ihme_db.sh#

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Make a Local Copy an IHME Dismod_at Database#

Syntax#

bin/ihme_db.sh [ -- user ] relative_dir database

Purpose#

This script copies a dismod_at database to a local directory and then runs the db2csv_command on the database. This script is only intended to be used by members of IHME and to be run from the IHME cluster. It can also be run on a computer that has mounted the /ihme/epi and /ihme/homes directories.

Download#

You must first change into a directory where you have write permission, download dismod_at.git , and then change into the dismod_at.git directory. This script can only be run from the download directory dismod_at.git.

python3#

You must inform dismod_at where the python3 executable is located. The setting for this is in the run_cmake.sh file. If that setting is not correct, change it, and then execute the command

bin/run_cmake.sh

absolute_dir#

We use absolute_dir to refer to an absolute path to a directory below which the database is stored before executing this script. You must have read permission below this directory (but do not need write permission). The default value for this directory is

absolute_dir =/ ihme/epi/at_cascade

–user#

The brackets around -- user indicate that this command line argument is optional. If it is present, absolute_dir is the home directory for the specified user; i.e.,

absolute_dir =/ ihme/homes/ user

relative_dir#

The command line argument relative_dir is the directory, relative to the absolute directory, where the database is stored before executing this script.

database#

The command line argument database is the local name of the database file; i.e., there are no / characters in database . The original database is stored in the location

absolute_dir / relative_dir / database

db2csv#

The original database is copied to the directory

ihme_db/ relative_dir

relative to the download directory dismod_at.git. We refer to this as the local directory. The db2csv_command is run on the database. The resulting CSV files are all in the local directory.