Merge remote-tracking branch 'origin/development' into sk/small-fixes

src/sbml/SBMLDocument.cpp

@@ -730,14 +730,20 @@ SBMLDocument::checkConsistency ()
 }
 
 
+unsigned int
+SBMLDocument::checkConsistencyWithStrictUnits ()
+{
+  return checkConsistencyWithStrictUnits(LIBSBML_OVERRIDE_ERROR);
+}
+
 /*
  * Performs a set of semantic consistency checks on the document.  Query
  * the results by calling getNumErrors() and getError().
  *
  * @return the number of failed checks (errors) encountered.
  */
 unsigned int
-SBMLDocument::checkConsistencyWithStrictUnits ()
+SBMLDocument::checkConsistencyWithStrictUnits (XMLErrorSeverityOverride_t strictErrorOverride /* = LIBSBML_OVERRIDE_ERROR */)
 {
   // keep a copy of the override status
   // and then override any change
@@ -781,7 +787,7 @@ SBMLDocument::checkConsistencyWithStrictUnits ()
   else
   {
     // log as errors
-    getErrorLog()->setSeverityOverride(LIBSBML_OVERRIDE_ERROR);
+    getErrorLog()->setSeverityOverride(strictErrorOverride);
     StrictUnitConsistencyValidator unit_validator;
     unit_validator.init();
     unsigned int nerrors = unit_validator.validate(*this);

src/sbml/SBMLDocument.h

@@ -305,7 +305,7 @@
 #include <sbml/SBMLErrorLog.h>
 #include <sbml/SBase.h>
 #include <sbml/SBMLTransforms.h>
-
+#include <sbml/xml/XMLError.h>
 
 #ifdef __cplusplus
 
@@ -318,7 +318,6 @@ LIBSBML_CPP_NAMESPACE_BEGIN
 class Model;
 class ConversionProperties;
 class SBMLVisitor;
-class XMLError;
 
 class SBMLValidator;
 class SBMLInternalValidator;
@@ -341,7 +340,10 @@ class SBMLLevelVersionConverter;
 #define OverdeterCheckOFF 0xdf
 #define PracticeCheckON   0x40
 #define PracticeCheckOFF  0xbf
+#define StrictUnitsCheckON 0x80
+#define StrictUnitsCheckOFF 0x7f
 #define AllChecksON       0x7f
+#define AllChecksONWithStrictUnits 0xff
 /** @endcond */
 
 
@@ -1005,12 +1007,36 @@ class LIBSBML_EXTERN SBMLDocument: public SBase
    * flag in the individual SBMLError objects returned by
    * SBMLDocument::getError(@if java long@endif) to determine the nature of the failures.
    *
+   * @param strictErrorOverride the severity of the error to use for strict units checking
+   *       by default unit validations will be flagged as an error using this method. Use
+   *       LIBSBML_OVERRIDE_WARNING to change this to a warning.
+   * 
    * @return the number of failed checks (errors) encountered.
    *
    * @see SBMLDocument::checkInternalConsistency()
    */
   unsigned int checkConsistencyWithStrictUnits ();
 
+  /**
+   * Performs consistency checking and validation on this SBML document
+   * using the ultra strict units validator that assumes that there
+   * are no hidden numerical conversion factors.
+   *
+   * If this method returns a nonzero value (meaning, one or more
+   * consistency checks have failed for SBML document), the failures may be
+   * due to warnings @em or errors.  Callers should inspect the severity
+   * flag in the individual SBMLError objects returned by
+   * SBMLDocument::getError(@if java long@endif) to determine the nature of the failures.
+   *
+   * @param strictErrorOverride the severity of the error to use for strict units checking
+   *       by default unit validations will be flagged as an error using this method. Use
+   *       LIBSBML_OVERRIDE_WARNING to change this to a warning.
+   * 
+   * @return the number of failed checks (errors) encountered.
+   *
+   * @see SBMLDocument::checkInternalConsistency()
+   */
+  unsigned int checkConsistencyWithStrictUnits (XMLErrorSeverityOverride_t strictErrorOverride);
 
   /**
    * Performs consistency checking and validation on this SBML document.

src/sbml/SBMLError.cpp

@@ -171,7 +171,8 @@ static struct sbmlCategoryString {
   { LIBSBML_CAT_MODELING_PRACTICE,      "Modeling practice"           },
   { LIBSBML_CAT_INTERNAL_CONSISTENCY,   "Internal consistency"        },
   { LIBSBML_CAT_SBML_L2V4_COMPAT,	"Translation to SBML L2V4"    },
-  { LIBSBML_CAT_SBML_L3V1_COMPAT, "Translation to SBML L3V1Core" }
+  { LIBSBML_CAT_SBML_L3V1_COMPAT, "Translation to SBML L3V1Core" },
+  { LIBSBML_CAT_STRICT_UNITS_CONSISTENCY, "Strict unit consistency"   }
 };
 
 static unsigned int sbmlCategoryStringTableSize

src/sbml/SBMLError.h

@@ -1039,6 +1039,9 @@ typedef enum
   , LIBSBML_CAT_SBML_COMPATIBILITY
     /*!< Category of errors that can only occur during attempted
      * translation from one Level/Version of SBML to another. */
+  , LIBSBML_CAT_STRICT_UNITS_CONSISTENCY
+    /*!< Category of errors that occur running the strict unit 
+     * validator. */
 
 } SBMLErrorCategory_t;
 

src/sbml/test/TestConsistencyChecks.cpp

@@ -150,10 +150,55 @@ START_TEST (test_strict_unit_consistency_checks)
   fail_unless(d->getError(0)->getErrorId() == 10513);
   fail_unless(d->getError(0)->getSeverity() == LIBSBML_SEV_ERROR);
 
+  d->getErrorLog()->clearLog();
+
+  // now once more as warning
+  errors = d->checkConsistencyWithStrictUnits(LIBSBML_OVERRIDE_WARNING);
+
+  fail_unless(errors == 1);
+  fail_unless(d->getError(0)->getErrorId() == 10513);
+  fail_unless(d->getError(0)->getSeverity() == LIBSBML_SEV_WARNING);
+
+
+
   delete d;
 }
 END_TEST
 
+START_TEST (test_check_consistency_settings)
+{
+  SBMLReader        reader;
+  SBMLDocument*     d;
+  unsigned int errors;
+  std::string filename(TestDataDirectory);
+  filename += "l3v1-units.xml";
+
+
+  d = reader.readSBML(filename);
+
+  if (d == NULL)
+  {
+    fail("readSBML(\"l3v1-units.xml\") returned a NULL pointer.");
+  }
+
+  errors = d->checkConsistency();
+
+  fail_unless(errors == 0);
+
+  d->getErrorLog()->clearLog();
+
+  // now enable the strict units check
+  d->setConsistencyChecks(LIBSBML_CAT_STRICT_UNITS_CONSISTENCY, true);
+
+  errors = d->checkConsistency();
+
+  fail_unless(errors == 1);
+  fail_unless(d->getError(0)->getErrorId() == 10513);
+  fail_unless(d->getError(0)->getSeverity() == LIBSBML_SEV_WARNING);
+
+  delete d;
+}
+END_TEST
 
 Suite *
 create_suite_TestConsistencyChecks (void)
@@ -164,6 +209,7 @@ create_suite_TestConsistencyChecks (void)
 
   tcase_add_test(tcase, test_consistency_checks);
   tcase_add_test(tcase, test_strict_unit_consistency_checks);
+  tcase_add_test(tcase, test_check_consistency_settings);
 
   suite_add_tcase(suite, tcase);
 

src/sbml/validator/SBMLInternalValidator.cpp

@@ -54,6 +54,7 @@
 #include <sbml/validator/MathMLConsistencyValidator.h>
 #include <sbml/validator/SBOConsistencyValidator.h>
 #include <sbml/validator/UnitConsistencyValidator.h>
+#include <sbml/validator/StrictUnitConsistencyValidator.h>
 #include <sbml/validator/OverdeterminedValidator.h>
 #include <sbml/validator/ModelingPracticeValidator.h>
 #include <sbml/validator/L1CompatibilityValidator.h>
@@ -176,6 +177,18 @@ SBMLInternalValidator::setConsistencyChecks(SBMLErrorCategory_t category,
 
     break;
 
+  case LIBSBML_CAT_STRICT_UNITS_CONSISTENCY:
+    if (apply)
+    {
+      mApplicableValidators |= StrictUnitsCheckON;
+    }
+    else
+    {
+      mApplicableValidators &= StrictUnitsCheckOFF;
+    }
+
+    break;
+
   case LIBSBML_CAT_OVERDETERMINED_MODEL:
     if (apply)
     {
@@ -274,6 +287,18 @@ SBMLInternalValidator::setConsistencyChecksForConversion(SBMLErrorCategory_t cat
 
     break;
 
+  case LIBSBML_CAT_STRICT_UNITS_CONSISTENCY:
+    if (apply)
+    {
+      mApplicableValidatorsForConversion |= StrictUnitsCheckON;
+    }
+    else
+    {
+      mApplicableValidatorsForConversion &= StrictUnitsCheckOFF;
+    }
+
+    break;
+
   case LIBSBML_CAT_OVERDETERMINED_MODEL:
     if (apply)
     {
@@ -329,6 +354,7 @@ SBMLInternalValidator::checkConsistency (bool writeDocument)
   bool units = ((mApplicableValidators & 0x10) == 0x10);
   bool over  = ((mApplicableValidators & 0x20) == 0x20);
   bool practice = ((mApplicableValidators & 0x40) == 0x40);
+  bool strictUnits = ((mApplicableValidators & 0x80) == 0x80);
 
   /* taken the state machine concept out for now
   if (LibSBMLStateMachine::isActive()) 
@@ -505,6 +531,25 @@ SBMLInternalValidator::checkConsistency (bool writeDocument)
     }
   }
 
+  if (strictUnits)
+  {
+    StrictUnitConsistencyValidator unit_validator;
+    unit_validator.init();
+    nerrors = unit_validator.validate(*doc);
+    total_errors += nerrors;
+    if (nerrors > 0) 
+    {
+      log->add( unit_validator.getFailures() );
+      /* only want to bail if errors not warnings */
+      if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0)
+      {
+        if (writeDocument)
+          SBMLDocument_free(doc);
+        return total_errors;
+      }
+    }
+  }
+
   /* do not even try if there have been unit warnings 
    * changed this as would have bailed */
   if (over)

src/sbml/validator/Validator.cpp

@@ -864,7 +864,8 @@ Validator::validate (const SBMLDocument& d)
 
   if (m != NULL)
   {
-    if (this->getCategory() == LIBSBML_CAT_UNITS_CONSISTENCY)
+    if (this->getCategory() == LIBSBML_CAT_UNITS_CONSISTENCY ||
+        this->getCategory() == LIBSBML_CAT_STRICT_UNITS_CONSISTENCY)
     {
       /* create list of formula units for validation */
       if (!m->isPopulatedListFormulaUnitsData())