnnotationsLocalFile(None, annotations_file)
@@ -66,21 +63,21 @@ def skip_if(condition, reason: str):
return decorator
def app_config(data_locator, backed=False, extra={}):
args = {
"embeddings__names": ["umap", "tsne", "pca"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
"adaptor__anndata_adaptor__backed": backed,
"single_dataset__datapath": data_locator,
"limits__diffexp_cellcount_max": None,
"limits__column_request_max": None,
}
def app_config(data_locator, backed=False, extra_server_config={}, extra_dataset_config={}):
config = AppConfig()
config.update(**args)
config.update(**extra)
config.update_server_config(
single_dataset__obs_names=None,
single_dataset__var_names=None,
adaptor__anndata_adaptor__backed=backed,
single_dataset__datapath=data_locator,
limits__diffexp_cellcount_max=None,
limits__column_request_max=None,
)
config.update_default_dataset_config(
embeddings__names=["umap", "tsne", "pca"], presentation__max_categories=100, diffexp__lfc_cutoff=0.01
)
config.update_server_config(**extra_server_config)
config.update_default_dataset_config(**extra_dataset_config)
config.complete_config()
return config