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]
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:
logger.exception(mse)
raise BackendException('database error: ' + 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, genomic_build, 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 ' \
'AND genomic_build=%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'] + '%',
input['genomic_build'],
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 as mse:
logger.exception(mse)
raise BackendException('database error')
def search(self, parameters):
self.validate_feature_search_input(parameters)
query = 'SELECT gene_name, genomic_build, internal_feature_id' \
' FROM {table_name}' \
' WHERE gene_name=%s' \
' AND genomic_build=%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
# sql_keyword = '%' + keyword + '%'
query_args = [
input['gene_name'], input['genomic_build'], 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['genomic_build'])
return items
except MySQLError as mse:
logger.exception(mse)
raise BackendException("MySQLError: {}".format(str(mse)))