diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index a9e6d876aadba9018dd4444ae655f5a6aad0219a..5626fa605a3c11fd1558d739a37e0a5eb7e7713b 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 2.9.2
+current_version = 2.9.3
commit = True
tag = True
tag_name = {new_version}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4424d57a3de2fa2a9cc2decb1ca06a0d4e178170..c4296ef6eebbdd329b63b27e12c4ebcd41992202 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -6,6 +6,7 @@ repos:
- id: end-of-file-fixer
exclude: .bumpversion.cfg
- id: check-merge-conflict
+ exclude: LICENSE
- id: check-added-large-files
- id: check-yaml
- id: check-json
diff --git a/hbp.yml b/hbp.yml
index 944af46cff5e075822bd8b6b25da28fdbc3016eb..6e6fcd1f7a02989a909a567bd775313a679dacc0 100644
--- a/hbp.yml
+++ b/hbp.yml
@@ -58,9 +58,9 @@ testing:
command: ./test.sh
release_management:
- current_version: 2.9.2
- current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.9.2.zip
- current_binary_release: https://pypi.python.org/pypi/portal-backend/2.9.2
+ current_version: 2.9.3
+ current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.9.3.zip
+ current_binary_release: https://pypi.python.org/pypi/portal-backend/2.9.3
release_script: 'publish.sh'
continuous_integration:
@@ -75,10 +75,10 @@ continuous_integration:
distribution:
docker_hub:
name: hbpmip/portal-backend
- current_tag: 2.9.2
+ current_tag: 2.9.3
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:2.9.2
+ command: docker pull hbpmip/portal-backend:2.9.3
planning:
github:
diff --git a/pom.xml b/pom.xml
index da8cae4dc32584e10eb4827871bb5a416b460145..f8c622e0f3366184d2322bd29b9089ed026cfbad 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<groupId>eu.hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
- <version>2.9.2</version><!-- BUMP_VERSION -->
+ <version>2.9.3</version><!-- BUMP_VERSION -->
<packaging>jar</packaging>
<name>portal-backend</name>
@@ -47,9 +47,9 @@
<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>2.9.6</woken-messages.version>
+ <woken-messages.version>3.0.1</woken-messages.version>
<javax-inject.version>1</javax-inject.version>
- <akka.version>2.5.20</akka.version>
+ <akka.version>2.5.21</akka.version>
<spring-context.version>4.3.4.RELEASE</spring-context.version>
<protobuf-java.version>3.1.0</protobuf-java.version>
diff --git a/src/main/java/eu/hbp/mip/StartupTasks.java b/src/main/java/eu/hbp/mip/StartupTasks.java
index fa58eaf924ef9826e7eadb6ac182b85acc2a9341..acbf8f0c9d1ccd557c0ffe4e118d841eab8f2b03 100644
--- a/src/main/java/eu/hbp/mip/StartupTasks.java
+++ b/src/main/java/eu/hbp/mip/StartupTasks.java
@@ -47,7 +47,7 @@ public class StartupTasks implements ApplicationListener<ApplicationReadyEvent>
for (int i = 0; i < 5; i++) {
try {
for (Dataset dataset : datasetsApi.fetchDatasets()) {
- final String code = dataset.dataset().code();
+ final String code = dataset.id().code();
Variable v = variableRepository.findOne(code);
if (v == null) {
LOGGER.info("Store additional variable {}", code);
diff --git a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
index 99d5b8497cd9fad5b2843b1621293e26d5f6dfe8..7798b0ab9069dedb526cc24d7e2e5849b19987c8 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -49,7 +49,7 @@ public class DatasetsApi extends WokenClientController {
for (Dataset d: fetchDatasets()) {
DatasetDescription dataset = new DatasetDescription();
LOGGER.info("Dataset {}", d);
- dataset.setCode(d.dataset().code());
+ dataset.setCode(d.id().code());
dataset.setLabel(d.label());
dataset.setDescription(d.description());
dataset.setAnonymisationLevel(d.anonymisationLevel().toString());
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 5e4620f9cec3b368d569003e921f9a1edaabc07c..d94514c6e78eda1e10c0db3459671dd2a3e770f8 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,6 +1,7 @@
package eu.hbp.mip.controllers;
import akka.dispatch.OnSuccess;
+import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.common.collect.Lists;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
@@ -269,11 +270,9 @@ public class ExperimentApi extends WokenClientController {
} else {
if (queryResult.error().nonEmpty()) {
experiment.setHasServerError(true);
- experiment.setResult(queryResult.error().get());
LOGGER.error("Experiment failed with message: " + queryResult.error().get());
- } else {
- experiment.setResult(queryResult.data().get().compactPrint());
}
+ experiment.setResult(new WokenConversions().toJson(queryResult));
experiment.setFinished(Date.from(queryResult.timestamp().toInstant()));
experimentRepository.save(experiment);
LOGGER.info("Experiment " + uuid + " updated (finished)");
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 21720df3028c9f4893555ee50bcaf59af91ce6be..bf89261eb14fab25a0adf5bf7dd3e07ff43235e6 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -2,11 +2,9 @@ package eu.hbp.mip.controllers;
import com.google.gson.Gson;
import eu.hbp.mip.akka.WokenClientController;
-import eu.hbp.mip.configuration.SecurityConfiguration;
import eu.hbp.mip.model.Mining;
import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
-import eu.hbp.mip.utils.HTTPUtil;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.slf4j.Logger;
@@ -22,7 +20,6 @@ import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import scala.Option;
-import java.io.IOException;
import java.sql.Date;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -61,7 +58,7 @@ public class MiningApi extends WokenClientController {
return ResponseEntity.status(HttpStatus.BAD_REQUEST).body("{\"error\":\"" + result.error().get() + "\"}");
} else {
Mining mining = new Mining(
- unwrap(result.jobId()),
+ result.jobId(),
result.node(),
unwrap(result.algorithm()),
result.type().mime(),
diff --git a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala b/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
index a0240df7d4bf4111be1ae4819266a6a120f377df..6abe7b362661e997730feae6a0790785ca13784e 100644
--- a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
+++ b/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
@@ -2,9 +2,10 @@ package ch.chuv.lren.mip.portal
import eu.hbp.mip.model.Variable
import ch.chuv.lren.woken.messages.datasets.DatasetId
+import ch.chuv.lren.woken.messages.query.QueryResult
import ch.chuv.lren.woken.messages.query.filters.FilterRule
import ch.chuv.lren.woken.messages.query.filters.FilterRule._
-import ch.chuv.lren.woken.messages.query.filters.queryFiltersProtocol._
+import ch.chuv.lren.woken.messages.query.queryProtocol._
import org.springframework.stereotype.Component
import spray.json._
@@ -24,4 +25,6 @@ class WokenConversions {
def toSqlWhere(filter: Option[FilterRule]): String = filter.fold("")(_.toSqlWhere)
+ def toJson(result: QueryResult): String =
+ result.toJson.compactPrint
}