OperationalError: (1046, 'No database selected') when querying json attribute

[vmr160030]

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Bug Report

OperationalError: (1046, 'No database selected') when querying json attribute

Description

Following the tutorial in datajoint docs here to use the json datatype. Using the same schema and Team table as in tutorial, I run into an error when querying the car attribute like so:Team & {'car.length': 100}. However, using this syntax works: Team & "car->>'$.length' < 50"

Reproducibility

Include:

• OS MacOS Monterey 12.4
• Python Version 3.8.18
• MySQL Ver 14.14 Distrib 5.7.24, for osx10.9 (x86_64) using EditLine wrapper
• MySQL Deployment Strategy: local-docker
• DataJoint Version: 0.14.1
• Complete error stack as a result of evaluating the above steps: { "name": "OperationalError", "message": "(1046, 'No database selected')", "stack": "--------------------------------------------------------------------------- OperationalError Traceback (most recent call last) File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/IPython/core/formatters.py:708, in PlainTextFormatter.call(self, obj) 701 stream = StringIO() 702 printer = pretty.RepresentationPrinter(stream, self.verbose, 703 self.max_width, self.newline, 704 max_seq_length=self.max_seq_length, 705 singleton_pprinters=self.singleton_printers, 706 type_pprinters=self.type_printers, 707 deferred_pprinters=self.deferred_printers) --> 708 printer.pretty(obj) 709 printer.flush() 710 return stream.getvalue()

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/IPython/lib/pretty.py:410, in RepresentationPrinter.pretty(self, obj) 407 return meth(obj, self, cycle) 408 if cls is not object \ 409 and callable(cls.dict.get('repr')): --> 410 return _repr_pprint(obj, self, cycle) 412 return _default_pprint(obj, self, cycle) 413 finally:

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/IPython/lib/pretty.py:778, in repr_pprint(obj, p, cycle) 776 """A pprint that just redirects to the normal repr function.""" 777 # Find newlines and replace them with p.break() --> 778 output = repr(obj) 779 lines = output.splitlines() 780 with p.group():

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/expression.py:646, in QueryExpression.repr(self) 635 def repr(self): 636 """ 637 returns the string representation of a QueryExpression object e.g. str(q1). 638 (...) 641 :rtype: str 642 """ 643 return ( 644 super().repr() 645 if config["loglevel"].lower() == "debug" --> 646 else self.preview() 647 )

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/expression.py:651, in QueryExpression.preview(self, limit, width) 649 def preview(self, limit=None, width=None): 650 """:return: a string of preview of the contents of the query.""" --> 651 return preview(self, limit, width)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/preview.py:13, in preview(query_expression, limit, width) 11 if width is None: 12 width = config["display.width"] ---> 13 tuples = rel.fetch(limit=limit + 1, format="array") 14 has_more = len(tuples) > limit 15 tuples = tuples[:limit]

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/fetch.py:258, in Fetch.call(self, offset, limit, order_by, format, as_dict, squeeze, download_path, *attrs) 256 ret = return_values[0] if len(attrs) == 1 else return_values 257 else: # fetch all attributes as a numpy.record_array or pandas.DataFrame --> 258 cur = self._expression.cursor( 259 as_dict=as_dict, limit=limit, offset=offset, order_by=order_by 260 ) 261 heading = self._expression.heading 262 if as_dict:

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/expression.py:633, in QueryExpression.cursor(self, offset, limit, order_by, as_dict) 631 sql += " LIMIT %d" % limit + (" OFFSET %d" % offset if offset else "") 632 logger.debug(sql) --> 633 return self.connection.query(sql, as_dict=as_dict)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/connection.py:342, in Connection.query(self, query, args, as_dict, suppress_warnings, reconnect) 340 cursor = self._conn.cursor(cursor=cursor_class) 341 try: --> 342 self._execute_query(cursor, query, args, suppress_warnings) 343 except errors.LostConnectionError: 344 if not reconnect:

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/connection.py:298, in Connection._execute_query(cursor, query, args, suppress_warnings) 296 cursor.execute(query, args) 297 except client.err.Error as err: --> 298 raise translate_query_error(err, query)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/datajoint-0.14.1-py3.8.egg/datajoint/connection.py:296, in Connection._execute_query(cursor, query, args, suppress_warnings) 293 if suppress_warnings: 294 # suppress all warnings arising from underlying SQL library 295 warnings.simplefilter("ignore") --> 296 cursor.execute(query, args) 297 except client.err.Error as err: 298 raise translate_query_error(err, query)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/cursors.py:153, in Cursor.execute(self, query, args) 149 pass 151 query = self.mogrify(query, args) --> 153 result = self._query(query) 154 self._executed = query 155 return result

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/cursors.py:322, in Cursor._query(self, q) 320 conn = self._get_db() 321 self._clear_result() --> 322 conn.query(q) 323 self._do_get_result() 324 return self.rowcount

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/connections.py:558, in Connection.query(self, sql, unbuffered) 556 sql = sql.encode(self.encoding, "surrogateescape") 557 self._execute_command(COMMAND.COM_QUERY, sql) --> 558 self._affected_rows = self._read_query_result(unbuffered=unbuffered) 559 return self._affected_rows

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/connections.py:822, in Connection._read_query_result(self, unbuffered) 820 else: 821 result = MySQLResult(self) --> 822 result.read() 823 self._result = result 824 if result.server_status is not None:

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/connections.py:1200, in MySQLResult.read(self) 1198 def read(self): 1199 try: -> 1200 first_packet = self.connection._read_packet() 1202 if first_packet.is_ok_packet(): 1203 self._read_ok_packet(first_packet)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/connections.py:772, in Connection._read_packet(self, packet_type) 770 if self._result is not None and self._result.unbuffered_active is True: 771 self._result.unbuffered_active = False --> 772 packet.raise_for_error() 773 return packet

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/protocol.py:221, in MysqlPacket.raise_for_error(self) 219 if DEBUG: 220 print("errno =", errno) --> 221 err.raise_mysql_exception(self._data)

File ~/opt/anaconda3/envs/mea/lib/python3.8/site-packages/pymysql/err.py:143, in raise_mysql_exception(data) 141 if errorclass is None: 142 errorclass = InternalError if errno < 1000 else OperationalError --> 143 raise errorclass(errno, errval)

OperationalError: (1046, 'No database selected')" }

Expected Behavior

I expected same query output as in tutorial.

Additional Research and Context

I have installed latest datajoint version from source using pip as conda seems to only pull older 0.13 version. Was also running into a separate error with the table definition line for unique index, which I then commented out of my code: unique index(car.length:decimal(4, 1)) # Add an index if this key is frequently accessed

Error: ("You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '(json_value(car, _utf8mb4'$.length' returning decimal(4, 1))))\n) ENGINE=InnoDB' at line 5", 'CREATE TABLE IF NOT EXISTS root_json.#team2 (\nname varchar(40) NOT NULL COMMENT "team name",\ncar json DEFAULT NULL COMMENT "A car belonging to a team (null to allow registering first but specifying car later)",\nPRIMARY KEY (name),\nunique index ((json_value(car, _utf8mb4'$.length' returning decimal(4, 1))))\n) ENGINE=InnoDB, COMMENT "A team within a company"')