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Merge pull request #313 from sbmlteam/model-hist
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allow model history without creator
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@skeating
skeating committed Apr 3, 2023
2 parents 7000862 + 29e085a commit e575643
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Showing 6 changed files with 559 additions and 124 deletions.
143 changes: 143 additions & 0 deletions src/sbml/SBase.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
#include <sbml/util/util.h>

#include <sbml/annotation/RDFAnnotation.h>
#include <sbml/annotation/Date.h>

#include <sbml/KineticLaw.h>
#include <sbml/SBMLError.h>
Expand Down Expand Up @@ -1064,6 +1065,31 @@ SBase::getModelHistory()
return mHistory;
}

Date*
SBase::getCreatedDate() const
{
return (mHistory != NULL) ? mHistory->getCreatedDate() : NULL;
}

Date*
SBase::getCreatedDate()
{
return (mHistory != NULL) ? mHistory->getCreatedDate() : NULL;
}


Date*
SBase::getModifiedDate(unsigned int n)
{
return (mHistory != NULL) ? mHistory->getModifiedDate(n) : NULL;
}

unsigned int
SBase::getNumModifiedDates()
{
return (mHistory != NULL) ? mHistory->getNumModifiedDates() : NULL;
}


/*
* @return @c true if the metaid of this SBML object is set, false
Expand Down Expand Up @@ -1150,6 +1176,22 @@ SBase::isSetModelHistory() const
}


bool
SBase::isSetCreatedDate() const
{
return (mHistory == NULL) ? false : mHistory->isSetCreatedDate();
}



bool
SBase::isSetModifiedDate() const
{
return (mHistory == NULL) ? false : mHistory->isSetModifiedDate();
}



/*
* Sets the metaid field of the given SBML object to a copy of metaid.
*/
Expand Down Expand Up @@ -2310,6 +2352,39 @@ SBase::setModelHistory(ModelHistory * history)
return status;
}

int
SBase::setCreatedDate(Date* date)
{
if (mHistory != NULL)
{
return mHistory->setCreatedDate(date);
}
else
{
mHistory = new ModelHistory();
mHistoryChanged = true;

return mHistory->setCreatedDate(date);

}
}

int
SBase::addModifiedDate(Date* date)
{
if (mHistory != NULL)
{
return mHistory->addModifiedDate(date);
}
else
{
mHistory = new ModelHistory();
mHistoryChanged = true;

return mHistory->addModifiedDate(date);

}
}

/** @cond doxygenLibsbmlInternal */
/*
Expand Down Expand Up @@ -2892,6 +2967,74 @@ SBase::unsetModelHistory()
}


int
SBase::unsetCreatedDate()
{
if (mHistory != NULL && mHistory->isSetCreatedDate())
{
mHistoryChanged = true;
}
else
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}

/* ModelHistory is only allowed on Model in L2
* but on any element in L3
*/
if (getLevel() < 3 && getTypeCode() != SBML_MODEL)
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}

Date* created = mHistory->getCreatedDate();
delete created;
mHistory->mCreatedDate = NULL;

if (mHistory->isSetCreatedDate() == true)
{
return LIBSBML_OPERATION_FAILED;
}
else
{
return LIBSBML_OPERATION_SUCCESS;
}
}


int
SBase::unsetModifiedDates()
{
if (mHistory != NULL && mHistory->isSetModifiedDate())
{
mHistoryChanged = true;
}
else
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}

/* ModelHistory is only allowed on Model in L2
* but on any element in L3
*/
if (getLevel() < 3 && getTypeCode() != SBML_MODEL)
{
return LIBSBML_UNEXPECTED_ATTRIBUTE;
}

List_freeItems(mHistory->getListModifiedDates(), Date_free, Date_t);

if (mHistory->getNumModifiedDates() > 0)
{
return LIBSBML_OPERATION_FAILED;
}
else
{
return LIBSBML_OPERATION_SUCCESS;
}
}


/*
* Returns the BiologicalQualifier associated with this resource,
* an empty string if the resource does not exist.
Expand Down
133 changes: 133 additions & 0 deletions src/sbml/SBase.h
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Original file line number Diff line number Diff line change
Expand Up @@ -975,6 +975,19 @@ class LIBSBML_EXTERN SBase
ModelHistory* getModelHistory() const;


/**
* Returns the "creation date" portion of the ModelHistory of this object.
*
* @return a Date object representing the creation date stored in
* this ModelHistory object.
*
* @note In SBML Level&nbsp;2, model history annotations were only
* permitted on the Model element. In SBML Level&nbsp;3, they are
* permitted on all SBML components derived from SBase.
*/
Date * getCreatedDate() const;


/**
* Returns the ModelHistory object, if any, attached to this object.
*
Expand All @@ -988,6 +1001,46 @@ class LIBSBML_EXTERN SBase
ModelHistory* getModelHistory();


/**
* Returns the "creation date" portion of the ModelHistory of this object.
*
* @return a Date object representing the creation date stored in
* this ModelHistory object.
*
* @note In SBML Level&nbsp;2, model history annotations were only
* permitted on the Model element. In SBML Level&nbsp;3, they are
* permitted on all SBML components derived from SBase.
*/
Date * getCreatedDate();


/**
* Get the nth Date object in the list of "modified date" values stored
* in the ModelHistory of this object.
*
* In the MIRIAM format for annotations, there can be multiple
* modification dates. The libSBML ModelHistory class supports this by
* storing a list of "modified date" values.
*
* @return the nth Date in the list of ModifiedDates of this
* ModelHistory or @c NULL if no such object exists.
*/
Date* getModifiedDate(unsigned int n);


/**
* Get the number of Date objects in the ModelHistory of this Iobject's list of
* "modified dates".
*
* In the MIRIAM format for annotations, there can be multiple
* modification dates. The libSBML ModelHistory class supports this by
* storing a list of "modified date" values.
*
* @return the number of ModifiedDates in this ModelHistory.
*/
unsigned int getNumModifiedDates();


/**
* Predicate returning @c true if this object's "metaid" attribute is set.
*
Expand Down Expand Up @@ -1163,6 +1216,30 @@ class LIBSBML_EXTERN SBase
bool isSetModelHistory() const;


/**
* Predicate returning @c true if this
* object has a ModelHistory object attached to it and the created date is set
*
* @return @c true if the CreatedDate of the ModelHistory of this object is set,
* @c false otherwise.
*
* @note In SBML Level&nbsp;2, model history annotations were only
* permitted on the Model element. In SBML Level&nbsp;3, they are
* permitted on all SBML components derived from SBase.
*/
bool isSetCreatedDate() const;


/**
* Predicate returning @c true or @c false depending on whether the
* ModelHistory's "modified date" of this object is set.
*
* @return @c true if the modification date value of this ModelHistory
* object is set, @c false otherwise.
*/
bool isSetModifiedDate() const;


/**
* Sets the value of the "id" attribute of this SBML object.
*
Expand Down Expand Up @@ -1697,6 +1774,32 @@ s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></b
int setModelHistory(ModelHistory * history);


/**
* Sets the creation date of the ModelHistory of this object.
*
* @param date a Date object representing the date to which the "created
* date" portion of this ModelHistory should be set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*/
int setCreatedDate(Date* date);


/**
* Adds a modified date to the ModelHistory of this object.
*
* @param date a Date object representing the date to which the "modified
* date" portion of this ModelHistory should be set.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
*/
int addModifiedDate(Date* date);


/** @cond doxygenLibsbmlInternal */
/**
* Sets the parent SBMLDocument of this SBML object.
Expand Down Expand Up @@ -2018,6 +2121,36 @@ s.setNotes("<body xmlns='http://www.w3.org/1999/xhtml'><p>here is my note</p></b
int unsetModelHistory();


/**
* Unsets the created date of the ModelHistory object attached to this object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @note In SBML Level&nbsp;2, model history annotations were only
* permitted on the Model element. In SBML Level&nbsp;3, they are
* permitted on all SBML components derived from SBase.
*/
int unsetCreatedDate();


/**
* Unsets the modified dates of the ModelHistory object attached to this object.
*
* @copydetails doc_returns_success_code
* @li @sbmlconstant{LIBSBML_OPERATION_SUCCESS, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_UNEXPECTED_ATTRIBUTE, OperationReturnValues_t}
* @li @sbmlconstant{LIBSBML_OPERATION_FAILED, OperationReturnValues_t}
*
* @note In SBML Level&nbsp;2, model history annotations were only
* permitted on the Model element. In SBML Level&nbsp;3, they are
* permitted on all SBML components derived from SBase.
*/
int unsetModifiedDates();


/**
* Returns the MIRIAM <em>biological qualifier</em> associated with the
* given resource.
Expand Down
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