Merge branches 'connect-to-real-data' and 'master' of github.com:seat…

…tleflu/incidence-mapper into connect-to-real-data

# Conflicts:
#	modelServR/R/returnModel.R
#	modelServR/R/saveModel.R

api_service/Dockerfile

@@ -38,7 +38,7 @@ ADD docker_scripts/entrypoint.sh docker_scripts/wsgi.ini ./
 # Add the rest of our library here
 ADD seattle_flu_incidence_mapper ./seattle_flu_incidence_mapper
 
-
+EXPOSE 80
 VOLUME [/model_store]
 
 CMD /app/entrypoint.sh

api_service/docker-compose.yml

@@ -1,42 +1,25 @@
 version: '3'
 
-
 services:
-  redis:
-    # We use management so we can have a nice gui
-    # Default login is guest/guest
-    image: redis
-    ports:
-      - "6379:6379"
-  # Our queue container
-  rabbit:
-    # We use management so we can have a nice gui
-    # Default login is guest/guest
-    image: rabbitmq:3.7-management
-    ports:
-    - "5672:5672"
-    - "8081:15672"
-  workers:
-    build:
-      context: .
-      dockerfile: Dockerfile
-    image: idm-docker-production.packages.idmod.org/sfim
-    command: python3 seattle_flu/app.py workers start
+  db:
+    image: postgres
+    restart: always
     environment:
-      - "DRAMATIQ_USE_PROD=True"
+      POSTGRES_USER: seattle_flu
+      POSTGRES_PASSWORD: seattle_flu
+
   service:
     build:
       context: .
       dockerfile: Dockerfile
     image: idm-docker-production.packages.idmod.org/sfim
     ports:
-      - 5000:5000
+      - 5000:80
     volumes:
-      - "/model_store:/model_store"
+      - "./test_model_store:/model_store"
     environment:
-    - "DEBUG=1"
-    - "FLASK_ENV=development"
-    - "DRAMATIQ_USE_PROD=True"
+    - "CREATE_DB=1"
+    - "SQLALCHEMY_URI=postgres+psycopg2://seattle_flu:@db"
 
 
 

api_service/docker_scripts/nginx.conf

@@ -33,8 +33,8 @@ http {
     #include /etc/nginx/conf.d/*.conf;
 
     server {
-        listen       5000 default_server;
-        listen       [::]:5000 default_server;
+        listen       80 default_server;
+        listen       [::]:80 default_server;
         server_name  _;
         #root         /usr/share/nginx/html;
 

api_service/docs/_static/jquery-3.2.1.js

@@ -1160,7 +1160,7 @@ setDocument = Sizzle.setDocument = function( node ) {
 	// Support: IE<10
 	// Check if getElementById returns elements by name
 	// The broken getElementById methods don't pick up programmatically-set names,
-	// so use a roundabout getElementsByName test
+	// so use a roundabout getElementsByName tests
 	support.getById = assert(function( el ) {
 		docElem.appendChild( el ).id = expando;
 		return !document.getElementsByName || !document.getElementsByName( expando ).length;
@@ -1280,7 +1280,7 @@ setDocument = Sizzle.setDocument = function( node ) {
 		// Regex strategy adopted from Diego Perini
 		assert(function( el ) {
 			// Select is set to empty string on purpose
-			// This is to test IE's treatment of not explicitly
+			// This is to tests IE's treatment of not explicitly
 			// setting a boolean content attribute,
 			// since its presence should be enough
 			// https://bugs.jquery.com/ticket/12359
@@ -1290,7 +1290,7 @@ setDocument = Sizzle.setDocument = function( node ) {
 
 			// Support: IE8, Opera 11-12.16
 			// Nothing should be selected when empty strings follow ^= or $= or *=
-			// The test attribute must be unknown in Opera but "safe" for WinRT
+			// The tests attribute must be unknown in Opera but "safe" for WinRT
 			// https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
 			if ( el.querySelectorAll("[msallowcapture^='']").length ) {
 				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
@@ -6229,7 +6229,7 @@ function addGetHookIf( conditionFn, hookFn ) {
 				return;
 			}
 
-			// Hook needed; redefine it so that the support test is not executed again.
+			// Hook needed; redefine it so that the support tests is not executed again.
 			return ( this.get = hookFn ).apply( this, arguments );
 		}
 	};

api_service/docs/_static/underscore-1.3.1.js

@@ -135,7 +135,7 @@
     return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
   };
 
-  // Return the first value which passes a truth test. Aliased as `detect`.
+  // Return the first value which passes a truth tests. Aliased as `detect`.
   _.find = _.detect = function(obj, iterator, context) {
     var result;
     any(obj, function(value, index, list) {
@@ -147,7 +147,7 @@
     return result;
   };
 
-  // Return all the elements that pass a truth test.
+  // Return all the elements that pass a truth tests.
   // Delegates to **ECMAScript 5**'s native `filter` if available.
   // Aliased as `select`.
   _.filter = _.select = function(obj, iterator, context) {
@@ -160,7 +160,7 @@
     return results;
   };
 
-  // Return all the elements for which a truth test fails.
+  // Return all the elements for which a truth tests fails.
   _.reject = function(obj, iterator, context) {
     var results = [];
     if (obj == null) return results;
@@ -170,7 +170,7 @@
     return results;
   };
 
-  // Determine whether all of the elements match a truth test.
+  // Determine whether all of the elements match a truth tests.
   // Delegates to **ECMAScript 5**'s native `every` if available.
   // Aliased as `all`.
   _.every = _.all = function(obj, iterator, context) {
@@ -183,7 +183,7 @@
     return result;
   };
 
-  // Determine if at least one element in the object matches a truth test.
+  // Determine if at least one element in the object matches a truth tests.
   // Delegates to **ECMAScript 5**'s native `some` if available.
   // Aliased as `any`.
   var any = _.some = _.any = function(obj, iterator, context) {

api_service/seattle_flu_incidence_mapper/swagger/swagger.yml

@@ -9,7 +9,6 @@ info:
   license:
     name: "Apache 2.0"
     url: "http://www.apache.org/licenses/LICENSE-2.0.html"
-host: "localhost"
 basePath: "/v1"
 tags:
 - name: "pathogen_model"
@@ -39,11 +38,26 @@ paths:
           schema:
             type: object
             additionalProperties: true
+            example: 
+              model_type: inla
+              observed:
+              - catchment
+              - encountered_week
+              - flu_shot
+              - n
+              - pathogen
+              - positive
+              - PUMA5CE
+              - sampling_location
+              - time_row
       responses:
         200:
           description: "successful operation"
           schema:
             type: "array"
+            items:
+              type: "object"
+
   /pathogen_models:
     get:
       tags:

api_service/setup.py

@@ -49,7 +49,9 @@
         'flask_sqlalchemy',
         'flask_marshmallow',
         'marshmallow-sqlalchemy',
-        "docker"
+        "docker",
+        'psycopg2',
+        ''
     ],
 
     extras_require={

docker-compose.production.yml

@@ -5,16 +5,30 @@ services:
     restart: always
     environment:
       POSTGRES_USER: seattle_flu
+  # placeholder for building worker
+  workers:
+    build:
+      context: .
+      dockerfile: Dockerfile.worker
+    image: idm-docker-production.packages.idmod.org/sfim-worker:${version:-latest}
+    command: touch t
   service:
       build:
         context: api_service
         dockerfile: Dockerfile
       image: idm-docker-production.packages.idmod.org/sfim-api:${version:-latest}
       volumes:
-      - "/model_store:/model_store"
+       - db-data:/var/lib/mysql/data
+      volumes:
+        - /model_store:/model_store
+        # pass docker so we can execute other containers
+        - /var/run/docker.sock:/var/run/docker.sock
       environment:
-        - SQLALCHEMY_URI=postgres://seattle_flu:@db
+        - SQLALCHEMY_URI=postgres+psycopg2://seattle_flu:@db
+        - "CREATE_DB=1"
+        #- "MODEL_HOST_PATH=`pwd`/test_model_store"
+        #- "DEBUG_TOKENS=1"
       depends_on:
       - db
       ports:
-       - "80:5000"
+       - "80:80"

modelServR/R/queryModel.R

@@ -65,8 +65,4 @@ queryLoadedModel <-
       jsonlite::write_json(model, file.path(outputDir, outputFile))
     }
     return(TRUE)
-  }
-
-#initializeModel <- function (modelId) {
-#  return(loadModelFileById(modelId))
-#}
+  }

modelServR/R/returnModel.R

@@ -1,3 +1,5 @@
+library(logging)
+
 #' loadModelFileById function for getting modeled data
 #'
 #' This function will load a model from the model_store_dir by Id
@@ -52,7 +54,7 @@ returnModel <- function(queryIn = jsonlite::toJSON(
                             cloudDir = Sys.getenv('MODEL_STORE', '/home/rstudio/seattle_flu/test_model_store')){
 
   basicConfig()
-  
+
   if(class(queryIn)== 'list'){
     queryList <- queryIn
     queryIn <- jsonlite::toJSON(queryIn)

modelServR/R/saveModel.R

@@ -1,4 +1,7 @@
 #' getHumanReadableModelIdFromModel: return human readable verion of model from query
+library(logging)
+
+
 #'
 #' @param model INLA model object that will generatie id from
 #'
@@ -55,14 +58,14 @@ getModelQueryObjectFromModel<- function(model, model_type = 'inla', latent = FAL
 #' @param query query object container the observed and the model_type attributes
 #'
 #' @import logging
-#' 
+#'
 #' @return An object containing the observed and the model_type fields
 #' @export
 #'
 getModelQueryObjectFromQuery <- function(query) {
   basicConfig()
   setLevel("FINEST")
-  
+
   logdebug("getModelQueryObjectFromQuery Src:", str(query))
   logdebug("$observed", attr(query, "observed"))
   result <- newEmptyObject()
@@ -95,7 +98,7 @@ getModelIdFromModel <- function(model) {
 getModelIdFromQuery <- function(query) {
   basicConfig()
   setLevel("FINEST")
-  
+
   #props <- getModelQueryObjectFromQuery(query)
   modelId <- as.character(jsonlite::toJSON(query, simplifyDataFrame=))
   logdebug("Model ID JSON:", jsonlite::toJSON(query, simplifyDataFrame=))
@@ -111,6 +114,8 @@ getModelIdFromQuery <- function(query) {
 #' @export
 #'
 saveModel <- function(model, modelStoreDir =  Sys.getenv('MODEL_STORE', '/home/rstudio/seattle_flu/test_model_store')) {
+  basicConfig()
+  setLevel("FINEST")
   ts <- Sys.time()
   attr(ts, "tzone") <- 'UTC'
   ts <- paste0(as.character(ts), 'Z')
@@ -139,13 +144,13 @@ saveModel <- function(model, modelStoreDir =  Sys.getenv('MODEL_STORE', '/home/r
     created = ts
   )
 
-  print("Saving RDS")
+  loginfo("Saving RDS")
   outfile <- xzfile(paste(modelStoreDir, '/', filename, '.RDS', sep = ''), 'wb', compress=9, encoding = 'utf8')
   saveRDS(model,file = outfile)
   close(outfile)
 
 
-  print("Saving smooth model")
+  loginfo("Saving smooth model")
   # all models output smooth
   newRow$latent <- FALSE
   write.csv(