ping543f / smartva-analyze

SmartVA-Analyze Desktop Application

SmartVA-Analyze is an application that implements the Tariff 2.0 Method for computer certification of verbal autopsies.

More information and the SmartVA-Analyze application can be found here: http://www.healthdata.org/verbal-autopsy/tools

The latest development version of the SmartVA-Analyze application can be found in releases. The application is available as a Windows graphical user interface (GUI), Windows command-line interface (CLI), and Linux binary.

The latest stable version of the SmartVA-Analyze application can be found here: http://www.healthdata.org/verbal-autopsy/tools

The SmartVA-Analyze application requires an input csv in the format of the PHMRC Full Questionnaire, PHMRC Shortened (SmartVA) Questionnaire, or WHO 2016 Questionnaire. The simplest workflow is to collect verbal autopsy data with ODK Collect and export the questionaire data via ODK Aggregate or ODK Briefcase.

Requirements

To compile the source code of SmartVA-Analyze, the following applications must be installed:

• Anaconda
• Docker

Build Instructions

To build the SmartVA-Analyze application as seen in releases, run one of the following commands:

Windows: build_script.bat

macOS, Linux: $ sh build_script.sh

Environment Instructions

To create your python environment, either create a conda environment or use the Docker image.

Windows:

$ conda create -n smartva python=2.7.13 wxpython=3.*
$ activate smartva
$ pip install -r requirements.txt -r requirements-dev.txt - r requirements-win.txt

macOS, Linux:

$ conda create -n smartva python=2.7.13 wxpython=3.*
$ source activate smartva
$ pip install -r requirements.txt -r requirements-dev.txt

or

$ docker build -t smartva-build-linux -f ./pkg/docker/linux-build/Dockerfile ./pkg/docker
$ docker build -t smartva-dev -f pkg/docker/dev/Dockerfile .
$ docker run -it --rm -v `pwd`:/home/smartva/smartva smartva-dev

Run Instructions

To test your python environment, run the following command to show the available options.

$ python app.py --help

Usage: app.py [OPTIONS] INPUT OUTPUT

Options:
  --country TEXT                  Data origin country abbreviation. "LIST"
                                  displays all. Default is "Unknown".
  --hiv BOOLEAN                   Data is from an HIV region. Default is True.
  --malaria BOOLEAN               Data is from a Malaria region. Default is
                                  True.
  --hce BOOLEAN                   Use Health Care Experience (HCE) variables.
                                  Default is True.
  --freetext BOOLEAN              Use "free text" variables. Default is True.
  --figures BOOLEAN               Generate charts and figures output. Default
                                  is True.
  --language [english|chinese|spanish]
                                  Language used for output files.
  --version                       Show the version and exit.
  --legacy-format                 Output files in a format that matches
                                  SmartVA v1.2
  --help                          Show this message and exit.

Example

$ mkdir ./test/example/output
$ python app.py "./test/example/input/PHMRC_short_example.csv" "./test/example/output" --hiv=False
$ python app.py "./test/example/input/WHO_2016_1_5_1_example.csv" "./test/example/output" --language=chinese --country=CHN

Test Instructions

All tests are run using pytest:

$ python -m pytest