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Required modification to setup:

The following requirements are not available on the test server:

sudo apt install ant
sudo apt-get install openjfx
export JAVA_HOME=

Install node and typescript:

sudo apt-get install npm
sudo apt-get install nodejs
sudo npm install -g typescript
sudo ln -s `which nodejs` /usr/bin/node

Installation of BioAssay Express

The following files are required for the installation:

  • optbae.zip
  • log4j.properties
  • curation20170603.zip (timestamp may vary)

In the following it is assumed that these files are in user directory. NOTE: if log4j.properties is not found, the BAE service will fail at start-up; see Common.java for loading details.

Export master from github

mkdir git
cd git
git clone https://github.com/cdd/bioassay-express.git bae
git clone https://github.com/cdd/bioassay-template.git bax
git clone https://github.com/aclarkxyz/web_molkit.git WebMolKit

Compiling bioassay-template (bax, optional)

cd bax
ant

Use precompiled pkg/BioAssayTemplate.jar file.

Compiling bae

cd ~/git/bae
ant

Copy the default configuration

sudo mkdir /opt/bae
cd /opt/bae
sudo cp  ~/log4j.properties .
sudo unzip ~/optbae.zip
sudo mkdir assays

Run the junit tests

cd ~/git/bae
ant junit

Load the curated assay information

cd ~/git/bae
csh baeconsole transfer importassays ~/curation20170603.zip --init /opt/bae

Add the log directory

sudo mkdir /opt/bae/logs
sudo chmod 777 /opt/bae/logs

Correct user/group credentials

Install the war file

sudo cp pkg/BioAssayExpress.war /var/lib/tomcat8/webapps

Check authentication settings on mongo DB

  • Server must be password protected and mongod started with the --auth flag
  • provide the user credentials either in the config.json file or as environment variables

Add baseURI to config.json

To prevent the possibility of Redirect/Phishing via HTTP Host Injection (CDD-01-003 Web) it is recommended to add baseURI to config.json.

Access the server

Server installations:

Updating an existing server

If you update the software on an existing server and run into a problem, it is best to clean up the existing installation first.

ant clean

Authentication support

Check that the OAuth keys are correct.