diff --git a/src/main/java/eu/hbp/mip/StartupTasks.java b/src/main/java/eu/hbp/mip/StartupTasks.java
index 880603a9cae3f020a3968b586f29ff76593e8be5..a72e119529fb6fcd497b8ad90fc0b60d4dd7c14a 100644
--- a/src/main/java/eu/hbp/mip/StartupTasks.java
+++ b/src/main/java/eu/hbp/mip/StartupTasks.java
@@ -1,6 +1,12 @@
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;
@@ -10,10 +16,13 @@ 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;
@@ -21,12 +30,18 @@ public class StartupTasks implements ApplicationListener<ApplicationReadyEvent>
@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 (ch.chuv.lren.woken.messages.datasets.Dataset dataset: datasetsApi.fetchDatasets()) {
+ for (Dataset dataset: datasetsApi.fetchDatasets()) {
final String code = dataset.dataset().code();
Variable v = variableRepository.findOne(code);
if (v == null) {
@@ -38,6 +53,18 @@ public class StartupTasks implements ApplicationListener<ApplicationReadyEvent>
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/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
index 28d101a18b28b1dd980a202e72efa41a38c964ab..99d5b8497cd9fad5b2843b1621293e26d5f6dfe8 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -5,15 +5,17 @@
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 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.DatasetDescription;
import io.swagger.annotations.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -21,6 +23,8 @@ import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;
import scala.Option;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Set;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
@@ -35,19 +39,22 @@ public class DatasetsApi extends WokenClientController {
@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 {
- JsonArray datasets = new JsonArray();
- fetchDatasets().stream().map(d -> {
- JsonObject jsObject = new JsonObject();
- jsObject.addProperty("code", d.dataset().code());
- jsObject.addProperty("label", d.label());
- datasets.add(jsObject);
- return jsObject;
- });
+ 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) {
@@ -58,8 +65,8 @@ public class DatasetsApi extends WokenClientController {
}
- public Set<ch.chuv.lren.woken.messages.datasets.Dataset> fetchDatasets() throws Exception {
+ public List<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());
+ return new ArrayList<>(scala.collection.JavaConversions.asJavaCollection(result.datasets()));
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 97d5943420ae4a47d6631e591079e21f80ffe358..b497da478cf525a7cf03934ba72bd4e1acfc4f3e 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;
+ }
+}