diff --git a/src/main/java/eu/hbp/mip/StartupTasks.java b/src/main/java/eu/hbp/mip/StartupTasks.java
index 598e05b178d6964e37879acac0c50a2acf81864e..d7dc3e0958bc1613ee6afa13fbb4a8d6b9ddc836 100644
--- a/src/main/java/eu/hbp/mip/StartupTasks.java
+++ b/src/main/java/eu/hbp/mip/StartupTasks.java
@@ -17,7 +17,6 @@ import org.springframework.stereotype.Component;
@Component
-@DependsOn("wokenCluster")
public class StartupTasks implements ApplicationListener<ApplicationReadyEvent> {
private static final Logger LOGGER = LoggerFactory.getLogger(StartupTasks.class);
@@ -43,32 +42,32 @@ public class StartupTasks implements ApplicationListener<ApplicationReadyEvent>
// 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) )
// Try 5 times, to be more robust in the face of cluster failures / slow startup
- LOGGER.info("Prefill variable repository with datasets...");
- for (int i = 0; i < 5; i++) {
- try {
- StringBuilder fetchedDatasets = new StringBuilder();
- for (Dataset dataset : datasetsApi.fetchDatasets()) {
- final String code = dataset.id().code();
- fetchedDatasets.append(code).append(' ');
- Variable v = variableRepository.findOne(code);
- if (v == null) {
- LOGGER.info("Store additional variable {}", code);
- v = new Variable(code);
- variableRepository.save(v);
- }
- }
- LOGGER.info("Datasets fetched from Woken: " + fetchedDatasets.toString());
- variablesRepositoryOk = true;
- break;
- } catch (Exception e) {
- variablesRepositoryOk = false;
- LOGGER.error("Cannot initialise the variable repository. Is the connection to Woken working?", e);
- }
- }
+ // LOGGER.info("Prefill variable repository with datasets...");
+ // for (int i = 0; i < 5; i++) {
+ // try {
+ // StringBuilder fetchedDatasets = new StringBuilder();
+ // for (Dataset dataset : datasetsApi.fetchDatasets()) {
+ // final String code = dataset.id().code();
+ // fetchedDatasets.append(code).append(' ');
+ // Variable v = variableRepository.findOne(code);
+ // if (v == null) {
+ // LOGGER.info("Store additional variable {}", code);
+ // v = new Variable(code);
+ // variableRepository.save(v);
+ // }
+ // }
+ // LOGGER.info("Datasets fetched from Woken: " + fetchedDatasets.toString());
+ // variablesRepositoryOk = true;
+ // break;
+ // } catch (Exception e) {
+ // variablesRepositoryOk = false;
+ // LOGGER.error("Cannot initialise the variable repository. Is the connection to Woken working?", e);
+ // }
+ // }
- if (!variablesRepositoryOk) {
- System.exit(1);
- }
+ // if (!variablesRepositoryOk) {
+ // System.exit(1);
+ // }
/*
for (String variableJson: variablesApi.loadVariables()) {
diff --git a/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java b/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java
deleted file mode 100644
index 1af3fdafcbd0ac8347079c66e75a172ee1ed0a6b..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package eu.hbp.mip.akka;
-
-import akka.cluster.Cluster;
-import ch.chuv.lren.woken.messages.Ping;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.actuate.health.Health;
-import org.springframework.boot.actuate.health.HealthIndicator;
-import org.springframework.stereotype.Component;
-import scala.Option;
-
-
-@Component
-public class AkkaClusterHealthCheck extends WokenClientController implements HealthIndicator {
-
- @Autowired
- private Cluster wokenCluster;
-
- @Override
- public Health health() {
- if (wokenCluster.state().getLeader() == null) {
- return Health.down().withDetail("Error", "No leader in the cluster").build();
- } else if (!wokenCluster.state().allRoles().contains("woken")) {
- return Health.down().withDetail("Error", "Woken server cannot be seen in the cluster").build();
- }
- try {
- askWoken(new Ping(Option.apply("woken")), 5);
- return Health.up().build();
- } catch (Exception e) {
- return Health.down().withDetail("Error", "Cannot reach Woken: " + e.toString()).build();
- }
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/akka/ExperimentActor.java b/src/main/java/eu/hbp/mip/akka/ExperimentActor.java
deleted file mode 100644
index 7431d7928e056a22c019dd5bb539b9e2c27a1cbc..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/akka/ExperimentActor.java
+++ /dev/null
@@ -1,59 +0,0 @@
-package eu.hbp.mip.akka;
-
-import akka.actor.AbstractActor;
-import ch.chuv.lren.woken.messages.query.QueryResult;
-import eu.hbp.mip.model.Experiment;
-import eu.hbp.mip.repositories.ExperimentRepository;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.config.ConfigurableBeanFactory;
-import org.springframework.context.annotation.Scope;
-import org.springframework.stereotype.Component;
-
-import java.util.Date;
-import java.util.UUID;
-
-/**
- * Created by mirco on 30.11.16.
- */
-
-@Component
-@Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE)
-public class ExperimentActor extends AbstractActor {
-
- @Autowired
- private ExperimentRepository experimentRepository;
-
- private static final Logger LOGGER = LoggerFactory.getLogger(ExperimentActor.class);
-
- public Receive createReceive() {
- return receiveBuilder()
- .match(QueryResult.class, this::handleQueryResult)
- .matchAny(o -> LOGGER.info("received unknown message " + o))
- .build();
- }
-
- private void handleQueryResult(QueryResult queryResult) {
- LOGGER.info("ActorExperiment - onReceive method has been called");
- UUID uuid = UUID.fromString(this.getSelf().path().name());
- LOGGER.info("\n\nExperimentActor received response from woken for UUID: \n" + uuid.toString());
- Experiment experiment = experimentRepository.findOne(uuid);
- if (experiment == null) {
- LOGGER.error("Experiment with UUID=" + uuid + " not found in DB");
- getContext().stop(getSelf());
- } else {
- if (queryResult.error().nonEmpty()) {
- experiment.setHasServerError(true);
- experiment.setResult(queryResult.error().get());
- } else {
- // TODO: use new WokenConversions().toJson(queryResult)
- experiment.setResult(queryResult.data().get().compactPrint());
- }
- experiment.setFinished(Date.from(queryResult.timestamp().toInstant()));
- experimentRepository.save(experiment);
- LOGGER.info("Experiment " + uuid + " updated (finished)");
- getContext().stop(getSelf());
- }
- }
-}
diff --git a/src/main/java/eu/hbp/mip/akka/SpringActorProducer.java b/src/main/java/eu/hbp/mip/akka/SpringActorProducer.java
deleted file mode 100644
index ade82c181488d6c727aa653f6097aa1ac1ef5eb8..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/akka/SpringActorProducer.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package eu.hbp.mip.akka;
-
-import akka.actor.Actor;
-import akka.actor.IndirectActorProducer;
-import org.springframework.context.ApplicationContext;
-
-
-public class SpringActorProducer implements IndirectActorProducer {
-
- private final ApplicationContext applicationContext;
- private final String actorBeanName;
-
- public SpringActorProducer(ApplicationContext applicationContext,
- String actorBeanName) {
- this.applicationContext = applicationContext;
- this.actorBeanName = actorBeanName;
- }
-
- @Override
- public Actor produce() {
- return (Actor) applicationContext.getBean(actorBeanName);
- }
-
- @Override
- public Class<? extends Actor> actorClass() {
- return (Class<? extends Actor>) applicationContext.getType(actorBeanName);
- }
-}
diff --git a/src/main/java/eu/hbp/mip/akka/SpringExtension.java b/src/main/java/eu/hbp/mip/akka/SpringExtension.java
deleted file mode 100644
index 5fe0698be44193fcdc8761297f429cb456aadd40..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/akka/SpringExtension.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package eu.hbp.mip.akka;
-
-import akka.actor.AbstractExtensionId;
-import akka.actor.ExtendedActorSystem;
-import akka.actor.Extension;
-import akka.actor.Props;
-import org.springframework.context.ApplicationContext;
-
-/*
- * Created by mirco on 24.10.16.
- */
-
-public class SpringExtension
- extends AbstractExtensionId<SpringExtension.SpringExt> {
-
- public static final SpringExtension SPRING_EXTENSION_PROVIDER
- = new SpringExtension();
-
- private SpringExtension()
- {
- /* Private constructor for singleton */
- }
-
- @Override
- public SpringExt createExtension(ExtendedActorSystem system) {
- return new SpringExt();
- }
-
- public static class SpringExt implements Extension {
- private volatile ApplicationContext applicationContext;
-
- public void initialize(ApplicationContext applicationContext) {
- this.applicationContext = applicationContext;
- }
-
- public Props props(String actorBeanName) {
- return Props.create(
- SpringActorProducer.class, applicationContext, actorBeanName);
- }
- }
-}
diff --git a/src/main/java/eu/hbp/mip/akka/WokenClientController.java b/src/main/java/eu/hbp/mip/akka/WokenClientController.java
deleted file mode 100644
index e6ef3cdd79e7c0a6eaafdf2d72350f55e8f8e8f2..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/akka/WokenClientController.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package eu.hbp.mip.akka;
-
-import akka.actor.ActorRef;
-import akka.actor.ActorSystem;
-import akka.cluster.pubsub.DistributedPubSub;
-import akka.cluster.pubsub.DistributedPubSubMediator;
-import akka.pattern.Patterns;
-import akka.util.Timeout;
-import ch.chuv.lren.woken.messages.RemoteMessage;
-import ch.chuv.lren.woken.messages.query.Query;
-import ch.chuv.lren.woken.messages.query.QueryResult;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import scala.concurrent.Await;
-import scala.concurrent.ExecutionContext;
-import scala.concurrent.Future;
-import scala.concurrent.duration.Duration;
-
-import java.util.function.Function;
-
-/**
- * Base class for controllers using Woken services
- */
-public abstract class WokenClientController {
-
- protected final Logger LOGGER = LoggerFactory.getLogger(this.getClass());
-
- @Autowired
- private ActorSystem actorSystem;
-
- @Value("#{'${akka.woken.path:/user/entrypoint}'}")
- private String wokenPath;
-
- @SuppressWarnings("unchecked")
- protected <A extends RemoteMessage, B> B askWoken(A message, int waitInSeconds) throws Exception {
- LOGGER.info("Trying to reach remote Akka actor " + wokenPath + "...");
-
- DistributedPubSubMediator.Send queryMessage = new DistributedPubSubMediator.Send(wokenPath, message, false);
- Timeout timeout = new Timeout(Duration.create(waitInSeconds, "seconds"));
-
- Future<Object> future = Patterns.ask(wokenMediator(), queryMessage, timeout);
-
- B result = (B) Await.result(future, timeout.duration());
- LOGGER.info("Akka actor returned a result for message of class " + message.getClass());
- return result;
- }
-
- protected <A extends RemoteMessage, B> ResponseEntity requestWoken(A message, int waitInSeconds, Function<B, ResponseEntity> handleResponse) {
- try {
- B result = askWoken(message, waitInSeconds);
- return handleResponse.apply(result);
- } catch (Exception e) {
- final String msg = "Cannot receive result from woken: " + e.getMessage();
- LOGGER.error(msg, e);
- return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body(msg);
- }
- }
-
- protected <A extends Query> ResponseEntity askWokenQuery(A query, int waitInSeconds, Function<QueryResult, ResponseEntity> handleResponse) {
- try {
- QueryResult result = askWoken(query, waitInSeconds);
- return handleResponse.apply(result);
- } catch (Exception e) {
- final String msg = "Cannot receive algorithm result from woken: " + e.getMessage();
- LOGGER.error(msg, e);
- return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).body(msg);
- }
- }
-
- protected <A extends Query> Future<Object> sendWokenQuery(A query, int waitInSeconds) {
- LOGGER.info("Akka is trying to reach remote " + wokenPath);
-
- DistributedPubSubMediator.Send queryMessage = new DistributedPubSubMediator.Send(wokenPath, query, false);
-
- return Patterns.ask(wokenMediator(), queryMessage, waitInSeconds);
- }
-
- protected ExecutionContext getExecutor() {
- return actorSystem.dispatcher();
- }
-
- private ActorRef wokenMediator() {
- return DistributedPubSub.get(actorSystem).mediator();
- }
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java b/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java
deleted file mode 100644
index 4531d4d3070a9a34eb2dbbb617e6edccf225706e..0000000000000000000000000000000000000000
--- a/src/main/java/eu/hbp/mip/configuration/AkkaConfiguration.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package eu.hbp.mip.configuration;
-
-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 ch.chuv.lren.woken.utils.ConfigurationLoader;
-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;
-import org.springframework.context.ApplicationContext;
-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;
-
-/**
- * Created by mirco on 24.10.16.
- */
-
-@Configuration
-@ComponentScan
-public class AkkaConfiguration {
-
- protected final Logger LOGGER = LoggerFactory.getLogger(this.getClass());
-
- @Autowired
- private ApplicationContext applicationContext;
-
- private final Config config;
-
- {
- Config appConfig = ConfigFactory.parseResourcesAnySyntax("application.conf")
- .withFallback(ConfigFactory.parseResourcesAnySyntax("kamon.conf"));
- config = ConfigurationLoader.appendClusterConfiguration(appConfig).resolve();
- }
-
- @Bean
- public ExtendedActorSystem actorSystem() {
- LOGGER.info("Step 1/3: Starting actor system...");
- LOGGER.info("Create actor system at " + wokenClusterHost() + ":" + wokenClusterPort());
- ExtendedActorSystem system = (ExtendedActorSystem) ActorSystem.create(wokenClusterName(), config);
- SPRING_EXTENSION_PROVIDER.get(system).initialize(applicationContext);
- return system;
- }
-
- @Bean
- @DependsOn("actorSystem")
- public Cluster wokenCluster() {
- Cluster cluster = Cluster.get(actorSystem());
- LOGGER.info("Connect to Woken cluster nodes at " + String.join(",", wokenPath()));
- Semaphore semaphore = new Semaphore(1);
- cluster.registerOnMemberUp( () -> {
- LOGGER.info("Step 2/3: Cluster up, registering the actors...");
-
- // Do not call wokenMediator() here to avoid recursive loops
- ActorRef mediator = DistributedPubSub.get(actorSystem()).mediator();
-
- LOGGER.info("Woken Mediator available at " + mediator.path().toStringWithoutAddress());
-
- semaphore.release();
- });
-
- 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);
- }
- }
-
- final Runnable leaveCluster = () -> cluster.leave(cluster.selfAddress());
- actorSystem().registerOnTermination(leaveCluster);
-
- cluster.registerOnMemberRemoved( () -> {
- LOGGER.info("Exiting...");
- cluster.leave(cluster.selfAddress());
- actorSystem().registerOnTermination(() -> System.exit(0));
- actorSystem().terminate();
- });
-
- Runtime.getRuntime().addShutdownHook(new Thread(leaveCluster)
- );
-
- LOGGER.info("Step 3/3: Cluster connected to Woken.");
-
- return cluster;
- }
-
- @Bean
- public String wokenClusterHost() {
- return config.getString("clustering.ip");
- }
-
- @Bean
- public String wokenClusterName() {
- return config.getString("clustering.cluster.name");
- }
-
- @Bean
- public Integer wokenClusterPort() {
- return config.getInt("clustering.port");
- }
-
- @Bean
- public List<String> wokenPath() {
- return config.getStringList("akka.cluster.seed-nodes");
- }
-
-}
diff --git a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java b/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
index a6ae893f9df932db208fc5680e44df012dbd4d0c..a5b514dfb815c9df88c0475b7c3ce24df1f06803 100644
--- a/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
+++ b/src/main/java/eu/hbp/mip/configuration/WebConfiguration.java
@@ -20,7 +20,6 @@ import springfox.documentation.swagger2.annotations.EnableSwagger2;
@Configuration
@EnableSwagger2
@EnableSpringDataWebSupport
-@DependsOn("wokenCluster")
public class WebConfiguration {
@Bean
diff --git a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
index c7bd005aee68488280f16ec4ac079ef5c9756de4..4faac4ee5502fce220445a26de559aa04e9c5632 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -4,11 +4,6 @@
package eu.hbp.mip.controllers;
-
-import ch.chuv.lren.woken.messages.datasets.Dataset;
-import ch.chuv.lren.woken.messages.datasets.DatasetsQuery;
-import ch.chuv.lren.woken.messages.datasets.DatasetsResponse;
-import eu.hbp.mip.akka.WokenClientController;
import eu.hbp.mip.model.DatasetDescription;
import io.swagger.annotations.*;
import org.slf4j.Logger;
@@ -30,40 +25,9 @@ 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 extends WokenClientController {
+public class DatasetsApi {
private static final Logger LOGGER = LoggerFactory.getLogger(DatasetsApi.class);
- @ApiOperation(value = "Get dataset list", response = Dataset.class, responseContainer = "List")
- @RequestMapping(method = RequestMethod.GET)
- @Cacheable(value = "datasets")
- public ResponseEntity getDatasets(
- ) {
- LOGGER.info("Get list of datasets");
-
- try {
- List<DatasetDescription> datasets = new ArrayList<>();
- for (Dataset d: fetchDatasets()) {
- DatasetDescription dataset = new DatasetDescription();
- LOGGER.info("Dataset {}", d);
- dataset.setCode(d.id().code());
- dataset.setLabel(d.label());
- dataset.setDescription(d.description());
- dataset.setAnonymisationLevel(d.anonymisationLevel().toString());
- datasets.add(dataset);
- }
-
- 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);
- }
-
- }
- public List<ch.chuv.lren.woken.messages.datasets.Dataset> fetchDatasets() throws Exception {
- DatasetsResponse result = askWoken(new DatasetsQuery(Option.empty()), 30);
- return new ArrayList<>(scala.collection.JavaConversions.asJavaCollection(result.datasets()));
- }
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 2c626060818dc93ee79b1029ced677ce1412e8cf..3035889605e555189c2c2ff93eba40ccaa820a10 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -6,7 +6,7 @@ import com.google.gson.*;
import com.google.common.collect.Lists;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
-import eu.hbp.mip.akka.WokenClientController;
+
import eu.hbp.mip.model.*;
import eu.hbp.mip.repositories.ExperimentRepository;
import eu.hbp.mip.repositories.ModelRepository;
@@ -35,7 +35,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/experiments", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/experiments", description = "the experiments API")
-public class ExperimentApi extends WokenClientController {
+public class ExperimentApi {
private static final Logger LOGGER = LoggerFactory.getLogger(ExperimentApi.class);
@@ -62,16 +62,7 @@ public class ExperimentApi extends WokenClientController {
@Autowired
private ExperimentRepository experimentRepository;
- @ApiOperation(value = "Send a request to the workflow to run an experiment", response = Experiment.class)
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity<String> runExperiment(@RequestBody ExperimentQuery expQuery) {
- LOGGER.info("Run an experiment");
-
- Experiment experiment = saveExperiment(expQuery);
- sendExperiment(experiment);
- return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
- }
@ApiOperation(value = "Create an experiment on Exareme", response = Experiment.class)
@RequestMapping(value = "/exareme", method = RequestMethod.POST)
@@ -367,38 +358,6 @@ public class ExperimentApi extends WokenClientController {
return new ResponseEntity<>(gsonOnlyExposed.toJson(experiment.jsonify()), HttpStatus.OK);
}
- private void sendExperiment(final Experiment experiment) {
- User user = userInfo.getUser();
-
- // this runs in the background. For future optimization: use a thread pool
- final ch.chuv.lren.woken.messages.query.ExperimentQuery experimentQuery = experiment
- .prepareQuery(user.getUsername());
- final ExecutionContext ec = getExecutor();
-
- Future<Object> response = sendWokenQuery(experimentQuery, 24 * 3600);
- response.onSuccess(new OnSuccess<Object>() {
- public void onSuccess(Object result) {
- QueryResult queryResult = (QueryResult) result;
- UUID uuid = experiment.getUuid();
- LOGGER.info("\n\nExperimentActor received response from woken for UUID: \n" + uuid.toString());
- Experiment experiment = experimentRepository.findOne(uuid);
- if (experiment == null) {
- LOGGER.error("Experiment with UUID=" + uuid + " not found in DB");
- } else {
- if (queryResult.error().nonEmpty()) {
- experiment.setHasServerError(true);
- LOGGER.error("Experiment failed with message: " + queryResult.error().get());
- }
- // TODO: use new WokenConversions().toJson(queryResult)
- experiment.setResult(queryResult.data().get().compactPrint());
- experiment.setFinished(Date.from(queryResult.timestamp().toInstant()));
- experimentRepository.save(experiment);
- LOGGER.info("Experiment " + uuid + " updated (finished)");
- }
- }
- }, ec);
- }
-
private void finishExperiment(Experiment experiment) {
experiment.setFinished(new Date());
experimentRepository.save(experiment);
diff --git a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index 5eaf651b756c1536bddb6aea8431bf55eedccb7a..10f1e2276931dcc137c02f31cbf5a2aa3f01549b 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -1,7 +1,7 @@
package eu.hbp.mip.controllers;
import com.google.gson.*;
-import eu.hbp.mip.akka.WokenClientController;
+
import ch.chuv.lren.woken.messages.query.MethodsQuery$;
import ch.chuv.lren.woken.messages.query.MethodsResponse;
import io.swagger.annotations.Api;
@@ -21,7 +21,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/methods", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/methods", description = "the methods API")
-public class MethodsApi extends WokenClientController {
+public class MethodsApi {
private static final Logger LOGGER = LoggerFactory.getLogger(MethodsApi.class);
@@ -36,20 +36,6 @@ public class MethodsApi extends WokenClientController {
@Value("#{'${services.workflows.workflowAuthorization}'}")
private String workflowAuthorization;
- @ApiOperation(value = "List available methods and validations", response = String.class)
- @Cacheable(value = "methods", unless = "#result.getStatusCode().value()!=200")
- @RequestMapping(method = RequestMethod.GET)
- public ResponseEntity listAvailableMethodsAndValidations() {
- LOGGER.info("List available methods and validations");
-
- return requestWoken(MethodsQuery$.MODULE$, 10, r -> {
- MethodsResponse result = (MethodsResponse) r;
- JsonObject catalog = new JsonParser().parse(result.methods().compactPrint()).getAsJsonObject();
-
- return ResponseEntity.ok(gson.toJson(catalog));
- });
- }
-
@ApiOperation(value = "List Exareme algorithms and validations", response = String.class)
@Cacheable(value = "exareme", unless = "#result.getStatusCode().value()!=200")
@RequestMapping(value = "/exareme", method = RequestMethod.GET)
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index edee07b8dad31bcd62c7759a048f9edb82103446..a585098261f35176c3710ce2aeb73f3e20bd4e70 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -3,7 +3,7 @@ package eu.hbp.mip.controllers;
import eu.hbp.mip.utils.HTTPUtil;
import com.google.gson.Gson;
-import eu.hbp.mip.akka.WokenClientController;
+
import eu.hbp.mip.model.Mining;
import eu.hbp.mip.model.User;
import eu.hbp.mip.model.UserInfo;
@@ -34,7 +34,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/mining", produces = { APPLICATION_JSON_VALUE })
@Api(value = "/mining", description = "the mining API")
-public class MiningApi extends WokenClientController {
+public class MiningApi {
private static final Logger LOGGER = LoggerFactory.getLogger(MiningApi.class);
private static final Gson gson = new Gson();
@@ -45,27 +45,6 @@ public class MiningApi extends WokenClientController {
@Value("#{'${services.exareme.miningExaremeUrl:http://localhost:9090/mining/query}'}")
public String miningExaremeQueryUrl;
- @ApiOperation(value = "Run an algorithm", response = String.class)
- @Cacheable(value = "mining", condition = "#query != null and (#query.getAlgorithm().getCode() == 'histograms' or #query.getAlgorithm().getCode() == 'histograms')", key = "#query.toString()", unless = "#result.getStatusCode().value()!=200")
- @RequestMapping(method = RequestMethod.POST)
- public ResponseEntity runAlgorithm(@RequestBody eu.hbp.mip.model.MiningQuery query) {
- LOGGER.info("Run an algorithm");
- User user = userInfo.getUser();
-
- return askWokenQuery(query.prepareQuery(user.getUsername()), 120, result -> {
- if (result.error().nonEmpty()) {
- LOGGER.error(result.error().get());
- return ResponseEntity.status(HttpStatus.BAD_REQUEST)
- .body("{\"error\":\"" + result.error().get() + "\"}");
- } else {
- Mining mining = new Mining(result.jobId(), result.node(), unwrap(result.algorithm()),
- result.type().mime(), Date.from(result.timestamp().toInstant()),
- result.data().get().compactPrint());
- return ResponseEntity.ok(gson.toJson(mining.jsonify()));
- }
- });
- }
-
@ApiOperation(value = "Create an histogram on Exareme", response = String.class)
@RequestMapping(value = "/exareme", method = RequestMethod.POST)
public ResponseEntity runExaremeMining(@RequestBody List<HashMap<String, String>> queryList) {
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
index 6d7cce1c7819b64d168f06f94c817177fd461567..e41afded17f4779e0b41516e3ab8b796124a43b3 100644
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
@@ -13,7 +13,7 @@ import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
-import eu.hbp.mip.akka.WokenClientController;
+
import eu.hbp.mip.model.Algorithm;
import eu.hbp.mip.model.MiningQuery;
import eu.hbp.mip.model.Variable;
@@ -43,7 +43,7 @@ import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@RestController
@RequestMapping(value = "/variables", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/variables", description = "the variables API")
-public class VariablesApi extends WokenClientController {
+public class VariablesApi {
private static final Logger LOGGER = LoggerFactory.getLogger(VariablesApi.class);
@@ -79,36 +79,7 @@ public class VariablesApi extends WokenClientController {
return ResponseEntity.ok(variablesObjects);
}
- @ApiOperation(value = "Get variables available for a dataset", response = List.class, responseContainer = "List")
- @Cacheable(value = "availableVariables",
- unless = "#result.getStatusCode().value()!=200")
- @RequestMapping(value = "/availableVariables", method = RequestMethod.GET)
- public ResponseEntity getAvailableVariables(
- @ApiParam(value = "List of datasets : ds1,ds2,...") @RequestParam(value = "datasets") String datasets) {
-
- LOGGER.info("Get available variables for datasets " + datasets);
-
- List<Variable> dsAsVariables = Arrays.stream(datasets.split(",")).map(Variable::new).collect(Collectors.toList());
- WokenConversions conv = new WokenConversions();
-
- VariablesForDatasetsQuery query = new VariablesForDatasetsQuery(conv.toDatasets(dsAsVariables), true);
-
- return requestWoken(query, 30, r -> {
- VariablesForDatasetsResponse response = (VariablesForDatasetsResponse) r;
-
- if (response.error().isDefined()) {
- return ResponseEntity.status(HttpStatus.NOT_FOUND).body(response.error().get());
- } else {
- List<Variable> variables = new ArrayList<>();
- for (VariableMetaData var: JavaConversions.setAsJavaSet(response.variables())) {
- variables.add(new Variable(var.code()));
- }
- return ResponseEntity.ok(variables);
- }
- });
-
- }
-
+
@ApiOperation(value = "Get a variable", response = Object.class)
@Cacheable("variable")
diff --git a/src/main/resources/log4j2.xml b/src/main/resources/log4j2.xml
index 57becf5e642e1601d4024194e4eff427698d3986..c5c8d43bb2256424e434b9f4f859f00834630afd 100644
--- a/src/main/resources/log4j2.xml
+++ b/src/main/resources/log4j2.xml
@@ -10,7 +10,13 @@
<Root level="${env:LOG_LEVEL:-INFO}">
<AppenderRef ref="Console"/>
</Root>
- <Logger name="akka.actor.LocalActorRefProvider(akka://woken)" level="INFO">
+ <Logger name="akka.actor.LocalActorRefProvider(akka://
+ <Logger name="io.netty" level="${env:NETTY_LOG_LEVEL:-ERROR}">
+ <AppenderRef ref="Console"/>
+ </Logger>
+ </Loggers>
+</Configuration>
+woken)" level="INFO">
<AppenderRef ref="Console"/>
</Logger>
<Logger name="akka.cluster" level="${env:AKKA_CLUSTER_LOG_LEVEL:-INFO}">
@@ -30,9 +36,4 @@
</Logger>
<Logger name="akka.stream.impl" level="${env:AKKA_STREAM_LOG_LEVEL:-INFO}">
<AppenderRef ref="Console"/>
- </Logger>
- <Logger name="io.netty" level="${env:NETTY_LOG_LEVEL:-ERROR}">
- <AppenderRef ref="Console"/>
- </Logger>
- </Loggers>
-</Configuration>
+ </Logger>
\ No newline at end of file