diff --git a/docker/README.md b/docker/README.md
index 5d523406839cba97ac0df926752a81074409893d..419dd079818055f01a0e70f781e42d5221d80268 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -52,9 +52,8 @@ To use this image, you need a running instance of PostgreSQL and to configure th
### ENDPOINTS
-* WOKEN_URL: URL to woken machine learning server, default value is "http://172.22.0.1:8087".
-* WOKEN_HOST: default value is "woken".
-* WOKEN_AKKA_PORT default value is "8088".
+* WOKEN_PORT_8088_TCP_ADDR: default value is "woken".
+* WOKEN_PORT_8088_TCP_PORT default value is "8088".
* WOKEN_AKKA_PATH default value is "/user/entrypoint".
* EXAREME_URL: URL to Exareme server, default value is "http://hbps2.chuv.ch:9090".
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 345cfdd1c890abd2cb2e87eb4392d459de503f82..16a901f6b08c45917d5764a813c78a91a7952f69 100644
--- a/docker/config/application.tmpl
+++ b/docker/config/application.tmpl
@@ -82,14 +82,11 @@ endpoints:
sentitive: false
services:
- woken:
- experimentUrl: {{ default .Env.WOKEN_URL "http://172.22.0.1:8087" }}/experiment
- listMethodsUrl: {{ default .Env.WOKEN_URL "http://172.22.0.1:8087" }}/list-methods
exareme:
miningExaremeUrl: {{ default .Env.EXAREME_URL "http://hbps2.chuv.ch:9090" }}/mining/query
akka:
woken:
- host: {{ default .Env.WOKEN_HOST "woken" }}
- port: {{ default .Env.WOKEN_AKKA_PORT "8088" }}
+ host: {{ default .Env.WOKEN_PORT_8088_TCP_ADDR "woken" }}
+ port: {{ default .Env.WOKEN_PORT_8088_TCP_PORT "8088" }}
path: {{ default .Env.WOKEN_AKKA_PATH "/user/entrypoint" }}
diff --git a/pom.xml b/pom.xml
index 483704b6beb6f7e4f77a78da04a2d30dfe7e0608..95a350b908473c2c5131a40368a368b9574f2a12 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>2.3.0</woken-messages.version>
+ <woken-messages.version>2.3.1</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>
@@ -73,6 +73,10 @@
</repositories>
<dependencies>
+ <dependency>
+ <groupId>org.springframework.boot</groupId>
+ <artifactId>spring-boot-starter-logging</artifactId>
+ </dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-actuator</artifactId>
@@ -217,6 +221,11 @@
<artifactId>akka-cluster-tools_2.11</artifactId>
<version>${akka.version}</version>
</dependency>
+ <dependency>
+ <groupId>com.typesafe.akka</groupId>
+ <artifactId>akka-slf4j_2.11</artifactId>
+ <version>${akka.version}</version>
+ </dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index 1a63229034ea9edc8f6c5fc75f53a3c8514b73fb..d0e0db36aa029c95bebed143ff9755682dba899e 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -201,10 +201,10 @@ public class ExperimentApi extends WokenClientController {
@ApiOperation(value = "List available methods and validations", response = String.class)
@Cacheable(value = "methods", unless = "#result.getStatusCode().value()!=200")
@RequestMapping(path = "/methods", method = RequestMethod.GET)
- public ResponseEntity listAvailableMethodsAndValidations() throws IOException {
+ public ResponseEntity listAvailableMethodsAndValidations() {
LOGGER.info("List available methods and validations");
- return askWoken(MethodsQuery$.MODULE$, 5, r -> {
+ return askWoken(MethodsQuery$.MODULE$, 10, r -> {
MethodsResponse result = (MethodsResponse) r;
// >> Temporary : should return result.methods() in the future
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 3d3cd0c6a8ffae7224a37084f5279e8d13a3cad4..5b784fba15f1d93de20c5199112f9e34834070e7 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -2,11 +2,14 @@ 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 io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -15,7 +18,6 @@ import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
-import java.io.IOException;
import java.sql.Date;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -31,13 +33,17 @@ public class MiningApi extends WokenClientController {
private static final Logger LOGGER = LoggerFactory.getLogger(MiningApi.class);
private static final Gson gson = new Gson();
+ @Autowired
+ private SecurityConfiguration securityConfiguration;
+
@ApiOperation(value = "Run an algorithm", response = String.class)
- @Cacheable(value = "mining", condition = "#query.getAlgorithm().getCode() == 'histograms'", key = "#query.toString()", unless = "#result.getStatusCode().value()!=200")
+ @Cacheable(value = "mining", condition = "#query != null and #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) throws IOException {
+ public ResponseEntity runAlgorithm(@RequestBody eu.hbp.mip.model.MiningQuery query) {
LOGGER.info("Run an algorithm");
+ User user = securityConfiguration.getUser();
- return askWokenQuery(query.prepareQuery(), 120,
+ return askWokenQuery(query.prepareQuery(user.getUsername()), 120,
result -> {
if (result.error().nonEmpty()) {
LOGGER.error(result.error().get());
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
index 8278bef8af34f5861e2569dcb3fc5bf255a09a98..c55cec4b05e2334b45df5e946ce96f598a8f1672 100644
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
@@ -9,10 +9,8 @@ import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
-import eu.hbp.mip.configuration.SecurityConfiguration;
import eu.hbp.mip.model.Algorithm;
import eu.hbp.mip.model.MiningQuery;
-import eu.hbp.mip.model.User;
import eu.hbp.mip.model.Variable;
import io.swagger.annotations.*;
import org.postgresql.util.PGobject;
@@ -50,9 +48,6 @@ public class VariablesApi {
@Value("#{'${spring.featuresDatasource.main-table:features}'}")
private String featuresMainTable;
- @Autowired
- private SecurityConfiguration securityConfiguration;
-
@ApiOperation(value = "Get variables", response = List.class, responseContainer = "List")
@Cacheable("variables")
@RequestMapping(method = RequestMethod.GET)
@@ -153,15 +148,13 @@ public class VariablesApi {
) {
LOGGER.info("Get query for histograms");
- User user = securityConfiguration.getUser();
-
String sqlQuery = String.format(
"SELECT histogram_groupings FROM meta_variables where upper(target_table)='%s'", featuresMainTable.toUpperCase());
SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
data.next();
String histogramGroupings = data.getString("histogram_groupings");
- MiningQuery query = new MiningQuery(user.getUsername());
+ MiningQuery query = new MiningQuery();
query.addVariable(new Variable(code));
List<String> newGroups = Arrays.asList(histogramGroupings.split(","));
List<Variable> groupings = query.getGrouping();
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 09bd4a576449a8397d5b7fb81a98801d4d2e6725..1b03306c3c048901c411309cdb3c59f15fe66d60 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -4,6 +4,7 @@ import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.gson.Gson;
import eu.hbp.mip.utils.TypesConvert;
import eu.hbp.mip.woken.messages.datasets.DatasetId;
+import eu.hbp.mip.woken.messages.query.ExecutionPlan;
import eu.hbp.mip.woken.messages.query.UserId;
import eu.hbp.mip.woken.messages.query.filters.FilterRule;
import eu.hbp.mip.woken.messages.variables.FeatureIdentifier;
@@ -17,25 +18,19 @@ import java.util.List;
*/
public class MiningQuery {
- private String user;
private List<Variable> variables;
private List<Variable> covariables;
private List<Variable> grouping;
private String filters;
private Algorithm algorithm;
- public MiningQuery(String user) {
- this.user = user;
+ public MiningQuery() {
this.variables = new LinkedList<>();
this.covariables = new LinkedList<>();
this.grouping = new LinkedList<>();
this.filters = "";
}
- public String getUser() {
- return user;
- }
-
public List<Variable> getVariables() {
return variables;
}
@@ -82,7 +77,7 @@ public class MiningQuery {
this.algorithm = algorithm;
}
- public eu.hbp.mip.woken.messages.query.MiningQuery prepareQuery() {
+ public eu.hbp.mip.woken.messages.query.MiningQuery prepareQuery(String user) {
eu.hbp.mip.woken.messages.query.AlgorithmSpec scalaAlgorithm = new eu.hbp.mip.woken.messages.query.AlgorithmSpec(
algorithm.getCode(), TypesConvert.algoParamsToScala(algorithm.getParameters()));
@@ -102,7 +97,7 @@ public class MiningQuery {
Option<FilterRule> filters = conv.toFilterRule(filtersJson);
return new eu.hbp.mip.woken.messages.query.MiningQuery(userId,
- variablesSeq, covariablesSeq, groupingSeq, filters, datasets, scalaAlgorithm);
+ variablesSeq, covariablesSeq, groupingSeq, filters, datasets, scalaAlgorithm, Option.<ExecutionPlan>empty());
}
@Override
diff --git a/src/main/java/eu/hbp/mip/utils/TypesConvert.java b/src/main/java/eu/hbp/mip/utils/TypesConvert.java
index b4270bde5666fb60f7feeafc85829b604ee8093e..d00d026761855011b7a97d5848ecdca7d5b87a2c 100644
--- a/src/main/java/eu/hbp/mip/utils/TypesConvert.java
+++ b/src/main/java/eu/hbp/mip/utils/TypesConvert.java
@@ -19,7 +19,9 @@ public class TypesConvert {
public static scala.collection.immutable.List<FeatureIdentifier> variablesToIdentifiers(List<Variable> vars) {
List<FeatureIdentifier> varIds = new LinkedList<>();
for (Variable v: vars) {
- varIds.add(new VariableId(v.getCode()));
+ if (!v.getCode().isEmpty()) {
+ varIds.add(new VariableId(v.getCode()));
+ }
}
return JavaConversions.asScalaBuffer(varIds).toList();
}
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 0e90d1f3b512fd3f4f4cd931d216464b308d669e..5960326ec8df4f3596aacdcc7cf60ef14e138726 100644
--- a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
+++ b/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
@@ -9,7 +9,10 @@ import spray.json._
@Component
class WokenConversions {
- def toFilterRule(json: String): Option[FilterRule] = Some(json).map(_.parseJson.convertTo[FilterRule])
+ def toFilterRule(json: String): Option[FilterRule] = json match {
+ case "" => None
+ case _ => Some(json).map(_.parseJson.convertTo[FilterRule])
+ }
def toDatasets(commaSeparatedSets: String): Set[DatasetId] = commaSeparatedSets match {
case "" => Set()