data mining is not processed during project upload

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.
    * 

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();