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Canonicalizes different MathML encodings of equivalent formulae

Home Page: https://mir.fi.muni.cz/mathml-normalization/

License: Apache License 2.0

Java 100.00%

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mathmlcan's Issues

WstxEOFException: Unexpected EOF in prolog

Hello, I am getting a strange exception when trying to index some documents. The exception is as follows:

May 09, 2018 8:42:41 PM cz.muni.fi.mir.mathmlcanonicalization.modules.ElementMinimizer execute
SEVERE: error while parsing the input file. 
com.ctc.wstx.exc.WstxEOFException: Unexpected EOF in prolog
 at [row,col {unknown-source}]: [1,0]
	at com.ctc.wstx.sr.StreamScanner.throwUnexpectedEOF(StreamScanner.java:686)
	at com.ctc.wstx.sr.BasicStreamReader.handleEOF(BasicStreamReader.java:2134)
	at com.ctc.wstx.sr.BasicStreamReader.nextFromProlog(BasicStreamReader.java:2040)
	at com.ctc.wstx.sr.BasicStreamReader.next(BasicStreamReader.java:1069)
	at cz.muni.fi.mir.mathmlcanonicalization.modules.ElementMinimizer.minimizeElements(ElementMinimizer.java:134)
	at cz.muni.fi.mir.mathmlcanonicalization.modules.ElementMinimizer.execute(ElementMinimizer.java:84)
	at cz.muni.fi.mir.mathmlcanonicalization.MathMLCanonicalizer.executeStreamModules(MathMLCanonicalizer.java:375)
	at cz.muni.fi.mir.mathmlcanonicalization.MathMLCanonicalizer.canonicalize(MathMLCanonicalizer.java:326)
	at cz.muni.fi.mias.math.MathTokenizer.parseMathML(MathTokenizer.java:304)
	at cz.muni.fi.mias.math.MathTokenizer.processFormulae(MathTokenizer.java:280)
	at cz.muni.fi.mias.math.MathTokenizer.reset(MathTokenizer.java:246)
	at org.apache.lucene.index.DefaultIndexingChain$PerField.invert(DefaultIndexingChain.java:613)
	at org.apache.lucene.index.DefaultIndexingChain.processField(DefaultIndexingChain.java:359)
	at org.apache.lucene.index.DefaultIndexingChain.processDocument(DefaultIndexingChain.java:318)
	at org.apache.lucene.index.DocumentsWriterPerThread.updateDocument(DocumentsWriterPerThread.java:241)
	at org.apache.lucene.index.DocumentsWriter.updateDocument(DocumentsWriter.java:465)
	at org.apache.lucene.index.IndexWriter.updateDocument(IndexWriter.java:1526)
	at org.apache.lucene.index.IndexWriter.updateDocument(IndexWriter.java:1500)
	at cz.muni.fi.mias.indexing.Indexing.indexDocsThreaded(Indexing.java:145)
	at cz.muni.fi.mias.indexing.Indexing.indexFiles(Indexing.java:89)
	at cz.muni.fi.mias.MIaS.main(MIaS.java:39)

I run a command:

java -jar MIaS-1.6.6-4.10.4-SNAPSHOT.jar -conf ~/sandbox/mias/mias.properties -overwrite ~/sandbox/mias/data/samples/sample-mathml.xhtml ~/sandbox/mias/data/samples

My setup is:

MathMLCan: develop branch
MIaS: master branch
MIaSMath: master branch

$ java -version
java version "1.8.0_171"
Java(TM) SE Runtime Environment (build 1.8.0_171-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

The `mias.properties` configuration is:

INDEXDIR=~/sandbox/mias/indexes/index-0
UPDATE=false
THREADS=16
MAXRESULTS=10000
DOCLIMIT=-1
FORMULA_DOCUMENTS=true

The `sample-mathml.xhtml` file is as simple as:

<?xml version="1.0" encoding="UTF-8"?>
<html xmlns="http://www.w3.org/1999/xhtml">
  <head>
    <meta http-equiv="Content-Type" content="application/xhtml+xml; charset=UTF-8" />
  </head>
  <body>
    <math>
      <mfrac linethickness="1">
        <!-- numerator -->
        <mrow>
          <mi> x </mi>
          <mo> + </mo>
          <mi mathcolor="red"> y </mi>
          <mo> + </mo>
          <mi> z </mi>
        </mrow>
        <!-- denominator -->
        <mrow>
          <mi> x </mi>
          <mphantom>
            <mo> + </mo>
            <mi> y </mi>
          </mphantom>
          <mo> + </mo>
          <mi> z </mi>
        </mrow>
      </mfrac>
      <mfenced open=":" close="?">
      </mfenced>
    </math>
  </body>
</html>

Is there please any help out there or any ideas what could be a problem here?

Blank 'xmlns' is sometimes unnecessarily added to elements during canonicalization

Operator to identifier conversion (OperatorNormalizer module)

Opposite conversion (mo -> mi) should be allowed, e.g. for function identifiers: exp sin cos tan tg cot cotan cotg ctg ctn sec csc cosec arcsin arccos arctan arccot arcsec arccsc sinh cosh tanh coth cesh csch arcsinh arcosh artanh arcoth arsech arcsch log lg ln

Remove empty elements

Empty mi and mn elements (or those containing whitespace) can be removed.

Removing operators can break MathML validity

OperatorNormalizer should not remove mo element if it is a required argument of its parent. This can change formula meaning and even create invalid MathML from a valid input.

Configure to remove top level mrow

TableConvertor module

New module should convert between table representations and other possibilities - e.g. binomial coefficients can be expressed by mtable elements or mfrac elements with linethickness=0

Special treatment of 'mathvariant' attribute (ElementMinimizer module)

Default value should be removed, which is mathvariant='normal' except for single character mi (see http://www.w3.org/TR/MathML3/chapter3.html#presm.mi)
Variety of values could be normalized into less number of them

MfencedReplacer use default attributes sometimes

See https://mir.fi.muni.cz/apps/MathCalEval/canonicoutput/view/23058/

OperatorNormalizer changes formula meaning

https://mir.fi.muni.cz/apps/MathCalEval/canonicoutput/view/22144

In case when the operator * does not mean multiplication it should not be removed.
If we really need to remove infix * I suggest checking if it has operands.

Add more operators for conversion from mi

MrowNormalizer - fenced expression format

Apart from removing redundant mrow elements, MrowNormalizer also adds mrow to transform detected fenced expressions to the form:

<mrow><mo>(</mo><mrow> ... </mrow><mo>)</mo></mrow>

I'm not sure what should be preferred in case when this format breaks the rules for mrow minimizing (only one element in inner mrow, etc.) Should the redundant elements be removed or should the exact format be kept?

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