Hyrax - THREDDS Configuration

From OPeNDAP Documentation

1 Overview

Hyrax now uses its own implementation of the THREDDS catalog services and supports most of the THREDDS catalog service stack. The implementation relies on two DispatchHandlers in the OLFS and utilizes XSLT to provide HTML versions (presentation views) for human consumption.

  1. Dynamic THREDDS catalogs for holdings provided by the BES are provided by the opendap.bes.BESThreddsDispatchHandler.
  2. Static THREDDS catalogs are provided by the opendap.threddsHandler.StaticCatalogDispatch. The static catalogs allow catalog "graphs" to be decoupled from the filesystem "graph" of the data holdings, thus allowing data providers the ability to present and organize data collections independently of how they are organized in the underlying filesystem.

Static THREDDS catalogs are "rooted" in a master catalog file, catalog.xml, located in the (persistent) content directory for the OLFS (Typically $CATALINA_HOME/content/opendap). The default catalog.xml that comes with Hyrax contains a simple catalogRef element that points to the dynamic THREDDS catalogs generated from the BES holdings. The default catalog example also contains a (commented out) datasetScan element that provides (if enabled) a simple demonstration of the datasetScan capabilities. Additional catalog components may be added to the catalog.xml file to build (potentially large) static catalogs.

  • THREDDS datasetScan elements are now fully supported and can be used as a tool for altering the catalog presentation of any part of the BES catalog. These alterations include (but are not limited too) renaming, auto proxy generation, filtering, and metadata injection.

More details about the handlers, their configuration options, and other information can be found here.


1.1 THREDDS Catalog Documentation

Rather than provide an exhaustive explanation of the THREDDS catalog functionality and configuration I will appeal to the existing documents provided by our fine colleagues at UNIDATA:



2 Configuration Instructions

  • The current default (olfs.xml) file comes with THREDDS configured correctly.
  • The THREDDS master catalog is stored in the file $CATALINA_HOME/content/opendap/catalog.xml it can be edited to provide additional static catalog access.

3 datasetScan Support

The datasetScan element is a powerful tool that can be used to sculpt the catalog's presentation of the BES catalog content. The Hyrax implementation has a couple of key points that need to be considered when developing an instance of the datasetScan element in your THREDDS catalog.

3.1 location attribute

The location attribute specifies the place in the BES catalog graph that the datasetScan will be rooted. This value must be expressed relative to the BES catalog root (BES.Catalog.catalog.RootDirectory) and not in terms of the underlying BES host file system.

Example
If BES.Catalog.catalog.RootDirectory=/usr/share/hyrax and the data directory to which you wish to apply the datasetScan is (in filesystem terms) located at /Users/share/hyrax/data/nc then the associated datasetScan element's location attribute would have a value of /data/nc
<datasetScan name="DatasetScanExample" path="hyrax" location="/data/nc">

3.2 name attribute

The name attribute specifies name that will be used to in the presentation (HTML) view for the catalog containing the datasetScan is viewed.

3.3 path attribute

The path attribute specifies the place in the THREDDS catalog graph that the datasetScan will be rooted. In effect it is a relative URL for the service. If path begins with a "/" then it is an absolute path - rooted at the server and port of the web server. The values of the path attribute should NEVER contain "catalog.xml" or "catalog.html". The service will create these endpoints dynamically.

Relative path example
Consider a catalog accessed with the URL: http://localhost:8080/opendap/thredds/v27/Landsat/catalog.xml and that contains this datasetScan element:

<datasetScan name="DatasetScanExample" path="hyrax" location="/data/nc" /> </source>

In the client catalog the datasetScan becomes this catalogRef element:
<thredds:catalogRef
    name="DatasetScanExample"
    xlink:title="DatasetScanExample"
    xlink:href="hyrax/catalog.xml"
    xlink:type="simple"
/>


And the top of datasetScan catalog graph will be found at the URL
http://localhost:8080/opendap/thredds/v27/Landsat/hyrax/catalog.xml
Absolute path examples
Consider a catalog accessed with the URL: http://localhost:8080/opendap/thredds/v27/Landsat/catalog.xml and that contains this datasetScan element:
<datasetScan name="DatasetScanExample" path="/hyrax" location="/data/nc" />
In the client catalog the datasetScan becomes this catalogRef element:
<thredds:catalogRef
     name="DatasetScanExample"
     xlink:title="DatasetScanExample"
     xlink:href="/hyrax/catalog.xml"
     xlink:type="simple"
/>
Then the top of datasetScan catalog graph will be found at the URL
http://localhost:8080/hyrax/catalog.xml
Which is probably not what you want! This catalogRef directs the catalog crawler away from the Hyrax THREDDS service and to an undefined (as far as Hyrax is concerned) endpoint, one that most likely will generate a 404 (Not Found) response from the Web Server.
When using absolute paths you must be sure to prefix the path with the Hyrax THREDDS service path or you will direct the clients away from the service. In these examples the Hyrax THREDDS service path would be /opendap/thredds/" (look at the URLs in the above examples) If we change the datasetScan path attribute value to /opendap/thredds/myDatasetScan:
<datasetScan name="DatasetScanExample" path="'/opendap/thredds/myDatasetScan" location="/data/nc" />
In the client catalog the datasetScan becomes this catalogRef element:
<thredds:catalogRef
    name="DatasetScanExample"
    xlink:title="DatasetScanExample"
    xlink:href="/opendap/thredds/myDatasetScan/catalog.xml"
    xlink:type="simple"
/>
Now the top of datasetScan catalog graph will be found at the URL
http://localhost:8080/opendap/thredds/myDatasetScan/catalog.xml
which keeps the URL referencing the Hyrax THREDDS service and not some other part of the web service stack.

3.4 useHyraxServices attribute

The Hyrax version of the datasetScan element employs the extra attribute useHyraxServices. This allows the datasetScan to automatically generate Hyrax data services definitions and access links for datasets in the catalog. The datasetScan can be used to augment the list of services (when useHyraxServices is set to true) or it can be used to completely replace the Hyrax service stack (when useHyraxServices is set to false).

  • If no services are referenced in the datasetScan and useHyraxServices is set to true, then Hyrax will provide catalogs with service definitions and access elements for all the datasets that the BES identifies as data.
  • If no services are referenced in the datasetScan and useHyraxServices is set to false, then the catalogs generated by the datasetScan will have no service definitions or access elements.

By default useHyraxServices is set to true.

3.5 Functions

DatasetScan allows you to apply the following functions to the names of the datasets in the datasetScan catalog graph.

3.5.1 Filter

A datasetScan element can specify which files and directories it will include with a filter element (also see THREDDS server catalog spec for details). The filter element allows users to specify which datasets are to be included in the generated catalogs. A filter element can contain any number of include and exclude elements. Each include or exclude element may contain either a wildcard or a regExp attribute. If the given wildcard pattern or regular expression matches a dataset name, that dataset is included or excluded as specified. By default, includes and excludes apply only to atomic datasets (regular files). You can specify that they apply to atomic and/or collection datasets (directories) by using the atomic and collection attributes.
<filter>
    <exclude wildcard="*not_currently_supported" />
    <include regExp="/data/h5/dir2" collection="true" />
</filter>

3.5.2 Sort

Datasets at each collection level are listed in ascending order by name. With a sort element you can specify that they are to be sorted in reverse order:
<sort>
    <lexigraphicByName increasing="false" />
</sort>

3.5.3 Namer

If no namer element is specified, all datasets are named with the corresponding BES catalog dataset name. By adding a namer element, you can specify more human readable dataset names.
<namer>
    <regExpOnName regExp="/data/he/dir1" replaceString="AVHRR" />
    <regExpOnName regExp="(.*)\.h5" replaceString="$1.hdf5" />
    <regExpOnName regExp="(.*)\.he5" replaceString="$1.hdf5_eos" />
    <regExpOnName regExp="(.*)\.nc" replaceString="$1.netcdf" />
</namer>

3.5.4 addTimeCoverage

A datasetScan element may contain an addTimeCoverage element. The addTimeCoverage element indicates that a timeCoverage metadata element should be added to each dataset in the collection and describes how to determine the time coverage for each dataset in the collection.
<addTimeCoverage 
    datasetNameMatchPattern="([0-9]{4})([0-9]{2})([0-9]{2})([0-9]{2})_gfs_211.nc$"
    startTimeSubstitutionPattern="$1-$2-$3T$4:00:00"
    duration="60 hours"
/>
for the dataset named 2005071812_gfs_211.nc, results in the following timeCoverage element:
 <timeCoverage>
    <start>2005-07-18T12:00:00</start>
    <duration>60 hours</duration>
  </timeCoverage>

3.5.5 addProxies

For real-time data you may want to have a special link that points to the "latest" data in the collection. Here, latest is simply means the last filename in a list sorted by name, so its only the latest if the time stamp is in the filename and the name sorts correctly by time.
<addProxies>
    <simpleLatest name="simpleLatest" />
    <latestComplete name="latestComplete" lastModifiedLimit="60.0" />
</addProxies>