{"type":"doc","content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"_parentId":{"value":"289964033"}},"macroMetadata":{"macroId":{"value":"82d72198-5284-4145-8465-451265ade804"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"9aefda6a-52fa-4ab7-b4da-b6740ac86c2f"}},{"type":"heading","attrs":{"level":1},"content":[{"text":"Download OpenSpecimen","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"table","attrs":{"layout":"default","width":1800.0,"localId":"15e18716-a853-43ba-8ebb-6ed128ded78c"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Enterprise Edition","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Email contact@openspecimen.org","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Community Edition","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Download the code from Github","type":"text","marks":[{"type":"link","attrs":{"href":"https://github.com/krishagni/openspecimen"}}]},{"text":" and follow steps on ","type":"text"},{"text":"How to build from code?","type":"text","marks":[{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"How to build from source code?","versionAtSave":"59"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115955"}}]},{"text":")","type":"text"}]}]}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Prerequisites","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Database: MySQL 8.0 or Oracle 11g/12c","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Set JAVA_HOME (Refer to ","type":"text"},{"text":"this","type":"text","marks":[{"type":"link","attrs":{"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/289964033/Deployment+steps#Deploymentsteps-Java17changes(LinuxandUbuntu)"}}]},{"text":" section for Java 17 changes)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Tomcat 9 and its service","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"MySQL prerequisites","type":"text","marks":[{"type":"textColor","attrs":{"color":"#326ca6"}},{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"MySQL prerequisites","versionAtSave":"29"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115772"}}]}]}]}]},{"type":"paragraph","content":[{"text":"Please visit the respective download centers and download the latest version available for your operating system:","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}}]}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"MySQL","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}},{"type":"link","attrs":{"href":"https://dev.mysql.com/downloads/mysql/"}}]},{"text":" (Ignore if you are going to use Oracle)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Java","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}},{"type":"link","attrs":{"href":"https://java.com/en/download/manual.jsp"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Tomcat","type":"text"},{"text":" (Use the Tomcat zip provided into OpenSpecimen build zip)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Apache for Linux","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}},{"type":"link","attrs":{"href":"https://httpd.apache.org/download.cgi"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Apache for Windows","type":"text","marks":[{"type":"textColor","attrs":{"color":"#282b28"}},{"type":"link","attrs":{"href":"https://www.apachehaus.com/cgi-bin/download.plx"}}]}]}]}]},{"type":"paragraph","content":[{"text":"Note","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}},{"type":"strong"}]},{"text":": ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"Make sure ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ff6600"}}]},{"text":"MySQL prerequisites","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ff6600"}},{"type":"link","attrs":{"href":"https://openspecimen.atlassian.net/wiki/x/fAYR"}}]},{"text":" are configured correctly before moving on to the next steps","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ff6600"}}]},{"text":".","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ff6600"}},{"type":"strong"}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Create Database","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"paragraph","content":[{"text":"Note: Applicable only for a fresh install","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"table","attrs":{"layout":"default","width":1800.0,"localId":"413ac7a1-4e07-4481-81b0-d2b05bbcbf4a"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Database","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"MySQL","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"create 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","type":"text"},{"text":"Database Configuration","type":"text","marks":[{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"Database Configuration","versionAtSave":"27"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115693"}}]},{"text":" to set the proper privileges.","type":"text"}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Configure Tomcat context.xml","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"paragraph","content":[{"text":"Note: This section is applicable for the fresh install and upgrading OpenSpecimen from older versions before v5.0.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"paragraph","content":[{"text":"For Linux, configure the PID.txt path using the instructions here: ","type":"text"},{"text":"How to run Tomcat using PID on Linux?","type":"text","marks":[{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"How to run Tomcat using PID on Linux?","versionAtSave":"3"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/263454759"}}]}]},{"type":"paragraph","content":[{"text":"Refer to the attached ","type":"text"},{"text":"context.xml","type":"text","marks":[{"type":"link","attrs":{"href":"https://openspecimen.atlassian.net/wiki/download/attachments/289964033/context.xml?version=1&modificationDate=1537782425437&cacheVersion=1&api=v2"}}]},{"text":" for reference.","type":"text"}]},{"type":"paragraph","content":[{"text":"Configure the data source name in $TOMCAT_HOME/conf/context.xml using the snippet below.","type":"text"}]},{"type":"codeBlock","content":[{"text":"\" password=\"\"\n driverClassName=\"\"\n url=\"\"\n testOnBorrow=\"true\" validationQuery=\"select 1 from dual\" />","type":"text"}]},{"type":"paragraph"},{"type":"table","attrs":{"layout":"default","width":1800.0,"localId":"33234bf5-4b4f-4645-8f5b-197a53000b91"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph"}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"MySQL","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Oracle","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Driver class 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$TOMCAT_HOME/conf/context.xml","type":"text","marks":[{"type":"textColor","attrs":{"color":"#091e42"}}]}]},{"type":"codeBlock","attrs":{"language":"xml"},"content":[{"text":"","type":"text"}]},{"type":"paragraph","content":[{"text":"Notes: The word \"openspecimen\" above could be different based on your configuration. E.g. \"os-test\", \"os-prod\" etc.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Deployment","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Unzip the installer file. Let's call the new folder OSPM_HOME","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Change directory to OSPM_HOME","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Edit \"openspecimen.properties\"","type":"text","marks":[{"type":"textColor","attrs":{"color":"#0000ff"}}]}]},{"type":"paragraph","content":[{"text":"Note: If the data & plugin directory is not present at the specified path, installer script will create data & plugin directory at the specified path provided in the openspecimen.properties file.","type":"text"}]},{"type":"table","attrs":{"layout":"full-width","width":1512.7938,"localId":"dbb85a58-4043-48ff-b9d2-fab87a2e35a8"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"Field","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"Description","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"Values","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"app.name","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"This field is useful for deploying multiple OpenSpecimen instances on the same Tomcat server. E.g. You can use \"os-test\" and \"os-prod\".","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"Typically this is \"openspecimen\".","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"tomcat.dir","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"The absolute path to the Tomcat 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\"openspecimen/data\"","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"app.log_conf","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"Folder where the OpenSpecimen logs should be created","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"If left empty logs are created in \"app.data_dir/logs\"","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"datasource.jndi","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"Name of datasource configured in \"context.xml\"","type":"text","marks":[{"type":"textColor","attrs":{"color":"#333333"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"Usually, it is \"jdbc/openspecimen\".","type":"text","marks":[{"type":"textColor","attrs":{"color":"#333333"}}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"datasource.type","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"\"fresh\": If your database schema is created by OpenSpecimen from scratch.","type":"text"}]},{"type":"paragraph","content":[{"text":"\"Upgrade\": if your database schema is upgraded from a caTissue database.","type":"text"}]},{"type":"paragraph","content":[{"text":"Note: The name is a bit misleading, we will fix this in v5.2.","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"\"fresh\" or \"upgrade\"","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"database.type","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"MySQL or Oracle","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"\"mysql\" or \"oracle\"","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[160.29]},"content":[{"type":"paragraph","content":[{"text":"plugin.dir","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[671.62]},"content":[{"type":"paragraph","content":[{"text":"Absolute path to the plugin directory.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[680.89]},"content":[{"type":"paragraph","content":[{"text":"Best practice:","type":"text"}]},{"type":"paragraph","content":[{"text":"Create a folder in parallel to 'tomcat.dir' with the name \"openspecimen/plugins\"","type":"text"}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Install / Upgrade","type":"text","marks":[{"type":"textColor","attrs":{"color":"#0000ff"}}]}]},{"type":"paragraph","content":[{"text":"For installing new or upgrading OpenSpecimen from previous versions use the below command:","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]}]},{"type":"table","attrs":{"layout":"default","width":1800.0,"localId":"1fa00065-f1f7-4a8b-8fe0-b38e8d11de2e"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Operating system","type":"text","marks":[{"type":"strong"}]}]}]},{"type":"tableHeader","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Command","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Linux","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"./install.sh ","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"Windows","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1},"content":[{"type":"paragraph","content":[{"text":"./install.bat ","type":"text"}]}]}]}]},{"type":"paragraph","content":[{"text":"Example :","type":"text","marks":[{"type":"strong"}]},{"text":" ","type":"text"},{"text":"./install.sh /usr/local/openspecimen/tomcat-as/conf/openspecimen.properties","type":"text","marks":[{"type":"strong"}]}]},{"type":"paragraph","content":[{"text":"Notes for upgrade: ","type":"text","marks":[{"type":"strong"}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Download the build zip using the details provided by OpenSpecimen support team. ","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Once the build zip is extracted, copy the paid plugins (if any) under the new_plugins directory.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"The installer scripts automatically copies the new WAR and plugin and take the backup of existing WAR and plugins into $os_data/old_builds directory.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Stop the Tomcat if running","type":"text","marks":[{"type":"textColor","attrs":{"color":"#333333"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Take the backup of the custom plugins if any","type":"text","marks":[{"type":"textColor","attrs":{"color":"#333333"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Take the backup of the database before upgrade","type":"text","marks":[{"type":"textColor","attrs":{"color":"#333333"}}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Starting/Stopping OpenSpecimen","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"table","attrs":{"layout":"full-width","width":1069.4124,"localId":"b84c89ff-1d15-4c07-83a2-bd524562ca5a"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[103.36]},"content":[{"type":"paragraph","content":[{"text":"Windows","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[966.05]},"content":[{"type":"paragraph","content":[{"text":"Start: Go to Task manager => Services tab => Click on Apache Tomcat 9 service => Click on ","type":"text"},{"text":"Start ","type":"text","marks":[{"type":"strong"}]},{"text":"link. (In left panel)","type":"text"}]},{"type":"paragraph","content":[{"text":"Stop: Go to Task manager => Services tab => Click on Apache Tomcat 9 service => Click on ","type":"text"},{"text":"Stop","type":"text","marks":[{"type":"strong"}]},{"text":" link. (In left panel)","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[103.36]},"content":[{"type":"paragraph","content":[{"text":"Linux","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[966.05]},"content":[{"type":"paragraph","content":[{"text":"The installer starts OpenSpecimen automatically. If not started, run the following command:","type":"text"}]},{"type":"paragraph","content":[{"text":"Start","type":"text"},{"text":": $TOMCAT_HOME/bin/startup.sh","type":"text","marks":[{"type":"em"}]},{"type":"hardBreak"}]},{"type":"paragraph","content":[{"text":"Stop: ","type":"text"},{"text":"$TOMCAT_HOME/bin/shutdown.sh -force","type":"text","marks":[{"type":"em"}]}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Accessing OpenSpecimen","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Open a browser: Chrome, Firefox, Safari, IE (11 and above only)","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Type in: ","type":"text"},{"text":"http://:/openspecimen/","type":"text","marks":[{"type":"link","attrs":{"href":"http://128.199.204.227:8080/openspecimen/v20.do"}}]},{"type":"hardBreak"},{"text":"E.g. ","type":"text"},{"text":"http://localhost:8080/openspecimen","type":"text","marks":[{"type":"link","attrs":{"href":"http://localhost:8080/openspecimen"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Username: admin (password: Login@123)","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Additional Configuration","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Email Configuration","type":"text","marks":[{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"Email Configuration","versionAtSave":"14"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115964"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Locale Configuration","type":"text","marks":[{"type":"link","attrs":{"href":"https://openspecimen.atlassian.net/wiki/x/A4A_/"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"LDAP Configuration","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}},{"type":"link","attrs":{"__confluenceMetadata":{"isRenamedTitle":true,"linkType":"page","contentTitle":"LDAP Configuration","versionAtSave":"36"},"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/1115962"}}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Java 17 changes (Linux and Ubuntu)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"paragraph","content":[{"text":"OpenSpecimen version 10.1 onwards.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Install Java 17 using the below command.","type":"text"}]}]}]},{"type":"table","attrs":{"layout":"default","width":588.9707999999999,"localId":"07873855-28dd-4236-b361-40783b5e7c8e"},"content":[{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[95.51]},"content":[{"type":"paragraph","content":[{"text":"Ubuntu","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[493.46]},"content":[{"type":"paragraph","content":[{"text":"sudo apt install openjdk-17-jdk openjdk-17-jre","type":"text"}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[95.51]},"content":[{"type":"paragraph","content":[{"text":"RedHat","type":"text"}]}]},{"type":"tableCell","attrs":{"colspan":1,"rowspan":1,"colwidth":[493.46]},"content":[{"type":"paragraph","content":[{"text":"sudo dnf install java-17-openjdk-devel java-17-openjdk","type":"text"}]}]}]}]},{"type":"paragraph","content":[{"text":"2. Change the existing JAVA_HOME directory path in .bashrc file and point to the Java 17 directory.","type":"text"}]},{"type":"paragraph","content":[{"text":"3. Check the Java version using the below command.","type":"text"}]},{"type":"paragraph","content":[{"text":" # java -version","type":"text"}]},{"type":"paragraph","content":[{"text":"4. Edit the $Tomcat_Dir/bin/setenv.sh file and remove the below lines.","type":"text"}]},{"type":"paragraph","content":[{"text":" \"-XX:PermSize=64m -XX:MaxPermSize=512m\"","type":"text"}]},{"type":"paragraph","content":[{"text":"5. Add the below-mentioned Java specific startup parameters required by Tomcat in $Tomcat_Dir/bin/catalina.sh file.","type":"text"}]},{"type":"paragraph","content":[{"text":" JDK_JAVA_OPTIONS=\"$JDK_JAVA_OPTIONS --add-opens=java.base/","type":"text"},{"text":"java.net","type":"text","marks":[{"type":"link","attrs":{"href":"http://java.net/"}}]},{"text":"=ALL-UNNAMED","type":"text"}]},{"type":"paragraph","content":[{"text":"6. Deploy the OpenSpecimen build.","type":"text"}]},{"type":"paragraph"},{"type":"heading","attrs":{"level":2},"content":[{"text":"Java 17 changes (Windows)","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"paragraph","content":[{"text":"OpenSpecimen version 10.1 onwards.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#3366ff"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Rename the existing Java folder under C drive ","type":"text"},{"text":"C:\\Program Files\\Java to C:\\Program Files\\Java_bkp","type":"text","marks":[{"type":"textColor","attrs":{"color":"#1f1f1f"}}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Uninstall the old java from the control Panel","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Download and install the Java 17 from ","type":"text"},{"text":"here","type":"text","marks":[{"type":"link","attrs":{"href":"https://download.oracle.com/java/17/archive/jdk-17.0.7_windows-x64_bin.msi"}}]},{"text":".","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Change the Java environment variables and insert the new path to the JDK folder.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Check the Java version using below command once the installation is complete.","type":"text"},{"type":"hardBreak"},{"text":" # java -version","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Edit the service.bat file inside $Tomcat_Home/bin/service.bat location.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Find the following string \"","type":"text"},{"text":"--JvmOptions9","type":"text","marks":[{"type":"strong"}]},{"text":"\" in the service.bat file and add the below line.","type":"text"},{"type":"hardBreak"},{"text":" --add-opens=java.base/java.lang=ALL-UNNAMED#","type":"text"},{"type":"hardBreak"},{"type":"hardBreak"},{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"inline-media-image","parameters":{"width":"700","id":"a030fff1-743d-40ca-985c-735397ca5473","collection":"contentId-289964033","height":""}}},{"type":"hardBreak"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Edit the catalina.sh file, which can be found under $Tomcat_Home/bin/catalina.bat directory.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Add the below parameter under the \"JDK_JAVA_OPTIONS\" options.","type":"text"},{"type":"hardBreak"},{"text":" JDK_JAVA_OPTIONS=\"$JDK_JAVA_OPTIONS --add-opens=java.base/","type":"text"},{"text":"java.net","type":"text","marks":[{"type":"link","attrs":{"href":"http://java.net"}}]},{"text":"=ALL-UNNAMED\"","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Deploy the OpenSpecimen build.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Upload workflow licence in OpenSpecimen","type":"text","marks":[{"type":"link","attrs":{"href":"https://openspecimen.atlassian.net/wiki/spaces/CAT/pages/289964033/Deployment+steps#Upload-workflow-licence-in-OpenSpecimen"}}]}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Navigate to Home → Extras → Licenses","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Click on upload license.","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Choose the provided license file and click on upload.","type":"text"}]}]}]},{"type":"paragraph"}],"version":1}