This PR sets up the infrastructure change necessary to enable Access DB files to be read in place i.e., without the need to copy them to the db_extraction task folder.
To test this PR, first install the orderly.sharedfile plugin
Then edit the orderly_config.yml to update the singledb, doubledb and doubledb2 fields. I have added detailed instructions in the README file.
Note: I have included orderly_config.yml in the repo for demonstration. As the settings will be user-specific, you don't need to add this file to version control. That is, don't push it to the repo.
Delete all the access database files from the db_extraction folder.
Then as before run
orderly2::orderly_run('db_extraction', parameters = list(pathogen = "Ebola"))
This PR sets up the infrastructure change necessary to enable Access DB files to be read in place i.e., without the need to copy them to the db_extraction task folder. To test this PR, first install the orderly.sharedfile plugin
remotes::install_github("mrc-ide/orderly.sharedfile")Then edit the orderly_config.yml to update the singledb, doubledb and doubledb2 fields. I have added detailed instructions in the README file. Note: I have included orderly_config.yml in the repo for demonstration. As the settings will be user-specific, you don't need to add this file to version control. That is, don't push it to the repo.
Delete all the access database files from the db_extraction folder.
Then as before run
orderly2::orderly_run('db_extraction', parameters = list(pathogen = "Ebola"))