def annotation_xml(item: libsbml.SBase) -> str:
"""Create Annotation string for the item.
:param item: SBML object for which MathML content is to be generated
:return: Annotation string for the item
"""
if item.isSetAnnotation():
return f"<pre>{item.getAnnotationString().decode('utf-8')}</pre>"
return ""
def cvterm(item: libsbml.SBase) -> str:
"""Create HTML code fragment enclosing cvterm data for the item.
:param item: SBML object for which cvterm data has to be displayed
:return: HTML code fragment enclosing cvterm data for the item
"""
if item.isSetAnnotation():
return f'<div class="cvterm">{annotation_to_html(item)}</div>'
return ""
def cvterms(cls, sbase: libsbml.SBase) -> Optional[List]:
"""Parse CVTerms information.
:param sbase: SBase instance
"""
if not sbase.isSetAnnotation():
return None
cvterms = []
for kcv in range(sbase.getNumCVTerms()):
cv: libsbml.CVTerm = sbase.getCVTerm(kcv)
# qualifier
q_type = cv.getQualifierType()
if q_type == libsbml.MODEL_QUALIFIER:
qualifier = ModelQualifierType[cv.getModelQualifierType()]
elif q_type == libsbml.BIOLOGICAL_QUALIFIER:
qualifier = BiologicalQualifierType[
cv.getBiologicalQualifierType()]
else:
raise ValueError(f"Unsupported qualifier type: '{q_type}'")
resources = [
cv.getResourceURI(k) for k in range(cv.getNumResources())
]
cvterms.append({
"qualifier": qualifier,
"resources": resources,
})
# add SBO term as CVTerm
if sbase.isSetSBOTerm():
sbo = sbase.getSBOTermID()
sbo_in_cvs: bool = False
for cv in cvterms:
for resource in cv["resources"]:
if sbo in resource:
sbo_in_cvs = True
break
if not sbo_in_cvs:
cvterms = [{
"qualifier": "BQB_IS",
"resources": [f"https://identifiers.org/{sbo}"],
}] + cvterms
return cvterms
def annotation_html(item: libsbml.SBase) -> str:
"""Create annotation HTML content for the item.
:param item: SBML object for which annotation HTML content is to be generated
:return: HTML code fragment enclosing annotation for item
"""
info = '<div class="cvterm">'
if item.getSBOTerm() != -1:
info += f"""
<a href="{item.getSBOTermAsURL()}" target="_blank">
{item.getSBOTermID()}
</a><br />
"""
if item.isSetAnnotation():
info += annotation_to_html(item)
info += "</div>"
return info