How to access the e-Ecology database

Connecting other programs to the UvA-BiTS database (e.g. R, Access, ArcGIS)

This page provides information on how to set up an Open Database Connectivity (ODBC) which will enable many software packages to extract data directly from the database.

Last updated by Judy Shamoun-Baranes on February 6, 2012.

General Information

The UvA-BiTS database is a spatial postgreSQL ([1]).

The UvA-BiTS database can be directly accessed through the UvA-BiTS phpPgAdmin web service ([2]) by people working directly within the University of Amsterdam network.

You can also access the database from other programs by installing an ODBC driver for postgreSQL and establishing a "User Data Source".

In order to access the database you must first have a user name and password provided to you by SARA. (Current contact person is Lykle Voort.)

The public server is at

 server : public.flysafe.sara.nl
 port : 5432
 ssl : required

The UvA-BiTS data can be found in schema gps.

Setting up an ODBC connection

ODBC (Open Database connectivity) is a standard method of sharing data between databases and other programs. ODBC drivers use SQL to gain access to data from sources outside the program. Therefore, in order to connect between your database and other programs you must set up an ODBC connection.

Step 1: Download and install the most recent ODBC driver for postgreSQL. [3]

Step 2: Set up an ODBC connection

Do the following (variations may exist between windows operating systems):

1. Go to start | Control panel | Administrative tools | Data sources (ODBC). If you are having trouble finding it, type "ODBC" into the Search box at the top of the Control Panel window.
2. Go to User DSN (first tab in Data sources).
3. Click ADD.
4. In the window Create New Data Source select PostgreSQL ANSI and click FINISH.
5. The ODBC Driver Setup window opens. Data source name: give your data source a name (e.g. GPS). Keep it simple and easily identifiable since this is the name you will use to identify your database from other applications; this will be the ODBC driver name.
6. In the same window fill in the following information: database flysafe, Server public.flysafe.sara.nl, User Name your user name, SSL Mode require, Port 5432, Password your password. Click TEST to test your connection. When the window is completed click SAVE.
7. Back in the User DSN window you should now see the ODBC driver you just named. Click OK.

After completing these steps many other programs will now recognize your database and be able to communicate with it.

Connecting to the database in R

The text file provides a very short example that will give an idea of how to connect to the database via the ODBC driver you have just established.

Here you provide the name of the database file or the user DSN name for a given ODBC data source (as described above).

db.file <-"GPS"

Load the RODBC library. Visit the CRAN repository <http://cran.r-project.org/web/packages/> for a list of contributed packages and instructions for installation. Packages may be installed using the GUI interface or using ?install.packages.

library(RODBC)

Establish a connection to the database, the following code is used if reading from an ODBC data source.

db <- odbcConnect(db.file) 

View the table names in the database.

sqlTables(db)

View the field (column) names of a specific table.

sqlColumns(db, table.name)

Query the database, returning data from table gps.uva_tracking_speed_limited, for device_info_serial 1 as dataframe "test".

test <- sqlQuery(db, query = paste("SELECT * FROM gps.uva_tracking_speed_limited 
 WHERE device_info_serial = 1 AND latitude IS NOT NULL ORDER BY date_time ASC", sep = '' ))

Connecting to the database in Access

You can now connect to the database via Access. You have two options. One is to import the data; once this is done your database is not automatically updated but does not require a link to the database.

The second option (described below) is to create a dynamic link to the database. (You must be connected to the network.) In this case you are always viewing updated data that is in the actual SARA database. '

1. Open a new database in Access 2007-2010.
2. Go to External data | ODBC Database.
3. It is recommended that you select Link to the data source by creating a linked table. Click OK.
4. In Select Data Source click on the tab Machine Data Source.
5. Select the data source name you created when setting up the ODBC connection (e.g. GPS), then click OK.
6. Select the tables you want to import and click OK.

1. Open a new database in Access 2003.
2. Go to File | Get external data | Link tables.
3. In Files of type, select ODBC databases.
4. In Select data source click on the tab Machine Data Source.
5. Select the data source name you created when setting up the ODBC connection (e.g. GPS), then click OK.
6. Select the tables you want to import and click OK.

You now have access to your selected tables in the database. Have fun.