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[WIP] Patch for anndata 0.7 (#1132)

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* Fix JSON encoding bug introduced by anndata 0.7

* Add anndata csr and csc classes to allowed matrix proxy inputs
This commit is contained in:
Sidney Bell
2020-01-28 16:12:43 -08:00
committed by GitHub
parent 3dd50e5676
commit a927d733c2
4 changed files with 22 additions and 19 deletions
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2
server/app/rest_api/rest.py
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@@ -45,7 +45,7 @@ class ConfigAPI(Resource):
},
"links": {"about-dataset": current_app.config["ABOUT_DATASET"]},
"parameters": {**current_app.data.get_config_parameters(uid=cxguid, collection=anno_collection)},
"library_versions": {"cellxgene": cellxgene_version, "anndata": anndata_version},
"library_versions": {"cellxgene": cellxgene_version, "anndata": str(anndata_version)},
}
}

2
server/app/scanpy_engine/matrix_proxy.py
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@@ -38,6 +38,8 @@ class MatrixProxy_anndata_h5py(MatrixProxyView):
"anndata.h5py.h5sparse.backed_csc_matrix",
"anndata.h5py.h5sparse.backed_csr_matrix",
"h5py._hl.dataset.Dataset",
"anndata._core.sparse_dataset.backed_csr_matrix",
"anndata._core.sparse_dataset.backed_csc_matrix",
)
@classmethod

2
server/app/util/matrix_proxy.py
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@@ -73,6 +73,8 @@ class MatrixProxy(_ArrayProxyBase):
"numpy.ndarray": True,
"scipy.sparse.csc.csc_matrix": True,
"scipy.sparse.csr.csr_matrix": True,
"anndata._core.sparse_dataset.backed_csr_matrix": "MatrixProxy_anndata_h5py",
"anndata._core.sparse_dataset.backed_csc_matrix": "MatrixProxy_anndata_h5py",
}
proxy_registry = None
last_cache_token = None

35
server/requirements.txt
View File

@@ -1,18 +1,17 @@
# TEMP anndata 0.7 breaks cellxgene - workaround
anndata==0.6.22post1
click>=6.7
fastobo>=0.6.1
Flask>=1.0.2
Flask-Caching>=1.4.0
Flask-Compress>=1.4.0
Flask-Cors>=3.0.6
Flask-RESTful>=0.3.6
flatbuffers>=1.10.0
fsspec>=0.4.4
numpy>=1.15.2
pandas>=0.24.2
scipy>=1.3.0
tables==3.5.1
# TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression
h5py==2.9.0
requests>=2.22.0
anndata>=0.6.2
click>=6.7
fastobo>=0.6.1
Flask>=1.0.2
Flask-Caching>=1.4.0
Flask-Compress>=1.4.0
Flask-Cors>=3.0.6
Flask-RESTful>=0.3.6
flatbuffers>=1.10.0
fsspec>=0.4.4
numpy>=1.15.2
pandas>=0.24.2
scipy>=1.3.0
tables==3.5.1
# TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression
h5py==2.9.0
requests>=2.22.0