def annotation_to_html(item: libsbml.SBase) -> str:
"""Render HTML representation of given annotation.
:param item: SBase instance
"""
lines = []
for kcv in range(item.getNumCVTerms()):
cv = item.getCVTerm(kcv)
q_type = cv.getQualifierType()
if q_type == 0:
qualifier = miriam.ModelQualifierType[cv.getModelQualifierType()]
elif q_type == 1:
qualifier = miriam.BiologicalQualifierType[
cv.getBiologicalQualifierType()]
lines.append("".join(
['<span class="collection">', qualifier, "</span>"]))
items = []
for k in range(cv.getNumResources()):
uri = cv.getResourceURI(k)
tokens = uri.split("/")
resource_id = tokens[-1]
link = "".join(
['<a href="', uri, '" target="_blank">', resource_id, "</a>"])
items.append(link)
lines.append("; ".join(items))
res = "<br />".join(lines)
return res
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