Merge pull request #106 from sbmlteam/sk-addtemplates

Sk addtemplates

deviser/base_files/BaseTexFile.py

@@ -39,8 +39,8 @@
 # ------------------------------------------------------------------------ -->
 
 
+from ..util import global_variables, strFunctions
 from . import BaseFile
-from ..util import strFunctions
 
 
 class BaseTexFile(BaseFile.BaseFile):
@@ -57,27 +57,40 @@ def __init__(self, name, extension, object_desc):
         BaseFile.BaseFile.__init__(self, name, extension)
 
         # change the comment delimiter and line length
-        self.comment = '%'
+        self.comment = "%"
         self.line_length = 72
 
-        self.package = object_desc['name']
-        self.fullname = object_desc['fullname']
-        self.sbml_classes = object_desc['baseElements']
-        self.offset = object_desc['offset']
-        self.plugins = object_desc['plugins']
-        self.enums = object_desc['enums']
-        self.level = object_desc['base_level']
-        self.version = object_desc['base_version']
-        self.pkg_version = object_desc['pkg_version']
-        if object_desc['required']:
-            self.reqd_status = 'true'
+        if global_variables.is_sbml:
+            self.package = object_desc["name"]
+            self.fullname = object_desc["fullname"]
+            self.sbml_classes = object_desc["baseElements"]
+            self.offset = object_desc["offset"]
+            self.plugins = object_desc["plugins"]
+            self.enums = object_desc["enums"]
+            self.level = object_desc["base_level"]
+            self.version = object_desc["base_version"]
+            self.pkg_version = object_desc["pkg_version"]
+            if object_desc["required"]:
+                self.reqd_status = "true"
+            else:
+                self.reqd_status = "false"
         else:
-            self.reqd_status = 'false'
+            self.package = ''
+            self.fullname = global_variables.package_full_name
+            self.sbml_classes = object_desc["baseElements"]
+            self.offset = object_desc["offset"]
+            self.plugins = []
+            self.enums = object_desc["enums"]
+            self.level = object_desc["base_level"]
+            self.version = object_desc["base_version"]
+            self.pkg_version = 0
+            self.reqd_status = "false"
+
 
         self.prim_class = []
 
-        self.start_b = '{'
-        self.end_b = '}'
+        self.start_b = "{"
+        self.end_b = "}"
 
         # expand the information for the classes
         self.fulltexname = strFunctions.texify(self.fullname)
@@ -86,8 +99,12 @@ def __init__(self, name, extension, object_desc):
         self.sort_attribute_names(self.sbml_classes)
         self.sort_enum_names(self.enums)
 
-        self.full_pkg_command = '\\{0}Package'.format(self.fulltexname)
-        self.brief_pkg_command = '\\{0}'.format(self.upper_package)
+        if global_variables.is_sbml:
+            self.full_pkg_command = "\\{0}Package".format(self.fulltexname)
+        else:
+            self.full_pkg_command = "\\{0}".format(self.fulltexname)
+
+        self.brief_pkg_command = "\\{0}".format(self.upper_package)
 
     ########################################################################
 
@@ -99,14 +116,14 @@ def sort_class_names(self, classes):
         """
         if classes is not None:
             for i in range(0, len(classes)):
-                name = classes[i]['name']
+                name = classes[i]["name"]
                 texname = strFunctions.texify(name)
-                classes[i]['texname'] = texname
+                classes[i]["texname"] = texname
                 # hack for render
-                if name == 'Ellipse' or name == 'Rectangle':
-                    texname = 'Render' + name
-                    classes[i]['texname'] = texname
-                if name == 'RelAbsVector':
+                if name == "Ellipse" or name == "Rectangle":
+                    texname = "Render" + name
+                    classes[i]["texname"] = texname
+                if name == "RelAbsVector":
                     self.prim_class.append(classes[i])
 
     @staticmethod
@@ -118,28 +135,12 @@ def sort_attribute_names(classes):
         """
         if classes is not None:
             for i in range(0, len(classes)):
-                attribs = classes[i]['attribs']
+                attribs = classes[i]["attribs"]
                 BaseTexFile.update_attrib_dicts(attribs)
-                # for j in range(0, len(attribs)):
-                #     if attribs[j]['type'] in ['lo_element', 'element',
-                #                               'inline_lo_element']:
-                #         name = attribs[j]['element']
-                #     else:
-                #         name = attribs[j]['name']
-                #     texname = strFunctions.texify(name)
-                #     attribs[j]['texname'] = texname
             for i in range(0, len(classes)):
-                if 'lo_attribs' in classes[i]:
-                    lo_attribs = classes[i]['lo_attribs']
+                if "lo_attribs" in classes[i]:
+                    lo_attribs = classes[i]["lo_attribs"]
                     BaseTexFile.update_attrib_dicts(lo_attribs)
-                    # for j in range(0, len(lo_attribs)):
-                    #     if lo_attribs[j]['type'] in ['lo_element', 'element',
-                    #                                  'inline_lo_element']:
-                    #         name = lo_attribs[j]['element']
-                    #     else:
-                    #         name = lo_attribs[j]['name']
-                    #     texname = strFunctions.texify(name)
-                    #     lo_attribs[j]['texname'] = texname
 
     @staticmethod
     def update_attrib_dicts(my_list):
@@ -149,13 +150,12 @@ def update_attrib_dicts(my_list):
         :param my_list: the list which we update.
         """
         for j in range(0, len(my_list)):
-            if my_list[j]['type'] in ['lo_element', 'element',
-                                      'inline_lo_element']:
-                name = my_list[j]['element']
+            if my_list[j]["type"] in ["lo_element", "element", "inline_lo_element"]:
+                name = my_list[j]["element"]
             else:
-                name = my_list[j]['name']
+                name = my_list[j]["name"]
             texname = strFunctions.texify(name)
-            my_list[j]['texname'] = texname
+            my_list[j]["texname"] = texname
 
     @staticmethod
     def sort_enum_names(enums):
@@ -166,9 +166,9 @@ def sort_enum_names(enums):
         """
         if enums is not None:
             for i in range(0, len(enums)):
-                name = enums[i]['name']
+                name = enums[i]["name"]
                 texname = strFunctions.texify(name)
-                enums[i]['texname'] = texname
+                enums[i]["texname"] = texname
 
     def write_to_do(self, text):
         """
@@ -177,8 +177,7 @@ def write_to_do(self, text):
 
         :param text: the text describing the TODO.
         """
-        self.write_text_line('\\TODO{0}{1}{2}'.format(self.start_b, text,
-                                                      self.end_b))
+        self.write_text_line("\\TODO{0}{1}{2}".format(self.start_b, text, self.end_b))
         self.skip_line()
 
     def write_text_line(self, line):

deviser/code_files/ExtensionHeaderFile.py

@@ -419,6 +419,10 @@ def write_all_elements(self):
             prefixed_name = '{0}{1}'.format(global_variables.prefix, name)
             new_element = dict({'name': prefixed_name})
             elements.append(new_element)
+        others = ['List', 'ListNode', 'ExpectedAttributes']
+        for name in others:
+            new_element = dict({'name': name})
+            elements.append(new_element)
         self.write_classes(elements)
         new_length = len(elements)
         for i in range(new_length, no_elements, -1):
@@ -483,7 +487,8 @@ def write_fwd_file(self):
         self.write_cppns_end()
         # if we are in another library and using either ASTNode or XMLNode
         # we need to declare these here
-        if global_variables.uses_ASTNode or global_variables.uses_XMLNode:
+        # don't need xmlnode for now
+        if global_variables.uses_ASTNode:
             self.write_libsbml_fwd()
         self.write_end_class_or_struct()
         self.write_defn_end()

deviser/code_files/OtherLibraryFiles.py

@@ -428,9 +428,9 @@ def print_document_errors(self, fileout):
             docname = SF.remove_prefix(doc['name'], remove_package=False,
                                        remove_doc_prefix=True)
         libname = SF.get_library_suffix(gv.library_name)
-        if not libname.endswith('ml'):
-            libname = libname + 'ml'
-        fileout.copy_line_verbatim((10 * '') + 'if ( errorId == {0}{1}Allowed'
+#        if not libname.endswith('ml'):
+#            libname = libname + 'ml'
+        fileout.copy_line_verbatim((10 * ' ') + 'if ( errorId == {0}{1}Allowed'
                                    'CoreAttributes\n'.format(libname, docname))
         level = False
         version = False

deviser/code_files/ValidationFiles.py

@@ -106,13 +106,15 @@ def create_rule_structure(self):
         rules = ValidationRulesGeneral\
             .ValidationRulesGeneral(self.fullname, number, self.package,
                                     self.pkg_ref, self.level, self.version,
-                                    self.pkg_version, self.reqd_status)
+                                    self.pkg_version, self.reqd_status,
+                                    global_variables.language)
         rules.determine_rules()
         self.class_rules += rules.rules
-        if global_variables.is_package:
-            number = self.offset + 20200
-        else:
-            number = 20200
+        number = self.offset + 20200 if global_variables.is_sbml else 20100
+#        if global_variables.is_package:
+#            number = self.offset + 20200
+#        else:
+#            number = 20200
         for i in range(0, len(self.plugins)):
             rules = ValidationRulesForPlugin.ValidationRulesForPlugin(
                 self.plugins[i], self.fullname, number,
@@ -130,6 +132,15 @@ def create_rule_structure(self):
                                          self.pkg_ref)
             rules.determine_rules()
             self.class_rules += rules.rules
+            if not global_variables.is_sbml:
+                for att in self.sbml_classes[i]['attribs']:
+                    if att['type'] == 'lo_element':
+                        rules.rules = []
+                        number += 100
+                        rules.number = number
+                        rules.add_lo_rules()
+                        self.class_rules += rules.rules
+
             number += 100
         self.populate_error_list()
 
@@ -437,28 +448,36 @@ def is_package(i, text_string, length):
             is_package = True
         return [is_package, len_word]
 
-    @staticmethod
-    def replace_name(i, text_string, length):
+    def replace_name(self, i, text_string, length):
         in_name = True
         return_name_rep = ''
+        # we dont want to lower the s of SBase
+        # or name if it starts with the prefix for the language
+        isSBase = False
+        is_language_prefix = False
+        num_letters = 0
         while in_name and i < length:
             letter = text_string[i]
             if i != length-1:
                 next_letter = text_string[i+1]
             else:
                 next_letter = ' '
             if letter == '\\':
-                isSBase = False
-                # we dont want to lower the s of SBase
-                if next_letter == 'S' or next_letter == 's':
-                    test_str = text_string[i+1:i+7]
-                    if test_str.lower() == 'sbase ':
-                        isSBase = True
+                if global_variables.is_sbml:
+                    isSBase = self.is_sbase(text_string, i, next_letter)
+                else:
+                    [is_language_prefix, num_letters] = self.is_language_prefix(text_string, i, next_letter)
                 if isSBase:
                     return_name_rep += '\'S'
+                    i += 1
+                elif is_language_prefix:
+                    return_name_rep += '<'
+                    for j in range(0, num_letters):
+                        return_name_rep += '{0}'.format(text_string[i + j + 1].upper())
+                    i += num_letters
                 else:
                     return_name_rep += '<{0}'.format(next_letter.lower())
-                i += 1
+                    i += 1
             elif next_letter == ' ' or next_letter == '.':
                 if isSBase:
                     return_name_rep += '{0}\''.format(letter)
@@ -471,6 +490,27 @@ def replace_name(i, text_string, length):
             continue
         return [i-1, return_name_rep]
 
+    def is_language_prefix(self, text, index, next_letter):
+        prefix = global_variables.language.upper()
+        if not prefix.startswith(next_letter):
+            return [False, 0]
+        length_prefix = len(prefix)
+        match = True
+        for i in range(0, length_prefix):
+            if prefix[i] != text[index + i + 1]:
+                match = False
+        return [match, length_prefix]
+
+    @staticmethod
+    def is_sbase(text, index, next_letter):
+        if len(text) < index + 7:
+            return False
+        if next_letter == 'S' or next_letter == 's':
+            test_str = text[index + 1:index + 7]
+            if test_str.lower() == 'sbase ':
+                return True
+        return False
+
     @staticmethod
     def replace_uri(i, text_string, length):
         in_uri = True

deviser/code_files/templates/ConstructorException.h

@@ -1,7 +1,7 @@
 #ifndef SBML_CONSTRUCTOR_EXCEPTION_H
 #define SBML_CONSTRUCTOR_EXCEPTION_H
 
-#include <common/extern.h>
+#include <sbml/common/extern.h>
 #include <sbml/SBMLNamespaces.h>
 
 #ifdef __cplusplus

deviser/code_files/templates/Error.h

@@ -1,7 +1,7 @@
 #ifndef SBMLError_h
 #define SBMLError_h
 
-#include <common/extern.h>
+#include <sbml/common/extern.h>
 <verbatim>
 #include <xml/XMLError.h>
 </verbatim>
@@ -21,17 +21,6 @@ typedef enum
 , SBMLNotUTF8                               = 10001 /*!< File does not use UTF-8 encoding. */
 , SBMLUnrecognizedElement                   = 10002 /*!< Encountered unrecognized element. */
 , SBMLNotSchemaConformant                   = 10003 /*!< Document does not conform to the SBML_Lang XML schema. */
-, SBMLInvalidMathElement                    = 10201
-, SBMLMissing<Annotation>Namespace            = 10401 /*!< Missing declaration of the XML namespace for the annotation. */
-, SBMLDuplicate<Annotation>Namespaces         = 10402 /*!< Multiple annotations using the same XML namespace. */
-, SBMLNamespaceIn<Annotation>             = 10403 /*!< The SBML_Lang XML namespace cannot be used in an <Annotation> object. */
-, SBMLMultiple<Annotation>s                   = 10404 /*!< Only one <Annotation> object is permitted under a given SBML_Lang object. */
-, SBML<Annotation>NotElement                  = 10405
-, SBMLNotesNotInXHTMLNamespace              = 10801 /*!< Notes must be placed in the XHTML XML namespace. */
-, SBMLNotesContainsXMLDecl                  = 10802 /*!< XML declarations are not permitted in Notes objects. */
-, SBMLNotesContainsDOCTYPE                  = 10803 /*!< XML DOCTYPE elements are not permitted in Notes objects. */
-, SBMLInvalidNotesContent                   = 10804 /*!< Invalid notes content found. */
-, SBMLOnlyOneNotesElementAllowed            = 10805 /*!< Only one Notes subobject is permitted on a given SBML_Lang object. */
 <add_specific_errors/>
 , SBMLUnknownCoreAttribute                  = 99994 /*!< Encountered an unknown attribute in the SBML_Lang Core namespace. */
 , SBMLCodesUpperBound                   = 99999 /*!< Upper boundary of libSBML-specific diagnostic codes. */

deviser/code_files/templates/ErrorLog.h

@@ -4,8 +4,8 @@
 
 #include <sbml/common/extern.h>
 <verbatim>
-#include <sbml/xml/XMLError.h>
-#include <sbml/xml/XMLErrorLog.h>
+#include <xml/XMLError.h>
+#include <xml/XMLErrorLog.h>
 </verbatim>
 #include <sbml/SBMLError.h>