Standalone install on Windows 10 in console

Change {..} to the actual path

Download files
1. https://git-scm.com/download/win
2. https://tomcat.apache.org/download-80.cgi # 9.0.37
3. https://dev.mysql.com/downloads/mysql/ # 8.0.23
4. https://downloads.gradle-dn.com/distributions/gradle-4.10.2-bin.zip # MUST BE VERSION 4.x
5. https://dev.mysql.com/downloads/connector/j/ # MUST BE 8.0.20 if mysql version is 8.0.23, copy mysql-connector-java-8.0.20.jar to {..}/apache-tomcat-9.0.37/lib
6. https://nodejs.org/en/download/ # 14.16.0
7. https://github.com/mimi3421/openspecimen/releases # release v8.0.b1

Environment

set PATH={..}\server\gradle-6.8.3\bin;{..}\node-v14.16.0-win-x64\node_modules\.bin;{..}\Git\bin;{..}\Java\jdk1.8.0_241\bin;{..}\mysql-8.0.23-winx64\bin;{..}\node-v14.16.0-win-x64

set JAVA_HOME={..}\Java\jdk1.8.0_241

set CLASSPATH={..}\apache-tomcat-9.0.37\lib

set TOMCAT_HOME={..}\apache-tomcat-9.0.37

Initialize mysql

Create my.ini in {..}/mysql-8.0.23-winx64

#https://dev.mysql.com/doc/refman/8.0/en/option-files.html
[mysqld]
port=3306
basedir={..}\MySql
datadir={..}\DataBase\MySql
max_connections=200
max_connect_errors=10
character-set-server=utf8
default-storage-engine=INNODB
default_authentication_plugin=mysql_native_password
disable_log_bin
skip-log-bin

[mysql]
default-character-set=utf8

[client]
port=3306
default-character-set=utf8

Initialization

mysqld --initialize --console
# Markdown the original random root password from the output

Create database

# Use heidisql or other mysql client to create databse and user, change root password to PASSWORD
# DROP DATABASE openspecimen
CREATE DATABASE openspecimen

Prepare tomcat

Create openspecimen.properties in ${TOMCAT_HOME}/conf

#######################################################################
# Windows users, please note the directories should be separated using 
# forward slashes as in below example:
# D:/openspecimen/tomcat
# D:/opnespecimen/data
# D:/openspecimen/plugins
#######################################################################

# This field is useful for deploying multiple OpenSpecimen 
# instances on the one Tomcat server. E.g. "os-test" and 
# "os-prod".
app.name=openspecimen

# Name of datasource configured in  the Tomcat's context.xml.
# Usually, it is "jdbc/openspecimen".
datasource.jndi=jdbc/openspecimen 

# Value can be mysql or oracle
database.type=mysql

# Value can be fresh or upgrade.
# This should be "upgrade" if the database was initially upgraded from caTissue.
# Note: This should be fresh for all other cases.
datasource.type=fresh

# Absolute path where Tomcat is installed
tomcat.dir={..}/apache-tomcat-9.0.37

# Absolute path to OpenSpecimen data directory.
# Best practice: Create a folder in parallel to 'tomcat.dir' with 
# the name "openspecimen/data"
app.data_dir={..}/OpenSpeciemen/data
 
# Absolute path to OpenSpecimen data directory.
# Best practice: Create a folder in parallel to 'tomcat.dir' with 
# the name "openspecimen/plugins"
plugin.dir={..}/OpenSpeciemen/plugins

# Optional. Absolute path of the customised logging configuration file.
# The configuration file should follow log4j configuration rules.
app.log_conf=

Add lines in ${TOMCAT_HOME}/conf/context.xml inside <Context>. Must use root user or user with SUPER privilege if binary logging is enabled in mysql.

<Resource name="jdbc/openspecimen" auth="Container" type="javax.sql.DataSource"
      maxTotal="100" maxIdle="30" maxWaitMillis="10000"
      username="root" password="PASSWORD"
      driverClassName="com.mysql.cj.jdbc.Driver"
      url="jdbc:mysql://localhost:3306/openspecimen?serverTimezone=UTC&amp;characterEncoding=utf8&amp;useUnicode=true&amp;useSSL=true"
      testOnBorrow="true" validationQuery="select 1 from dual" />
<Environment
      name="config/openspecimen"
      value="{..}/apache-tomcat-9.0.37/conf/openspecimen.properties"
      type="java.lang.String"/>

Install npm modules

Install git

Set npm mirrors if needed

npm config set registry https://registry.npm.taobao.org
# npm config get registry # Check if success

Install module

pushd {..}\openspecimen-8.0.b1\www
npm install bower
npm install grunt-cli

Add {..}/node_modules/.bin to PATH

Prepare openspecimen compile

Edit {..}/openspecimen-8.0.b1/build.properties
```
app_home={..}/apache-tomcat-9.0.37
```

Add mirrors of maven if needed in {..}/openspecimen-8.0.b1/build.gradle

repositories {
    maven {
      url 'https://maven.aliyun.com/repository/public/'
    }
  mavenCentral()
}

Comple everything with gradle

pushd {..}\openspecimen-8.0.b1\www

# grunt must be installed locally
npm install grunt --save-dev
npm install
bower install

cd ..

# Comple and put generated WAR file to app_home/webapps setted in {..}/openspecimen-8.0.b1/build.properties
gradle deploy 

# The following is not needed

# Comple jar only
# gradle compileJava 

# Comple and generate WAR file only
# gradle build

Start the daemon

Set the port in {..}/apache-tomcat-9.0.37/conf/server.xml . The default is 8080

<Connector port="8080" protocol="HTTP/1.1"
               connectionTimeout="20000"
               redirectPort="8443" />

Add tomcat-user：{..}/apache-tomcat-9.0.37/conf/tomcat-users.xml

<tomcat-users>

...
<role rolename="admin-gui"/>
  <role rolename="manager-gui"/>
  <user username="tomcat" password="tomcat" roles="admin-gui,manager-gui"/>
  
...
</tomcat-users>

Start standalone

mysqld --standalone --console
{..}\apache-tomcat-9.0.37\bin\catalina.bat start

Test from browser

# Check app status, username tomcat password tomcat
http://localhost:8080/manager/html
# The site, username admin password Login@123
http://localhost:8080/openspecimen

OpenSpecimen

An Open Source Biobanking Informatics Platform Developed by Krishagni Solutions (India)

Introduction

OpenSpecimen (formerly known as caTissue Plus) is a Free & Open Source biobank/biospecimen management software. At the heart of OpenSpecimen is that “biospecimens without high quality data is of no value”. OpenSpecimen is used across the globe in some of the most respected biobanks of various sizes and diseases. OpenSpecimen streamlines management of biospecimens across collection, consent, QC, request and distribution. Finally, OpenSpecimen is highly configurable and customizable. E.g., adding a custom field or form can be done in minutes by a non-IT person.

Krishagni Solutions (India) actively develops newer versions of OpenSpecimen as well provides professional support. Support includes phone/email, data migration, customizations, integrations, training, and so forth.

For more details visit: www.openspecimen.org

Features

Planned and unplanned biospecimen collections
Storage and Inventory management
Role based user authentication and authorization
Participants and informed consents
Path reports
Clinical and pathology annotations
Specimen request and distribution
Shipping and tracking
Track specimen lifecycle events
Reports: Data query, Pivot table, Export as CSV, Scheduled reports
Custom fields and forms
Complete audit trial
Bulk Operation to upload CSV data
Token based specimen label generation
Barcode printing
REST APIs
Integration with clinical databases
Integration with instruments
Real time notifications

Upcoming features

Patient family relationships (family pedigree)
Invoicing
Tissue Microarray
Highly configurable user interface
Mobile and tablet apps

Online Resources

Website: http://www.openspecimen.org Forums: http://forums.openspecimen.org Help: http://help.openspecimen.org Email: mailto:contact@openspecimen.org

License

OpenSpecimen is released under BSD 3 Style license. https://github.com/krishagni/openspecimen/blob/trunk/LICENSE.md

Contact Information

Project Lead: Srikanth Adiga Email: srikanth.adiga@openspecimen.org

mimi3421/openspecimen