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.
* refactor cli to improve ux and enable easy incorporation of prepare as a subcommand
* switches to use click, which removes some boilerplate and gets us some improved ux for free
* changes the entry point for the cli
* changes the name of the browser option to --open and makes the default false
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
