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c7f2032dd7
* Add user-generated annotations tests to the server Partially completes https://github.com/chanzuckerberg/cellxgene/issues/969 * Auto-format python code * @skip_if: passing lambdas > than property strings * Respond to feedback from @bkmartinjr
51 lines
1.5 KiB
Python
51 lines
1.5 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.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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"layout": ["umap"],
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"max_category_items": 100,
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"obs_names": None,
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"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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data = MatrixDataLoader(data_locator.abspath()).open(args)
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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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