diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 5962090f74f78857c05f67ba9e901b9e20305c10..31a6e60666439467deb16631989ca8fc4191b7d7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -63,15 +63,11 @@ import lcsb.mapviewer.model.log.LogType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.graph.DataMining;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.LayoutStatus;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
@@ -103,7 +99,6 @@ import lcsb.mapviewer.services.search.db.drug.IDrugService;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.utils.InvalidDataMiningInputFile;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
/**
@@ -123,16 +118,6 @@ public class ProjectService implements IProjectService {
*/
private static final int OUT_OF_MEMORY_BACKUP_BUFFER_SIZE = 10000;
- /**
- * How much time (out of 1.00) is used for creation of the data from file.
- */
- private static final double CREATION_OF_DATA = 0.50;
-
- /**
- * How much time (out of 1.00) is used for uploading of the data from file.
- */
- private static final double UPLOAD_OF_DATA = 0.50;
-
/**
* Default class logger.
*/
@@ -737,72 +722,10 @@ public class ProjectService implements IProjectService {
}, annotators, params.getAnnotatorsParamsAsMap());
logger.debug("Annotations updated");
}
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, 0.0, params);
- processDataMining(topModel, topModel.getDataMiningSets(), new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, progress, params);
- }
-
- });
- updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, IProgressUpdater.MAX_PROGRESS, params);
logger.debug("Model created");
}
- /**
- * Process data mining files and assign suggested connections to the model.
- *
- * @param model
- * model where the suggested connections will be added
- * @param dataMiningSets
- * set of files to process
- * @param progressUpdater
- * callback function informing higher layer about progress
- * @throws InvalidDataMiningInputFile
- * thrown when one of the files is invalid
- */
- private void processDataMining(Model model, List<DataMiningSet> dataMiningSets,
- final IProgressUpdater progressUpdater) throws InvalidDataMiningInputFile {
- Set<Element> nodes = new HashSet<>();
- nodes.addAll(model.getElements());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- nodes.addAll(connection.getSubmodel().getElements());
- }
- Set<Reaction> reactions = new HashSet<Reaction>();
- reactions.addAll(model.getReactions());
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- reactions.addAll(connection.getSubmodel().getReactions());
- }
-
- int fileCounter = 0;
- final int filesCount = dataMiningSets.size();
- for (DataMiningSet dmSet : dataMiningSets) {
-
- final double offset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount;
- IProgressUpdater secondPartUpdater = new IProgressUpdater() {
-
- @Override
- public void setProgress(double progress) {
- progressUpdater.setProgress((progress * CREATION_OF_DATA) / ((double) filesCount) + offset);
- }
- };
- Set<DataMining> result = dataMiningService.parseData(dmSet, nodes, reactions, secondPartUpdater);
- double size = result.size();
- double count = 0;
-
- double updateOffset = IProgressUpdater.MAX_PROGRESS * fileCounter / filesCount
- + CREATION_OF_DATA / ((double) filesCount);
- for (DataMining missingConnection : result) {
- missingConnection.setType(dmSet.getType());
- missingConnection.getElement().addDataMining(missingConnection);
- count++;
- progressUpdater.setProgress(updateOffset + IProgressUpdater.MAX_PROGRESS * count / size * UPLOAD_OF_DATA);
- }
- }
- }
-
/**
* Updates status of the generating project.
*
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index a2df3103ff7b7ddb87c133e239c1777945e42e6f..2e07d435d48f1d608aef1c3065e27d45de805b81 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -571,33 +571,6 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
- @Test
- public void testCreateComplexWithDataMining() throws Exception {
- String name = "Some_id";
- try {
- String filename = "testFiles/complexModel/complex_model_with_data_mining.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- boolean dmFound = false;
- for (Element element : model.getElements()) {
- if (element.getDataMining().size() > 0) {
- dmFound = true;
- }
- }
- assertTrue("Cannot find data mining information for the model", dmFound);
- projectService.removeProject(project, null, false, adminToken);
- String token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
- assertNull(projectService.getProjectByProjectId(name, token));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
protected Project createComplexProject(String projectId, String filename) throws IOException, SecurityException {
CreateProjectParams params = new CreateProjectParams();