Merge branch '921-progress-bar-during-adding-removing-project' into 'master'

Resolve "progress bar during adding/removing project"

Closes #921

See merge request !1432

CHANGELOG

 minerva (16.1.0~alpha.0) stable; urgency=medium
   * Improvement: possibility to register map in minerva-net (#1595)
-  * Small improvement: export to image allows to define size of the image (#955)
+  * Small improvement: export to image allows to define size of the image
+    (#955)
+  * Small improvement: progress bar on project upload changed into more verbose
+    statements (#921)
   * Small improvement: AVOGADRO unit type from SBML is parsed properly (#1612)
   * Small improvement: data overlays have automatically generated legend (#205,
     #1061)

annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java

@@ -38,6 +38,7 @@ import lcsb.mapviewer.model.user.annotator.AnnotatorConfigParameter;
 import lcsb.mapviewer.model.user.annotator.AnnotatorData;
 import lcsb.mapviewer.modelutils.map.ClassTreeNode;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.persist.dao.user.UserAnnotationSchemaDao;
 
 /**
  * This class annotates all elements in the model.
@@ -77,13 +78,17 @@ public class ModelAnnotator {
    */
   private List<IElementAnnotator> defaultAnnotators;
 
+  private UserAnnotationSchemaDao userAnnotationSchemaDao;
+
   /**
    * Constructor
    */
   @Autowired
-  public ModelAnnotator(final MiriamConnector miriamConnector, final List<IElementAnnotator> availableAnnotators) {
+  public ModelAnnotator(final MiriamConnector miriamConnector, final List<IElementAnnotator> availableAnnotators,
+      final UserAnnotationSchemaDao userAnnotationSchemaDao) {
     this.miriamConnector = miriamConnector;
     this.availableAnnotators = availableAnnotators;
+    this.userAnnotationSchemaDao = userAnnotationSchemaDao;
     defaultAnnotators = new ArrayList<>();
     for (final IElementAnnotator annotator : availableAnnotators) {
       if (annotator.isDefault()) {
@@ -107,7 +112,7 @@ public class ModelAnnotator {
   /**
    * Performs all possible and automatic annotations on the model.
    * 
-   * @param annotationSchema
+   * @param inputAnnotationSchema
    *          information about {@link ElementAnnotator} objects that should be
    *          used for a given classes
    * @param model
@@ -115,8 +120,12 @@ public class ModelAnnotator {
    * @param progressUpdater
    *          callback function used for updating progress of the function
    */
-  public void performAnnotations(final Model model, final IProgressUpdater progressUpdater,
-      final UserAnnotationSchema annotationSchema) {
+  public void performAnnotations(final Model model, final IProgressUpdater progressUpdater, final UserAnnotationSchema inputAnnotationSchema) {
+
+    UserAnnotationSchema annotationSchema = inputAnnotationSchema;
+    if (annotationSchema != null && annotationSchema.getId() > 0) {
+      annotationSchema = userAnnotationSchemaDao.getById(annotationSchema.getId());
+    }
 
     progressUpdater.setProgress(0);
     List<Model> models = new ArrayList<>();

frontend-js/src/main/js/gui/admin/MapsAdminPanel.js

@@ -264,7 +264,7 @@ MapsAdminPanel.prototype._createProjectTableRow = function () {
     } else {
       promise = self.getServerConnector().unregisterProjectInMinervaNet(projectId);
     }
-    return Promise.resolve(promise).catch(GuiConnector.alert).finally(function(){
+    return Promise.resolve(promise).catch(GuiConnector.alert).finally(function () {
       GuiConnector.hideProcessing();
       return self.getServerConnector().getProject(projectId);
     })
@@ -357,7 +357,35 @@ MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
   }
   var status = project.getStatus();
   if (project.getStatus().toLowerCase() !== "ok" && project.getStatus().toLowerCase() !== "failure") {
-    status += ' (' + project.getProgress().toFixed(2) + ' %)';
+    var step;
+    if (status === "Parsing data") {
+      step = 1;
+    } else if (status === "Uploading to db") {
+      step = 2;
+    } else if (status === "Annotating") {
+      step = 3;
+    } else if (status === "Generating images") {
+      step = 4;
+    } else if (status === "Validating miriam data") {
+      step = 5;
+    } else if (status === "Caching pubmed data") {
+      step = 6;
+    } else if (status === "Caching miriam data") {
+      step = 7;
+    } else if (status === "Caching chemical data") {
+      step = 8;
+    } else if (status === "Caching drug data") {
+      step = 9;
+    } else if (status === "Caching miRNA data") {
+      step = 10;
+    } else if (status === "Project removing") {
+      status = "Removing project, please wait";
+    } else {
+      status += ' (' + project.getProgress().toFixed(2) + ' %)';
+    }
+    if (step !== undefined) {
+      status += " step " + step + " ( of 10)";
+    }
   }
 
   var isAdmin = user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.IS_ADMIN)) ||

model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java

@@ -58,7 +58,7 @@ public class UserAnnotationSchema implements Serializable {
    */
   @Id
   @GeneratedValue(strategy = GenerationType.IDENTITY)
-  private Integer id;
+  private int id;
 
   /**
    * {@link User} for which annotation schema is defined.
@@ -187,8 +187,8 @@ public class UserAnnotationSchema implements Serializable {
   }
 
   /**
-   * Adds (or updates) {@link UserClassAnnotators class annotator} information to
-   * {@link #classAnnotators}.
+   * Adds (or updates) {@link UserClassAnnotators class annotator} information
+   * to {@link #classAnnotators}.
    * 
    * @param ca
    *          object to add/update

persist/src/main/java/lcsb/mapviewer/persist/dao/user/UserAnnotationSchemaDao.java

+package lcsb.mapviewer.persist.dao.user;
+
+import org.springframework.stereotype.Repository;
+
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.persist.dao.BaseDao;
+
+@Repository
+public class UserAnnotationSchemaDao extends BaseDao<UserAnnotationSchema> {
+
+  public UserAnnotationSchemaDao() {
+    super(UserAnnotationSchema.class);
+  }
+}