Observational Health Data Sciences and Informatics development

development:architecture

Anonymous (anonymous@undisclosed.example.com) — 2014-12-03T15:58:31+0000

OHDSI Architecture Overview

development:best_practices_estimation

Anonymous (anonymous@undisclosed.example.com) — 2020-03-09T05:18:13+0000

OHDSI Best Practices for Estimating Population-Level Effects :!: This document is under development. Changes can be proposed and discussed via the OHDSI Forum and in the Population-Level Estimation Workgroup meetings. General principles * Transparency: others should be able to reproduce your study in every detail using the information you provide.

development:data_architecture

Anonymous (anonymous@undisclosed.example.com) — 2016-08-23T13:24:43+0000

Data Architecture In this document we describe various conventions used in the processing and storage of data within the OHDSI architecture. Data within the OHDSI data architecture falls into one of four categories including Source Data, Standardized Data, Derived Data and Administrative Data.

development:database_migration_management

Anonymous (anonymous@undisclosed.example.com) — 2015-04-24T13:18:18+0000

Background The OHDSI WebAPI services executable creates and maintains some read/write tables in the OHDSI database schema for services that need to persist data. These tables are not part of the Common Data Model. They are used by the OHDSI WebAPI services to save data such as analytical results, cohort definitions and operational data such as batch job execution statuses.

development:guidelines

Anonymous (anonymous@undisclosed.example.com) — 2017-02-02T14:43:42+0000

Developer Guidelines This page discusses the approach to software development used by the OHDSI community. For information on the development of statistical methods please see the Research Methods section of the wiki. Please refer to the Architecture section of the wiki for a broad overview of general components of an OHDSI based application.

development:issue_tracker

Anonymous (anonymous@undisclosed.example.com) — 2016-02-08T15:14:00+0000

Open Issues on GitHub Achilles Common Data Model CDM Vocabulary Cyclops

development:methods

Anonymous (anonymous@undisclosed.example.com) — 2014-11-11T05:26:45+0000

Observational Research Methods and Tools * Cyclops * Self Controlled Cohort method * Empirical Calibratio

development:ohdsi_code_style_for_r

Anonymous (anonymous@undisclosed.example.com) — 2020-04-06T13:39:47+0000

OHDSI code style for R This has moved here:

development:ohdsi_code_style_for_sql

Anonymous (anonymous@undisclosed.example.com) — 2020-04-06T13:40:33+0000

OHDSI code style for SQL This has moved here:

development:ohdsi_content_delivery_network

Anonymous (anonymous@undisclosed.example.com) — 2015-02-09T16:51:19+0000

Overview OHDSI uses the AWS cloudfront content delivery network (CDN). The OHDSI CDN domain name is “cdn.ohdsi.org”. The OHDSI CDN will host OHDSI specific javascript files and potentially other content that requires low latency delivery. If you have a file that you need to host in the OHDSI CDN please send an email to

development:ohdsi_documentation_guidelines

Anonymous (anonymous@undisclosed.example.com) — 2015-02-06T07:53:28+0000

OHDSI documentation guidelines For R packages we use the standards for documenting those, so use in-line documentation (using Roxygen) to document functions which are collected in a package manual, and optionally vignettes (using KNITR) to describe how to use a package.

development:ohdsi_github_projects

Anonymous (anonymous@undisclosed.example.com) — 2016-10-18T18:43:24+0000

Updated can be found here Access to OHDSI project source code Github is the source control repository for all OHDSI projects. Here is the main URL for OHDSI Github projects: OHDSI collaborative development model OHDSI developers use Github flow with the fork and pull collaborative development model.

development:ohdsi_github_projects_v2

Anonymous (anonymous@undisclosed.example.com) — 2017-02-02T14:41:53+0000

Github Contributor Best Practices Contributors: Anthony Sena, Chris Knoll, Frank DeFalco, Peter Rijnbeek Overview For reference, we reviewed some common release/code management articles such as Gitflow and alternatives to form the basis of this article. The goal with this approach was to keep the code management process as simple as possible while leveraging the functionality available in Git and GitHub. We've also formally adopted the semantic versioning scheme for all software which is alre…

development:ohdsi_jenkins_ci_server

Anonymous (anonymous@undisclosed.example.com) — 2015-03-16T06:31:03+0000

How to get access The OHDSI Jenkins CI Server User Interface is here: Anyone can view the status of the build jobs in Jenkins using the above URL without needing to log into the server. If you want to setup your own Jenkins build jobs request an OHDSI Jenkins account by sending an email to

development:ohdsi_nexus_maven_repository

Anonymous (anonymous@undisclosed.example.com) — 2021-12-10T14:05:14+0000

Overview The WebAPI war file can be downloaded from the OHDSI nexus repository, using a URL in the following format: https://repo.ohdsi.org/nexus/repository/releases/org/ohdsi/WebAPI//WebAPI-.war For example, if the WebAPI release number was

development:ohdsi_travis_ci_server

Anonymous (anonymous@undisclosed.example.com) — 2015-06-30T02:58:23+0000

The OHDSI Travis CI page can be found here: . Travis builds are automatically triggered by pushes to the repositories. On build status change (e.g. a build failure) e-mails are sent to the administrators. To add a repository to the list, two things need to be done: 1. Add a .travix.yml file to the repository 2. Add the repository to Travis

development:openssl

Anonymous (anonymous@undisclosed.example.com) — 2016-11-12T03:47:23+0000

Using OpenSSL to create an SSL Certificate This page will detail how to use OpenSSL to create a Certificate Authority and how to generate a Secure Socket Layer (SSL) certificate for use with a web server such as Apache Tomcat. This is useful when you need to use SSL on a local development machine. As a general rule of thumb, if you need an SSL certificate for use on either a production or non-production instance, you should contact your organization's IT team to obtain a certificate that will w…

development:optimizing_spring_builds_in_netbeans

Anonymous (anonymous@undisclosed.example.com) — 2015-03-05T13:47:10+0000

Background It is much faster to use a Spring-boot run maven build goal to launch the embedded tomcat container in a Spring-boot application than to use the standard NetBeans approach of packaging and (re)-deploying the application in the tomcat server on each build. The Spring-boot run approach takes under 40 secs to launch the application.

development:overview

Anonymous (anonymous@undisclosed.example.com) — 2017-07-07T18:16:15+0000

OHDSI Development Software The OHDSI developer community is committed to the development of open-source, high-quality, and easy to use tools for making the most out of observational health data. * OHDSI-In-A-Box: a virtual machine loaded with the entire OHDSI Stack for educational use

development:projects

Anonymous (anonymous@undisclosed.example.com) — 2014-11-11T15:27:06+0000

Active Projects * ACHILLES - Population-level summarization of dataset in CDM format * HERACLES * HERMES * LAERTES * CYCLOPS * White Rabbit

development:roadmap

Anonymous (anonymous@undisclosed.example.com) — 2017-07-27T17:49:30+0000

OHDSI Architecture Roadmap The OHDSI Archiecture's current state is represented by Version 2. Future versions are proposed technology roadmaps. Version 3 is a draft architecture roadmap that is open for public comment. Please direct feedback to fdefalco@ohdsi.org or fdefalco@its.jnj.com.

development:security

Anonymous (anonymous@undisclosed.example.com) — 2018-03-20T13:33:06+0000

This page describes the details of the security implementation in WebAPI. DEPENDENCIES The security subsystem is built on top of Apache Shiro framework. Apache Shiro is a powerful and easy-to-use Java security framework that performs authentication, authorization, cryptography, and session management. With Shiro’s easy-to-understand

development:sql

Anonymous (anonymous@undisclosed.example.com) — 2015-02-03T14:35:40+0000

CDM data can live on different databases. SqlRender package provides a way to translate SQL statements across dialects. I relies on a CSV table that translates from source dialect to target dialect.Because of temporal issues, the source has to be MSSQLServer dialect.

development:style_guide

Anonymous (anonymous@undisclosed.example.com) — 2017-09-19T20:10:50+0000

Web Development Style Guide Typography Fonts The following font stack should be used for OHDSI based web applications: font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", "Segoe UI Symbol";

development:unit_testing_in_r

Anonymous (anonymous@undisclosed.example.com) — 2020-04-06T13:51:36+0000

This has moved to

development:webapi

Anonymous (anonymous@undisclosed.example.com) — 2015-09-19T21:24:21+0000

Here is a link to the automatically generated documentation for the WebAPI services: