Reorganized core app to be more modular, allows for FileField swagger

neuroscout/api_spec.py

@@ -0,0 +1,25 @@
+# Setup API docs and Swagger
+from .core import app
+from .auth import add_auth_to_swagger
+from apispec import APISpec
+from flask_apispec.extension import FlaskApiSpec
+import webargs as wa
+from apispec.ext.marshmallow import MarshmallowPlugin
+
+file_plugin = MarshmallowPlugin()
+spec = APISpec(
+    title='neuroscout',
+    version='v1',
+    plugins=[file_plugin],
+    openapi_version='2.0'
+)
+app.config.update({
+    'APISPEC_SPEC': spec})
+add_auth_to_swagger(spec)
+
+docs = FlaskApiSpec(app)
+
+
+@file_plugin.map_to_openapi_type('file', None)
+class FileField(wa.fields.Raw):
+    pass

neuroscout/core.py

@@ -7,43 +7,30 @@
 from flask_security import Security
 from flask_security.confirmable import confirm_email_token_status, confirm_user
 from flask_cors import CORS
-from apispec import APISpec
-from flask_apispec.extension import FlaskApiSpec
 
-from .basic import create_app, file_plugin
-from .models import db
+from .basic import create_app
+from .models import db, user_datastore
 
 app = create_app()
 mail = Mail(app)
 cache = Cache(
     config={'CACHE_TYPE': 'filesystem', 'CACHE_DIR': app.config['CACHE_DIR']})
 cache.init_app(app)
 # Enable CORS
-cors = CORS(app,
-            resources={r"/api/*": {"origins": "*"},
-                       r"/swagger/": {"origins": "*"}})
+cors = CORS(
+    app,
+    resources={r"/api/*": {"origins": "*"}, r"/swagger/": {"origins": "*"}})
 
-# Setup Flask-Security and JWT
-from .auth import authenticate, load_user, add_auth_to_swagger
-from .models import *
+# These imports require the above
+from .auth import authenticate, load_user
+from .utils.factory import route_factory
+from .api_spec import docs
 
+# Setup Flask-Security and JWT
 security = Security(app, user_datastore)
 jwt = JWT(app, authenticate, load_user)
 
-
-# Setup API and Swagger
-from .utils.core import route_factory
-spec = APISpec(
-    title='neuroscout',
-    version='v1',
-    plugins=[file_plugin],
-    openapi_version='2.0'
-)
-app.config.update({
-    'APISPEC_SPEC': spec})
-add_auth_to_swagger(spec)
-docs = FlaskApiSpec(app)
-
+# Set up API routes
 route_factory(
     app, docs,
     [

neuroscout/resources/analysis/reports.py

@@ -1,18 +1,18 @@
+import datetime
+import tempfile
+from hashids import Hashids
+import webargs as wa
 from flask_apispec import doc, use_kwargs, MethodResource, marshal_with
 from flask import current_app
+
 from ...models import Report, NeurovaultCollection
 from ...database import db
 from ...worker import celery_app
-import webargs as wa
-from marshmallow import fields
-from ..utils import owner_required, abort, fetch_analysis
 from ...schemas.analysis import (
     ReportSchema, AnalysisCompiledSchema, NeurovaultCollectionSchema)
 from ...utils.db import put_record
-
-import datetime
-import tempfile
-from hashids import Hashids
+from ..utils import owner_required, abort, fetch_analysis
+from ...api_spec import FileField
 
 
 def _validation_hash(analysis_id):
@@ -58,7 +58,7 @@ def get(self, analysis):
 
 @marshal_with(ReportSchema)
 @use_kwargs({
-    'run_id': wa.fields.DelimitedList(fields.Int(),
+    'run_id': wa.fields.DelimitedList(wa.fields.Int(),
                                       description='Run id(s).'),
     'sampling_rate': wa.fields.Number(description='Sampling rate in Hz'),
     'scale': wa.fields.Boolean(description='Scale columns for plotting'),
@@ -110,15 +110,6 @@ def get(self, analysis, run_id=None):
         return report
 
 
-# Use current_app
-# file_plugin = MarshmallowPlugin()
-#
-#
-# @file_plugin.map_to_openapi_type('file', None)
-class FileField(wa.fields.Raw):
-    pass
-
-
 @doc(tags=['analysis'])
 class AnalysisUploadResource(MethodResource):
     @doc(summary='Upload fitlins analysis tarball.',

neuroscout/resources/predictor.py

@@ -73,3 +73,9 @@ def get(self, **kwargs):
             query = query.filter(
                 getattr(PredictorEvent, param).in_(kwargs[param]))
         return dump_pe(query)
+
+
+class PredictorCreateResource(MethodResource):
+    @doc(tags=['predictors'], summary='Create a new predictor')
+    def post(self, **kwargs):
+        return {}

neuroscout/utils/core.py

@@ -1,16 +1,6 @@
 """
     Misc. utilities useful across package.
 """
-from .. import resources
-
-
-def route_factory(app, docs, pairings, prepend='/api/'):
-    """ Create API routes and add to app """
-    for res_name, route in pairings:
-        res = getattr(resources, res_name)
-        app.add_url_rule(prepend + route,
-                         view_func=res.as_view(res_name.lower()))
-        docs.register(res)
 
 
 def listify(obj):

neuroscout/utils/factory.py

@@ -0,0 +1,11 @@
+from .. import resources
+from ..models import *
+
+
+def route_factory(app, docs, pairings, prepend='/api/'):
+    """ Create API routes and add to app """
+    for res_name, route in pairings:
+        res = getattr(resources, res_name)
+        app.add_url_rule(prepend + route,
+                         view_func=res.as_view(res_name.lower()))
+        docs.register(res)