Hi everyone
First message to the list. I've been using SQLAlchemy for quite some
time, mostly with MySQL and some SQLite. Now, we are moving our DB
system to Postgres and I'm converting some scripts that parse data
into our databases to Postgres.
I'm having a recurring error on using COPY FROM. The Python code is
this
<after starting and having a successful connection>
curr_path2 = os.getcwd()
trans = conn.begin()
conn.execute("COPY precursor (spectrum_number, scan_begin, scan_end,
mass, mtoz, elution_time_begin, spectral_analysis_id, charge) FROM
'%s' " % curr_path2)
trans.commit()
The error I'm getting, with different input files, sometimes on
different lines, is the following:
Traceback (most recent call last):
File "pp_ipad_parser3.py", line 434, in <module>
"FROM '%s' " % curr_path2)
File "C:\Python25\lib\site-packages\sqlalchemy-0.4.7p1-py2.5.egg
\sqlalchemy\engine\base.py", line 844, in execute
return Connection.executors[c](self, object, multiparams, params)
File "C:\Python25\lib\site-packages\sqlalchemy-0.4.7p1-py2.5.egg
\sqlalchemy\engine\base.py", line 854, in _execute_tex
t
self.__execute_raw(context)
File "C:\Python25\lib\site-packages\sqlalchemy-0.4.7p1-py2.5.egg
\sqlalchemy\engine\base.py", line 916, in __execute_ra
w
self._cursor_execute(context.cursor, context.statement,
context.parameters[0], context=context)
File "C:\Python25\lib\site-packages\sqlalchemy-0.4.7p1-py2.5.egg
\sqlalchemy\engine\base.py", line 960, in _cursor_exec
ute
self._handle_dbapi_exception(e, statement, parameters, cursor)
File "C:\Python25\lib\site-packages\sqlalchemy-0.4.7p1-py2.5.egg
\sqlalchemy\engine\base.py", line 942, in _handle_dbap
i_exception
raise exceptions.DBAPIError.instance(statement, parameters, e,
connection_invalidated=is_disconnect)
sqlalchemy.exceptions.DataError: (DataError) missing data for column
"spectral_analysis_id"
CONTEXT: COPY precursor, line 360: "13177 13177 13177
555.2051 1662.59362792969 64.374"
"COPY precursor (spectrum_number, scan_begin, scan_end, mass, mtoz,
elution_time_begin, spectral_analysis_id, charge) F
ROM 'C:/Users/nuin/workspace/OCBN/src/ipad_parser_1/temp2.csv' " {}
The files are tab-delimited ones, and I have checked their integrity
and the lines where the errors are occurring are fine. Running the
same command by using the -c parameter of psql doesn't give me any
errors and the copy finishes successfully. I have searched different
forums and web sites trying to find a solution for this problem, but I
couldn't find anything that would resemble the error I'm having.
I'd like to thank in advance for any help
Paulo Nuin
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