Merge branch 'master' into Production

added new annotations

README.textile

@@ -0,0 +1,62 @@
+h1. EEGBase
+
+h2. An database portal specialized for EEG/ERP experiments
+
+h3. "http://eegdatabase.kiv.zcu.cz":http://eegdatabase.kiv.zcu.cz
+
+EEG Database enables community researchers to store, update, download and search data and metadata from EEG/ERP experiments. The system is developed as a standalone product; the database access is available through a web interface.
+
+h2. Technical Overview
+
+EEGBase as a web application uses modern web and database technologies:
+* SQL and NoSQL databases
+** PostgreSQL
+** Elasticsearch
+* Application
+** Spring MVC architecture
+** Hibernate JPA
+** Wicket framework
+* Web Server
+** Jetty
+
+h2. Getting Started
+* Prerequisites
+** Installed PostgreSQL v9.2 (http://www.postgresql.org/)
+** Installed Jetty 	web server and servlet container v7.5.0 (http://www.eclipse.org/jetty/)
+** Installed Java SE 6 JDK (http://www.oracle.com/technetwork/java/javase/downloads/index.html) 
+** Installed and "configured":https://github.com/INCF/eeg-database/wiki/Elasticsearch Elasticsearch v1.3 (http://www.elasticsearch.org/);
+** Installed your favourite IDE (Eclipse, Netbeans, IntelliJ etc.) with configured GIT
+* EEG Database
+** Create new database in PostgreSQL (default name is "eeg"); tables will be created automatically by Hibernate framework
+** Clone eegdatabase GITHub repository to local destination
+** Open eegdatabase Maven project in your IDE and let the Maven to download dependencies
+** Edit database accesses in @eeb-database/src/main/webapp/WEB-INF/db.properties.sample@ and save the file as @db.properties@
+** Set-up run and deployment configuration
+*** Select Jetty as a main deploying server
+*** Edit Jetty start up options; increase permanent generation memory size @-XX:MaxPermSize=256m@
+*** Set-up deployment artefacts
+** Set-up Java SE 6 JDK as a default project SDK
+* Frequent problems
+** Ensure you have set JAVA_HOME variable in system environment variables
+** Elasticsearch requires JAVA 7.
+** Jetty port (8080 by default) is occupied by another service application (e.g. Apache Tomcat, Glassfish).
+** db.properties file is not set properly.
+** DB user has not enough privileges to the database schema.
+
+h1. License
+
+<pre>
+This software is licensed under the Apache 2 license, quoted below.
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not 
+use this file except in compliance with the License. You may obtain a copy of 
+the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software 
+distributed under the License is distributed on an "AS IS" BASIS, WITHOUT 
+WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the 
+License for the specific language governing permissions and limitations under 
+the License.
+</pre>

src/main/java/cz/zcu/kiv/eegdatabase/data/dao/SimplePersonDao.java

@@ -171,10 +171,12 @@ public Map getInfoForAccountOverview(Person loggedPerson) {
 
     public boolean userNameInGroup(String userName, int groupId) {
         String hqlQuery = "select p.personId from Person p left join p.researchGroupMemberships rgm where p.username = :userName and rgm.researchGroup.researchGroupId = :groupId";
+        String ownerGroupQuery = "from ResearchGroup r where r.researchGroupId = :groupId and r.person.username = :userName";
         String[] paramNames = {"userName", "groupId"};
         Object[] values = {userName, groupId};
         List list = getHibernateTemplate().findByNamedParam(hqlQuery, paramNames, values);
-        return (list.size() > 0);
+        List ownerList = getHibernateTemplate().findByNamedParam(ownerGroupQuery, paramNames,values);
+        return (list.size() > 0 || ownerList.size() > 0);
     }
 
     public List<Person> getPersonSearchResults(List<SearchRequest> requests) throws NumberFormatException {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/Artifact.java

@@ -39,6 +39,7 @@
 /**
  * Artifact generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "ARTEFACT")
 public class Artifact implements java.io.Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/Digitization.java

@@ -37,6 +37,7 @@
 /**
  * Digitization generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "DIGITIZATION")
 public class Digitization implements Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/ElectrodeConf.java

@@ -38,6 +38,7 @@
 /**
  * ElectrodeConf generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "ELECTRODE_CONF")
 public class ElectrodeConf implements Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/ElectrodeSystem.java

@@ -41,6 +41,7 @@
 /**
  * ElectrodeSystem generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "ELECTRODE_SYSTEM")
 public class ElectrodeSystem implements Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/Person.java

@@ -53,6 +53,7 @@
 /**
  * Person generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "PERSON")
 public class Person implements Serializable, Comparable<Person>, IAutoCompletable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/ResearchGroup.java

@@ -47,6 +47,7 @@
 /**
  * ResearchGroup generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "RESEARCH_GROUP")
 public class ResearchGroup implements java.io.Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/Scenario.java

@@ -55,6 +55,7 @@
 /**
  * Scenario generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "SCENARIO")
 @XmlRootElement

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/SubjectGroup.java

@@ -44,6 +44,7 @@
 /**
  * SubjectGroup generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "SUBJECT_GROUP")
 public class SubjectGroup implements java.io.Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/data/pojo/Weather.java

@@ -47,6 +47,7 @@
 /**
  * Weather generated by hbm2java
  */
+@Form
 @Entity
 @Table(name = "WEATHER")
 public class Weather implements java.io.Serializable {

src/main/java/cz/zcu/kiv/eegdatabase/wui/core/group/ResearchGroupServiceImpl.java

@@ -302,6 +302,10 @@ public List<ResearchGroup> getUnique(ResearchGroup example) {
     @Override
     @Transactional
     public ResearchGroupMembershipId createMemberhip(ResearchGroupMembership newInstance) {
+        if (newInstance.getId() == null) {
+            ResearchGroupMembershipId id = new ResearchGroupMembershipId(newInstance.getPerson().getPersonId(), newInstance.getResearchGroup().getResearchGroupId());
+            newInstance.setId(id);
+        }
         return membershipDao.create(newInstance);
     }
 

src/test/java/cz/zcu/kiv/eegdatabase/services/ArtifactServiceTest.java

@@ -0,0 +1,97 @@
+/*******************************************************************************
+ * This file is part of the EEG-database project
+ *
+ * ==========================================
+ *
+ * Copyright (C) 2013 by University of West Bohemia (http://www.zcu.cz/en/)
+ *
+ * ***********************************************************************************************************************
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
+ * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ *
+ * ***********************************************************************************************************************
+ *
+ * ArtifactServiceTest.java, 2014/08/10 00:01 Jan Stebetak
+ ******************************************************************************/
+package cz.zcu.kiv.eegdatabase.services;
+
+import cz.zcu.kiv.eegdatabase.data.TestUtils;
+import cz.zcu.kiv.eegdatabase.data.dao.PersonDao;
+import cz.zcu.kiv.eegdatabase.data.dao.ResearchGroupDao;
+import cz.zcu.kiv.eegdatabase.data.pojo.Artifact;
+import cz.zcu.kiv.eegdatabase.data.pojo.Person;
+import cz.zcu.kiv.eegdatabase.data.pojo.ResearchGroup;
+import cz.zcu.kiv.eegdatabase.logic.Util;
+import cz.zcu.kiv.eegdatabase.wui.core.common.ArtifactService;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by Honza on 10.8.14.
+ */
+@Transactional
+public class ArtifactServiceTest extends AbstractServicesTest {
+
+    @Autowired
+    private ArtifactService artifactService;
+
+    @Autowired
+    private ResearchGroupDao researchGroupDao;
+    @Autowired
+    private PersonDao personDao;
+    private Artifact artifact;
+    private ResearchGroup researchGroup;
+
+    @Before
+    public void setUp() throws Exception {
+        Person person = TestUtils.createPersonForTesting("test@test.com", Util.ROLE_ADMIN);
+
+        personDao.create(person);
+
+        researchGroup = new ResearchGroup();
+        researchGroup.setDescription("test-description");
+        researchGroup.setTitle("test-title");
+        researchGroup.setPerson(person);
+        researchGroupDao.create(researchGroup);
+        artifact = new Artifact();
+        artifact.setCompensation("test comp");
+        artifact.setRejectCondition("test condition");
+    }
+
+    @Test
+    public void testCreateArtifact() {
+        int artifactCountBefore = artifactService.getAllRecords().size();
+        int id = artifactService.create(artifact);
+        assertEquals(artifactCountBefore + 1, artifactService.getAllRecords().size());
+        assertEquals(id, artifact.getArtifactId());
+    }
+
+
+    @Test
+    public void testCreateArtifactGroupRel() {
+        int artifactCountBefore = artifactService.getAllRecords().size();
+        int artifactGroupBefore = artifactService.getRecordsByGroup(researchGroup.getResearchGroupId()).size();
+        int id = artifactService.create(artifact);
+        assertEquals(artifactCountBefore + 1, artifactService.getAllRecords().size());
+
+        List<Artifact> list = artifactService.getRecordsByGroup(researchGroup.getResearchGroupId());
+        assertEquals(artifactGroupBefore, list.size());
+        assertFalse(artifactService.hasGroupRel(id));
+    }
+
+}

src/test/java/cz/zcu/kiv/eegdatabase/services/DiseaseServiceTest.java

@@ -0,0 +1,111 @@
+/*******************************************************************************
+ * This file is part of the EEG-database project
+ *
+ * ==========================================
+ *
+ * Copyright (C) 2013 by University of West Bohemia (http://www.zcu.cz/en/)
+ *
+ * ***********************************************************************************************************************
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
+ * the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
+ * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations under the License.
+ *
+ * ***********************************************************************************************************************
+ *
+ * DiseaseServiceTest.java, 2014/08/08 00:01 Jan Stebetak
+ ******************************************************************************/
+package cz.zcu.kiv.eegdatabase.services;
+
+import cz.zcu.kiv.eegdatabase.data.TestUtils;
+import cz.zcu.kiv.eegdatabase.data.dao.PersonDao;
+import cz.zcu.kiv.eegdatabase.data.dao.ResearchGroupDao;
+import cz.zcu.kiv.eegdatabase.data.pojo.Disease;
+import cz.zcu.kiv.eegdatabase.data.pojo.Person;
+import cz.zcu.kiv.eegdatabase.data.pojo.ResearchGroup;
+import cz.zcu.kiv.eegdatabase.logic.Util;
+import cz.zcu.kiv.eegdatabase.wui.core.common.DiseaseService;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+/**
+ * Created by Honza on 8.8.14.
+ */
+@Transactional
+public class DiseaseServiceTest extends AbstractServicesTest {
+
+    @Autowired
+    private DiseaseService diseaseService;
+
+    @Autowired
+    private ResearchGroupDao researchGroupDao;
+    @Autowired
+    private PersonDao personDao;
+    private Disease disease;
+    private ResearchGroup researchGroup;
+
+    @Before
+    public void setUp() throws Exception {
+        Person person = TestUtils.createPersonForTesting("test@test.com", Util.ROLE_ADMIN);
+
+        personDao.create(person);
+
+        researchGroup = new ResearchGroup();
+        researchGroup.setDescription("test-description");
+        researchGroup.setTitle("test-title");
+        researchGroup.setPerson(person);
+        researchGroupDao.create(researchGroup);
+        disease = createDisease("new Disease");
+    }
+
+    @Test
+    public void testCreateDisease() {
+        int diseaseCountBefore = diseaseService.getAllRecords().size();
+        int diseaseID = diseaseService.create(disease);
+        assertEquals(diseaseCountBefore + 1, diseaseService.getAllRecords().size());
+        assertEquals(diseaseID, disease.getDiseaseId());
+    }
+
+
+    @Test
+    public void testCreateDiseaseGroupRel() {
+        int diseaseCountBefore = diseaseService.getAllRecords().size();
+        int diseaseGroupBefore = diseaseService.getRecordsByGroup(researchGroup.getResearchGroupId()).size();
+        diseaseService.createGroupRel(disease, researchGroup);
+        int id = diseaseService.create(disease);
+        assertEquals(diseaseCountBefore + 1, diseaseService.getAllRecords().size());
+
+        List<Disease> list = diseaseService.getRecordsByGroup(researchGroup.getResearchGroupId());
+        assertEquals(diseaseGroupBefore + 1, list.size());
+        assertTrue(diseaseService.hasGroupRel(id));
+    }
+
+
+    @Test
+    public void testCanSaveTitle() {
+        diseaseService.createGroupRel(disease, researchGroup);
+        int id = diseaseService.create(disease);
+        assertTrue(diseaseService.canSaveTitle(disease.getTitle(), researchGroup.getResearchGroupId(), id));
+        assertFalse(diseaseService.canSaveTitle(disease.getTitle(), researchGroup.getResearchGroupId(), -1));
+    }
+
+    private Disease createDisease(String title) {
+        Disease newDisease = new Disease();
+        newDisease.setTitle(title);
+        newDisease.setDescription("This is new testing Disease");
+        return newDisease;
+    }
+}