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Creating Your First SQL Datasource

To illustrate creating a Datasource, we'll use a public database of research data called “Rfam” as an example: https://docs.rfam.org/en/latest/database.html

First, navigate to the PocketQuery administration by following the link in the Apps menu:

PocketQuery in the Apps Menu

This will take you to the PocketQuery administration. Here, Confluence administrators can create all sorts of PocketQuery Entities. To get started, we need to create our first Datasource. Click on the Datasources panel which brings you to the Datasources tab:

Datasources panel in the PocketQuery administration

On the Datasources tab, click the Let’s setup my first Datasource button, to get started with creating your first Datasource:

Button to set up datasource

This will open a form that lets you specify a name for your Datasource (we’re going with “Rfam”, as this the name of the research database we’re using) and the type of your Datasource. As we are connecting to a MySQL 5 database, choose the “MySQL 5” type here:

Dropdown with Datasource types

Once you have selected a type, more fields will show up. To connect to a SQL Datasource, you’ll typically need a JDBC URL, a user, and a password. To connect to our public research database, these are the values you need to enter:

PQ_create-datasource2.jpg

#

Field

Value

1

JDBC URL

jdbc:mysql://mysql-rfam-public.ebi.ac.uk:4497/Rfam

2

User

rfamro

3

Password

No password - leave blank

4

Description (Optional)

A public database containing research data. Rfam is a collection of non-coding RNA families represented by manually curated sequence alignments, consensus secondary structures, and predicted homologues. More info: https://docs.rfam.org/en/latest/database.html

After entering all the details, click the Test Connection button and see if you can connect to the database:

Screen with successful connection test

All good? Awesome! Hit the Create Datasource button and we’re done creating our first Datasource!

Continue with “Creating Your First SQL Query

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