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common


License

License
GroupId

GroupId

io.igia.i2b2.cdi.common
ArtifactId

ArtifactId

common
Last Version

Last Version

0.3.3
Release Date

Release Date
Type

Type

jar
Description

Description

common
Project URL

Project URL

https://github.com/igia/i2b2-cdi-ext/
Project Organization

Project Organization

igia
Source Code Management

Source Code Management

https://github.com/igia/i2b2-cdi-ext/

Download common

Filename Size
common-0.3.3.pom
common-0.3.3.jar 69 KB
common-0.3.3-sources.jar 55 KB
common-0.3.3-javadoc.jar 330 KB
Browse

How to add to project

<!-- https://jarcasting.com/artifacts/io.igia.i2b2.cdi.common/common/ -->
<dependency>
    <groupId>io.igia.i2b2.cdi.common</groupId>
    <artifactId>common</artifactId>
    <version>0.3.3</version>
</dependency>
// https://jarcasting.com/artifacts/io.igia.i2b2.cdi.common/common/
implementation 'io.igia.i2b2.cdi.common:common:0.3.3'
// https://jarcasting.com/artifacts/io.igia.i2b2.cdi.common/common/
implementation ("io.igia.i2b2.cdi.common:common:0.3.3")
'io.igia.i2b2.cdi.common:common:jar:0.3.3'
<dependency org="io.igia.i2b2.cdi.common" name="common" rev="0.3.3">
  <artifact name="common" type="jar" />
</dependency>
@Grapes(
@Grab(group='io.igia.i2b2.cdi.common', module='common', version='0.3.3')
)
libraryDependencies += "io.igia.i2b2.cdi.common" % "common" % "0.3.3"
[io.igia.i2b2.cdi.common/common "0.3.3"]

Dependencies

There are no dependencies for this project. It is a standalone project that does not depend on any other jars.

Project Modules

There are no modules declared in this project.

I2b2 CDI Demo Installation

I2b2 CDI (Clinical Data Infrastructure) application provides generic and simple way to imports patients data and clinical concepts from csv files into i2b2. I2b2 framework provides data storage and querying the data with the help of clinical concepts (i.e. Ontology). This application monitors remote directories in SFTP server and downloads files from those remote directories when it senses new files. Those files are then uploaded to i2b2 database.

To set up the complete environment for this application, we will need setting up following:

  • I2b2 framework (Consist of webclient, wildfly and postgres database)
  • SFTP server
  • Postgres database (I2b2 CDI application uses this for temporary purpose)
  • I2b2 CDI application

docker-compose file provided in this repository helps to quickly set up all these required components. Please note that you should change values for username and password related environment variables in docker-compose files before setting up environments.

Prerequisite

Following software/tools must be installed:

Pull the repository for the I2b2 CDI

Provide your partner's user id and password.

git clone https://github.com/igia/i2b2-cdi-ext.git
cd i2b2-cdi-ext/i2b2-cdi-app/src/main/docker

Setup I2b2 framework

docker-compose up -d i2b2-pg i2b2-web i2b2-wildfly

Note: Verify that i2b2 webclient runs successfully on http://localhost/webclient, by successfully logging in and running a query to get all males.

Clean default i2b2 instance

docker-compose up i2b2-python-delete-data

Note: Verify that there is no ontology available in the webclient.

Setup I2b2 CDI Application

It consist of 3 components:

  • SFTP : To upload files
  • Postgresql database : This will be used as staging database
  • I2b2 CDI Application : To download files, read data, transform and insert to i2b2 database.
docker-compose up -d i2b2-cdi-sftp i2b2-cdi-pg i2b2-cdi-app

Check logs to ensure there are no errors.

docker logs -f i2b2-cdi-sftp
docker logs -f i2b2-cdi-pg
docker logs -f i2b2-cdi-app

Note : If your i2b2 database connection and credentials are different than what have been specified in docker-compose file, you will need to update below environment variables in docker-compose:

  • APP_DATASOURCE_I2B2_URL
  • APP_DATASOURCE_I2B2_USERNAME
  • APP_DATASOURCE_I2B2_PASSWORD

Load concepts

  • Login to sftp server using default credentials and upload demo zip file in concept folder.
  • Verify that the concept herirarchy is seen in webclient and a query for Labs/Blood/LDL gives 0 patients.

Load facts

  • Login to sftp server using default credentials and upload demo zip file in data folder.
  • Verify that the LDL query above gives some patients count.

License and Copyright

MPL 2.0 w/ HD
See LICENSE file.
See HEALTHCARE DISCLAIMER file.
© Persistent Systems, Inc.

io.igia.i2b2.cdi.common

igia

Enabling the development, deployment, and sharing of healthcare technology.

Versions

Version
0.3.3
0.3.1