All posts by Lee Hachadoorian

Installing PostgreSQL/PostGIS on Linux Mint 18

NOTE: This guide is not tested for Ubuntu, but should work the same way.

I recently upgraded Linux Mint to version 18. As with the previous time I upgraded the OS, I wanted to upgrade PostgreSQL and PostGIS as well. If you are upgrading from a previous version of PostgreSQL/PostGIS and have data you want to bring over to your new cluster, you have to begin with a dump of your old data. In the terminal:

pg_dump -Fc my_db > my_db.backup

The extension *.backup is arbitrary, but is the one that is expected by pgAdmin.

After that the next step for me was installing Linux Mint 17. If you’re not installing/upgrading an OS, your next step might involve going straight to installing/upgrading PostgreSQL 9.5/PostGIS 2.2. If you are not yet using the ubuntugis-unstable PPA, go ahead and set that up. This will give you access to the latest PostGIS, GDAL/OGR drivers, SpatiaLite, QGIS, etc. In spite of the name, the repository is very stable and widely used.

sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo add-apt update

Then install PostgreSQL and PostGIS:

sudo apt-get install postgresql-9.5-postgis-2.2 postgresql-contrib-9.5 pgadmin3

Since the PostGIS package depends on PostgreSQL, you should get everything you need. If you use pgAdmin III for server management, that has to be added separately, as I have done here.

Before you can restore your database you have to have a cluster to restore it to. When you install Postgres on a Debian-based Linux distro, the installer will automatically create a database cluster named main with a data directory in /var/lib/postgresql/9.5/main. But it’s fairly common to run a server with a small root partition, and have the database cluster, which can grow very large, on a separate data partition. If you follow the PostgreSQL docs for initializing a new cluster, it will work, but your new cluster will not start at system startup, and if your database client connects to localhost:5432 the connection will go to the default cluster created during installation.

WARNING: I am about to show you how to delete a database cluster. This assumes that you have done a fresh install and the main cluster created during install is empty, or that you have a backup of your database as I demonstrated at the beginning of this article. If you are attempting an upgrade (i.e., not a fresh install) but do not know whether your data is backed up, STOP and make sure that you have a backup!

First, decide where you are going to store your data. PG documentation recommends not creating a cluster at the root of a partition. For example, if you want to have your cluster on a partition named /data, you should create your cluster in a folder on that partition, not as the root folder /data. In the example below, I create a cluster named pg_data. A folder of this name should not exist,* and will be created for you.

sudo pg_dropcluster --stop 9.5 main
sudo pg_createcluster -d /data --start 9.5 pg_data

The first statement will stop the default cluster and drop it (destroying all data in the process). The second statement will create the folder /pg_data in the /data partition, set the folder owner to the postgres system user, initialize the cluster, and start it. New clusters are assigned the next available port beginning with 5432. Because we have dropped the default cluster, the new cluster will be assigned port 5432. If you did not drop the default cluster, or have other clusters on this server, the new cluster will be assinged 5433 or the next available port number.

After executing these commands, you can see the results using pg_lsclusters (no options, does not need sudo). If you have run the commands above, you should see the first line in the following output. I have also mocked up what you would see if you create two additional clusters:

Ver Cluster Port Status Owner    Data directory Log file
9.5 pg_data 5432 online postgres /data/pg_data  /var/log/postgresql/postgresql-9.5-main.log
9.5 tmp     5433 down   postgres /data/tmp      /var/log/postgresql/postgresql-9.5-tmp.log
9.5 tmp2    5434 down   postgres /data/tmp2     /var/log/postgresql/postgresql-9.5-tmp2.log

Remember that port 5432 is the default PostgreSQL port. Note that the dummy clusters I have “created” above use ports 5433 and 5434, because 5432 was already taken. If you want to be able to access the database without specifying the port number, make sure to drop the default cluster first.

The cluster will be initialized to use trust authentication, which means that all local users can log in without a password. The cluster will also automatically have a postgres user. It is usually good practice to create a SUPERUSER role to manage the database instead of logging in as postgres. However, we have to log in with postgres at least once to create the SUPERUSER role we will use for the rest of our database management.

Still at the command line, use createuser (a utility command installed installed with PostgreSQL) to create a login role:

creatuser -U postgres -P -s superusername

The given options mean:

  • -U postgres: log in to the server as postgres to issue the CREATE ROLE statement
  • -P: prompt for a password for the new user
  • -s: make the new user a SUPERUSER (including CREATEDB and CREATEROLE privileges)

If you set the role name to match your Linux user (e.g. jsmith), you will be able to launch psql without specifying the username. If you also create a database named for the user, psql will automatically log in to that database. Obviously, this is probably something you don’t want to do in an enterprise setting, but can be useful for a development laptop.

Now you need to edit the environment file. In Ubuntu/LM, it will be located in /etc/postgresql/9.5/ (in our example, /etc/postgresql/9.5/pg_data), and will need to be edited as root. The file is named environment (no extension, just “environment”). Open it and add the following two lines:

POSTGIS_ENABLE_OUTDB_RASTERS=1
POSTGIS_GDAL_ENABLED_DRIVERS=ENABLE_ALL

Close and save. Now restart the postgres service, or just reboot, so that postgres restarts using the new cluster.

With a typical PostgreSQL dump/restore, the restore will create the database and load any functions, as well as schemas and data. When upgrading the PostGIS extension, the new PostGIS version will have different (and possibly incompatible) spatial functions, so we want to:

  1. Create the database
  2. Enable the new PostGIS extension to create the new spatial functions and necessary structures (such as the spatial_ref_sys table)
  3. Only then do we load the data, which we do using a special script rather than the standard pg_restore command.

I do the following steps in pgAdmin. First, create a connection to the server:

pgAdminNewServerRegistration

In pgAdmin it is easy to create a database graphically (not shown here) by right-clicking on the Databases “can” and choosing New Database, or just open the SQL Editor window to follow the commands below. If you prefer to use psql, now that you have added your system user as a database superuser, you can

psql postgres

Either way, you end up at a SQL editor. You are in the postgres database, which should be used only for system data, so create a new database to store your “real” data.

CREATE DATABASE my_db WITH OWNER superusername;

Now create the necessary PostGIS extensions. The only one that is really necessary is PostGIS. Some other ones commonly used for geospatial analysis include:

  • Topology support
  • The TIGER geocoder (which requires the fuzzystrmatch extension)
  • SFCGAL for 3D analysis (which used to require jumping through a lot of hoops, but is now quite easy to install)

You need to issue the SQL commands in the correct DB, so in pgAdmin, close the SQL Editor, connect to the new database, and reopen the SQL Editor. Or, in psql:

\connect my_db

Now create the extensions:

CREATE EXTENSION postgis;
CREATE EXTENSION postgis_topology;
CREATE EXTENSION fuzzystrmatch;
CREATE EXTENSION postgis_tiger_geocoder;
CREATE EXTENSION postgis_sfcgal;

If you are restoring a previous database, now you are ready to reload your data. PostGIS provides a Perl data loader, postgis_restore.pl, that will not attempt to recreate the spatial functions, since they are already there (although deprecated functions will be missing and will require special handling if you have database applications which make use of them). Any aspatial data will be loaded in the usual manner, so it is harmless to use this instead of pg_restore. The data loader will not, by default, be in your PATH, so either navigate to the PostGIS contrib directory, as I show below, or be prepared to type in the entire path when you call the command. Then pass in the name of the dump file and pipe the result to psql:

cd /usr/share/postgresql/9.5/contrib/postgis-2.2/
perl postgis_restore.pl ~/my_db.dump | psql -U superusername my_db 2> ~/postgis_restore_errors.txt

Go get a cup of coffee. In fact, go out to dinner. Maybe see a movie.

The PostGIS installer also installs the graphical shapeloader (front end to shp2pgsql-gui). As a final tweak, you might want to configure this as a pgAdmin plugin, so that you have easy access to it when working with pgAdmin (and it will launch with the database connection details taken from the pgAdmin environment). To do so, open (as root) the file /usr/share/pgadmin3/plugins.d/plugins.ini. Then add the following section:

;
; pgShapeLoader (Linux):
; Added manually by <user> on <date>
Title=PostGIS Shapefile and DBF loader
Command=$$PGBINDIR/shp2pgsql-gui -U $$USERNAME -d $$DATABASE -p $$PORT -h $$HOSTNAME
Description=Open a PostGIS ESRI Shapefile or Plain dbf loader console to the current database.
KeyFile=$$PGBINDIR/shp2pgsql-gui
Platform=unix
ServerType=postgresql
Database=Yes
SetPassword=No

This will create a new entry in the pgAdmin Plugins menu.

That’s it! You should now have a working PostGIS installation. The first thing I did was fire up QGIS, connect to the database, and load some of my old projects to make sure everything was working. Happy geoprocessing!

* pg_createcluster can be used to bring an existing PostgreSQL data directory into the cluster management architecture. However, if you are doing a major upgrade of PostgreSQL or PostGIS, you need to do a dump and restore anyway. You cannot upgrade the cluster “in place”. So these instructions emphasize creation of a new, empty cluster, followed by a restore of your old database. For information on bringing an existing data PostgreSQL data directory into the cluster management architecture, please read the pg_createcluster documentation.

References:

 

 

 

Setting a custom data directory for a new PostreSQL installation on Linux

When you install Postgres on a Debian-based Linux distro (in my case, Linux Mint 18), the installer will automatically create a database cluster with a data directory in /var/lib/postgresql/9.5/main. But it’s fairly common to run a server with a small root partition, and have the database cluster, which can grow very large, on a separate data partition.

I didn’t have any trouble using initdb to initialize the cluster in the desired location. But at system boot, the server automatically started using the default data cluster, not the one I had created. The PostgreSQL documentation on how to customize server start was pretty obtuse.

Fortunately, Debian-based distros ship with some utilities that allow you to create multiple data clusters, and integrates them all into a multicluster management architecture:

Some important points about pg_createcluster:

  1. An existing cluster will be added to the list of clusters, rather than reinitialized. This was important, because I had already run a load script overnight to restore a database dumped from a prior version of Postgres/PostGIS.
  2. PostgreSQL uses the default port number 5432. New clusters will be automatically initialized to use a new port one number higher than the highest existing Postgres port (5433 for the second cluster, 5434 for the third cluster, etc.).

I did not need the default cluster. I also intend to run only one cluster on this machine, and wanted it to use the standard port (5432). pg_dropcluster and pg_createcluster both take the Postgres version number (9.5 in my case) and cluster name as arguments. The default cluster is named “main”. My computer is named tycho, so I decided to name my cluster “tycho_main” so that it would be clear this was not the default cluster. So I ran the following commands:

sudo pg_dropcluster 9.5 main
sudo pg_createcluster -d /data/pg_data --start 9.5 tycho_main

pg_dropcluster does take --stop as an option to stop a running server, but I already had both servers stopped. The -d option to pg_createcluster is where you set the data directory for the new cluster, and the --start option start the cluster immediately after adding it to the list of available clusters.

After running those commands, I confirmed I could connect to the running server. Then I rebooted to make sure the server started at boot, which it did.

Done and done.

NOTE: Tablespaces can also be used within the database to determine where the database stores the data. The primary use case for this, however, is if the DBA wants to store data that is accessed with varying frequency on media of different speed: commonly accessed tables on fast hard drives or solid state drives, infrequently accessed tables on slow hard drives. It adds complexity to the installation, and is not really intended for the case where the DBA wants the entire database cluster on one partition, but in a nonstandard location.

Installing PostgreSQL/PostGIS on Linux Mint 17

Linux Mint 17 (based on Ubuntu 14.04) was released before the Summer, but I finally got around to upgrading from Linux Mint 13. I was previously running PostgreSQL 9.0 / PostGIS 2.0, and it was time to upgrade those as well. If you are upgrading from previous version of PostgreSQL/PostGIS and have data you want to bring over to your new cluster, you have to begin with a dump of your old data:

pg_dump -Fc my_db > my_db.dump

The extension *.dump is arbitrary. Some people prefer *.backup. I should have timed the process for this post, but expect something in the order of hours. For smallish DBs (tens to hundreds of gigabytes), I have seen compression ratios of about 10-20%. Not sure what to expect for much larger DBs. Continue reading Installing PostgreSQL/PostGIS on Linux Mint 17

Load PostGIS geometries in R without rgdal

As I said in my last post, rgdal lacks some of the features of GDAL, including the ability to subset columns and rows the source layer, and I demonstrated a workaround. The workaround relied upon the RPostgreSQL package, and this raises a question: Is it possible to transfer geographic data from PostGIS to R just using RPostgreSQL?

It is, and in fact, this may be necessary if you are working on Windows. Continue reading Load PostGIS geometries in R without rgdal

Subsetting in readOGR

The function readOGR in the rgdal package is used to bring vector spatial data sources into R. readOGR() relies upon OGR (part of the GDAL/OGR library) for format conversion. Unfortunately, while OGR supports the ability to subset columns (with the -select switch) or rows (with the -where switch), or even to request a layer using a full SQL statement, none of that functionality is available in readOGR. Every so often this gets discussed in the mailing lists, but the functionality has not yet been implemented.

If your data is already in a SQL database though, you’re in luck. You can accomplish the same thing within R by creating a spatial view in-database, loading the spatial view with readOGR, then dropping the view. I’ve created a function that does just that for PostGIS data sources. Continue reading Subsetting in readOGR

Hexbinning

Hexbinning is a method for visualizing point data when many similar values mean there is a lot of overplotting. Although it originated in the data visualization field as a an enhancement to the traditional XY scatterplot, within the last few years hexbinning has been used more and more in cartography. (See this great blog post by Zachary Forest Johnson which traces this history and explains how to create hexbin maps using D3.js.)

I wanted to map police stops under the NYPD Stop and Frisk program (official source, easier to use version from NYCLU), but at city or borough scale, this just looks like a continuous carpet of dots. Visualizing that kind of dense point data is exactly what hexbinning is for.
Continue reading Hexbinning

Finding Islands (or the Converse)

areawater

I have a PostGIS polygon layer with a lot of small “islands” (actually, lakes and ponds), polygons which are not touching any other polygons. I wanted to delete them from the layer, or rather, since I wanted to keep a version with and without the islands, I wanted to copy only the polygons with neighbors to a new table. I’ll show the solution first, and then how I got there. Continue reading Finding Islands (or the Converse)