anuga 1.3.5__zip

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/utilities/tests/test_xml_tools.py

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+#!/usr/bin/env python
+
+
+import unittest
+from tempfile import mkstemp, mktemp
+
+import os
+
+from anuga.utilities.xml_tools import *
+
+class Test_xml_tools(unittest.TestCase):
+
+    def setUp(self):
+        pass
+
+    def tearDown(self):
+        pass
+
+    def test_generate_xml(self):
+	"""Test that xml code is generated from XMLobject model
+	"""
+
+            
+        X1 = XML_element(tag='first element',
+                         value=XML_element(tag='some text',
+                                           value='hello world'))
+
+        text_elements = []
+        for i in range(10):
+            X = XML_element(tag='title %d' %i,
+                            value='example text %d' %i)
+            text_elements.append(X)
+
+        
+        X2 = XML_element(tag='second element',
+                         value=XML_element(tag='texts',
+                                           value=text_elements))
+        X3 = XML_element(tag='third element',
+                         value='42')        
+        
+            
+
+        doc = XML_element(value=[X1, X2, X3])
+
+        #print doc.pretty_print()        
+        #print doc
+
+        assert doc['second element']['texts']['title 4'] == 'example text 4'
+        
+        assert doc.has_key('first element')
+
+        
+
+    def test_xml2object(self):
+        """Test that XML_document can be generated from file
+        """
+
+        tmp_fd , tmp_name = mkstemp(suffix='.xml', dir='.')
+        fid = os.fdopen(tmp_fd, 'w')
+        
+	xml_string = """<?xml version="1.0" encoding="iso-8859-1"?>
+  <ga_license_file>
+    <metadata>
+      <author>Ole Nielsen</author>
+      <svn_keywords>
+        <author>$Author$</author>  
+        <date>$Date$</date>
+        <revision>$Revision$</revision>
+        <url>$URL:$</url>
+        <id>$Id$</id>
+      </svn_keywords>
+    </metadata>
+    <datafile>
+      <filename>bathymetry.asc</filename>
+      <checksum>%s</checksum>
+      <publishable>Yes</publishable>
+      <accountable>Jane Sexton</accountable>
+      <source>Unknown</source>
+      <IP_owner>Geoscience Australia</IP_owner>
+      <IP_info>This is a test</IP_info>
+    </datafile>
+  </ga_license_file>
+""" %('1234')
+
+	fid.write(xml_string)
+	fid.close()
+
+        fid = open(tmp_name)
+	reference = fid.read()
+        reflines = reference.split('\n')
+	
+        xmlobject = xml2object(fid, verbose=True)
+
+
+        #print xmlobject.pretty_print()
+        
+        xmllines = str(xmlobject).split('\n')
+
+        #for line in reflines:
+        #    print line
+        #print    
+        #for line in xmllines:
+        #    print line            
+
+            
+        assert len(reflines) == len(xmllines)
+
+        for i, refline in enumerate(reflines):
+            msg = '%s != %s' %(refline.strip(), xmllines[i].strip())
+            assert refline.strip() == xmllines[i].strip(), msg
+
+        # Check dictionary behaviour    
+        for tag in xmlobject['ga_license_file'].keys():
+            xmlobject['ga_license_file'][tag]
+
+        assert xmlobject['ga_license_file']['datafile']['accountable'] == 'Jane Sexton'
+
+        #print
+        #print xmlobject['ga_license_file']['datafile']
+        #print xmlobject['ga_license_file']['metadata']
+        #print xmlobject['ga_license_file']['datafile']
+        #print xmlobject['ga_license_file']['datafile']['accountable']        
+        #print xmlobject['ga_license_file']['datafile'].keys()
+
+        #for tag in xmlobject['ga_license_file'].keys():
+        #    print xmlobject['ga_license_file'][tag]
+	    	
+        # Clean up
+        fid.close()
+        os.remove(tmp_name)
+
+
+
+
+    def test_xml2object_empty_fields(self):
+        """Test that XML_document can be generated from file
+        This on tests that empty fields are treated as ''
+        """
+
+        tmp_fd , tmp_name = mkstemp(suffix='.xml', dir='.')
+        fid = os.fdopen(tmp_fd, 'w')
+        
+	xml_string = """<?xml version="1.0" encoding="iso-8859-1"?>
+  <ga_license_file>
+    <metadata>
+      <author>Ole Nielsen</author>
+      <svn_keywords>
+        <author>$Author$</author>  
+        <date>$Date$</date>
+        <revision>$Revision$</revision>
+        <url>$URL:$</url>
+        <id>$Id$</id>
+      </svn_keywords>
+    </metadata>
+    <datafile>
+      <filename>bathymetry.asc</filename>
+      <checksum>%s</checksum>
+      <publishable></publishable>
+      <accountable>Jane Sexton</accountable>
+      <source>Unknown</source>
+      <IP_owner>Geoscience Australia</IP_owner>
+      <IP_info>This is a test</IP_info>
+    </datafile>
+  </ga_license_file>
+""" %('1234')
+
+	fid.write(xml_string)
+	fid.close()
+
+        fid = open(tmp_name)
+	reference = fid.read()
+        reflines = reference.split('\n')
+	
+        xmlobject = xml2object(fid, verbose=True)
+
+
+        #print xmlobject.pretty_print()
+        
+        xmllines = str(xmlobject).split('\n')
+
+        #for line in reflines:
+        #    print line
+        #print    
+        #for line in xmllines:
+        #    print line            
+
+            
+        ##assert len(reflines) == len(xmllines)
+        x = xmlobject['ga_license_file']['datafile']['publishable']
+        msg = 'Got %s, should have been an empty string' %x
+        assert x == '', msg
+        
+
+        for i, refline in enumerate(reflines):
+            msg = '%s != %s' %(refline.strip(), xmllines[i].strip())
+            assert refline.strip() == xmllines[i].strip(), msg
+
+        # Check dictionary behaviour    
+        for tag in xmlobject['ga_license_file'].keys():
+            xmlobject['ga_license_file'][tag]
+
+        assert xmlobject['ga_license_file']['datafile']['accountable'] == 'Jane Sexton'
+
+
+        
+
+        #print
+        #print xmlobject['ga_license_file']['datafile']
+        #print xmlobject['ga_license_file']['metadata']
+        #print xmlobject['ga_license_file']['datafile']
+        #print xmlobject['ga_license_file']['datafile']['accountable']        
+        #print xmlobject['ga_license_file']['datafile'].keys()
+
+        #for tag in xmlobject['ga_license_file'].keys():
+        #    print xmlobject['ga_license_file'][tag]
+	    	
+        # Clean up
+        fid.close()
+        os.remove(tmp_name)
+
+
+	
+
+    def test_generate_and_read_back(self):
+	"""Test that xml code generated from XMLobject model
+        can be read back.
+	"""
+
+            
+        X1 = XML_element(tag='first_element',
+                         value=XML_element(tag='some_text',
+                                           value='hello world'))
+
+        text_elements = []
+        for i in range(10):
+            X = XML_element(tag='title_%d' %i,
+                            value='example text %d' %i)
+            text_elements.append(X)
+
+        
+        X2 = XML_element(tag='second_element',
+                         value=XML_element(tag='texts',
+                                           value=text_elements))
+        X3 = XML_element(tag='third_element',
+                         value='42')        
+        
+            
+        # Need to have one main element according to minidom
+        main = XML_element(tag='all', value=[X1, X2, X3])
+        xmldoc = XML_element(value=main)
+        #print xmldoc
+
+        tmp_fd , tmp_name = mkstemp(suffix='.xml', dir='.')
+        fid = os.fdopen(tmp_fd, 'w')
+
+        fid.write(str(xmldoc))
+        fid.close()
+
+        # Now read it back
+        xmlobject = xml2object(tmp_name, verbose=True)        
+        #print xmlobject
+
+        assert str(xmldoc) == str(xmlobject)
+
+        os.remove(tmp_name)
+
+
+    def test_duplicate_tags(self):
+	"""Test handling of duplicate tags.
+	"""
+
+        X1 = XML_element(tag='datafile',
+                         value=XML_element(tag='some_text',
+                                           value='hello world'))
+
+        
+        X2 = XML_element(tag='second_element',
+                         value=XML_element(tag='texts',
+                                           value='egg and spam'))
+        X3 = XML_element(tag='datafile',
+                         value='42')        
+
+
+        # Need to have one main element according to minidom
+        main = XML_element(tag='all', value=[X1, X2, X3])
+        xmldoc = XML_element(value=main)
+        #print xmldoc
+
+        tmp_fd , tmp_name = mkstemp(suffix='.xml', dir='.')
+        fid = os.fdopen(tmp_fd, 'w')
+
+        fid.write(str(xmldoc))
+        fid.close()
+
+        # Now read it back
+        xmlobject = xml2object(tmp_name, verbose=True)        
+        #print xmlobject
+
+        assert str(xmldoc) == str(xmlobject)
+
+        assert xmlobject['all'].has_key('datafile')
+
+        
+        assert len(xmlobject['all']['datafile']) == 2
+        #print xmlobject['all']['datafile']
+
+        os.remove(tmp_name)
+
+################################################################################
+
+if __name__ == "__main__":
+    suite = unittest.makeSuite(Test_xml_tools, 'test')
+    runner = unittest.TextTestRunner()
+    runner.run(suite)
+        
+

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/utilities/where_close.py

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+#!/usr/bin/python -tt
+#=======================================================================
+#                        General Documentation
+
+"""Single-function module.
+
+   See function docstring for description.
+"""
+
+#-----------------------------------------------------------------------
+#                       Additional Documentation
+#
+# RCS Revision Code:
+#   $Id: where_close.py,v 1.2 2004/04/28 00:28:15 jlin Exp $
+#
+# Modification History:
+# - 19 Mar 2004:  Original by Johnny Lin, Computation Institute,
+#   University of Chicago.  Passed reasonable tests.
+#
+# Notes:
+# - Written for Python 2.2.2.
+# - Function is based on code from the MA module by Paul F. Dubois.
+#   Some snippets of code in this function are copied directly from 
+#   lines in that module.
+# - Module docstrings can be tested using the doctest module.  To
+#   test, execute "python where_close.py".
+# - See import statements throughout for packages/modules required.
+#
+# Copyright (c) 2004 by Johnny Lin.  For licensing, distribution 
+# conditions, contact information, and additional documentation see
+# the URL http://www.johnny-lin.com/py_pkgs/gemath/doc/;
+
+# This library is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License as
+# published by the Free Software Foundation; either version 2.1 of the
+# License, or (at your option) any later version.
+
+# This library is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+# USA.
+
+# You can contact Johnny Lin at his email address or at the University
+# of Chicago, Department of the Geophysical Sciences, 5734 S. Ellis
+# Ave., Chicago, IL 60637, USA.
+
+#=======================================================================
+
+
+
+#--------------------------- General Function --------------------------
+
+def where_close(x, y, rtol=1.e-5, atol=1.e-8):
+    """Mask of where x and y are element-wise "equal" to each other.
+
+    Returns a long integer array with elements equal to 1 where x and 
+    y are "equal", and 0 otherwise.  If x or y are floating point, 
+    "equal" means where abs(x-y) <= atol + rtol * abs(y).  This is 
+    essentially the same algorithm used in the numeric function 
+    allclose.  If x and y are integer, "equal" means strict equality.  
+    Shape and size of output is the same as x and y; if one is an 
+    array and the other is scalar, shape and size of the output is the 
+    same as the array.  Output is a numeric array, unless both inputs 
+    are scalar in which the output is a Python integer scalar.
+
+    Positional Input Arguments:
+    * x:  Scalar or numeric array, Python list/tuple of any size and 
+      shape.  Floating or integer type.
+    * y:  Scalar or numeric array, Python list/tuple of any size and 
+      shape.  Floating or integer type.
+
+    Keyword Input Arguments:
+    * rtol:   "Relative" tolerance.  Default is 1.e-5.  Used in the
+              comparison between x and y only if the two are floating 
+              point.
+    * atol:   "Absolute" tolerance.  Default is 1.e-8.  Used in the
+              comparison between x and y only if the two are floating 
+              point.
+
+    Examples:
+    >>> import numpy as N
+    >>> from where_close import where_close
+    >>> x = [20.,  -32., -1., 2.            , 5., 29.]
+    >>> y = [20.1, -31., -1., 2.000000000001, 3., 28.99]
+    >>> ind = where_close(x, y)
+    >>> ['%.1g' % ind[i] for i in range(len(ind))]
+    ['0', '0', '1', '1', '0', '0']
+
+    >>> x = N.array([1,  5,  7, -2, 10])
+    >>> y = N.array([1, -5, 17, -2,  0])
+    >>> ind = where_close(x, y)
+    >>> ['%.1g' % ind[i] for i in range(len(ind))]
+    ['1', '0', '0', '1', '0']
+    """
+    import numpy as N
+    abs = N.absolute
+
+
+    #- Make sure input is numeric type:
+
+    xN = N.array(x)
+    yN = N.array(y)
+
+
+    #- Safe compare if floating.  Strict compare if integer.  Any other
+    #  type returns an error:
+
+    if (xN.dtype.char in N.typecodes['Float']) or \
+       (yN.dtype.char in N.typecodes['Float']):
+        return N.less_equal(abs(xN-yN), atol+rtol*abs(yN))
+
+    elif (xN.dtype.char in N.typecodes['Integer']) and \
+         (yN.dtype.char in N.typecodes['Integer']):
+        return N.equal(xN, yN)
+
+    else:
+        raise ValueError, "where_close:  Inputs must be Float or Integer"
+
+
+
+
+#-------------------------- Main:  Test Module -------------------------
+
+#- Define additional examples for doctest to use:
+
+__test__ = { 'Additional Examples':
+    """
+    >>> from where_close import where_close
+    >>> import numpy as N
+    >>> x = [20.,  -32., -1., 2.            , 5., 29.]
+    >>> y = [20.1, -31., -1., 2.000000000001, 3., 28.99]
+    >>> x = N.reshape(x, (2,3))
+    >>> y = N.reshape(y, (2,3))
+    >>> ind = where_close(x, y)
+    >>> ['%.1g' % ind[0,i] for i in range(3)]
+    ['0', '0', '1']
+    >>> ['%.1g' % ind[1,i] for i in range(3)]
+    ['1', '0', '0']
+    >>> ind.shape
+    (2, 3)
+    >>> ind.dtype.char
+    '?'
+    >>> type(ind)
+    <type 'numpy.ndarray'>
+
+    >>> x = [20.,  -32., -1., 2.            , 5., 29.]
+    >>> y = [20.1, -31., -1., 2.000000000001, 3.]
+    >>> ind = where_close(x, y)
+    Traceback (most recent call last):
+        ...
+    ValueError: frames are not aligned
+
+    >>> x = [20, -32, -1]
+    >>> y = [20, -32]
+    >>> ind = where_close(x, y)
+    Traceback (most recent call last):
+        ...
+    ValueError: frames are not aligned
+
+    >>> x = [20,  -32, -1.0, 2, 5, 29]
+    >>> y = 2.
+    >>> ind = where_close(x, y)
+    >>> ['%.1g' % ind[i] for i in range(len(ind))]
+    ['0', '0', '0', '1', '0', '0']
+    >>> x = -32
+    >>> y = N.array([20.,  -32., -1., 2., 5., 29.])
+    >>> ind = where_close(x, y)
+    >>> ['%.1g' % ind[i] for i in range(len(ind))]
+    ['0', '1', '0', '0', '0', '0']
+    >>> x = -32
+    >>> y = -33.
+    >>> ind = where_close(x, y)
+    >>> print ind
+    0
+    >>> type(ind)
+    <type 'numpy.bool_'>
+    >>> x = -33
+    >>> y = -33.
+    >>> ind = where_close(x, y)
+    >>> print ind
+    1
+    >>> x = -33
+    >>> y = -33
+    >>> ind = where_close(x, y)
+    >>> print ind
+    1
+    >>> x = -3.
+    >>> y = -3.
+    >>> ind = where_close(x, y)
+    >>> print ind
+    1
+    """ }
+
+
+#- Execute doctest if module is run from command line:
+
+if __name__ == "__main__":
+    """Test the module.
+
+    Tests the examples in all the module documentation 
+    strings, plus __test__.
+
+    Note:  To help ensure that module testing of this file works, the
+    parent directory to the current directory is added to sys.path.
+    """
+    import doctest, sys, os
+    sys.path.append(os.pardir)
+    doctest.testmod(sys.modules[__name__])
+
+
+
+
+# ===== end file =====
+