Enum Tool

Enum Tool is a Python application designed to digest OME XML schema and produce meaningful output about enumerations.

Running the tool

$ ./enum-tool
Expecting single ome.xsd file path!
Usage: ./enum-tool (-t | -x | -d <file>) [path/to/ome.xsd]
Toolkit for working with enumerations from an OME XML Schema definition.

Options:
  -t            Dumps all enumerations in a visual tree
  -x            Displays the XPath expressions for each enumeration
  -d file       Diffs enumeration possible values from an XPath
            configuration file. This file is expected to have two sections
            the first containing the "old" and "new" XSD files and the
            second containing the XPath mappings. (See: example.cfg)

Examples:
  ./enum-tool -t schemas/ome.xsd
  ./enum-tool -x schemas/ome.xsd
  ./enum-tool -d example.cfg

Report bugs to OME-Devel <ome-devel@lists.openmicroscopy.org.uk

Examining enumeration structure

Enum Tool has two formats for providing information about enumerations within OME XML schemata:

  • XPath format

    $ ./enum-tool -x tmp/ome.xsd
/OME/Instrument/LightSource/Filament@Type
/OME/Image/DisplayOptions/GreyChannel@ColorMap
/OME/Experiment@Type
/OME/Image/ChannelInfo@PhotometricInterpretation
/OME/Image/Pixels@DimensionOrder
/OME/Instrument/Detector@Type
/OME/Instrument/Filter/ExFilter@Type
...

  • Tree/graph format

    $ ./enum-tool -t tmp/ome.xsd
+-- OME
+-- Image
  +-- DisplayOptions
    +-- Display(xs:string)
      +-- RGB
      +-- Grey
+-- OME
  +-- Experiment
    +-- Type(xs:string)
      +-- FP
      +-- FRET
      +-- Time-lapse
      +-- 4-D+
...

Using Enum Tool to compare enumerations in schemata (an example)

Enum Tool can be used to diff or compare two schema files by XPath. This is particularly useful when attempting to build XSL stylesheets to move from one schema version to another.

$ ./enum-tool -x tmp/old.xsd | sort > old
$ ./enum-tool -x tmp/new.xsd | sort > new

Now, using a spreadsheet or other visual differencing tool we build a mapping file, which outlines the new and old schema as well as an enumerated list of XPath mappings between the two schema.

[schemas]
old="../../Release/2008-09/V1/ome.xsd"
new="../../Working/ome.xsd"

[xpaths]
/OME/Image/MicrobeamManipulation@Type=/OME/Experiment/MicrobeamManipulation@Type
/OME/Experiment@Type=/OME/Experiment@Type
/OME/Image/ObjectiveRef@Medium=/OME/Image/ObjectiveSettings@Medium
/OME/Image/LogicalChannel/DetectorRef@Binning=/OME/Image/Pixels/Channel/DetectorSettings@Binning
/OME/Image/LogicalChannel@Mode=/OME/Image/Pixels/Channel@AcquisitionMode
/OME/Image/LogicalChannel@ContrastMethod=/OME/Image/Pixels/Channel@ContrastMethod
/OME/Image/LogicalChannel@IlluminationType=/OME/Image/Pixels/Channel@IlluminationType
/OME/Image/Pixels@DimensionOrder=/OME/Image/Pixels@DimensionOrder
/OME/Image/Pixels@PixelType=/OME/Image/Pixels@Type
/OME/Instrument/Detector@Type=/OME/Instrument/Detector@Type
/OME/Instrument/Filter@Type=/OME/Instrument/Filter@Type
/OME/Instrument/LightSource/Arc@Type=/OME/Instrument/LightSource/Arc@Type
/OME/Instrument/LightSource/Filament@Type=/OME/Instrument/LightSource/Filament@Type
/OME/Instrument/LightSource/Laser@LaserMedium=/OME/Instrument/LightSource/Laser@LaserMedium
/OME/Instrument/LightSource/Laser@Pulse=/OME/Instrument/LightSource/Laser@Pulse
/OME/Instrument/LightSource/Laser@Type=/OME/Instrument/LightSource/Laser@Type
/OME/Instrument/Microscope@Type=/OME/Instrument/Microscope@Type
/OME/Instrument/OTF/ObjectiveRef@Medium=/OME/Instrument/OTF/ObjectiveSettings@Medium
/OME/Instrument/OTF@PixelType=/OME/Instrument/OTF@Type
/OME/Instrument/Objective/Correction=/OME/Instrument/Objective@Correction
/OME/Instrument/Objective/Immersion=/OME/Instrument/Objective@Immersion

And finally, our diff:

$ ./enum-tool -d example.cfg
/OME/Instrument/Detector@Type:EM-CCD not in /OME/Instrument/Detector@Type
/OME/Instrument/Detector@Type:Unknown not in /OME/Instrument/Detector@Type
/OME/Instrument/LightSource/Arc@Type:Unknown not in /OME/Instrument/LightSource/Arc@Type
/OME/Instrument/LightSource/Filament@Type:Unknown not in /OME/Instrument/LightSource/Filament@Type
/OME/Instrument/LightSource/Laser@LaserMedium:Unknown not in /OME/Instrument/LightSource/Laser@LaserMedium
/OME/Instrument/LightSource/Laser@Type:Unknown not in /OME/Instrument/LightSource/Laser@Type
/OME/Instrument/Microscope@Type:Unknown not in /OME/Instrument/Microscope@Type
/OME/Instrument/Objective/Correction:Unknown not in /OME/Instrument/Objective@Correction
/OME/Instrument/Objective/Immersion:Unknown not in /OME/Instrument/Objective@Immersion

Acknowledgments

Thanks to Dave Kuhlman for his work on generateDS which Enum Tool makes heavy use of internally.

See also