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binary wire format with flatbuffers (#509)

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* 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
This commit is contained in:
Bruce Martin
2019-01-09 14:26:05 -08:00
committed by GitHub
parent 42e25a1a1f
commit b90447c387
41 changed files with 2317 additions and 266 deletions
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dev_docs/REST_API.md
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@@ -1,5 +1,7 @@
# cellxgene REST API 0.2 specification
_Note:_ this document lacks any information about the binary encoding utilized by various routes. This will be added at a later date.
Items marked as (_future_) are intended for future implementation, and are included in the design to round out the concept, and highlight what we would do when/if we needed more functionality. The (_future_) items are not currently used by the cellxgene web application, and may be omitted from any backend - see [Current Front-End Dependencies](#current-front-end-dependencies) for more details.
_Caveat emptor, partial spec_: this is a sketch for a spec, not a full spec, and some shortcuts have been taken in the authorship. Best practices for a REST API are assumed but not documented here, such as API versioning, reasonable choices for HTTP response codes, etc. In addition, for clarity the JSON examples will not always have all required quoting (eg, on keys) - the actual implementation should use legal JSON/CSV.