sgosline/srp-analytics repository overview

⁠Superfund Research Program Analytics

⁠Incoming Data

The incoming data will be formatted as a table with schema TBD. Currently we are just compiling the current data and not adding to it

⁠How to build your own docker image

If you prefer to build your own docker image, run these commands (turn off PNNL VPN).

git clone https://github.com/sgosline/srpAnalytics.git
cd srp-analytics
docker build . -t srp-analytics

(this building took 8 minutes in macbook pro since it installs all dependencies)

Then run like this

docker run -v $PWD:/tmp srp-analytics [your file here, for example to_be_processedt/7_PAH_zf_morphology_data_2020NOV11_tall.csv]

For faster running add --devel,

docker run -v $PWD:/tmp srp-analytics [your file here, for example to_be_processedt/7_PAH_zf_morphology_data_2020NOV11_tall.csv] --devel

To build the whole database:

sh build_db.sh

⁠How to run from docker hub

To create a data package, you simply need to add your data to the existing repository by running the following

docker pull sgosline/srp-analytics

(this pulling took 5 minutes in mackbook

Then run like this

docker run -v $PWD:/tmp sgosline/srp-analytics [your file here, for example test_input/7_PAH_zf_morphology_data_2020NOV11_tall.csv]

The results will be the four files for the data portal. Add the --devel flag if you are just testing the code.

⁠Data Input

Currently the code is designed to take a specific form of input to be processed by our benchmark dose analysis pipeline. The columns are defined in the table below:

⁠Data Output

The result of the pipeline will be six files, zipped up into a single resource.