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OHNLP Toolkit Environment Setup

Installation and Preparation Scripts for setting up OHNLP Toolkit configured for an example PASC/RECOVER NLP task

System Requirements and Recommendations

  • Java 9+ (11 recommended)
  • Unix-Based System
    • unzip must be installed (e.g. via apt-get install zip unzip)

Installation Instructions

  1. Clone this repository via git clone https://www.github.com/OHNLP/OHNLPTK_SETUP.git into an empty directory
  2. Execute ./install_or_update_ohnlptk.sh
  3. Once installation is complete, navigate to the created OHNLPTK_SETUP directory
  4. Edit configs/[run_nlp]_[ohdsi_cdm]_[ohdsi_cdm].json lines 5-17 and lines 36-56 to reflect your data warehouse settings

Instructions for Use

For a Local Run: Run run_pipeline_local.sh. You will be prompted for the configuration to use. Alternatively, run run_pipeline_local.sh your_config_name.json for non-interactive execution

For other environments: Executed package_modules_and_configs.sh and edit the run_pipeline_### appropriate to your environment and replace declared variables as appropriate.