nomcompile3: Build a set of nomenclature files

# - - -   w r i t e X M L F i l e

def writeXMLFile ( txny ):
    '''Write the XML representation of the taxonomy.

      [ txny is a Txny instance ->
          if file xml-file(Args()) can be opened new for writing ->
            file xml-file(Args))  :=  an XML representation of txny
          else ->
            Log()  +:=  error message(s)
            stop execution ]
    '''

The reader should be familiar with the XML generation techniques described in Python XML processing with lxml. In particular, the factory instance E builds new XML elements. We will also use et, which is a replacement for Python's standard elementTree module.

We'll start by building the et.Document instance, whose root is a taxonomySystem element.

    #-- 1 --
    # [ root  :=  a new rnc.TAXONOMY_SYSTEM_N et.Element
    #   doc  :=  a new et.ElementTree with that root element ]
    root = et.Element(rnc.TAXONOMY_SYSTEM_N, version=EXTERNAL_VERSION)
    doc = et.ElementTree ( root )

There are four required child elements. The first, representing the rank hierarchy, is built by Section 15.9, “Hier.writeXML(): Generate XML”.

    #-- 2 --
    # [ root  :=  root with an rnc.RANK_SET_N element added
    #             representing txny.hier ]
    txny.hier.writeXML ( root )

The second child of the root, containing the taxonomic tree, is build by Section 18.9, “TaxaTree.writeXML(): Generate XML output”.

    #-- 3 --
    # [ root  :=  root with an rnc.TAXONOMY_N element added
    #             representing the tree rooted in txny.taxaTree.root ]
    txny.taxaTree.writeXML ( root )

The third and fourth children, representing valid and collision codes, are generated by Section 24.5, “AbTab.writeXML()”. That completes the tree, so we can write it out.

    #-- 4 --
    # [ root  :=  root with an rnc.ABBR_SET_N element added
    #       representing codes in txny.abTab linked to specific
    #       taxa, and an rnc.COLLISION_SET_N element added
    #       representing collision codes in txny.abTab ]
    txny.abTab.writeXML ( root )

    #-- 5 --
    # [ if file (Args().xmlFileName) can be opened new for writing ->
    #     that file  :=  doc as XML
    #   else ->
    #     Log()  +:=  error message
    #     stop execution ]
    try:
        xmlFile = file ( Args().xmlFileName, 'w' )
        doc.write ( xmlFile, pretty_print=True )
        xmlFile.close()
    except IOError, detail:
        Log().fatal ( "Can't open the output XML file '%s': %s" %
            (Args.xmlFilName, detail) )