Process SNAP graphs with CWL

The described method targets processing Earth Observation data with the SNAP Graph Processing Tool (GPT) using docker and CWL.

CWL is used to invoke the SNAP gpt command line tool and deals with all the docker volume mounts required to process a Graph and EO data available on the host.

The examples rely on a simple SNAP graph applying the Calibration operator to a Sentinel-1 GRD acquisition:

<graph id="Graph">
  <version>1.0</version>
  <node id="Read">
    <operator>Read</operator>
    <sources/>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>${inFile}</file>
      <formatName>SENTINEL-1</formatName>
    </parameters>
  </node>
  <node id="Calibration">
    <operator>Calibration</operator>
    <sources>
      <sourceProduct refid="Read"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <sourceBands/>
      <auxFile>Product Auxiliary File</auxFile>
      <externalAuxFile/>
      <outputImageInComplex>false</outputImageInComplex>
      <outputImageScaleInDb>false</outputImageScaleInDb>
      <createGammaBand>false</createGammaBand>
      <createBetaBand>false</createBetaBand>
      <selectedPolarisations>${selPol}</selectedPolarisations>
      <outputSigmaBand>true</outputSigmaBand>
      <outputGammaBand>false</outputGammaBand>
      <outputBetaBand>false</outputBetaBand>
    </parameters>
  </node>
  <node id="Write">
    <operator>Write</operator>
    <sources>
      <sourceProduct refid="Calibration"/>
    </sources>
    <parameters class="com.bc.ceres.binding.dom.XppDomElement">
      <file>./cal.dim</file>
      <formatName>BEAM-DIMAP</formatName>
    </parameters>
  </node>
</graph>

This SNAP graph contains parameters:

${inFile} is the path to the Sentinel-1 manifest.xml file. This parameter is used in the Read Operator
${selPol} is the selected polarization and thus leaving an option to process VV or VH (typically). This parameter is used in the Calibration Operator

CWL is used to wrap the SNAP gpt executable:

gpt sar-calibration.xml -PselPol=${selPol} -PinFile=${inFile}

There are two approaches described to process this graph using CWL:

The SNAP graph is a local file and thus passed to CWL as a File (as a reference)
The SNAP graph XML content is part of the CWL (included as a value)