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getting_started_with_pbj
Johnsd11 edited this page Sep 25, 2024
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- Latest cTAKES version installed
- Python installed
- Artemis installed
- Download Apache ActiveMQ Artemis here: https://activemq.apache.org/components/artemis/download/
- Navigate to the downloaded apache-artemis-version folder in your command line
- Navigate into bin, then use these commands
./artemis create [name of your broker]for Mac and Linux orartemis create [name of your broker]for Windows (These commands will create a broker that is needed to run PBJ)
- You will be prompted to create a username and password, as well as
--allow-anonymous, PressYfor this option
- Now navigate into your brokers' bin folder
Optional: cTakes should run your broker for you but if it does not work, run the command./artemis runfor Mac and Linux orartemis runfor Windows to start the broker
For more information see apache-artemis documentation for further documentation.
- Start by creating an application configuration in your IDE (I will be using Intellij for this example)
- Create a name for it and copy down the information you see in the picture below

- In this next step you will need to have made an artimis broker as well as have python installed, we also recommend creating a venv for this project which you can do by following this guide
- In the program arguments section include these parameters
-p "PbjSentencePrinter"(path to program you would like to run)
-i "org/apache/ctakes/examples/notes/annotated"(path to input folder)
-a "[Destination of your Artemis Broker]"
-v "[Destinaiton of your virtual env]"
-o "output folder"

- Piper File Submitter
- UMLS Package Fetcher
- Dictionary Creator
- Simple Pipeline Fabricator
- Pipeline Installation Facility
- ctakes-pbj module
- Getting started with PBJ
- Python pbj-component
- Python pbj-pipeline
- Python pbj-scripts
- Python pbj-tools
- pbj-user-pipeline
- examples
- ctakes-assertion
- ctakes-assertion-zoner
- ctakes-chunker
- ctakes-clinical-pipeline
- ctakes-constituency-parser
- ctakes-context-tokenizer
- ctakes-core
- ctakes-coreference
- ctakes-dependency-parser
- ctakes-dictionary-lookup
- ctakes-dictionary-lookup-fast
- ctakes-distribution
- ctakes-dockhand
- ctakes-drug-ner
- ctakes-examples
- ctakes-fhir
- ctakes-gui
- ctakes-lvg
- ctakes-mastif-zoner
- ctakes-ne-contexts
- ctakes-pbj
- ctakes-pos-tagger
- ctakes-preprocessor
- ctakes-regression-test
- ctakes-relation-extractor
- ctakes-side-effect
- ctakes-smoking-status
- ctakes-template-filler
- ctakes-temporal
- ctakes-tiny-rest
- ctakes-type-system
- ctakes-utils
- ctakes-web-rest
- ctakes-ytex
- ctakes-ytex-uima
- ctakes-ytex-web