Component DB

Prerequisites:

In order to deploy or develop Component DB, you must have some support software installed. Follow the instructions below to achieve this.

# For red-hat based linux distribution run the following:
yum install -y gcc libgcc expect zlib-devel openssl-devel openldap-devel readline-devel git make cmake sed gawk autoconf automake wget mariadb mariadb-server curl unzip rsync
# For debian based linux distributions run the following:
apt-get install wget gcc git make cmake build-essential libcurses-ocaml-dev curl expect mariadb-client mariadb-server openssl libssl-dev libldap2-dev libsasl2-dev sed gawk unzip rsync

Versions used in production

• mariadb: 10.5.22
• Other dependencies are automatically downloaded and installed when running make support command.

Deployment

Below are the steps to be followed to deploy an installation of CDB. These steps are designed to be done as a standard non-root user account. Before starting ensure that you have set the root password for your mariadb installation (See Helpful Utility).

Deployment Procedure:

# Make a new directory to hold cdb and its support directories. (replace or set DESIRED_CDB_INSTALL_DIRECTORY var with a unix directory.)
mkdir $DESIRED_CDB_INSTALL_DIRECTORY
cd $DESIRED_CDB_INSTALL_DIRECTORY 
# get the distribution of Component DB (Alternativelly download a release zip and unzip it). 
git clone https://github.com/AdvancedPhotonSource/ComponentDB.git
# Navigate inside the distribution. 
cd ComponentDB
# Build support needed for the application
make support
# load enviornment variables with new support built. 
source setup.sh    
# Create deployment configuration
make configuration
# Create a clean db for the distribution 
make clean-db
# Prepare web portal configuraiton
make configure-web-portal

# Deploy plugins if needed using `make deploy-cdb-plugin`
# See https://github.com/AdvancedPhotonSource/ComponentDB/wiki/Plugins

# Deploy web portal
make deploy-web-portal    

# All done... output of the command below should print url to the deployed portal. 
echo "https://`hostname`:8181/cdb"

# Valid SSL certificates can also be applied using the following command:
# ./sbin/cdb_update_glassfish_ssl.sh KEY_FILE CRT_FILE # NOTE, this will prompt for the master password set during the `make support` step. 

Troubleshooting:

Managing Payara:

# Navigate to the ComponentDB distribution directory. 

# Viewing logs
tail -f ../support-`hostname -a`/payara/linux-x86_64/glassfish/domains/production/logs/server.log

# Restart payara server
./etc/init.d/cdb-glassfish restart

Other notes:

Setting Project:

The item project has been mostly static attribute, therefore there is no UI. Currently this can only be done within SQL.

-- Log into the mariadb shell with cdb database. 
use cdb;
-- Override the default project
update item_project set name='OPS' where id = 1;
-- Adding additional projects 
insert into item_project(name) values ('Upgrade');

Restart application to reset any caches for item_project.

# Navigate to the ComponentDB distribution directory. 
./etc/init.d/cdb-glassfish restart

Deployment Upgrade

# Navigate to cdb installation directory
cd $CDB_INSTALL_DIRECTORY

# Download the release package to cdb install dicrectory
# Using version 3.10 as an example. 
wget https://github.com/AdvancedPhotonSource/ComponentDB/archive/v3.10.0.tar.gz
tar -xvf v3.10.0.tar.gz
rm v3.10.0.tar.gz
cd ComponentDB-3.10.0

# Backup the database. 
make backup

# Verify db changes. 
cd db/sql/updates
# Check to see if the release has a updateTo(Version).sql script. 
# Follow instructions described in the top comments of the sql update file.
cd ../../../ # Navigate back to release directory

# Deploy plugins if needed using `make deploy-cdb-plugin`
# See https://github.com/AdvancedPhotonSource/ComponentDB/wiki/Plugins

make deploy-web-portal

Development

For detailed development instructions please refer to our developers guide.

Getting Started with development:

# first make a fork of this project. 
# create a desired development directory and cdb into it
mkdir $desired_dev_directory
cd $desired_dev_directory
git clone https://github.com/AdvancedPhotonSource/ComponentDB.git

# Getting support software
cd ComponentDb
make support 
# Get Netbeans
make support-netbeans

# Load up the environment 
source setup.sh

# Prepare Dev DB    
# mysql could be installed as part of ComponentDB support by running 'make support-mysql' 
# - Afterwards run `./etc/init.d/cdb-mysql start`
# if you have mysql installed and started run...
make clean-db   # sample-db will be coming later 

# Start development
make dev-config     

# Open Netbeans
netbeans & 

Preparing Netbeans

Once netbeans is open a few steps need to be taken to prepare netbeans for CDB development.

1. Open CDB Project: File > Open Project
2. Navigate to $desired_dev_directory/ComponentDB/src/java
3. Select CdbWebPortal and hit Open Project
4. Right click on CdbWebPortal top level under projects
5. Click "Resolve Missing Server Problem"
6. Add Server -> Payara Server

• Installation Location: $desired_dev_directory/support-hostname/netbeans/payara
• Version: 5.2022.5
• Use the wizard's download

7. Next -> Use Default Domain Location -> Finish add server instance wizard
8. Select the Newly added "Payara Server"
9. Copy over the required mysql client to new payara server.

# cd into the $desired_dev_directory/$distribution_directory
cp src/java/CdbWebPortal/lib/mariadb-java-client-3.1.0.jar ../support-`hostname`/netbeans/payara/glassfish/domains/domain1/lib/

10. Run the project

Python Web Service Development

The python web service is deprecated but is still a part of the distribution for legacy integrations.

# Code is located in $desired_dev_directory/ComponentDB/src/python
# For web service development (Use your favorite python editor) to test run web service using:
./sbin/cdbWebService.sh

License

Copyright (c) UChicago Argonne, LLC. All rights reserved.