def test_invalid_range_multiple_ranges(self):
with self.assertRaises(InvalidStageInputError):
emapaStageParser("1-10-4")
with self.assertRaises(InvalidStageInputError):
emapaStageParser("1--4")
def test_invalid_integer(self):
"""
non-integer should throw custom exception
"""
with self.assertRaises(InvalidStageInputError):
emapaStageParser("b")
def test_wildcard_all(self):
stages = emapaStageParser("all")
expected = range(1,29)
self.assertEqual(expected, stages)
stages = emapaStageParser("ALL")
self.assertEqual(expected, stages)
def test_invalid_range_non_integer(self):
with self.assertRaises(InvalidStageInputError):
emapaStageParser("1-b")
with self.assertRaises(InvalidStageInputError):
emapaStageParser("b-10")
with self.assertRaises(InvalidStageInputError):
emapaStageParser("x-z")
def test_invalid_range_empty_range(self):
with self.assertRaises(InvalidStageInputError):
emapaStageParser(" -4")
with self.assertRaises(InvalidStageInputError):
emapaStageParser("10 - ")
with self.assertRaises(InvalidStageInputError):
emapaStageParser(" - ")
def add_items(self, _user_key, emapa_id, stages_to_add):
"""
Parse stages_to_add into list of stages
throws InvalidStageInputError on invalid input
Adds clipboard record for every emapa_id, stage combo
"""
# find vocterm record
emapa_term = self.vocterm_dao.get_by_primary_id(emapa_id)
if not emapa_term:
raise InvalidEMAPAIDError("Cannot find term for EMAPA ID: %s" % emapa_id)
# parse stage input
stages = emapaStageParser(stages_to_add)
added_items = []
for stage in stages:
# only add stages valid for this term
if stage >= emapa_term.emapa_info.startstage \
and stage <= emapa_term.emapa_info.endstage:
set_member = self.add_item(_user_key, emapa_term._term_key, stage)
added_items.append(set_member)
else:
if "*" not in stages_to_add and "all" not in stages_to_add.lower():
raise InvalidStageInputError("%s is invalid for range %d-%d for %s(%s)" % \
(stage,
emapa_term.emapa_info.startstage,
emapa_term.emapa_info.endstage,
emapa_term.term,
emapa_id)
)
if added_items:
# adding a duplicate can cause sequencenums to have gaps
# so we normalize them here
# This is necessary, because EI requires sequencenums without gaps
self.clipboard_dao.normalize_sequencenums(_user_key)
return added_items
def test_range_input_same_stage(self):
stages = emapaStageParser("10-10")
expected = [10]
self.assertEqual(expected, stages)
def test_range_input(self):
stages = emapaStageParser("7-10")
expected = [7, 8, 9, 10]
self.assertEqual(expected, stages)
def test_list_input_unique(self):
stages = emapaStageParser("1, 10, 10, 10, 20")
expected = [1, 10, 20]
self.assertEqual(expected, stages)
def test_list_input(self):
stages = emapaStageParser("1, 11, 10")
expected = [1, 11, 10]
self.assertEqual(expected, stages)
def test_single_stage(self):
stages = emapaStageParser("10")
expected = [10]
self.assertEqual(expected, stages)
def test_wildcard_in_list (self):
stages = emapaStageParser("1, *, 20")
expected = range(1,29)
self.assertEqual(expected, stages)
def test_wildcard_asterisk(self):
stages = emapaStageParser("*")
expected = range(1,29)
self.assertEqual(expected, stages)
def test_range_and_list(self):
stages = emapaStageParser("1, 5-7, 20, 22-24")
expected = [1, 5,6,7, 20, 22,23,24]
self.assertEqual(expected, stages)
def test_invalid_range_left_greater_than_right(self):
with self.assertRaises(InvalidStageInputError):
emapaStageParser("10 - 2")
def test_empty_input(self):
stages = emapaStageParser("")
expected = []
self.assertEqual(expected, stages)
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