This is used to build tools which process and standardize data.

You cannot select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

Go to file

youainti 4831864805 adjusted paths and started writing something to link GBD and ICD10		3 years ago
raw_data/ICD- 10_(2019 version)/WHO	adding WHO ICD-10 Data	3 years ago
containers	reorganized python scripts into package, added requisit sql, and added shell scripts to notify me when the systems are up again.	3 years ago
development_sql	reorganized python scripts into package, added requisit sql, and added shell scripts to notify me when the systems are up again.	3 years ago
non-db_data_sources/GBD and ICD-10_(2019 version)	adjusted paths and started writing something to link GBD and ICD10	3 years ago
scripts	reorganized python scripts into package, added requisit sql, and added shell scripts to notify me when the systems are up again.	3 years ago
.gitignore	lots of updates while integrating rxnav and aact into one dockerfile	3 years ago
README.md	Added instructions to README, improved downloader and adjusted justfile recipe to accomodate downloader	3 years ago
justfile	lots of updates while integrating rxnav and aact into one dockerfile	3 years ago

README.md

ClinicalTrialsDataProcessing

This represents my

Prerequisites

Python >= 3.10 (requires match statement) Docker >= 20.10 Curl >= 7 Just >= 1.9

Usage

Basic usage

Check prerequisites

just check-status

Setup the underlying AACT database including downloading both the AACT dump and historical data.

just create
just select-trials
just count=1000 get-histories

replacing the 1000 in count=1000 with the number of trials you want to download.

Advanced Usage

If you need to reset the db without downloading the AACT dump

just rebuild
just select-trials
just count=1000 get-histories

Description of all the `just` recipes

Background information

This is designed to run on a linux machine with bash. If you are using a shell other than bash you should be aware of what is needed to run all of this using bash

If any of the discussions below don't make sense, talk to your sysadmin, a local linux user, or reach out to the author.

Just installation

I use the command runner just to automate/simplfy setting up the docker containers and running many of the python scripts. It is similar to make in many ways but is designed to do less.

Just can be installed from https://github.com/casey/just/

Python installation

This requires python 3.10 or above due to the use of match-case statements in the html parser.

Check which version of python you have by typing python --version. If you do not have the required version, I would recommend installing the conda python manager and setting up a conda environment with python 3.10. Instructions for doing so are on the internet.

Docker and Postgres

Docker is a tool to manage and run OCI containers. What this means in regards to this project is that docker makes it easy to setup containers.

Install docker based on instructions for your linux distribution.

Docker networking

I have the docker container for the database attached to a network called "pharmaceutical_research" because I have a container with pgadmin4 running on that docker network. This can be adjusted in the dockerfile.

I also have the database container open on port 5432, the typical postgresql database port.

Database logins

I have choosen the database user of root with a password of root because I don't really need this database to be secure. If you do need to think about the security of your database I would recommend you start by changing these.