datahub/metadata-ingestion/source_docs/s3_data_lake.md

S3 Data Lake

For context on getting started with ingestion, check out our metadata ingestion guide.

:::caution

This source is in Beta and under active development. Not yet considered ready for production.

:::

Setup

To install this plugin, run pip install 'acryl-datahub[s3]'. Note that because the profiling is run with PySpark, we require Spark 3.0.3 with Hadoop 3.2 to be installed (see compatibility for more details). If profiling, make sure that permissions for s3a:// access are set because Spark and Hadoop use the s3a:// protocol to interface with AWS (schema inference outside of profiling requires s3:// access).

The s3 connector extracts schemas and profiles from a variety of file formats (see below for an exhaustive list). Based on configuration, individual files or folders are ingested as tables, and profiles are computed similar to the SQL profiler. Enabling profiling will slow down ingestion runs.

Capabilities

Extracts:

• Row and column counts for each table
• For each column, if profiling is enabled:
  • null counts and proportions
  • distinct counts and proportions
  • minimum, maximum, mean, median, standard deviation, some quantile values
  • histograms or frequencies of unique values

This connector supports both local files as well as those stored on AWS S3 (which must be identified using the prefix s3://). Supported file types are as follows:

• CSV
• TSV
• JSON
• Parquet
• Apache Avro

Schemas for Parquet and Avro files are extracted as provided.

Schemas for schemaless formats (CSV, TSV, JSON) are inferred. For CSV and TSV files, we consider the first 100 rows by default, which can be controlled via the max_rows recipe parameter (see below) JSON file schemas are inferred on the basis of the entire file (given the difficulty in extracting only the first few objects of the file), which may impact performance. We are working on using iterator-based JSON parsers to avoid reading in the entire JSON object.

Capability	Status	Details
Platform Instance	✔️	link

Quickstart recipe

Check out the following recipe to get started with ingestion! See below for full configuration options.

For general pointers on writing and running a recipe, see our main recipe guide.

source:
  type: s3
  config:
    path_spec: 
      include: "s3://covid19-lake/covid_knowledge_graph/csv/nodes/*.*"
    aws_config:
      aws_access_key_id: *****
      aws_secret_access_key: *****
      aws_region: us-east-2
    env: "PROD"
    profiling:
      enabled: false

sink:
  # sink configs

Config details

Note that a . is used to denote nested fields in the YAML recipe.

Field	Required	Default	Description
path_spec.include	✅		Path to table (s3 or local file system). Name variable {table} is used to mark the folder with dataset. In absence of {table}, file level dataset will be created. Check below examples for more details.
path_spec.exclude			list of paths in glob pattern which will be excluded while scanning for the datasets
path_spec.table_name		{table}	Display name of the dataset.Combination of named variableds from include path and strings
path_spec.file_types		["csv", "tsv", "json", "parquet", "avro"]	Files with extenstions specified here (subset of default value) only will be scanned to create dataset. Other files will be omitted.
env		PROD	Environment to use in namespace when constructing URNs.
platform		Autodetected	Platform to use in namespace when constructing URNs. If left blank, local paths will correspond to file and S3 paths will correspond to s3.
platform_instance			Platform instance for datasets and containers
spark_driver_memory		4g	Max amount of memory to grant Spark.
aws_config.aws_region	If ingesting from AWS S3		AWS region code.
aws_config.aws_access_key_id		Autodetected (Required for s3 profiling)	See https://boto3.amazonaws.com/v1/documentation/api/latest/guide/credentials.html
aws_config.aws_secret_access_key		Autodetected (Required for s3 profiling)	See https://boto3.amazonaws.com/v1/documentation/api/latest/guide/credentials.html
aws_config.aws_session_token		Autodetected	See https://boto3.amazonaws.com/v1/documentation/api/latest/guide/credentials.html
max_rows		100	Maximum number of rows to use when inferring schemas for TSV and CSV files.
profile_patterns.allow		*	List of regex patterns for tables to profile (a must also be ingested for profiling). Defaults to all.
profile_patterns.deny			List of regex patterns for tables to not profile (a must also be ingested for profiling). Defaults to none.
profile_patterns.ignoreCase		True	Whether to ignore case sensitivity during pattern matching of tables to profile.
profiling.enabled		False	Whether profiling should be done.
profiling.profile_table_level_only		False	Whether to perform profiling at table-level only or include column-level profiling as well.
profiling.max_number_of_fields_to_profile		None	A positive integer that specifies the maximum number of columns to profile for any table. None implies all columns. The cost of profiling goes up significantly as the number of columns to profile goes up.
profiling.include_field_null_count		True	Whether to profile for the number of nulls for each column.
profiling.include_field_min_value		True	Whether to profile for the min value of numeric columns.
profiling.include_field_max_value		True	Whether to profile for the max value of numeric columns.
profiling.include_field_mean_value		True	Whether to profile for the mean value of numeric columns.
profiling.include_field_median_value		True	Whether to profile for the median value of numeric columns.
profiling.include_field_stddev_value		True	Whether to profile for the standard deviation of numeric columns.
profiling.include_field_quantiles		True	Whether to profile for the quantiles of numeric columns.
profiling.include_field_distinct_value_frequencies		False	Whether to profile for distinct value frequencies.
profiling.include_field_histogram		False	Whether to profile for the histogram for numeric fields.
profiling.include_field_sample_values		True	Whether to profile for the sample values for all columns.

Valid path_spec.include

s3://my-bucket/foo/tests/bar.avro # single file table   
s3://my-bucket/foo/tests/*.* # mulitple file level tables
s3://my-bucket/foo/tests/{table}/*.avro #table without partition
s3://my-bucket/foo/tests/{table}/*/*.avro #table where partitions are not specified
s3://my-bucket/foo/tests/{table}/*.* # table where no partitions as well as data type specified
s3://my-bucket/{dept}/tests/{table}/*.avro # specifying key wards to be used in display name
s3://my-bucket/{dept}/tests/{table}/{partition_key[0]}={partition[0]}/{partition_key[1]}={partition[1]}/*.avro # specify partition key and value format
s3://my-bucket/{dept}/tests/{table}/{partition[0]}/{partition[1]}/{partition[2]}/*.avro # specify partition value only format
s3://my-bucket/{dept}/tests/{table}/{partition[0]}/{partition[1]}/{partition[2]}/*.* # for all extensions
s3://my-bucket/*/{table}/{partition[0]}/{partition[1]}/{partition[2]}/*.* # table is present at 2 levels down in bucket
s3://my-bucket/*/*/{table}/{partition[0]}/{partition[1]}/{partition[2]}/*.* # table is present at 3 levels down in bucket

Valid path_spec.exclude

• /tests/
• s3://my-bucket/hr/**
• **/tests/*.csv
• s3://my-bucket/foo/*/my_table/**

Notes

• {table} represents folder for which dataset will be created.
• include path must end with (. or *.[ext]) to represent leaf level.
• if *.[ext] is provided then only files with specified type will be scanned.
• /*/ represents single folder.
• {partition[i]} represents value of partition.
• {partition_key[i]} represents name of the partition.
• While extracting, “i” will be used to match partition_key to partition.
• all folder levels need to be specified in include. Only exclude path can have ** like matching.
• exclude path cannot have named variables ( {} ).
• Folder names should not contain {, }, *, / in their names.
• {folder} is reserved for internal working. please do not use in named variables.

If you would like to write a more complicated function for resolving file names, then a transformer would be a good fit.

:::caution

Specify as long fixed prefix ( with out /*/ ) as possible in path_spec.include. This will reduce the scanning time and cost, specifically on AWS S3

:::

:::caution

Running profiling against many tables or over many rows can run up significant costs. While we've done our best to limit the expensiveness of the queries the profiler runs, you should be prudent about the set of tables profiling is enabled on or the frequency of the profiling runs.

:::

:::caution

If you are ingesting datasets from AWS S3, we recommend running the ingestion on a server in the same region to avoid high egress costs.

:::

Compatibility

Profiles are computed with PyDeequ, which relies on PySpark. Therefore, for computing profiles, we currently require Spark 3.0.3 with Hadoop 3.2 to be installed and the SPARK_HOME and SPARK_VERSION environment variables to be set. The Spark+Hadoop binary can be downloaded here.

For an example guide on setting up PyDeequ on AWS, see this guide.

Questions

If you've got any questions on configuring this source, feel free to ping us on our Slack!