diff --git a/src/main/java/eu/hbp/mip/MIPApplication.java b/src/main/java/eu/hbp/mip/MIPApplication.java
index 489fe56d50708eb98a1d1da7c7bef7121b0ee0c4..df70ba78a5ba397676f1ad1533895e86a67c4f89 100644
--- a/src/main/java/eu/hbp/mip/MIPApplication.java
+++ b/src/main/java/eu/hbp/mip/MIPApplication.java
@@ -4,7 +4,6 @@
package eu.hbp.mip;
-import ch.chuv.lren.mip.portal.Reporting;
import org.springframework.boot.SpringApplication;
import org.springframework.boot.autoconfigure.SpringBootApplication;
@@ -12,7 +11,6 @@ import org.springframework.boot.autoconfigure.SpringBootApplication;
public class MIPApplication {
public static void main(String[] args) {
- new Reporting().init();
SpringApplication.run(MIPApplication.class, args);
}
diff --git a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
index f48d4d8e268848275a9343a1b4eaf990fbe25da0..40a2f064f795a1b21814ed815ceef315eb46fad7 100644
--- a/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ExperimentApi.java
@@ -1,7 +1,6 @@
package eu.hbp.mip.controllers;
import akka.dispatch.OnSuccess;
-import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.gson.*;
import com.google.common.collect.Lists;
import com.google.gson.Gson;
diff --git a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
index 6f6e7745459889f8467d6f0013ba11426f585498..3ac19450cccf0b5b709d3380a9c87443659e4f5c 100644
--- a/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/ModelsApi.java
@@ -4,7 +4,6 @@
package eu.hbp.mip.controllers;
-import ch.chuv.lren.mip.portal.WokenConversions;
import ch.chuv.lren.woken.messages.query.filters.FilterRule;
import com.github.slugify.Slugify;
import com.google.gson.Gson;
@@ -293,17 +292,17 @@ public class ModelsApi {
allVars.addAll(model.getDataset().getHeader());
allVars.addAll(model.getDataset().getGrouping());
- WokenConversions conv = new WokenConversions();
- String filtersJson = model.getQuery().getFilters();
- Option<FilterRule> filters = conv.toFilterRule(filtersJson);
- String filtersSQL = conv.toSqlWhere(filters);
+ // WokenConversions conv = new WokenConversions();
+ // String filtersJson = model.getQuery().getFilters();
+ // Option<FilterRule> filters = conv.toFilterRule(filtersJson);
+ // String filtersSQL = conv.toSqlWhere(filters);
- Gson gson = new Gson();
- JsonObject jsonModel = gson.fromJson(gson.toJson(model, Model.class), JsonObject.class);
- jsonModel.get("dataset").getAsJsonObject()
- .add("data", dataUtil.getDataFromVariables(allVars, filtersSQL));
+ // Gson gson = new Gson();
+ // JsonObject jsonModel = gson.fromJson(gson.toJson(model, Model.class), JsonObject.class);
+ // jsonModel.get("dataset").getAsJsonObject()
+ // .add("data", dataUtil.getDataFromVariables(allVars, filtersSQL));
- return gson.fromJson(jsonModel, Model.class);
+ return model; //gson.fromJson(jsonModel, Model.class);
}
}
diff --git a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
index e41afded17f4779e0b41516e3ab8b796124a43b3..0eae7e7cf5bfcd84f75505f7d9dfb2f0596d6469 100644
--- a/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
+++ b/src/main/java/eu/hbp/mip/controllers/VariablesApi.java
@@ -5,7 +5,6 @@
package eu.hbp.mip.controllers;
-import ch.chuv.lren.mip.portal.WokenConversions;
import ch.chuv.lren.woken.messages.variables.VariableMetaData;
import ch.chuv.lren.woken.messages.variables.VariablesForDatasetsQuery;
import ch.chuv.lren.woken.messages.variables.VariablesForDatasetsResponse;
diff --git a/src/main/java/eu/hbp/mip/model/Experiment.java b/src/main/java/eu/hbp/mip/model/Experiment.java
index e2def32c37b446fde76ca609792569036b8b22e6..7149063be3968c4cda72a9e6fa6f69d868131afb 100644
--- a/src/main/java/eu/hbp/mip/model/Experiment.java
+++ b/src/main/java/eu/hbp/mip/model/Experiment.java
@@ -1,6 +1,5 @@
package eu.hbp.mip.model;
-import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.gson.*;
import com.google.gson.annotations.Expose;
import com.google.gson.reflect.TypeToken;
@@ -88,47 +87,6 @@ public class Experiment {
*/
}
- public ExperimentQuery prepareQuery(String user) {
- if (model == null || model.getQuery() == null)
- return new ExperimentQuery(null, null, null, false,null, null, Option.empty(), null, null, null, null, null, null);
-
- List<AlgorithmSpec> algorithms = new LinkedList<>();
- Type algoList = new TypeToken<LinkedList<eu.hbp.mip.model.Algorithm>>(){}.getType();
- List<eu.hbp.mip.model.Algorithm> algos = new Gson().fromJson(this.algorithms, algoList);
- for (eu.hbp.mip.model.Algorithm a: algos) {
- algorithms.add(new AlgorithmSpec(a.getCode(), TypesConvert.algoParamsToScala(a.getParameters()), Option.empty()));
- }
-
- List<ValidationSpec> validations = new LinkedList<>();
- Type validList = new TypeToken<LinkedList<eu.hbp.mip.model.ExperimentValidator>>(){}.getType();
- List<eu.hbp.mip.model.ExperimentValidator> valids = new Gson().fromJson(this.validations, validList);
- for (ExperimentValidator v: valids) {
- validations.add(new ValidationSpec(v.getCode(), TypesConvert.algoParamsToScala(v.getParameters())));
- }
-
- scala.collection.immutable.List<FeatureIdentifier> variablesSeq =
- TypesConvert.variablesToIdentifiers(model.getQuery().getVariables());
- scala.collection.immutable.List<FeatureIdentifier> covariablesSeq =
- TypesConvert.variablesToIdentifiers(model.getQuery().getCovariables());
- scala.collection.immutable.List<FeatureIdentifier> groupingSeq =
- TypesConvert.variablesToIdentifiers(model.getQuery().getGrouping());
- scala.collection.immutable.List<AlgorithmSpec> algorithmsSeq = JavaConversions.asScalaBuffer(algorithms).toList();
- scala.collection.immutable.List<ValidationSpec> validationsSeq = JavaConversions.asScalaBuffer(validations).toList();
-
- WokenConversions conv = new WokenConversions();
- scala.collection.immutable.SortedSet<DatasetId> trainingDatasets = conv.toDatasets(model.getQuery().getTrainingDatasets());
- scala.collection.immutable.SortedSet<DatasetId> testingDatasets = conv.toDatasets(model.getQuery().getTestingDatasets());
- scala.collection.immutable.SortedSet<DatasetId> validationDatasets = conv.toDatasets(model.getQuery().getValidationDatasets());
-
- String filtersJson = model.getQuery().getFilters();
- Option<FilterRule> filters = conv.toFilterRule(filtersJson);
- UserId userId = new UserId(user);
-
- // TODO: covariablesMustExist argument should be set from a user intention? Or maybe automatically selected based on the list of algorithms???
- return new ExperimentQuery(userId, variablesSeq, covariablesSeq, false, groupingSeq, filters, Option.empty(),
- trainingDatasets, testingDatasets, algorithmsSeq, validationDatasets,
- validationsSeq, Option.empty());
- }
public JsonObject jsonify() {
JsonObject exp = gson.toJsonTree(this).getAsJsonObject();
diff --git a/src/main/java/eu/hbp/mip/model/MiningQuery.java b/src/main/java/eu/hbp/mip/model/MiningQuery.java
index 016899377030f8fb767d22083d338aa98ff8a509..cf33a4ecb04a833a093b453ae6b8c3a0f30794b3 100644
--- a/src/main/java/eu/hbp/mip/model/MiningQuery.java
+++ b/src/main/java/eu/hbp/mip/model/MiningQuery.java
@@ -1,6 +1,5 @@
package eu.hbp.mip.model;
-import ch.chuv.lren.mip.portal.WokenConversions;
import com.google.gson.Gson;
import eu.hbp.mip.utils.TypesConvert;
import ch.chuv.lren.woken.messages.datasets.DatasetId;
@@ -87,28 +86,6 @@ public class MiningQuery {
this.algorithm = algorithm;
}
- public ch.chuv.lren.woken.messages.query.MiningQuery prepareQuery(String user) {
-
- ch.chuv.lren.woken.messages.query.AlgorithmSpec scalaAlgorithm = new ch.chuv.lren.woken.messages.query.AlgorithmSpec(
- algorithm.getCode(), TypesConvert.algoParamsToScala(algorithm.getParameters()), Option.empty());
-
- scala.collection.immutable.List<FeatureIdentifier> variablesSeq =
- TypesConvert.variablesToIdentifiers(getVariables());
- scala.collection.immutable.List<FeatureIdentifier> covariablesSeq =
- TypesConvert.variablesToIdentifiers(getCovariables());
- scala.collection.immutable.List<FeatureIdentifier> groupingSeq =
- TypesConvert.variablesToIdentifiers(getGrouping());
- UserId userId = new UserId(user);
-
- WokenConversions conv = new WokenConversions();
- scala.collection.immutable.SortedSet<DatasetId> datasets = conv.toDatasets(getDatasets());
- String filtersJson = getFilters();
- Option<FilterRule> filters = conv.toFilterRule(filtersJson);
-
- return new ch.chuv.lren.woken.messages.query.MiningQuery(userId,
- variablesSeq, covariablesSeq, true, groupingSeq, filters, Option.empty(), datasets, scalaAlgorithm, Option.empty());
- }
-
@Override
public String toString() {
return new Gson().toJson(this);
diff --git a/src/main/scala/ch.chuv.lren/mip/portal/Reporting.scala b/src/main/scala/ch.chuv.lren/mip/portal/Reporting.scala
deleted file mode 100644
index e14987957ec6e1f0876b463f3a5b9e1d0f635002..0000000000000000000000000000000000000000
--- a/src/main/scala/ch.chuv.lren/mip/portal/Reporting.scala
+++ /dev/null
@@ -1,11 +0,0 @@
-package ch.chuv.lren.mip.portal
-
-import ch.chuv.lren.woken.errors._
-
-class Reporting {
-
- def init(): Unit = {
- reportErrorsToBugsnag()
- }
-
-}
diff --git a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala b/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
deleted file mode 100644
index 6abe7b362661e997730feae6a0790785ca13784e..0000000000000000000000000000000000000000
--- a/src/main/scala/ch.chuv.lren/mip/portal/WokenConversions.scala
+++ /dev/null
@@ -1,30 +0,0 @@
-package ch.chuv.lren.mip.portal
-
-import eu.hbp.mip.model.Variable
-import ch.chuv.lren.woken.messages.datasets.DatasetId
-import ch.chuv.lren.woken.messages.query.QueryResult
-import ch.chuv.lren.woken.messages.query.filters.FilterRule
-import ch.chuv.lren.woken.messages.query.filters.FilterRule._
-import ch.chuv.lren.woken.messages.query.queryProtocol._
-import org.springframework.stereotype.Component
-import spray.json._
-
-import scala.collection.JavaConverters._
-import scala.collection.immutable.{SortedSet, TreeSet}
-
-@Component
-class WokenConversions {
-
- def toFilterRule(json: String): Option[FilterRule] = json match {
- case "" => None
- case _ => Some(json).map(_.parseJson.convertTo[FilterRule])
- }
-
- def toDatasets(datasets: java.util.List[Variable]): SortedSet[DatasetId] =
- datasets.asScala.map(v => DatasetId(v.getCode)).toSet.to[TreeSet]
-
- def toSqlWhere(filter: Option[FilterRule]): String = filter.fold("")(_.toSqlWhere)
-
- def toJson(result: QueryResult): String =
- result.toJson.compactPrint
-}