Merge branch 'master' into release-0.2

.gitignore

@@ -118,3 +118,9 @@ wrappers/python/fbs/
 #ONNX example
 examples/models/onnx_resnet50/cpu_codegen/Function_0_codegen.cpp
 examples/models/onnx_resnet50/resnet.onnx
+
+#openapi
+engine/src/main/resources/static/seldon.json
+api-frontend/src/main/resources/static/seldon.json
+wrappers/python/seldon.json
+

CHANGELOG.md

@@ -1,5 +1,39 @@
 # Change Log
 
+## [v0.2.3](https://github.com/SeldonIO/seldon-core/tree/v0.2.3) (2018-09-17)
+[Full Changelog](https://github.com/SeldonIO/seldon-core/compare/v0.2.2...v0.2.3)
+
+**Closed issues:**
+
+- R wrapper s2i environment documentation missing Model file extension [\#219](https://github.com/SeldonIO/seldon-core/issues/219)
+- Provide example using ONNX via Intel nGraph for inference [\#214](https://github.com/SeldonIO/seldon-core/issues/214)
+- how to explore grafana dashboard for seldon-core  in  web ui [\#209](https://github.com/SeldonIO/seldon-core/issues/209)
+- APPLICATION FAILED TO START - Example python notebook \(fx-market-predictor\) [\#208](https://github.com/SeldonIO/seldon-core/issues/208)
+- dev guide doc: develop/test changes locally? [\#202](https://github.com/SeldonIO/seldon-core/issues/202)
+- Service orchestrator updated when surrounding deployment changed [\#199](https://github.com/SeldonIO/seldon-core/issues/199)
+- UnknownHostException: seldon-deployment [\#194](https://github.com/SeldonIO/seldon-core/issues/194)
+- grafana dashboard [\#192](https://github.com/SeldonIO/seldon-core/issues/192)
+- Add image versions to all wrapper images [\#136](https://github.com/SeldonIO/seldon-core/issues/136)
+- Status is not created in Custom Resource on initial create or update [\#74](https://github.com/SeldonIO/seldon-core/issues/74)
+
+**Merged pull requests:**
+
+- Update SeldonDeployment status for lifecycle conditions [\#223](https://github.com/SeldonIO/seldon-core/pull/223) ([cliveseldon](https://github.com/cliveseldon))
+- Update use of python wrappers to version 0.2 [\#222](https://github.com/SeldonIO/seldon-core/pull/222) ([cliveseldon](https://github.com/cliveseldon))
+- Support for ONNX exported models for inference [\#221](https://github.com/SeldonIO/seldon-core/pull/221) ([cliveseldon](https://github.com/cliveseldon))
+- Private repo build and run [\#220](https://github.com/SeldonIO/seldon-core/pull/220) ([gsunner](https://github.com/gsunner))
+- Nodejs s2i wrapper for JavaScript models [\#218](https://github.com/SeldonIO/seldon-core/pull/218) ([SachinVarghese](https://github.com/SachinVarghese))
+- Update seldon metrics [\#217](https://github.com/SeldonIO/seldon-core/pull/217) ([cliveseldon](https://github.com/cliveseldon))
+- fix oauth\_port check in api-tester [\#213](https://github.com/SeldonIO/seldon-core/pull/213) ([cliveseldon](https://github.com/cliveseldon))
+- Add configurable timeouts for REST and gRPC [\#211](https://github.com/SeldonIO/seldon-core/pull/211) ([cliveseldon](https://github.com/cliveseldon))
+- Config circular bug [\#210](https://github.com/SeldonIO/seldon-core/pull/210) ([cliveseldon](https://github.com/cliveseldon))
+- Update for flatbuffers python wrappers [\#205](https://github.com/SeldonIO/seldon-core/pull/205) ([cliveseldon](https://github.com/cliveseldon))
+- Experimental Flatbuffers based protocol for python wrapper [\#204](https://github.com/SeldonIO/seldon-core/pull/204) ([cliveseldon](https://github.com/cliveseldon))
+- Change wrappers to be versioned and update examples and docs [\#201](https://github.com/SeldonIO/seldon-core/pull/201) ([cliveseldon](https://github.com/cliveseldon))
+- Update istio example notebook [\#200](https://github.com/SeldonIO/seldon-core/pull/200) ([cliveseldon](https://github.com/cliveseldon))
+- Allow Annotations to allow customizations [\#197](https://github.com/SeldonIO/seldon-core/pull/197) ([cliveseldon](https://github.com/cliveseldon))
+- Removed subtype from deployment example [\#195](https://github.com/SeldonIO/seldon-core/pull/195) ([hanneshapke](https://github.com/hanneshapke))
+
 ## [v0.2.2](https://github.com/SeldonIO/seldon-core/tree/v0.2.2) (2018-07-18)
 [Full Changelog](https://github.com/SeldonIO/seldon-core/compare/v0.2.1...v0.2.2)
 

api-frontend/Makefile

@@ -6,7 +6,7 @@ VERSION_FILE=target/version.txt
 write_version:
 	ls target/seldon-apife-*.jar | sed -n 's/target\/seldon-apife-\(.*\).jar$$/\1/p' > $(VERSION_FILE) && cat $(VERSION_FILE)
 
-build_jar: update_proto
+build_jar: update_proto update_swagger
 	mvn clean verify -Dlicense.useMissingFile -B
 
 build_image: build_jar write_version
@@ -52,3 +52,5 @@ port_forward_api_server:
 	POD_NAME=$$(kubectl --namespace default get pod -l app=seldon-apiserver-container-app -o template --template="{{(index .items 0).metadata.name}}") && \
 		kubectl port-forward $${POD_NAME} 8080:8080
 
+update_swagger:
+	cp -v ../openapi/apife.oas3.json src/main/resources/static/seldon.json

api-frontend/Makefile.ci

@@ -7,7 +7,7 @@ LOCAL_PRIVATE_REPO=127.0.0.1:5000
 build: clean build_image
 
 
-build_jar: update_proto
+build_jar: update_proto update_swagger
 	@set -x && mvn clean verify -Dlicense.useMissingFile -B
 
 write_version: build_jar
@@ -47,3 +47,5 @@ update_proto: download_protos
 	cp -vr ../proto/k8s/k8s.io src/main/proto
 	cp -v ../proto/k8s/v1.proto src/main/proto
 
+update_swagger:
+	cp -v ../openapi/apife.oas3.json src/main/resources/static/seldon.json

api-frontend/pom.xml

@@ -5,12 +5,12 @@
 	<parent>
 		<groupId>org.springframework.boot</groupId>
 		<artifactId>spring-boot-starter-parent</artifactId>
-		<version>1.5.7.RELEASE</version>
+		<version>1.5.17.RELEASE</version>
 	</parent>
 
 	<groupId>io.seldon.apife</groupId>
 	<artifactId>seldon-apife</artifactId>
-	<version>0.2.3</version>
+	<version>0.2.4</version>
 	<packaging>jar</packaging>
 
 	<name>api-frontend</name>
@@ -35,6 +35,26 @@
 		</extensions>
 
 		<plugins>
+			<plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.2</version>
+                <executions>
+                    <execution>
+                        <id>jacoco-initialize</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>jacoco-report</id>
+                        <phase>test</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>		
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>license-maven-plugin</artifactId>
@@ -146,12 +166,12 @@
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-core</artifactId>
-			<version>2.8.6</version>
+			<version>2.8.11</version>
 		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
-			<version>2.8.6</version>
+			<version>2.8.11.2</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-lang</groupId>
@@ -175,7 +195,7 @@
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpclient</artifactId>
-			<version>4.3.4</version>
+			<version>4.5.6</version>
 		</dependency>
 
 		<dependency>
@@ -228,7 +248,7 @@
 		<dependency>
 			<groupId>mysql</groupId>
 			<artifactId>mysql-connector-java</artifactId>
-			<version>5.1.40</version>
+			<version>5.1.47</version>
 		</dependency>
 		<dependency>
     		<groupId>org.apache.kafka</groupId>

api-frontend/src/main/java/io/seldon/apife/api/rest/RestClientController.java

@@ -29,6 +29,7 @@
 import org.springframework.http.MediaType;
 import org.springframework.http.RequestEntity;
 import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseStatus;
@@ -122,7 +123,7 @@ String ping() {
         return "pong";
     }
 
-
+	@CrossOrigin(origins = "*")
 	@RequestMapping(value = "/api/v0.1/predictions", method = RequestMethod.POST, consumes = "application/json; charset=utf-8", produces = "application/json; charset=utf-8")
 	    public ResponseEntity<String> prediction(RequestEntity<String> requestEntity,Principal principal) {
 
@@ -172,6 +173,7 @@ public ResponseEntity<String> prediction(RequestEntity<String> requestEntity,Pri
 
 	}
 
+	@CrossOrigin(origins = "*")
 	@RequestMapping(value = "/api/v0.1/feedback", method = RequestMethod.POST, consumes = "application/json; charset=utf-8", produces = "application/json; charset=utf-8")
 	@ResponseStatus(value = HttpStatus.OK)
 	public void feedback(RequestEntity<String> requestEntity, Principal principal) 

api-frontend/src/main/java/io/seldon/apife/config/SimpleCorsFilter.java

@@ -0,0 +1,48 @@
+package io.seldon.apife.config;
+
+import java.io.IOException;
+
+import javax.servlet.Filter;
+import javax.servlet.FilterChain;
+import javax.servlet.FilterConfig;
+import javax.servlet.ServletException;
+import javax.servlet.ServletRequest;
+import javax.servlet.ServletResponse;
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+
+import org.springframework.core.Ordered;
+import org.springframework.core.annotation.Order;
+import org.springframework.stereotype.Component;
+
+@Component
+@Order(Ordered.HIGHEST_PRECEDENCE)
+public class SimpleCorsFilter implements Filter {
+
+    public SimpleCorsFilter() {
+    }
+
+    @Override
+    public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain) throws IOException, ServletException {
+        HttpServletResponse response = (HttpServletResponse) res;
+        HttpServletRequest request = (HttpServletRequest) req;
+        response.setHeader("Access-Control-Allow-Origin", "*");
+        response.setHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS, DELETE");
+        response.setHeader("Access-Control-Max-Age", "3600");
+        //response.setHeader("Access-Control-Allow-Headers", "x-requested-with, authorization");
+        response.setHeader("Access-Control-Allow-Headers", "API-Key, accept, Content-Type, x-requested-with, authorization");
+        if ("OPTIONS".equalsIgnoreCase(request.getMethod())) {
+            response.setStatus(HttpServletResponse.SC_OK);
+        } else {
+            chain.doFilter(req, res);
+        }
+    }
+
+    @Override
+    public void init(FilterConfig filterConfig) {
+    }
+
+    @Override
+    public void destroy() {
+    }
+}

cluster-manager/README.txt

@@ -1,4 +1,7 @@
 Local testing:
 
+export ENGINE_CONTAINER_IMAGE_PULL_POLICY=IfNotPresent
 export SELDON_CLUSTER_MANAGER_POD_NAMESPACE=seldon
 export ENGINE_CONTAINER_IMAGE_AND_VERSION=seldonio/engine:<VERSION>
+
+mvn spring-boot:run

cluster-manager/pom.xml

@@ -4,7 +4,7 @@
   <groupId>io.seldon.clustermanager</groupId>
   <artifactId>seldon-cluster-manager</artifactId>
   <packaging>jar</packaging>
-  <version>0.2.3</version>
+  <version>0.2.4</version>
   <name>seldon-cluster-manager</name>
   <url>http://maven.apache.org</url>
 
@@ -81,7 +81,7 @@
     <dependency>
       <groupId>io.kubernetes</groupId>
       <artifactId>client-java</artifactId>
-      <version>1.0.0</version>
+      <version>3.0.0</version>
       <scope>compile</scope>
     </dependency>
 
@@ -102,6 +102,26 @@
     </extensions>
 
     <plugins>
+			<plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.2</version>
+                <executions>
+                    <execution>
+                        <id>jacoco-initialize</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>jacoco-report</id>
+                        <phase>test</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>    
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>license-maven-plugin</artifactId>

cluster-manager/src/main/java/io/seldon/clustermanager/ClusterManagerProperites.java

@@ -23,7 +23,8 @@ public class ClusterManagerProperites {
     private int engineContainerPort;
     private int engineGrpcContainerPort;
     private String engineContainerImageAndVersion;
-    private String engineContainerImagePullPolicy;
+    private String engineContainerImagePullPolicy = "IfNotPresent";
+    private String engineContainerServiceAccountName = "default";
     private int puContainerPortBase;
     private String namespace;
 
@@ -59,7 +60,15 @@ public void setEngineContainerImagePullPolicy(String engineContainerImagePullPol
         this.engineContainerImagePullPolicy = engineContainerImagePullPolicy;
     }
 
-    public int getPuContainerPortBase() {
+    public String getEngineContainerServiceAccountName() {
+		return engineContainerServiceAccountName;
+	}
+
+	public void setEngineContainerServiceAccountName(String engineContainerServiceAccountName) {
+		this.engineContainerServiceAccountName = engineContainerServiceAccountName;
+	}
+
+	public int getPuContainerPortBase() {
         return puContainerPortBase;
     }
 

cluster-manager/src/main/java/io/seldon/clustermanager/k8s/Constants.java

@@ -20,4 +20,8 @@ public class Constants {
     public static final String STATE_CREATING = "Creating";
     public static final String STATE_FAILED = "Failed";
     public static final String STATE_AVAILABLE = "Available";
+
+    public static final String ENGINE_JAVA_OPTS_ANNOTATION = "seldon.io/engine-java-opts";
+    public static final String REST_READ_TIMEOUT_ANNOTATION = "seldon.io/rest-read-timeout";
+    public static final String GRPC_READ_TIMEOUT_ANNOTATION = "seldon.io/grpc-read-timeout";
 }

cluster-manager/src/main/java/io/seldon/clustermanager/k8s/DeploymentWatcher.java

@@ -125,7 +125,6 @@ public int watchDeployments(int resourceVersion,int resourceVersionProcessed) th
                         // put this logic in new class
                     }
                 }
-
             }
         }
         catch(RuntimeException e)

cluster-manager/src/main/java/io/seldon/clustermanager/k8s/KubeCRDHandler.java

@@ -22,7 +22,7 @@
 public interface KubeCRDHandler {
 
 	public void updateRaw(String json,String seldonDeploymentName);
-	public void updateSeldonDeployment(SeldonDeployment mlDep);
+	public void updateSeldonDeploymentStatus(SeldonDeployment mlDep);
 	public SeldonDeployment getSeldonDeployment(String name);
 	public ExtensionsV1beta1DeploymentList getOwnedDeployments(String seldonDeploymentName);
 	public V1ServiceList getOwnedServices(String seldonDeploymentName);

cluster-manager/src/main/java/io/seldon/clustermanager/k8s/KubeCRDHandlerImpl.java

@@ -52,6 +52,8 @@ public class KubeCRDHandlerImpl implements KubeCRDHandler {
 
 	private final String namespace;
 
+	private boolean replaceStatusResource = true; // Whether to use the status CR endpoint (available from k8s 1.10 (alpha) 1.11 (beta)
+
 	@Autowired
     public KubeCRDHandlerImpl(ClusterManagerProperites clusterManagerProperites) {
 		this.namespace = StringUtils.isEmpty(clusterManagerProperites.getNamespace()) ? "default" : clusterManagerProperites.getNamespace();
@@ -75,9 +77,9 @@ public void updateRaw(String json,String seldonDeploymentName) {
 
 
 	}
-
+	
 	@Override
-	public void updateSeldonDeployment(SeldonDeployment mldep) {
+	public void updateSeldonDeploymentStatus(SeldonDeployment mldep) {
 
 		try
 		{
@@ -96,7 +98,18 @@ public void updateSeldonDeployment(SeldonDeployment mldep) {
 			logger.debug("Updating seldondeployment "+mlDeployment.getMetadata().getName());
 			ApiClient client = Config.defaultClient();
 			CustomObjectsApi api = new CustomObjectsApi(client);
-			api.replaceNamespacedCustomObject(GROUP, VERSION, namespace, KIND_PLURAL, mlDeployment.getMetadata().getName(),json.getBytes());
+			if (replaceStatusResource)
+			{
+				try 
+				{
+					api.replaceNamespacedCustomObjectStatus(GROUP, VERSION, namespace, KIND_PLURAL, mlDeployment.getMetadata().getName(),json.getBytes());
+				} catch (ApiException e) {
+					replaceStatusResource = false; // Stop using the /status endpoint (maybe because the k8s version does not have this <1.10)
+					logger.warn("Failed to update deployment in kubernetes ",e);
+				}
+			}
+			if (!replaceStatusResource)
+				api.replaceNamespacedCustomObject(GROUP, VERSION, namespace, KIND_PLURAL, mlDeployment.getMetadata().getName(),json.getBytes());
 		} catch (InvalidProtocolBufferException e) {
 			logger.error("Failed to update deployment in kubernetes ",e);
 		} catch (ApiException e) {