mobile_covid19_tracker

Construct close contact from mobile tracking data. For users coming from makselab's Project COVID19 K-core tracker (https://github.com/makselab/COVID19) Please refer to the "running for research" section.

Production

Deployment code for calculation pipeline as backend of an actual app.

Staging

Pipeline of detecting and generating close contact network. Requires deployment of Elasticsearch and Airflow

Running for research

To running for research on 'COVID19 K-core tracker'. Please download staging folder only. And following the below.

1. Install Elasticsearch ver. >= 7.6 (https://www.elastic.co/)
2. Install necessary packages by pip install requirements.txt
3. Download the data and extract any folder.
4. Edit config_params.yaml to set parameters of generating network. Set "track.person" field to "levels" and modify the location of files and temp/output folder accordingly. See the comments for details.
5. Edit config_status.yaml to make sure the time in "grandata" field is later the the "last run".
6. cd staging/ and in staging folder, run python src/data_ingest.py. This step automatically ingest the raw data into elasticsearch.
7. Run python research/level_expansion.py to generate close contact network. You can setting up how many chuncks you are going to expand by modifying the max_chunk variable in it. The I/O file/folder and paramter is controled by the config_params.yaml.