Merge pull request #110 from sbmlteam/sk-fix-errors

Sk fix errors
sbmlteam · Nov 9, 2023 · 662bdfb · 662bdfb
2 parents 73aaec9 + e34820f
commit 662bdfb
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Showing 16 changed files with 53 additions and 44 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [2.7, 3.7, 3.8, 3.9, '3.10', 3.11]
+        python-version: [3.7, 3.8, 3.9, '3.10', 3.11]
         platform: [windows-latest, ubuntu-latest, macos-latest]
 
     runs-on: ${{ matrix.platform }}

diff --git a/deviser/code_files/ValidationFiles.py b/deviser/code_files/ValidationFiles.py
@@ -103,11 +103,12 @@ def create_rule_structure(self):
             number = self.offset
         else:
             number = 0
+        full_package = f'{global_variables.package_full_name} Package' if global_variables.is_sbml else global_variables.language
         rules = ValidationRulesGeneral\
             .ValidationRulesGeneral(self.fullname, number, self.package,
                                     self.pkg_ref, self.level, self.version,
                                     self.pkg_version, self.reqd_status,
-                                    global_variables.language)
+                                    full_package)
         rules.determine_rules()
         self.class_rules += rules.rules
         number = self.offset + 20200 if global_variables.is_sbml else 20100

diff --git a/deviser/pytest_files/test_cpp/test-extension/DistribSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/DistribSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry distribErrorTable[] =
 {
   // 1510100
   { DistribUnknown,
-    "Unknown error from Distrib",
+    "Unknown error from DISTRIB",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Distrib",
-    { ""
+    "Unknown error from DISTRIB",
+    { "L3V1 Distrib V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry distribErrorTable[] =
     "Version 2, an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version2/distrib/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Distrib V1 Section 3.1"
+    { "L3V1 Distrib V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry distribErrorTable[] =
     "Distributions Package must use the "
     "'http://www.sbml.org/sbml/level3/version2/distrib/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Distrib V1 Section 3.1"
+    { "L3V1 Distrib V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/FooSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/FooSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry fooErrorTable[] =
 {
   // 110100
   { FooUnknown,
-    "Unknown error from Foo",
+    "Unknown error from FOO",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Foo",
-    { ""
+    "Unknown error from FOO",
+    { "L3V1 Foo V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry fooErrorTable[] =
     "SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/foo/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Foo V1 Section 3.1"
+    { "L3V1 Foo V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry fooErrorTable[] =
     "Foo Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/foo/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Foo V1 Section 3.1"
+    { "L3V1 Foo V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/GroupsSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/GroupsSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry groupsErrorTable[] =
 {
   // 4010100
   { GroupsUnknown,
-    "Unknown error from Groups",
+    "Unknown error from GROUPS",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Groups",
-    { ""
+    "Unknown error from GROUPS",
+    { "L3V1 Groups V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry groupsErrorTable[] =
     "an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/groups/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Groups V1 Section 3.1"
+    { "L3V1 Groups V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry groupsErrorTable[] =
     "Groups Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/groups/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Groups V1 Section 3.1"
+    { "L3V1 Groups V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/QualSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/QualSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry qualErrorTable[] =
 {
   // 3010100
   { QualUnknown,
-    "Unknown error from Qual",
+    "Unknown error from QUAL",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Qual",
-    { ""
+    "Unknown error from QUAL",
+    { "L3V1 Qual V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry qualErrorTable[] =
     "3 Version 1, an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/qual/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Qual V1 Section 3.1"
+    { "L3V1 Qual V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry qualErrorTable[] =
     "Qualitative Models Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/qual/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Qual V1 Section 3.1"
+    { "L3V1 Qual V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/RefsSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/RefsSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry refsErrorTable[] =
 {
   // 110100
   { RefsUnknown,
-    "Unknown error from Refs",
+    "Unknown error from REFS",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Refs",
-    { ""
+    "Unknown error from REFS",
+    { "L3V1 Refs V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry refsErrorTable[] =
     "Version 1, an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/refs/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Refs V1 Section 3.1"
+    { "L3V1 Refs V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry refsErrorTable[] =
     "SID References Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/refs/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Refs V1 Section 3.1"
+    { "L3V1 Refs V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/RenderSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/RenderSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry renderErrorTable[] =
 {
   // 1310100
   { RenderUnknown,
-    "Unknown error from Render",
+    "Unknown error from RENDER",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Render",
-    { ""
+    "Unknown error from RENDER",
+    { "L3V1 Render V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry renderErrorTable[] =
     "an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/render/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Render V1 Section 3.1"
+    { "L3V1 Render V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry renderErrorTable[] =
     "Render Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/render/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Render V1 Section 3.1"
+    { "L3V1 Render V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/TestSBMLErrorTable.h b/deviser/pytest_files/test_cpp/test-extension/TestSBMLErrorTable.h
@@ -53,11 +53,11 @@ static const packageErrorTableEntry testErrorTable[] =
 {
   // 10010100
   { TestUnknown,
-    "Unknown error from Test",
+    "Unknown error from TEST",
     LIBSBML_CAT_GENERAL_CONSISTENCY,
     LIBSBML_SEV_ERROR,
-    "Unknown error from Test",
-    { ""
+    "Unknown error from TEST",
+    { "L3V1 Test V1 Section"
     }
   },
 
@@ -70,7 +70,7 @@ static const packageErrorTableEntry testErrorTable[] =
     "Version 1, an SBML document must declare "
     "'http://www.sbml.org/sbml/level3/version1/test/version1' as the "
     "XMLNamespace to use for elements of this package.",
-    { "L3V1 Test V1 Section 3.1"
+    { "L3V1 Test V1 Section"
     }
   },
 
@@ -83,7 +83,7 @@ static const packageErrorTableEntry testErrorTable[] =
     "testAttributes Package must use the "
     "'http://www.sbml.org/sbml/level3/version1/test/version1' namespace, "
     "declaring so either explicitly or implicitly.",
-    { "L3V1 Test V1 Section 3.1"
+    { "L3V1 Test V1 Section"
     }
   },
 

diff --git a/deviser/pytest_files/test_cpp/test-extension/TestcaseExtension.cpp b/deviser/pytest_files/test_cpp/test-extension/TestcaseExtension.cpp
@@ -665,4 +665,6 @@ ExtraLong_isValidString(const char* code)
 
 
 
-LIBSBML_CPP_NAMESPACE_END
+LIBSBML_CPP_NAMESPACE_END
+
+
diff --git a/deviser/pytest_files/test_cpp/test-extension/TestcaseExtension.h b/deviser/pytest_files/test_cpp/test-extension/TestcaseExtension.h
@@ -746,4 +746,6 @@ LIBSBML_CPP_NAMESPACE_END
 
 
 
-#endif /* !TestcaseExtension_H__ */
+#endif /* !TestcaseExtension_H__ */
+
+
diff --git a/deviser/pytest_files/test_examples/test_examples.py b/deviser/pytest_files/test_examples/test_examples.py
@@ -54,6 +54,8 @@ def test_specific_xml_fail(name, start, stop, number):
     """
     assert 0 == ret.run_specific_xml_fail_tests(name, start, stop, number)
 
+
+#########################################################################################################
 # fails
 # @pytest.mark.parametrize('name', [
 #     ('base_class'),

diff --git a/deviser/util/global_variables.py b/deviser/util/global_variables.py
@@ -192,10 +192,11 @@ def set_globals(lang, base, doc, prfix, lib, is_pack, pkg_prefix,
                 specifications=[], depend=[], library_vers=[],
                 my_copyright='', annot_elem='', notes_elem='', use_id_1=True,
                 use_name_1=True, ast=False, xml=False, top_name=''):
+    global is_sbml
+    is_sbml = True
     global language
     language = lang
     if language != 'sbml':
-        global is_sbml
         is_sbml = False
 
     global namespaces

diff --git a/deviser/validation/ValidationRulesForClass.py b/deviser/validation/ValidationRulesForClass.py
@@ -86,7 +86,7 @@ def __init__(self, object_desc, spec_name, number, package, pkg_ref):
         # constants for rules
         if global_variables.is_sbml:
             self.up_package = strFunctions.upper_first(self.package)
-            self.lib_ref = 'L3V1 {0} V1 Section 3.1'.format(self.up_package)
+            self.lib_ref = 'L3V1 {0} V1 Section'.format(self.up_package)
         else:
             self.up_package = self.package.upper()
             self.lib_ref = '{0} L{1}V{2} Section '.format(self.up_package, self.level, self.version)

diff --git a/deviser/validation/ValidationRulesGeneral.py b/deviser/validation/ValidationRulesGeneral.py
@@ -71,7 +71,7 @@ def __init__(self, spec_name, number, package, pkg_ref, level, version,
         self.tc = 'TBC'
         # constants for rules
         if global_variables.is_sbml:
-            self.lib_ref = 'L3V1 {0} V1 Section 3.1'.format(self.up_package)
+            self.lib_ref = 'L3V1 {0} V1 Section'.format(self.up_package)
             self.up_package = strFunctions.upper_first(self.package)
         else:
             self.lib_ref = '{0} L{1}V{2} Section '.format(self.up_package.upper(), self.level, self.version)
@@ -195,7 +195,7 @@ def write_unknown_rule(self):
         ref = ''
         sev = 'ERROR'
         lib_sev = '{0}_SEV_ERROR'.format(global_variables.up_full_lib)
-        short = 'Unknown error from {0}'.format(self.up_package.upper())*10
+        short = 'Unknown error from {0}'.format(self.up_package.upper())
         tc = global_variables.unknown_error
         return dict({'number': self.number, 'text': text,
                      'reference': ref, 'severity': sev, 'typecode': tc,

diff --git a/deviser/validation/ValidationXMLFiles.py b/deviser/validation/ValidationXMLFiles.py
@@ -67,6 +67,7 @@ def __init__(self, lib_object, verbose=False):
         self.pkg_version = lib_object['pkg_version']
         self.pkg_ref = 'NA'
         self.reqd_status = lib_object['required']
+        self.full_package_command = lib_object['name'] + ' Package'
 
         self.tree = query.create_object_tree(lib_object, False)
 
@@ -127,7 +128,7 @@ def determine_rules(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, self.full_package_command)
         rules.determine_rules()
         self.class_rules += rules.rules
         number = self.offset + 20200