phenopipe iap setup

Phenopipe IAP Server Setup

First you need to install MongoDb 3.4.

System Configuration

Create a new system user and group for running the phenopipe application:

sudo adduser -r -m -s /sbin/nologin phenopipe

Next create the directory to which we want to install the application and give our user access:

sudo mkdir /var/www/phenopipe
sudo chown phenopipe:phenopipe /var/www/phenopipe/

If you don't have git installed already install it. (e.g. for centOS)

yum install git

Building the application

To build and install the application you have to download the source code to your server via

git clone --recursive https://github.com/Gregor-Mendel-Institute/PhenoBox-System.git

Now you have to create/adapt some configuration files in order to build it successfully. Under 'PhenoBox-System/phenopipe-iap-server/src/main/resources/' you have to add a file called 'shared_folder_map.properties'. This file should contain the mapping from your smb file share (its SMB URL) to the local mount point. It should look like the following.

smb\://url.of.your.server/share=/your/local/mountpoint/

Afterwards you have to run the following commands as the phenopipe user (e.g. sudo -u phenopipe bash):

cd PhenoBox-System/phenopipe-iap-server
./gradlew build
tar -xvf build/distributions/phenopipe-iap-server.tar -C /var/www/phenopipe/
sudo chown -R phenopipe:phenopipe /var/www/phenopipe/phenopipe-iap-server/

Installation and Autostart

Now that the application is built we have to create a service to start it automatically Using systemd we can do the following: Create the service description at /etc/systemd/system/phenopipe-iap-server.service This file should look like this:

[Unit]
Description=Phenopipe IAP analysis service
Wants=network-online.target
After=network-online.target

[Service]
ExecStart=/var/www/phenopipe/phenopipe-iap-server/bin/phenopipe-iap-server

User=phenopipe
Group=phenopipe

[Install]
WantedBy=multi-user.target

To start and enable the service do the following:

sudo systemctl daemon-reload
sudo sytemctl enable phenopipe-iap-server

Now the server should start everytime you restart the system.

IAP Configuration

During the first run of the application initialization IAP will create a hidden directory (.iap_2.0) in the home folder of the user running the process (e.g. /home/phenopipe). In this folder there is the configuration file of IAP (iap.ini). In this file you have to make all necessary configurations to be able to use IAP correctly.

You can either create an appropriate configuration on a client computer where you have access to IAPs GUI and the copy the relevant parts to the server or edit the file directly. Passwords must be set on the server because a different key is used on each machine. You can encrypt the passwords on the server using the following command:

/var/wwww/phenopipe/phenopipe-iap-server/bin/phenopipe-iap-server -encrypt-pw yourPassword

where phenopipe-iap-server is the built executable of the phenopipe server. This will give you something like this encrypted:N5YAdxcaKq8=. Take the whole output and paste it in the appropriate place in the config file.

The most important part is the configuration of the grid storage: This is an example configuration with one grid storage instance

[GRID-STORAGE]
    n = 1
    retry-count in case of error = 0
    Data Source Read-Timeout (s) = 240
    Experiment-Navigation Mode-radio-selection = Group by type then coordinator//Group by type then import user//Group by import user group then import user//[x]Group by coordinator then type//Group by import user then coordinator//Group by type only
    Sort Substances upon Loading = true
    Sort Conditions upon Loading = true
    connections per host = 5
    connect timeout = 300000
    threads allowed to wait for connection = 10000
    socket timeout = 300000
    max wait time = 300000
    socket keep alive = true
    auto connect retry = true
    Load missing input from LT storage = false
    User Name Mapping = oldname/newname
    User Name Mapping = 
    
    [GRID-STORAGE-1]
    enabled = true
    title = Store
    database_name = storage
    host = 127.0.0.1
    port = 27017
    login = your_monogodb_username
    password = <yourEncryptedPw>

You may also want to configure a VFS for file storage to not store all the images inside the mongodb as described in the IAP documentation

For general system settings edit the [SYSTEM] section of the configuration

[SYSTEM]
Issue GC Memory Usage Threshold Percent = 60
Reduce Workload Memory Usage Threshold Percent = 70
cpu_n = 4
cpu_use_half_n = false
Detect Idle Tasks = true
Reduce Workload in Low Memory Situation = false
Issue GC upon high memory use = false