Logbook

Prerequisites:

In order to deploy or develop Logbook, 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 mysql mysql-libs mysql-server mysql-devel curl unzip
# For debian based linux distributions run the following:
apt-get install wget gcc git make cmake build-essential libcurses-ocaml-dev curl expect mysql-server libmysqlclient-dev openssl libssl-dev libldap2-dev libsasl2-dev sed gawk unzip

Deployment

For detailed deployment instructions please refer to our administrators guide.

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 web portal
make deploy-web-portal
# Deploy REST web service
make deploy-web-service

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

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

Automated Tests

To get started with running the API test suite the BELY app needs to be running on local machine.

Prereqs

# API requirements 
pip install -r  tools/developer_tools/python-client/test/requirements.txt

Manual Test

source setup.sh
# Deploy test-db data
make test-db
# Test API 
# Navigate to python-client directory
cd tools/developer_tools/python-client/
# Optionally genreate latest version of API. 
./generatePyClient.sh http://localhost:8080/bely
# Run tests
pytest test/api_test.py

Single Command Test

This will backup the db, deploy test db, run test, and restore backup.

source setup.sh
make test

Python Web Service Development

# 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.