I am using pyspark in databricks to append data to a sql table via ADF pipelines. Code is sown below:
log_status_df_all = spark.createDataFrame(log_status_df_all)
log_status_df_all.write.format("com.microsoft.sqlserver.jdbc.spark").mode(write_mode).option("url", url).option("dbtable", 'Logs_Collection_Status').option("user", username).option("password", password).save()
log_status_df_all.show()
On some days I am get the error message:
com.microsoft.sqlserver.jdbc.SQLServerException: There is already an object named '<table_name>' in the database.
Upon simply re-running the pipeline the table is updated with no issues; therefore the code is working. How can I prevent this from happening again? Is it an error when multiple pipelines try writing to the same table at the same time?
The rest of the error message is shown below:
---------------------------------------------------------------------------
Py4JJavaError Traceback (most recent call last)
<command-3143827225825384> in <module>
8
9 log_collection_df = spark.createDataFrame(log_collection_df)
---> 10 write_df_sql(log_collection_df, 'Logs_Collection_Status', 'overwrite')
11
<command-1421348210166948> in write_df_sql(df, table, write_mode)
14
15
---> 16 spark_df.write.format("com.microsoft.sqlserver.jdbc.spark").mode(write_mode).option("url", url).option("dbtable", table_name).option("user", username).option("password", password).save()
17
18 #backup table
/databricks/spark/python/pyspark/sql/readwriter.py in save(self, path, format, mode, partitionBy, **options)
735 self.format(format)
736 if path is None:
--> 737 self._jwrite.save()
738 else:
739 self._jwrite.save(path)
/databricks/spark/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py in __call__(self, *args) 1255 answer = self.gateway_client.send_command(command) 1256 return_value
= get_return_value(
-> 1257 answer, self.gateway_client, self.target_id, self.name) 1258 1259 for temp_arg in temp_args:
/databricks/spark/python/pyspark/sql/utils.py in deco(*a, **kw)
61 def deco(*a, **kw):
62 try:
---> 63 return f(*a, **kw)
64 except py4j.protocol.Py4JJavaError as e:
65 s = e.java_exception.toString()
/databricks/spark/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
326 raise Py4JJavaError(
327 "An error occurred while calling {0}{1}{2}.\n".
--> 328 format(target_id, ".", name), value)
329 else:
330 raise Py4JError(
Py4JJavaError: An error occurred while calling o661.save. : com.microsoft.sqlserver.jdbc.SQLServerException: There is already an object named 'Logs_Collection_Status' in the database. at com.microsoft.sqlserver.jdbc.SQLServerException.makeFromDatabaseError(SQLServerException.java:258) at com.microsoft.sqlserver.jdbc.SQLServerStatement.getNextResult(SQLServerStatement.java:1535) at com.microsoft.sqlserver.jdbc.SQLServerStatement.doExecuteStatement(SQLServerStatement.java:845) at com.microsoft.sqlserver.jdbc.SQLServerStatement$StmtExecCmd.doExecute(SQLServerStatement.java:752) at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:7151) at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:2478) at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeCommand(SQLServerStatement.java:219) at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeStatement(SQLServerStatement.java:199) at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeUpdate(SQLServerStatement.java:680) at com.microsoft.sqlserver.jdbc.spark.BulkCopyUtils$.executeUpdate(BulkCopyUtils.scala:456) at com.microsoft.sqlserver.jdbc.spark.BulkCopyUtils$.mssqlCreateTable(BulkCopyUtils.scala:495) at com.microsoft.sqlserver.jdbc.spark.SingleInstanceConnector$.createTable(SingleInstanceConnector.scala:33) at com.microsoft.sqlserver.jdbc.spark.Connector.write(Connector.scala:60) at com.microsoft.sqlserver.jdbc.spark.DefaultSource.createRelation(DefaultSource.scala:51) at org.apache.spark.sql.execution.datasources.SaveIntoDataSourceCommand.run(SaveIntoDataSourceCommand.scala:45) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:70) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult(commands.scala:68) at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:86) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:152) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:140) at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$5.apply(SparkPlan.scala:193) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:189) at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:140) at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:117) at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:115) at org.apache.spark.sql.DataFrameWriter$$anonfun$runCommand$1.apply(DataFrameWriter.scala:711) at org.apache.spark.sql.DataFrameWriter$$anonfun$runCommand$1.apply(DataFrameWriter.scala:711) at org.apache.spark.sql.execution.SQLExecution$$anonfun$withCustomExecutionEnv$1.apply(SQLExecution.scala:113) at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:243) at org.apache.spark.sql.execution.SQLExecution$.withCustomExecutionEnv(SQLExecution.scala:99) at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:173) at org.apache.spark.sql.DataFrameWriter.runCommand(DataFrameWriter.scala:711) at org.apache.spark.sql.DataFrameWriter.saveToV1Source(DataFrameWriter.scala:307) at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:293) at sun.reflect.GeneratedMethodAccessor841.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:380) at py4j.Gateway.invoke(Gateway.java:295) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:251) at java.lang.Thread.run(Thread.java:748)
The issue has now been resolved.
Previous code:
if condition1==True:
write_mode = 'overwrite'
elif condition2==True:
write_mode = 'append'
log_status_df_all = spark.createDataFrame(log_status_df_all)
log_status_df_all.write.format("com.microsoft.sqlserver.jdbc.spark").mode(write_mode).option("url", url).option("dbtable", 'Logs_Collection_Status').option("user", username).option("password", password).save()
log_status_df_all.show()
Current code:
write_mode = 'append'
log_status_df_all = spark.createDataFrame(log_status_df_all)
log_status_df_all.write.format("com.microsoft.sqlserver.jdbc.spark").mode(write_mode).option("url", url).option("dbtable", 'Logs_Collection_Status').option("user", username).option("password", password).save()
log_status_df_all.show()
Related
I am trying to pull data from a table where the dates are in timestamp format 2019-06-31 19:00:00
I want to have them in string format as 20190631
It works if I choose get_pandas_df instead of get_spark_df but I need it in get_spark_df
I have tried this so far:
start_date = '2019-06-15'
end_date = '2019-06-31'
records = QaasHook.get_spark_df("""
(SELECT name,
cast(date_format(startdt, '%Y%m%d') AS VARCHAR) AS stdt,
cast(amnt AS DOUBLE) AS amount,
cast(date_format(enddt, '%Y%m%d') AS VARCHAR) AS endt
FROM table_1
WHERE cast(date_format(startdt, '%Y%m%d') AS INT) >= {st_dt}
AND cast(date_format(enddt, '%Y%m%d') AS INT) <= {end_dt} )
""".format(st_dt = start_date.replace('-',''), end_dt = end_date.replace('-',''))
)
But I get an error on the format line as
Py4JJavaError Traceback (most recent call last)
<ipython-input-36-c72fafc06f37> in <module>
159 where cast(date_format(cph.d_chkdate,'%Y%m%d') as int) >= {st_dt} and cast(date_format(cph.d_chkdate,'%Y%m%d') as int) <= {end_dt})
--> 160 """.format(st_dt = start_date.replace('-',''), end_dt = end_date.replace('-',''))
161 )
162
/opt/pyenv/versions/3.7.4/lib/python3.7/site-packages/dss_airflow_utils/hooks/qaas_hook.py in get_spark_df(self, dbtable, options)
258 ", ".join(actual_options.keys()))
259 spark_op = spark_op.options(**actual_options)
--> 260 return spark_op.load()
261
262 def get_conn(self):
/opt/spark-3.0.0/python/pyspark/sql/readwriter.py in load(self, path, format, schema, **options)
182 return self._df(self._jreader.load(self._spark._sc._jvm.PythonUtils.toSeq(path)))
183 else:
--> 184 return self._df(self._jreader.load())
185
186 #since(1.4)
/opt/spark-3.0.0/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py in __call__(self, *args)
1303 answer = self.gateway_client.send_command(command)
1304 return_value = get_return_value(
-> 1305 answer, self.gateway_client, self.target_id, self.name)
1306
1307 for temp_arg in temp_args:
/opt/spark-3.0.0/python/pyspark/sql/utils.py in deco(*a, **kw)
129 def deco(*a, **kw):
130 try:
--> 131 return f(*a, **kw)
132 except py4j.protocol.Py4JJavaError as e:
133 converted = convert_exception(e.java_exception)
/opt/spark-3.0.0/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
326 raise Py4JJavaError(
327 "An error occurred while calling {0}{1}{2}.\n".
--> 328 format(target_id, ".", name), value)
329 else:
330 raise Py4JError(
Py4JJavaError: An error occurred while calling o527.load.
: java.sql.SQLException: Error executing query
at io.prestosql.jdbc.PrestoStatement.internalExecute(PrestoStatement.java:274)
at io.prestosql.jdbc.PrestoStatement.execute(PrestoStatement.java:227)
at io.prestosql.jdbc.PrestoPreparedStatement.<init>(PrestoPreparedStatement.java:80)
at io.prestosql.jdbc.PrestoConnection.prepareStatement(PrestoConnection.java:128)
at org.apache.spark.sql.execution.datasources.jdbc.JDBCRDD$.resolveTable(JDBCRDD.scala:58)
at org.apache.spark.sql.execution.datasources.jdbc.JDBCRelation$.getSchema(JDBCRelation.scala:226)
at org.apache.spark.sql.execution.datasources.jdbc.JdbcRelationProvider.createRelation(JdbcRelationProvider.scala:35)
at org.apache.spark.sql.execution.datasources.DataSource.resolveRelation(DataSource.scala:339)
at org.apache.spark.sql.DataFrameReader.loadV1Source(DataFrameReader.scala:279)
at org.apache.spark.sql.DataFrameReader.$anonfun$load$2(DataFrameReader.scala:268)
at scala.Option.getOrElse(Option.scala:189)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:268)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:203)
at sun.reflect.GeneratedMethodAccessor71.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Any help would be appreciated
I'm working with a Dask Cluster on GCP. I'm using this code to deploy it:
from dask_cloudprovider.gcp import GCPCluster
from dask.distributed import Client
enviroment_vars = {
'EXTRA_PIP_PACKAGES': '"gcsfs"'
}
cluster = GCPCluster(
n_workers=32,
docker_image='daskdev/dask:2021.2.0',
env_vars=enviroment_vars,
network='my-network',
#filesystem_size=150,
machine_type='e2-standard-16',
projectid='my-project-id',
zone='us-central1-a',
on_host_maintenance="MIGRATE"
client = Client(cluster)
Then I read csv files, with the following code:
import dask.dataframe as dd
import csv
col_dtypes = {
'var1': 'float64',
'var2': 'object',
'var3': 'object',
'var4': 'float64'
}
df = dd.read_csv('gs://my_bucket/files-*.csv', blocksize=None, dtype= col_dtypes)
df = df.persist()
Everything works fine, but when I try to do some queries, or calculation, I get an error. For instance this piece of code:
df.var1.value_counts().compute()
This is the output:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-14-711a7c21ed42> in <module>
----> 1 df.var1.value_counts().compute()
/opt/conda/lib/python3.8/site-packages/dask/base.py in compute(self, **kwargs)
279 dask.base.compute
280 """
--> 281 (result,) = compute(self, traverse=False, **kwargs)
282 return result
283
/opt/conda/lib/python3.8/site-packages/dask/base.py in compute(*args, **kwargs)
561 postcomputes.append(x.__dask_postcompute__())
562
--> 563 results = schedule(dsk, keys, **kwargs)
564 return repack([f(r, *a) for r, (f, a) in zip(results, postcomputes)])
565
/opt/conda/lib/python3.8/site-packages/distributed/client.py in get(self, dsk, keys, workers, allow_other_workers, resources, sync, asynchronous, direct, retries, priority, fifo_timeout, actors, **kwargs)
2653 should_rejoin = False
2654 try:
-> 2655 results = self.gather(packed, asynchronous=asynchronous, direct=direct)
2656 finally:
2657 for f in futures.values():
/opt/conda/lib/python3.8/site-packages/distributed/client.py in gather(self, futures, errors, direct, asynchronous)
1962 else:
1963 local_worker = None
-> 1964 return self.sync(
1965 self._gather,
1966 futures,
/opt/conda/lib/python3.8/site-packages/distributed/client.py in sync(self, func, asynchronous, callback_timeout, *args, **kwargs)
836 return future
837 else:
--> 838 return sync(
839 self.loop, func, *args, callback_timeout=callback_timeout, **kwargs
840 )
/opt/conda/lib/python3.8/site-packages/distributed/utils.py in sync(loop, func, callback_timeout, *args, **kwargs)
338 if error[0]:
339 typ, exc, tb = error[0]
--> 340 raise exc.with_traceback(tb)
341 else:
342 return result[0]
/opt/conda/lib/python3.8/site-packages/distributed/utils.py in f()
322 if callback_timeout is not None:
323 future = asyncio.wait_for(future, callback_timeout)
--> 324 result[0] = yield future
325 except Exception as exc:
326 error[0] = sys.exc_info()
/opt/conda/lib/python3.8/site-packages/tornado/gen.py in run(self)
760
761 try:
--> 762 value = future.result()
763 except Exception:
764 exc_info = sys.exc_info()
/opt/conda/lib/python3.8/site-packages/distributed/client.py in _gather(self, futures, errors, direct, local_worker)
1827 exc = CancelledError(key)
1828 else:
-> 1829 raise exception.with_traceback(traceback)
1830 raise exc
1831 if errors == "skip":
/opt/conda/lib/python3.8/site-packages/dask/optimization.py in __call__()
961 if not len(args) == len(self.inkeys):
962 raise ValueError("Expected %d args, got %d" % (len(self.inkeys), len(args)))
--> 963 return core.get(self.dsk, self.outkey, dict(zip(self.inkeys, args)))
964
965 def __reduce__(self):
/opt/conda/lib/python3.8/site-packages/dask/core.py in get()
149 for key in toposort(dsk):
150 task = dsk[key]
--> 151 result = _execute_task(task, cache)
152 cache[key] = result
153 result = _execute_task(out, cache)
/opt/conda/lib/python3.8/site-packages/dask/core.py in _execute_task()
119 # temporaries by their reference count and can execute certain
120 # operations in-place.
--> 121 return func(*(_execute_task(a, cache) for a in args))
122 elif not ishashable(arg):
123 return arg
/opt/conda/lib/python3.8/site-packages/dask/utils.py in apply()
33 def apply(func, args, kwargs=None):
34 if kwargs:
---> 35 return func(*args, **kwargs)
36 else:
37 return func(*args)
/opt/conda/lib/python3.8/site-packages/dask/dataframe/core.py in apply_and_enforce()
5474 return meta
5475 if is_dataframe_like(df):
-> 5476 check_matching_columns(meta, df)
5477 c = meta.columns
5478 else:
/opt/conda/lib/python3.8/site-packages/dask/dataframe/utils.py in check_matching_columns()
690 def check_matching_columns(meta, actual):
691 # Need nan_to_num otherwise nan comparison gives False
--> 692 if not np.array_equal(np.nan_to_num(meta.columns), np.nan_to_num(actual.columns)):
693 extra = methods.tolist(actual.columns.difference(meta.columns))
694 missing = methods.tolist(meta.columns.difference(actual.columns))
/opt/conda/lib/python3.8/site-packages/pandas/core/generic.py in __getattr__()
5268 or name in self._accessors
5269 ):
-> 5270 return object.__getattribute__(self, name)
5271 else:
5272 if self._info_axis._can_hold_identifiers_and_holds_name(name):
pandas/_libs/properties.pyx in pandas._libs.properties.AxisProperty.__get__()
/opt/conda/lib/python3.8/site-packages/pandas/core/generic.py in __getattr__()
5268 or name in self._accessors
5269 ):
-> 5270 return object.__getattribute__(self, name)
5271 else:
5272 if self._info_axis._can_hold_identifiers_and_holds_name(name):
AttributeError: 'DataFrame' object has no attribute '_data'
The version of Pandas in my docker file is 1.0.1, so I already try upgrading Pandas (to version 1.2.2), but it didn't work, what am I doing wrong?
My guess is that you have a version mismatch somewhere. What does client.get_versions(check=True) say?
I am using Koalas and I want to change the value of a column based on a condition.
In pandas I can do that using:
import pandas as pd
df_test = pd.DataFrame({
'a': [1,2,3]
,'b': ['one','two','three']})
df_test2 = pd.DataFrame({
'c': [2,1,3]
,'d': ['one','two','three']})
df_test.loc[df_test.a.isin(df_test2['c']),'b'] = 'four'
df_test.head()
a b
0 1 four
1 2 four
2 3 four
I am trying to use the same in Koalas, but I have this error:
---------------------------------------------------------------------------
PandasNotImplementedError Traceback (most recent call last)
<ipython-input-15-814219258adb> in <module>
5 new_loans['write_offs'] = 0
6
----> 7 new_loans.loc[(new_loans['ID'].isin(userinput_write_offs['id'])),'write_offs'] = 1
8 new_loans.loc[new_loans['write_offs']==1,'is_active'] = 0
9 new_loans = new_loans.sort_values(by = ['ZOHOID','Disb Date'])
/usr/local/lib/python3.7/dist-packages/databricks/koalas/base.py in isin(self, values)
894 )
895
--> 896 return self._with_new_scol(self.spark.column.isin(list(values)))
897
898 def isnull(self) -> Union["Series", "Index"]:
/usr/local/lib/python3.7/dist-packages/databricks/koalas/series.py in __iter__(self)
5871
5872 def __iter__(self):
-> 5873 return MissingPandasLikeSeries.__iter__(self)
5874
5875 if sys.version_info >= (3, 7):
/usr/local/lib/python3.7/dist-packages/databricks/koalas/missing/__init__.py in unsupported_function(*args, **kwargs)
21 def unsupported_function(*args, **kwargs):
22 raise PandasNotImplementedError(
---> 23 class_name=class_name, method_name=method_name, reason=reason
24 )
25
PandasNotImplementedError: The method `pd.Series.__iter__()` is not implemented. If you want to collect your data as an NumPy array, use 'to_numpy()' instead.
How could I do the same operation in Koalas?
UPDATE
Following this question: Assign Koalas Column from Numpy Result I have done:
df_test.loc[df_test.a.isin(df_test2['c'].to_list()),'b'] = 'four'
But now I have this error:
---------------------------------------------------------------------------
PythonException Traceback (most recent call last)
/usr/local/lib/python3.7/dist-packages/IPython/core/formatters.py in __call__(self, obj)
700 type_pprinters=self.type_printers,
701 deferred_pprinters=self.deferred_printers)
--> 702 printer.pretty(obj)
703 printer.flush()
704 return stream.getvalue()
/usr/local/lib/python3.7/dist-packages/IPython/lib/pretty.py in pretty(self, obj)
392 if cls is not object \
393 and callable(cls.__dict__.get('__repr__')):
--> 394 return _repr_pprint(obj, self, cycle)
395
396 return _default_pprint(obj, self, cycle)
/usr/local/lib/python3.7/dist-packages/IPython/lib/pretty.py in _repr_pprint(obj, p, cycle)
698 """A pprint that just redirects to the normal repr function."""
699 # Find newlines and replace them with p.break_()
--> 700 output = repr(obj)
701 lines = output.splitlines()
702 with p.group():
/usr/local/lib/python3.7/dist-packages/databricks/koalas/frame.py in __repr__(self)
10614 return self._to_internal_pandas().to_string()
10615
> 10616 pdf = self._get_or_create_repr_pandas_cache(max_display_count)
10617 pdf_length = len(pdf)
10618 pdf = pdf.iloc[:max_display_count]
/usr/local/lib/python3.7/dist-packages/databricks/koalas/frame.py in _get_or_create_repr_pandas_cache(self, n)
10606 def _get_or_create_repr_pandas_cache(self, n):
10607 if not hasattr(self, "_repr_pandas_cache") or n not in self._repr_pandas_cache:
> 10608 self._repr_pandas_cache = {n: self.head(n + 1)._to_internal_pandas()}
10609 return self._repr_pandas_cache[n]
10610
/usr/local/lib/python3.7/dist-packages/databricks/koalas/frame.py in _to_internal_pandas(self)
10602 This method is for internal use only.
10603 """
> 10604 return self._internal.to_pandas_frame
10605
10606 def _get_or_create_repr_pandas_cache(self, n):
/usr/local/lib/python3.7/dist-packages/databricks/koalas/utils.py in wrapped_lazy_property(self)
514 def wrapped_lazy_property(self):
515 if not hasattr(self, attr_name):
--> 516 setattr(self, attr_name, fn(self))
517 return getattr(self, attr_name)
518
/usr/local/lib/python3.7/dist-packages/databricks/koalas/internal.py in to_pandas_frame(self)
807 """ Return as pandas DataFrame. """
808 sdf = self.to_internal_spark_frame
--> 809 pdf = sdf.toPandas()
810 if len(pdf) == 0 and len(sdf.schema) > 0:
811 pdf = pdf.astype(
/usr/local/spark/python/pyspark/sql/pandas/conversion.py in toPandas(self)
136
137 # Below is toPandas without Arrow optimization.
--> 138 pdf = pd.DataFrame.from_records(self.collect(), columns=self.columns)
139 column_counter = Counter(self.columns)
140
/usr/local/spark/python/pyspark/sql/dataframe.py in collect(self)
594 """
595 with SCCallSiteSync(self._sc) as css:
--> 596 sock_info = self._jdf.collectToPython()
597 return list(_load_from_socket(sock_info, BatchedSerializer(PickleSerializer())))
598
/usr/local/lib/python3.7/dist-packages/py4j/java_gateway.py in __call__(self, *args)
1303 answer = self.gateway_client.send_command(command)
1304 return_value = get_return_value(
-> 1305 answer, self.gateway_client, self.target_id, self.name)
1306
1307 for temp_arg in temp_args:
/usr/local/spark/python/pyspark/sql/utils.py in deco(*a, **kw)
132 # Hide where the exception came from that shows a non-Pythonic
133 # JVM exception message.
--> 134 raise_from(converted)
135 else:
136 raise
/usr/local/spark/python/pyspark/sql/utils.py in raise_from(e)
PythonException:
An exception was thrown from the Python worker. Please see the stack trace below.
Traceback (most recent call last):
File "/opt/spark/python/lib/pyspark.zip/pyspark/worker.py", line 589, in main
func, profiler, deserializer, serializer = read_udfs(pickleSer, infile, eval_type)
File "/opt/spark/python/lib/pyspark.zip/pyspark/worker.py", line 447, in read_udfs
udfs.append(read_single_udf(pickleSer, infile, eval_type, runner_conf, udf_index=i))
File "/opt/spark/python/lib/pyspark.zip/pyspark/worker.py", line 254, in read_single_udf
f, return_type = read_command(pickleSer, infile)
File "/opt/spark/python/lib/pyspark.zip/pyspark/worker.py", line 74, in read_command
command = serializer._read_with_length(file)
File "/opt/spark/python/lib/pyspark.zip/pyspark/serializers.py", line 172, in _read_with_length
return self.loads(obj)
File "/opt/spark/python/lib/pyspark.zip/pyspark/serializers.py", line 458, in loads
return pickle.loads(obj, encoding=encoding)
File "/opt/spark/python/lib/pyspark.zip/pyspark/cloudpickle.py", line 1110, in subimport
__import__(name)
ModuleNotFoundError: No module named 'pandas'
Why is trying to use pandas?
Koalas package exposes Pandas Like APIs on high level for the users but under the hood implementation is done using PySpark APIs.
I observed that within the stack track log you have pasted, a pandas dataframe is being created from sdf spark Dataframe using toPandas() method and assigned to pdf.
In the implementation of toPandas() function, pandas and numpy are being imported.
check line numbers 809 & 138.
/usr/local/lib/python3.7/dist-packages/databricks/koalas/internal.py in to_pandas_frame(self)
807 """ Return as pandas DataFrame. """
808 sdf = self.to_internal_spark_frame
--> 809 pdf = sdf.toPandas()
810 if len(pdf) == 0 and len(sdf.schema) > 0:
811 pdf = pdf.astype(
/usr/local/spark/python/pyspark/sql/pandas/conversion.py in toPandas(self)
136
137 # Below is toPandas without Arrow optimization.
--> 138 pdf = pd.DataFrame.from_records(self.collect(), columns=self.columns)
139 column_counter = Counter(self.columns)
140
/usr/local/spark/python/pyspark/sql/dataframe.py in collect(self)
594 """
595 with SCCallSiteSync(self._sc) as css:
--> 596 sock_info = self._jdf.collectToPython()
597 return list(_load_from_socket(sock_info, BatchedSerializer(PickleSerializer())))
598
you can check out the implementation of toPandas() function at the following link:
https://github.com/apache/spark/blob/master/python/pyspark/sql/pandas/conversion.py
I am trying to pass a simple variable (string, list whatever I can get working) in to sql (using jaydebapi to AWS Redshift cluster.
The python/pandas code looks like this at moment. I think the %s is part of the problem:
id = (261894)
df = pd.read_sql_query(
'''
select * from purchases where customer_id = %s
''',
conn, params=[id])
exception is
ava.sql.SQLExceptionPyRaisable Traceback (most recent call last)
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in execute(self, *args, **kwargs)
1377 else:
-> 1378 cur.execute(*args)
1379 return cur
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in execute(self, operation, parameters)
497 self._close_last()
--> 498 self._prep = self._connection.jconn.prepareStatement(operation)
499 self._set_stmt_parms(self._prep, parameters)
java.sql.SQLExceptionPyRaisable: java.sql.SQLException: [Amazon](500310) Invalid operation: syntax error at or near "%"
Position: 70;
During handling of the above exception, another exception occurred:
java.sql.SQLExceptionPyRaisable Traceback (most recent call last)
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in rollback(self)
416 try:
--> 417 self.jconn.rollback()
418 except:
java.sql.SQLExceptionPyRaisable: java.sql.SQLException: [Amazon][JDBC](11680) Cannot use rollback while Connection is in auto-commit mode.
During handling of the above exception, another exception occurred:
DatabaseError Traceback (most recent call last)
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in execute(self, *args, **kwargs)
1381 try:
-> 1382 self.con.rollback()
1383 except Exception: # pragma: no cover
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in rollback(self)
418 except:
--> 419 _handle_sql_exception()
420
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in _handle_sql_exception_jpype()
155 exc_type = InterfaceError
--> 156 reraise(exc_type, exc_info[1], exc_info[2])
157
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in reraise(tp, value, tb)
56 if tb:
---> 57 raise value.with_traceback(tb)
58 raise value
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in rollback(self)
416 try:
--> 417 self.jconn.rollback()
418 except:
DatabaseError: java.sql.SQLException: [Amazon][JDBC](11680) Cannot use rollback while Connection is in auto-commit mode.
During handling of the above exception, another exception occurred:
DatabaseError Traceback (most recent call last)
in
5 select * from purchases where customer_id = %s
6 ''',
----> 7 conn, params=[id])
8
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in read_sql_query(sql, con, index_col, coerce_float, params, parse_dates, chunksize)
312 return pandas_sql.read_query(
313 sql, index_col=index_col, params=params, coerce_float=coerce_float,
--> 314 parse_dates=parse_dates, chunksize=chunksize)
315
316
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in read_query(self, sql, index_col, coerce_float, params, parse_dates, chunksize)
1411
1412 args = _convert_params(sql, params)
-> 1413 cursor = self.execute(*args)
1414 columns = [col_desc[0] for col_desc in cursor.description]
1415
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in execute(self, *args, **kwargs)
1384 ex = DatabaseError("Execution failed on sql: %s\n%s\nunable"
1385 " to rollback" % (args[0], exc))
-> 1386 raise_with_traceback(ex)
1387
1388 ex = DatabaseError(
C:\ProgramData\Anaconda3\lib\site-packages\pandas\compat\__init__.py in raise_with_traceback(exc, traceback)
402 if traceback == Ellipsis:
403 _, _, traceback = sys.exc_info()
--> 404 raise exc.with_traceback(traceback)
405 else:
406 # this version of raise is a syntax error in Python 3
C:\ProgramData\Anaconda3\lib\site-packages\pandas\io\sql.py in execute(self, *args, **kwargs)
1380 except Exception as exc:
1381 try:
-> 1382 self.con.rollback()
1383 except Exception: # pragma: no cover
1384 ex = DatabaseError("Execution failed on sql: %s\n%s\nunable"
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in rollback(self)
417 self.jconn.rollback()
418 except:
--> 419 _handle_sql_exception()
420
421 def cursor(self):
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in _handle_sql_exception_jpype()
154 else:
155 exc_type = InterfaceError
--> 156 reraise(exc_type, exc_info[1], exc_info[2])
157
158 def _jdbc_connect_jpype(jclassname, url, driver_args, jars, libs):
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in reraise(tp, value, tb)
55 value = tp(value)
56 if tb:
---> 57 raise value.with_traceback(tb)
58 raise value
59
C:\ProgramData\Anaconda3\lib\site-packages\jaydebeapi\__init__.py in rollback(self)
415 def rollback(self):
416 try:
--> 417 self.jconn.rollback()
418 except:
419 _handle_sql_exception()
DatabaseError: Execution failed on sql:
select * from purchases where customer_id = %s
java.sql.SQLException: [Amazon](500310) Invalid operation: syntax error at or near "%"
Position: 70;
unable to rollback
[39]
id = (261894)
[44]
Any thoughts on how I can get this to work? Do I need an alternative to %s?
try this:
id = (261894)
df = pd.read_sql_query( ''' select * from purchases where customer_id = ? ''', conn, params=[id])
it should work
I am trying to print a RDD using Spark in Ipython and when I do that I get this error:
---------------------------------------------------------------------------
Py4JJavaError Traceback (most recent call last)
<ipython-input-4-77015cd18335> in <module>()
---> 24 print inputData.collect()
25
26
/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/pyspark/rdd.pyc in collect(self)
771 """
772 with SCCallSiteSync(self.context) as css:
--> 773 port = self.ctx._jvm.PythonRDD.collectAndServe(self._jrdd.rdd())
774 return list(_load_from_socket(port, self._jrdd_deserializer))
775
/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/py4j-0.8.2.1-src.zip/py4j/java_gateway.py in __call__(self, *args)
536 answer = self.gateway_client.send_command(command)
537 return_value = get_return_value(answer, self.gateway_client,
--> 538 self.target_id, self.name)
539
540 for temp_arg in temp_args:
/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/pyspark/sql/utils.pyc in deco(*a, **kw)
34 def deco(*a, **kw):
35 try:
---> 36 return f(*a, **kw)
37 except py4j.protocol.Py4JJavaError as e:
38 s = e.java_exception.toString()
/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/py4j-0.8.2.1-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
298 raise Py4JJavaError(
299 'An error occurred while calling {0}{1}{2}.\n'.
--> 300 format(target_id, '.', name), value)
301 else:
302 raise Py4JError(
Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.collectAndServe.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 7.0 failed 1 times, most recent failure: Lost task 0.0 in stage 7.0 (TID 56, localhost): org.apache.spark.api.python.PythonException: Traceback (most recent call last):
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/worker.py", line 98, in main
command = pickleSer._read_with_length(infile)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 164, in _read_with_length
return self.loads(obj)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 421, in loads
return pickle.loads(obj)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/mllib/__init__.py", line 25, in <module>
ImportError: No module named numpy
at org.apache.spark.api.python.PythonRDD$$anon$1.read(PythonRDD.scala:138)
at org.apache.spark.api.python.PythonRDD$$anon$1.<init>(PythonRDD.scala:179)
at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:97)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1280)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1268)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1267)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1267)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:697)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:697)
at scala.Option.foreach(Option.scala:236)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:697)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1493)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1455)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1444)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:567)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1813)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1826)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1839)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1910)
at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:905)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:147)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:108)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:306)
at org.apache.spark.rdd.RDD.collect(RDD.scala:904)
at org.apache.spark.api.python.PythonRDD$.collectAndServe(PythonRDD.scala:373)
at org.apache.spark.api.python.PythonRDD.collectAndServe(PythonRDD.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:231)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:379)
at py4j.Gateway.invoke(Gateway.java:259)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:133)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:207)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.api.python.PythonException: Traceback (most recent call last):
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/worker.py", line 98, in main
command = pickleSer._read_with_length(infile)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 164, in _read_with_length
return self.loads(obj)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/serializers.py", line 421, in loads
return pickle.loads(obj)
File "/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip/pyspark/mllib/__init__.py", line 25, in <module>
ImportError: No module named numpy
at org.apache.spark.api.python.PythonRDD$$anon$1.read(PythonRDD.scala:138)
at org.apache.spark.api.python.PythonRDD$$anon$1.<init>(PythonRDD.scala:179)
at org.apache.spark.api.python.PythonRDD.compute(PythonRDD.scala:97)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:264)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)
at org.apache.spark.scheduler.Task.run(Task.scala:88)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
... 1 more
My current code is:
from pyspark.mllib.regression import LabeledPoint
from pyspark.mllib.tree import DecisionTree, DecisionTreeModel
from pyspark.mllib.util import MLUtils
import os.path
import numpy as np
print np.version.version
def extract(line):
return (line[1])
inputPath = os.path.join('file1.csv')
fileName = os.path.join(inputPath)
Data = sc.textFile(fileName).zipWithIndex().filter(lambda (line,rownum): rownum>0).map(lambda (line, rownum): line)
inputData = (Data
.map(lambda line: line.split(";"))
.filter(lambda line: len(line) >1 )
.map(extract)) # Map to tuples
# error comes a this line
print inputData.collect()
I have numpy already installed (sudo apt-get install python-numpy) and can print numpy version in Ipython using numpy.version.version
Why is this error coming and how to resolve it?
NOTE 1: My current bash_profile:
# Set the Spark Home as an environment variable.
export SPARK_HOME="$HOME/spark-1.5.0-bin-hadoop2.6"
# Define your Spark arguments for when running Spark.
export PYSPARK_SUBMIT_ARGS="--master local[2]"
# IPython alias for the use with SPARK.
alias IPYSPARK='PYSPARK_DRIVER_PYTHON=ipython PYSPARK_DRIVER_PYTHON_OPTS="notebook --profile=pyspark --ip=0.0.0.0" $SPARK_HOME/bin/pyspark'
I have also added following to my spark-env.sh.template file:
#!/usr/bin/env bash
# This file is sourced when running various Spark programs.
export PYSPARK_PYTHON=/usr/bin/python2.7
export PYSPARK_DRIVER_PYTHON=/usr/bin/ipython
NOTE 2: I am launching the Ipython notebook from inside a virtual environment.
NOTE 3: I have Spark 1.5.0 and numpy 1.8.2
UPDATE: output from sc.parallelize([],1).mapPartitions(lambda _: [(sys.executable, sys.path)]).first()
('/home/vagrant/pyEnv/bin/python2.7', ['', u'/tmp/spark-dbbcfd0b-413e-4406-8bd5-37de29d3fcc5/userFiles-6296ba2d-4ec5-4956-9904-828bda0c6424', '/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/pyspark.zip', '/home/vagrant/spark-1.5.0-bin-hadoop2.6/python/lib/py4j-0.8.2.1-src.zip', '/home/vagrant/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar', '/home/vagrant/spark-1.5.0-bin-hadoop2.6/python', '/home/vagrant', '/home/vagrant/pyEnv/lib/python2.7', '/home/vagrant/pyEnv/lib/python2.7/plat-x86_64-linux-gnu', '/home/vagrant/pyEnv/lib/python2.7/lib-tk', '/home/vagrant/pyEnv/lib/python2.7/lib-old', '/home/vagrant/pyEnv/lib/python2.7/lib-dynload', '/usr/lib/python2.7', '/usr/lib/python2.7/plat-x86_64-linux-gnu', '/usr/lib/python2.7/lib-tk', '/home/vagrant/pyEnv/local/lib/python2.7/site-packages', '/home/vagrant/pyEnv/lib/python2.7/site-packages'])