Sk/distrib units

src/sbml/SBMLDocument.cpp

@@ -2405,11 +2405,11 @@ SBMLDocument_checkConsistency (SBMLDocument_t *d)
 
 
 LIBSBML_EXTERN
-unsigned int SBMLDocument_validateSBML(SBMLDocument_t * d)
-{
+unsigned int SBMLDocument_validateSBML(SBMLDocument_t * d)
+{
   return (d != NULL) ? d->validateSBML() : SBML_INT_MAX;
-}
-
+}
+
 unsigned int
 SBMLDocument_checkInternalConsistency (SBMLDocument_t *d)
 {
@@ -2490,11 +2490,11 @@ SBMLDocument_getError (SBMLDocument_t *d, unsigned int n)
   return (d != NULL) ? d->getError(n) : NULL;
 }
 
-LIBSBML_EXTERN
-const SBMLErrorLog_t *
-SBMLDocument_getErrorLog(SBMLDocument_t *d)
-{
-  return (d != NULL) ? d->getErrorLog() : NULL;
+LIBSBML_EXTERN
+const SBMLErrorLog_t *
+SBMLDocument_getErrorLog(SBMLDocument_t *d)
+{
+  return (d != NULL) ? d->getErrorLog() : NULL;
 }
 
 LIBSBML_EXTERN

src/sbml/packages/distrib/extension/DistribASTPlugin.cpp

@@ -45,6 +45,7 @@
 #include <sbml/xml/XMLNamespaces.h>
 #include <sbml/math/L3ParserSettings.h>
 #include <sbml/packages/distrib/extension/DistribExtension.h>
+#include <sbml/units/UnitFormulaFormatter.h>
 
 /** @cond doxygenIgnored */
 
@@ -265,8 +266,30 @@ double DistribASTPlugin::evaluateASTNode(const ASTNode * node, const Model * m)
 
 UnitDefinition * DistribASTPlugin::getUnitDefinitionFromPackage(UnitFormulaFormatter* uff, const ASTNode * node, bool inKL, int reactNo) const
 {
-  //OK, this *definitely* could be actually coded, so we could do unit checking on draws from distributions.  But it will be a fair amount of work to get right.
-  return NULL;
+    UnitDefinition* ud = NULL;
+    switch (node->getType())
+    {
+    case AST_DISTRIB_FUNCTION_UNIFORM:
+    case AST_DISTRIB_FUNCTION_NORMAL:
+    case AST_DISTRIB_FUNCTION_BINOMIAL:
+    case AST_DISTRIB_FUNCTION_CAUCHY:
+    case AST_DISTRIB_FUNCTION_CHISQUARE:
+    case AST_DISTRIB_FUNCTION_EXPONENTIAL:
+    case AST_DISTRIB_FUNCTION_GAMMA:
+    case AST_DISTRIB_FUNCTION_LAPLACE:
+    case AST_DISTRIB_FUNCTION_LOGNORMAL:
+    case AST_DISTRIB_FUNCTION_POISSON:
+    case AST_DISTRIB_FUNCTION_RAYLEIGH:
+    case AST_DISTRIB_FUNCTION_BERNOULLI:
+
+        ud = uff->getUnitDefinitionFromArgUnitsReturnFunction(node, inKL, reactNo);
+        break;
+
+    default:
+        break;
+    }
+    return ud;
+
 }
 
 #endif /* __cplusplus */

src/sbml/packages/distrib/extension/DistribSBMLDocumentPlugin.cpp

@@ -43,6 +43,8 @@
 #include <sbml/packages/distrib/validator/DistribSBMLError.h>
 #include <sbml/packages/distrib/validator/DistribConsistencyValidator.h>
 #include <sbml/packages/distrib/validator/DistribIdentifierConsistencyValidator.h>
+#include <sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.h>
+#include <sbml/packages/distrib/validator/DistribUnitConsistencyValidator.h>
 
 
 using namespace std;
@@ -167,7 +169,11 @@ DistribSBMLDocumentPlugin::checkConsistency()
   unsigned char applicableValidators = doc->getApplicableValidators();
   bool id = ((applicableValidators & 0x01) ==0x01);
   bool core = ((applicableValidators & 0x02) ==0x02);
+  bool math = ((applicableValidators & 0x08) == 0x08);
+  bool units = ((applicableValidators & 0x10) == 0x10);
 
+  DistribMathMLConsistencyValidator math_validator;
+  DistribUnitConsistencyValidator unit_validator;
   DistribIdentifierConsistencyValidator id_validator;
   DistribConsistencyValidator core_validator;
 
@@ -200,7 +206,32 @@ DistribSBMLDocumentPlugin::checkConsistency()
       }
     }
   }
+  if (math)
+  {
+      math_validator.init();
+      nerrors = math_validator.validate(*doc);
+      total_errors += nerrors;
+      if (nerrors > 0)
+      {
+          log->add(math_validator.getFailures());
+          /* only want to bail if errors not warnings */
+          if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0)
+          {
+              return total_errors;
+          }
+      }
+  }
 
+  if (units)
+  {
+      unit_validator.init();
+      nerrors = unit_validator.validate(*doc);
+      total_errors += nerrors;
+      if (nerrors > 0)
+      {
+          log->add(unit_validator.getFailures());
+      }
+  }
   return total_errors;
 }
 

src/sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.cpp

@@ -0,0 +1,80 @@
+
+/** @cond doxygenLibsbmlInternal */
+
+/**
+ * @file DistribMathMLConsistencyValidator.cpp
+ * @brief Definition of DistribMathMLConsistencyValidator.
+ * @author SBMLTeam
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2020 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. University of Heidelberg, Heidelberg, Germany
+ *     3. University College London, London, UK
+ *
+ * Copyright (C) 2019 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ * 3. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation. A copy of the license agreement is provided in the
+ * file named "LICENSE.txt" included with this software distribution and also
+ * available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ */
+
+#ifndef doxygen_ignore
+
+#include <sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.h>
+
+/**
+ * Compile ConsistencyConstraints
+ */
+#include "constraints/DistribMathMLConsistencyConstraints.cpp"
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+
+/**
+ * Initializes this Validator with a set of Constraints
+ */
+void
+DistribMathMLConsistencyValidator::init()
+{
+#define  AddingConstraintsToValidator 1
+#include "constraints/DistribMathMLConsistencyConstraintsDeclared.cxx"
+}
+
+
+
+
+LIBSBML_CPP_NAMESPACE_END
+
+
+
+#endif /* doxygen_ignore */
+
+
+/** @endcond */
+

src/sbml/packages/distrib/validator/DistribMathMLConsistencyValidator.h

@@ -0,0 +1,102 @@
+
+/** @cond doxygenLibsbmlInternal */
+
+/**
+ * @file DistribMathMLConsistencyValidator.h
+ * @brief Definition of DistribMathMLConsistencyValidator.
+ * @author SBMLTeam
+ *
+ * <!--------------------------------------------------------------------------
+ * This file is part of libSBML. Please visit http://sbml.org for more
+ * information about SBML, and the latest version of libSBML.
+ *
+ * Copyright (C) 2020 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. University of Heidelberg, Heidelberg, Germany
+ *     3. University College London, London, UK
+ *
+ * Copyright (C) 2019 jointly by the following organizations:
+ *     1. California Institute of Technology, Pasadena, CA, USA
+ *     2. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2013-2018 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ * 3. University of Heidelberg, Heidelberg, Germany
+ *
+ * Copyright (C) 2009-2013 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. EMBL European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
+ *
+ * Copyright (C) 2006-2008 by the California Institute of Technology,
+ * Pasadena, CA, USA
+ *
+ * Copyright (C) 2002-2005 jointly by the following organizations:
+ * 1. California Institute of Technology, Pasadena, CA, USA
+ * 2. Japan Science and Technology Agency, Japan
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation. A copy of the license agreement is provided in the
+ * file named "LICENSE.txt" included with this software distribution and also
+ * available online as http://sbml.org/software/libsbml/license.html
+ * ------------------------------------------------------------------------ -->
+ */
+
+
+#ifndef DistribMathMLConsistencyValidator_H__
+#define DistribMathMLConsistencyValidator_H__
+
+
+
+
+#ifdef __cplusplus
+
+
+#include <sbml/packages/distrib/validator/DistribValidator.h>
+
+
+LIBSBML_CPP_NAMESPACE_BEGIN
+
+
+class DistribMathMLConsistencyValidator : public DistribValidator
+{
+public:
+
+  DistribMathMLConsistencyValidator()
+    : DistribValidator( LIBSBML_CAT_MATHML_CONSISTENCY)
+  {
+  }
+
+
+  virtual ~DistribMathMLConsistencyValidator()
+  {
+  }
+
+
+  /**
+   * Initializes this Validator with a set of Constraints
+   */
+  virtual void init();
+
+
+};
+
+
+
+LIBSBML_CPP_NAMESPACE_END
+
+
+
+
+#endif /* __cplusplus */
+
+
+
+
+#endif /* !DistribMathMLConsistencyValidator_H__ */
+
+
+
+/** @endcond */
+

src/sbml/packages/distrib/validator/DistribSBMLError.h

@@ -69,8 +69,10 @@ typedef enum
   DistribUnknown                                              = 1510100
 , DistribNSUndeclared                                         = 1510101
 , DistribElementNotInNs                                       = 1510102
+, DistribMathnumber                                           = 1510201
 , DistribDuplicateComponentId                                 = 1510301
 , DistribIdSyntaxRule                                         = 1510302
+, DistribUnitsRule                                            = 1510501
 , DistribAttributeRequiredMissing                             = 1520101
 , DistribAttributeRequiredMustBeBoolean                       = 1520102
 , DistribAttributeRequiredMustHaveValue                       = 1520103

src/sbml/packages/distrib/validator/DistribSBMLErrorTable.h

@@ -92,6 +92,19 @@ static const packageErrorTableEntry distribErrorTable[] =
     }
   },
 
+    // 1510201
+      { DistribMathnumber,
+        "Element not in Distrib namespace",
+        LIBSBML_CAT_GENERAL_CONSISTENCY,
+        LIBSBML_SEV_ERROR,
+        "Wherever they appear in an SBML document, elements and attributes from the "
+        "Distributions Package must use the "
+        "'http://www.sbml.org/sbml/level3/version1/distrib/version1' namespace, "
+        "declaring so either explicitly or implicitly.",
+        { "L3V1 Distrib V1 Section 3.1"
+        }
+      },
+
   // 1510301
   { DistribDuplicateComponentId,
     "Duplicate 'id' attribute value",
@@ -114,6 +127,16 @@ static const packageErrorTableEntry distribErrorTable[] =
     }
   },
 
+    // 1510501
+ { DistribUnitsRule,
+   "Invalid units",
+   LIBSBML_CAT_GENERAL_CONSISTENCY,
+   LIBSBML_SEV_ERROR,
+   "The unit supplied to an argument must be correct.",
+   { "L3V1 Distrib V1 Section"
+   }
+ },
+
   // 1520101
   { DistribAttributeRequiredMissing,
     "Required distrib:required attribute on <sbml>",