Following are the servers, database, and code repositories participating in the project.

$DATA_DIR variable

Please note regarding directory paths: In this documentation we use the Bash-style prefix $DATA_DIR for clarity rather than the current absolute path (/home/atushar/dengue_data), which is subject to change.

Servers

There are two servers involved in the hosting and updating of the dengue-cases database. To get access to the UMass server, contact Nicholas Reich. The page UMass-Server-Access lays out the process for connecting to the virtual machine (VM) that houses the database. To get access to the JHSPH server, contact Joshua Kaminsky.

JHSPH server: idmodeling1.jhsph.edu

This server is to which the Thai MOPH collaborators uses SFTP to upload Access and CSV files. Directories of interest:

• idmodeling1.jhsph.edu:/home/sasithan/incoming: Destination of the files.
• idmodeling1.jhsph.edu:/home/suthanun/incoming: Former destination (documented here should we need to go back to older files).

UMass server: sphhs-bioepi01.umass.edu

This server runs the Postgres server that serves the dengue_cases database (see below) and is where the import process takes place.

Directories of interest:

• $DATA_DIR/dengue-data-new-repo (base_dir variable in R): Cloned copy of the GitHub repository.
• $DATA_DIR/dengue_data (base_data_dir variable): Parent data directory that has subdirectories for raw and processed data.
• $DATA_DIR/raw: Contains unprocessed MOPH data. Files are located either here (archive data from previous years) or under $DATA_DIR/raw/rolling for current data.
• $DATA_DIR/original_data (original_data_dir variable): Contains a normalized version of the CSV files in $DATA_DIR/raw. It is these files that are actually imported into the database.
• $DATA_DIR/peripheral_data (peripheral_data_dir variable): Contains unique-geocodes.rds, which has TIS 1099 codes used during import.

Codebases

The data import codebase is located on GitHub at https://github.com/reichlab/dengue-data , and a local copy is cloned at sphhs-bioepi01.umass.edu:/$DATA_DIR/dengue-data-new-repo. The master branch is the currently running one, and it is where main line development takes place.

Locations of other codebases are found in Use-Cases.

Database

The the dengue_cases Postgres database is served on sphhs-bioepi01.umass.edu at port 6392. For details on connecting to it from R or the command line, see the relevant sections in the document accessing dengue database server. See Dengue-Cases-Database for database details including namespaces, functions, and tables.