diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index a0c10f8e63abfd3df157ed44d700aa9cceea78b6..1c6836a274bbebd34431846d566a5fc2c66ee298 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 2.8.1
+current_version = 2.8.4
commit = True
tag = True
tag_name = {new_version}
diff --git a/hbp.yml b/hbp.yml
index 02066a86c0d140fed69d9ea6531cec471db509b7..5151973f18ab9302f37721a915118fb66869ebd5 100644
--- a/hbp.yml
+++ b/hbp.yml
@@ -58,9 +58,9 @@ testing:
command: ./test.sh
release_management:
- current_version: 2.8.1
- current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.8.1.zip
- current_binary_release: https://pypi.python.org/pypi/portal-backend/2.8.1
+ current_version: 2.8.4
+ current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.8.4.zip
+ current_binary_release: https://pypi.python.org/pypi/portal-backend/2.8.4
release_script: 'publish.sh'
continuous_integration:
@@ -75,10 +75,10 @@ continuous_integration:
distribution:
docker_hub:
name: hbpmip/portal-backend
- current_tag: 2.8.1
+ current_tag: 2.8.4
url: https://hub.docker.com/r/hbpmip/portal-backend/
badge: https://img.shields.io/badge/docker-hbpmip%2Fportal--backend-008bb8.svg
- command: docker pull hbpmip/portal-backend:2.8.1
+ command: docker pull hbpmip/portal-backend:2.8.4
planning:
github:
diff --git a/pom.xml b/pom.xml
index 965b0c07a7ef5332bd378e9268413dbc7f4d9027..76a85838526cc5c1aaa9bae903ff6b8acb192250 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<groupId>eu.hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
- <version>2.8.1</version><!-- BUMP_VERSION -->
+ <version>2.8.4</version><!-- BUMP_VERSION -->
<packaging>jar</packaging>
<name>portal-backend</name>
@@ -47,7 +47,7 @@
<spring-data-jpa.version>1.10.11.RELEASE</spring-data-jpa.version>
<spring-boot-starter-actuator.version>1.4.7.RELEASE</spring-boot-starter-actuator.version>
<aspectjweaver.version>1.8.9</aspectjweaver.version>
- <woken-messages.version>2.7.5</woken-messages.version>
+ <woken-messages.version>2.8.1</woken-messages.version>
<javax-inject.version>1</javax-inject.version>
<akka.version>2.5.12</akka.version>
<spring-context.version>4.3.4.RELEASE</spring-context.version>
@@ -249,6 +249,12 @@
<version>${scala.release.version}</version>
<scope>compile</scope>
</dependency>
+
+ <dependency>
+ <groupId>com.bugsnag</groupId>
+ <version>[3.0,4.0)</version>
+ <artifactId>bugsnag</artifactId>
+ </dependency>
</dependencies>
<build>
diff --git a/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java b/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java
index 4f4ae846fc8b0e89d3a87c334f03a32948026846..59375f7ab4916753bf108ead11e9a37d9ebd59cd 100644
--- a/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java
@@ -4,9 +4,11 @@ import akka.actor.ActorRef;
import akka.actor.ActorSystem;
import akka.actor.ExtendedActorSystem;
import akka.cluster.Cluster;
+import akka.cluster.Member;
import akka.cluster.pubsub.DistributedPubSub;
import com.typesafe.config.Config;
import com.typesafe.config.ConfigFactory;
+import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@@ -15,6 +17,7 @@ import org.springframework.context.annotation.*;
import java.util.List;
import java.util.concurrent.Semaphore;
+import java.util.concurrent.TimeUnit;
import static eu.hbp.mip.akka.SpringExtension.SPRING_EXTENSION_PROVIDER;
@@ -73,11 +76,18 @@ class AkkaConfiguration {
semaphore.release();
});
- try {
- semaphore.acquire();
- Thread.sleep(5000);
- } catch (InterruptedException e) {
- LOGGER.warn("Cannot wait for Akka cluster start", e);
+ for (Member member: cluster.state().getMembers()) {
+ LOGGER.info("Member " + StringUtils.join(member.getRoles(), ",") + " at " + member.address().toString() + " is in the cluster");
+ }
+
+ if (cluster.state().members().size() < 2) {
+ LOGGER.info("Waiting for Woken cluster connection...");
+ try {
+ semaphore.tryAcquire(5, TimeUnit.MINUTES);
+ Thread.sleep(5000);
+ } catch (InterruptedException e) {
+ LOGGER.warn("Cannot wait for Akka cluster start", e);
+ }
}
Runtime.getRuntime().addShutdownHook(new Thread(() -> {
diff --git a/src/main/java/eu/hbp/mip/configuration/BugsnagConfig.java b/src/main/java/eu/hbp/mip/configuration/BugsnagConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..c399706049a7cb4b1a7129c2174c13bc4f8721c0
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/configuration/BugsnagConfig.java
@@ -0,0 +1,13 @@
+package eu.hbp.mip.configuration;
+
+import com.bugsnag.Bugsnag;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+@Configuration
+public class BugsnagConfig {
+ @Bean
+ public Bugsnag bugsnag() {
+ return new Bugsnag("dff301aa15eb795a6d8b22b600586f77");
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index 9000271a9dfa9f0624ea3e26cc310c84a34279c0..c3d1de874308576c07f27304e167f56a85bc6605 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -135,7 +135,9 @@ public class ModelsApi {
configRepository.save(model.getConfig());
queryRepository.save(model.getQuery());
- datasetRepository.save(model.getDataset());
+ if (model.getDataset() != null) {
+ datasetRepository.save(model.getDataset());
+ }
modelRepository.save(model);
LOGGER.info("Model saved (also saved model.config and model.query)");
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index c3a306017259dcdf71443909de06e7ba195cc3ea..00a3d11f5f408e249ef05805963f6978db6f5fd5 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -103,7 +103,7 @@ public class Experiment {
Type algoList = new TypeToken<LinkedList<eu.hbp.mip.model.Algorithm>>(){}.getType();
List<eu.hbp.mip.model.Algorithm> algos = new Gson().fromJson(this.algorithms, algoList);
for (eu.hbp.mip.model.Algorithm a: algos) {
- algorithms.add(new AlgorithmSpec(a.getCode(), TypesConvert.algoParamsToScala(a.getParameters())));
+ algorithms.add(new AlgorithmSpec(a.getCode(), TypesConvert.algoParamsToScala(a.getParameters()), Option.empty()));
}
List<ValidationSpec> validations = new LinkedList<>();
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 51cb91c3a7dc033c247be43617e0ed168ed1d39b..908ef52193221feec68520c88662d9e3ac7b5b56 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -90,7 +90,7 @@ public class MiningQuery {
public ch.chuv.lren.woken.messages.query.MiningQuery prepareQuery(String user) {
ch.chuv.lren.woken.messages.query.AlgorithmSpec scalaAlgorithm = new ch.chuv.lren.woken.messages.query.AlgorithmSpec(
- algorithm.getCode(), TypesConvert.algoParamsToScala(algorithm.getParameters()));
+ algorithm.getCode(), TypesConvert.algoParamsToScala(algorithm.getParameters()), Option.empty());
scala.collection.immutable.List<FeatureIdentifier> variablesSeq =
TypesConvert.variablesToIdentifiers(getVariables());