Configuring TDS With DatasetScan

TDS User's Guide Configuring TDS With DatasetScan

Overview

The datasetScan element allows you to serve all files in a directory tree. The files must be homogenous so that the same metadata can be applied to all of them.

Note: See the Server-Side Catalog Specification for the formal definition of the datasetScan element XML.

Here is a minimal catalog containing a datasetScan element:

<?xml version="1.0" encoding="UTF-8"?>
<catalog name="Unidata Workshop 2006 - NCEP Model Data" version="1.0.1"
    xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
    xmlns:xlink="http://www.w3.org/1999/xlink">
  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />

  <datasetScan name="NCEP Data" path="ncep" location="/data/ldm/pub/native/grid/NCEP/" >
    <serviceName>myserver</serviceName>
  </datasetScan>
</catalog>

The main points are:

The path attribute on the datasetScan element is the part of the URL that identifies this datasetScan and is used to map URLs to a file on disk.
The location attribute on the datasetScan element gives the location of the dataset collection on the local file system.
The (path, location) of every datasetScan defines an implicit datasetRoot. The datasetRoot path therefore must be unique across all datasetRoots in the server.

In the catalog that the TDS server sends to a client, the datasetScan element is shown as a catalog reference:

<catalog name="Unidata Workshop 2006 - NCEP Model Data" version="1.0.1"
    xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
    xmlns:xlink="http://www.w3.org/1999/xlink">

  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <catalogRef xlink:href="/thredds/catalog/ncep/catalog.xml" xlink:title="NCEP Data" name="" />
</catalog>

The catalog will be generated dynamically on the server when requested, by scanning the server’s directory /data/ldm/pub/native/grid/NCEP/. For example, if the directory looked like:

/data/ldm/pub/native/grid/NCEP/
  GFS/
    CONUS_191km/
      GFS_CONUS_191km_20061107_0000.grib1
      GFS_CONUS_191km_20061107_0000.grib1.gbx9
      GFS_CONUS_191km_20061107_0600.grib1
      GFS_CONUS_191km_20061107_1200.grib1
    CONUS_80km/
      ...
    ...
  NAM/
    ...
  NDFD/
    ...

The result of a request for /thredds/catalog/ncep/catalog.xml might look like:

<catalog ...>
  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <dataset name="NCEP Data">
    <metadata inherited="true">
      <serviceName>myserver</serviceName>
    </metadata>
    <catalogRef xlink:title="GFS" xlink:href="GFS/catalog.xml" name="" />
    <catalogRef xlink:title="NAM" xlink:href="NAM/catalog.xml" name="" />
    <catalogRef xlink:title="NDFD" xlink:href="NDFD/catalog.xml" name="" />
  </dataset>
</catalog>

And for a /thredds/catalog/ncep/GFS/CONUS_191km/catalog.xml request:

<catalog ...>
  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <dataset name="ncep/GFS/CONUS_191km">
    <metadata inherited="true">
      <serviceName>myserver</serviceName>
    </metadata>
    <dataset name="GFS_CONUS_191km_20061107_0000.grib1"
             urlPath="ncep/GFS/CONUS_191km/GFS_CONUS_191km_20061107_0000.grib1" />
    <dataset name="GFS_CONUS_191km_20061107_0000.grib1.gbx"
             urlPath="ncep/GFS/CONUS_191km/GFS_CONUS_191km_20061107_0000.grib1.gbx" />
    <dataset name="GFS_CONUS_191km_20061107_0000.grib1"
             urlPath="ncep/GFS/CONUS_191km/GFS_CONUS_191km_20061107_0600.grib1" />
    <dataset name="GFS_CONUS_191km_20061107_0000.grib1"
             urlPath="ncep/GFS/CONUS_191km/GFS_CONUS_191km_20061107_1200.grib1" />
  </dataset>
</catalog>

Note that:

Files are turned into dataset elements, subdirectories are turned into nested catalogRef elements.
All the catalog URLs are relative. If the original catalog URL is http://server:8080/thredds/catalog.xml then the first catalogRef /thredds/catalog/ncep/catalog.xml resolves to http://server:8080/thredds/catalog/ncep/catalog.xml. From that catalog, the catalogRef GFS/catalog.xml resolves to http://server:8080/thredds/catalog/ncep/GFS/catalog.xml.
The dataset access URLs are built from the service base and the dataset urlPath (see THREDDS URL construction). So the dataset URLs from the above catalog would be http://server:8080/thredds/dodsC/ncep/GFS/CONUS_191km/GFS_CONUS_191km_20061107_0000.grib1. (You don’t have to worry about these URLs, as they are all generated automatically).
Each datasetScan element must reference a service element (whether directly, as above, or inherited).
Because the TDS uses the set of all given path values to map URLs to datasets, each datasetScan path MUST be unique across all config catalogs on a given TDS installation.

Inherited Metadata

The datasetScan element is an extension of a dataset element, and it can contain any of the metadata elements that a dataset can. Typically, you want all of its contained datasets to inherit the metadata, so add an inherited metadata element contained in the datasetScan element, for example:

<catalog name="Unidata Workshop 2006 - NCEP Model Data" version="1.0.1"
    xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0">

  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <datasetScan name="NCEP Data" path="ncep" location="/data/ldm/pub/native/grid/NCEP/">
    <metadata inherited="true">
      <serviceName>myserver</serviceName>
      <authority>unidata.ucar.edu:</authority>
      <dataType>Grid</dataType>
    </metadata>
  </datasetScan>
</catalog>

Including Only Desired Files

A datasetScan element can specify which files and directories it will include with a filter element.

Note: See the Server-Side Catalog Specification for the formal definition of the filter element XML.

When no filter element is given, all files and directories are included in the generated catalog(s). Adding a filter element to your datasetScan element allows you to include (and/or exclude) the files and directories as you desire. For instance, the following filter and selector elements will only include files that end in .grib1 and exclude any file that ends with *_0000.grib1:

<filter>
  <include wildcard="*.grib1"/>
  <exclude wildcard="*_0000.grib1"/>
</filter>

You can specify which files to include or exclude using either wildcard patterns (with the wildcard attribute) or regular expressions (with the regExp attribute). If the wildcard or regular expression matches the dataset name, the dataset is included or excluded as specified. By default, includes and excludes apply only to regular files (atomic datasets). You can specify that they apply to directories (collection datasets) as well by using the atomic and collection attributes.

For instance, the additional selector in this filter element means that only directories that don’t start with CONUS will be cataloged (since the default value of atomic is true, we have to explicitly set it to false if we only want to filter directories):

<filter>
  <include wildcard="*.grib1"/>
  <exclude wildcard="*_0000.grib1"/>
  <exclude wildcard="CONUS*" atomic="false" collection="true"/>
</filter>

Its a good idea to always use a filter element with explicit includes, so if stray files accidentally get into your data directories, they won’t generate erroneous catalog entries. This is known as whitelisting.

<?xml version="1.0" encoding="UTF-8"?>
<catalog name="Unidata Workshop 2006 - NCEP Model Data" version="1.0.1"
    xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
    xmlns:xlink="http://www.w3.org/1999/xlink">

  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <datasetScan name="NCEP Data" path="ncep" location="/data/ldm/pub/native/grid/NCEP/" >
    <serviceName>myserver</serviceName>
    <filter>
      <include wildcard="*.grib1"/>
      <include wildcard="*.grib2"/>
      <exclude wildcard="*.gbx"/>
    </filter>
  </datasetScan>
</catalog>

Complicated matching can be done with regular expressions, e.g.:

<filter>
  <include regExp="PROFILER_.*_2013110[67]_[0-9]{4}\.nc"/>
</filter>

A few gotchas to remember:

to match any number of characters, use .*, not *
in the above, we use a \ to escape the . character, to require a literal . character. Note that only one backslash is needed. (Inside a Java String, one needs to use \\, but not here in the catalog).

<?xml version="1.0" encoding="UTF-8"?>
<catalog name="Unidata Workshop 2006 - NCEP Model Data" version="1.0.1"
    xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0"
    xmlns:xlink="http://www.w3.org/1999/xlink">

  <service name="myserver" serviceType="OpenDAP" base="/thredds/dodsC/" />
  <datasetScan name="NCEP Data" path="ncep" location="/data/ldm/pub/native/grid/NCEP/" >
    <serviceName>myserver</serviceName>
    <filter>
      <include regExp="PROFILER_wind_06min_2013110[67]_[0-9]{4}\.nc"/>
    </filter>
    <addTimeCoverage
          datasetNameMatchPattern="PROFILER_wind_06min_([0-9]{4})([0-9]{2})([0-9]{2})_([0-9]{2})([0-9]{2}).nc$"
          startTimeSubstitutionPattern="$1-$2-$3T$4:$5:00" duration="1 hour"/>
  </datasetScan>
</catalog>

Sorting Datasets

Datasets at each collection level are listed in ascending order by name. To specify that they are to be sorted in reverse order:

<filesSort increasing="false" />

Note that the sort is done before renaming.

Adding A Link To The “Latest” Dataset

You may want to have a special link that points to the “latest” data in the collection, especially for data that is constantly being updated, e.g., real-time data. Here, latest 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).

The simplest way to enable this is to add the attribute addLatest="true" to the datasetScan element. The latest resolver service will be automatically added to the catalog.

<datasetScan name="GRIB2 Data" path="grib2" location="c:/data/grib2/" serviceName="myserver"
    addLatest="true" >
 ...
</datasetScan>

The <addLatest> child element allows more options in configuring the latest service:

<datasetScan name="GRIB2 Data" path="grib2" location="c:/data/grib2/" serviceName="myserver" >
  <addLatest name="Latest Run" top="false" lastModifiedLimit="60000" />
</datasetScan>

where the addLatest attributes mean:

name: the name of the dataset in the catalog (default latest)
top: place link on top (try) or bottom (false) of the catalogScan (default true)
lastModifiedLimit: files whose last modified date is less than this amount (in minutes, may be fractional) are excluded (default 0).

Note: See the Server-Side Catalog Specification for the formal definition of the addLatest element XML.

Adding `timeCoverage` Elements

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 datasets in the collection.

Currently, the addTimeCoverage element can only construct start/duration timeCoverage elements and uses the dataset name to determine the start time. As described in the Naming Datasets section of this document, the addTimeCoverage element applies a regular expressions match to the dataset name. If the match succeeds, any regular expression capturing groups are used in the start time replacement string to build the start time string. These attributes values are used to determine the time coverage:

The datasetNameMatchPattern attribute value is used for a regular expression match on the dataset name. If a match is found, a timeCoverage element is added to the dataset. The match pattern should include capturing groups which allow the match to save substrings from the dataset name.
The startTimeSubstitutionPattern attribute value has all capture group references ("$n") replaced by the corresponding substring that was captured during the match. The resulting string is used as the start value of the resulting timeCoverage element.
The duration attribute value is used as the duration value of the resulting timeCoverage element.

For example, the addTimeCoverage element:

<datasetScan name="GRIB2 Data" path="grib2" location="c:/data/grib2/" serviceName="myserver">
  <addTimeCoverage
    datasetNameMatchPattern="([0-9]{4})([0-9]{2})([0-9]{2})_([0-9]{2})([0-9]{2}).grib1$"
    startTimeSubstitutionPattern="$1-$2-$3T$4:00:00"
 duration="60 hours" />
</datasetScan>

results in the following timeCoverage element:

<timeCoverage>
   <start>2005-07-18T12:00:00</start>
   <duration>60 hours</duration>
</timeCoverage>

A variation is the addition of the datasetPathMatchPattern attribute. It can be used instead of the datasetNameMatchPattern attribute and changes the target of the match from the dataset name to the dataset path. If both attributes are used, the datasetNameMatchPattern attribute takes precedence.

Naming Datasets

By default, datasets are named with the corresponding file name. By adding a namer element, you can specify a more human readable dataset names. The following namer looks for datasets named GFS or NCEP and renames them with the corresponding replace string:

<namer>
  <regExpOnName regExp="GFS" replaceString="NCEP GFS model data" />
  <regExpOnName regExp="NCEP" replaceString="NCEP model data"/>
</namer>

More complex renaming is possible as well. The namer uses a regular expressions match on the dataset name. If the match succeeds, any regular expression capturing groups are used in the replacement string.

A capturing group is a part of a regular expression enclosed in parenthesis. When a regular expression with a capturing group is applied to a string, the substring that matches the capturing group is saved for later use. The captured strings can then be substituted into another string in place of capturing group references,$n, where n is an integer indicating a particular capturing group. (The capturing groups are numbered according to the order in which they appear in the match string.)

For example, the regular expression Hi (.), how are (.)? when applied to the string Hi Fred, how are you? would capture the strings Fred and you. Following with a capturing group replacement in the string $2 are $1 would result in the string “you are Fred.”

Here’s an example namer:

<namer>
  <regExpOnName regExp="([0-9]{4})([0-9]{2})([0-9]{2})_([0-9]{2})([0-9]{2})"
                replaceString="NCEP GFS 191km Alaska $1-$2-$3 $4:$5:00 GMT"/>
</namer>

The regular expression has five capturing groups:

The first capturing group, ([0-9]{4}), captures four digits, in this case the year.
The second capturing group, ([0-9]{2}), captures two digits, in this case the month.
The third capturing group, ([0-9]{2}), captures two digits, in this case the day of the month.
The fourth capturing group, ([0-9]{2}), captures two digits, in this case the hour of the day.
The fifth capturing group, ([0-9]{2}), captures two digits, in this case the minutes of the hour.

When applied to the dataset name GFS_Alaska_191km_20051011_0000.grib1, the strings 2005, 10, 11, 00, and 00 are captured. After replacing the capturing group references in the replaceString attribute value, we get the name NCEP GFS 191km Alaska 2005-10-11 00:00:00 GMT. So, when cataloged, this dataset would end up as something like this:

<dataset name="NCEP GFS 191km Alaska 2005-10-11 00:00:00 GMT"
         urlPath="models/NCEP/GFS/Alaska_191km/GFS_Alaska_191km_20051011_0000.grib1"/>