This is a python/R/geospatial docker image that builds upon rocker/geospatial:4.1.2.
A second repo, gwells_geocode_and_archive_data will contain scripts that will download gwells.csv, reverse-geocode the lat-long, create data quality variables and save the results to a repo of ever-increasing size. The python scripts come from Simon Norris code.
A third repo, gwells_shiny will read these csv and display them.
Lots of code for the Dockerfile comes from this image by Thomas Schaffer, and there is more useful stuff there.
Here is more info than required:
Here is the lines of codes I use to build the image and upload it to dockerhub (my username is morglum):
docker build -t monrstudio .
docker tag monrstudio morglum/monrstudio
docker push morglum/monrstudio
Here is a line of code to start the server with "yourpasswordhere". The rstudio server will be available at 127.0.0.1:8787
docker run -d --rm -p 8787:8787 -e PASSWORD=yourpasswordhere --name monrstudio -v ~/git/montest:/tmp/workingdir -w /tmp/workingdir monrstudio
The -d (detached) starts the server but allows us to keep working in the terminal.
The -v (volume) allows us to work on code that is available locally.
The -w (working dir) sets the current work directory to /tmp/workingdir
This is how to SSH into the docker after starting it :
docker exec -it monrstudio bash
Once in Rstudio, one can use reticulate to set the conda environment to gwells_locationqa using this code:
library(reticulate)
use_condaenv(condaenv = "gwells_locationqa", required= TRUE)
We do not use reticulate in this project, because reticulate converts functions to R. The geocoding and qa scripts are closer to shell commands. They do not take a table in memory as input and do not return a table in memory as output. Instead, they read a CSV file and write to a different CSV file.
The easiest way I found to run the python scripts from the gwells_locationqa environment is to create a shell script that activates the environment and calls the .py file, like so:
#!/bin/bash
#set -euxo pipefail
eval "$(conda shell.bash hook)"
conda activate gwells_locationqa
cp /GWELLS_LocationQA/gwells_locationqa.py /tmp/workingdir/gwells_locationqa.py
python gwells_locationqa.py geocode not_an_api_key