Working with PostgreSQL

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PostgreSQL on edegan.com

We have a dedicated Postgres server available for use by interns, affiliates, and researchers. It is available by SSH directly and through the RDP.

Connecting to the dbase server

To connect through the RDP get a copy of PuTTY (put PuTTY.exe on your desktop) from: 

E:/installs

The preferred way to connect is from the RDP where you can stay inside the private network, and have gigabit connection speeds. Connect to: 

researcher@192.168.2.92

It is possible to connect from other machines over the Internet. You shouldn't do this unless you have to but in this case connect via SSH to: 

reseacher@199.188.177.215
 or
researcher@ssh.edegan.com

All of the data files (tab-delimited text) that need to be loaded in and out of a dbase for your project should be stored in: 

/bulk/YourDbase

Note: To make your life easy, map the database's bulk drive on your RDP account. Follow the instructions to do this. We refer to the database server's bulk drive as either dbase/bulk or as Z:, as this is the drive letter most commonly mapped to.

Working with psql

After you have ssh'd onto the server change directory to your data directory: 

cd /bulk/yourdir

Then connect a database: 

psql DBName

Note: to use a local copy of psql (if you have it installed locally), connect using the username researcher and DBname: 

psql -h dbase.edegan.com -U researcher dbname

You MUST store all of your SQL commands in a file named yourfilename.sql that is stored in: 

E:/projects/YourProject/

There are NO EXCEPTIONS to this. All of your code must go into a .sql file. Even exploratory code. You can copy out of there line by line to run code.

Useful PostgreSQL commands

Useful commands are: 

\q             Quits
\l             List all dbases available to your username
\i basics.sql  Run script basics.sql
\dt            List tables
\d tablename   Shows the schema of the table
\r             Reset the query buffer
Ctrl-c         Abort the current query
q              Go back to the prompt when viewing a dataset
\COPY          Psql's version of copy (See below)

Dumping and Restoring a Database

This can be done in pgAdmin in Windows, but the commands (needed on Linux with SSH access) are:

To dump a db: 

pg_dump mydb > db.backup

To reload this database: 

pg_restore -d DBName db.backup

We typically use compression (Postgres' format custom), so the best command is: 

pg_dump -Fc dbase > dbase_fc.dump
pg_restore -Fc -d DBName db.backup

All backups are stored in /bulk/backups. You can drop a database after it has been dumped with: 

dropdb dbase

To selectively restore a single table use the -t tablename option. See https://www.postgresql.org/docs/9.2/static/app-pgrestore.html for the other options.

SQL Commands

CREATE, DROP, \COPY

There is a list of SQL commands that may help.

Make/delete tables and functions with CREATE and DROP: 

CREATE TABLE tablename AS
  SELECT * FROM tablename WHERE date_prod >= '2002-01-01';

DROP TABLE tablename;

CREATE TABLE tablename (
 field1 varchar(100),
 field2 int,
 field3 date,
 field4 real
);

Functions can be written in Perl, Python and other languages. See below for more information. 

CREATE FUNCTION getreal (text) RETURNS real AS $$
    if ($_[0]=~/^\d{1,}\.\d{0,}$/) { return $_[0]; }
    return undef;
$$ LANGUAGE plperl;
 
DROP Function correctyear(int,int);

Do not do any of the following: 

Populate data with COPY, INSERT and UPDATE:

 INSERT INTO tablename VALUES ('San Francisco', 46, 50, 0.25, '1994-11-27');

 COPY tablename FROM '/home/user/weather.txt'; --http://www.postgresql.org/docs/8.4/interactive/sql-copy.html

 UPDATE tablename SET kind = 'Dramatic' WHERE kind = 'Drama';
 
 UPDATE accounts SET (contact_last_name, contact_first_name) =
     (SELECT last_name, first_name FROM salesmen
     WHERE salesmen.id = accounts.sales_id);

Instead, always build stack of tables using: 

CREATE TABLE tablename AS
  SELECT * FROM tablename WHERE ...;

DROP TABLE tablename;

Always load/unload data using the PostgreSQL specific copy function below. Always load tab-delimited data that is UTF-8 encoded, with PC or UNIX line endings, and that has a header row. NEVER DEVIATE FROM THIS. 

Load using:
\COPY tablename FROM 'filename.txt' WITH DELIMITER AS E'\t' HEADER NULL AS '' CSV

Unload (copy to txt file) using:
\COPY tablename TO 'filename.txt' WITH DELIMITER AS E'\t' HEADER NULL AS '' CSV

SELECT

Retrieve results with SELECT: 

SELECT x.a y.a FROM x,y WHERE x.a=y.a

SELECT * FROM x LEFT OUTER JOIN y ON x.a=y.a;

SELECT * FROM
	(SELECT ) AS x
LEFT OUTER JOIN 
	(SELECT ) AS y
ON x.a=y.a;

SELECT COUNT (*) FROM ( ) AS Temp;

SELECT COUNT (*) FROM Acq;

SELECT x, min(y) FROM tablename GROUP BY x;

SELECT * FROM tablename LIMIT 10;

SELECT 
	CASE WHEN a > b THEN 1
	ELSE  2 
	END As Colname,
FROM tablename;

Get information on a table: 

SELECT column_name, data_type FROM information_schema.columns WHERE table_name = 'tablename';

ALTER

DON'T DO THIS. CREATE A NEW TABLE INSTEAD!

Change a table with ALTER: 

ALTER TABLE tablename ADD COLUMN colname real;

ALTER TABLE tablename RENAME COLUMN product_no TO product_number;

EXPLAIN

Find out how a query will be executed with EXPLAIN (a Postgre command): 

EXPLAIN ANALYZE SELECT * FROM x;

CREATE OR DROP INDEX

If the dbase is large or you just need things to run faster, add an index to your key fields. 

CREATE UNIQUE INDEX title_idx ON films (title);
CREATE INDEX title_idx ON films (title);
DROP INDEX title_idx;

See https://www.postgresql.org/docs/9.5/static/sql-createindex.html for more options

SEQUENCES

If you want to create a sequence: 

CREATE SEQUENCE serial START 101;

To use the sequence call: 

nextval('serial');

Perl Functions

NOTE: Perl and Python Functions only work the the dbase server, not the RDP (where perl has a dependency error in plperl.dll and python has unknown issues).

PLPerl was installed into Template1 (and hence all new databases) when the server was first set up.

An example perl function is: 

 CREATE OR REPLACE FUNCTION getint (text) RETURNS int AS $$
 	if ($_[0]) {
 		my $var=$_[0];
 		if ($var=~/^\d\d\d\d\d\d\d+$/) {
 			return 1;
 		}
 		return undef;
 	}
 	return undef;
 $$ LANGUAGE plperl;

Python Functions

Installing python in a database - if Python is not already installed

Source: https://www.postgresql.org/docs/9.4/static/plpython-funcs.html

To get into database via terminal: 

 1) ssh researcher@ssh.edegan.com
 2) cd \folder_name
 3) psql database_name

Creating Functions: 

CREATE FUNCTION pymax (a integer, b integer)
   RETURNS integer
AS $$
   if a > b:
     return a
   return b
 $$ LANGUAGE plpythonu;

PostGIS Resources

See:

Useful PostGIS functions for spatial joins

sum(expression): aggregate to return a sum for a set of records
count(expression): aggregate to return the size of a set of records
ST_Area(geometry) returns the area of the polygons
ST_AsText(geometry) returns WKT text
ST_Buffer(geometry, distance): For geometry: Returns a geometry that represents all points whose distance from this Geometry is less than or equal to distance. Calculations are in the Spatial Reference System of this Geometry. For geography: Uses a planar transform wrapper.
ST_Contains(geometry A, geometry B) returns the true if geometry A contains geometry B
ST_Distance(geometry A, geometry B) returns the minimum distance between geometry A and geometry B
ST_DWithin(geometry A, geometry B, radius) returns the true if geometry A is radius distance or less from geometry B
ST_GeomFromText(text) returns geometry
ST_Intersection(geometry A, geometry B): Returns a geometry that represents the shared portion of geomA and geomB. The geography implementation does a transform to geometry to do the intersection and then transform back to WGS84
ST_Intersects(geometry A, geometry B) returns the true if geometry A intersects geometry B
ST_Length(linestring) returns the length of the linestring
ST_Touches(geometry A, geometry B) returns the true if the boundary of geometry A touches geometry B
ST_Within(geometry A, geometry B) returns the true if geometry A is within geometry B
geometry_a && geometry_b: Returns TRUE if A’s bounding box overlaps B’s.
geometry_a = geometry_b: Returns TRUE if A’s bounding box is the same as B’s.
ST_SetSRID(geometry, srid): Sets the SRID on a geometry to a particular integer value.
ST_SRID(geometry): Returns the spatial reference identifier for the ST_Geometry as defined in spatial_ref_sys table.
ST_Transform(geometry, srid): Returns a new geometry with its coordinates transformed to the SRID referenced by the integer parameter.
ST_Union(): Returns a geometry that represents the point set union of the Geometries.
substring(string [from int] [for int]): PostgreSQL string function to extract substring matching SQL regular expression.
ST_Relate(geometry A, geometry B): Returns a text string representing the DE9IM relationship between the geometries.
ST_GeoHash(geometry A): Returns a text string representing the GeoHash of the bounds of the object.

Native functions for geography

ST_AsText(geography) returns text
ST_GeographyFromText(text) returns geography
ST_AsBinary(geography) returns bytea
ST_GeogFromWKB(bytea) returns geography
ST_AsSVG(geography) returns text
ST_AsGML(geography) returns text
ST_AsKML(geography) returns text
ST_AsGeoJson(geography) returns text
ST_Distance(geography, geography) returns double
ST_DWithin(geography, geography, float8) returns boolean
ST_Area(geography) returns double
ST_Length(geography) returns double
ST_Covers(geography, geography) returns boolean
ST_CoveredBy(geography, geography) returns boolean
ST_Intersects(geography, geography) returns boolean
ST_Buffer(geography, float8) returns geography [1]
ST_Intersection(geography, geography) returns geography [1]

Functions for Linear Referencing

ST_LineInterpolatePoint(geometry A, double measure): Returns a point interpolated along a line.
ST_LineLocatePoint(geometry A, geometry B): Returns a float between 0 and 1 representing the location of the closest point on LineString to the given Point.
ST_Line_Substring(geometry A, double from, double to): Return a linestring being a substring of the input one starting and ending at the given fractions of total 2d length.
ST_Locate_Along_Measure(geometry A, double measure): Return a derived geometry collection value with elements that match the specified measure.
ST_Locate_Between_Measures(geometry A, double from, double to): Return a derived geometry collection value with elements that match the specified range of measures inclusively.
ST_AddMeasure(geometry A, double from, double to): Return a derived geometry with measure elements linearly interpolated between the start and end points. If the geometry has no measure dimension, one is added.

3-D Functions

ST_3DClosestPoint — Returns the 3-dimensional point on g1 that is closest to g2. This is the first point of the 3D shortest line.
ST_3DDistance — For geometry type Returns the 3-dimensional cartesian minimum distance (based on spatial ref) between two geometries in projected units.
ST_3DDWithin — For 3d (z) geometry type Returns true if two geometries 3d distance is within number of units.
ST_3DDFullyWithin — Returns true if all of the 3D geometries are within the specified distance of one another.
ST_3DIntersects — Returns TRUE if the Geometries “spatially intersect” in 3d - only for points and linestrings
ST_3DLongestLine — Returns the 3-dimensional longest line between two geometries
ST_3DMaxDistance — For geometry type Returns the 3-dimensional cartesian maximum distance (based on spatial ref) between two geometries in projected units.
ST_3DShortestLine — Returns the 3-dimensional shortest line between two geometries

Relevant PostgreSQL Commands

\dt *.* Show all tables
\q Exit table

To make a circle

SELECT ST_Buffer([desired point], [desired radius], 'quad_segs=8') 
FROM [desired table]

quad_segs=8 indicates circle

 

For more precision in circle: 

SELECT ST_Transform(geometry( 
    ST_Buffer(geography( 
        ST_Transform( [desired point], 4326 )), 
            [desired radius]')), 
            900913) FROM [desired table]

4326 and 900913 represent particular precision.

Decimal Degrees

We are working with longitude and latitude in decimal degrees. See https://en.wikipedia.org/wiki/Decimal_degrees

When converting radius to km, multiply by 111.3199. For area, multiple by (111.3199)^2=12,392.12013601.

Configuring a copy of Postgres on Windows

If you'd like to set up a copy of PostgreSQL on your windows laptop or desktop, the following instructions may be helpful.

Adding PostgresSQL to the PATH

Add PostgreSQL to the path if it isn't already: 

Control Panel->System->Advanced->Environmental Variables
Add: C:\Program Files\PostgreSQL\9.0\bin

or from a cmd window (though sometimes this doesn't stick): 

SET PATH=%PATH%;C:\Program Files\PostgreSQL\9.0\bin;

PostgreSQL and Perl

To use PLPerl on windows, you will need to be careful to mix and match the right versions of PostgreSQL and Perl.

Perl version 5.10.1 (a 64bit build is available from ActiveState) works with PostgreSQL 9.0.1 (64bit build 1500). To see your PostgreSQL version type: 

psql -c "select version();" template1

To see your perl version type: 

perl -v

With these two versions together you should be able to add plperl to template1 (which all new dbs will inherit) with the command: 

createlang plperl template1

There is a list of commands/client applications, with links to documentation, which is useful.

Basic Performance Tuning

Note that the dbase server at ssh.edegan.com does not use the settings below. Its configuration is much more aggressive.

You will almost surely want to 'performance tune' your postgresql database, as the default settings are near useless. In particular edit postgresql.conf (which is in the data directory of your install) to change: 

shared_buffers = 512MB	#Use about 10-15% of available RAM, to a max of 512Mb on windows
effective_cache_size = 3GB #Use half to 3/4 of available RAM, depending on your pref
work_mem = 128MB # This is the memory allocated to each query sort
maintenance_work_mem = 256MB #This is for vacuum, and a max of 256 is recommended.

Note that with work_mem this is the allocation to each sort. Each query you run may do many sorts and you may have many users, so this can explode quickly. 128Mb is an aggresive setting that assumes only a single user. See the various documentation resources, especially the official performance optimization page for more information.

Restart the server (on windows use the 'services' control panel) for many changes to take effect: 

pg_ctl restart

Creating Users and Dbases

Create a user using pgAdmin or the createuser command: 

createuser username

And then create a database again using pgAdmin or the createdb command: 

createdb -O username DBName


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