[SCIDB-124] SciServer/Compute sql.pandas_read_sql not working

Thu, 13 May 2021 03:09:36 +0000

I got a kind of timeout error when simply trying this:

# import the hscdata module to talk to the database
from hscdata import sql# SQL script
# for details of each database column, please refer to the schema browser linked from the previous cell
script = '''
SELECT
    object_id
    ,spec.ra
    ,spec.dec
    ,spec.z0
    ,spec.reliability0
    ,phot.g_cmodel_mag
    ,phot.r_cmodel_mag
    ,phot.i_cmodel_mag
    ,phot.patch_s
    ,phot.tract
FROM
    scidb_25.gal_specline AS spec JOIN
    pdr2_dud.forced AS phot USING (object_id)
WHERE
    phot.isprimary AND
    pdr2_dud.search_cosmos(object_id) AND
    phot.i_cmodel_mag < 22
    --- feel free to include more constraints here
'''# query the database.  you will get the result in pandas dataframe
data = sql.pandas_read_sql(script)

-->

/python-extra/lib/python3.9/site-packages/hscdata/config.py:35: UserWarning: Waiting for the db connection information... warnings.warn('Waiting for the db connection information...') --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-2-36c45ed638a2> in <module> 27 28 # query the database. you will get the result in pandas dataframe ---> 29 data = sql.pandas_read_sql(script)/python-extra/lib/python3.9/site-packages/hscdata/sql.py in pandas_read_sql(sql, index_col, coerce_float, params, parse_dates, columns, chunksize) 29 raise ValueError('Use pandas_read_sql_chunked instead.') 30 ---> 31 with connect2db() as conn: 32 return pandas.read_sql( 33 sql=sql, con=conn, index_col=index_col,/usr/local/lib/python3.9/contextlib.py in __enter__(self) 115 del self.args, self.kwds, self.func 116 try: --> 117 return next(self.gen) 118 except StopIteration: 119 raise RuntimeError("generator didn't yield") from None/python-extra/lib/python3.9/site-packages/hscdata/sql.py in connect2db() 55 @contextlib.contextmanager 56 def connect2db(): ---> 57 conn = psycopg2.connect(config.sql_dsn) 58 try: 59 yield conn/python-extra/lib/python3.9/site-packages/hscdata/config.py in __getattr__(self, key) 23 24 def __getattr__(self, key): ---> 25 self._wait_until_config_ready() 26 return getattr(self._config, key) 27 /python-extra/lib/python3.9/site-packages/hscdata/config.py in _wait_until_config_ready(self) 39 time.sleep(1) 40 else: ---> 41 raise RuntimeError('Failed to get db connection information') 42 43 RuntimeError: Failed to get db connection information

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[SCIDB-124] SciServer/Compute sql.pandas_read_sql not working