diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 011209f07cb1d8dfe265becbf234916b550c1227..a8a9c0e160044c46d7b182f1b6f0f26f9fcb6cd7 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
[bumpversion]
-current_version = 2.6.2
+current_version = 2.6.8
commit = True
tag = True
tag_name = {new_version}
diff --git a/docker/README.md b/docker/README.md
index 33262bddeb289cca0a33a980fcd462b8e3fc4d9b..6e66dafa60dc9a73a74d27303d2b3b670b4766ce 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
@@ -64,3 +63,10 @@ To use this image, you need a running instance of PostgreSQL and to configure th
* CONTEXT_PATH: context path appended to all services running in this container. Default to "/services".
* SESSION_TIMEOUT: Timeout in milliseconds for session expiration. Default to 2592000.
+
+### PROXY
+
+* HTTP_PROXY_HOST: HTTP proxy host
+* HTTP_PROXY_PORT: HTTP proxy port
+* HTTPS_PROXY_HOST: HTTPS proxy host
+* HTTPS_PROXY_PORT: HTTPS proxy port
diff --git a/docker/config/application.tmpl b/docker/config/application.tmpl
index 45110f4b688d291c030c1e72df085f40bae34c8b..911af6200bda7587d08d1543ad269d969fba3c81 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 2b1ca22d1c42ceccd4d8d6fe9ac40e363f729a43..36a069dc7bc2abcbe1391a3ef1d56007ab4e8896 100755
--- a/docker/run.sh
+++ b/docker/run.sh
@@ -10,4 +10,16 @@ fi
if [ ! -z "$FEATURES_DB_SERVER" ]; then
OPTS="$OPTS -wait tcp://$FEATURES_DB_SERVER -timeout 60s"
fi
-dockerize $OPTS java -jar /usr/share/jars/portal-backend.jar
+if [ ! -z "$HTTP_PROXY_HOST" ]; then
+ JAVA_OPTIONS="$JAVA_OPTIONS -Dhttp.proxyHost=$HTTP_PROXY_HOST"
+fi
+if [ ! -z "$HTTP_PROXY_PORT" ]; then
+ JAVA_OPTIONS="$JAVA_OPTIONS -Dhttp.proxyPort=$HTTP_PROXY_PORT"
+fi
+if [ ! -z "$HTTPS_PROXY_HOST" ]; then
+ JAVA_OPTIONS="$JAVA_OPTIONS -Dhttps.proxyHost=$HTTPS_PROXY_HOST"
+fi
+if [ ! -z "$HTTPS_PROXY_PORT" ]; then
+ JAVA_OPTIONS="$JAVA_OPTIONS -Dhttps.proxyPort=$HTTPS_PROXY_PORT"
+fi
+dockerize $OPTS java ${JAVA_OPTIONS} -jar /usr/share/jars/portal-backend.jar
diff --git a/hbp.yml b/hbp.yml
index 95e575825136d6ba677d02bc320eaf7f57ac0371..e01490c0f87191ff2af7e0945146fba41c165875 100644
--- a/hbp.yml
+++ b/hbp.yml
@@ -58,9 +58,9 @@ testing:
command: ./test.sh
release_management:
- current_version: 2.6.2
- current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.6.2.zip
- current_binary_release: https://pypi.python.org/pypi/portal-backend/2.6.2
+ current_version: 2.6.8
+ current_code_release: https://github.com/HBPMedical/portal-backend/archive/2.6.8.zip
+ current_binary_release: https://pypi.python.org/pypi/portal-backend/2.6.8
release_script: 'publish.sh'
continuous_integration:
@@ -75,10 +75,10 @@ continuous_integration:
distribution:
docker_hub:
name: hbpmip/portal-backend
- current_tag: 2.6.2
+ current_tag: 2.6.8
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:2.6.2
+ command: docker pull hbpmip/portal-backend:2.6.8
planning:
github:
diff --git a/pom.xml b/pom.xml
index 3f71142f10524f829b335c825c5760dc5ad9d8eb..4c827b642da5b1e4aa48c6aaba539084b1b944dc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -5,7 +5,7 @@
<groupId>eu.hbp.mip</groupId>
<artifactId>portal-backend</artifactId>
- <version>2.6.2</version><!-- BUMP_VERSION -->
+ <version>2.6.8</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>2.4.9</woken-messages.version>
+ <woken-messages.version>2.6.3</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/StartupTasks.java b/src/main/java/eu/hbp/mip/StartupTasks.java
new file mode 100644
index 0000000000000000000000000000000000000000..a72e119529fb6fcd497b8ad90fc0b60d4dd7c14a
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/StartupTasks.java
@@ -0,0 +1,70 @@
+package eu.hbp.mip;
+
+import ch.chuv.lren.woken.messages.datasets.Dataset;
+import com.google.gson.Gson;
+import eu.hbp.mip.controllers.DatasetsApi;
+import eu.hbp.mip.controllers.MiningApi;
+import eu.hbp.mip.controllers.VariablesApi;
+import eu.hbp.mip.model.Algorithm;
+import eu.hbp.mip.model.MiningQuery;
+import eu.hbp.mip.model.Variable;
+import eu.hbp.mip.repositories.VariableRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.context.event.ApplicationReadyEvent;
+import org.springframework.context.ApplicationListener;
+import org.springframework.stereotype.Component;
+
+import java.util.Collections;
+
+@Component
+public class StartupTasks implements ApplicationListener<ApplicationReadyEvent> {
+
+ private static final Logger LOGGER = LoggerFactory.getLogger(StartupTasks.class);
+ private static final Gson gson = new Gson();
+
+ @Autowired
+ private VariableRepository variableRepository;
+
+ @Autowired
+ private DatasetsApi datasetsApi;
+
+ @Autowired
+ private VariablesApi variablesApi;
+
+ @Autowired
+ private MiningApi miningApi;
+
+ @Override
+ public void onApplicationEvent(ApplicationReadyEvent event) {
+ // 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 {
+ for (Dataset dataset: datasetsApi.fetchDatasets()) {
+ final String code = dataset.dataset().code();
+ Variable v = variableRepository.findOne(code);
+ if (v == null) {
+ v = new Variable(code);
+ variableRepository.save(v);
+ }
+ }
+ } catch (Exception e) {
+ LOGGER.error("Cannot initialise the variable repository. Is the connection to Woken working?", e);
+ }
+
+ /*
+ for (String variableJson: variablesApi.loadVariables()) {
+ String code = gson.fromJson(variableJson, Variable.class).getCode();
+ MiningQuery histogram = new MiningQuery();
+ histogram.setAlgorithm(new Algorithm("histogram", "histogram", false));
+ histogram.setVariables(Collections.singletonList(new Variable(code)));
+ histogram.setCovariables(Collections.emptyList());
+ histogram.setGrouping(Collections.emptyList());
+ // TODO: need to get groupings from Woken
+ }
+ */
+
+ LOGGER.info("MIP Portal backend is ready!");
+ }
+}
diff --git a/src/main/java/eu/hbp/mip/akka/WokenClientController.java b/src/main/java/eu/hbp/mip/akka/WokenClientController.java
index 3cc463857d927b17e4210cce5013eac638939a28..2504d6468feaad808d19fffa52f29da4baeac77c 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 052486a5e47d840b21511c1279310ab2a31d6685..99d5b8497cd9fad5b2843b1621293e26d5f6dfe8 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -5,21 +5,27 @@
package eu.hbp.mip.controllers;
-import com.google.gson.Gson;
-import eu.hbp.mip.model.Dataset;
-import eu.hbp.mip.model.Variable;
-import eu.hbp.mip.repositories.VariableRepository;
+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 com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import eu.hbp.mip.akka.WokenClientController;
+import eu.hbp.mip.model.DatasetDescription;
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.cache.annotation.Cacheable;
+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.ArrayList;
+import java.util.List;
+import java.util.Set;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -27,35 +33,40 @@ 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();
-
- @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);
- if (v == null) {
- v = new Variable(dataset);
- variableRepository.save(v);
- }
- }
- }
@ApiOperation(value = "Get dataset list", response = Dataset.class, responseContainer = "List")
@RequestMapping(method = RequestMethod.GET)
+ @Cacheable(value = "datasets")
public ResponseEntity getDatasets(
) {
- LOGGER.info("Get dataset list");
+ 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.dataset().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);
+ }
- return ResponseEntity.ok(datasets.split(","));
}
+ 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/MethodsApi.java b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
index f25187d58f31ff93087a0c6cf2d6031e5aa92525..b275f889d2f955a8b52cdf25dde3696789a0274c 100644
--- a/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MethodsApi.java
@@ -35,11 +35,11 @@ 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
- JsonObject catalog = new JsonParser().parse(result.methods()).getAsJsonObject();
+ JsonObject catalog = new JsonParser().parse(result.methods().compactPrint()).getAsJsonObject();
InputStream is = MethodsApi.class.getClassLoader().getResourceAsStream(EXAREME_ALGO_JSON_FILE);
InputStreamReader isr = new InputStreamReader(is);
BufferedReader br = new BufferedReader(isr);
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 14dda0f5ad3b7b0b8cc622359485e882c7b49819..655d159d09dbf6554efdc1d2e197a30e547d84a4 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -44,7 +44,10 @@ public class MiningApi extends WokenClientController {
public String queryUrl;
@ApiOperation(value = "Run an algorithm", response = String.class)
- @Cacheable(value = "mining", condition = "#query != null and #query.getAlgorithm().getCode() == 'histograms'", key = "#query.toString()", unless = "#result.getStatusCode().value()!=200")
+ @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");
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
index c55cec4b05e2334b45df5e946ce96f598a8f1672..1c284f1bbb406e3907ee28888d88aa250757ad5d 100644
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
@@ -166,7 +166,7 @@ public class VariablesApi {
}
- private List<String> loadVariables() {
+ public List<String> loadVariables() {
String sqlQuery = String.format(
"SELECT * FROM meta_variables where upper(target_table)='%s'", featuresMainTable.toUpperCase());
SqlRowSet data = metaJdbcTemplate.queryForRowSet(sqlQuery);
diff --git a/src/main/java/eu/hbp/mip/model/DatasetDescription.java b/src/main/java/eu/hbp/mip/model/DatasetDescription.java
new file mode 100644
index 0000000000000000000000000000000000000000..c77c50aeab3a4256ecadf78aa2f25f89a05a0b92
--- /dev/null
+++ b/src/main/java/eu/hbp/mip/model/DatasetDescription.java
@@ -0,0 +1,46 @@
+package eu.hbp.mip.model;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import io.swagger.annotations.ApiModel;
+
+@ApiModel
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public class DatasetDescription {
+
+ private String code;
+ private String label;
+ private String description;
+ private String anonymisationLevel;
+
+ public String getCode() {
+ return code;
+ }
+
+ public void setCode(String code) {
+ this.code = code;
+ }
+
+ public String getLabel() {
+ return label;
+ }
+
+ public void setLabel(String label) {
+ this.label = label;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ public String getAnonymisationLevel() {
+ return anonymisationLevel;
+ }
+
+ public void setAnonymisationLevel(String anonymisationLevel) {
+ this.anonymisationLevel = anonymisationLevel;
+ }
+}
diff --git a/src/main/resources/application.conf b/src/main/resources/application.conf
index 23a49772785dc1100acb9ab6230c082ff841b80c..711776afa4ac564da86946c61b2af8c3b6c0f104 100644
--- a/src/main/resources/application.conf
+++ b/src/main/resources/application.conf
@@ -14,17 +14,6 @@ akka {
event-stream = off
}
- serializers {
- query-result-serializer = "ch.chuv.lren.woken.messages.query.QueryResultSerializer"
- }
-
- serialization-bindings {
- "ch.chuv.lren.woken.messages.query.QueryResult" = query-result-serializer
- }
- enable-additional-serialization-bindings = off
- allow-java-serialization = on
- warn-about-java-serializer-usage = on
-
}
remote {
diff --git a/tests/docker-compose.yml b/tests/docker-compose.yml
index 99c80d8e2bd87822115ae8e4387867adce99bd70..881353667065f7c1994068560e71516021dc1ab2 100644
--- a/tests/docker-compose.yml
+++ b/tests/docker-compose.yml
@@ -43,7 +43,7 @@ services:
- db
meta_db_setup:
- image: "hbpmip/sample-meta-db-setup:0.4.3"
+ image: "hbpmip/sample-meta-db-setup:0.5.1"
container_name: "meta-db-setup"
restart: "no"
networks:
@@ -59,7 +59,7 @@ services:
- db
sample_db_setup:
- image: "hbpmip/sample-data-db-setup:0.5.0"
+ image: "hbpmip/sample-data-db-setup:0.5.1"
container_name: "data-db-setup"
restart: "no"
networks: