Software notes

Installing eagle-i Repository on orchestra:

ssh into orchestra

ssh ecommonsId@orchestra.med.harvard.edu

navigate to the working directory and make a project folder in tomcat .
```
cd /www/dev.some.website.hms.harvard.edu/tomcat
mkdir blink
```

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

unzip the folder

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

create additional folders in the project folder that are needed to install the repository
```
mkdir datarepo
cd datarepo
mkdir lib
```
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/* .
```
also place a copy of the derby jars in tomcat's lib folder
```
../../repository-1.7-MS1.02/lib/* ../../../lib/
```
create a symbolic link in the tomcat folder to the docroot folder
```
cd ../../../
ln -s ../docroot/ webapps
```

copy the ROOT.war from the unzipped repository folder into the docroot folder

cd /www/dev.some.website.hms.harvard.edu/docroot
cp ../tomcat/blink/repository-1.7-MS1.02/webapps/ROOT.war .

Additional configurations needed to continue installation:

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
```

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.some.website.hms.harvard.edu/tomcat/blink

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

dev.some.website.hms.harvard.edu
- docroot
  - ROOT.war
  - (additional files that were set up by RITG)
- support
- tomcat
  - blink
    - datarepo
      - lib
        2 derby jars
    - repository-1.7.-MS1.02
  - conf
    - catalina.properties
  - lib
    - 2 derby jars
    - (additional folders that were set up by RITG)
  - webapps -> ../docroot/

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

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.

Now exit out of the interactive shell and start tomcat

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

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

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
```

Additional references:

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

Child pages

Software notes

Installing eagle-i Repository on orchestra:

Additional references: