def test_get_last_mirror_time(self):
db = SQLData(config_section='clinvar')
last_mirror_time = db.get_last_mirror_time("variant_summary")
assert_that(last_mirror_time,
greater_than_or_equal_to(datetime(2015, 1, 1)))
assert_that(
calling(db.get_last_mirror_time).with_args(
"table_that_does_not_exist"), raises(Exception))
def _test_EscapeString(self):
'''
Test adding weird characters into database
This is commented out because it will pollute your database
'''
utf8_example = "\xF0\x9F\x92\xA9a"
db = SQLData(config_section="pubmed", db_host="localhost")
d = {'PMID': 1, 'xml': utf8_example, 'medline_xml_filename_id': 11}
last_insert_id = db.insert("medline_xml", d)
print(last_insert_id)
db.delete("medline_xml", d)
def test_fetch_with_no_results(self):
db = SQLData(config_section='clinvar')
sql_query = 'select distinct variant_name from variant_summary where AlleleID = "Not-An-Allele-ID"'
assert_that(len(db.fetchall(sql_query)), is_(0))
assert_that(db.fetchrow(sql_query), is_(None))
assert_that(db.fetchID(sql_query), is_(None))
#TODO: update with correct data point to test
#sql_query_with_ID ='select distinct variant_name as ID from variant_summary where AlleleID = "15041"'
#assert_that(db.fetchID(sql_query_with_ID), is_('NM_014855.2:c.80_83delGGATinsTGCTGTAAACTGTAACTGTAAA'))
sql_query_with_missing_ID = 'select distinct variant_name from variant_summary where AlleleID = "15041"'
assert_that(
calling(db.fetchID).with_args(sql_query_with_missing_ID),
raises(Exception))
def test_non_existing_db(self):
db = SQLData(dataset='ThisDBDoesNotExist')
assert_that(
calling(db.fetchall).with_args("select * from my_table"),
raises(Exception))
assert_that(
calling(db.fetchrow).with_args("select * from my_table"),
raises(Exception))
assert_that(
calling(db.fetchID).with_args("select * from my_table"),
raises(Exception))
def test_non_existing_table(self):
db = SQLData(config_section='clinvar')
assert_that(
calling(db.fetchall).with_args("select * from my_table"),
raises(Exception))
assert_that(
calling(db.fetchrow).with_args("select * from my_table"),
raises(Exception))
assert_that(
calling(db.fetchID).with_args("select * from my_table"),
raises(Exception))
def test_truncate_str(self):
s = "NP_775931.3:p.(Pro504delinsArgGluProGlnIleProProArgGlyCysLysGlyAlaGluPheAlaProArgTrpGlnArgLysTrpArgGlnProProCysArgLeuValLeuCysValLeuTrpGluGlyProGlyValSerArgArgGlyGluLeuGluGlyAlaProCysGlyCysHisArgArgLysGlyLeuThrTrpGlyGlyGluPheTrpLysAlaGlyAlaLeuGlyProAlaGlyArgGlyHisGlnSerProAsnAlaGlnLeuLeuHisSerValSerProThrProGluAspGlnValSerAlaAlaProLeuLeuAlaArgAlaLeuHisTrpGlyAlaLysGlyTrpArgProCysArgTrpProCysProProTrpAlaSerArgProLeuArgGlyTrpProValLeuProIleThrSerLeuGlyGlnSerHisHisLeuLeuSerIleLysLeuProGlnArgLeuArgProProGlyLeuHisGlnProSerProProGlyLeuArgValArgTrpAlaSerSerProSerMetGlyGlyAsn)"
db = SQLData(dataset='medgen')
s_truncated = db.trunc_str(s, 200)
assert_that(len(s_truncated), is_(200))