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Last pushed: 10 months ago
Short Description
Experiment Hub
Full Description

Docker Container for ExperimentHub Server

Table of Contents


This Docker Container provides an isolated environment for modifying the
metadata records in the ExperimentHub database. It can be used for testing only
or the modified database can be dumped and used to replace the production db.

The docker can be used by anyone who has the password for the 'read only' user
on the production server. With these credentials, a copy of the mysql
production database is downloaded locally to the docker container. From within
an R session, global options are set to point code from ExperimentHubData and
ExperimentHub to the local db. Changes to the metadata (inserts, modifications
or extractions) are made to the docker db instead of production.

<a name="setup"></a>

Setting up the docker container

<a name="prerequisites"></a>


Set the environment variable MYSQL_REMOTE_PASSWORD to the password found in
the "ExperimentHub production server" section of the Google Doc "Credentials
For Bioconductor Cloud resources".

The container will not work properly unless this is set.

You can set it by doing:


where XXX is replaced with the correct password.

Install docker.
If you are on Mac or Windows,
install docker toolbox

Also install Docker Compose.

Clone the HubServer code to the same directory as this README:

git clone

Or if you already have this repository checked out elsewhere
on your system, make a symbolic link to it in the current directory
(the same directory as this README).

Create a directory called "data" in the same directory as
this README.

<a name="run"></a>

Run The Container

Open a terminal window (a Docker Quickstart Terminal if
you are on Mac or windows) and change to the same
directory where this README is. Issue the command:

docker-compose up

This command will pull down the database contents
from the production ExperimentHub server
and then
start a local server.

When you see a line like this:

experimenthub_1 | == Shotgun/WEBrick on

...the ExperimentHub server is running in the container.

To verify that it is running, you can determine its URL
(in the next section).

<a name="url"></a>

Determining URL of server

If you are on linux, the URL of the server is likely

If you are in the cloud you need to use the public DNS name of your instance
as your IP address.

If you are using boot2docker (deprecated by Docker Toolbox),
you can determine your Docker host's IP address with the command
boot2docker ip. If this returns, your URL
would be

If you are using Docker Toolbox, the command to determine
your Docker host's IP address is

docker-machine ip default

If this returns, your URL would be

<a name="use"></a>

Using the container

Start a new R session in a new terminal window. Assuming your server URL is, enter the following at the R prompt:

## used by ExperimentHubData to insert metadata
## used by ExperimentHub to get metadata

Replace the URL with your actual URL, of course. These options must be set
before loading ExperimentHub and ExperimentHubData.


Now you can run recipes, etc. and the insertions will happen inside the docker
container, not in the production database.

<a name="test"></a>

Testing the changes

You can interact with the docker db with R or mysql.

R session

To view the docker db from R you must first convert the mysql db to sqlite. From another terminal window do

docker exec -ti experimenthubdocker_experimenthub_1 bash

That will log you in to the experimenthub server container. Then do the following:

cd /HubServer/
ruby convert_db.rb 

That will convert the mysql database to sqlite. You can then type


to exit the container, start R and set the variables as described in Using the container. ExperimentHub should recognize that there are changes and download the new sqlite database, but if not you can remove the old one from your cache to trigger a copy.

mysql session

mysql is not exposed to the host, so you need to do this from the mysql machine. Run

docker ps

to see a list of containers that are running. One will have the string 'db' in it. Let's say the full name is 'db1'. Connect to the container with:

docker exec -ti db_1 bash

From within the resulting prompt start mysql and query the db as usual:

mysql -p -u hubuser

When you are satisfied that the changes you have made are
correct, you can update the production database (see next
section). If you have messed up and you don't want to
push your changes to production, you can just exit
the container (press Control-C in the window where it is
running) and start over again.

<a name="push"></a>

Pushing changes to production

You need to back up the database inside the docker
container. You can do it like this:

 docker exec experimenthubdocker_experimenthub_1 bash /bin/

Note that experimenthub_experimenthub_1 is the name of the
docker container that has the experiment hub server on it; this
name may vary, the docker ps command will give you the
accurate container name.

Now in the data directory on your local machine,
there is a file called experimenthub.sql.gz. Upload this to the production machine.

Log into the production machine and make a backup of production db:

mysqldump -p -u hubuser experimenthub | gzip > dbdump_YYYY_MM_DD_fromProd.sql.gz

Drop the old db and create an empty one:

mysql -p -u root
drop database experimenthub;
create database experimenthub;

Fill the empty with the modified db:

zcat dbdump_YYYY_MM_DD_fromDocker.sql.gz | mysql -p -u root experimenthub
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