Merge pull request #312 from sbmlteam/python-example

converted setNamesFromIds.cpp example into a python file

Makefile.in

@@ -290,6 +290,7 @@ examples =                                                          \
   examples/python/renameSId.py                                      \
   examples/python/stringInput.py                                    \
   examples/python/setIdFromNames.py                                 \
+  examples/python/setNamesFromIds.py                                \
   examples/python/translateMath.py                                  \
   examples/python/unsetAnnotation.py                                \
   examples/python/unsetNotes.py                                     \

docs/src/libsbml-python-example-files.txt

@@ -85,6 +85,10 @@ Promote all local parameters in the model to global parameters.
 Program that renames all SIds that also have names specified. The new
 identifiers will be derived from the name, with all invalid characters removed.
 
+@li @ref setNamesFromId.py "setNamesFromId.py":
+Program that changes all objects' "name" attribute values to match
+their "id" attribute values.
+
 @li @ref stripPackage.py "stripPackage.py":
 Strips the given SBML Level 3 package from the given SBML file.
 
@@ -302,6 +306,10 @@ An example of creating a model using SBML Level 3 Qualitative Models.
 @example createSimpleModel.py
 An example of creating a simple SBML Level 3 model.
 
+@example setNamesFromIds.py
+Program that changes all objects' "name" attribute values to match
+their "id" attribute values.
+
 */
 <!-- The following is for [X]Emacs users.  Please leave in place. -->
 <!-- Local Variables: -->

examples/python/setNamesFromIds.py

@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+##
+## @file    setNamesFromIds.py
+## @brief   Utility program, renaming all Names to match their ids. 
+##
+## @author  Frank T. Bergmann
+## 
+## 
+## <!--------------------------------------------------------------------------
+## This sample program is distributed under a different license than the rest
+## of libSBML.  This program uses the open-source MIT license, as follows:
+##
+## Copyright (c) 2013-2018 by the California Institute of Technology
+## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
+## and the University of Heidelberg (Germany), with support from the National
+## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
+##
+## Permission is hereby granted, free of charge, to any person obtaining a
+## copy of this software and associated documentation files (the "Software"),
+## to deal in the Software without restriction, including without limitation
+## the rights to use, copy, modify, merge, publish, distribute, sublicense,
+## and/or sell copies of the Software, and to permit persons to whom the
+## Software is furnished to do so, subject to the following conditions:
+##
+## The above copyright notice and this permission notice shall be included in
+## all copies or substantial portions of the Software.
+##
+## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+## DEALINGS IN THE SOFTWARE.
+##
+## Neither the name of the California Institute of Technology (Caltech), nor
+## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
+## of Heidelberg, nor the names of any contributors, may be used to endorse
+## or promote products derived from this software without specific prior
+## written permission.
+## ------------------------------------------------------------------------ -->
+## 
+## 
+
+import sys
+import os.path
+import time 
+import libsbml
+
+# This class implements an identifier transformer, that means it can be used
+# to rename all sbase elements. 
+class SetNamesFromId(libsbml.IdentifierTransformer):
+  def __init__(self):
+    # call the constructor of the base class
+    libsbml.IdentifierTransformer.__init__(self)
+
+  # The function actually doing the transforming. This function is called 
+  # once for each SBase element in the model. 
+  def transform(self, element):
+    # return in case we don't have a valid element
+    if element is None or element.getTypeCode() == libsbml.SBML_LOCAL_PARAMETER:
+        return libsbml.LIBSBML_OPERATION_SUCCESS
+
+    # or if there is nothing to do
+    if element.isSetId() == False or element.getId() == element.getName():
+        return libsbml.LIBSBML_OPERATION_SUCCESS
+
+   	# set it
+    element.setName(element.getId())
+
+    return libsbml.LIBSBML_OPERATION_SUCCESS
+
+def main (args):
+  """Usage: setNamesFromIds filename output
+  """
+  if len(args) != 3:
+    print(main.__doc__)
+    sys.exit(1)
+
+  filename = args[1]
+  output = args[2]
+
+  # read the document
+  start = time.time() * 1000
+  document = libsbml.readSBMLFromFile(filename)
+  stop = time.time() * 1000
+
+  print ("")
+  print ("            filename: {0}".format( filename))
+  print ("      read time (ms): {0}".format( stop - start))
+
+  # stop in case of serious errors
+  errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR)
+  if errors > 0:
+      print ("            error(s): {0}".format(errors))
+      document.printErrors()
+      sys.exit (errors)
+
+  # get a list of all elements, as we will need to know all identifiers
+  allElements = document.getListOfAllElements()
+
+  # create the transformer
+  trans = SetNamesFromId()
+
+  # rename the identifiers (using the elements we already gathered before)
+  start = time.time() * 1000
+  document.getModel().renameIDs(allElements, trans)
+  stop = time.time() * 1000
+  print ("    rename time (ms): {0}".format(stop - start))
+
+  # write to file
+  start = time.time() * 1000
+  libsbml.writeSBMLToFile(document, output)
+  stop = time.time() * 1000
+  print ("     write time (ms): {0}".format(stop - start))
+  print ("")
+
+  # if we got here all went well ... 
+
+if __name__ == '__main__':
+  main(sys.argv)  

src/bindings/python/CMakeLists.txt

@@ -623,6 +623,13 @@ if(WITH_CHECK)
             setIdFromNames.out.xml
         )
         ADJUST_PYTHONPATH(test_python_setIdFromNames)    
+
+        add_test(NAME test_python_setNamesFromIds
+            COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/examples/python/setNamesFromIds.py
+            ${CMAKE_SOURCE_DIR}/examples/sample-models/from-spec/level-3/enzymekinetics.xml
+            setNamesFromIds.out.xml
+        )
+        ADJUST_PYTHONPATH(test_python_setNamesFromIds)    
 
         add_test(NAME test_python_unsetAnnotation
             COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_SOURCE_DIR}/examples/python/unsetAnnotation.py