From 4749cc5103ac826c6f4fe7c089a5f843044721e5 Mon Sep 17 00:00:00 2001
From: Sarah <s.keating@ucl.ac.uk>
Date: Thu, 29 Sep 2022 17:02:19 +0100
Subject: [PATCH 1/5] generating matlab files

---
 deviser/base_files/BaseMatlabFile.py | 164 +++++++++++++++++----------
 deviser/parseXML/ParseXML.py         |  23 +++-
 deviser/util/generateMatlab.py       |  95 ++++++++++++++++
 3 files changed, 219 insertions(+), 63 deletions(-)
 create mode 100644 deviser/util/generateMatlab.py

diff --git a/deviser/base_files/BaseMatlabFile.py b/deviser/base_files/BaseMatlabFile.py
index 47eae8307..3b2016a37 100644
--- a/deviser/base_files/BaseMatlabFile.py
+++ b/deviser/base_files/BaseMatlabFile.py
@@ -41,6 +41,7 @@
 
 from . import BaseFile
 from ..util import strFunctions as SF
+from ..util import query
 
 
 class BaseMatlabFile(BaseFile.BaseFile):
@@ -56,7 +57,7 @@ def __init__(self, name, object_desc, filetype):
         self.matlab_comment_line = 68 * '%'
         self.long_matlab_comment_line = 78 * '%'
         self.short_matlab_comment_line = 32 * '%'
-        self.matlab_big_space = 70 * ' '
+        self.matlab_big_space = 55 * ' '
 
         self.package = object_desc['name']
         self.up_pack = self.package.upper()
@@ -68,6 +69,8 @@ def __init__(self, name, object_desc, filetype):
         self.level = object_desc['base_level']
         self.version = object_desc['base_version']
         self.pkg_version = object_desc['pkg_version']
+        self.num_versions = 1 if 'num_versions' not in object_desc else object_desc['num_versions']
+
         if object_desc['required']:
             self.reqd_status = 'true'
         else:
@@ -178,19 +181,16 @@ def write_value_types(self):
             self.write_get_class_values_types(sbmlclass)
             self.skip_line(2)
 
-    def write_some_common_lines(self):
+    def write_function_args(self):
         """
         Utility function to write some common output.
-        TODO a more descriptive name wouldn't go amiss.
         The first line closes a matlab function argument list.
         """
-        self.write_line(self.matlab_big_space + 'version, pkgVersion)')
-        self.write_more_common_lines()
+        self.write_line_verbatim(self.matlab_big_space + 'version, pkgVersion)')
 
-    def write_more_common_lines(self):
+    def write_function_setup(self):
         """
-        Another utility function
-        TODO yep, this one also needs a better name!
+        Utility function to write some common output.
         """
         self.up_indent()
         self.write_line('if (~isValidLevelVersionCombination(level,'
@@ -232,7 +232,8 @@ def write_get_plugin_values_types(self, plugin):
                                  'get{0}{1}ValueType(level, ...'.
                                  format(self.up_pack, plugin['sbase']))
 
-        self.write_some_common_lines()
+        self.write_function_args()
+        self.write_function_setup()
         num_fields = 1
         self.write_line('SBMLfieldnames = {')
         self.write_line('\'uint\', ...')
@@ -259,7 +260,8 @@ def write_get_class_values_types(self, sbmlclass):
         self.write_line_verbatim('function [SBMLfieldnames, nNumberFields] = '
                                  'get{0}ValueType(level, ...'.
                                  format(sbmlclass['name']))
-        self.write_some_common_lines()
+        self.write_function_args()
+        self.write_function_setup()
 
         num_fields = 9
         self.write_line('SBMLfieldnames = {')
@@ -314,7 +316,8 @@ def write_get_plugin_default_values(self, plugin):
         self.write_line_verbatim('function [SBMLfieldnames, nNumberFields] = '
                                  'get{0}{1}DefaultValues(level, ...'.
                                  format(self.up_pack, plugin['sbase']))
-        self.write_some_common_lines()
+        self.write_function_args()
+        self.write_function_setup()
 
         num_fields = 1
         self.write_line('SBMLfieldnames = {')
@@ -347,7 +350,8 @@ def write_get_class_default_values(self, sbmlclass):
                                  ' = get{0}DefaultValues(level, ...'.
                                  format(sbmlclass['name']))
 
-        self.write_some_common_lines()
+        self.write_function_args()
+        self.write_function_setup()
 
         num_fields = 9
         self.write_line('SBMLfieldnames = {')
@@ -390,6 +394,25 @@ def get_type(self, attrib):
         else:
             return att_type
 
+    def write_attribute(self, attrib, version, num_fields):
+        if attrib['version_info'][version]:
+            if attrib['name'] == 'math':
+                self.write_line('\'{0}\', ...'.format(attrib['name']))
+            else:
+                self.write_line('\'{0}_{1}\', ...'.format(self.package,
+                                                          attrib['name']))
+            num_fields += 1
+            if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
+                self.write_line('\'isSet{0}_{1}\', ...'.
+                                format(self.package,
+                                       SF.lower_first(attrib['name'])))
+                num_fields += 1
+        return num_fields
+
+    def get_lo_attributes(self, extension):
+        element = query.get_class(extension['name'], extension['root'])
+        return element['lo_attribs']
+
     def write_get_plugin_fieldname(self, plugin):
         """
         Writes a "getXXXFieldnames() Matlab function for a plugin
@@ -401,31 +424,48 @@ def write_get_plugin_fieldname(self, plugin):
         self.write_line_verbatim('function [SBMLfieldnames, nNumberFields]'
                                  ' = get{0}{1}Fieldnames(level, ...'.
                                  format(self.up_pack, plugin['sbase']))
-
-        self.write_some_common_lines()  # writes "nNumberFields = 0;" (etc.)
-
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('\'{0}_version\', ...'.format(self.package))
-        # e.g. "'qual_version', ..."
-        num_fields = 1
-
-        for extension in plugin['extension']:
-            self.write_line('\'{0}_{1}\', ...'.
-                            format(self.package,
-                                   SF.lower_first(extension['name'])))
-            num_fields += 1
-        for extension in plugin['lo_extension']:
-            self.write_line('\'{0}_{1}\', ...'.
-                            format(self.package,
-                                   SF.lower_first(extension['name'])))
-            num_fields += 1
-        for attrib in plugin['attribs']:
-            self.write_line('\'{0}_{1}\', ...'.
-                            format(self.package,
-                                   SF.lower_first(attrib['name'])))
-            num_fields += 1
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
+        self.write_function_args()
+        self.write_function_setup()
+
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if plugin['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                for extension in plugin['extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('\'{0}_{1}\', ...'.
+                                        format(self.package,
+                                               SF.lower_first(extension['name'])))
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute(attrib, i, num_fields)
+
+                for extension in plugin['lo_extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('\'{0}_{1}\', ...'.
+                                        format(self.package,
+                                               SF.lower_first(extension['name'])))
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute(attrib, i, num_fields)
+                for attrib in plugin['attribs']:
+                    num_fields = self.write_attribute(attrib, i, num_fields)
+                self.write_line('\'level\', ...')
+                self.write_line('\'version\', ...')
+                self.write_line('\'{0}_version\', ...'.format(self.package))
+                # e.g. "'qual_version', ..."
+                num_fields += 3
+
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
+            self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
+                self.up_indent()
 
         self.write_ends()
 
@@ -441,29 +481,33 @@ def write_get_class_fieldname(self, sbmlclass):
                                  ' = get{0}Fieldnames(level, ...'.
                                  format(sbmlclass['name']))
 
-        self.write_some_common_lines()
-
-        num_fields = 9
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('\'typecode\', ...')
-        self.write_line('\'metaid\', ...')
-        self.write_line('\'notes\', ...')
-        self.write_line('\'annotation\', ...')
-        self.write_line('\'cvterms\', ...')
-        self.write_line('\'sboTerm\', ...')
-        for attrib in sbmlclass['attribs']:
-            if attrib['name'] == 'math':
-                self.write_line('\'{0}\', ...'.format(attrib['name']))
-            else:
-                self.write_line('\'{0}_{1}\', ...'.format(self.package,
-                                                          attrib['name']))
-            num_fields += 1
-        self.write_line('\'level\', ...')
-        self.write_line('\'version\', ...')
-        self.write_line('\'{0}_version\', ...'.format(self.package))
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
-
+        self.write_function_args()
+        self.write_function_setup()
+
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if sbmlclass['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                num_fields = 9
+                self.write_line('\'typecode\', ...')
+                self.write_line('\'metaid\', ...')
+                self.write_line('\'notes\', ...')
+                self.write_line('\'annotation\', ...')
+                self.write_line('\'cvterms\', ...')
+                self.write_line('\'sboTerm\', ...')
+                for attrib in sbmlclass['attribs']:
+                    num_fields = self.write_attribute(attrib, i, num_fields)
+                self.write_line('\'level\', ...')
+                self.write_line('\'version\', ...')
+                self.write_line('\'{0}_version\', ...'.format(self.package))
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
+            self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.up_indent()
         self.write_ends()
 
     def write_get_fieldname_function(self, functionType):
diff --git a/deviser/parseXML/ParseXML.py b/deviser/parseXML/ParseXML.py
index 0e3ed1c48..94e10c1fa 100644
--- a/deviser/parseXML/ParseXML.py
+++ b/deviser/parseXML/ParseXML.py
@@ -849,8 +849,11 @@ def update_element_description(self, node, version_count, element):
         :param element: element to be updated
         :return: nothing
         """
+        element['version_info'][version_count] = True
+
         # <attribute> node(s) are listed within an <element> node
         for attr in node.getElementsByTagName('attribute'):
+
             # Add the dictionary for attribute `attr` to the list.
             element['attribs'].append(
                 self.get_attribute_description(self, attr, version_count))
@@ -886,6 +889,11 @@ def get_element_description(self, node, version_count):
                      minNumListOfChildren="0"
                      maxNumListOfChildren="0" abstract="false">
         '''
+        version_info = []
+        for i in range(0, self.num_versions):
+            version_info.append(False)
+        version_info[version_count] = True
+
         element_name = self.get_element_class_name(self, node)
         # e.g. "DynElement"
         if not element_name:
@@ -959,7 +967,8 @@ def get_element_description(self, node, version_count):
                             'min_lo_children': min_lo_children,
                             'num_versions': self.num_versions,
                             'version': version_count,
-                            'childrenOverwriteElementName': children_overwrite
+                            'childrenOverwriteElementName': children_overwrite,
+                            'version_info': version_info
                             })
             if add_decls is not None:
                 element['addDecls'] = add_decls
@@ -982,6 +991,7 @@ def update_plugin_description(self, node, version_count, plugin):
         :param plugin: existing plugin dict to update
         :return: nothing
         """
+        plugin['version_info'][version_count] = True
         for reference in node.getElementsByTagName('reference'):
             temp = self.find_element(self.elements,
                                      self.get_value(reference, 'name'))
@@ -1024,6 +1034,11 @@ def get_plugin_description(self, node, version_count):
               </attributes>
             </plugin>
         '''
+        version_info = []
+        for i in range(0, self.num_versions):
+            version_info.append(False)
+        version_info[version_count] = True
+
         ext_point = self.get_value(node, 'extensionPoint')  # e.g. "Model"
         plugin = None
         # check whether we have an element with this
@@ -1069,7 +1084,8 @@ def get_plugin_description(self, node, version_count):
             plugin_dict = dict({'sbase': ext_point,
                                 'extension': plug_elements,
                                 'attribs': attributes,
-                                'lo_extension': plug_lo_elements})
+                                'lo_extension': plug_lo_elements,
+                                'version_info': version_info})
 
             if add_decls is not None:
                 if os.path.exists(self.temp_dir + '/' + add_decls):
@@ -1128,7 +1144,8 @@ def populate_elements_for_version(self, pkg_node):
                                                element['lo_class_name'],
                                            'xml_name': element['elementName'],
                                            'min_lo_children':
-                                               element['min_lo_children']}))
+                                               element['min_lo_children'],
+                                           'version_info': element['version_info']}))
                 self.sbml_elements.append(element)
 
     def populate_plugins_for_version(self, pkg_node):
diff --git a/deviser/util/generateMatlab.py b/deviser/util/generateMatlab.py
new file mode 100644
index 000000000..a7500a630
--- /dev/null
+++ b/deviser/util/generateMatlab.py
@@ -0,0 +1,95 @@
+#!/usr/bin/env python
+#
+# @file    generateExamples.py
+# @brief   function for generating code examples
+# @author  Frank Bergmann
+# @author  Sarah Keating
+#
+# <!--------------------------------------------------------------------------
+#
+# 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
+
+from deviser.base_files import BaseMatlabFile
+from deviser.parseXML import ParseXML
+from deviser.util import global_variables
+
+
+def generate_matlab_for(filename, overwrite=True):
+    global_variables.running_tests = False
+    parser = ParseXML.ParseXML(filename)
+    ob = dict()
+    if global_variables.code_returned == \
+            global_variables.return_codes['success']:
+        # catch a problem in the parsing
+        try:
+            ob = parser.parse_deviser_xml()
+        except:
+            global_variables.code_returned \
+                = global_variables.return_codes['parsing error']
+    if global_variables.code_returned == \
+            global_variables.return_codes['success']:
+        name = ob['name'.lower()]
+        try:
+            if global_variables.is_package:
+                generate_matlab_code(name, ob)
+        except:
+            global_variables.code_returned \
+                = global_variables.return_codes['unknown error - please report']
+
+
+def generate_matlab_code(name, ob):
+    filetypes = ['sf', 'dv', 'vt']
+    for t in filetypes:
+        ex = BaseMatlabFile.BaseMatlabFile(name, ob, t)
+        ex.write_file()
+        ex.close_file()
+
+
+
+def main(args):
+    if len(args) != 2:
+        global_variables.code_returned = \
+            global_variables.return_codes['missing function argument']
+        print ('Usage: generateCode.py xmlfile')
+    else:
+        generate_matlab_for(args[1])
+    if global_variables.code_returned == \
+            global_variables.return_codes['success']:
+        print('code successfully written')
+    else:
+        print('writing code failed')
+
+    return global_variables.code_returned
+
+if __name__ == '__main__':
+    main(sys.argv)

From 761cba0fc5ef3a461067bd22f7df127940c54dc8 Mon Sep 17 00:00:00 2001
From: Sarah <s.keating@ucl.ac.uk>
Date: Tue, 11 Oct 2022 16:27:55 +0100
Subject: [PATCH 2/5] multiple pkg versions

---
 deviser/base_files/BaseMatlabFile.py | 218 ++++++++++++++++++---------
 deviser/util/generateMatlab.py       |   1 -
 2 files changed, 148 insertions(+), 71 deletions(-)

diff --git a/deviser/base_files/BaseMatlabFile.py b/deviser/base_files/BaseMatlabFile.py
index 3b2016a37..858780d26 100644
--- a/deviser/base_files/BaseMatlabFile.py
+++ b/deviser/base_files/BaseMatlabFile.py
@@ -104,11 +104,11 @@ def write_file(self):
         self.write_line('%%%% ADD isExtension')
         self.write_line('%%%% ADD isExtension')   # TODO both necessary?
         if self.filetype == 'sf':
-            self.write_is_extension('Fieldname')
+            self.write_is_extension()
         elif self.filetype == 'dv':
-            self.write_is_extension('DefaultValue')
+            self.write_is_extension()
         elif self.filetype == 'vt':
-            self.write_is_extension('ValueType')
+            self.write_is_extension()
         self.write_line('%%%% END isExtension')
         self.skip_line(2)
         self.write_line('%%%% ADD getFieldname')
@@ -234,20 +234,41 @@ def write_get_plugin_values_types(self, plugin):
 
         self.write_function_args()
         self.write_function_setup()
-        num_fields = 1
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('\'uint\', ...')
-        for extension in plugin['extension']:
-            self.write_line('\'structure\', ...'.format())
-            num_fields += 1
-        for extension in plugin['lo_extension']:
-            self.write_line('\'structure\', ...')
-            num_fields += 1
-        for attrib in plugin['attribs']:
-            self.write_line('{0}, ...'.format(self.get_value_type(attrib)))
-            num_fields += 1
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if plugin['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                for extension in plugin['extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('\'structure\', ...'.format())
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute_vt(attrib, i, num_fields)
+                for extension in plugin['lo_extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('\'structure\', ...')
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute_vt(attrib, i, num_fields)
+                for attrib in plugin['attribs']:
+                    num_fields = self.write_attribute_vt(attrib, i, num_fields)
+                self.write_line('\'uint\', ...')
+                self.write_line('\'uint\', ...')
+                self.write_line('\'uint\', ...'.format(v))
+                # e.g. "'qual_version', ..."
+                num_fields += 3
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
+
+            self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
+                self.up_indent()
+
         self.write_ends()
 
     def write_get_class_values_types(self, sbmlclass):
@@ -263,21 +284,29 @@ def write_get_class_values_types(self, sbmlclass):
         self.write_function_args()
         self.write_function_setup()
 
-        num_fields = 9
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('\'{0}\', ...'.format(sbmlclass['typecode']))
-        for _ in range(0, 3):
-            self.write_line('\'char\', ...')
-        self.write_line('\'structure\', ...')
-        self.write_line('\'int\', ...')
-        for attrib in sbmlclass['attribs']:
-            self.write_line('{0}, ...'.format(self.get_value_type(attrib)))
-            num_fields += 1
-        self.write_line('\'uint\', ...')
-        self.write_line('\'uint\', ...')
-        self.write_line('\'uint\', ...')  # .format(self.package))
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if sbmlclass['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                num_fields = 9
+                self.write_line('\'{0}\', ...'.format(sbmlclass['typecode']))
+                for _ in range(0, 3):
+                    self.write_line('\'char\', ...')
+                self.write_line('\'structure\', ...')
+                self.write_line('\'int\', ...')
+                for attrib in sbmlclass['attribs']:
+                    num_fields = self.write_attribute_vt(attrib, i, num_fields)
+                self.write_line('\'uint\', ...')
+                self.write_line('\'uint\', ...')
+                self.write_line('\'uint\', ...')  # .format(self.package))
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
+            self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.up_indent()
         self.write_ends()
 
     def get_value_type(self, attrib):
@@ -292,9 +321,11 @@ def get_value_type(self, attrib):
             return '\'char\''
         elif att_type == 'bool':
             return '\'bool\''
-        elif att_type == 'uint' or att_type == 'int':
+        elif att_type == 'uint':
             return '\'uint\''
-        elif att_type == 'lo_element':
+        elif att_type == 'int':
+            return '\'int\''
+        elif att_type == 'lo_element' or att_type == 'inline_lo_element':
             return '\'structure\''
         elif att_type == 'element':
             if att_name == 'math':
@@ -319,25 +350,42 @@ def write_get_plugin_default_values(self, plugin):
         self.write_function_args()
         self.write_function_setup()
 
-        num_fields = 1
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('int32(pkgVersion), ...')
-        for extension in plugin['extension']:
-            self.write_line('[], ...'.format())
-            num_fields += 1
-        for extension in plugin['lo_extension']:
-            self.write_line('[], ...')
-            num_fields += 1
-        for attrib in plugin['attribs']:
-            self.write_line('{0}, ...'.format(self.get_type(attrib)))
-            num_fields += 1
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if plugin['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                for extension in plugin['extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('[], ...'.format())
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute_dv(attrib, i, num_fields)
+                for extension in plugin['lo_extension']:
+                    if extension['version_info'][i]:
+                        self.write_line('[], ...')
+                        num_fields += 1
+                        attribs = self.get_lo_attributes(extension)
+                        for attrib in attribs:
+                            num_fields = self.write_attribute_dv(attrib, i, num_fields)
+                for attrib in plugin['attribs']:
+                    num_fields = self.write_attribute_dv(attrib, i, num_fields)
+                self.write_line('int32(3), ...')
+                self.write_line('int32(1), ...')
+                self.write_line('int32({0}), ...'.format(v))
+                # e.g. "'qual_version', ..."
+                num_fields += 3
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
 
-        self.down_indent()
-        for _ in range(0, 3):
-            self.write_line('end;')
             self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
+                self.up_indent()
+
+        self.write_ends()
 
     def write_get_class_default_values(self, sbmlclass):
         """
@@ -353,21 +401,29 @@ def write_get_class_default_values(self, sbmlclass):
         self.write_function_args()
         self.write_function_setup()
 
-        num_fields = 9
-        self.write_line('SBMLfieldnames = {')
-        self.write_line('\'{0}\', ...'.format(sbmlclass['typecode']))
-        for _ in range(0, 3):
-            self.write_line('\'\', ...')
-        self.write_line('[], ...')
-        self.write_line('int32(-1), ...')
-        for attrib in sbmlclass['attribs']:
-            self.write_line('{0}, ...'.format(self.get_type(attrib)))
-            num_fields += 1
-        self.write_line('3, ...')
-        self.write_line('int32(version), ...')
-        self.write_line('int32(pkgVersion), ...')  # .format(self.package))
-        self.write_line('};')
-        self.write_line('nNumberFields = {0};'.format(num_fields))
+        v = 1
+        for i in range(0, self.num_versions):
+            num_fields = 0
+            if sbmlclass['version_info'][i]:
+                self.write_line('SBMLfieldnames = {')
+                num_fields = 9
+                self.write_line('\'{0}\', ...'.format(sbmlclass['typecode']))
+                for _ in range(0, 3):
+                    self.write_line('\'\', ...')
+                self.write_line('[], ...')
+                self.write_line('int32(-1), ...')
+                for attrib in sbmlclass['attribs']:
+                    num_fields = self.write_attribute_dv(attrib, i, num_fields)
+                self.write_line('int32(3), ...')
+                self.write_line('int32(1), ...')
+                self.write_line('int32({0}), ...'.format(v))
+                self.write_line('};')
+                self.write_line('nNumberFields = {0};'.format(num_fields))
+            self.down_indent()
+            v = v + 1
+            if v <= self.num_versions:
+                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.up_indent()
         self.write_ends()
 
     def get_type(self, attrib):
@@ -385,7 +441,7 @@ def get_type(self, attrib):
             return '\'\''
         elif att_type in ['bool', 'uint', 'int']:
             return 'int32(0)'
-        elif att_type == 'lo_element':
+        elif att_type in ['lo_element', 'inline_lo_element']:
             return '[]'
         elif att_type == 'element':
             return '\'\'' if att_name == 'math' else '[]'
@@ -409,6 +465,30 @@ def write_attribute(self, attrib, version, num_fields):
                 num_fields += 1
         return num_fields
 
+    def write_attribute_dv(self, attrib, version, num_fields):
+        if attrib['version_info'][version]:
+            if attrib['name'] == 'math':
+                self.write_line('\'{0}\', ...'.format(attrib['name']))
+            else:
+                self.write_line('{0}, ...'.format(self.get_type(attrib)))
+            num_fields += 1
+            if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
+                self.write_line('int32(0), ...')
+                num_fields += 1
+        return num_fields
+
+    def write_attribute_vt(self, attrib, version, num_fields):
+        if attrib['version_info'][version]:
+            if attrib['name'] == 'math':
+                self.write_line('\'{0}\', ...'.format(attrib['name']))
+            else:
+                self.write_line('{0}, ...'.format(self.get_value_type(attrib)))
+            num_fields += 1
+            if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
+                self.write_line('\'bool\', ...')
+                num_fields += 1
+        return num_fields
+
     def get_lo_attributes(self, extension):
         element = query.get_class(extension['name'], extension['root'])
         return element['lo_attribs']
@@ -565,11 +645,9 @@ def write_get_fieldname_function(self, functionType):
         self.write_line('end;')
         self.down_indent()
 
-    def write_is_extension(self, functionType):
+    def write_is_extension(self):
         """
         Write an isXXXExtension() function in the Matlab file.
-
-        TODO the functionType argument isn't used
         """
         self.write_line('function extend = is{0}Extension(typecode)'.
                         format(self.up_pack))
diff --git a/deviser/util/generateMatlab.py b/deviser/util/generateMatlab.py
index a7500a630..d9ca79a94 100644
--- a/deviser/util/generateMatlab.py
+++ b/deviser/util/generateMatlab.py
@@ -75,7 +75,6 @@ def generate_matlab_code(name, ob):
         ex.close_file()
 
 
-
 def main(args):
     if len(args) != 2:
         global_variables.code_returned = \

From 5d416b62e70d46f234cf36808f1a1eec242f4be1 Mon Sep 17 00:00:00 2001
From: Sarah <s.keating@ucl.ac.uk>
Date: Thu, 13 Oct 2022 13:16:26 +0100
Subject: [PATCH 3/5] fix syntax issues

---
 deviser/base_files/BaseMatlabFile.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/deviser/base_files/BaseMatlabFile.py b/deviser/base_files/BaseMatlabFile.py
index 858780d26..9a791a33e 100644
--- a/deviser/base_files/BaseMatlabFile.py
+++ b/deviser/base_files/BaseMatlabFile.py
@@ -198,7 +198,7 @@ def write_function_setup(self):
         self.up_indent()
         self.write_line('error (\'invalid level/version combination\');')
         self.down_indent()
-        self.write_line('end;')
+        self.write_line('end')
         self.skip_line()
 
         self.write_line('SBMLfieldnames = [];')
@@ -216,9 +216,8 @@ def write_ends(self):
         Another utility function, used a number of times.
         Write the `end` keywords at the end of a code block.
         """
-        self.down_indent()
         for _ in range(0, 3):
-            self.write_line('end;')
+            self.write_line('end')
             self.down_indent()
 
     def write_get_plugin_values_types(self, plugin):
@@ -305,7 +304,7 @@ def write_get_class_values_types(self, sbmlclass):
             self.down_indent()
             v = v + 1
             if v <= self.num_versions:
-                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
                 self.up_indent()
         self.write_ends()
 
@@ -422,7 +421,7 @@ def write_get_class_default_values(self, sbmlclass):
             self.down_indent()
             v = v + 1
             if v <= self.num_versions:
-                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
                 self.up_indent()
         self.write_ends()
 
@@ -586,7 +585,7 @@ def write_get_class_fieldname(self, sbmlclass):
             self.down_indent()
             v = v + 1
             if v <= self.num_versions:
-                self.write_line('else if (pkgVersion == {0})'.format(v))
+                self.write_line('elseif (pkgVersion == {0})'.format(v))
                 self.up_indent()
         self.write_ends()
 

From 8c146aab0201e3698fc52fb2aea78cf8973e9849 Mon Sep 17 00:00:00 2001
From: Sarah <s.keating@ucl.ac.uk>
Date: Sat, 15 Oct 2022 14:36:31 +0100
Subject: [PATCH 4/5] tweaks

---
 deviser/base_files/BaseMatlabFile.py | 73 +++++++++++++++-------------
 1 file changed, 40 insertions(+), 33 deletions(-)

diff --git a/deviser/base_files/BaseMatlabFile.py b/deviser/base_files/BaseMatlabFile.py
index 9a791a33e..bd338e3c5 100644
--- a/deviser/base_files/BaseMatlabFile.py
+++ b/deviser/base_files/BaseMatlabFile.py
@@ -449,21 +449,6 @@ def get_type(self, attrib):
         else:
             return att_type
 
-    def write_attribute(self, attrib, version, num_fields):
-        if attrib['version_info'][version]:
-            if attrib['name'] == 'math':
-                self.write_line('\'{0}\', ...'.format(attrib['name']))
-            else:
-                self.write_line('\'{0}_{1}\', ...'.format(self.package,
-                                                          attrib['name']))
-            num_fields += 1
-            if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
-                self.write_line('\'isSet{0}_{1}\', ...'.
-                                format(self.package,
-                                       SF.lower_first(attrib['name'])))
-                num_fields += 1
-        return num_fields
-
     def write_attribute_dv(self, attrib, version, num_fields):
         if attrib['version_info'][version]:
             if attrib['name'] == 'math':
@@ -492,6 +477,32 @@ def get_lo_attributes(self, extension):
         element = query.get_class(extension['name'], extension['root'])
         return element['lo_attribs']
 
+    def write_attribute(self, attrib, version, num_fields):
+        if attrib['version_info'][version]:
+            if attrib['name'] == 'math':
+                self.write_structure_cell(attrib['name'], '', 0, 5)
+            else:
+                self.write_structure_cell(attrib['name'], self.package)
+            num_fields += 1
+            if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
+                self.write_structure_cell('isSet{0}_{1}'.format(self.package, SF.lower_first(attrib['name'])),
+                                          '', 0, 7)
+                num_fields += 1
+        return num_fields
+
+    def write_structure_cell(self, attrib, plugin, is_sbml=1, sbml_type=20):
+        if plugin == '':
+            if is_sbml:
+                self.write_line_verbatim('{0}\'{2}\', \'{2}\', \'\', {3}, {4}{1}, ...'
+                                         .format(self.open_br, self.close_br, attrib, is_sbml, sbml_type))
+            else:
+                self.write_line_verbatim('{0}\'{2}\', \'\', \'\', {3}, {4}{1}, ...'
+                                         .format(self.open_br, self.close_br, attrib, is_sbml, sbml_type))
+
+        else:
+            self.write_line_verbatim('{0}\'{2}_{3}\', \'{3}\', \'{2}\', {4}, {5}{1}, ...'
+                                     .format(self.open_br, self.close_br, plugin, attrib, is_sbml, sbml_type))
+
     def write_get_plugin_fieldname(self, plugin):
         """
         Writes a "getXXXFieldnames() Matlab function for a plugin
@@ -513,9 +524,7 @@ def write_get_plugin_fieldname(self, plugin):
                 self.write_line('SBMLfieldnames = {')
                 for extension in plugin['extension']:
                     if extension['version_info'][i]:
-                        self.write_line('\'{0}_{1}\', ...'.
-                                        format(self.package,
-                                               SF.lower_first(extension['name'])))
+                        self.write_structure_cell(SF.lower_first(extension['name']), self.package)
                         num_fields += 1
                         attribs = self.get_lo_attributes(extension)
                         for attrib in attribs:
@@ -523,18 +532,16 @@ def write_get_plugin_fieldname(self, plugin):
 
                 for extension in plugin['lo_extension']:
                     if extension['version_info'][i]:
-                        self.write_line('\'{0}_{1}\', ...'.
-                                        format(self.package,
-                                               SF.lower_first(extension['name'])))
+                        self.write_structure_cell(SF.lower_first(extension['name']), self.package)
                         num_fields += 1
                         attribs = self.get_lo_attributes(extension)
                         for attrib in attribs:
                             num_fields = self.write_attribute(attrib, i, num_fields)
                 for attrib in plugin['attribs']:
                     num_fields = self.write_attribute(attrib, i, num_fields)
-                self.write_line('\'level\', ...')
-                self.write_line('\'version\', ...')
-                self.write_line('\'{0}_version\', ...'.format(self.package))
+                self.write_structure_cell('level', '', 0, 0)
+                self.write_structure_cell('version', '', 0, 0)
+                self.write_structure_cell('version', self.package, 1, 20)
                 # e.g. "'qual_version', ..."
                 num_fields += 3
 
@@ -569,17 +576,17 @@ def write_get_class_fieldname(self, sbmlclass):
             if sbmlclass['version_info'][i]:
                 self.write_line('SBMLfieldnames = {')
                 num_fields = 9
-                self.write_line('\'typecode\', ...')
-                self.write_line('\'metaid\', ...')
-                self.write_line('\'notes\', ...')
-                self.write_line('\'annotation\', ...')
-                self.write_line('\'cvterms\', ...')
-                self.write_line('\'sboTerm\', ...')
+                self.write_structure_cell('typecode', '', 0, 0)
+                self.write_structure_cell('metaid', '', 1, 20)
+                self.write_structure_cell('notes', '', 1, 1)
+                self.write_structure_cell('annotation', '', 1, 2)
+                self.write_structure_cell('cvterms', '', 0, 4)
+                self.write_structure_cell('sboTerm', '', 1, 20)
                 for attrib in sbmlclass['attribs']:
                     num_fields = self.write_attribute(attrib, i, num_fields)
-                self.write_line('\'level\', ...')
-                self.write_line('\'version\', ...')
-                self.write_line('\'{0}_version\', ...'.format(self.package))
+                self.write_structure_cell('level', '', 0, 0)
+                self.write_structure_cell('version', '', 0, 0)
+                self.write_structure_cell('version', self.package, 1, 20)
                 self.write_line('};')
                 self.write_line('nNumberFields = {0};'.format(num_fields))
             self.down_indent()

From c642608c9f7a607caddf140aeee970038626858c Mon Sep 17 00:00:00 2001
From: Sarah <s.keating@ucl.ac.uk>
Date: Wed, 26 Oct 2022 16:22:17 +0100
Subject: [PATCH 5/5] fixing generation

---
 deviser/base_files/BaseMatlabFile.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/deviser/base_files/BaseMatlabFile.py b/deviser/base_files/BaseMatlabFile.py
index bd338e3c5..017a9eacd 100644
--- a/deviser/base_files/BaseMatlabFile.py
+++ b/deviser/base_files/BaseMatlabFile.py
@@ -485,8 +485,7 @@ def write_attribute(self, attrib, version, num_fields):
                 self.write_structure_cell(attrib['name'], self.package)
             num_fields += 1
             if self.get_type(attrib) == 'int32(0)' or self.get_type(attrib) == '0/0':
-                self.write_structure_cell('isSet{0}_{1}'.format(self.package, SF.lower_first(attrib['name'])),
-                                          '', 0, 7)
+                self.write_structure_cell(attrib['name'], self.package, 0, 7)
                 num_fields += 1
         return num_fields
 
@@ -500,8 +499,14 @@ def write_structure_cell(self, attrib, plugin, is_sbml=1, sbml_type=20):
                                          .format(self.open_br, self.close_br, attrib, is_sbml, sbml_type))
 
         else:
-            self.write_line_verbatim('{0}\'{2}_{3}\', \'{3}\', \'{2}\', {4}, {5}{1}, ...'
-                                     .format(self.open_br, self.close_br, plugin, attrib, is_sbml, sbml_type))
+            if sbml_type == 7:
+                sbmlname = 'isSet{0}_{1}'.format(self.package, SF.lower_first(attrib))
+                self.write_line_verbatim('{0}\'{6}\', \'{3}\', \'{2}\', {4}, {5}{1}, ...'
+                                         .format(self.open_br, self.close_br, plugin, attrib, is_sbml, sbml_type,
+                                                 sbmlname))
+            else:
+                self.write_line_verbatim('{0}\'{2}_{3}\', \'{3}\', \'{2}\', {4}, {5}{1}, ...'
+                                         .format(self.open_br, self.close_br, plugin, attrib, is_sbml, sbml_type))
 
     def write_get_plugin_fieldname(self, plugin):
         """