From c9c43887e853d0122bce16a4f67d4d1b984a668c Mon Sep 17 00:00:00 2001
From: Ludovic Claude <ludovic.claude54@gmail.com>
Date: Thu, 15 Mar 2018 18:45:41 +0100
Subject: [PATCH] Update woken-messages to 2.5.2, /datasets return
[{code,label}] from Woken
---
docker/README.md | 1 -
docker/config/application.tmpl | 1 -
docker/run.sh | 2 +-
pom.xml | 2 +-
.../hbp/mip/akka/WokenClientController.java | 45 +++++++----------
.../eu/hbp/mip/controllers/DatasetsApi.java | 49 +++++++++++++++----
.../eu/hbp/mip/controllers/MethodsApi.java | 2 +-
7 files changed, 60 insertions(+), 42 deletions(-)
diff --git a/docker/README.md b/docker/README.md
index 33262bdde..419dd0798 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -24,7 +24,6 @@ To use this image, you need a running instance of PostgreSQL and to configure th
* FEATURES_DB_USER: User to use when connecting to the science database, default value is "postgres".
* FEATURES_DB_PASSWORD: Password to use when connecting to the science database.
* FEATURES_DB_MAIN_TABLE: Table that contains the scientific data to use, default value is "features".
-* DATASETS (temporary hack): list of datasets available in the features table
### OAUTH2 LOGIN
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 3be9dac65..16a901f6b 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -21,7 +21,6 @@ spring:
username: {{ default .Env.FEATURES_DB_USER "postgres" }}
password: {{ .Env.FEATURES_DB_PASSWORD }}
driver-class-name: org.postgresql.Driver
- datasets: {{ .Env.DATASETS }}
jpa:
hibernate:
dialect: org.hibernate.dialect.PostgreSQL9Dialect
diff --git a/docker/run.sh b/docker/run.sh
index 2b1ca22d1..a89331926 100755
--- a/docker/run.sh
+++ b/docker/run.sh
@@ -10,4 +10,4 @@ fi
if [ ! -z "$FEATURES_DB_SERVER" ]; then
OPTS="$OPTS -wait tcp://$FEATURES_DB_SERVER -timeout 60s"
fi
-dockerize $OPTS java -jar /usr/share/jars/portal-backend.jar
+dockerize $OPTS java ${JAVA_OPTS} -jar /usr/share/jars/portal-backend.jar
diff --git a/pom.xml b/pom.xml
index 3f71142f1..d39be85f1 100644
--- a/pom.xml
+++ b/pom.xml
@@ -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>2.4.9</woken-messages.version>
+ <woken-messages.version>2.5.2</woken-messages.version>
<javax-inject.version>1</javax-inject.version>
<akka.version>2.5.9</akka.version>
<spring-context.version>4.3.4.RELEASE</spring-context.version>
diff --git a/src/main/java/eu/hbp/mip/akka/WokenClientController.java b/src/main/java/eu/hbp/mip/akka/WokenClientController.java
index 3cc463857..2504d6468 100644
--- a/src/main/java/eu/hbp/mip/akka/WokenClientController.java
+++ b/src/main/java/eu/hbp/mip/akka/WokenClientController.java
@@ -31,7 +31,7 @@ import java.util.function.Function;
*/
public abstract class WokenClientController {
- private final Logger LOGGER = LoggerFactory.getLogger(this.getClass());
+ protected final Logger LOGGER = LoggerFactory.getLogger(this.getClass());
@Autowired
private ActorSystem actorSystem;
@@ -44,6 +44,7 @@ public abstract class WokenClientController {
private ActorRef wokenClient;
+ @SuppressWarnings("unused")
@PostConstruct
public void initClusterClient() {
LOGGER.info("Start Woken client " + wokenReceptionistPath);
@@ -56,7 +57,8 @@ public abstract class WokenClientController {
return Collections.singleton(ActorPaths.fromString(wokenReceptionistPath));
}
- protected <A, B> ResponseEntity askWoken(A message, int waitInSeconds, Function<B, ResponseEntity> handleResponse) {
+ @SuppressWarnings("unchecked")
+ protected <A, B> B askWoken(A message, int waitInSeconds) throws Exception {
LOGGER.info("Akka is trying to reach remote " + wokenPath);
ClusterClient.Send queryMessage = new ClusterClient.Send(wokenPath, message, true);
@@ -64,35 +66,29 @@ public abstract class WokenClientController {
Future<Object> future = Patterns.ask(wokenClient, queryMessage, timeout);
- B result;
+ return (B) Await.result(future, timeout.duration());
+ }
+
+ protected <A, B> ResponseEntity requestWoken(A message, int waitInSeconds, Function<B, ResponseEntity> handleResponse) {
try {
- result = (B) Await.result(future, timeout.duration());
+ B result = askWoken(message, waitInSeconds);
+ return handleResponse.apply(result);
} catch (Exception e) {
- LOGGER.error("Cannot receive algorithm result from woken: " + e.getMessage(), e);
- return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).build();
+ final String msg = "Cannot receive result from woken: " + e.getMessage();
+ LOGGER.error(msg, e);
+ return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body(msg);
}
-
- return handleResponse.apply(result);
}
-
protected <A extends Query> ResponseEntity askWokenQuery(A query, int waitInSeconds, Function<QueryResult, ResponseEntity> handleResponse) {
- LOGGER.info("Akka is trying to reach remote " + wokenPath);
-
- ClusterClient.Send queryMessage = new ClusterClient.Send(wokenPath, query, true);
- Timeout timeout = new Timeout(Duration.create(waitInSeconds, "seconds"));
-
- Future<Object> future = Patterns.ask(wokenClient, queryMessage, timeout);
-
- QueryResult result;
try {
- result = (QueryResult) Await.result(future, timeout.duration());
+ QueryResult result = askWoken(query, waitInSeconds);
+ return handleResponse.apply(result);
} catch (Exception e) {
- LOGGER.error("Cannot receive algorithm result from woken: " + e.getMessage(), e);
- return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).build();
+ final String msg = "Cannot receive algorithm result from woken: " + e.getMessage();
+ LOGGER.error(msg, e);
+ return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body(msg);
}
-
- return handleResponse.apply(result);
}
protected <A extends Query> Future<Object> sendWokenQuery(A query, int timeout) {
@@ -103,11 +99,6 @@ public abstract class WokenClientController {
return Patterns.ask(wokenClient, queryMessage, timeout);
}
- protected ActorRef createActor(String actorBeanName, String actorName) {
- return actorSystem.actorOf(SpringExtension.SPRING_EXTENSION_PROVIDER.get(actorSystem)
- .props(actorBeanName), actorName);
- }
-
protected ExecutionContext getExecutor() {
return actorSystem.dispatcher();
}
diff --git a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
index 052486a5e..f4f67edd9 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -5,7 +5,12 @@
package eu.hbp.mip.controllers;
+import ch.chuv.lren.woken.messages.datasets.DatasetsQuery;
+import ch.chuv.lren.woken.messages.datasets.DatasetsResponse;
import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import eu.hbp.mip.akka.WokenClientController;
import eu.hbp.mip.model.Dataset;
import eu.hbp.mip.model.Variable;
import eu.hbp.mip.repositories.VariableRepository;
@@ -13,21 +18,25 @@ import io.swagger.annotations.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
+import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
+import scala.Option;
import javax.annotation.PostConstruct;
+import java.util.Set;
+import java.util.stream.Stream;
+
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/datasets", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/datasets", description = "the datasets API")
-public class DatasetsApi {
+public class DatasetsApi extends WokenClientController {
private static final Logger LOGGER = LoggerFactory.getLogger(DatasetsApi.class);
private static final Gson gson = new Gson();
@@ -35,15 +44,15 @@ public class DatasetsApi {
@Autowired
private VariableRepository variableRepository;
- @Value("#{'${spring.featuresDatasource.datasets:adni,ppmi,edsd}'}")
- private String datasets;
-
@PostConstruct
- public void init() {
- for (String dataset: datasets.split(",")) {
- Variable v = variableRepository.findOne(dataset);
+ public void init() throws Exception {
+ // Pre-fill the local variable repository with the list of datasets, interpreted here as variables
+ // (a bit like a categorical variable can be split into a set of variables (a.k.a one hot encoding in Data science) )
+ for (ch.chuv.lren.woken.messages.datasets.Dataset dataset: fetchDatasets()) {
+ final String code = dataset.dataset().code();
+ Variable v = variableRepository.findOne(code);
if (v == null) {
- v = new Variable(dataset);
+ v = new Variable(code);
variableRepository.save(v);
}
}
@@ -55,7 +64,27 @@ public class DatasetsApi {
) {
LOGGER.info("Get dataset list");
- return ResponseEntity.ok(datasets.split(","));
+ try {
+ JsonArray datasets = new JsonArray();
+ Stream<JsonObject> values = fetchDatasets().stream().map(d -> {
+ JsonObject jsObject = new JsonObject();
+ jsObject.addProperty("code", d.dataset().code());
+ jsObject.addProperty("label", d.label());
+ datasets.add(jsObject);
+ return jsObject;
+ });
+
+ return ResponseEntity.ok(datasets);
+ } catch (Exception e) {
+ final String msg = "Cannot receive datasets from woken: " + e.getMessage();
+ LOGGER.error(msg, e);
+ return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body(msg);
+ }
+
}
+ private Set<ch.chuv.lren.woken.messages.datasets.Dataset> fetchDatasets() throws Exception {
+ DatasetsResponse result = askWoken(new DatasetsQuery(Option.empty()), 30);
+ return scala.collection.JavaConversions.setAsJavaSet(result.datasets());
+ }
}
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index f25187d58..5e7f36b2d 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -35,7 +35,7 @@ public class MethodsApi extends WokenClientController {
public ResponseEntity listAvailableMethodsAndValidations() {
LOGGER.info("List available methods and validations");
- return askWoken(MethodsQuery$.MODULE$, 10, r -> {
+ return requestWoken(MethodsQuery$.MODULE$, 10, r -> {
MethodsResponse result = (MethodsResponse) r;
// >> Temporary : should return result.methods() in the future
--
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