Restv2 feature branch merge to master (#284)

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

server/app/app.py

@@ -9,11 +9,13 @@ from flask_cors import CORS
 from flask_restful_swagger_2 import get_swagger_blueprint
 
 from .rest_api.rest import get_api_resources
+from .util.utils import Float32JSONEncoder
 from .web import webapp
 
 REACTIVE_LIMIT = 1_000_000
 
 app = Flask(__name__, static_folder="web/static")
+app.json_encoder = Float32JSONEncoder
 cache = Cache(app, config={"CACHE_TYPE": "simple", "CACHE_DEFAULT_TIMEOUT": 860000})
 Compress(app)
 CORS(app)
@@ -54,9 +56,12 @@ def run_scanpy(args):
     )
 
     from .scanpy_engine.scanpy_engine import ScanpyEngine
-    app.data = ScanpyEngine(args.data_directory, schema="data_schema.json",
-                            graph_method=args.layout, diffexp_method=args.diffexp)
-    app.run(host="127.0.0.1", debug=True, port=args.port)
+    app.data = ScanpyEngine(args.data_directory, layout_method=args.layout, diffexp_method=args.diffexp)
+    if args.bind_all:
+        host = "0.0.0.0"
+    else:
+        host = "127.0.0.1"
+    app.run(host=host, debug=True, port=args.port)
 
 
 def main():
@@ -64,6 +69,10 @@ def main():
     parser.add_argument("--title", "-t", help="Title to display -- if this is omitted the title will be the name "
                                               "of the directory from the data_directory arg")
     parser.add_argument("--port", help="Port to run server on.", type=int, default=5005)
+    parser.add_argument(
+        "--bind-all",
+        help="Bind to all interfaces (this makes the server accessible beyond this computer)",
+        action="store_true")
     subparsers = parser.add_subparsers(dest="cellxgene_command")
     try:
         from .scanpy_engine.scanpy_engine import ScanpyEngine