Merge pull request #20 from qbicsoftware/hotfix/mysql-connector

Hotfix/mysql connector

Author: sven1103

.travis.yml

@@ -18,6 +18,9 @@ branches:
   only:
   - master
   - development
+  - /^release\/.*$/
+  - /^hotfix\/.*$/
+  - /^[vV]?\d+\.\d+\.\d+$/ # matches e.g., v1.2.3, 1.2.3, V1.2.3
 
 # added to make logs look cleaner, crisper, certified fresh
 before_install: unset _JAVA_OPTIONS 

pom.xml

@@ -6,13 +6,17 @@
 	<parent>
 		<groupId>life.qbic</groupId>
 		<artifactId>portlet-parent-pom</artifactId>
-		<version>1.4.0</version>
+		<version>3.1.0</version>
 	</parent>
 	<artifactId>user-db-portlet</artifactId>
-	<version>1.8.0</version>
+	<version>1.8.1</version>
 	<name>User Database Portlet</name>
 	<url>http://github.com/qbicsoftware/user-db-portlet</url>
 	<packaging>war</packaging>
+	<properties>
+		<vaadin.version>7.7.8</vaadin.version>
+		<vaadin.plugin.version>7.7.8</vaadin.plugin.version>
+	</properties>
 	<!-- we only need to tell maven where to find our parent pom and other QBiC 
 		dependencies -->
 	<repositories>
@@ -27,7 +31,7 @@
 			</snapshots>
 			<id>nexus-snapshots</id>
 			<name>QBiC Snapshots</name>
-			<url>https://qbic-repo.am10.uni-tuebingen.de/repository/maven-snapshots</url>
+			<url>http://qbic-repo.qbic.uni-tuebingen.de:8081/repository/maven-snapshots</url>
 		</repository>
 		<repository>
 			<releases>
@@ -40,7 +44,7 @@
 			</snapshots>
 			<id>nexus-releases</id>
 			<name>QBiC Releases</name>
-			<url>https://qbic-repo.am10.uni-tuebingen.de/repository/maven-releases</url>
+			<url>http://qbic-repo.qbic.uni-tuebingen.de:8081/repository/maven-releases</url>
 		</repository>
 	</repositories>
 	<!-- To avoid inconsistencies across projects, plase check which librares 
@@ -52,22 +56,22 @@
 		<dependency>
 			<groupId>life.qbic</groupId>
 			<artifactId>portal-utils-lib</artifactId>
-			<version>1.6.0</version>
+			<version>2.2.1</version>
 		</dependency>
 		<dependency>
 			<groupId>life.qbic</groupId>
 			<artifactId>core-utils-lib</artifactId>
-			<version>1.2.1</version>
+			<version>1.7.0</version>
 		</dependency>
 		<dependency>
 			<groupId>life.qbic</groupId>
 			<artifactId>openbis-client-lib</artifactId>
-			<version>1.1.4</version>
+			<version>1.4.0</version>
 		</dependency>
 		<dependency>
 			<groupId>life.qbic</groupId>
 			<artifactId>data-model-lib</artifactId>
-			<version>1.3.0</version>
+			<version>1.11.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.mariadb.jdbc</groupId>

src/main/java/life/qbic/portal/portlet/UserDBPortletUI.java

@@ -4,6 +4,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;
@@ -26,10 +27,10 @@
 import com.vaadin.ui.Layout;
 import com.vaadin.ui.TabSheet;
 import com.vaadin.ui.VerticalLayout;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
 import com.vaadin.ui.Button.ClickEvent;
 import com.vaadin.ui.Button.ClickListener;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
 import life.qbic.datamodel.persons.Affiliation;
 import life.qbic.datamodel.persons.CollaboratorWithResponsibility;
 import life.qbic.datamodel.persons.Person;
@@ -213,19 +214,25 @@ private void initTabs() {
       }
       Map<String, ProjectInfo> userProjects = new HashMap<String, ProjectInfo>();
 
-      List<Project> openbisProjects = new ArrayList<Project>();
+      List<Project> openbisProjectsForUser = new ArrayList<Project>();
+      Set<String> spaces = new HashSet<>(openbis.getUserSpaces(userID));
 
-      openbisProjects = openbis.getOpenbisInfoService()
-          .listProjectsOnBehalfOfUser(openbis.getSessionToken(), userID);
+      List<Project> allOpenbisProjects = openbis.listProjects();
+      for (Project p : allOpenbisProjects) {
+        String space = p.getSpace().getCode();
+        if (spaces.contains(space)) {
+          openbisProjectsForUser.add(p);
+        }
+      }
 
       Map<String, ProjectInfo> dbProjects = dbControl.getProjectMap();
-      for (Project p : openbisProjects) {
+      for (Project p : openbisProjectsForUser) {
         String desc = Objects.toString(p.getDescription(), "");
         desc = desc.replaceAll("\n+", ". ");
-        String projectID = p.getIdentifier();
+        String projectID = p.getIdentifier().getIdentifier();
         String code = p.getCode();
         if (dbProjects.get(projectID) == null)
-          userProjects.put(projectID, new ProjectInfo(p.getSpaceCode(), code, desc, "", -1));
+          userProjects.put(projectID, new ProjectInfo(p.getSpace().getCode(), code, desc, "", -1));
         else {
           ProjectInfo info = dbProjects.get(projectID);
           info.setDescription(desc);
@@ -253,8 +260,7 @@ private Map<String, Integer> fillMaxInputLengthMap() {
       res.putAll(dbControl.getColsMaxLengthsForTable("persons"));
       res.putAll(dbControl.getColsMaxLengthsForTable("organizations"));
     } catch (SQLException e) {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
+      logger.error(e.toString());
     }
     return res;
   }
@@ -271,8 +277,8 @@ private boolean canUsePortlet() {
         }
       }
     } catch (Exception e) {
-      e.printStackTrace();
       logger.error("Could not fetch user groups. User won't be able to use portlet.");
+      logger.error(e.toString());
     }
     return false;
   }
@@ -292,8 +298,8 @@ private boolean isAdmin() {
           }
         }
       } catch (Exception e) {
-        e.printStackTrace();
         logger.error("Could not fetch user groups. User won't be able to use portlet.");
+        logger.error(e.toString());
       }
       return false;
     }
@@ -361,9 +367,9 @@ public void valueChange(ValueChangeEvent event) {
               dbControl.getCollaboratorsOfProject(project);
           // get openbis experiments and type
           Map<String, String> existingExps = new HashMap<String, String>();
-          for (Experiment e : openbis.getExperimentsForProject2(project)) {
-            String type = expTypeCodeTranslation.get(e.getExperimentTypeCode());
-            String id = e.getIdentifier();
+          for (Experiment e : openbis.getExperimentsOfProjectByCode(project)) {
+            String type = expTypeCodeTranslation.get(e.getType().getCode());
+            String id = e.getIdentifier().getIdentifier();
             if (type != null)
               existingExps.put(id, type);
           }
@@ -613,8 +619,7 @@ private void successfulCommit() {
     try {
       Thread.sleep(1000);
     } catch (InterruptedException e) {
-      // TODO Auto-generated catch block
-      e.printStackTrace();
+      logger.error(e.toString());
     }
     initTabs();
   }

src/main/java/life/qbic/userdb/views/PersonInput.java

@@ -17,7 +17,6 @@
 
 import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import com.vaadin.data.Property.ValueChangeEvent;
 import com.vaadin.data.Property.ValueChangeListener;
 import com.vaadin.data.Validator;
@@ -33,11 +32,9 @@
 import com.vaadin.ui.HorizontalLayout;
 import com.vaadin.ui.TextField;
 import com.vaadin.ui.themes.ValoTheme;
-import ch.systemsx.cisd.common.collection.RegExValidator;
 import life.qbic.datamodel.persons.Affiliation;
 import life.qbic.datamodel.persons.Person;
 import life.qbic.portal.Styles;
-import life.qbic.userdb.helpers.EmailFreeValidator;
 import life.qbic.userdb.helpers.RegExHelper;
 
 public class PersonInput extends HorizontalLayout {

src/main/java/life/qbic/userdb/views/ProjectView.java

@@ -41,7 +41,6 @@
 import com.vaadin.ui.TextField;
 import com.vaadin.ui.VerticalLayout;
 import com.vaadin.ui.themes.ValoTheme;
-import ch.systemsx.cisd.common.concurrent.TimerUtilities;
 import life.qbic.datamodel.identifiers.SampleCodeFunctions;
 import life.qbic.datamodel.persons.Affiliation;
 import life.qbic.datamodel.persons.CollaboratorWithResponsibility;