mathdom-devel — For general discussion about MathDOM

Re: [MathDOM] MathDOM 0.8 won't start

[Mario C. <mar...@to...>]

Hello Stefan,
thanks for your reply: I was using pyparsing 1.5.1 (last version)

I downgraded to 1.4.2 and now it works!

Thanks a lot

Mario

On Fri, Dec 19, 2008 at 3:24 PM, Stefan Behnel <ste...@be...> wrote:
> Hi,
>
> sorry for the late reply.
>
> Mario Ceresa wrote:
>> I have a problem after I just downloaded and installed MathDOM 0.8.
>>
>> I tried to do:
>>
>> from mathml.lmathdom import MathDOM
>>
>> but it crashes with:
>> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
>> in p_case(self, p_arithmetic_exp, p_bool_expression)
>>     289                   Suppress(CaselessKeyword('END'))
>>     290                   )
>> --> 291         p_case.setParseAction(self._parse_case)
>>     292         return p_case
>>     293
>>
>> AttributeError: 'NoneType' object has no attribute 'setParseAction'
>> ________________________________________________________________
>>
>> It seems to me related to these warning that I receive just before the
>> exception is thrown:
>>
>> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:288:
>> SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
>> ParserElement
>>   Suppress(CaselessKeyword('ELSE')) + p_arithmetic_exp +
>> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:289:
>> SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
>> ParserElement
>>   Suppress(CaselessKeyword('END'))
>
> I just tested and it works for me with pyparsing 1.4.2. What version of
> pyparsing are you using?
>
> Stefan
>

Re: [MathDOM] MathDOM 0.8 won't start

[Stefan B. <ste...@be...>]

Hi,

sorry for the late reply.

Mario Ceresa wrote:
> I have a problem after I just downloaded and installed MathDOM 0.8.
> 
> I tried to do:
> 
> from mathml.lmathdom import MathDOM
> 
> but it crashes with:
> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
> in p_case(self, p_arithmetic_exp, p_bool_expression)
>     289                   Suppress(CaselessKeyword('END'))
>     290                   )
> --> 291         p_case.setParseAction(self._parse_case)
>     292         return p_case
>     293
> 
> AttributeError: 'NoneType' object has no attribute 'setParseAction'
> ________________________________________________________________
> 
> It seems to me related to these warning that I receive just before the
> exception is thrown:
> 
> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:288:
> SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
> ParserElement
>   Suppress(CaselessKeyword('ELSE')) + p_arithmetic_exp +
> /usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:289:
> SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
> ParserElement
>   Suppress(CaselessKeyword('END'))

I just tested and it works for me with pyparsing 1.4.2. What version of
pyparsing are you using?

Stefan

[MathDOM] MathDOM 0.8 won't start

[Mario C. <mar...@to...>]

Hello,
I have a problem after I just downloaded and installed MathDOM 0.8.

I tried to do:

from mathml.lmathdom import MathDOM

but it crashes with:
__________________________________________________________
AttributeError                            Traceback (most recent call last)

/home/whitehat/<ipython console> in <module>()

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/lmathdom.py
in <module>()
     35
     36 from mathml           import MATHML_NAMESPACE_URI, UNARY_FUNCTIONS
---> 37 from mathml.xmlterm   import SaxTerm, dom_to_tree, serialize_dom
     38 from mathml.datatypes import Decimal, Complex, Rational, ENotation
     39

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/xmlterm.py
in <module>()
     79
     80 from mathml             import MATHML_NAMESPACE_URI
---> 81 from mathml.termparser  import term_parsers
     82 from mathml.termbuilder import tree_converters
     83

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
in <module>()
    537 term_parsers = TermParsing()
    538
--> 539 parser = InfixTermParser().p_arithmetic_exp()
    540 term_parsers.register_converter('infix_bool',
InfixBoolExpressionParser().p_bool_exp())
    541 term_parsers.register_converter('infix_term',      parser)

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
in __get__(self, instance, owner)
     69         if instance is None:
     70             return self
---> 71         result = self.function(instance)
     72         def return_result():
     73             return result

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
in p_arithmetic_exp(self)
    267         p_identifier = self.tokenizer.p_identifier()
    268         p_function   = self.p_function(p_arithmetic_exp)
--> 269         p_case       = self.p_case(p_arithmetic_exp,
self.p_bool_expression)
    270
    271         # numeric values = attribute | number | expression

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py
in p_case(self, p_arithmetic_exp, p_bool_expression)
    289                   Suppress(CaselessKeyword('END'))
    290                   )
--> 291         p_case.setParseAction(self._parse_case)
    292         return p_case
    293

AttributeError: 'NoneType' object has no attribute 'setParseAction'
________________________________________________________________

It seems to me related to these warning that I receive just before the
exception is thrown:

/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:288:
SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
ParserElement
  Suppress(CaselessKeyword('ELSE')) + p_arithmetic_exp +
/usr/lib/python2.5/site-packages/mathdom-0.8-py2.5.egg/mathml/termparser.py:289:
SyntaxWarning: Cannot combine element of type <type 'NoneType'> with
ParserElement
  Suppress(CaselessKeyword('END'))

But I don't know how to move on... Any help is greatly appreciated

Thanks

Mario

Re: [MathDOM] Problem running MathDOM

[Stefan B. <ste...@be...>]

Hi,

chrystiano araujo wrote:
>     You helped me a lot. i've already installed the lxml1.0. and it's
> functioning.

Good.


>     But now, there is another doubt.
>     can you help me again?

I would prefer it if you wrote to the mailing list. Admittedly, there are not
a lot of subscribers currently, but at least your questions get archived that
way, so that others can find them on the web.


>     I have to make a Mathml parser with python.  So i have to study
> mathdom a lot, don't I?

What do you need a MathML parser for? How is that more than a validating XML
parser?

(and how is that different from what MathDOM already gives you?)


> and i have only 3 examples as documentation, i think it's not enough.

As I said, look at the Python scripts that come with MathDOM. They use quite a
big part of the API, so they may give you enough hints already.


>  doc.serialize("python")
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.5/site-packages/mathml/mathdom.py", line
> 441, in serialize
>     return serialize_dom(self._document, output_format, converter)
>   File "/usr/local/lib/python2.5/site-packages/mathml/xmlterm.py", line
> 134, in serialize_dom
>     tree = dom_to_tree(doc_or_element)
>   File "/usr/local/lib/python2.5/site-packages/mathml/xmlterm.py", line
> 216, in dom_to_tree
>     tree = _recursive_dom_to_tree(root)
>   File "/usr/local/lib/python2.5/site-packages/mathml/xmlterm.py", line
> 188, in _recursive_dom_to_tree
>     name = operator.mathtype()
>   File "/usr/lib/python2.5/site-packages/_xmlplus/dom/FtNode.py", line
> 83, in __getattr__
>     return getattr(FtNode, name)
> AttributeError: class FtNode has no attribute 'mathtype'

Hmm, ok, now that's using the PyXML implementation of MathDOM. I'll have to
check what's not working here. Any reason you can't keep using MathDOM with
lxml? It's the preferred way anyway.

Regards,
Stefan

Re: [MathDOM] Problem running MathDOM with latest lxml

[Stefan B. <ste...@be...>]

Hi,

sorry for the late reply.

chrystiano araujo wrote:
> i've been using mathdom-0.7.
> 
> there is a doubt. Could you help me, please??
> 
> In a Quick example:
> 
>>>> from mathml.lmathdom import MathDOM                                
>     # use lxml implementation
>>>> doc = MathDOM.fromString("+2^x+4*-5i/6", "infix_term")          #
> parse infix term
>>>> [ n.value() for n in doc.xpath(u'//math:cn[@type="integer"]') ]    #
> find integers
>  x [2, 4, 6]
>>>> for apply_tag in doc.xpath(u'//math:apply[math:plus]'):            
>    # replace '+' with '-'
> 
> ...     apply_tag.set_operator(u'minus') tthis line, there is a error
>  Traceback (most recent call last):
>   File "<stdin>", line 2, in <module>
> AttributeError: 'etree._Element' object has no attribute 'set_operator'

I assume you are using a recent version of lxml? The way lxml sets up custom
element classes (which are used by MathDOM to implement the MathML namespace)
has changed in lxml 1.1. I'll fix MathDOM as soon as possible and release a
0.7.2, but it's not as simple as "change this 0 to 1 and it works".

Please use lxml 1.0.x for now, which you can get here:
http://codespeak.net/lxml/

Ready-to-install binaries are here:
http://cheeseshop.python.org/pypi/lxml/1.0.4
http://cheeseshop.python.org/pypi/lxml/1.0.3


> if do you have any documentation of mathdom, send to me, please.

Admittedly, MathDOM is pretty much underdocumented. However, it's not that
hard to use, so you should get along once you've got it running. Take a look
at the test scripts that come with the distribution.

Regards,
Stefan

[MathDOM] How to read and evaluate MathML files?

[Roman S. <sa...@we...>]

Hello list

currently I am working on my Bachelors Thesis on storing characteristics 
(mathematical formulas), containing several parameters as variables, in 
an ontology. To instantiate the variable the parameters (real-values) 
are extracted from different concepts in the ontology.

I decided to encode the characteristics via MathML and to store them as 
XMLLiterals which are to be found as datatype properties in the ontology.

The project I am working with uses a Java written GUI that enables the 
user to instantiate the ontology without writing any OWL but with using 
drag´n drop and wysiwyg mechanisms.

One of my tasks is to implement a feature which enables the user to type 
in formulas (e.g (x + 5*y) * 42) without using MathML. These formulas 
should be encoded in MathML and they should be stored in the ontology. 
On the other hand the program has to be able to instantiate the 
variables of the given formulas and eventually calculate and return the 
result.

My task is not to write a MathML parser but to implement an exisiting 
one.  Unfortunately I could not find anything that matches my 
requirements (written in Java).

MathDom looks very promising to me and with Jython I might be able to 
use it as a part of  my program. Unfortunately I am not very familiar 
with Python and I could not find a helpful documentation (sorry, if 
there is one). I would really appreciate if you could show me how to 
read exisiting MathML streams and to return Java (or Python) expressions.

Thank you,

Roman

Re: [MathDOM] Re: Packaging MathDOM, patching lxml

[Stefan B. <beh...@gk...>]

Stefan Behnel wrote:
> Jeff Kowalczyk wrote:
>> The other option is to include a private copy of the full lxml source and
>>  apply your patch in place, then have setup.py build and install that in
>> a private subdir. If the runtime test for a patched lxml in the default 
>> python path fails, have the import statement import the private copy.
>
> With the modified setup.py, you can easily ship lxml with MathDOM. The test
>  for a patched version also has an option. But lxml is not yet included in 
> the build process. Once it *is* built, all you have to do is copy the 
> resulting lxml directory (containing the files etree.so, _elementpath.py 
> and __init__.py) into the mathml directory. Since the only module that 
> depends on lxml is mathml.lmathdom, Python will simply look there first and
>  find the correct version. The tests and examples will *not* find the 
> patched version, but they are not of interest to an installation anyway.
> 
>> lxml is becoming a core product, even Zope has considered making it a 
>> dependency. I don't think it will be practical to apply post-release 
>> patching to lxml in anything but experimental setups or package-private 
>> copies.
> 
> Ok, sounds reasonable. So maybe it would help to integrate the build 
> processes of lxml and MathDOM. In that case I'd prefer shipping only the 
> generated C-code for lxml, i.e. lxml/etree.c, to strip the additional Pyrex
>  dependency (the latest official Pyrex version is still broken when used 
> with GCC4, so that is really the right thing to do). I'll have to look into
>  that.

Now that I looked into it, I do no longer think a package private copy of lxml
is a good choice. Lxml is part of the API of the mathml.lmathdom module, so
existing code will import it directly, i.e. break if it is moved. Multiple
installed copies will really confuse users and make its usage difficult. So I
finally think that installing the patched version independently is the best
choice. I'll keep bugging the lxml maintainer to get my patches in there.

Stefan

[MathDOM] Re: Packaging MathDOM, patching lxml

[Stefan B. <beh...@gk...>]

Jeff Kowalczyk wrote:
> I don't think mathdom should have split packages. The mathdom setup.py doesn't
> need options for that, just runtime import autodetection of whether lxml is
> available, or pyxml as the fallback.

The PyXML version is not a fallback. It's a different implementation based on
the XML DOM Level 2 API, while the lxml version is based on the ElementTree
API with XIST-like extensions. While I could implement a certain level of
compatibility methods (and I partially did already), I will definitely not
reimplement the entire APIs, so the general usage of both APIs will stay
different. So in a way it's two packages in one - you have to choose.


> My question was whether mathdom doesn't
> run (with degraded functionality) on a stock lxml-0.8, in which case you'd need
> to test for your patched functions in addition to a successful 'import lxml'
> statement.

No, because it is based on an implementation style that I had to patch into
lxml (namespace implementation by element subclassing), so it will definitely
not work with any release version of lxml until that patch is merged. It's
pretty simple to test though:
.>>> from lxml.etree import ElementBase, SaxTreeBuilder
will fail on unpatched systems.


> 'pymathdom' is a reasonable name if you think 'mathdom' name will conflict.
> Gentoo would call the package 'dev-python/mathdom', so this isn't a problem. In
> general, I prefer the distro package name to be the same as the python package
> name.

Like 'mathml'? :) That would be the first to conflict. Actually, one of the
reasons for bundling PyMathML with MathDOM was such a conflict...

I still think 'mathml' is a good name for the installed package while
'mathdom' is a good name for the main module. Currently, to the best of my
knowledge, MathDOM is the only Python implementation of Content MathML there
is, so conflicts are unlikely. *cross-fingers*


> I think the direction to go (for Gentoo packaging anyway) is simply to have a
> modified ebuild that optionally builds lxml with your lxml patch. The mechanism
> is called a USE variable, the Gentoo user would add +mathdom to his lxml
> configuration, a rebuild would trigger, and your patch would apply. 

Ok, fine.


> This is all fine for the bleeding edge Gentoo experimenter, but I think that
> going forward any lxml patches mathdom prefers will have to be accepted
> upstream lxml, or mathdom will need to implement rejected extensions itself in
> an intermediary C, pyrex, or python code.

I'm actually pretty sure the main patches that make MathDOM work will be
accepted. MathDOM is a perfect example why they are great. :) Namespace
implementation is exemplified in XIST and it's the best way of doing custom
data binding and XML driven APIs/GUIs/etc.
http://www.livinglogic.de/Python/xist/Howto.html


> The other option is to include a private copy of the full lxml source and apply
> your patch in place, then have setup.py build and install that in a private
> subdir. If the runtime test for a patched lxml in the default python path
> fails, have the import statement import the private copy.

With the modified setup.py, you can easily ship lxml with MathDOM. The test
for a patched version also has an option. But lxml is not yet included in the
build process. Once it *is* built, all you have to do is copy the resulting
lxml directory (containing the files etree.so, _elementpath.py and
__init__.py) into the mathml directory. Since the only module that depends on
lxml is mathml.lmathdom, Python will simply look there first and find the
correct version. The tests and examples will *not* find the patched version,
but they are not of interest to an installation anyway.


> lxml is becoming a core product, even Zope has considered making it a
> dependency. I don't think it will be practical to apply post-release patching
> to lxml in anything but experimental setups or package-private copies.

Ok, sounds reasonable. So maybe it would help to integrate the build processes
of lxml and MathDOM. In that case I'd prefer shipping only the generated
C-code for lxml, i.e. lxml/etree.c, to strip the additional Pyrex dependency
(the latest official Pyrex version is still broken when used with GCC4, so
that is really the right thing to do). I'll have to look into that.

Stefan

[MathDOM] Re: Packaging MathDOM, patching lxml

[Stefan B. <beh...@gk...>]

Stefan Behnel wrote:
> I may consider changing setup.py to check for their availability, too. That
> would make it easier for maintainers to split up the package. If you do that,
> I'd really appreciate it if you provided both packages, though.
> 
> If it fits the package naming convention, you may call them
> 
> python-mathdom-lxml
> and
> python-mathdom-pyxml
> and the complete package
> python-mathdom
> 
> or something in that line.

The setup.py in the current CVS version now has a couple of configuration
options that should help packagers:

-----------------
# python setup.py --help-mathdom
MathDOM package install options:
    --name=XXX           : force package name to XXX
    --contrib-lxml       : include lxml sources in 'contrib/lxml/'  (False)
    --no-contrib-lxml    : do not include lxml sources
    --require-imports    : check if required packages are installed (False)
    --no-require-imports : do not check installation
    --pyxml              : build *only* 'mathdom-pyxml' package
    --lxml               : build *only* 'mathdom-lxml'  package

    Current build config : lxml (True), pyxml (True), forced name (None)
-----------------

You can checkout my lxml branch (see README) into "contrib/lxml/" in the
MathDOM source directory and have it included automatically using
"--contrib-lxml". It is not built automatically, though.

Is that ok for you?

Stefan

[MathDOM]Packaging MathDOM, patching lxml

[Stefan B. <beh...@gk...>]

Hi!

I changed the subject to help finding it on the mailing list.

Jeff Kowalczyk wrote:
> I'm curious to try MathDOM on my Gentoo Linux system. Idly curious, I d=
on't
> have any real math tasks to use it on, but I planned to at least packag=
e up
> MathDOM for Gentoo as a result of the experimentation.

Sure, go ahead :) I already noticed it's been packaged up for Darwin/Mac-=
OS,
and I'd really like to see it in other places.


> Thanks for writing it.

Was for my own needs, but it's grown bigger. :)


> Could you clarify the web page documentation regarding whether your pat=
ch:
> http://mathdom.sourceforge.net/bigfat.patch has been, or will be, accep=
ted or
> rejected upstream by lxml's maintainers?

A smaller part is in lxml-0.8 (released yesterday), so I'll release a new
patch against that version soon. Other parts are still pending but most o=
f it
will be merged into lxml's SVN fairly soon, I hope.

The patch is a rather big collection of single patches, so it will take s=
ome
time until all of them are accepted and merged. None has been rejected so=
 far
and there are actually people using them so it's likely that they will be
accepted in one way or another.


> It also isnt stated whether this patch (and a rebuilt lxml) is required=
 for
> MathDOM to use lxml (over pyxml), nor if the patch has side effects not=
iced by
> other lxml-using programs.

No side effects were found so far, but I guess that's mainly because thos=
e
that are there conform with the intention of lxml (heading for ElementTre=
e
conformance). Most of the patch adds additional (independent) functionali=
ty.

While you can use MathDOM with PyXML (that's intended), the PyXML version=
 does
not currently support XSLT and RelaxNG validation, so I encourage all use=
rs to
stick to the lxml version. No XSLT support means no support for Presentat=
ional
MathML export and the like, so that's a rather big draw back. Literal ter=
ms
are equally well supported in both versions.

If you like, you can make distinct packages, one that excludes
mathml/lmathdom.py and does not depend on lxml and one that excludes
mathml/mathdom.py and does not depend on PyXML. Even the tests should wor=
k
since they test for the availability of both modules. I hope I took enoug=
h
care to make the rest only depend on the Python stdlib.

I may consider changing setup.py to check for their availability, too. Th=
at
would make it easier for maintainers to split up the package. If you do t=
hat,
I'd really appreciate it if you provided both packages, though.

If it fits the package naming convention, you may call them

python-mathdom-lxml
and
python-mathdom-pyxml
and the complete package
python-mathdom

or something in that line.


> Gentoo ebuilds make it easy to add patches to the build process. If the=
 patch
> is already accepted by upstream lxml, or is just a generally useful pat=
ch, I
> could add a USE variable and the conditional patch to dev-python/lxml-0=
.7. They
> may not accept it into mainline portage, but it would be there in
> bugs.gentoo.org for any who were interested.

Right, Gentoo 'gen=E8re tout' (generates everything - french) :) - longes=
t OS
installation ever :) So I guess separate packages would be the way to go.=
 I'll
include that in the CVS version, so you can be the first to test it... :)

Stefan