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8180be83b8
* Introduce a config file to cellxgene The config file format is in yaml. The default config is located in server/common/default_config.py. A user may create a yaml file that contains a subset of these fields. It can be used during cellxgene launch, or for hosted cellxgene. The code has also been refactored. Much of the logic to check arguments has moved from launch to app config. It is now possible to set the tiledb context parameters using the config file. Other feature will soon be handled in a similar way.
56 lines
1.7 KiB
Python
56 lines
1.7 KiB
Python
import shutil
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import tempfile
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from os import path
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import pandas as pd
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from server.common.annotations import AnnotationsLocalFile
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from server.common.data_locator import DataLocator
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from server.common.app_config import AppConfig
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from server.data_common.fbs.matrix import encode_matrix_fbs
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from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
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def data_with_tmp_annotations(ext: MatrixDataType, annotations_fixture=False):
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tmp_dir = tempfile.mkdtemp()
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annotations_file = path.join(tmp_dir, "test_annotations.csv")
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if annotations_fixture:
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shutil.copyfile(f"test/test_datasets/pbmc3k-annotations.csv", annotations_file)
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args = {
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"embeddings__names": ["umap"],
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"presentation__max_categories": 100,
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"single_dataset__obs_names": None,
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"single_dataset__var_names": None,
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"diffexp__lfc_cutoff": 0.01,
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}
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fname = {
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MatrixDataType.H5AD: "../example-dataset/pbmc3k.h5ad",
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MatrixDataType.CXG: "test/test_datasets/pbmc3k.cxg",
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}[ext]
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data_locator = DataLocator(fname)
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config = AppConfig()
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config.update(**args)
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config.update(single_dataset__datapath=data_locator.path)
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config.complete_config()
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data = MatrixDataLoader(data_locator.abspath()).open(config)
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annotations = AnnotationsLocalFile(None, annotations_file)
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return data, tmp_dir, annotations
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def make_fbs(data):
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df = pd.DataFrame(data)
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return encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns)
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def skip_if(condition, reason: str):
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def decorator(f):
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def wraps(self, *args, **kwargs):
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if condition(self):
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self.skipTest(reason)
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else:
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f(self, *args, **kwargs)
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return wraps
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return decorator
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