#include <CMIRIAMResource.h>

Inheritance diagram for CMIRIAMResources:

Collaboration diagram for CMIRIAMResources:

Public Member Functions
void	addMIRIAMResource (CMIRIAMResource *pMIRIAMResource)

bool	autoUpdateMIRIAMResources (CProcessReport *pProcessReport)

	CMIRIAMResources (const std::string &name="MIRIAM Resources", const CCopasiContainer *pParent=NULL)

	CMIRIAMResources (const CMIRIAMResources &src, const CCopasiContainer *pParent=NULL)

	CMIRIAMResources (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)

virtual bool	elevateChildren ()

const unsigned C_INT32 &	getMIRIAMLastUpdateDate () const

const CMIRIAMResource &	getMIRIAMResource (const size_t index) const

size_t	getMIRIAMResourceIndex (const std::string &URI) const

const CMIRIAMResources &	getMIRIAMResources () const

const unsigned C_INT32 &	getMIRIAMUpdateFrequency () const

size_t	getResourceIndexFromDisplayName (const std::string &displayName) const

const CCopasiParameterGroup &	getResourceList () const

void	initializeParameter ()

void	setMIRIAMUpdateFrequencyInDays (const size_t &days)

bool	updateMIRIAMResources (CProcessReport *pProcessReport)

bool	updateMIRIAMResourcesFromFile (CProcessReport *pProcessReport, const std::string &filename)

virtual	~CMIRIAMResources ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)

void	addParameter (CCopasiParameter *pParameter)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)

index_iterator	beginIndex () const

name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")

void	clear ()

index_iterator	endIndex () const

name_iterator	endName () const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const std::string &name) const

std::string	getKey (const size_t &index) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

CCopasiParameter::Type	getType (const size_t &index) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual void	print (std::ostream *ostream) const

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

size_t	size () const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CCopasiContainer pParent=NULL, const std::string &objectType="Parameter")

virtual CCopasiObjectName	getCN () const

virtual const std::string &	getKey () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const CCopasiParameter::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

bool	isValidValue (const bool &value) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const CCopasiObjectName &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)

virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Private Member Functions
void	createDisplayNameMap ()

void	createURIMap ()

unsigned C_INT32	getActDateInSeconds ()

void	setMIRIAMLastUpdateDate ()

Private Attributes
std::map< std::string, size_t >	mDisplayName2Resource

unsigned C_INT32 *	mpLastUpdateDate

CCopasiParameterGroup *	mpMIRIAMResources

unsigned C_INT32 *	mpUpdateFrequency

std::map< std::string, size_t >	mURI2Resource

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 173 of file CMIRIAMResource.h.

Constructor & Destructor Documentation

CMIRIAMResources::CMIRIAMResources	(	const std::string &	name = `"MIRIAM Resources"`,
		const CCopasiContainer *	pParent = `NULL`
	)

Default constructor

Parameters

const	std::string & name (default: MIRIAM Resources)
const	CCopasiContainer * pParent (default: NULL)

Definition at line 29 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                      :
   CCopasiParameterGroup(name, pParent),
   mpLastUpdateDate(NULL),
   mpUpdateFrequency(NULL),
   mpMIRIAMResources(NULL)
 {initializeParameter();}

CMIRIAMResources::CMIRIAMResources	(	const CMIRIAMResources &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters

const	CMIRIAMResources & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 37 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                     :
   CCopasiParameterGroup(src, pParent),
   mpLastUpdateDate(NULL),
   mpUpdateFrequency(NULL),
   mpMIRIAMResources(NULL)
 {initializeParameter();}

CMIRIAMResources::CMIRIAMResources	(	const CCopasiParameterGroup &	group,
		const CCopasiContainer *	pParent = `NULL`
	)

Specific constructor

Parameters

const	CCopasiParameterGroup & group
const	CCopasiContainer * pParent (default: NULL)

Definition at line 45 of file CMIRIAMResource.cpp.

References initializeParameter().

                                                                     :
   CCopasiParameterGroup(group, pParent),
   mpLastUpdateDate(NULL),
   mpUpdateFrequency(NULL),
   mpMIRIAMResources(NULL)
 {initializeParameter();}

CMIRIAMResources::~CMIRIAMResources ( )

virtual

Destructor

Definition at line 466 of file CMIRIAMResource.cpp.

467 {}

Member Function Documentation

void CMIRIAMResources::addMIRIAMResource ( CMIRIAMResource * pMIRIAMResource )

Add a MIRIAM Resource to the list of MIRIAM Resources

Parameters

CMIRIAMResource * pMIRIAMResource

Definition at line 67 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::addParameter(), and mpMIRIAMResources.

 {
   mpMIRIAMResources->addParameter(mimriamResource);
 }

bool CMIRIAMResources::autoUpdateMIRIAMResources ( CProcessReport * pProcessReport )

Automatically update the resources when the last update is older than the current date minus the update interval.

Parameters

CProcessReport * pProcessReport

Returns: bool success

Definition at line 323 of file CMIRIAMResource.cpp.

References getActDateInSeconds(), mpLastUpdateDate, mpUpdateFrequency, and updateMIRIAMResources().

 {
   if ((*mpLastUpdateDate + *mpUpdateFrequency) <= getActDateInSeconds())
     {return updateMIRIAMResources(pProcessReport);}
 
   return false;
 }

void CMIRIAMResources::createDisplayNameMap ( )

private

Initialize the display name to resource index map

Definition at line 344 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getMIRIAMDisplayName(), getMIRIAMResource(), mDisplayName2Resource, and mpMIRIAMResources.

Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().

 {
   mDisplayName2Resource.clear();
 
   size_t Index = 0;
 
   CCopasiParameterGroup::index_iterator it = mpMIRIAMResources->beginIndex();
   CCopasiParameterGroup::index_iterator end = mpMIRIAMResources->endIndex();
 
   for (; it != end; ++it)
     {
       mDisplayName2Resource[getMIRIAMResource(Index).getMIRIAMDisplayName()] = Index;
       Index++;
     }
 }

void CMIRIAMResources::createURIMap ( )

private

Initialize the URI to resource index map

Definition at line 360 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CMIRIAMResource::getIdentifiersOrgURL(), CMIRIAMResource::getMIRIAMDeprecated(), CMIRIAMResource::getMIRIAMURI(), mpMIRIAMResources, and mURI2Resource.

Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().

 {
   mURI2Resource.clear();
 
   size_t Index = 0;
   CMIRIAMResource * pResource = NULL;
 
   CCopasiParameterGroup::index_iterator it = mpMIRIAMResources->beginIndex();
   CCopasiParameterGroup::index_iterator end = mpMIRIAMResources->endIndex();
 
   for (; it != end; ++it)
     {
       pResource = static_cast< CMIRIAMResource * >(*it);
       mURI2Resource[pResource->getMIRIAMURI() + ":"] = Index;
       mURI2Resource[pResource->getIdentifiersOrgURL() + "/"] = Index;
 
       const CCopasiParameterGroup * pDeprecated = &pResource->getMIRIAMDeprecated();
       CCopasiParameterGroup::index_iterator itDeprecated = pDeprecated->beginIndex();
       CCopasiParameterGroup::index_iterator endDeprecated = pDeprecated->endIndex();
 
       for (; itDeprecated != endDeprecated; ++itDeprecated)
         {
           std::string Deprecated = *(*itDeprecated)->getValue().pSTRING;
 
           //Deprecated URL style URIs do not use the ':' separator.
           if (Deprecated[Deprecated.length() - 1] != '/')
             {
               Deprecated += ":";
             }
 
           mURI2Resource[Deprecated] = Index;
         }
 
       Index++;
     }
 }

bool CMIRIAMResources::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 331 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), and mpMIRIAMResources.

Referenced by initializeParameter(), updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().

 {
   bool success = true;
 
   CCopasiParameterGroup::index_iterator it = mpMIRIAMResources->beginIndex();
   CCopasiParameterGroup::index_iterator end = mpMIRIAMResources->endIndex();
 
   for (; it != end; ++it)
     *it = elevate<CMIRIAMResource, CCopasiParameterGroup>(*it);
 
   return success;
 }

unsigned C_INT32 CMIRIAMResources::getActDateInSeconds ( )

private

Retrieve the current date ins seconds

Definition at line 320 of file CMIRIAMResource.cpp.

References C_INT32.

Referenced by autoUpdateMIRIAMResources(), initializeParameter(), and setMIRIAMLastUpdateDate().

321 {return (unsigned C_INT32) time(NULL);}

C_INT32

#define C_INT32

Definition: copasi.h:90

const unsigned C_INT32 & CMIRIAMResources::getMIRIAMLastUpdateDate ( ) const

Retrieve the day the resources where last updated

Returns: const unsigned C_INT32 & lastUpdateDay

Definition at line 78 of file CMIRIAMResource.cpp.

References mpLastUpdateDate.

79 {return * mpLastUpdateDate;}

CMIRIAMResources::mpLastUpdateDate

unsigned C_INT32 * mpLastUpdateDate

Definition: CMIRIAMResource.h:325

const CMIRIAMResource & CMIRIAMResources::getMIRIAMResource ( const size_t index ) const

Retrieve the indexed resource

Parameters

const size_t index

Returns: const CMIRIAMResource & resource

Definition at line 397 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::getGroup(), CCopasiRootContainer::getUnknownMiriamResource(), mpMIRIAMResources, and CCopasiParameterGroup::size().

Referenced by createDisplayNameMap(), CMIRIAMResourceObject::extractId(), CMIRIAMResourceObject::getDisplayName(), CMIRIAMResourceObject::getIdentifiersOrgURL(), CMIRIAMResourceObject::getURI(), and CQMiriamWidget::updateResourcesList().

 {
   if (index >= mpMIRIAMResources->size())
     return CCopasiRootContainer::getUnknownMiriamResource();
 
   return * static_cast< CMIRIAMResource * >(mpMIRIAMResources->getGroup(index));
 }

size_t CMIRIAMResources::getMIRIAMResourceIndex ( const std::string & URI ) const

Retrieve the index of the resource with the given URI

Parameters

const std::string & URI

Returns: size_t index

Definition at line 405 of file CMIRIAMResource.cpp.

References C_INVALID_INDEX, and mURI2Resource.

Referenced by CMIRIAMResourceObject::getResource(), and CMIRIAMResourceObject::isValid().

 {
   size_t index = C_INVALID_INDEX;
 
   std::map< std::string , size_t >::const_iterator it = mURI2Resource.lower_bound(URI);
   std::map< std::string , size_t >::const_iterator end = mURI2Resource.upper_bound(URI);
 
   if (it == mURI2Resource.begin())
     return index;
 
   it--;
 
   for (; it != end; ++it)
     {
       // Check whether the URI base of the candidate matches.
       if (URI.compare(0, it->first.length(), it->first) == 0)
         {
           index =  it->second;
           break;
         }
     }
 
   return index;
 }

const CMIRIAMResources & CMIRIAMResources::getMIRIAMResources ( ) const

Retrieve the list of MIRIAM Resources

Returns: CMIRIAMResources & MIRIAMResources

Definition at line 72 of file CMIRIAMResource.cpp.

73 {return * this;}

const unsigned C_INT32 & CMIRIAMResources::getMIRIAMUpdateFrequency ( ) const

Retrieve the of interval between updates

Returns: const unsigned C_INT32 & updateFrequency

Definition at line 81 of file CMIRIAMResource.cpp.

References mpUpdateFrequency.

82 {return * mpUpdateFrequency;}

CMIRIAMResources::mpUpdateFrequency

unsigned C_INT32 * mpUpdateFrequency

Definition: CMIRIAMResource.h:330

size_t CMIRIAMResources::getResourceIndexFromDisplayName ( const std::string & displayName ) const

Retrieve the index of the resource with the given display name

Parameters

const std::string & displayName

Returns: size_t index

Definition at line 430 of file CMIRIAMResource.cpp.

References C_INVALID_INDEX, and mDisplayName2Resource.

Referenced by CMIRIAMResourceObject::setDisplayName().

 {
   // Check if the display name is a know resource
   std::map< std::string, size_t>::const_iterator it =
     mDisplayName2Resource.find(displayName.c_str());
 
   // If we did not find the resource we set it to unknown
   if (it == mDisplayName2Resource.end())
     {
       // unknown is indicated by an invalid index.
       return C_INVALID_INDEX;
     }
 
   return it->second;
 }

const CCopasiParameterGroup & CMIRIAMResources::getResourceList ( ) const

Retrieve the list of MIRIAM resource as a CCopasiParameterGroup

Returns: const CCopasiParameterGroup & resourceList

Definition at line 75 of file CMIRIAMResource.cpp.

References mpMIRIAMResources.

Referenced by CConfigurationFile::load(), and CQMiriamWidget::updateResourcesList().

76 {return * mpMIRIAMResources;}

CMIRIAMResources::mpMIRIAMResources

CCopasiParameterGroup * mpMIRIAMResources

Definition: CMIRIAMResource.h:335

void CMIRIAMResources::initializeParameter ( )

Allocates all group parameters and assures that they are properly initialized.

Definition at line 53 of file CMIRIAMResource.cpp.

References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), C_INT32, createDisplayNameMap(), createURIMap(), elevateChildren(), getActDateInSeconds(), CCopasiParameter::getValue(), mpLastUpdateDate, mpMIRIAMResources, mpUpdateFrequency, CCopasiParameter::Value::pUINT, and CCopasiParameter::UINT.

Referenced by CMIRIAMResources(), and CConfigurationFile::load().

 {
   mpLastUpdateDate = assertParameter("LastUpdateDate", CCopasiParameter::UINT,
                                      (unsigned C_INT32) getActDateInSeconds())->getValue().pUINT;
   mpUpdateFrequency = assertParameter("Frequency", CCopasiParameter::UINT,
                                       (unsigned C_INT32) 604800)->getValue().pUINT;
   mpMIRIAMResources = assertGroup("Resources");
 
   elevateChildren();
 
   createDisplayNameMap();
   createURIMap();
 }

void CMIRIAMResources::setMIRIAMLastUpdateDate ( )

private

Set the last update date to the current time

Definition at line 314 of file CMIRIAMResource.cpp.

References getActDateInSeconds(), and mpLastUpdateDate.

Referenced by updateMIRIAMResources(), and updateMIRIAMResourcesFromFile().

315 {*mpLastUpdateDate = getActDateInSeconds();}

CMIRIAMResources::getActDateInSeconds

unsigned C_INT32 getActDateInSeconds()

Definition: CMIRIAMResource.cpp:320

CMIRIAMResources::mpLastUpdateDate

unsigned C_INT32 * mpLastUpdateDate

Definition: CMIRIAMResource.h:325

void CMIRIAMResources::setMIRIAMUpdateFrequencyInDays ( const size_t & days )

Set the days between updates

Parameters

const size_t & days

Definition at line 317 of file CMIRIAMResource.cpp.

References C_INT32, and mpUpdateFrequency.

318 {*mpUpdateFrequency = (unsigned C_INT32)(days * 24 * 60 * 60);}

C_INT32

#define C_INT32

Definition: copasi.h:90

CMIRIAMResources::mpUpdateFrequency

unsigned C_INT32 * mpUpdateFrequency

Definition: CMIRIAMResource.h:330

bool CMIRIAMResources::updateMIRIAMResources ( CProcessReport * pProcessReport )

Update the MIRIAM resources

Parameters

CProcessReport * pProcessReport

Returns: bool success

Definition at line 206 of file CMIRIAMResource.cpp.

References ArrayOf_USCORExsd_USCOREstring::__ptr, ArrayOf_USCORExsd_USCOREstring::__size, ns2__getDataTypeURIsResponse::_getDataTypeURIsReturn, CMIRIAMResource::addDeprecatedURL(), CProcessReport::addItem(), CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), createDisplayNameMap(), createURIMap(), elevateChildren(), CCopasiMessage::ERROR, CProcessReport::finishItem(), MiriamWebServicesSoapBindingProxy::getDataTypePattern(), MiriamWebServicesSoapBindingProxy::getDataTypesName(), ns2__getDataTypesNameResponse::getDataTypesNameReturn, MiriamWebServicesSoapBindingProxy::getDataTypeURI(), MiriamWebServicesSoapBindingProxy::getDataTypeURIs(), MCAnnotation, mpMIRIAMResources, pdelete, CProcessReport::progressItem(), CMIRIAMResource::setMIRIAMCitation(), CMIRIAMResource::setMIRIAMDisplayName(), setMIRIAMLastUpdateDate(), CMIRIAMResource::setMIRIAMPattern(), CMIRIAMResource::setMIRIAMURI(), CProcessReport::setName(), MiriamWebServicesSoapBindingProxy::soap_fault_detail(), MiriamWebServicesSoapBindingProxy::soap_fault_string(), and SOAP_OK.

Referenced by autoUpdateMIRIAMResources().

 {
   if (pProcessReport)
     pProcessReport->setName("MIRIAM Resources Update...");
 
   bool success = true;
   MiriamWebServicesSoapBindingProxy * pProxy = new MiriamWebServicesSoapBindingProxy();
 
   CCopasiParameterGroup * pTmpCpyCMIRIAMResources = new CCopasiParameterGroup("Resources");
 
   CMIRIAMResource * pMIRIAMResource = NULL;
   std::string Name, URI, Deprecated, Pattern, IsDeprecated;
   int itNames = 0, itURIs = 0, sizeNames = 0, sizeURIs = 0;
   unsigned C_INT32 processStep = 0, processSteps;
   size_t hUpdateStep;
   struct ns2__getDataTypesNameResponse DataTypesName;
 
   if (pProxy->getDataTypesName(DataTypesName) == SOAP_OK)
     {
       sizeNames = DataTypesName.getDataTypesNameReturn->__size;
       processSteps = sizeNames + 2;
       hUpdateStep = pProcessReport->addItem("Update Process", processStep, &processSteps);
 
       if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
         return false;
 
       for (itNames = 0; itNames < sizeNames; itNames++)
         {
           struct ns2__getDataTypeURIsResponse DataTypeURIs;
 
           if (DataTypesName.getDataTypesNameReturn->__ptr[itNames] != "")
             Name = DataTypesName.getDataTypesNameReturn->__ptr[itNames];
 
           pMIRIAMResource = new CMIRIAMResource(Name, NULL);
 
           if ((pProxy->getDataTypeURI(Name, URI) == SOAP_OK)
               && (pProxy->getDataTypeURIs(Name, DataTypeURIs) == SOAP_OK)
               && (pProxy->getDataTypePattern(Name, Pattern) == SOAP_OK))
             {
               sizeURIs = DataTypeURIs._getDataTypeURIsReturn->__size;
 
               if (sizeURIs != 0)
                 {
                   for (itURIs = 0; itURIs < sizeURIs; itURIs++)
                     {
                       Deprecated = DataTypeURIs._getDataTypeURIsReturn->__ptr[itURIs];
 
                       if (Deprecated != URI)
                         pMIRIAMResource->addDeprecatedURL(Deprecated);
                     }
                 }
 
               pMIRIAMResource->setMIRIAMDisplayName(Name);
               pMIRIAMResource->setMIRIAMURI(URI);
               pMIRIAMResource->setMIRIAMPattern(Pattern);
               pMIRIAMResource->setMIRIAMCitation(URI == "urn:miriam:arxiv" ||
                                                  URI == "urn:miriam:doi" ||
                                                  URI == "urn:miriam:pubmed" ||
                                                  URI == "urn:miriam:isbn");
 
               pTmpCpyCMIRIAMResources->addParameter(pMIRIAMResource);
             }
           else
             success = false;
 
           processStep++;
 
           if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
             return false;
         }
 
       processStep++;
 
       if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
         return false;
     }
   else
     success = false;
 
   if (success)
     {
       // TODO add a resource for local objects, i.e., within the current model.
 
       setMIRIAMLastUpdateDate();
       *mpMIRIAMResources = *pTmpCpyCMIRIAMResources;
       elevateChildren();
       createDisplayNameMap();
       createURIMap();
     }
   else
     CCopasiMessage(CCopasiMessage::ERROR,
                    MCAnnotation + 3,
                    pProxy->soap_fault_string(),
                    pProxy->soap_fault_detail());
 
   pdelete(pTmpCpyCMIRIAMResources);
 
   processStep++;
 
   if (pProcessReport && !pProcessReport->progressItem(hUpdateStep)) return false;
 
   if (pProcessReport) pProcessReport->finishItem(hUpdateStep);
 
   pdelete(pProxy);
 
   return success;
 }

bool CMIRIAMResources::updateMIRIAMResourcesFromFile	(	CProcessReport *	pProcessReport,
		const std::string &	filename
	)

Update the MIRIAM resources using a local filename

Parameters

CProcessReport * pProcessReport

Returns: bool success

Definition at line 84 of file CMIRIAMResource.cpp.

References CMIRIAMResource::addDeprecatedURL(), CProcessReport::addItem(), CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), createDisplayNameMap(), createURIMap(), elevateChildren(), mpMIRIAMResources, pdelete, CProcessReport::progressItem(), CMIRIAMResource::setMIRIAMCitation(), CMIRIAMResource::setMIRIAMDisplayName(), setMIRIAMLastUpdateDate(), CMIRIAMResource::setMIRIAMPattern(), and CMIRIAMResource::setMIRIAMURI().

Referenced by DataModelGUI::miriamDownloadFinished().

 {
   bool success = true;
 
   CCopasiParameterGroup * pTmpCpyCMIRIAMResources = new CCopasiParameterGroup("Resources");
   CMIRIAMResource * pMIRIAMResource = NULL;
   std::string Name, URI, Deprecated, Pattern, IsDeprecated;
   int itNames = 0, itURIs = 0, sizeNames = 0, sizeURIs = 0;
   unsigned C_INT32 processStep = 0, processSteps = 1;
 
   size_t hUpdateStep;
 
   if (pProcessReport)
     hUpdateStep = pProcessReport->addItem("Parsing MIRIAM XML", processStep, &processSteps);
 
   // parse file into memory
   XMLInputStream stream(filename.c_str());
 
   if (stream.isError()) return false;
 
   XMLNode root(stream);
 
   ++processStep;
 
   if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
     return false;
 
   sizeNames = root.getNumChildren();
   processSteps = sizeNames + 2;
 
   if (pProcessReport)
     hUpdateStep = pProcessReport->addItem("Add Items", processStep, &processSteps);
 
   if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
     return false;
 
   // read all datatype elements
   for (itNames = 0; itNames < sizeNames; itNames++)
     {
       XMLNode dataType = root.getChild(itNames);
 
       // only parse dataType elements
       if (dataType.getName() != "datatype") continue;
 
       // extract name
       Name = dataType.getChild("name").getChild(0).getCharacters();
       pMIRIAMResource = new CMIRIAMResource(Name, NULL);
 
       XMLNode uris = dataType.getChild("uris");
       sizeURIs = uris.getNumChildren();
 
       // extract uri & deprecated uris
       URI.clear();
 
       if (sizeURIs != 0)
         {
           for (itURIs = 0; itURIs < sizeURIs; itURIs++)
             {
               XMLNode uri = uris.getChild(itURIs);
 
               if (URI.empty())
                 URI = uri.getChild(0).getCharacters();
 
               Deprecated = uri.getAttrValue("deprecated");
 
               if (Deprecated == "true")
                 pMIRIAMResource->addDeprecatedURL(uri.getChild(0).getCharacters());
             }
         }
 
       // set name
       pMIRIAMResource->setMIRIAMDisplayName(Name);
 
       if (URI.empty() || Name.empty())
         {
           // ignore invalid item
           delete pMIRIAMResource;
           continue;
         }
 
       pMIRIAMResource->setMIRIAMURI(URI);
       pMIRIAMResource->setMIRIAMPattern(dataType.getAttrValue("pattern"));
       pMIRIAMResource->setMIRIAMCitation(URI == "urn:miriam:arxiv" ||
                                          URI == "urn:miriam:doi" ||
                                          URI == "urn:miriam:pubmed" ||
                                          URI == "urn:miriam:isbn");
 
       pTmpCpyCMIRIAMResources->addParameter(pMIRIAMResource);
 
       processStep++;
 
       if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
         return false;
     }
 
   processStep++;
 
   if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
     return false;
 
   if (success)
     {
       // TODO add a resource for local objects, i.e., within the current model.
 
       setMIRIAMLastUpdateDate();
       *mpMIRIAMResources = *pTmpCpyCMIRIAMResources;
       elevateChildren();
       createDisplayNameMap();
       createURIMap();
     }
 
   pdelete(pTmpCpyCMIRIAMResources);
 
   processStep++;
 
   if (pProcessReport && !pProcessReport->progressItem(hUpdateStep))
     return false;
 
   return success;
 }