Merge branch '2023.06.x'

* 2023.06.x: MCR-2647 update database configuration (#935) enable docker builds for version 2023.06 in github workflow Bump ckeditor-wordcount-plugin from 1.17.6 to 1.17.12 in /mir-module MCR-3010 Duplicate warnings about old absolute include mechanism congest logs (#936) MIR-1241 Response mir facets should be dynamic (#901) Sort pom (#937) MCR-2647 fix db config updates LICENSE.txt due to plugin updates MIR-1231 Expect dates in ISO8601 to be in ISO8601 basic format. MIR-1257 sort 'register PI' menu entries MIR-1226 rework subject editor (#885) MIR-1248 check if @valueURI contains # - is a classification accordingly MIR-1251 add support for arbitrary classification facets w/o the need for specialized SOLR fields MIR-1254 optionally allow HTML content in validateion messages MIR-1231 Expect dates in ISO8601 to be in ISO8601 basic format. Allow to depict intervalls in that format too. No timezones are supported. MIR-1250 Set q.alt parameter on /find request handler (#914) MCR-2647 update to hibernate 6.3 and H2 2.2 (#907) MCR-2966 move Saxon ready stylesheets to /xslt
MyCoRe-Org · Dec 21, 2023 · 983bad4 · 983bad4
2 parents dd5cbe6 + d1e3383
commit 983bad4
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1 @@
+docker
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -88,16 +88,16 @@ jobs:
         export FIREFOX_BIN=$(which firefox-esr)
         export SELENIUM_BROWSER=firefox
 
-        mvn -B -P!standard-with-extra-repos -Djetty clean install
+        mvn -B -P!standard-with-extra-repos -U -Djetty clean install
         mvn -P!standard-with-extra-repos -B javadoc:javadoc
     - name: Login to Docker Hub
-      if: contains('refs/heads/2022.06.x refs/heads/main', github.ref) && github.event_name=='push' && success()
+      if: contains('refs/heads/2022.06.x refs/heads/2023.06.x refs/heads/main', github.ref) && github.event_name=='push' && success()
       uses: docker/login-action@v2
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}
     - name: Build the mir Docker images and push them
-      if: contains('refs/heads/2022.06.x refs/heads/main', github.ref) && github.event_name=='push' && success()
+      if: contains('refs/heads/2022.06.x refs/heads/2023.06.x refs/heads/main', github.ref) && github.event_name=='push' && success()
       run: |
         docker build . --file Dockerfile --tag mycoreorg/mir:${GITHUB_REF_NAME}
         docker build mir-webapp/src/main/solr/ --file mir-webapp/src/main/solr/Dockerfile --tag mycoreorg/mir-solr:${GITHUB_REF_NAME}

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -645,7 +645,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
@@ -59,8 +59,56 @@ 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/mir/mir/bin/mir.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"
+    grep -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
@@ -74,19 +122,19 @@ 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 "${SOLR_CLASSIFICATION_CORE}" ]; then
@@ -113,28 +161,27 @@ function setDockerValues() {
           echo "MCR.Save.FileSystem=${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
+    downloadDriver https://repo1.maven.org/maven2/com/zaxxer/HikariCP/5.1.0/HikariCP-5.1.0.jar
 }
 
 function setUpMyCoRe {
     echo "Set up MyCoRe!"
     /opt/mir/mir/bin/mir.sh create configuration directory
     setDockerValues
     setupLog4jConfig
-    sed -ri "s/<mapping-file>META-INF\/mycore-viewer-mappings.xml<\/mapping-file>/&\n    <mapping-file>META-INF\/mir-module-mappings.xml<\/mapping-file>\n    <mapping-file>META-INF\/mycore-acl-mappings.xml<\/mapping-file>\n    <mapping-file>META-INF\/mycore-jobqueue-mappings.xml<\/mapping-file>/" "${MCR_CONFIG_DIR}resources/META-INF/persistence.xml"
-    sed -ri "s/(<\/properties>)/<property name=\"hibernate\.connection\.provider_class\" value=\"org\.hibernate\.connection\.C3P0ConnectionProvider\" \/>\n<property name=\"hibernate\.c3p0\.min_size\" value=\"2\" \/>\n<property name=\"hibernate\.c3p0\.max_size\" value=\"50\" \/>\n<property name=\"hibernate\.c3p0\.acquire_increment\" value=\"2\" \/>\n<property name=\"hibernate\.c3p0\.max_statements\" value=\"30\" \/>\n<property name=\"hibernate\.c3p0\.timeout\" value=\"1800\" \/>\n\1/" "${MCR_CONFIG_DIR}resources/META-INF/persistence.xml"
+    /opt/mir/mir/bin/mir.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/mir/mir/bin/setup.sh
 }
 

diff --git a/docker-log4j2.xml b/docker-log4j2.xml
@@ -22,5 +22,11 @@
         </root>
         <logger name="org.hibernate" level="error" />
         <logger name="org.mycore.frontend.editor.validation" level="info" />
+        <logger name="org.mycore.common.xml.MCRURIResolver" >
+            <filters>
+                <MarkerFilter marker="tryResolveXML" onMatch="NEUTRAL" onMismatch="ACCEPT"/>
+                <MCRUniqueFilter onMatch="DENY" onMismatch="ACCEPT"/>
+            </filters>
+        </logger>
     </loggers>
 </configuration>
diff --git a/mir-cli/LICENSE.txt b/mir-cli/LICENSE.txt
@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -645,7 +645,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/mir-common-resources/LICENSE.txt b/mir-common-resources/LICENSE.txt
@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -645,7 +645,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/mir-it/LICENSE.txt b/mir-it/LICENSE.txt
@@ -1,7 +1,7 @@
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
@@ -645,7 +645,7 @@ the "copyright" line and a pointer to where the full notice is found.
     GNU General Public License for more details.
 
     You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 Also add information on how to contact you by electronic and paper mail.
 
@@ -664,11 +664,11 @@ might be different; for a GUI interface, you would use an "about box".
   You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
+<https://www.gnu.org/licenses/>.
 
   The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+<https://www.gnu.org/licenses/why-not-lgpl.html>.
diff --git a/mir-it/pom.xml b/mir-it/pom.xml
@@ -81,7 +81,7 @@
                 <artifactItem>
                   <groupId>com.h2database</groupId>
                   <artifactId>h2</artifactId>
-                  <version>1.3.176</version>
+                  <version>2.2.224</version>
                 </artifactItem>
               </artifactItems>
             </configuration>

diff --git a/mir-it/src/test/integration/resources/META-INF/persistence.xml b/mir-it/src/test/integration/resources/META-INF/persistence.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<persistence xmlns="http://xmlns.jcp.org/xml/ns/persistence"
+<persistence xmlns="https://jakarta.ee/xml/ns/persistence"
              xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-             xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/persistence http://xmlns.jcp.org/xml/ns/persistence/persistence_2_2.xsd"
-             version="2.2">
+             xsi:schemaLocation="https://jakarta.ee/xml/ns/persistence https://jakarta.ee/xml/ns/persistence/persistence_3_0.xsd"
+             version="3.0">
   <persistence-unit name="MyCoRe" transaction-type="RESOURCE_LOCAL">
     <!-- http://stackoverflow.com/questions/15026302/multiple-jars-single-persistence-unit-solution -->
     <mapping-file>META-INF/mycore-base-mappings.xml</mapping-file>
@@ -14,14 +14,15 @@
     <!-- required for MIR only: -->
     <mapping-file>META-INF/mir-module-mappings.xml</mapping-file>
     <properties>
-      <property name="javax.persistence.jdbc.driver" value="org.h2.Driver" />
-      <property name="javax.persistence.jdbc.url" value="jdbc:h2:${MCR.Home.Integration}/${MCR.AppName}/data/h2/mir" />
-      <property name="javax.persistence.jdbc.user" value="sa" />
-      <property name="javax.persistence.jdbc.password" value="" />
+      <property name="jakarta.persistence.jdbc.driver" value="org.h2.Driver" />
+      <property name="jakarta.persistence.jdbc.url" value="jdbc:h2:${MCR.Home.Integration}/${MCR.AppName}/data/h2/mir" />
+      <property name="jakarta.persistence.jdbc.user" value="sa" />
+      <property name="jakarta.persistence.jdbc.password" value="" />
       <property name="hibernate.cache.use_second_level_cache" value="false" />
       <property name="hibernate.hbm2ddl.auto" value="update" />
       <property name="hibernate.jdbc.batch_size" value="0" />
       <property name="hibernate.show_sql" value="false" />
+      <property name="hibernate.auto_quote_keyword" value="true" />
     </properties>
   </persistence-unit>
 </persistence>
diff --git a/mir-it/src/test/java/org/mycore/mir/it/controller/MIREditorController.java b/mir-it/src/test/java/org/mycore/mir/it/controller/MIREditorController.java
@@ -9,6 +9,7 @@
 import org.openqa.selenium.StaleElementReferenceException;
 import org.openqa.selenium.TimeoutException;
 import org.openqa.selenium.WebElement;
+import org.openqa.selenium.support.ui.ExpectedConditions;
 
 public abstract class MIREditorController extends MIRTestController {
 
@@ -44,7 +45,8 @@ protected void setHTMLAreaText(String childElementName, String text) {
     protected void clickRepeater(String field) {
         driver
             .waitAndFindElement(
-                By.xpath(".//button[contains(@name, '" + field + "') and contains(@name, '_xed_submit_insert')]"))
+                By.xpath(".//button[contains(@name, '" + field + "') and contains(@name, '_xed_submit_insert')]"),
+                ExpectedConditions::elementToBeClickable)
             .click();
     }