Software

Installing eagle-i Repository on orchestra:

1. ssh into orchestra

   ssh ecommonsId@orchestra.med.harvard.edu
   

2. navigate to the working directory and make a project folder in tomcat . 

   cd /www/dev.some.website.hms.harvard.edu/tomcat
   mkdir blink
   

3. get the latest distribution of the repository software

   cd blink/
   wget http://infra.search.eagle-i.net:8081/nexus/content/repositories/releases/org/eagle-i/eagle-i-repository-dist/1.7-MS1.02/eagle-i-repository-dist-1.7-MS1.02-dist.zip
   

4. unzip the folder

   unzip eagle-i-repository-dist-1.7-MS1.02-dist.zip
   

5. create additional folders in the project folder that are needed to install the repository

   mkdir datarepo
   cd datarepo
   mkdir lib
   

6. now copy the required derby jars from the unzipped repository folder to the newly created lib folder

   cd lib
   cp ../../repository-1.7-MS1.02/lib/* .
   

7. also place a copy of the derby jars in tomcat's lib folder

   ../../repository-1.7-MS1.02/lib/* ../../../lib/
   

8. create a symbolic link in the tomcat folder to the docroot folder

   cd ../../../
   ln -s ../docroot/ webapps
   

The folder structure in the website directory should now look like this:

• dev.some.website.hms.harvard.edu
  • docroot
  • support
  • tomcat
    • blink
      • datarepo
        • lib
          • 2 derby jars
      • repository-1.7.-MS1.02
    • webapps -> ../docroot/

Additional configurations needed to continue installation:

1. Edit the .jkmounts file (https://wiki.med.harvard.edu/Orchestra/TomcatHosting#Content_Placement_and_Tomcat_Con) because we need to serve the repository at the root.  The .jkmounts file should only have the following line in it.

   /* = devalaskau24
   

2. Add a catalina.properties file in tomcat's conf folder with the following content, making sure to update the locations:

   org.eaglei.repository.home=/www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo
   derby.system.home=/www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo
   common.loader=${catalina.base}/blink/.config,${catalina.base}/blink/conf,${catalina.base}/lib,/www/dev.some.website.hms.harvard.edu/tomcat/lib/*.jar,${catalina.home}/lib,${catalina.home}/lib/*.jar
   org.eaglei.home=/www/dev.alaska.u24.hms.harvard.edu/tomcat/blink
   

In order to perform the rest of the installation of the repository, we now need to enter orchestra's interactive LSF (https://wiki.med.harvard.edu/Orchestra/IntroductionToLSF#Interactive_Jobs)

bsub -Is -q shared_int_2h bash

1. Navigate to the unzipped repository distribution /etc/ folder and run the prepare-install script

   cd blink/repository-1.7-MS1.02/
   ./etc/prepare-install.sh USERNAME PASSWORD ../datarepo/
   

   Where USERNAME and PASSWORD are the initial admin creds for the repository.
2. Now exit out of the interactive shell and start tomcat

   exit
   tomcatctl start dev.some.website.hms.harvard.edu
   

3. Re-enter the interactive LSF to complete the installation

   bsub -Is -q shared_int_2h bash
   ./etc/finish-install.sh USERNAME PASSWORD https://dev.some.website.hms.harvard.edu
   

4. Finally, edit the configuration file in the datarepo folder to have the sesame property point to the correct place.

   eaglei.repository.sesame.dir = /www/dev.some.website.hms.harvard.edu/tomcat/blink/datarepo/sesame
   

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Additional references:

• https://open.med.harvard.edu/display/eaglei/Repository+Installation+and+Administrator+Guide#RepositoryInstallationandAdministratorGuide-InstallandConfigureRepository