https://github.com/dataforgoodfr/batch4_diafoirus_mimic
Dockerized postgres running Mimic
https://github.com/dataforgoodfr/batch4_diafoirus_mimic
Last synced: 6 days ago
JSON representation
Dockerized postgres running Mimic
- Host: GitHub
- URL: https://github.com/dataforgoodfr/batch4_diafoirus_mimic
- Owner: dataforgoodfr
- License: mit
- Created: 2018-03-31T21:14:10.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-05-09T17:19:55.000Z (over 7 years ago)
- Last Synced: 2024-04-24T10:06:56.583Z (almost 2 years ago)
- Language: Shell
- Size: 22.5 KB
- Stars: 0
- Watchers: 5
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Mimic Database installation with Docker
What we are going to do here is to break down every steps required for setting up a working environment.
The goal is:
* To ease your life so you don't lose too much type trying to figure out non-important stuff (non-related to our main goal)
* To have a common environment for all team members, so communication and workflow can spread more easily.
The database will be run inside a Docker container. You'll have access to this container through ports mapping.
If you don't know anything about Docker, you may want to start by following the quick [Get Started](https://docs.docker.com/get-started/) tutorial. Moreover, [this blog post](https://blog.docker.com/2016/03/containers-are-not-vms/) should explain why a Docker container is useful, and what are the differences between a container and a classic virtual machine.
Starting from now, we assume that [Docker is installed](https://docs.docker.com/install/) on your machine, as well as [docker-compose](https://docs.docker.com/compose/install/), a program we will use to build the Docker container.
## 1. Clone this Github repository on your machine
$ git clone git@github.com:dataforgoodfr/batch4_diafoirus_mimic.git
$ cd batch4_diafoirus_mimic
## 2. Get the data
Now, move to the directory we'll use for storing the data
$ cd mimic_data/csv
`NOTE` For the following command, your access to the database must first have been granted by **Physionet.org**.
**Warning:** replace `{EMAIL}` with the email you used to log in physionet.org.
$ wget --user {EMAIL} --ask-password -A csv.gz -m -p -E -k -K -np -nd https://physionet.org/works/MIMICIIIClinicalDatabaseDemo/files/
*You will be prompted to enter your physionet.org password.*
`NOTE` This is **only the test database** (light version). We are currently working on making sure that everything works with the actual/enormous database.
This will download all the `csv.gz` (compressed CSV) files that composed the database. The compressed CSVs are about 6 GB in total, so it may take a while!
---
If the automatic dowloads with `wget` fails on the very big files, you can [download each of them manually here](https://physionet.org/works/MIMICIIIClinicalDatabase/files/) `right clic -> save target` (access restricted to granted users only, of course)
Then go back to the root of our directory
$ cd ../..
## 3. Build the image and run the container
This is the magic command :)
$ sudo docker-compose up --build
**This will take a while** (probably a few hours), since it has to copy all the data to the container's system.
*`NOTE` Sometimes, the process will exit quickly, with this message `ERROR: Service 'postgres' failed to build`. In that case, try re-launching the same command, as it can work with no problem the second time.*
When it's done, the container should be up and running with a seeded postgres on port `5432`. You're now free to connect to it (user: `mimic`, password: `mimic`)
If you want to connect to the database through the terminal keep reading, otherwise **congratulations, you are all set!**
`NOTE` You can stop the container using `CTRL-C`
## 4. Restart the container
When you reboot your machine and you want to relauch the container, you can use the `docker-compose` command we used earlier, but add the `-d` flag to run the container as *daemon* (= as a background task)
$ sudo docker-compose up --build -d
----------------
The following steps are optionnal, or are just provided as complementary observations.
### Log into the container's shell
$ sudo docker exec -it mimic /bin/bash
You should have a shell access to the container.
`NOTE` after this command, you are executing **inside** the container, and not on your local machine anymore. You can exit the container with `CTRL-C`.
### Connect to postgres
$ psql -U mimic
### Run SQL queries
To list all the tables within the database
$ \d
If you don't see anything returning from this command, there is a problem :)
Otherwise, congratulations! You can start querying the database, for example...
$ SELECT row_id FROM admissions limit 10;
... should return a list of the first 10 indexes of the `admissions` table.
`NOTE` don't forget the `;` at the end of any SQL queries...