def search(self, keyword, field):
self.validate_search_field(keyword, field)
query = 'SELECT mirna_name, platform, value_field, internal_feature_id ' \
'FROM {table_name} WHERE {search_field} LIKE %s LIMIT %s'.format(
table_name=self.get_table_name(),
search_field=field
)
# Format the keyword for MySQL string matching
sql_keyword = '%' + keyword + '%'
query_args = [sql_keyword, FOUND_FEATURE_LIMIT]
try:
db = get_sql_connection()
cursor = db.cursor(DictCursor)
cursor.execute(query, tuple(query_args))
items = []
for row in cursor.fetchall():
items.append(row)
# Generate human readable labels
for item in items:
item['feature_type'] = MIRN_FEATURE_TYPE
item['label'] = build_feature_label(item)
return items
except MySQLError:
raise BackendException('database error', keyword, field)
def field_value_search(self, keyword, field):
self.validate_field_search_input(keyword, field)
query = 'SELECT DISTINCT {search_field} FROM {table_name} WHERE {search_field} LIKE %s LIMIT %s'.format(
table_name=self.get_table_name(),
search_field=field
)
# Format the keyword for MySQL string matching
sql_keyword = '%' + keyword + '%'
query_args = [sql_keyword, FOUND_FEATURE_LIMIT]
logging.debug("CLOUDSQL_QUERY_GEXP_FIELDS: {}".format(query))
try:
db = get_sql_connection()
cursor = db.cursor(DictCursor)
cursor.execute(query, tuple(query_args))
items = []
for row in cursor.fetchall():
items.append(row[field])
return items
except MySQLError as mse:
raise BackendException("MySQLError: {}".format(str(mse)))
def search(self, parameters):
self.validate_feature_search_input(parameters)
query = 'SELECT gene_name, probe_name, platform, relation_to_gene, relation_to_island, ' \
'value_field, internal_feature_id ' \
'FROM {table_name} ' \
'WHERE gene_name=%s ' \
'AND probe_name LIKE %s ' \
'AND platform LIKE %s ' \
'AND relation_to_gene LIKE %s ' \
'AND relation_to_island LIKE %s ' \
'LIMIT %s'.format(table_name=self.get_table_name()
)
# Fills in '' for fields that were not specified in the parameters
input = defaultdict(lambda: '', parameters)
# Format the keyword for MySQL string matching
query_args = [
input['gene_name'], '%' + input['probe_name'] + '%',
'%' + input['platform'] + '%',
'%' + input['relation_to_gene'] + '%',
'%' + input['relation_to_island'] + '%', FOUND_FEATURE_LIMIT
]
try:
db = get_sql_connection()
cursor = db.cursor(DictCursor)
cursor.execute(query, tuple(query_args))
items = []
for row in cursor.fetchall():
items.append(row)
# Generate human readable labels
for item in items:
item['feature_type'] = METH_FEATURE_TYPE
item['label'] = self.build_feature_label(item)
return items
except MySQLError:
raise BackendException('database error')
def search(self, parameters):
self.validate_feature_search_input(parameters)
query = 'SELECT gene_name, platform, generating_center, value_label, internal_feature_id' \
' FROM {table_name}' \
' WHERE gene_name=%s'\
' AND platform LIKE %s' \
' AND generating_center LIKE %s'\
' LIMIT %s'.format(table_name=self.get_table_name()
)
logging.debug("CLOUDSQL_QUERY_GEXP_SEARCH: {}".format(query))
# Fills in '' for fields that were not specified in the parameters
input = defaultdict(lambda: '', parameters)
# Format the keyword for MySQL string matching
# sql_keyword = '%' + keyword + '%'
query_args = [
input['gene_name'], '%' + input['platform'] + '%',
'%' + input['center'] + '%', FOUND_FEATURE_LIMIT
]
try:
db = get_sql_connection()
cursor = db.cursor(DictCursor)
cursor.execute(query, tuple(query_args))
items = []
for row in cursor.fetchall():
items.append(row)
# Generate human readable labels
for item in items:
item['feature_type'] = GEXP_FEATURE_TYPE
item['label'] = self.build_feature_label(
item['gene_name'], item)
return items
except MySQLError as mse:
raise BackendException("MySQLError: {}".format(str(mse)))