Git Product home page Git Product logo

logicahealth / komet Goto Github PK

View Code? Open in Web Editor NEW
17.0 25.0 5.0 76.56 MB

Informatics Analytic Architecture—A dynamic semantic architecture for the analysis of models, logic, and language.

Home Page: http://informatics-architecture.net/isaac.web/index.html

License: Apache License 2.0

Java 99.10% CSS 0.62% AppleScript 0.01% Swift 0.01% HTML 0.27% XSLT 0.01%
isaac stamp-versioning java-8 javafx informatics terminology terminology-management terminology-extraction snomed loinc rxnorm solor

komet's Introduction

ISAAC: Informatics Analytic Architecture

Knowledge%20Snapshot%20Build Actions Status

A dynamic semantic architecture for the analysis of models, logic, and language.

Environment

  • Java 11 (Oracle or OpenJDK) (Java 8 support deprecated, and on another branch of the source code)
  • Maven 3.5 or newer

JDK 11 notes

Launch the GUI using sh.komet.fx.stage.Komet, rather than MainApp, to avoid all sorts of JavaFX problems with modular java.

Linux Issues

To allow the debugger to work properly when debugging an FX GUI app, you likely will need to disable screengrab.

-Dsun.awt.disablegrab=true

KOMET notes

To enable the GUI to load content directly from your Maven repository, set the parameter as appropriate:

 -DM2_PATH=/mnt/STORAGE/Work/Maven/repository/

developer flags...

-DSHOW_BETA_FEATURES=true 
-DISAAC_DEBUG=true

Apple Issues

Use "jenv exec mvn clean install" to get maven using the correct jdk.

IntelliJ issues

Be aware... newer versions of IntelliJ "should" make this a non issue as is indicated in the last post in that file:

It looks like IDEA solves this for you (like everything else). When loading a large project and letting it thrash, it will open a dialog to up the memory settings. Entering 2048 for Xmx and clicking "Shutdown", then restarting IDEA makes IDEA start up with more memory. This seems to work well for Mac OS, though it never seems to persist for me on Windows (not sure about IDEA 12).

Gitflow

This project uses GitFlow: https://nvie.com/posts/a-successful-git-branching-model/ There are tools in the maven package to make branching easier IF you want the version number in all of the poms changed to match to the feature branch name. If you do NOT want to change the poms when you make a feature branch, you should probably use another mechanism to branch.

Creating a feature branch

mvn gitflow:feature-start

You will be prompted for the feature name:

What is a name of feature branch? feature/: F2

Finishing a feature branch

mvn gitflow:feature-finish

Deploying to a repository

  • Option 1: To deploy, set a profile in your settings.xml with the repository you want to deploy to, patterned after these entries:
  <profile>
      <id>release-deploy</id>
      <properties>
        <altDeploymentRepository>central::default::http://artifactory.isaac.sh/artifactory/libs-release-local</altDeploymentRepository>
      </properties>
  </profile>

  <profile>
      <id>snapshot-deploy</id>
      <properties>
         <altDeploymentRepository>central::default::http://artifactory.isaac.sh/artifactory/libs-snapshot-local</altDeploymentRepository>
      </properties>
  </profile>
  • Option 2: just use the parameter:
-DaltDeploymentRepository=central::default::http://artifactory.isaac.sh/artifactory/libs-snapshot-local

Note, in either case, the value 'central' is a variable that needs to align with a 'server' section in your settings.xml file.

  <server>
    <id>central</id>
    <username>your server username</username>
    <password>your server password</password>
  </server>

Then you can deploy to the repository of your choice using the following command:

mvn clean deploy -Psnapshot-deploy

Bitbucket Pipelines

There is a Bitbucket pipelines configuration provided, which builds the source on openjdk11. It also provides a custom deploy step you can run. Before running the custom (snapshot) deploy step in bitbucket, you need to set the following three variables in your bitbucket pipelines configuration:

DEPLOYMENT_SNAPSHOT_REPO
REPO_USERNAME
REPO_PASSWORD

#GitFlow Implementation We use the Git-Flow Maven plugin hosted on GitHub by Aleksandr Mashchenko

https://github.com/aleksandr-m/gitflow-maven-plugin

Travis

Travis is already configured for this repository. See the .travis.yml file for how to configure it, if you are forking and want to use travis on your own server.

Jenkins

The provided Jenkinsfile runs this as a jenkins pipeline. See comments in the Jenkinsfile for details on what plugins need to be installed on your Jenkins server to build this code.

Performing a release

Make sure that offline is set to false in your settings.xml file.

$ mvn gitflow:release-start gitflow:release-finish\
         -DreleaseVersion=4.64 -DdevelopmentVersion=4.65-SNAPSHOT\
         -DpostReleaseGoals="clean deploy"

$ mvn gitflow:release -Prelease

Other tips

To turn off messages such as the following from JAXB:

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.sun.xml.bind.v2.runtime.reflect.opt.Injector (file:/home/tra/.m2/repository/com/sun/xml/bind/jaxb-impl/2.3.0/jaxb-impl-2.3.0.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int)
WARNING: Please consider reporting this to the maintainers of com.sun.xml.bind.v2.runtime.reflect.opt.Injector
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Add the following flag to the java start command

--add-opens java.base/java.lang=ALL-UNNAMED

komet's People

Contributors

aks8m avatar ashleyswegel avatar cemadmin avatar darmbrust avatar happyfacade avatar kec avatar marc-medley avatar susancastillo avatar theadityakedia avatar

Stargazers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

Watchers

 avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar  avatar

komet's Issues

Request for setup/installation documentation

Hello there! I'm currently evaluating terminology management tools for my team. I'd like to set up Komet locally, but Java is not my usual ecosystem for running web apps, so I'm not sure intuitively how to do this, and the documentation seems rather sparse.

Is it possible to describe step by step how to install a local instance of Komet on Mac, Windows, or Linux?

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.