Installation

Prerequisites

To run this pipeline, you need the following prerequisites:

Setup

  1. Clone the repository for local installation:

    git clone https://github.com/oucru-id/tb-to-fhir-deeplex.git
cd tb-to-fhir-deeplex

  2. Install Nextflow:

    curl -s https://get.nextflow.io | bash

  3. Testing the Nextflow install:

    nextflow -v

  4. Create and activate a virtual environment:

    python3 -m venv venv
source venv/bin/activate

  5. Get Access Token to FHIR Server: Notes: need to fill input_sso.json first

    python3 scripts/get_access_token.py

  6. Basic Run:

    nextflow run main.nf

  7. Search for Patient UUID: Notes: need to get an access token first

    python scripts/get_patient_by_nik.py --nik 1234567890 --fhir_base_url "https://<BASE_URL>/fhir"

  8. Run and Upload to FHIR Server: Notes: need to get an access token and mapping patient UUID first before running the pipeline

```bash
nextflow run main.nf \
  --fhir_server_url "https://<BASE_URL>/fhir"
```

Setup (Docker)

  1. Pull Docker image:

    docker pull robind1/tb-to-fhir-deeplex:v1.4.1

  2. Get Access Token to FHIR Server: Notes: need to fill input_sso.json first

    docker run --rm \
  -v /your/host/data:/pipeline/data \
  robind1/tb-to-fhir-deeplex:v1.4.1 \
  get-token --sso /pipeline/data/input_sso.json --out /pipeline/data/access_token.json

  3. Basic Run:

    docker run --rm \
  -v /your/host/data:/pipeline/data \
  -v /your/host/results:/pipeline/results \
  robind1/tb-to-fhir-deeplex:v1.4.1 \
  run main.nf

  4. Search for Patient UUID: Notes: need to get an access token first

    docker run --rm \
  -v /your/host/data:/pipeline/data \
  robind1/tb-to-fhir-deeplex:v1.4.1 \
  get-patient \
  --nik 1234567890 \
  --fhir_base_url "https://<BASE_URL>/fhir"

  5. Run and Upload to FHIR Server: Notes: need to get an access token and mapping patient UUID first before running the pipeline

    docker run --rm \
  -v /your/host/data:/pipeline/data \
  -v /your/host/results:/pipeline/results \
  robind1/tb-to-fhir-deeplex:v1.4.1 \
  run main.nf --fhir_server_url "https://<BASE_URL>/fhir"