* dead code and route removal
* more dead code cleanup
* fix scanpy_engine tests
* lint
* add missing catch in filter parsing
* update scanpy NaN tests
* more fbs tests and dead test removal
* remove forced default for content type negotiation
* bit of cleanup
* more fbs test cleanup
* lint
* remove swagger
* swagger cleanup
* lint
* correctly handle lack of templates
* more dead code removal
* remove unused files
* fix dev build
* lint
* 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
* Scanpy engine now required
Without the --engine param we need to error if scanpy engine cannot be imported rather than waiting for all engines
* CLI options and help matches proposal
(but not all options hooked up yet)
* Flesh out top level args
* Move computation args to engine
* CLI input file (#374)
* Fix test command
(tests still won't work)
* Input is file instead of directory
- also renamed example file
* Csweaver/debug (#376)
* Respect debug flag for logging flask calls
* Add loading messages
* max categories (#377)
* Add max categories
* Rename max_categories to category_selection_limit
* ensure whole numbers
* Add empty filter case
* Filtering dataframes moved to engine instead of rest
* minor changes from PR review
* Minor fixes from PR review
Pass {} instead of none if no filter
chain exceptions
typos
* Use HTTPStatus for all responses
More informative than just the code as an int
* Fill out REST error handling
* Test error routes
* Use HTTP Status for tests too
* factor mime type request into function
* Better mimetype errors
* 404 -> 400 error for bad key
Move to new REST v0.2 communication between front and back-end. This is a first cut implementation which is functional, but will need follow-up enhancements for performance, error checking, etc. Protocol spec is in docs directory.
* Add filtering via indexing
* Using new filter specs
Indexing working
* Added filtering by annotation value
* factor out common methods
* Documentation
* create enum for axis (obs/var)
* Better description for filter's return
* Add boolean to enumerated types
* Augmented enum for scanpy axis
* Create schema for annotations
Based on datatype within scanpy/anndata
+ tests
* remove obsolete schema parse script
* Update rest api to remove old routes and add schema route
* Separate development requirements
* Warning for unsupported datatypes
* include -r requirements.txt in dev
* Merged downcast warnings
* Fixed bug where names were NaNs
Needed to include the index too when creating the series
* Add config endpoint
* Generate app features from CLI selections
* Move features to driver
* Add tests for schema
* Clearer version wording
* python3 version of super
* version from engine to package level
* move features to driver
* Revise layout function to match the new spec
* GET for layout/obs
* PUT Layout (#211)
* PUT Layout
* Csweaver/annotations (#212)
* Update scanpy engine to support the rest v0.2 annotation requests
* GET endpoint for obs annotations + tests
* Documentation
* Test annotations in scanpy engine
* Description for annotation-keys param
* annotation->annotations
* clarified return for annotations
* Use URL query list for annotations fields
* parse_filter parses v0.2 GET filters (#215)
* parse_filter parses v0.2 GET filters
* Don't allow index filters from query params
* Better variable conversion
* Parse filter improvements
- uses default dict
- renamed filter -> query_filter
* Cleanup Tasks (#216)
* Add test_api back into travis build
* Do custom JSON encoding the correct way
* Run cellxgene server in test setup
* Cleanup new tests too
* Option to bind to all interfaces (#225)
app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces.
Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns.
Test plan: browsed to <ip>:5005/api/v0.2/config on a different host.
* Add filtering via indexing
* Using new filter specs
Indexing working
* Added filtering by annotation value
* factor out common methods
* Documentation
* create enum for axis (obs/var)
* Better description for filter's return
* Add boolean to enumerated types
* Augmented enum for scanpy axis
* Create schema for annotations
Based on datatype within scanpy/anndata
+ tests
* remove obsolete schema parse script
* Update rest api to remove old routes and add schema route
* Separate development requirements
* Warning for unsupported datatypes
* include -r requirements.txt in dev
* Merged downcast warnings
* Fixed bug where names were NaNs
Needed to include the index too when creating the series
* Add config endpoint
* Generate app features from CLI selections
* Move features to driver
* Add tests for schema
* Clearer version wording
* python3 version of super
* version from engine to package level
* move features to driver
* Revise layout function to match the new spec
* GET for layout/obs
* PUT Layout (#211)
* PUT Layout
* Csweaver/annotations (#212)
* Update scanpy engine to support the rest v0.2 annotation requests
* GET endpoint for obs annotations + tests
* Documentation
* Test annotations in scanpy engine
* Description for annotation-keys param
* annotation->annotations
* clarified return for annotations
* Use URL query list for annotations fields
* parse_filter parses v0.2 GET filters (#215)
* parse_filter parses v0.2 GET filters
* Don't allow index filters from query params
* Better variable conversion
* Parse filter improvements
- uses default dict
- renamed filter -> query_filter
* Cleanup Tasks (#216)
* Add test_api back into travis build
* Do custom JSON encoding the correct way
* Run cellxgene server in test setup
* Cleanup new tests too
* Option to bind to all interfaces (#225)
app.run("0.0.0.0") instead of app.run("127.0.0.1") binds to all interfaces.
Note: There are comments on the internet that says that the flask server is not up to the task of production serving. I don't think that such scalability concerns apply here, but I was able to get cellxgene working with twistd relatively easily, and we could switch to that if there are scalability concerns.
Test plan: browsed to <ip>:5005/api/v0.2/config on a different host.
* Fix merge errors
- import warnings was improperly deleted
- scanpy engine tests were totally wrong
* Fix merge error with driver
* PUT /annotations (#235)
* Add query param for annotation name
* fix descriptions, eliminate else clause
* first cut at initial data load on rest 0.2 api
* Annotation var (#248)
* Fix bug strings are always objects in pandas
* Add axis to annotation method
* Add /annotation/var to REST api
* Csweaver/expressiondata (#242)
* Refactor expression method for REST v2
* Add message to QueryStringError
* Fix range filters
* Add GET route for /data
* /data PUT route
* rename expression to data_frame
* clarification of error
* Improve accept type handling
* support all schema types for 0.2 REST API
* remove REST 0.1 code; connect var annotations loading
* config reducer; use config to set data set title; remove obsolete templating code for data set title
* REST 0.2 expression conversion support
* partial port of expression to REST 0.2
* diffexp (#273)
* Add diffexp method to scanpy
and test
* Minor tweaks to diffexp
Get a minimal working version to unblock FE development
* Fixing things git deleted
* cleanup print statements
* Add index test
* additional, partial REST 0.2 bring up of diffexp
* Ignore unstructured annotations for data (#275)
This is a temp hack, need to figure out how to include data.uns if there is only one gene
* diffexp REST 0.2 port finish
* ignore unstructured annotaitons on all routes except layout
* correctly use varDataCache; maintain state during world rebuild
* correct varDataCache use
* temporarily disable all memoization
* refinements to expression data caching
* clear cell sets upon regraph/reset
* update version of REST to 0.2
* Travis build fixes
- comment out cache import
- fix duplicate test name
* Remove dependency from travis
* clarify semantics of config variables
* move generic action helpers into util
