Databases and SQL

Selecting Data

Overview

Teaching: 10 min
Exercises: 5 min
Questions
  • How can I get data from a database?

Objectives
  • Explain the difference between a table, a record, and a field.

  • Explain the difference between a database and a database manager.

  • Write a query to select all values for specific fields from a single table.

A relational database is a way to store and manipulate information. Databases are arranged as tables. Each table has columns (also known as fields) that describe the data, and rows (also known as records) which contain the data.

When we are using a spreadsheet, we put formulas into cells to calculate new values based on old ones. When we are using a database, we send commands (usually called queries) to a database manager: a program that manipulates the database for us. The database manager does whatever lookups and calculations the query specifies, returning the results in a tabular form that we can then use as a starting point for further queries.

Changing Database Managers

Every database manager — Oracle, IBM DB2, PostgreSQL, MySQL, Microsoft Access, and SQLite — stores data in a different way, so a database created with one cannot be used directly by another. However, every database manager can import and export data in a variety of formats, like .csv, so it is possible to move information from one to another.

Queries are written in a language called SQL, which stands for “Structured Query Language”. SQL provides hundreds of different ways to analyze and recombine data. We will only look at a handful of queries, but that handful accounts for most of what scientists do.

Getting Into and Out Of SQLite

In order to use the SQLite commands interactively, we need to enter into the SQLite console. So, open up a terminal, and run

$ cd /path/to/survey/data/
$ sqlite3 survey.db

The SQLite command is sqlite3 and you are telling SQLite to open up the survey.db. You need to specify the .db file otherwise, SQLite will open up a temporary, empty database.

To get out of SQLite, type out .exit or .quit. For some terminals, Ctrl-D can also work. If you forget any SQLite . (dot) command, type .help.

Before we get into using SQLite to select the data, let’s take a look at the tables of the database we will use in our examples:

Person: people who took readings.

id personal family
dyer William Dyer
pb Frank Pabodie
lake Anderson Lake
roe Valentina Roerich
danforth Frank Danforth

Site: locations where readings were taken.

name lat long
DR-1 -49.85 -128.57
DR-3 -47.15 -126.72
MSK-4 -48.87 -123.4

Visited: when readings were taken at specific sites.

id site dated
619 DR-1 1927-02-08
622 DR-1 1927-02-10
734 DR-3 1930-01-07
735 DR-3 1930-01-12
751 DR-3 1930-02-26
752 DR-3 -null-
837 MSK-4 1932-01-14
844 DR-1 1932-03-22

Survey: the actual readings.

taken person quant reading
619 dyer rad 9.82
619 dyer sal 0.13
622 dyer rad 7.8
622 dyer sal 0.09
734 pb rad 8.41
734 lake sal 0.05
734 pb temp -21.5
735 pb rad 7.22
735 -null- sal 0.06
735 -null- temp -26.0
751 pb rad 4.35
751 pb temp -18.5
751 lake sal 0.1
752 lake rad 2.19
752 lake sal 0.09
752 lake temp -16.0
752 roe sal 41.6
837 lake rad 1.46
837 lake sal 0.21
837 roe sal 22.5
844 roe rad 11.25

Notice that three entries — one in the Visited table, and two in the Survey table — don’t contain any actual data, but instead have a special -null- entry: we’ll return to these missing values later.

Checking If Data is Available

On the shell command line, change the working directory to the one where you saved survey.db. If you saved it at your Desktop you should use

$ cd Desktop
$ ls | grep survey.db
survey.db

If you get the same output, you can run

$ sqlite3 survey.db
SQLite version 3.8.8 2015-01-16 12:08:06
Enter ".help" for usage hints.
sqlite>

that instructs SQLite to load the database in the survey.db file.

For a list of useful system commands, enter .help.

All SQLite-specific commands are prefixed with a . to distinguish them from SQL commands. Type .tables to list the tables in the database.

.tables
Person   Site     Survey   Visited

You can change some SQLite settings to make the output easier to read. First, set the output mode to display left-aligned columns. Then turn on the display of column headers.

.mode column
.header on

To exit SQLite and return to the shell command line, you can use either .quit or .exit.

For now, let’s write an SQL query that displays scientists’ names. We do this using the SQL command SELECT, giving it the names of the columns we want and the table we want them from. Our query and its output look like this:

SELECT family, personal FROM Person;
family personal
Dyer William
Pabodie Frank
Lake Anderson
Roerich Valentina
Danforth Frank

The semicolon at the end of the query tells the database manager that the query is complete and ready to run. We have written our commands in upper case and the names for the table and columns in lower case, but we don’t have to: as the example below shows, SQL is case insensitive.

SeLeCt FaMiLy, PeRsOnAl FrOm PeRsOn;
family personal
Dyer William
Pabodie Frank
Lake Anderson
Roerich Valentina
Danforth Frank

You can use SQL’s case insensitivity to your advantage. For instance, some people choose to write SQL keywords (such as SELECT and FROM) in capital letters and field and table names in lower case. This can make it easier to locate parts of an SQL statement. For instance, you can scan the statement, quickly locate the prominent FROM keyword and know the table name follows. Whatever casing convention you choose, please be consistent: complex queries are hard enough to read without the extra cognitive load of random capitalization. One convention is to use UPPER CASE for SQL statements, to distinguish them from tables and column names. This is the convention that we will use for this lesson.

While we are on the topic of SQL’s syntax, one aspect of SQL’s syntax that can frustrate novices and experts alike is forgetting to finish a command with ; (semicolon). When you press enter for a command without adding the ; to the end, it can look something like this:

SELECT id FROM Person
...>
...>

This is SQL’s prompt, where it is waiting for additional commands or for a ; to let SQL know to finish. This is easy to fix! Just type ; and press enter!

Now, going back to our query, it’s important to understand that the rows and columns in a database table aren’t actually stored in any particular order. They will always be displayed in some order, but we can control that in various ways. For example, we could swap the columns in the output by writing our query as:

SELECT personal, family FROM Person;
personal family
William Dyer
Frank Pabodie
Anderson Lake
Valentina Roerich
Frank Danforth

or even repeat columns:

SELECT id, id, id FROM Person;
id id id
dyer dyer dyer
pb pb pb
lake lake lake
roe roe roe
danforth danforth danforth

As a shortcut, we can select all of the columns in a table using *:

SELECT * FROM Person;
id personal family
dyer William Dyer
pb Frank Pabodie
lake Anderson Lake
roe Valentina Roerich
danforth Frank Danforth

Selecting Site Names

Write a query that selects only the name column from the Site table.

Solution

SELECT name FROM Site;
name
DR-1
DR-3
MSK-4

Query Style

Many people format queries as:

SELECT personal, family FROM person;

or as:

select Personal, Family from PERSON;

What style do you find easiest to read, and why?

Key Points