Fix /datasets service

src/main/java/eu/hbp/mip/StartupTasks.java

 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!");
     }
 }

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()));
     }
 }

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");

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);

src/main/java/eu/hbp/mip/model/DatasetDescription.java

+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;
+    }
+}