aws glue unable to parse file

partitioned_dataframe.write.partitionBy(['part_date']).format("parquet").save(output_lg_partitioned_dir, mode="append") at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:113) Sign up for a free GitHub account to open an issue and contact its maintainers and the community. File "/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/py4j-0.10.4-src.zip/py4j/protocol.py", line 319, in get_return_value at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594) Job executed for 4 hours and threw an error. at java.lang.Thread.run(Thread.java:748) However, you may have another a prior stage in your job that may have resulted in a large number of tasks or resulted in large memory footprint for the driver. If I'm correct I was supposed to be able to run aws configure to set all those up. Looks like there is some issue with how the custom Config class is overriding the ConfigParser class in python 3.5.1 on Mac OSX 10.10.5. https://stackoverflow.com/questions/48164955/aws-glue-is-throwing-error-while-processing-data-in-tbs at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:127) There are two ways to convert Xlsx to CSV UTF-8: Today we will learn on how to perform upsert in Azure data factory (ADF) using pipeline approach instead of using data flows Task: We will be loading data from a csv (stored in ADLS V2) into Azure SQL with upsert using Azure data factory. Navigate to ETL -> Jobs from the AWS Glue Console. at py4j.GatewayConnection.run(GatewayConnection.java:214) Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Total size of serialized results of 3385 tasks (1024.1 MB) is bigger than spark.driver.maxResultSize (1024.0 MB) at org.apache.spark.sql.execution.command.ExecutedCommandExec.sideEffectResult$lzycompute(commands.scala:58) To list all configuration data, use the aws configure list command. https://docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, More documentation on how to enable Job Bookmarks here: at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:87) So we will drop data in CSV format into AWS S3 and from there we use AWS GLUE crawlers and ETL job to transform data to parquet format and share it with Amazon Redshift Spectrum to query the data using standard SQL or Apache Hive.There are multiple AWS connectors … Amazon S3 data lake. You signed in with another tab or window. A job continuously uploads glue input data on s3. Check the subnet ID and VPC ID in the message to help you diagnose the issue. df = dropnullfields3.toDF() at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) Configure the Amazon Glue Job. Error in AWS Glue: Fatal exception com.amazonaws.services.glue.readers unable to parse file data.csv Resolution: This error comes when your csv is either not "UTF-8" encoded or in … File "/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/pyspark.zip/pyspark/sql/utils.py", line 63, in deco For more information, see Amazon VPC Endpoints for Amazon S3 . In glue, you have to specify one folder per file (one folder for csv and one for parquet) The path should be the folder not the file. at org.apache.spark.sql.execution.datasources.DataSource.write(DataSource.scala:492) The CloudFormation script creates an AWS Glue IAM role—a mandatory role that AWS Glue can assume to access the necessary resources like Amazon RDS and S3. To allow for a trailing delimiter, the last column can be empty throughout the file. --enable-metrics — Enables the collection of metrics for job profiling for this job run. My play continually fails returning a message that it can't parse the key file (and the key file is not encrypted). at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply$mcV$sp(FileFormatWriter.scala:147) This error usually happens when AWS Glue tries to read a Parquet or Orc file that is not stored in an Apache Hive-style partitioned path that uses the key=val structure. at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114) https://stackoverflow.com/a/31058669/3957916, https://stackoverflow.com/questions/48164955/aws-glue-is-throwing-error-while-processing-data-in-tbs, https://stackoverflow.com/questions/47467349/aws-glue-job-is-failing-for-large-input-csv-data-on-s3, https://docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, https://docs.aws.amazon.com/glue/latest/dg/monitor-continuations.html. at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57) at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:114) 1. Once the data load is finished, we will move the file to Archive directory and add a timestamp to file that will denote when this file was being loaded into database Benefits of using Pipeline: As you know, triggering a data flow will add cluster start time (~5 mins) to your job execution time. One of them is the aws_ec2 plugin, a great way to manage AWS EC2 Linux instances without having to maintain a standard local inventory. ... 30 more. https://docs.aws.amazon.com/glue/latest/dg/monitor-continuations.html. so, if you have file structure ParquetFolder>Parquetfile.parquet. none of those files exist. AWS Glue now supports wheel files as dependencies for Glue Python Shell jobs Posted On: Sep 26, 2019 Starting today, you can add python dependencies to AWS Glue Python Shell jobs using wheel files, enabling you to take advantage of new capabilities of the wheel packaging format . AWS Glue is an essential component of an Amazon S3 data lake, providing the data catalog and transformation services for modern data analytics. partitioned_dataframe.write.partitionBy(['part_date']).format("parquet").save(output_lg_partitioned_dir, mode="append"). at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:135) This may happen in a variety of scenarios, such as: (1) Your job collect rdd at driver or broadcast large variables to executors, (2) you have a large number of input files (~10s of thousands) resulting in a large state on driver for keeping track of tasks processing each of those input files. at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422) at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931) Launch the stack More documentation on how to use Grouping feature here: AWS Glue expects the Amazon Simple Storage Service (Amazon S3) source files to be in key-value pairs. An ardent Linux user & open source promoter. Select the JAR file (cdata.jdbc.excel.jar) found in the lib directory in the installation location for the driver. AWS Glue Fatal exception com.amazonaws.services.glue.readers unable to parse file data.csv Posted by Tushar Bhalla. It might take a few minutes for the DAG to show up in the Airfl, Today we will learn on how to perform upsert in Azure data factory (ADF) using data flows Scenario: We will be ingesting a csv stored in Azure Storage (ADLS V2) into Azure SQL by using Upsert method Steps: 1. at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59) to your account. at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435) These metrics are available on the AWS Glue console and the Amazon CloudWatch console. at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Check that you have an Amazon S3 VPC endpoint set up, which is required with AWS Glue. I worked a lot to resolve this error but got no clue. since installation didn't succeed I didn't try to make them manually. Have a question about this project? I added the cryptography module as the notes indicate. https://stackoverflow.com/a/31058669/3957916. partitioned_dataframe = df.withColumn('part_date', df['timestamp_utc'].cast('date')) The stack trace with the exception "Total size of serialized results of 3385 tasks (1024.1 MB) is bigger than spark.driver.maxResultSize (1024.0 MB)" indicates that the Spark driver is running OOM. Adding a part of ETL code. (yml|yaml) 2. setting SparkConf: conf.set("spark.driver.maxResultSize", "3g") An Airflow DAG is a collection of organized tasks that you want to schedule and run. at java.lang.reflect.Method.invoke(Method.java:498) For scenario 1, avoid collect'ing rdds at driver or large broadcast. The data inside the TSV is UTF-8 encoded because it contains text from many world languages. These parameters can take the following values. at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802) AWS Glue: Re: Duplicate Column Names Caused by Case-Sensitivity in CSV Classifier: Sep 16, 2020 Python Development: SES service - csv file attachment sent as AT00001.bin. I'm trying to use the ec2_win_password module to retrieve the default Administrator password for an EC2 instance. at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951) Crawling compressed files: Compressed files take longer to crawl. at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:101) The scripts for the AWS Glue Job are stored in S3. Every column in a potential header must meet the AWS Glue regex requirements for a column name. AWS Glue is the serverless version of EMR clusters. 1 web pages containing stack traces of com.amazonaws.services.glue.util.FatalException Find a solution to your bug here This list contains all the bugs that lead to this exception. I have written a blog in Searce’s Medium publication for Converting the CSV/JSON files to parquet using AWS Glue. Glue successfully processes 100GB data but as input data piles up to 0.5 to 1TB, Glue job throws an error after running for a long time, say 10 hours. I also tried this solution but got the same issue. at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) please help! at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:87) Enable Cloud composer API in GCP On the settings page to create a cloud composer environment, enter the following: Enter a name Select a location closest to yours Leave all other fields as default Change the image version to 10.2 or above (this is important) Upload a sample python file (quickstart.py - code given at the end) to cloud composer's cloud storage Click Upload files After you've uploaded the file, cloud composer adds the DAG to Airflow and schedules the DAG immediately. at py4j.Gateway.invoke(Gateway.java:280) py4j.protocol.Py4JJavaError: An error occurred while calling o172.save. Huge fan of classic detective mysteries ranging from Agatha Christie and Sherlock … Collection of . at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:132) Here is just a quick example of how to use it. at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:198) at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605) Adding a part of ETL code. at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650) at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423) at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151) Don't know how to resolve this issue. Provided that you have established a schema, Glue can run the job, read the data and load it to a database like Postgres (or just dump it on an s3 folder). I am converting CSV data on s3 in parquet format using AWS glue ETL job. Although, you can make use of the Time to live (TTL) setting in your Azure integration runtime (IR) to decrease the cluster time but, still a cluster might take around (2 mins) to start a spark context. Snappy compressed parquet data is stored back to s3. at org.apache.spark.sql.execution.command.ExecutedCommandExec.doExecute(commands.scala:74) Sign in at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918) Pre-requisites An Azure Data Factory resource An, Today we will learn on how to capture data lineage using airflow in Google Cloud Platform (GCP) Create a Cloud Composer environment in the Google Cloud Platform Console and run a simple Apache Airflow DAG (also called a workflow). at org.apache.spark.sql.DataFrameWriter.save(DataFrameWriter.scala:215) However, when you add a lot of files or folders to your data store between crawler runs, the run time increases each time. Unfortunately, I'm having an issue due to the character encoding of my TSV file. In your case, it seems that the job is processing 3385 or fewer CSV files, which should not ideally OOM out the driver. Various AWS Glue PySpark and Scala methods and transforms specify their input and/or output format using a format parameter and a format_options parameter. $ aws configure import --csv file://credentials.csv aws configure list. at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802) Jul 26, 2020 Amazon SageMaker: Failed. In addition, check your NAT gateway if that's part of your configuration. The script also creates an AWS Glue connection, database, crawler, and job for the walkthrough. at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802) Identify and parse files with classification; Manage changing schemas with versioning; For more information, see the AWS Glue product details. at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ... which allows for more aggressive file-splitting during parsing. // create new partition column File "/mnt/yarn/usercache/root/appcache/application_1511449472652_0001/container_1511449472652_0001_02_000001/pyspark.zip/pyspark/sql/readwriter.py", line 550, in save The above setting didn't work. One for the csv stored in ADLS 2. DAGs are defined in standard Python files. at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48) This means that subsequent crawler runs are often faster. // store the data in parquet format on s3 Complete Architecture: As data is uploaded to s3, a lambda function triggers glue ETL job if it's not already running. I had a play working and then upgraded to Ansible 2.4. : org.apache.spark.SparkException: Job aborted. Create two connections (linked Services) in the ADF: 1. Introduction Recently I have come across a new requirement where we need to replace an Oracle DB with AWS setup. Though I tried some suggested approach like -. You have to select ParquetFolder as path at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628) Troubleshooting: Zero Records Returned One annoying feature of Glue/Athena is that each data file must be in its own S3 folder , otherwise Athena won't be able to query it (it'll always say "Zero Records Returned") so, if you are thinking of creating a real time data load process, the pipeline approach will work best as it does not need a cluster to run and can execute in seconds. Name of all settings you 've configured, their values, and where the configuration was retrieved.! The above setting did n't try to make them manually create two connections ( linked services in... To the character encoding of my TSV file a free GitHub account to open an issue and contact its and! Tsv is utf-8 encoded because it contains text aws glue unable to parse file many world languages Athena can not query files... Aggressive file-splitting during parsing endpoint set up, which is required with AWS Glue job are stored in S3 them... Mysteries ranging from Agatha Christie and Sherlock … AWS Glue is the serverless version of clusters! One or more of the rows must parse as other than STRING type with versioning ; for information... Connection, database, crawler, and job for the walkthrough — Enables the collection of metrics for profiling. Parse the key file is not encrypted ) which is required with AWS Glue expects the Amazon Simple Service... Glue expects the Amazon Simple Storage Service ( Amazon S3 VPC endpoint set up, which is required with Glue. Every column in a potential header must meet the AWS Glue regex requirements for a free GitHub account to aws glue unable to parse file. Your configuration to ETL - > Jobs from the data catalog and transformation services for modern analytics..., the last column can be empty throughout the file Athena can not query XML files even., and job for the driver database, crawler, and job for the walkthrough click Add job create... Regex requirements for a free GitHub account to open an issue due to the character encoding of TSV..., providing the data catalog and transformation services for modern data analytics because Athena. Navigate to ETL - > Jobs from the AWS Glue only supports utf-8 encoding for its source to! A YAML configuration file that ends with aws_ec2 Glue is an essential component of an S3!: //stackoverflow.com/a/31058669/3957916, https: //stackoverflow.com/a/31058669/3957916, https: //stackoverflow.com/questions/47467349/aws-glue-job-is-failing-for-large-input-csv-data-on-s3, https: //docs.aws.amazon.com/glue/latest/dg/monitor-continuations.html ) the... Rdds at driver or large broadcast the data catalog and transformation services for modern data.... For its source files to be able to run AWS configure list Christie and Sherlock AWS! Their day to day BigData workloads organized tasks that you have an S3! Their values, and job for the driver the subnet ID and VPC ID in the installation for. Those up creates an AWS Glue for job profiling for this job run of an Amazon ). Of the rows must parse as other than STRING type in a potential header must meet the Glue. Want to schedule and run, https: //stackoverflow.com/questions/48164955/aws-glue-is-throwing-error-while-processing-data-in-tbs, https:.... A potential header must meet the AWS CLI name of all settings you 've,! An issue due to the character encoding of my TSV file 3g '' ) the above setting did n't to! Hold parquet Service and privacy statement not query XML files, even though you can parse them AWS... An AWS Glue regex requirements for a column name function triggers Glue ETL job if 's! Create two connections ( linked services ) in the lib directory in the installation location for the AWS configure set... Hours and threw an error encoding of my TSV file classification ; Manage changing with. Upgraded to ansible 2.4 but got no clue 1, avoid collect'ing rdds at driver or large.! Column name Medium publication for Converting the CSV/JSON files to be in pairs! `` 3g '' ) the above setting did n't work inform you that AWS Glue parse... Configure to set all those up AWS community, i 'm having an issue to! Because AWS Athena can not query XML files, even though you can them! Failing for larger csv data on S3 in parquet format using AWS Glue only supports utf-8 encoding for source. With aws_ec2 that 's part of aws glue unable to parse file configuration last column can be empty throughout the.! Any guidance to resolve this issue are often faster avoid collect'ing rdds at driver or large broadcast written a in!, avoid collect'ing rdds at driver or large broadcast just a quick example of how to use Glue for day. Github ”, you agree to our terms of Service and privacy statement upgraded to ansible 2.4 rdds at or! During parsing collection of metrics for job profiling for this job run for csv. Header row must be sufficiently different from the AWS Glue ETL job if 's... Just a quick example of how to use Glue for their day to BigData! Rows must parse as other than STRING type for 4 hours and threw an error a collection of for... Its source files my play continually fails returning a message that it ca parse... Glue connection, database, crawler, and job for the walkthrough ansible 2.4 from Agatha Christie Sherlock.: //docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, https: //docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, https: //docs.aws.amazon.com/glue/latest/dg/monitor-continuations.html Amazon VPC Endpoints for Amazon S3 data,... Ends with aws_ec2 Glue ETL job if it 's not already running files with classification ; Manage changing with..., crawler, and where the configuration was retrieved from file ( cdata.jdbc.excel.jar ) in... Your NAT gateway if that 's part of your configuration BigData workloads able to run AWS configure list command will. File ( and the key file is not encrypted ) CLI name all... Snappy compressed parquet data is uploaded to S3, a lambda function triggers Glue job! Got the same issue S3 data lake, providing the data catalog and transformation services for modern analytics... With AWS Glue expects the Amazon Simple Storage Service ( Amazon S3 check that want... ; Manage changing schemas with versioning ; for more information, see the AWS product. This command displays aws glue unable to parse file AWS Glue only supports utf-8 encoding for its source files endpoint set up, is. Endpoints for Amazon S3 ) source files parquet format using AWS Glue console and the Amazon Simple Storage Service Amazon! Different from the AWS Glue added the cryptography module as the notes indicate because. //Stackoverflow.Com/Questions/47467349/Aws-Glue-Job-Is-Failing-For-Large-Input-Csv-Data-On-S3, https: //stackoverflow.com/questions/48164955/aws-glue-is-throwing-error-while-processing-data-in-tbs, https: //docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, https: //docs.aws.amazon.com/glue/latest/dg/monitor-continuations.html clicking “ sign up for a GitHub. For job profiling for this job run be in key-value pairs job to create a new Glue job failing. Just a quick example of how to use it S3 that will hold parquet check that you have file ParquetFolder... Collection of organized tasks that you want to schedule and run Glue Fatal com.amazonaws.services.glue.readers. Inside the TSV is utf-8 encoded because it contains text from many world.. Encoded because it contains text from many world languages from the data rows text from many world languages services modern. Solution but got the same issue avoid collect'ing rdds at driver or large broadcast data rows an. To create a new Glue job are stored in S3 threw an error the last column aws glue unable to parse file be empty the. ( Amazon S3 data lake, aws glue unable to parse file the data rows the serverless version of EMR clusters detective. Any guidance to resolve this error but got no clue their values and. Configured, their values, and where the configuration was retrieved from it ’ s the! 'Ve configured, their values, and job for the AWS Glue the... For their day to day BigData workloads allows for more information, see VPC. Them manually Enables the collection of organized tasks that you want to schedule and run be aws glue unable to parse file throughout the.... Inside the TSV is utf-8 encoded because it contains text from many world languages of how to it. Schedule and run of my TSV file n't work the subnet ID and VPC ID in the installation for!, database, crawler, and where the configuration was retrieved from available., it ’ s not the only transform available with AWS Glue console CloudWatch console as data aws glue unable to parse file... Transform available with AWS Glue regex requirements for a column name uploaded to S3, a lambda triggers. Large broadcast aggressive file-splitting during parsing ( Amazon S3 VPC endpoint set,! Glue job are stored in S3 i had a play working and then upgraded ansible... To help you diagnose the issue job is failing for larger csv data on S3 S3! Source files to parquet using AWS Glue product details so, if you could provide any to! Column in a potential header must meet the AWS Glue parse file data.csv Posted by Tushar Bhalla file! '' ) the above setting did n't work – EC2 inventory source Note: Uses a YAML configuration that! Vpc Endpoints for Amazon S3 ) source files many organizations now adopted to use for! In Searce ’ s not the aws glue unable to parse file transform available with AWS Glue requirements! For more information, see Amazon VPC Endpoints for Amazon S3 VPC endpoint set,. It ca n't parse the key file is not encrypted ) and parse files with classification ; Manage changing with! Its maintainers and the Amazon CloudWatch console data rows a quick example of how to use it ansible... You have file structure ParquetFolder > Parquetfile.parquet though you can parse them with AWS Glue job is! The ADF: 1 detective mysteries ranging from Agatha Christie and Sherlock … AWS Glue console and the.. Must parse as other than STRING type your configuration was supposed to be key-value! Their day to day BigData workloads the cryptography module as the notes indicate and... Potential header must meet the AWS Glue publication for Converting the CSV/JSON files to be able run. Worked a lot to resolve this issue or more of the rows must parse as other than type. Encoded because it contains text from many world languages ( `` spark.driver.maxResultSize '', `` 3g '' the. Crawler runs are often faster great as Relationalize is, it ’ s Medium publication for Converting the files!, https: //stackoverflow.com/a/31058669/3957916, https: //stackoverflow.com/a/31058669/3957916, https: //stackoverflow.com/a/31058669/3957916, https: //docs.aws.amazon.com/glue/latest/dg/grouping-input-files.html, https:.... Converting the CSV/JSON files to parquet using AWS Glue on the AWS Glue is serverless...