def _add_emapa_highlights(self, terms, termSearch):
"""
add term_highlight and synonym_highlight to each term in terms
"""
# prepare search tokens for highlighting
termSearchTokens = splitSemicolonInput(termSearch)
# prepare term_highlight and synonym_highlight
# only set synonym_highlight if there is no highlight
# on the term
for term in terms:
setattr(term, "term_highlight", "")
setattr(term, "synonym_highlight", "")
term.term_highlight = highlightEMAPA(term.term, termSearchTokens)
# if term could not be highlighted, try synonyms
if '<mark>' not in term.term_highlight:
for synonym in term.synonyms:
# try to highlight each synonym
synonym_highlight = highlightEMAPA(synonym.synonym, termSearchTokens)
if '<mark>' in synonym_highlight:
# set first synonym match and exit
term.synonym_highlight = synonym_highlight
break
def _build_search_query(self, search_query):
query = VocTerm.query
if search_query.has_valid_param("isobsolete"):
isobsolete = search_query.get_value("isobsolete")
query = query.filter(VocTerm.isobsolete==isobsolete)
if search_query.has_valid_param("_vocab_key"):
query = query.filter(VocTerm._vocab_key==search_query.get_value("_vocab_key"))
if search_query.has_valid_param("_term_key"):
query = query.filter(VocTerm._term_key==search_query.get_value("_term_key"))
if search_query.has_valid_param("term"):
term = search_query.get_value("term")
term = term.lower()
query = query.filter(db.func.lower(VocTerm.term)==term)
if search_query.has_valid_param("vocab_name"):
vocab_name = search_query.get_value("vocab_name")
vocab_name = vocab_name.lower()
vocab_alias = db.aliased(Vocab)
query = query.join(vocab_alias, VocTerm.vocab)
query = query.filter(db.func.lower(vocab_alias.name)==vocab_name)
# Specific to EMAPA Browser stage searching
if search_query.has_valid_param('stageSearch'):
stageSearch = search_query.get_value('stageSearch')
stages = emapaStageParser(stageSearch)
if stages:
stages = [int(stage) for stage in stages]
emapa_alias = db.aliased(VocTermEMAPA)
emaps_alias = db.aliased(VocTermEMAPS)
sub_term = db.aliased(VocTerm)
sq = db.session.query(sub_term) \
.join(emapa_alias, sub_term.emapa_info) \
.join(emaps_alias, emapa_alias.emaps_infos) \
.filter(emaps_alias._stage_key.in_(stages)) \
.filter(sub_term._term_key==VocTerm._term_key) \
.correlate(VocTerm)
query = query.filter(sq.exists())
# Specific to EMAPA Browser term searching
if search_query.has_valid_param('termSearch'):
termSearch = search_query.get_value('termSearch')
termSearch = termSearch.lower()
termsToSearch = splitSemicolonInput(termSearch)
# query IDs, terms, and synonyms then UNION all
# search accession ID
accession_alias = db.aliased(Accession)
sub_term1 = db.aliased(VocTerm)
id_sq = db.session.query(sub_term1) \
.join(accession_alias, sub_term1.all_accession_ids) \
.filter(db.func.lower(accession_alias.accid).in_(termsToSearch)) \
.filter(sub_term1._term_key==VocTerm._term_key) \
.correlate(VocTerm)
# search terms
sub_term2 = db.aliased(VocTerm)
term_sq = db.session.query(sub_term2) \
.filter(db.or_(
db.func.lower(VocTerm.term).like(term) for term in termsToSearch \
)) \
.filter(sub_term2._term_key==VocTerm._term_key) \
.correlate(VocTerm)
# search synonyms
synonym_alias = db.aliased(Synonym)
sub_term3 = db.aliased(VocTerm)
synonym_sq = db.session.query(sub_term3) \
.join(synonym_alias, sub_term3.synonyms) \
.filter(db.or_(
db.func.lower(synonym_alias.synonym).like(term) for term in termsToSearch \
)) \
.filter(sub_term3._term_key==VocTerm._term_key) \
.correlate(VocTerm)
# perform union
query1 = query.filter(id_sq.exists())
query2 = query.filter(term_sq.exists())
query3 = query.filter(synonym_sq.exists())
query = query1.union(query2).union(query3)
# handle sorts
sorts = []
if len(search_query.sorts) > 0:
for sort_name in search_query.sorts:
if sort_name == "sequencenum":
sorts.append(VocTerm.sequencenum.asc())
elif sort_name == "term":
sorts.append(VocTerm.term.asc())
else:
sorts.append(VocTerm.sequencenum.asc())
query = query.order_by(*sorts)
return query
