A consistent error with running the command docker run --rm --entrypoint "./cleanAD/update_table.sh" to perform the AD specimen table update was that the config.yml file could not be located within the directory (although this was not a problem when running the generate-table.R script locally in an RStudio instance). This PR uses system.file() to locate the config file, which worked in testing.
I also added a line to the dockerfile that checks for changes to the github repository, and invalidates the cache if it finds them. This allows to use cacheing to build the previous more time consuming layers of the image, without skipping over changes to the actual code in the repo.
A consistent error with running the command
docker run --rm --entrypoint "./cleanAD/update_table.sh"to perform the AD specimen table update was that the config.yml file could not be located within the directory (although this was not a problem when running the generate-table.R script locally in an RStudio instance). This PR uses system.file() to locate the config file, which worked in testing.I also added a line to the dockerfile that checks for changes to the github repository, and invalidates the cache if it finds them. This allows to use cacheing to build the previous more time consuming layers of the image, without skipping over changes to the actual code in the repo.