Merge branch 'develop'

* develop: UBO-340 Fixed genre selection UBO-340 Fixed indentation UBO-363 Fixed NullPointerException in MCRUserMatcherLDAP (#426) UBO-362-FSU040THUL-5049 Allow setting of partOf and state class during list import (#425) IM-154 add decimal format on response page Fix wrong grep command in docker-entrypoint.sh UBO-358 FSU040THUL-3822 Do not throw exception when object has both parent and multiple children (#420) UBO-359 FSU040THUL-4433 Remove parent div once it has been processed (#421) UBO-283 - add missing dependency for jobqueue UBO-283 switch also docker image to tomcat 10 (#419) UBO-283 Migrate to MyCoRe 2023.06.x (#335)
MyCoRe-Org · Nov 1, 2024 · 5065300 · 5065300
2 parents 8d3ff58 + c44e49f
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diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM tomcat:jdk17-temurin-focal
+FROM tomcat:10-jdk17-temurin-jammy
 RUN groupadd -r mcr -g 501 && \
     useradd -d /home/mcr -u 501 -m -s /bin/bash -g mcr mcr
 WORKDIR /usr/local/tomcat/

diff --git a/README.md b/README.md
@@ -21,11 +21,9 @@ ubo-cli/target/bin/ubo.sh create configuration directory
 create database ubo;
 grant all privileges on ubo.* to ubo@localhost identified by 'ubo';
 ```
-- setup your database and JDBC configuration in persistence.xml and **REMOVE** the following lines
+- setup your database and JDBC configuration in persistence.xml, update mappings with:
 ```
-<mapping-file>META-INF/mycore-iview2-mappings.xml</mapping-file>
-<mapping-file>META-INF/mycore-viewer-mappings.xml</mapping-file>
-<mapping-file>META-INF/mycore-ifs-mappings.xml</mapping-file>
+ubo-cli/target/bin/ubo.sh reload mappings in jpa configuration file
 ```
 ```
 vi ~/.mycore/ubo/resources/META-INF/persistence.xml
@@ -34,7 +32,7 @@ vi ~/.mycore/ubo/resources/META-INF/persistence.xml
 - copy jdbc driver to ~/.mycore/ubo/lib, eg. for h2
 ```
 cd ~/.mycore/ubo/lib
-wget https://repo1.maven.org/maven2/com/h2database/h2/1.4.200/h2-1.4.200.jar
+wget https://repo1.maven.org/maven2/com/h2database/h2/2.2.224/h2-2.2.224.jar
 cd -
 ```
 ## Solr 

diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
@@ -55,8 +55,56 @@ function downloadDriver {
   fi
 }
 
+function migrateC3P0toHikari {
+    # check if c3p0 is used (if any c3p0-* file present)
+    if ls "${MCR_CONFIG_DIR}lib/c3p0-"*.jar 1> /dev/null 2>&1; then
+      echo "Migrate from c3p0 to HikariCP"
+      # delete old c3p0 drivers
+      rm "${MCR_CONFIG_DIR}lib/c3p0-"*.jar
+      rm "${MCR_CONFIG_DIR}lib/mchange-commons-java-"*.jar
+      rm "${MCR_CONFIG_DIR}lib/hibernate-c3p0-"*.jar
+
+      # delete old database drivers
+      rm "${MCR_CONFIG_DIR}lib/postgresql-42.2.9.jar"
+      rm "${MCR_CONFIG_DIR}lib/mariadb-java-client-2.5.4.jar"
+      rm "${MCR_CONFIG_DIR}lib/h2-1.4.200.jar"
+      rm "${MCR_CONFIG_DIR}lib/mysql-connector-java-8.0.19.jar"
+
+      # delete old configuration and add new configuration
+      if grep -q "hibernate.c3p0" "${PERSISTENCE_XML}"; then
+        sed -ri "s/.*hibernate.c3p0.*//" "${PERSISTENCE_XML}"
+        sed -ri "s/(<property name=\"hibernate.connection.provider_class\" value=\")(.*)(\" \/>)/\1org.hibernate.hikaricp.internal.HikariCPConnectionProvider\3/" "${PERSISTENCE_XML}"
+        sed -ri "s/(<\/properties>)/<property name=\"hibernate.hikari.maximumPoolSize\" value=\"30\" \/>\n<property name=\"hibernate.hikari.minimumIdle\" value=\"2\" \/>\n<property name=\"hibernate.hikari.idleTimeout\" value=\"30000\" \/>\n<property name=\"hibernate.hikari.maxLifetime\" value=\"1800000\" \/>\n<property name=\"hibernate.hikari.leakDetectionThreshold\" value=\"9000\" \/>\n<property name=\"hibernate.hikari.registerMbeans\" value=\"true\" \/>\n\1/" "${PERSISTENCE_XML}"
+      fi
+
+      /opt/ubo/ubo-cli/target/bin/ubo.sh reload mappings in jpa configuration file
+    else
+      echo "No c3p0 driver found. Skip migration."
+    fi
+}
+
+function migrateJavaxPropertiesToJakarta() {
+  if grep -q "javax.persistence" "${PERSISTENCE_XML}"; then
+    echo "Migrate properties in persistence.xml from javax to jakarta"
+    sed -ri "s/(<property name=\")javax.persistence(.*\" value=\".*\" \/>)/\1jakarta.persistence\2/" "${PERSISTENCE_XML}"
+  fi
+  if grep -q "xmlns.jcp.org" "${PERSISTENCE_XML}"; then
+    echo "Migrate xmlns in persistence.xml from jcp.org to jakarta.ee"
+    sed -ri "s/xmlns=\".+persistence\"/xmlns=\"https:\/\/jakarta.ee\/xml\/ns\/persistence\"/" "${PERSISTENCE_XML}"
+    echo "Migrate schemaLocation in persistence.xml from jcp.org to jakarta.ee"
+    sed -ri "s/(xsi:schemaLocation=\").*jcp.org.*(\")/\1https:\/\/jakarta.ee\/xml\/ns\/persistence https:\/\/jakarta.ee\/xml\/ns\/persistence\/persistence_3_0.xsd\2/" "${PERSISTENCE_XML}"
+  fi
+  if grep -q "version=\"2" "${PERSISTENCE_XML}"; then
+    echo "Migrate version in persistence.xml from 2.* to 3.0"
+    sed -ri "s/version=\"2.*\"/version=\"3.0\"/" "${PERSISTENCE_XML}"
+  fi
+}
+
 function setDockerValues() {
     echo "Set Docker Values to Config!"
+
+    migrateJavaxPropertiesToJakarta
+
     if [ -n "${SOLR_URL}" ]; then
       sed -ri "s/#?(MCR\.Solr\.ServerURL=).+/\1${SOLR_URL_ESCAPED}/" "${MYCORE_PROPERTIES}";
     fi
@@ -70,23 +118,33 @@ function setDockerValues() {
     fi
 
     if [ -n "${JDBC_NAME}" ]; then
-      sed -ri "s/(name=\"javax.persistence.jdbc.user\" value=\").*(\")/\1${JDBC_NAME_ESCAPED}\2/" "${PERSISTENCE_XML}"
+      sed -ri "s/(name=\"jakarta.persistence.jdbc.user\" value=\").*(\")/\1${JDBC_NAME_ESCAPED}\2/" "${PERSISTENCE_XML}"
     fi
 
     if [ -n "${JDBC_PASSWORD}" ]; then
-      sed -ri "s/(name=\"javax.persistence.jdbc.password\" value=\").*(\")/\1${JDBC_PASSWORD_ESCAPED}\2/" "${PERSISTENCE_XML}"
+      sed -ri "s/(name=\"jakarta.persistence.jdbc.password\" value=\").*(\")/\1${JDBC_PASSWORD_ESCAPED}\2/" "${PERSISTENCE_XML}"
     fi
 
     if [ -n "${JDBC_DRIVER}" ]; then
-      sed -ri "s/(name=\"javax.persistence.jdbc.driver\" value=\").*(\")/\1${JDBC_DRIVER_ESCAPED}\2/" "${PERSISTENCE_XML}"
+      sed -ri "s/(name=\"jakarta.persistence.jdbc.driver\" value=\").*(\")/\1${JDBC_DRIVER_ESCAPED}\2/" "${PERSISTENCE_XML}"
     fi
 
     if [ -n "${JDBC_URL}" ]; then
-      sed -ri "s/(name=\"javax.persistence.jdbc.url\" value=\").*(\")/\1${JDBC_URL_ESCAPED}\2/" "${PERSISTENCE_XML}"
+      sed -ri "s/(name=\"jakarta.persistence.jdbc.url\" value=\").*(\")/\1${JDBC_URL_ESCAPED}\2/" "${PERSISTENCE_XML}"
     fi
 
-    if [ -n "${SOLR_CLASSIFICATION_CORE}" ]; then
-      sed -ri "s/(name=\"hibernate.default_schema\" value=\").*(\")/\1${HIBERNATE_SCHEMA_ESCAPED}\2/" "${PERSISTENCE_XML}"
+    if [ -n "${JDBC_SCHEMA}" ]; then
+      if grep -q "hibernate.default_schema" "${PERSISTENCE_XML}"; then
+        sed -ri "s/(name=\"hibernate.default_schema\" value=\").*(\")/\1${JDBC_SCHEMA_ESCAPED}\2/" "${PERSISTENCE_XML}"
+      else
+        sed -ri "s/(<\/properties>)/<property name=\"hibernate.default_schema\" value=\"${JDBC_SCHEMA_ESCAPED}\" \/>\n\1/" "${PERSISTENCE_XML}"
+      fi
+
+      if grep -q "hibernate.hbm2ddl.create_namespaces" "${PERSISTENCE_XML}"; then
+        sed -ri "s/(name=\"hibernate.hbm2ddl.create_namespaces\" value=\").*(\")/\1true\2/" "${PERSISTENCE_XML}"
+      else
+        sed -ri "s/(<\/properties>)/<property name=\"hibernate.hbm2ddl.create_namespaces\" value=\"true\" \/>\n\1/" "${PERSISTENCE_XML}"
+      fi
     fi
 
     sed -ri "s/(name=\"hibernate.hbm2ddl.auto\" value=\").*(\")/\1update\2/" "${PERSISTENCE_XML}"
@@ -97,43 +155,38 @@ function setDockerValues() {
           echo "MCR.datadir=${MCR_DATA_DIR}">>"${MYCORE_PROPERTIES}"
     fi
 
+    if grep -q "MCR.Solr.NestedDocuments=" "${MYCORE_PROPERTIES}" ; then
+      sed -ri "s/#?(MCR\.Solr\.NestedDocuments=).+/\1true/" "${MYCORE_PROPERTIES}"
+    else
+      echo "MCR.Solr.NestedDocuments=true">>"${MYCORE_PROPERTIES}";
+    fi
+
     if  grep -q "MCR.Save.FileSystem=" "${MYCORE_PROPERTIES}" ; then
           sed -ri "s/#?(MCR\.Save\.FileSystem=).+/\1${MCR_SAVE_DIR_ESCAPED}/" "${MYCORE_PROPERTIES}"
     else
           echo "MCR.Save.FileSystem=${MCR_SAVE_DIR}">>"${MYCORE_PROPERTIES}"
     fi
 
+    migrateC3P0toHikari
+
     case $JDBC_DRIVER in
-      org.postgresql.Driver) downloadDriver "https://jdbc.postgresql.org/download/postgresql-42.2.9.jar";;
-      org.mariadb.jdbc.Driver) downloadDriver "https://repo.maven.apache.org/maven2/org/mariadb/jdbc/mariadb-java-client/2.5.4/mariadb-java-client-2.5.4.jar";;
-      org.hsqldb.jdbcDriver) downloadDriver "https://repo.maven.apache.org/maven2/org/hsqldb/hsqldb/2.5.0/hsqldb-2.5.0.jar";;
-      org.h2.Driver) downloadDriver "https://repo.maven.apache.org/maven2/com/h2database/h2/1.4.200/h2-1.4.200.jar";;
-      com.mysql.jdbc.Driver) downloadDriver "https://repo.maven.apache.org/maven2/mysql/mysql-connector-java/8.0.19/mysql-connector-java-8.0.19.jar";;
+      org.postgresql.Driver) downloadDriver "https://jdbc.postgresql.org/download/postgresql-42.7.0.jar";;
+      org.mariadb.jdbc.Driver) downloadDriver "https://repo.maven.apache.org/maven2/org/mariadb/jdbc/mariadb-java-client/3.3.0/mariadb-java-client-3.3.0.jar";;
+      org.h2.Driver) downloadDriver "https://repo1.maven.org/maven2/com/h2database/h2/2.2.224/h2-2.2.224.jar";;
+      com.mysql.jdbc.Driver) downloadDriver "https://repo1.maven.org/maven2/com/mysql/mysql-connector-j/8.2.0/mysql-connector-j-8.2.0.jar";;
     esac
 
     mkdir -p "${MCR_CONFIG_DIR}lib"
 
-    downloadDriver https://repo1.maven.org/maven2/org/hibernate/hibernate-c3p0/5.3.9.Final/hibernate-c3p0-5.3.9.Final.jar
-    downloadDriver https://repo1.maven.org/maven2/com/mchange/c3p0/0.9.5.2/c3p0-0.9.5.2.jar
-    downloadDriver https://repo1.maven.org/maven2/com/mchange/mchange-commons-java/0.2.15/mchange-commons-java-0.2.15.jar
-
-
-    if [ -f "${MCR_CONFIG_DIR}jwt.secret" ]; then
-      echo "jwt.secret already exists."
-    else
-      echo "jwt.secret does not exists, create it.."
-      openssl rand -out "${MCR_CONFIG_DIR}jwt.secret" 4096
-    fi;
+    downloadDriver https://repo1.maven.org/maven2/com/zaxxer/HikariCP/5.1.0/HikariCP-5.1.0.jar
 }
 
 function setUpMyCoRe {
     /opt/ubo/ubo-cli/target/bin/ubo.sh create configuration directory
     setDockerValues
     setupLog4jConfig
-    sed -ri "s/(<\/properties>)/<property name=\"hibernate\.connection\.provider_class\" value=\"org\.hibernate\.connection\.C3P0ConnectionProvider\" \/>\n<property name=\"hibernate\.c3p0\.min_size\" value=\"2\" \/>\n<property name=\"hibernate\.c3p0\.max_size\" value=\"50\" \/>\n<property name=\"hibernate\.c3p0\.acquire_increment\" value=\"2\" \/>\n<property name=\"hibernate\.c3p0\.max_statements\" value=\"30\" \/>\n<property name=\"hibernate\.c3p0\.timeout\" value=\"1800\" \/>\n\1/" "${PERSISTENCE_XML}"
-    sed -ri "s/<mapping-file>META-INF\/mycore-viewer-mappings.xml<\/mapping-file>//" "${PERSISTENCE_XML}"
-    sed -ri "s/<mapping-file>META-INF\/mycore-iview2-mappings.xml<\/mapping-file>//" "${PERSISTENCE_XML}"
-    sed -ri "s/<mapping-file>META-INF\/mycore-ifs-mappings.xml<\/mapping-file>//" "${PERSISTENCE_XML}"
+    /opt/ubo/ubo-cli/target/bin/ubo.sh reload mappings in jpa configuration file
+    sed -ri "s/(<\/properties>)/<property name=\"hibernate.hikari.maximumPoolSize\" value=\"30\" \/>\n<property name=\"hibernate.hikari.minimumIdle\" value=\"2\" \/>\n<property name=\"hibernate.hikari.idleTimeout\" value=\"30000\" \/>\n<property name=\"hibernate.hikari.maxLifetime\" value=\"1800000\" \/>\n<property name=\"hibernate.hikari.leakDetectionThreshold\" value=\"9000\" \/>\n<property name=\"hibernate.hikari.registerMbeans\" value=\"true\" \/>\n\1/" "${MCR_CONFIG_DIR}resources/META-INF/persistence.xml"
     /opt/ubo/ubo-cli/target/bin/ubo.sh init superuser
     /opt/ubo/ubo-cli/target/bin/ubo.sh update all classifications from directory /opt/ubo/ubo-cli/src/main/setup/classifications
     /opt/ubo/ubo-cli/target/bin/ubo.sh update permission create-mods for id POOLPRIVILEGE with rulefile /opt/ubo/ubo-cli/src/main/setup/acl/acl-rule-always-allowed.xml described by always allowed

diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <groupId>org.mycore</groupId>
     <artifactId>mycore-parent</artifactId>
-    <version>49</version>
+    <version>55</version>
   </parent>
 
   <groupId>org.mycore.ubo</groupId>
@@ -53,13 +53,14 @@
     <java.target.version>17</java.target.version>
     <jquery.ui.version>1.13.2</jquery.ui.version>
     <jquery.version>3.5.1</jquery.version>
-    <mycore.version>2022.06.3-SNAPSHOT</mycore.version>
+    <mycore.version>2023.06.3-SNAPSHOT</mycore.version>
     <node.version>v16.0.0</node.version>
     <pica2mods.version>2.10</pica2mods.version>
     <sortpom.sortDeps>scope,groupId,artifactId</sortpom.sortDeps>
     <sortpom.sortFile>https://gist.githubusercontent.com/yagee-de/dfd3698c1b49173dbf251f74eb6a9297/raw/406460c088ff3cb6354e4ae6b40535e6f841607d/mycore_sort.xml</sortpom.sortFile>
     <sortpom.sortProps>true</sortpom.sortProps>
     <timestamp>${maven.build.timestamp}</timestamp>
+    <tomcat.version>10.1.11</tomcat.version>
     <yarn.version>v1.22.10</yarn.version>
   </properties>
 
@@ -74,6 +75,31 @@
         </plugin>
       </plugins>
     </pluginManagement>
+
+    <plugins>
+      <plugin>
+        <groupId>com.github.ekryd.sortpom</groupId>
+        <artifactId>sortpom-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>verify-sort-pom</id>
+            <goals>
+              <goal>sort</goal>
+            </goals>
+            <phase>verify</phase>
+            <configuration>
+              <createBackupFile>false</createBackupFile>
+              <expandEmptyElements>false</expandEmptyElements>
+              <spaceBeforeCloseEmptyElement>true</spaceBeforeCloseEmptyElement>
+              <keepBlankLines>true</keepBlankLines>
+              <sortDependencies>${sortpom.sortDeps}</sortDependencies>
+              <sortOrderFile>${sortpom.sortFile}</sortOrderFile>
+              <sortProperties>${sortpom.sortProps}</sortProperties>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
   </build>
 
   <repositories>
@@ -179,7 +205,7 @@
         </property>
       </activation>
       <properties>
-        <cargo.container>jetty9x</cargo.container>
+        <cargo.container>jetty12x</cargo.container>
       </properties>
       <build>
         <pluginManagement>
@@ -281,6 +307,11 @@
         <artifactId>bucket4j-core</artifactId>
         <version>8.9.0</version>
       </dependency>
+      <dependency>
+        <groupId>com.h2database</groupId>
+        <artifactId>h2</artifactId>
+        <version>2.2.224</version>
+      </dependency>
       <dependency>
         <groupId>jakarta.servlet</groupId>
         <artifactId>jakarta.servlet-api</artifactId>