diff --git a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
index 3c71e92602b3e6a8569883af3987c6065817f054..e14a623cf58f50f92f8e672375a8cc278c44c6fb 100644
--- a/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/DatasetsApi.java
@@ -19,6 +19,8 @@ import org.springframework.web.bind.annotation.RestController;
import static org.springframework.http.MediaType.APPLICATION_JSON_VALUE;
+// TODO: deprecate this
+
@RestController
@RequestMapping(value = "/datasets", produces = {APPLICATION_JSON_VALUE})
@Api(value = "/datasets", description = "the datasets API")
diff --git a/src/main/java/eu/hbp/mip/controllers/MiningApi.java b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
index 6245ed42a849c38b0c223439d52af64a38ab37eb..10619819da6908b7abef15c96b6140aee5234f6b 100644
--- a/src/main/java/eu/hbp/mip/controllers/MiningApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/MiningApi.java
@@ -77,25 +77,26 @@ public class MiningApi extends WokenClientController {
LOGGER.error("Cannot receive algorithm result from exareme" + e.getMessage(), e);
return ResponseEntity.status(HttpStatus.SERVICE_UNAVAILABLE).build();
}
+ } else {
+
+ 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(),
+ result.algorithm(),
+ result.shape(),
+ Date.from(result.timestamp().toInstant()),
+ result.data().get().compactPrint()
+ );
+ return ResponseEntity.ok(gson.toJson(mining.jsonify()));
+ }
+ });
}
-
- 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(),
- result.algorithm(),
- result.shape(),
- Date.from(result.timestamp().toInstant()),
- result.data().get().compactPrint()
- );
- return ResponseEntity.ok(gson.toJson(mining.jsonify()));
- }
- });
}
private static boolean isExaremeAlgo(eu.hbp.mip.model.MiningQuery query) {
diff --git a/src/main/java/eu/hbp/mip/model/Dataset.java b/src/main/java/eu/hbp/mip/model/Dataset.java
index 69fc5ed9902450a5bb03c84f7304311a1a21fdb7..d7d1e486a42ffebfadcdeead915652747ce52e74 100644
--- a/src/main/java/eu/hbp/mip/model/Dataset.java
+++ b/src/main/java/eu/hbp/mip/model/Dataset.java
@@ -13,6 +13,8 @@ import java.util.Date;
import java.util.LinkedList;
import java.util.List;
+// TODO: deprecate
+
@Entity
@Table(name = "`dataset`")
@ApiModel
@@ -24,6 +26,7 @@ public class Dataset {
private Date date = null;
+ // Aka covariables
@ElementCollection
@CollectionTable(name = "dataset_header", joinColumns = @JoinColumn(name = "dataset_code"))
private List<String> header = new LinkedList<>();
@@ -36,6 +39,7 @@ public class Dataset {
@CollectionTable(name = "dataset_variable", joinColumns = @JoinColumn(name = "dataset_code"))
private List<String> variable = new LinkedList<>();
+ // TODO:
@Transient
@JsonProperty(access = JsonProperty.Access.READ_ONLY)
private Object data = null;
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index c84c21b1a6983549e2a13c13b8edba5b4001bf67..fff0611d7f94321d5842c9fdd3ed9eb55a5a6349 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -119,11 +119,10 @@ public class Experiment {
scala.collection.immutable.List<AlgorithmSpec> algorithmsSeq = JavaConversions.asScalaBuffer(algorithms).toList();
scala.collection.immutable.List<ValidationSpec> validationsSeq = JavaConversions.asScalaBuffer(validations).toList();
- // TODO - set values
WokenConversions conv = new WokenConversions();
- scala.collection.immutable.Set<DatasetId> trainingDatasets = conv.toDatasets("");
- scala.collection.immutable.Set<DatasetId> testingDatasets = conv.toDatasets("");
- scala.collection.immutable.Set<DatasetId> validationDatasets = conv.toDatasets("");
+ scala.collection.immutable.Set<DatasetId> trainingDatasets = conv.toDatasets(model.getQuery().getTrainingDatasets());
+ scala.collection.immutable.Set<DatasetId> testingDatasets = conv.toDatasets(model.getQuery().getTestingDatasets());
+ scala.collection.immutable.Set<DatasetId> validationDatasets = conv.toDatasets(model.getQuery().getValidationDatasets());
String filtersJson = model.getQuery().getFilters();
Option<FilterRule> filters = conv.toFilterRule(filtersJson);
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 0b0c9a76fa4ab979267777bde4305974e05a3b70..49d8cadb2b743ebe532726ca208808d01d458b8d 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -29,6 +29,7 @@ public class MiningQuery {
this.variables = new LinkedList<>();
this.covariables = new LinkedList<>();
this.grouping = new LinkedList<>();
+ this.datasets = new LinkedList<>();
this.filters = "";
}
@@ -99,9 +100,8 @@ public class MiningQuery {
TypesConvert.variablesToIdentifiers(getGrouping());
UserId userId = new UserId(user);
- // TODO - set values
WokenConversions conv = new WokenConversions();
- scala.collection.immutable.Set<DatasetId> datasets = conv.toDatasets("");
+ scala.collection.immutable.Set<DatasetId> datasets = conv.toDatasets(getDatasets());
String filtersJson = getFilters();
Option<FilterRule> filters = conv.toFilterRule(filtersJson);
diff --git a/src/main/java/eu/hbp/mip/model/Query.java b/src/main/java/eu/hbp/mip/model/Query.java
index fd12294288b8fa50149ecb603f4bd1acb3d8715d..5d372447da74b2194b4b6605795ee015c816112c 100644
--- a/src/main/java/eu/hbp/mip/model/Query.java
+++ b/src/main/java/eu/hbp/mip/model/Query.java
@@ -24,8 +24,6 @@ public class Query {
@GeneratedValue(strategy = GenerationType.SEQUENCE)
private Long id = null;
- private String request = null;
-
@ManyToMany
@JoinTable(name = "query_variable", joinColumns = {
@JoinColumn(name = "id", nullable = false, updatable = false) },
@@ -47,6 +45,27 @@ public class Query {
nullable = false, updatable = false) })
private List<Variable> grouping = new LinkedList<>();
+ @ManyToMany
+ @JoinTable(name = "query_training_datasets", joinColumns = {
+ @JoinColumn(name = "id", nullable = false, updatable = false) },
+ inverseJoinColumns = { @JoinColumn(name = "code",
+ nullable = false, updatable = false) })
+ private List<Variable> trainingDatasets = new LinkedList<>();
+
+ @ManyToMany
+ @JoinTable(name = "query_testing_datasets", joinColumns = {
+ @JoinColumn(name = "id", nullable = false, updatable = false) },
+ inverseJoinColumns = { @JoinColumn(name = "code",
+ nullable = false, updatable = false) })
+ private List<Variable> testingDatasets = new LinkedList<>();
+
+ @ManyToMany
+ @JoinTable(name = "query_validation_datasets", joinColumns = {
+ @JoinColumn(name = "id", nullable = false, updatable = false) },
+ inverseJoinColumns = { @JoinColumn(name = "code",
+ nullable = false, updatable = false) })
+ private List<Variable> validationDatasets = new LinkedList<>();
+
@Column(columnDefinition = "text")
private String filters = "";
@@ -67,6 +86,7 @@ public class Query {
}
+ @JsonProperty("variables")
public List<Variable> getVariables() {
return variables;
}
@@ -95,21 +115,39 @@ public class Query {
this.grouping = grouping;
}
+ @JsonProperty("trainingDatasets")
+ public List<Variable> getTrainingDatasets() {
+ return trainingDatasets;
+ }
- public String getFilters() {
- return filters;
+ public void setTrainingDatasets(List<Variable> trainingDatasets) {
+ this.trainingDatasets = trainingDatasets;
}
- public void setFilters(String filters) {
- this.filters = filters;
+ @JsonProperty("testingDatasets")
+ public List<Variable> getTestingDatasets() {
+ return testingDatasets;
+ }
+
+ public void setTestingDatasets(List<Variable> testingDatasets) {
+ this.testingDatasets = testingDatasets;
}
- public String getRequest() {
- return request;
+ @JsonProperty("validationDatasets")
+ public List<Variable> getValidationDatasets() {
+ return validationDatasets;
}
- public void setRequest(String request) {
- this.request = request;
+ public void setValidationDatasets(List<Variable> validationDatasets) {
+ this.validationDatasets = validationDatasets;
+ }
+
+ public String getFilters() {
+ return filters;
+ }
+
+ public void setFilters(String filters) {
+ this.filters = filters;
}
}
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 5960326ec8df4f3596aacdcc7cf60ef14e138726..abdaa5d66f52446e5bcadb6d7e8fd99c09ef896b 100644
--- a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
+++ b/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
@@ -1,11 +1,14 @@
package ch.chuv.lren.mip.portal
+import eu.hbp.mip.model.Variable
import eu.hbp.mip.woken.messages.datasets.DatasetId
import eu.hbp.mip.woken.messages.query.filters.FilterRule
import eu.hbp.mip.woken.messages.query.filters.queryFiltersProtocol._
import org.springframework.stereotype.Component
import spray.json._
+import scala.collection.JavaConverters._
+
@Component
class WokenConversions {
@@ -14,9 +17,7 @@ class WokenConversions {
case _ => Some(json).map(_.parseJson.convertTo[FilterRule])
}
- def toDatasets(commaSeparatedSets: String): Set[DatasetId] = commaSeparatedSets match {
- case "" => Set()
- case _ => commaSeparatedSets.split(",").map(DatasetId).toSet
- }
+ def toDatasets(datasets: java.util.List[Variable]): Set[DatasetId] =
+ datasets.asScala.map(v => DatasetId(v.getCode)).toSet
}