Dapper comes with contains two configurable servlets: one provides provides OPeNDAP access to data (referred to as the Dapper servlet), while the other (known as the DChart servlet) provides an AJAX user interface to the OPeNDAP servlet.

Starting or stopping Dapper

Dapper is started with the dapper.sh command followed by the start argument:

    ./dapper.sh start

You must run this command from the Dapper distribution directory.

Debug information from the Tomcat container is available in logs/tomcat.log. Log info from Dapper is sent to logs/dapper.log while log info from DChart is sent to logs/dchart.log.

If you want to run Dapper in a terminal window and have all debug information sent to the terminal, you can use:

    ./dapper.sh run

Dapper is stopped with the stop argument:

    ./dapper.sh stop

Configuring the Dapper servlet

Dapper is configured with the etc/dapper.properties file. A sample configuration file is available in etc/dapper.properties.sample. Following are the configurable properties:

Property	Type	Required	Description
dapper.cdp_databases	string	no	Comma separated list of databases for the CDP to use
dapper.max_profiles	string	no	Maximum number of profiles to serve in one data request. Default is 1000
dapper.netcdf_directory	string	no	A directory that contains netCDF files to be served by the netCDF service. This directory can contain other directories and Dapper will also server netCDF files from those directories. The default value is empty (no netCDF directories).
dapper.user	string	yes	Database user name
dapper.password	string	yes	Database user password
dapper.dbhost	string	no	Host name of MySQL server (default localhost)
dapper.dbport	int	no	Port number of MySQL server (default 3306)
dapper.timeout	int	no	Maximum time in seconds to devote to one request (default 60)
dapper.disable_proxy	boolean	no	Disable proxying (and conversion) of remote netCDF datasets to OPeNDAP (default false)
dapper.aggconfig	string	no	Configuration file for aggregating data. (default etc/aggs.xml)

Configuring Dapper aggregations

Dapper allows you to aggregate multiple netCDF files into a single logical netCDF file. This is configured through an aggregation configuration file that is located (by default) in etc/aggs.xml.

Dapper supports two kinds of aggregations:

• Variable aggregations combine the variables from multiple netCDF files into one logical netCDF file
• Outer aggregations concatenate the outer dimension of variables with the same name in multiple files into a logical variable where the outer dimension has a size equal to the sum of the sizes of the outer dimension in the original netCDF files.

Outer aggregations can be nested in variable aggregations. Dapper can aggregate netCDF files that are available as local files as well as by HTTP or OPeNDAP.

Here's a sample aggregation configuration file (available in etc/aggs.xml.sample) that aggregates several netCDF files containing NCAR/NCEP reanalysis data:

 <scichart>
     <aggregation cacheTime="86400" id="www.cdc.noaa.gov/Datasets/ncep.reanalysis.dailyavgs/pressure" type="variable">
         <aggregation type="outer" dim="time">
             <dataset url="http://www.cdc.noaa.gov/Datasets/ncep.reanalysis.dailyavgs/pressure/air.2006.nc"/>
             <dataset url="http://www.cdc.noaa.gov/Datasets/ncep.reanalysis.dailyavgs/pressure/air.2007.nc"/>
         </aggregation>
         <aggregation type="outer" dim="time">
             <dataset url="http://www.cdc.noaa.gov/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.2006.nc"/>
             <dataset url="http://www.cdc.noaa.gov/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.2007.nc"/>
         </aggregation>
     </aggregation>
 < /scichart> 

If you copy this file to etc/aggs.xml and restart the server and point your browser to:

http://localhost:8080/dods/aggregations/www.cdc.noaa.gov/Datasets/ncep.r...

you will see that these four URls have been consolidated into a single logical OPeNDAP url.

Dapper aggregation file schema

The scichart element is the root element of the Dapper aggregation file.

Tag	Children	Children	Description
<scichart>	aggregation+	yes	Root element of document

Tag	Children	Children	Description
<aggregation>	dataset+ | aggregation	yes	Defines an aggregation. Only variable aggregations are allowed to have a nested aggregation.
Attribute	Type	Required	Description
id	string	yes	unique id for this aggregation. The OPeNDAP URL for the aggregation will be at "/dods/aggregations/<id>.nc"
cacheTime	integer	no	Time (in seconds) to cache metadata associated with this aggregation. Default is 3600 (1 hour)
type	"variable"|"outer"	yes	Aggregation method
dim	string	yes (for outer aggregations)	Name of the dimension to use to concatenate datasets. Only applies to outer aggregations.

Dataset to include in an aggregation

Tag	Children	Required?	Description
<dataset>
Attribute	Type	Required	Description
url	string	yes	url of the dataset.Aggregations can include file:, http:, or dods: url schemes.

 

Configuring the DChart servlet

DChart is configured with the dchart/etc/config.xml XML file. If the file is missing the servlet will be disabled.

A sample configuration file ( available in dchart/etc/config.xml.sample) is below:

<scichart>
    <title>
    <![CDATA[
	<h1>My Dapper Server</h1>
	<h2>Change me in config.xml</h2>
    ]]>
    </title>
    <property name="opendap.cache.expires" value="3600"/>  <!-- Max cache age in second -->
    <property name="opendap.cache.capacity" value="100000" /> <!-- Max number of items in cache -->
    <datasets>
	<dataset category="Gridded example" name="NCAR Reanalysis" url="file://test/data/agg/air.2006.0.2.nc" type="grid" >
	    <description>
	        Gridded data example
	    </description>
        </dataset>
        <dataset category="In-situ example" url="http://localhost:8080/dods/dapperexample/argo_sample.cdp" name="Argo Pacific profiles">
	    <variables>
	        <include name="PSAL" mapto="Salinity"/>
	        <include name="TEMP" mapto="Temperature"/>
	    </variables>
	    <description>
	        In-situ data example
	    </description>
	</dataset>
    </datasets>
</scichart>

Many more examples are available in the dchart/etc directory, including the configuration file used at PMEL (dchart/etc/config.xml.pmel).

DChart configuration file schema

The scichart element is the root element of the DChart configuration file.

Tag	Children	Children	Description
<scichart>	property+ | datasets | title	yes	Root element of document

The property element defines name value pairs to pass to the DChart servlet.

Two properties are currently defined:

• opendap.cache.expires specifies how long (in seconds) DChart should cache data from an Opendap server.
• opendap.cache.capacity specifies the maximum number of Opendap requests to store in the DChart Opendap cache.

Tag	Children	Required?	Description
<property>		no	Name/value pair
Attribute	Type	Required	Description
name	string	yes	Property name
value	string	yes	Property value

Contains all of the <dataset> elements and defines the base URL of the Opendap data server.

Tag	Children	Required?	Description
<datasets>	dataset+	yes	Container for dataset element
Attribute	Type	Required	Description
default_category	string	no	Default category to use for datasets
base	string	yes	Base URL of Opendap server

Use the dataset element to include datasets from the base URL specified by the <datasets> element.

Tag	Children	Required?	Description
<dataset>	variables | description | ranges | attributes	yes	Include a dataset in DChart
Attribute	Type	Required	Description
default	true|false	no	If true, this dataset will be selected when DChart is initialized in the client browser.
url	string	yes	url of the dataset. DChart supports file:, http:, or dods: schemes for the url.
category	string	no	Category in which to place dataset
type	"time"|"profile"|"grid"	no	Indicates whether the dataset is a time series, profile or gridded. If missing, DChart will assume that the dataset is a profile unless the dataset has the string "_time_" in the URL which implies a time series
name	string	yes	Label DChart uses to display this dataset

The description element is used to configure a link from a dataset to a description of the dataset. For example:

	    <description>
              <![CDATA[
                More info on this dataset is available <a href="http://www.example.com">here</a>.
              ]]>
	    </description>
		      

Tag	Children	Required?	Description
<description>		no	Dataset description

Specifies default ranges to use for the dataset. Only time ranges are currently supported.

Tag	Children	Required?	Description
<ranges>	range	no	Default dataset ranges

Specifies a range. Only time ranges are currently supported. Dates are formatted as "DD/MMM/YYYY HH:MM:SS" or [^|$][+/-]delta, where ^ is the first date in the dataset, $ is the last date in the dataset, and delta is a time interval in seconds.All times are assumed to be GMT.

Examples:

<!-- Fixed time interval -->
<ranges>                         
  <range type="t" low="01/Jan/2004 00:00:00" high="31/Dec/2005 00:00:00"/>
</ranges>

<!-- Low value is 1 hour before last time point in dataset -->                        
<ranges>                         
  <range type="t" low="$-3600"/>
</ranges>

Tag	Children	Required?	Description
<range>		yes	Default range
Attribute	Type	Required	Description
type	"t"	yes
high	Date	no	Upper date value of range
low	Date	no	Lower date value of range

Specifies miscellaneous attributes for the dataset.

Tag	Children	Required?	Description
<attributes>	stationName	no	Dataset attributes

Name of Dapper variable or attribute that contains the station name. This name will be displayed when a user clicks on a station in the DChart map.

Tag	Children	Required?	Description
<stationName>			Determine station name to display in DChart user interface.
Attribute	Type	Required	Description
variable	string	yes	Name of Dapper variable or attribute to use for station name

The variables element contains configuration info on the variables in a particular dataset.

Tag	Children	Required?	Description
<variable>	include* | exclude* | default	no	Configuration info on variables in a dataset

Include a variable from a Dapper dataset in DChart dataset and (optionally) rename the variable. For example, if a Dapper dataset contains the variable "PSAL" and you want to display it as "Salinity", you would add:

<include name="PSAL" mapto="Salinity"/>

to the configuration file.

Tag	Children	Required?	Description
<include>			Include variables from a dataset
Attribute	Type	Required	Description
name	string	yes	Name of variable to include
mapto	string	yes	Display the variable with the value of this attribute

Exclude a variable from a Dapper dataset in DChart.

Tag	Children	Required?	Description
<exclude>			Exclude variables from a dataset
Attribute	Type	Required	Description
name	string	yes	Name of variable to include

Specifies the variable to select when a user selects a DChart dataset.

Tag	Children	Required?	Description
<default>			Default selected variable in a dataset
Attribute	Type	Required	Description
name	string	yes	Name of variable

 

Tomcat configuration

Dapper is packaged with the Jakarta Tomcat Server. By default, the Tomcat server is configured to run on ports 8080 (for HTTP) and 8005 (for shutdown notices). If you already have a server running on either of these ports, you will need to reconfigure Tomcat. The following describes how to change these ports to 9090 and 9005:

• Edit the file jakarta/conf/server.xml in a text editor.
• Change the line containing:

  <Server port="8005"

  to

  <Server port="9005"

• Change the line containing:

  <Connector port="8080"

  to

  <Connector port="9090"

• Save the file and restart the server

 

More information on configuring Tomcat is available at the Tomcat site.