LibreClinica-odm module as a part of parent build process

.gitignore

@@ -1,4 +1,6 @@
 target/
+odm/src/main/java/
+odm/target/
 pom.xml.tag
 pom.xml.releaseBackup
 pom.xml.versionsBackup
@@ -8,9 +10,11 @@ release.properties
 .project
 .settings/
 .idea/
+LibreClinica.iml
 OpenClinica.iml
 web/src/main/resources/datainfo.properties
 core/*.iml
+odm/*.iml
 web/*.iml
 ws/*.iml
 .DS_Store
@@ -20,10 +24,6 @@ ws/.DS_Store
 
 # git
 *.orig
-/ws/*.iml
-/web/OpenClinica-web.iml
-/core/OpenClinica-core.iml
-/core/OpenClinica-core.iml
 
 # netbeans
 nb-configuration.xml

core/pom.xml

@@ -1,12 +1,12 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
-    <artifactId>OpenClinica-core</artifactId>
+    <artifactId>LibreClinica-core</artifactId>
     <packaging>jar</packaging>
-    <name>OpenClinica Core</name>
+    <name>LibreClinica Core</name>
     <parent>
-        <groupId>org.akaza.openclinica</groupId>
-        <artifactId>OpenClinica</artifactId>
-      <version>3.14</version>
+        <groupId>org.libreclinica</groupId>
+        <artifactId>LibreClinica</artifactId>
+      <version>0.3.0</version>
     </parent>
     <dependencies>
 		<dependency>
@@ -125,13 +125,11 @@
 		<dependency>
 			<groupId>commons-fileupload</groupId>
 			<artifactId>commons-fileupload</artifactId>
-			<version>1.2.1</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>1.4</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
@@ -231,10 +229,11 @@
             <version>1.4</version>
         </dependency>
 		<dependency>
-    		<groupId>org.akaza.openclinica.odm</groupId>
-			<artifactId>openclinica-odm</artifactId>
+    		<groupId>org.libreclinica.odm</groupId>
+			<artifactId>LibreClinica-odm</artifactId>
+			<version>2.2</version>
 		</dependency>
-		         <dependency>
+		 <dependency>
 			<groupId>org.mvel</groupId>
 			<artifactId>mvel2</artifactId>
 			<version>2.0.19</version>
@@ -254,16 +253,24 @@
 		</dependency>
 
 		<dependency>
-    <groupId>org.codehaus.jackson</groupId>
-    <artifactId>jackson-core-lgpl</artifactId>
-    <version>1.8.1</version>
-</dependency>
+    		<groupId>org.codehaus.jackson</groupId>
+    		<artifactId>jackson-core-lgpl</artifactId>
+    		<version>1.8.1</version>
+		</dependency>
 
-<dependency>
-    <groupId>org.codehaus.jackson</groupId>
-    <artifactId>jackson-mapper-lgpl</artifactId>
-    <version>1.8.1</version>
-</dependency>
+		<dependency>
+			<groupId>org.codehaus.jackson</groupId>
+			<artifactId>jackson-mapper-lgpl</artifactId>
+			<version>1.8.1</version>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.saxon</groupId>
+			<artifactId>saxon</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.saxon</groupId>
+			<artifactId>saxon-dom</artifactId>
+		</dependency>
 	</dependencies>
 	<!-- @pgawade 16-NOV-2010 unit tests through maven -->
 

core/src/main/java/org/akaza/openclinica/dao/core/CoreResources.java

@@ -362,8 +362,8 @@ private Properties setDataInfoProperties() {
         DATAINFO.setProperty("rss.more", rss_more);
 
         String supportURL = DATAINFO.getProperty("supportURL");
-        if (supportURL == null || supportURL.isEmpty())
-            supportURL = "https://www.openclinica.com/support";
+        if (supportURL == null || supportURL.trim().isEmpty())
+            supportURL = "";
         DATAINFO.setProperty("supportURL", supportURL);
 
         DATAINFO.setProperty("show_unique_id", "1");

core/src/main/java/org/akaza/openclinica/dao/extract/DatasetDAO.java

@@ -704,7 +704,7 @@ public DatasetBean initialDatasetData(int datasetId) {
     }
 
     protected String getDefinitionCrfItemSql(String sedIds, String itemIds) {
-        return "select item.*, sed.study_event_definition_id as sed_id, sed.name as sed_name, crf.crf_id, crf.name as crf_name"
+        return "select DISTINCT item.*, sed.study_event_definition_id as sed_id, sed.name as sed_name, crf.crf_id, crf.name as crf_name"
             + " from study_event_definition sed, event_definition_crf edc, crf, crf_version cv,item_form_metadata ifm, item"
             + " where sed.study_event_definition_id in " + sedIds + " and item.item_id in " + itemIds
             + " and sed.study_event_definition_id = edc.study_event_definition_id and edc.crf_id = crf.crf_id"

core/src/main/java/org/akaza/openclinica/dao/hibernate/AbstractDomainDao.java

@@ -10,6 +10,7 @@
 import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.internal.SessionImpl;
+import org.hibernate.query.Query;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.orm.hibernate5.HibernateTemplate;
@@ -32,27 +33,27 @@ public String getDomainClassName() {
     public T findById(Integer id) {
         getSessionFactory().getStatistics().logSummary();
         String query = "from " + getDomainClassName() + " do  where do.id = :id";
-        org.hibernate.Query q = getCurrentSession().createQuery(query);
-        q.setInteger("id", id);
-        return (T) q.uniqueResult();
+        Query<T> q = getCurrentSession().createQuery(query);
+        q.setParameter("id", id);
+        return q.uniqueResult();
     }
 
     @SuppressWarnings("unchecked")
     @Transactional
     public ArrayList<T> findAll() {
         getSessionFactory().getStatistics().logSummary();
         String query = "from " + getDomainClassName() + " do";
-        org.hibernate.Query q = getCurrentSession().createQuery(query);
-        return (ArrayList<T>) q.list();
+        Query<T> q = getCurrentSession().createQuery(query);
+        return new ArrayList<T>(q.list());
     }
 
     @SuppressWarnings("unchecked")
 	public T findByOcOID(String OCOID){
     	 getSessionFactory().getStatistics().logSummary();
          String query = "from " + getDomainClassName() + " do  where do.oc_oid = :oc_oid";
-         org.hibernate.Query q = getCurrentSession().createQuery(query);
-         q.setString("oc_oid", OCOID);
-         return (T) q.uniqueResult();
+         Query<T> q = getCurrentSession().createQuery(query);
+         q.setParameter("oc_oid", OCOID);
+         return q.uniqueResult();
     }
 
     @Transactional
@@ -65,19 +66,17 @@ public T saveOrUpdate(T domainObject) {
     @Transactional
     public Serializable save(T domainObject) {
         getSessionFactory().getStatistics().logSummary();
-        Serializable id = getCurrentSession().save(domainObject);
-        return id;
+        return getCurrentSession().save(domainObject);
     }
 
-
-
+    @SuppressWarnings("unchecked")
     @Transactional
-    public T findByColumnName(Object id,String key) {
-    String query = "from " + getDomainClassName() + " do where do."+key +"= ?";
-    org.hibernate.Query q = getCurrentSession().createQuery(query);
-    q.setParameter(0, id);
-    return (T) q.uniqueResult();
-    } 
+    public T findByColumnName(Object id, String key) {
+        String query = "from " + getDomainClassName() + " do where do." + key + " = :key_value";
+        Query<T> q = getCurrentSession().createQuery(query);
+        q.setParameter("key_value", id);
+        return q.uniqueResult();
+    }    
 
     public Long count() {
         return (Long) getCurrentSession().createQuery("select count(*) from " + domainClass().getName()).uniqueResult();
@@ -107,7 +106,8 @@ public Session getCurrentSession(String schema) {
                     //CoreResources.setSchema(sessionImpl.connection());
                 }
             } catch (SQLException e) {
-                logger.error(e.getMessage(), e);            }
+                logger.error(e.getMessage(), e);
+            }
         }
         return session;
     }
@@ -120,6 +120,4 @@ public void setHibernateTemplate(HibernateTemplate hibernateTemplate) {
         this.hibernateTemplate = hibernateTemplate;
     }
 
-
-
 }

core/src/main/java/org/akaza/openclinica/dao/hibernate/CompositeIdAbstractDomainDao.java

@@ -6,6 +6,7 @@
 import org.akaza.openclinica.domain.CompositeIdDomainObject;
 import org.hibernate.Session;
 import org.hibernate.SessionFactory;
+import org.hibernate.query.Query;
 import org.springframework.orm.hibernate5.HibernateTemplate;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -25,8 +26,8 @@ public String getDomainClassName() {
     public ArrayList<T> findAll() {
         getSessionFactory().getStatistics().logSummary();
         String query = "from " + getDomainClassName() + " do";
-        org.hibernate.Query q = getCurrentSession().createQuery(query);
-        return (ArrayList<T>) q.list();
+        Query<T> q = getCurrentSession().createQuery(query);
+        return new ArrayList<T>(q.list());
     }
 
     @Transactional
@@ -41,16 +42,15 @@ public Serializable save(T domainObject) {
         getSessionFactory().getStatistics().logSummary();
         Serializable id = getCurrentSession().save(domainObject);
         return id;
-    }
-
-
+    }    
 
+    @SuppressWarnings("unchecked")
     @Transactional
     public T findByColumnName(Object id,String key) {
-    String query = "from " + getDomainClassName() + " do where do."+key +"= ?";
-    org.hibernate.Query q = getCurrentSession().createQuery(query);
-    q.setParameter(0, id);
-    return (T) q.uniqueResult();
+    String query = "from " + getDomainClassName() + " do where do."+key +"= :id";
+    Query<T> q = getCurrentSession().createQuery(query);
+    q.setParameter("id", id);
+    return q.uniqueResult();
     } 
 
     public Long count() {

core/src/main/java/org/akaza/openclinica/dao/hibernate/StudyUserRoleDao.java

@@ -4,6 +4,7 @@
 
 import org.akaza.openclinica.domain.datamap.StudyUserRole;
 import org.akaza.openclinica.domain.user.UserAccount;
+import org.hibernate.query.Query;
 
 public class StudyUserRoleDao extends CompositeIdAbstractDomainDao<StudyUserRole> {
 
@@ -16,11 +17,11 @@ public Class<StudyUserRole> domainClass() {
     public ArrayList<StudyUserRole> findAllUserRolesByUserAccount(UserAccount userAccount, int studyId, int parentStudyId) {
         String query = "from " + getDomainClassName()
                 + "   where   user_name=:username  AND  status_id=1  AND  ( study_id=:studyId OR study_id=:parentStudyId) ";
-        org.hibernate.Query q = getCurrentSession().createQuery(query);
+        Query<StudyUserRole> q = getCurrentSession().createQuery(query);
         q.setParameter("username", userAccount.getUserName());
-        q.setInteger("studyId", studyId);
-        q.setInteger("parentStudyId", parentStudyId);
-        return (ArrayList<StudyUserRole>) q.list();
+        q.setParameter("studyId", studyId);
+        q.setParameter("parentStudyId", parentStudyId);
+        return new ArrayList<StudyUserRole>(q.list());
     }
 
 }

core/src/main/java/org/akaza/openclinica/domain/datamap/CrfVersion.java

@@ -56,7 +56,7 @@ public class CrfVersion extends DataMapDomainObject {
     private List<Section> sections;
     private List<EventDefinitionCrf> eventDefinitionCrfs;
     private Set decisionConditions = new HashSet(0);
-    private Set<ItemGroupMetadata> itemGroupMetadatas;;
+    private Set<ItemGroupMetadata> itemGroupMetadatas;
 
     public CrfVersion() {
     }
@@ -211,7 +211,7 @@ public void setXform(String xform) {
         this.xform = xform;
     }
 
-    @Column(name = "xformName")
+    @Column(name = "xform_name")
     public String getXformName() {
         return xformName;
     }

core/src/main/java/org/akaza/openclinica/domain/rule/RuleSetRuleBean.java

@@ -44,7 +44,6 @@
 @Entity
 @Table(name = "rule_set_rule")
 @GenericGenerator(name = "id-generator", strategy = "native", parameters = { @Parameter(name = "sequence_name", value = "rule_set_rule_id_seq") })
-@Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
 public class RuleSetRuleBean extends AbstractAuditableMutableDomainObject implements Serializable {
 
     RuleSetBean ruleSetBean;

core/src/main/java/org/akaza/openclinica/job/XsltTransformJob.java

@@ -100,7 +100,7 @@ public class XsltTransformJob extends QuartzJobBean {
     private AuditEventDAO auditEventDAO;
     private DatasetDAO datasetDao;
 
-    private final TransformerFactory transformerFactory = TransformerFactory.newInstance();
+    private final TransformerFactory transformerFactory = new net.sf.saxon.TransformerFactoryImpl();
 
     // POST PROCESSING VARIABLES
     public static final String POST_PROC_DELETE_OLD = "postProcDeleteOld";

core/src/main/resources/migration/2.5/changeLogCreateTables.xml

@@ -5,7 +5,7 @@
         <validCheckSum>30d56b8377711e93debdac333aa217d</validCheckSum>
         <preConditions onFail="MARK_RAN">
             <dbms type="postgresql" />
-            <sqlCheck expectedResult="t"> <![CDATA[select substring(replace((string_to_array(version(), ' '))[2],'.','')from 1 for 2)::integer < 90 ]]></sqlCheck>
+            <sqlCheck expectedResult="t"> <![CDATA[select current_setting('server_version_num')::integer < 90000 ]]></sqlCheck>
         </preConditions>
         <sql splitStatements="false">
             DROP LANGUAGE IF EXISTS plpgsql;

core/src/main/resources/migration/lc-1.0.0/update_to_spring5.xml

@@ -67,4 +67,51 @@
             </column>
         </addColumn>
     </changeSet>
+    <changeSet author="cha" id="1555001321719-11">
+        <addColumn tableName="oc_qrtz_job_details">
+            <column name="is_nonconcurrent" type="boolean"></column>
+        </addColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-12">
+        <addColumn tableName="oc_qrtz_job_details">
+            <column name="is_update_data" type="boolean"></column>
+        </addColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-13">
+        <addColumn tableName="oc_qrtz_fired_triggers">
+            <column name="is_nonconcurrent" type="boolean"></column>
+        </addColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-14">
+        <addColumn tableName="oc_qrtz_fired_triggers">
+            <column name="is_update_data" type="boolean"></column>
+        </addColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-15">
+        <addColumn tableName="oc_qrtz_fired_triggers">
+            <column name="sched_time" type="BIGINT">
+                <constraints nullable="false"/>
+            </column>
+        </addColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-16">
+    	<dropColumn tableName="oc_qrtz_job_details">
+            <column name="is_volatile"/>
+        </dropColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-17">
+    	<dropColumn tableName="oc_qrtz_job_details">
+            <column name="is_stateful"/>
+        </dropColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-18">
+    	<dropColumn tableName="oc_qrtz_fired_triggers">
+            <column name="is_volatile"/>
+        </dropColumn>
+    </changeSet>
+    <changeSet author="cha" id="1555001321719-19">
+    	<dropColumn tableName="oc_qrtz_triggers">
+            <column name="is_volatile"/>
+        </dropColumn>
+    </changeSet>
 </databaseChangeLog>