missing 'column' at 'partition athena
database (str, optional) â Glue/Athena catalog: Database name. The data is parsed only when you run the query. Because some columns have stats, but not all columns, the stats gathering scripts must have used something like for all indexed columns. Join The Startupâs +777K followers. Fetching the CommonPrefixes will avoid parsing through the entire S3 file structure thus making it faster and leaner. 1 To just create an empty table with schema only you can use WITH NO DATA (see CTAS reference).Such a query will not generate charges, as you do not scan any data. Thus I have updated the code to execute batches of 1000 partitions. First, if the data was accidentally added, you can remove the data files that cause the difference in schema, drop the partition, and re-crawl the data. Amazon Athena uses a managed Data Catalog to store information and schemas about the databases and tables that you create for your data stored in Amazon S3. After all the geeky coding comes the most easy part of click-click-run-done. Useful when you have columns with undetermined or mixed data types. When you run MSCK REPAIR TABLE or SHOW CREATE TABLE, Athena returns a ParseException error: 3. You must use ALTER TABLE to DROP the partitions if you really want them to go away. Problem Statement Amazon Athena uses a managed Data Catalog to store information and schemas about the databases and tables that you create for your data stored in ⦠AWS Glue allows database names with hyphens. Below youâll find some column labels (not necessarily all of them) that we need to apply in order to be able to write readable queries for our tables. Looping over the S3 structure by fetching CommonPrefixes and iterating over them again to fetch the inner partition list to have the final partition list. The last piece of code is encapsulated in an if..else block to check if the result set is empty to avoid triggering an empty query. MY TASK: Configure SAS Application to access AWS S3 bucket by using Athena jdbc/odbc driver . This example has 2 levels of partitions i.e. dtype (Dict[str, str], optional) â Dictionary of columns names and Athena/Glue types to be casted. When you run MSCK REPAIR TABLE or SHOW CREATE TABLE, Athena returns a ParseException error: To resolve this issue, recreate the database with a name that doesn't contain special characters other than underscore (_). Schedule a demo of Upsolver. 2. I have used the splitlines() method to separate the resultset into a list. There are a few ways to fix this issue. For now lets just understand that itâs the physical division of data in S3 similar to a folder structure in file system where the column on which the partition is created becomes the object (folder) under which the data set would be stored. Want to skip the coding in Spark/Hadoop and partition your data with just a few clicks? 2. Parameters can be hard coded inside the params or passed while running the Glue Job. # Create Alter Query for Athena if len(resultSet) != 0: queryString = "ALTER TABLE " + params['tableName'] + " ADD IF NOT EXISTS PARTITION(" + repr(resultSet) + ")" queryString = queryString.replace("{", "") queryString = queryString.replace("}", "") queryString = queryString.replace(",", ") PARTITION(") queryString = queryString.replace("'", "") queryString = queryString.replace("year=", "year='") queryString = queryString.replace("/", "', ") print("Alter Query String ⦠The above function is used to parse the S3 object structure to gather the partition list using the aws sdk list_objects_v2 method. Get smarter at building your thing. Medium is an open platform where 170 million readers come to find insightful and dynamic thinking. This is a mess and needs fixing. Create Alter Table query to Update Partitions in Athena. Still, the benefits of including the partition column in a secondary index can be significant. NOTE: I have created this script to add partition as current date +1(means tomorrowâs date). Write on Medium, args = getResolvedOptions(sys.argv, ['region', 'database', 'tableName', 'athenaResultBucket', 'athenaResultFolder', 's3Bucket', 's3Folder', 'timeout']), s3Client = boto3.client('s3', region_name=params['region']), #s3_filename = athena_to_s3(athenaClient, params), # Read Athena Query Result file and create a list of partitions present in athena meta, # Parse S3 folder structure and create partition list, # Compare Athena Partition List with S3 Partition List, https://github.com/gautam-shanbhag/AWS-Load-New-Partitions-Programmatically.git, API versioning and evolution with proxies, Tips for Storing Secrets with AWS SSM Parameter Store, Building a Fast and Reliable Reverse Proxy With YARP, Programmatic approach by running a simple, Passing parameters through ETL Job to set. In the following example, the database name is alb-database1. So for example, if weâre partitioning by day. Error 6766: Is a Directory Learn more, Follow the writers, publications, and topics that matter to you, and youâll see them on your homepage and in your inbox. However, constraint violations in SQL output do require an I/O request. Like the previous articles, our data is JSON data. In the scenario where partitions are not updated frequently, it would be best to run MSCK REPAIR TABLE to keep the schema in sync with complete dataset. Your one day is one table partition. For example, Apache Spark, Hive, Presto read partition metadata directly from Glue Data Catalog and do not support partition projection . One record per line: For our unpartitioned data, we placed the data files in our S3 bucket in a flat list of objects without any hierarchy. table (str, optional) â Glue/Athena catalog: Table name. However, it might be worth questioning your partitioning strategy. Please follow for more such easy and interesting write ups. By signing up, you will create a Medium account if you donât already have one. I believe in taking ownership of projects and proactively contributing towards the enhancement of the overall business solution. Partitioned columns don't exist within the table data itself, so if you use a column name that has the same name as a column in the table itself, you get an error. Currently working with Verizon Connect as a Big Data Engineer. Clients for connecting to AWS Athena and AWS S3. Tried below ways : Step -1 : Athena ODBC driver -- Failed ( SAS Says currently no plug-in available ) Step -2 : Athena JDBC driver -- Failed ( Proxy connectivity issue -- as we are connecting through proxy server ) This is a part which should be tweaked depending on your partition level. And lastly the cleanup()method is used to delete the temporary result file, Athena folder (and Bucket if required â uncomment the last line). Another way which I find to be more cost effective would be to have a python script to compare the Athena metadata with the S3 data structure and add the new partitions without having the overhead of scanning all the files in the bucket. This is the method that I am going to focus on in this article. In this article, we will look at the various approaches which help us achieve adding partitioning programmatically. To begin with, the basic commands to add a partition in the catalog are :MSCK REPAIR TABLEorALTER TABLE ADD PARTITION. That's correct. Parse S3 folder structure to fetch complete partition list, 4. If your table has defined partitions, the partitions might not yet be loaded into the AWS Glue Data Catalog or the internal Athena data catalog. Create an Athena "database" First you will need to create a database that Athena uses to access your data. Updated On : 02/March/2021 || Published On : 11/May/2020 || Version : 3, version 3 : Updated python script to ignore temp folders in s3 and batch execution on query due to athena query string limit, version 2 : Null check handling for athena and s3 partition list. The added test in that PR is for a table with a struct that has evolved with a new field that is not in an old partition. You need to explicitly add the partitions in metadata store. Thank you for reading till the end. The result set is a text file stored in temp S3 {bucket}.{folder}. You can use either of the above two approaches (direct calling or with function timeout). Function checks if bucket exists in S3 to store temporary Athena result set, if not we can create a temporary bucket using s3client or throw an error depending on the requirement. Explore, If you have a story to tell, knowledge to share, or a perspective to offer â welcome home. @zhenxiao I've run the tests from #4939 on this branch and it does not pass. âqueryStringâ failed to satisfy constraint: Member must have length less than or equal to 262144To overcome this scenario, it was better to run the partitions in batches. And you need to tell Glue those are also the partitions. After some experimentation, Athena will not drop references to objects deleted by S3 operations, or at least not immediately -- it's possible that "eventual consistency" will fix the problem at some point, but if you're expecting it to happen in the short term you need to do it yourself. Starting from a CSV file with a datetime column, I wanted to create an Athena table, partitioned by date. As per my usecase, I had to encapsulate the Athena query function with a timeout. With Athena the metadata actually resides in the AWS Glue Data Catalog and the physical data sits on S3. Hope you found it worthy. The term "partition" usually means a complete partition specification, i.e., you can construct a path into HDFS that contains data files (and not folders for the next level partition values). Partition key DATE_SID is not inside any index, because it is assume only one DATE_SID per partition. Athena creates metadata only when a table is created. One record per file. 2) Create external tables in Athena from the workflow for the files. For more information, see Partitioning Data . A basic google search led me to this page , but It was lacking some more detailing. Scan AWS Athena schema to identify partitions already stored in the metadata. Set subtraction of Athena partition list from S3 partition list would give us the list of newly created / missing partitions. The Parthenon Marbles (Greek: ÎλÏ
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ΠαÏθενÏνα), also known as the Elgin Marbles (/ Ë É l É¡ ɪ n /), are a collection of Classical Greek marble sculptures made under the supervision of the architect and sculptor Phidias and his assistants. It's still a database but data is stored in text files in S3 - I'm using Boto3 and Python to automate my infrastructure. Second, you can drop the individual partition and then run MSCK REPAIR within Athena to re-create the partition ⦠boto3 is the most widely used python library to connect and access AWS components. Till then Keep Smiling and Keep Coding âï¸ð !! Create a Glue job using the given script file and use a glue trigger to schedule the job using a cron expression or event trigger. Main Function for create the Athena Partition on daily. Here is a listing of that data in S3: With the above structure, we must use ALTER TABLEstatements in order to load each partition one-by-one into our Athena table. Partitions are logical entities in a metadata store such as Glue Data Catalog or Hive Metastore which are mapped to Folders which are physical entities where data is stored on S3. It will return âfalseâ boolean if something goes wrong while execution. One record per line: Previously, we partitioned our data into folders by the numPetsproperty. Create List to identify new partitions by subtracting Athena List from S3 List, 5. Even if a table definition contains the partition projection configuration, other tools will not use those values. If you see this error, update your table to match the partitioning on disk. The Athena Parthenos, a colossal gold and ivory statue of the goddess Athena created between 447 and 438 BC by the renowned ancient Athenian sculptor Pheidias (lived c. 480 â c. 430 BC) that originally stood in the naos of the Parthenon on the Athenian Akropolis, is one of the most famous of all ancient Greek statues.. Column stats for DATE_SID, the join key, is missing for 20120517 partition, the end date of the query. For example, missing a required column, such as PartitionKey, when using Azure Table output can be identified without an I/O request. They were originally part of the temple of the Parthenon and other buildings on the Acropolis of Athens. Because its always better to have one day additional partition, so we donât need wait until the lambda will trigger for that particular date. A humongous query was formed and when it was executed, Athena had a query length limitation ie. Just shared my personal experience working on a POC which I thought would help others like me. One thing that is missing are the column names, because that information isnât present in the myki data files. Review our Privacy Policy for more information about our privacy practices. The above function is used to run queries on Athena using athenaClient i.e. Click here to return to Amazon Web Services homepage. For this, I have used a very cool, neat and easy python library, NOTE : To add external library to Glue Job is itself a neat trick to cover in a separate blog (Will update once its ready). What is suitable : - is to create an Hive table on top of the current not partitionned data, - create a second Hive table for hosting the partitionned data (the same columns + the partition column), Use MSCK REPAIR TABLE or ALTER TABLE ADD PARTITION to load the partition information into the catalog. Using Decimals proved to be more challenging than we expected as it ⦠While creating a table in Athena we mention the partition columns, however, the partitions are not reflected until added explicitly, thus you do not get any records on querying the table. Funny, enthusiastic, self proclaimed smart techie who would be ignored if passed by but would be a crazy hyper active madness when you get to know með. athenaClient will run the query and the output would be stored in a S3 location which is used while calling the API. In the Athena Query Editor, test query the columns that you configured for the table. NOTE : To add variations to schema I have set year column to be string and month column to be int thus the query had to be formed respectively. Select a table and click Edit schema in the top right to update the columns. There are several data errors that can only be detected after making a call to the output sink, which can slow down processing. "universe_partitioned" (id, name, eyecolor, haircolor, gender, year) ⦠When secondary indexes have the partition column as a part of their key, and use the same or equivalent partition scheme, the indexes are partitioned ⦠Here are our unpartitioned files: Here are our partitioned files: Youâll notice that the partitioned data is grouped into âfoldersâ. year and month. Do like the blog, comment your feedback and improvements and also let me know if you need any help understanding it. Get smarter at building your thing. The timestamp column is not "suitable" for a partition (unless you want thousands and thousand of partitions). In case of tables partitioned on one or more columns, when new data is loaded in S3, the metadata store does not get updated with the new partitions. A simple calling to the mentioned functions to fetch the result filename for parsing. This error happens when the database name specified in the DDL statement contains a hyphen ("-"). There is a specific handling to filter out default spark null partitions which could exist at S3 locations with partitions which creates folders like _SUCCESS, _temporary, __HIVE_DEFAULT_PARTITION__.The existence of such folders can cause issues with query formation thus its better to ignore. Itâs easy and free to post your thinking on any topic. Subscribe to receive The Startup's top 10 most read stories â delivered straight into your inbox, once a week. Take a look. 3) Load partitions by running a script dynamically to load partitions in the newly created Athena tables Output path is mentioned in ResultConfiguration :: OutputLocation key, This function will call the athena_query method and wait till it is executed on Athena. 1. Data Engineer/Software Developer/Lead with Masters in Data Analytics from Dublin City University having 6+ years of work experience in Data Pipelines, Core Development, Reporting, Visualizations, DB & Data Technologies with progressive growth. 'region' = AWS Region'database' = Athena Database'tableName' = Athena table to update partitions'athenaResultBucket' = Temporary bucket to hold athena query result'athenaResultFolder' = Temporary folder to store athena query result's3Bucket' = S3 Bucket from where the table is created's3Folder' = S3 Folder from where the table is created'timeout' = Athena query timeout. This would motivate me to keep writing and sharing my experiences. Thanks Verizon Connect for giving me this awesome opportunity to work for some really cool projects of migrating a legacy on-premise data server to AWS thereby, getting my hands dirty while working on neat POCs on AWS. âSHOW PARTITIONS foobarâ & âALTER TABLE foobar ADD IF NOT EXISTS PARTITION(year=â2020', month=03) PARTITION( year=â2020', month=04)â. For use cases where streaming data or continuous data is added and partition is normally done on a date column or new partitions are created on daily/weekly/monthly basis we could use a GLUE Crawler (can be expensive in case of very huge data sets and files). The following get-table-metadata example returns metadata information about the counties table, including including column names and their datatypes, from the sampledb database of the AwsDataCatalog data catalog. Find out more about partitioning strategy for Athena by watching our on-demand webinar: ETL for Amazon Athena: 6 Things You Must Know, or by reading our previous guide on ETLing Amazon Kinesis to Athena using SQL. Refer : âAWS Partitionsâ for detailed information. To keep Athena Table metadata updated without the need to run these commands manually we can use the following : In AWS S3, partitions play an important role when querying data in Amazon Athena/Presto or Redshift Spectrum since, it limits the volume of data scanned, dramatically accelerating queries and reducing costs. Get smarter at building your thing. Pagination of S3 objects is handled using the NextContinuationToken as AWS API returns max 1000 objects in a single API call. Here, expert and undiscovered voices alike dive into the heart of any topic and bring new ideas to the surface. Specify the data ranges and relevant patterns for each partition column, or use a custom template. I am not an AWS expert but pursuing to be one. ALTER table date_partition_table ADD PARTITION (b=CAST('2017-01-01' AS DATE)); line 1:38: missing 'column' at 'partition' (service: amazonathena; status code: 400; error code: invalidrequestexception; In order to load the partitions automatically, we need to put the column name and value i⦠UPDATE : Recently I came across a scenario where my table schema got updated and all partitions had to be reloaded (approximately 6000 partitions). Note: Since Spectrum and Athena use the same AWS Glue Data Catalog we could use the simpler Athena client to add the partition to the table. The main execution of the python scripts starts from this line. This error can occur if you partition your ORC or Parquet data (see Using Partition Columns). One record per file. However, underscores (_) are the only special characters that Athena supports in database, table, view, and column names. As you can see, Glue crawler, while often being the easiest way to create tables, can be the most expensive one as well. And thatâs how Athena would know to scan less data if you filter by time. AWS Glue allows database names with hyphens. Athena table creation options comparison. Like the previous articles, our data is JSON data. The test creates a schema with a struct, add a partition with that schema, and ⦠RE: Question 1. Added About Me Section. But, in case you miss to specify the partition column, Athena creates a new partition INSERT INTO "marvel". Follow to join The Startupâs +8 million monthly readers & +777K followers. Athena in still fresh has yet to ⦠If you create an external table and then change the partition structure, for example by renaming a column, you must then re-create the external table. All rights reserved. However, by ammending the folder name, we can have Athena load the partitions automatically. Hi JBailey . Finally comes the part where the Alter Table partition query is formed by creating a complete query string and altering the string as per the syntax. 3. getResolvedOptions is used to read and parse Glue job parameters. Check your inboxMedium sent you an email at to complete your subscription. However, underscores (_) are the only special characters that Athena supports in database, table, view, and column names. Function returns the temporary filename for parsing further. Few words about float, decimal and double. Athena query result is a .txt format file hence, the result has to be parsed in a list for comparison to identify the newly created partitions. ALTER table date_partition_table ADD PARTITION (b=date '2017-01-01'); An error occurred in the following ALTER statement. It will do a full recomputation. If I have parquet files that don't have a DATE column specified, but instead have a DATE partition column, then the table is sucessfully created, but then querying it via Athena Console returns no rows. Partitions in itself would be a completely different topic to cover sometime later. The Partition Projection feature is available only in AWS Athena. 1) Parse and load files to AWS S3 into different buckets which will be queried through Athena. In the following example, the database name is alb-database1. © 2021, Amazon Web Services, Inc. or its affiliates. When I run an MSCK REPAIR TABLE or SHOW CREATE TABLE statement in Amazon Athena, I get an error like this: "FAILED: ParseException line 1:X missing EOF at '-' near 'keyword'". In Athena, a table and its partitions must use the same data formats but their schemas may differ. The biggest catch was to understand how the partitioning works. In this example, the partitions are the value from the numPetsproperty of the JSON data. QSM-00508 statistics missing on tables/columns QSM-00510 statistics missing on summaries QSM-00513 one or more of the workload tables is missing QSM-01092 mjv tries to rewrite a semi-join and primary key or rowid missing QSM-02117 missing GROUPING_ID or GROUPING functions on GROUP BY columns