Ciro Santilli @cirosantilli  40

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16S ribosomal RNA Updated 2025-07-16

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5S ribosomal RNA Updated 2025-07-16

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23S ribosomal RNA Updated 2025-07-16

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EF-Tu Updated 2025-07-16

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PostgreSQL getting started Updated 2025-07-16

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On Ubuntu 20.10 PostgreSQL 12.6, login with psql on my default username without sudo fails with: stackoverflow.com/questions/11919391/postgresql-error-fatal-role-username-does-not-exist

This is the one that worked on Ubuntu 21.04: stackoverflow.com/questions/11919391/postgresql-error-fatal-role-username-does-not-exist/38444152#38444152

sudo -u postgres createuser -s $(whoami)
createdb $(whoami)

Explanation:

sudo -u postgres uses the postgres user via peer authentication
-s in createuser -s: make it a superuser
createdb: TODO why do we have to create a table with the same name as the user? Otherwise login fails.

You can now run psql without any password. This works without password due to peer authentication:

sudo cat /etc/postgresql/12/main/pg_hba.conf

shows that peer authentication is available to all users apparently:

local   all             postgres                                peer

# TYPE  DATABASE        USER            ADDRESS                 METHOD

# "local" is for Unix domain socket connections only
local   all             all                                     peer

List users:

psql -c '\du'

output:

                                    List of roles
  Role name  |                         Attributes                         | Member of
-------------+------------------------------------------------------------+-----------
 ciro        | Superuser, Create role, Create DB                          | {}
 owning_user |                                                            | {}
 postgres    | Superuser, Create role, Create DB, Replication, Bypass RLS | {}

Delete user later on:

psql -c 'DROP USER username;'

Create a database:

createdb testdb0

Help toplevel:

help

Get help for Postgres commands such as \h and so on:

\?

List supported SQL commands:

\h

Show syntax for one type of command:

\h SELECT

List all databases:

psql -c '\l'

which shows:

    Name     |  Owner   | Encoding |   Collate   |    Ctype    |   Access privileges
-------------+----------+----------+-------------+-------------+-----------------------
 ciro        | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 postgres    | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
 template0   | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres          +
             |          |          |             |             | postgres=CTc/postgres
 template1   | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres          +
             |          |          |             |             | postgres=CTc/postgres
 testdb0     | postgres | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 |
(6 rows)

Delete a database:

psql -c 'DROP DATABASE "testdb0";'

If you didn't give a database from the command line e.g.:

psql

you can do that afterwards with:

\c testdb0

Let's create a table and test that it is working:

psql testdb0 -c 'CREATE TABLE table0 (int0 INT, char0 CHAR(16));'

List tables, no special tables:

psql testdb0 -c '\dt'

gives:

        List of relations
 Schema |  Name  | Type  | Owner
--------+--------+-------+-------
 public | table0 | table | ciro
(1 row)

View table schema: stackoverflow.com/questions/109325/postgresql-describe-table

psql testdb0 -c '\d+ table0'

output:

                                      Table "public.table0"
 Column |     Type      | Collation | Nullable | Default | Storage  | Stats target | Description
--------+---------------+-----------+----------+---------+----------+--------------+-------------
 int0   | integer       |           |          |         | plain    |              |
 char0  | character(16) |           |          |         | extended |              |

Insert some data into it and get the data out:

psql testdb0 -c "INSERT INTO table0 (int0, char0) VALUES (2, 'two'), (3, 'three'), (5, 'five'), (7, 'seven');"
psql testdb0 -c 'SELECT * FROM table0;'

output:

 int0 |      char0
------+------------------
    2 | two
    3 | three
    5 | five
    7 | seven
(4 rows)

Delete the table:

psql testdb0 -c 'DROP TABLE table0;'

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Create a test user in PostgreSQL Updated 2025-07-16

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In order to create a test user with password instead of peer authentication, let's create test user:

createuser -P user0
createdb user0

-P makes it prompt for the users password.

Alternatively, to create the password non-interactively stackoverflow.com/questions/42419559/postgres-createuser-with-password-from-terminal:

psql -c "create role NewRole with login password 'secret'"

Can't find a way using the createuser helper.

We can then login with that password with:

psql -U user0 -h localhost

which asks for the password we've just set, because the -h option turns off peer authentication, and turns off password authentication.

The password can be given non-interactively as shown at stackoverflow.com/questions/6405127/how-do-i-specify-a-password-to-psql-non-interactively with the PGPASSWORD environment variable:

PGPASSWORD=a psql -U user0 -h localhost

Now let's create a test database which user0 can access with an existing superuser account:

createdb user0db0
psql -c 'GRANT ALL PRIVILEGES ON DATABASE user0db0 TO user0'

We can check this permission with:

psql -c '\l'

which now contains:

                                  List of databases
   Name    |  Owner   | Encoding |   Collate   |    Ctype    |   Access privileges
-----------+----------+----------+-------------+-------------+-----------------------
 user0db0  | ciro     | UTF8     | en_GB.UTF-8 | en_GB.UTF-8 | =Tc/ciro             +
           |          |          |             |             | ciro=CTc/ciro        +
           |          |          |             |             | user0=CTc/ciro

The permission letters are explained at:

user0 can now do the usual table operations on that table:

PGPASSWORD=a psql -U user0 -h localhost user0db0 -c 'CREATE TABLE table0 (int0 INT, char0 CHAR(16));'
PGPASSWORD=a psql -U user0 -h localhost user0db0 -c "INSERT INTO table0 (int0, char0) VALUES (2, 'two'), (3, 'three'), (5, 'five'), (7, 'seven');"
PGPASSWORD=a psql -U user0 -h localhost user0db0 -c 'SELECT * FROM table0;'

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Peer authentication Updated 2025-07-16

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www.postgresql.org/docs/13/auth-peer.html

Uses the name of the current Linux user to login without a password.

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PostgreSQL logging Updated 2025-07-16

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stackoverflow.com/questions/722221/how-to-log-postgresql-queries

Ubuntu 21.10 has a certain default level of logging by default to:

/var/log/postgresql/postgresql-13-main.log

but it does not log everything, only/mostly errors it seems.

Setting:

log_statement = 'all'

under:

/etc/postgresql/13/main/postgresql.conf

and then restarting the server:

sudo service restart postgresql

just works.

Realtime monitoring for long queries instead: stackoverflow.com/questions/8597516/app-to-monitor-postgresql-queries-in-real-time

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PostgreSQL serialization failure Updated 2025-07-16

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When using SQL REPEATABLE READ isolation level and SQL SERIALIZABLE isolation level, concurrent transactions may fail with a serialization failure, and then you might need to retry them. You server code or your ORM must always account for that.

A good way to explore when it happens is to use the example