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To reload this database[[admin_classification: pg_restore -d DBName db.backup ==Working with psql== To connect your psql client to a db type (for localhost don't specify the host): psql -h host DBName Useful commands are: \q Quits ==SQL Commands== There is a list of [http://www.postgresql.org/docs/7.3/static/sql-commands.html SQL commandsIT Build| ]] that may help.
Working with PostgreSQL (view source)
Revision as of 11:40, 21 October 2019
, 11:40, 21 October 2019no edit summary
==Basic ConfigurationPostgreSQL 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. [[Help:Access_RDP_Sever#Mapping the Database Server as Z|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 [http://www.postgresql.org/docs/7.3/static/sql-commands.html 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: <nowiki>\COPY tablename FROM 'filename.txt' WITH DELIMITER AS E'\t' HEADER NULL AS '' CSV</nowiki> Unload (copy to txt file) using: <nowiki>\COPY tablename TO 'filename.txt' WITH DELIMITER AS E'\t' HEADER NULL AS '' CSV</nowiki> ===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: <nowiki> 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; </nowiki> ==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:*http://postgis.net/features/*https://www.census.gov/geo/maps-data/data/tiger-line.html *https://www.census.gov/geo/maps-data/data/tiger.html*https://en.wikipedia.org/wiki/GIS_file_formats ===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 [[File: CirclePostGIS.png]] 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.
There is a [http://www.postgresql.org/docs/7.3/static/reference-client.html 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:
pg_ctl restart
===Creating Users and Dbases===
Create a user using pgAdmin or the createuser command:
createuser ed_eganusername
And then create a database again using pgAdmin or the createdb command:
createdb -O ed_egan username DBName ==Dumping and Restoring a Database== This can be done in pgAdmin, but the commands are: To dump a db: pg_dump mydb > db.backup
