mirror of
https://github.com/chanzuckerberg/cellxgene.git
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b90447c387
* first flatbuffer schema * do not lint auto-generated files * add flatbuffers package * add flatbuffer module * wire up /data/X/T route * use flatbuffers for matrix data fetc * clarity and comments * add flatbuffer layout route * clean up obsolete code * fix tests * move flake8 config to setup.cfg * add comments * lint * rework layout routes for fbs * add more type support to fbs * lint * add flatbuffer support for annotations * function name improvements * fix botched merge with master * remove unused import * route cleanup for flatbuffers * rename function for clarity * add missing globals to Jest tests * fix client JS tests * fix routes for Python tests * comments for clarity * non-finite floating point hardening * more non-finite number handling * lint * fix tests for summarizeAnnotations * harden diffexp calculation against FP errors * cleanup unused code * lint * add encoding tests for flatbuffers * application type specified as strings * fix spelling error * improve variable names * add note about documentation gap * rename FBS DataFrame to Matrix
74 lines
1.6 KiB
Plaintext
74 lines
1.6 KiB
Plaintext
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/*
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Flatbuffers schema for use in cellxgene wire-format.
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Schema defines a general purpose, polymorphic, 2D matrix. Data is
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organized in a columnar layout. Each column is homomorphic, and
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several column types are supported:
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- IEEE 32 and 64 bit floats
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- signed and unsigned 32 bit integers
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- JSON/UTF8 encoded array (for other types)
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https://github.com/google/flatbuffers
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http://google.github.io/flatbuffers/
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NOTE: IF YOU MODIFY THIS FILE, YOU MUST RECOMPILE AND COMMIT
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RESULTING FILES TO THE REPO:
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* server/app/util/fbs/NetEncoding/*
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* client/src/util/stateManager/matrix_generated.js
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*/
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namespace NetEncoding;
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table Float32Array {
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data: [float32];
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}
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table Uint32Array {
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data: [uint32];
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}
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table Int32Array {
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data: [int32];
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}
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table Float64Array {
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data: [float64];
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}
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table JSONEncodedArray {
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// contains a UTF-8/JSON encoded array. Used to store other
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// types (or polymorphic arrays)
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data: [uint8];
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}
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union TypedArray {
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Float32Array,
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Int32Array,
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Uint32Array,
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Float64Array,
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JSONEncodedArray
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}
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// Extra level of indirection required because vector of union not yet supported
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table Column {
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u: TypedArray;
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}
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// 2D matrix stored in columnar layout
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//
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table Matrix {
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n_rows: uint32; // all columns have this length
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n_cols: uint32; // same as columns.length
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columns: [Column]; // length n_cols
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// optional row and column index, with same length as corresponding dimension.
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// If null, defaults to numeric index, ie, [0, n_rows) or [0, n_cols)
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col_index: TypedArray;
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row_index: TypedArray;
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}
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root_type Matrix;
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