ACAS (Assay Capture and Analysis System)

This repository Contains the source code for the main ACAS NodeJS/Web app.

The other required ACAS Open Source Projects can be found here:

• ACAS Roo Server
• ACAS Compound Registration Roo Server
• Racas

JM&Co offer a number of commercial ACAS modules. An introduction to ACAS with additional modules is available [here] (http://www.mcneilco.com/acas.html)

This Open Source release includes the Experiment Loader, Dose Response, and Compound Registration modules, as well as the various ACAS APIs.

ACAS Requirements

• Postgres (or optionally oracle)

Commercial Third-party (optional) requirements

• Oracle
• Compound Registration
• Chemaxon jchembase (with valid license to be obtained at sales [at] chemaxon.com See note in license section of this file)
• Chemaxon marvinjs (with valid license to be obtained at sales [at] chemaxon.com See note in license section of this file)

ACAS Documentation

Public Documentation Table of Contents

Release Notes

https://github.com/mcneilco/acas/releases

Docker installation instructions

ACAS has been configured to run a full stack in the docker environment. The instructions below outline the process of getting a basic working stack running on your system.

Some of the docker images in the ACAS stack are available in the mcneilco dockerhub repository while others (due to license restrictions) must be built by the developer.

Available Images:

• ACAS
• RACAS
• ACAS-Postgres

Images Built by Developer (instructions below):

• ACAS Roo Server
• ACAS Compound Registration Roo Server

Requirements

• Docker
• Docker for Mac
• Docker for Windows

Installation

Docker settings

Download and install docker for your operating system.

Memory

It is recommended to run the stack with at least 4GB of memory but is helpful to have up to 8GB available. Docker for mac and windows do not need to reserve the entire 8GB for itself so it's ok to give it a little extra if you have it available.

See docker instructions for you operating system to adjust

Make a working folder

mkdir -p ~/Documents/mcneilco/oss/

Building a working image for ACAS Roo Server

Due to license restrictions, this is one of the images that must be built by the developer.

Checkout

cd ~/Documents/mcneilco/oss/
git clone git@github.com:mcneilco/acas-roo-server.git
cd acas-roo-server

Build

docker build -t mcneilco/acas-roo-server-oss:latest .

Building a working image for Compound Registration ROO Server

Checkout

cd ~/Documents/mcneilco/oss/
git clone git@github.com:mcneilco/acas-cmpdreg-roo-server.git
cd acas-cmpdreg-roo-server

Add chemaxon jar file

• Go to https://www.chemaxon.com
• Login and/or Sign-Up
• Click Download > JChem Suite > JChem
• Scroll down to Archives and select 16.4.25.0, click Get Archive
• Download jchem-merged-lib-16.4.25.0.zip
• Unzip it and rename jchem.jar to jchem-16.4.25.0.jar

Add chemaxon jar file to a lib folder in the checkout

cd ~/Documents/mcneilco/oss/acas-cmpdreg-roo-server
mkdir lib
cd lib
cp <jchem-16.4.25.0.jar> .
cd ..

Build

docker build -t mcneilco/acas-cmpdreg-roo-server-oss:latest .

ACAS

The acas repository contains a docker-compose.yml file that orchestrates the creation of the ACAS stack. For this reason, it is helpful to have a clone of the ACAS repo even if you aren't doing ACAS development or don't need compound registration.

Checkout

cd ~/Documents/mcneilco/oss/
git clone git@github.com:mcneilco/acas.git
cd acas

Add chemaxon licenses and download marvin4js

mkdir -p chemaxon/licenses

Place your marvin4js-license.cxl and license.cxl (jchem base license) as follows:

cp <path/to/marvin4js-license.cxl> chemaxon/licenses
cp <path/to/license.cxl> chemaxon/licenses

Place your marvin4js download into a folder called "marvinjs" as follows:

cp -r <path/to/marvinjs-16.10.17-all> chemaxon/marvinjs

Start acas stack

cd ~/Documents/mcneilco/oss/acas
docker-compose up -d

Login

Visit http://localhost:3000 in your browser to login. You will need to create a user in order to access the web app:

curl localhost:3001/api/systemTest/getOrCreateACASBob
curl localhost:3001/api/systemTest/getOrCreateGlobalProject
curl localhost:3001/api/systemTest/getOrCreateGlobalProjectRole
curl localhost:3001/api/systemTest/giveBobRoles
curl localhost:3001/api/systemTest/getOrCreateCmpdRegBob
curl localhost:3001/api/systemTest/syncRoles

Optionally you could run the shell script docker_bob_setup.sh in this repository instead of manually curling each endpoint.

This will create a user "bob" with password "secret".

Viewing logs

docker-compose logs --tail=20 -f <service>

e.g. for all containers

docker-compose logs -f 

e.g. for only tomcat

docker-compose logs --tail=20 -f tomcat

Stop the web stack

docker-compose down

Troubleshooting

• There is a known timing issue where tomcat may try to connect to the database before the database is accepting connections. If this happens, try restarting tomcat.

docker-compose restart tomcat

Configuration

Environment variable configuration overrides

ACAS can read configuration overrides from environment variables prefixed with ACAS_. ACAS maps environment variable names to flat file configuration names by a 4 step process (e.g. ACAS_CLIENT_MODULEMENUS_LOGOTEXT=ACME Labs):

1. Match any environment variable name prefixed with ACAS_ and remove the prefix from the name.

Step output: CLIENT_MODULEMENUS_LOGOTEXT

2. Replace _ characters with . characters in the environment variable name.

Note, that you can escape substitution for flat file configs contain underscore by using double underscores __ in the environment variable.

Step output: ACAS.CLIENT.MODULEMENUS.LOGOTEXT

3. Do a case insensitive match of the now processed environment variable name with a flat file configuration name.

Match: client.moduleMenus.logoText

4. Replace the value in the flat file name with the value provided by the matched environment variable.

Final outcome: client.moduleMenus.logoText=ACME Labs

Example environment variables:

Simple override:

Replaces client.moduleMenus.logoText

ACAS_CLIENT_MODULEMENUS_LOGOTEXT=ACME Labs

Escape character usage using __

Replaces server.datafiles.relative_path (note this isn't a realistic example of a config you would ever override but demonstrates the escape sequence)

ACAS_SERVER_DATAFILES_RELATIVE__PATH=..

Override containing configs which will be replaced with other configs

Replaces client.service.cmpdReg.persistence.fullpath

docker-compose example which requires $$ to esacpe the $ override

environment:
  - ACAS_CLIENT_SERVICE_CMPDREG_PERSISTENCE_FULLPATH=http://$${client.service.cmpdReg.persistence.host}:$${client.service.persistence.port}/$${client.service.cmpdReg.persistence.path}/

Shell example requires escape $

ACAS_CLIENT_SERVICE_CMPDREG_PERSISTENCE_FULLPATH=http://\${client.service.cmpdReg.persistence.host}:\${client.service.persistence.port}/\${client.service.cmpdReg.persistence.path}/

or

ACAS_CLIENT_SERVICE_CMPDREG_PERSISTENCE_FULLPATH='http://${client.service.cmpdReg.persistence.host}:${client.service.persistence.port}/${client.service.cmpdReg.persistence.path}/'

License

[License] (./LICENSE)

ChemAxon license note: Subject to possession of valid license, you may use ChemAxon's proprietary software JChemBase and Marvin JS under John McNeil &Co., Inc's application as known as ACAS Compound Registration. Note that it is a restricted license, which is not valid for other (open source) applications. Terms and conditions of such license are covered by ChemAxon standard EULA (available at https://docs.chemaxon.com/display/docs/End+User+License+Agreement+(EULA)+LIC) with the exemption of bullet six (6) of section entitled 'YOU MAY NOT'. Please contact ChemAxon for obtaining the license at sales [at] chemaxon.com.

Copyright

[Copyright (c) 2012-2016 John McNeil & Co. Inc. All rights reserved.] (./COPYRIGHT.txt)