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server refactor (#1140)

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This PR contains a refactoring to make adding new features easier.

The new features include supporting the tiledb format, and the multi dataset application.

The refactoring includes

Simplifying the directory structure and files.
a class structure to handle annotations (currently one type: AnnotationsLocalFile).
a class to handle application configuration
a class structure to handle matrix data (currently AnndataAdaptor and CxgAdaptor). CxgAdaptor uses tiledb.
Algorithms that were previously dependent on the scanpy anndata object are now generalized to work with an abstract interface.
The multi dataset option is not fully supported yet, and so the option to use it is hidden.
Use "cli launch --dataroot ..."
To access this feature.

All combinations of app single dataset/ app multi dataset and AnndataAdaptor/CxgAdaptor work with all the features, such as annotations, ontologies, diffexp.
This commit is contained in:
bmccandless
2020-02-19 10:22:35 -08:00
committed by GitHub
parent 349c413d8b
commit 907cc634f5
116 changed files with 2697 additions and 3252 deletions
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server/test/decode_fbs.py
+8 -8
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@@ -2,17 +2,17 @@
Code to decode, for testing purposes, the flatbuffer encoded blobs.
This code will need to be updated if fbs/matrix.fbs changes.
For more information, see fbs/matrix.fbs and server/app/util/fbs/
For more information, see fbs/matrix.fbs and server/data_common/fbs/
"""
import json
import server.app.util.fbs.NetEncoding.TypedArray as TypedArray
import server.app.util.fbs.NetEncoding.Matrix as Matrix
import server.app.util.fbs.NetEncoding.Int32Array as Int32Array
import server.app.util.fbs.NetEncoding.Uint32Array as Uint32Array
import server.app.util.fbs.NetEncoding.Float32Array as Float32Array
import server.app.util.fbs.NetEncoding.Float64Array as Float64Array
import server.app.util.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray
import server.data_common.fbs.NetEncoding.TypedArray as TypedArray
import server.data_common.fbs.NetEncoding.Matrix as Matrix
import server.data_common.fbs.NetEncoding.Int32Array as Int32Array
import server.data_common.fbs.NetEncoding.Uint32Array as Uint32Array
import server.data_common.fbs.NetEncoding.Float32Array as Float32Array
import server.data_common.fbs.NetEncoding.Float64Array as Float64Array
import server.data_common.fbs.NetEncoding.JSONEncodedArray as JSONEncodedArray
def decode_typed_array(tarr):