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--- howto:molgenis_install [2015/08/20 14:28] – jp
+++ howto:molgenis_install [2018/10/09 10:12] (current) – external edit 127.0.0.1
@@ Line 15: / Line 15: @@
 </code>
-When you are done  ''java -version'' and ''javac -version'' should yield the Java 8 version and build number.
+When you are done  ''java -version'' and ''javac -version'' should yield the Java 8 version and build number.  **Note that version 8 is a requirement for the molgenis platform.**
 You will also need to install Tomcat 7.  This is straightforward with
@@ Line 23: / Line 23: @@
 </code>
+Molgenis uses MySQL for its backend - so this needs to be installed using the following:
+<code bash>
+sudo apt-get install mysql-server libmysql-java
+</code>
+During this installation of MySQL you will be prompted for the root password, make sure to use something memorable.
+Note that ''libmysql-java'' installs the JDBC connection driver to MySQL.  This JDBC Driver is a java class which needs to be made available to tomcat.  Two ways of doing this are either including ''/usr/share/java/mysql.jar'' in the tomcat7 user's CLASSPATH env variable or copying this file to the Tomcat ''lib'' directory as follows:
+<code bash>
+sudo cp -v /usr/share/java/mysql.jar /usr/share/tomcat7/lib
+</code>
+Note that Tomcat should be restarted after this file is copied over (for the class to be loaded).  This can be done with:
+<code bash>
+sudo service tomcat7 restart
+</code>
 ===== Installation Procedure =====
@@ Line 32: / Line 50: @@
     - First edit the tomcat defaults (these are found in ''/etc/default/tomcat7'').  This special location is used to store admin settings which are likely to change and you want to keep across updates. ''sudo vim /etc/default/tomcat7''
     - Add the following line ''JAVA_HOME=/usr/lib/jvm/java-8-oracle'' to the file to make sure the JVM is the oracle one we installed above
-    - In the JAVA_OPTS line:
+    - In the ''JAVA_OPTS'' line (this is used to set the JVM parameters):
       - **Change** ''-Xmx'' parameter to whatever its value to ''-Xmx1g''
       - **Add** The following two properties ''-Dmolgenis.home=/var/lib/molgenis -Dlog4j.configuration=log4j-molgenis.properties''
       - The resulting line should look something like:<code bash>
 JAVA_OPTS="-Djava.awt.headless=true -Xmx1g -XX:+UseConcMarkSweepGC -Dmolgenis.home=/var/lib/molgenis -Dlog4j.configuration=log4j-molgenis.properties"
+</code>
+    - After these changes to Tomcat you will need to restart the application server with:<code bash>
+sudo service tomcat7 restart
+</code>
+  - MySQL will also require some additional setup (basically creating a database, a username and a password).<code bash>
+mysql -u root -p -e "create database molgenis; grant all on molgenis.* to 'molgenis'@'localhost' identified by 'YOUR_PASSWORD_HERE'; flush privileges;"
+</code>
+  - Create a molgenis directory which is writable by the ''tomcat7'' user (this is used for state information).<code bash>sudo mkdir /var/lib/molgenis
+</code>
+    - Set the correct permissions with '' sudo chown tomcat7:tomcat7 /var/lib/molgenis''
+  - We need to create a properties file called ''molgenis-server.properties'' in the molgenis home directory (i.e. ''/var/lib/molgenis'') specified above.<code bash>
+sudo vim /var/lib/molgenis/molgenis-server.properties
+</code>
+    - This properties file should contain the following (please make sure to substitute the MySQL molgenis user password with the correct one):<code properties>
+#Molgenis server properties
+molgenis.version=13
+admin.password=MOLGENIS_ADMIN_PASSWORD_HERE_CHANGE!!!
+db_uri=jdbc\:mysql\://localhost/molgenis
+db_driver=com.mysql.jdbc.Driver
+db_user=molgenis
+db_password=MYSQL_MOLGENIS_PASSWORD_HERE_CHANGE!!!
+mail.host=localhost
+mail.port=25
+</code>
+    - Note: The ''admin.password'' property is the one which the user ''admin'' uses to log in the molgenis system (from the frontend).
+    - The file is sensitive as it contains passwords, and should therefore be secured using the following:<code bash>
+sudo chown tomcat7:tomcat7 /var/lib/molgenis/molgenis-server.properties
+sudo chmod 600 /var/lib/molgenis/molgenis-server.properties
 </code>
   - Download the latest version of molgenis web application file (this is in the form of a Java war).
     - Do this by searching for //molgenis-app// in the [[http://search.maven.org/|maven repository]]
     - Download the war file by using wget. e.g.<code bash>
-jp@maltabiobank:~/downloads$ wget http://search.maven.org/remotecontent?filepath=org/molgenis/molgenis-app/1.8.2/molgenis-app-1.8.2.war
+wget http://search.maven.org/remotecontent?filepath=org/molgenis/molgenis-app/1.19.0/molgenis-app-1.19.0.war -O molgenis-app-1.19.0.war</code>
-</code>
   - Rename the downloaded war file to ''ROOT.war'' (case important).  This is an annoying and necessary limitation
   - Make sure owner tomcat7 owns the file, ''sudo chown tomcat7:tomcat7 ROOT.war''
-  - Copy the newly renamed ''ROOT.war'' to the Tomcat webs directory (by default this is in ''/var/lib/tomcat7/webapps'')
+  - Copy the newly renamed ''ROOT.war'' to the Tomcat webs directory (by default this is in ''/var/lib/tomcat7/webapps'')<code bash>
-<code bash>
 sudo cp -vp ROOT.war /var/lib/tomcat7/webapps
 </code>
-  - If you want to follow what is going on, **before** copying set a ''tail -f /var/log/tomcat7/catalina.out''
+  - The above will automatically start deploying the molgenis app on Tomcat.  If you want to follow what is going on, **before** copying set a ''sudo tail -f /var/log/tomcat7/catalina.out''
-  -
+  - When the molgenis web application deploys you should see something like:
+<konsole>
+<nowiki>
+Aug 21, 2015 2:32:41 PM org.apache.catalina.startup.HostConfig deployWAR
+INFO: Deploying web application archive /var/lib/tomcat7/webapps/ROOT.war
+:33:04.641 [localhost-startStop-1] INFO  o.m.d.e.f.EmbeddedElasticSearchServiceFactory - Embedded elasticsearch server started, data path=[/var/lib/molgenis/data]
+:33:07.379 [localhost-startStop-1] INFO  o.m.d.version.MolgenisUpgradeService - MetaData version:13, current version:13 upgrade not needed
+:33:07.395 [localhost-startStop-1] INFO  o.m.a.WebAppConfig$$EnhancerBySpringCGLIB$$183b5b00 - Reindexing repositories....
+:33:09.499 [localhost-startStop-1] INFO  o.m.a.WebAppConfig$$EnhancerBySpringCGLIB$$183b5b00 - Reindexing done.
+:33:09.551 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity tags already exists. Skipping creation
+:33:09.576 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity packages already exists. Skipping creation
+:33:09.678 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity attributes already exists. Skipping creation
+:33:09.707 [localhost-startStop-1] WARN  o.m.data.mysql.MysqlRepository - Table for entity entities already exists. Skipping creation
+:33:34.421 [localhost-startStop-1] ERROR o.m.d.support.AbstractEntityMetaData - No idAttribute specified for entityFileMeta, this attribute is required
+:33:34.427 [localhost-startStop-1] ERROR o.m.d.support.AbstractEntityMetaData - No idAttribute specified for entityFileMeta, this attribute is required
+:33:52.166 [localhost-startStop-1] INFO  o.m.d.jpa.JpaRepositoryRegistrator - Registered JPA importer
+:33:52.167 [localhost-startStop-1] INFO  o.m.d.m.EmxImportServiceRegistrator - Registered EMX import service
+:33:52.940 [localhost-startStop-1] INFO  o.m.f.db.WebAppDatabasePopulator - initializing application database
+:34:40.345 [localhost-startStop-1] INFO  o.m.f.db.WebAppDatabasePopulator - initialized application database
+:34:40.920 [localhost-startStop-1] INFO  o.m.u.m.MenuManagerServiceImpl - Creating default menu from XML
+:34:43.557 [localhost-startStop-1] INFO  o.m.script.ScriptRunnerFactory - Registering Script type R.
+:34:45.561 [localhost-startStop-1] INFO  o.m.o.i.OntologyImporterServiceRegistrator - Registered ontology import service
+:34:51.415 [localhost-startStop-1] INFO  o.m.o.i.OntologyScriptInitializerImpl - Script entity "roc" has been added to the database!
+:34:51.417 [localhost-startStop-1] INFO  o.m.script.ScriptRunnerFactory - Registering Script type python.
+Aug 21, 2015 2:34:54 PM org.apache.coyote.AbstractProtocol start
+INFO: Starting ProtocolHandler ["http-bio-8080"]
+Aug 21, 2015 2:34:54 PM org.apache.catalina.startup.Catalina start
+INFO: Server startup in 133414 ms</nowiki>
+</konsole>
+You can access the molgenis web app by pointing your web browser to [[http://127.0.0.1:8080|http://127.0.0.1:8080]]