MySQL Hybrid Runner

• Requirements
• Metadata Ingestion
• Data Profiler
• Data Quality
• dbt Integration
• Enable Security
• Data Lineage
• Troubleshooting
• Reverse Metadata

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Requirements

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Metadata

-- Create user. If <hostName> is omitted, defaults to '%'
-- More details https://dev.mysql.com/doc/refman/8.0/en/create-user.html
CREATE USER '<username>'[@'<hostName>'] IDENTIFIED BY '<password>';
-- Grant select on a database
GRANT SELECT ON world.* TO '<username>';
-- Grant select on a database
GRANT SELECT ON world.* TO '<username>';
-- Grant select on a specific object
GRANT SELECT ON world.hello TO '<username>';
-- Grant show view to extract ddl
GRANT SHOW VIEW ON world.* to '<username>';

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Aurora MySQL IAM Authentication

1. Connect as an admin user with password authentication and create (or validate) the IAM DB user:

CREATE USER 'openmetadata_iam'@'%' IDENTIFIED WITH AWSAuthenticationPlugin AS 'RDS';
SHOW CREATE USER 'openmetadata_iam'@'%';

2. Grant minimum metadata permissions and verify:

GRANT SELECT, PROCESS, SHOW DATABASES, SHOW VIEW ON *.* TO 'openmetadata_iam'@'%';
FLUSH PRIVILEGES;
SHOW GRANTS FOR 'openmetadata_iam'@'%';

3. Attach the IAM policy to the AWS principal used by ingestion:

• Policy action must include rds-db:connect.
• Resource must be exactly: arn:aws:rds-db:<aws_region>:<aws_account_number>:dbuser:<rds_db_resource_id>/openmetadata_iam
• If ingestion runs on EC2/ECS/EKS, attach the policy to that runtime role.
• If ingestion runs locally, attach the policy to the IAM user/profile generating auth tokens.

4. Validate IAM login from the same host that runs ingestion:

curl -o global-bundle.pem https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem
TOKEN="$(aws rds generate-db-auth-token --hostname <cluster-endpoint> --port 3306 --region <aws_region> --username openmetadata_iam)"
mysql -h <cluster-endpoint> -P 3306 --ssl-ca=global-bundle.pem -u openmetadata_iam -p"$TOKEN"

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Lineage and Usage

-- Enable Logging
SET GLOBAL general_log='ON';
set GLOBAL log_output='table';
-- Grant SELECT on log table
GRANT SELECT ON mysql.general_log TO '<username>'@'<host>';

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Log Table Management

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Create a Manual Schedule to Rotate Logs

-- rotate general logs
CREATE PROCEDURE rotate_general_log()
BEGIN
  -- Step 1: Drop the backup table if it exists
  DROP TABLE IF EXISTS mysql.general_log_backup;
  -- Step 2: Copy current general_log table to backup
  CREATE TABLE mysql.general_log_backup AS SELECT * FROM mysql.general_log;
  -- Step 3: Truncate the general_log table (clears all records)
  TRUNCATE TABLE mysql.general_log;
END;
-- call this procedure
CALL rotate_general_log();
-- rotate slow logs
CREATE PROCEDURE rotate_slow_log()
BEGIN
  DROP TABLE IF EXISTS mysql.slow_log_backup;
  CREATE TABLE mysql.slow_log_backup AS SELECT * FROM mysql.slow_log;
  TRUNCATE TABLE mysql.slow_log;
END
-- call this procedure
CALL rotate_slow_log();

SELECT table_name, round(data_length/1024/1024, 2) AS size_in_mb
FROM information_schema.tables
WHERE table_schema = 'mysql' AND table_name IN ('general_log', 'slow_log', 'general_log_backup', 'slow_log_backup');

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Create Automatic Event to Clear Older Logs

CREATE EVENT mysql.cleanup_general_log ON SCHEDULE EVERY 7 DAY DO DELETE FROM mysql.general_log WHERE event_time < NOW() - INTERVAL 7 DAY;

• Rotating MySQL query logs
• RDS for MySQL database logs
• Aurora for MySQL database logs Best Practices:
• Monitor log table size regularly
• Implement a log rotation schedule
• Consider automating log cleanup after DAG execution
• Keep logging enabled only when needed for lineage extraction

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Profiler and Data Quality

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Metadata Ingestion

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Step 1: Add New Service

1. In the left navigation, click Connections.
2. On the Connections page, click Add New Service.

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Step 2: Select a Service and Connector

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Step 3: Add Service Name and Description

• Enter a unique, descriptive Service Name. Collate identifies services by their service name. Enter a name that distinguishes this deployment from other MySQL services you are ingesting metadata from.
• Optional: Enter a Description for the service.

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Step 4: Configure Connection Options

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Select Ingestion Runner

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Enter Connection Details

• Username: Specify the user to connect to MySQL. It should have enough privileges to read all the metadata.
• Auth Type: Basic Auth or IAM-based auth to connect to instances or cloud RDS.
  Tip: For Aurora MySQL IAM in Collate, use:

  • Username: openmetadata_iam
  • Auth Type: IAM
  • AWS Region: <aws_region> (for example, us-east-2)
  • Host and Port: <cluster-endpoint>:3306 (use cluster endpoint)
  • Basic Auth:
    • Password: Password to connect to MySQL.
  • IAM Based Auth:
    • AWS Access Key ID and AWS Secret Access Key: When you interact with AWS, you specify your AWS security credentials to verify who you are and whether you have permission to access the resources that you are requesting. AWS uses the security credentials to authenticate and authorize your requests (docs). Access keys consist of two parts: An access key ID (for example, AKIAIOSFODNN7EXAMPLE), and a secret access key (for example, wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEY). You must use both the access key ID and secret access key together to authenticate your requests. You can find further information on how to manage your access keys.
    • AWS Region: Each AWS Region is a separate geographic area in which AWS clusters data centers (docs). Because AWS can have instances in multiple regions, specify the region where the service you want to reach is located. The AWS Region is the only required parameter when configuring a connection. When connecting to services programmatically, AWS configurations can be extracted and used in different ways. You can find further information about configuring your credentials.
    • AWS Session Token (optional): If you are using temporary credentials to access your services, you will need to provide the AWS Access Key ID and AWS Secret Access Key. Also, these will include an AWS Session Token. You can find more information on Using temporary credentials with AWS resources.
    • Endpoint URL (optional): To connect programmatically to an AWS service, you use an endpoint. An endpoint is the URL of the entry point for an AWS web service. The AWS SDKs and the AWS Command Line Interface (AWS CLI) automatically uses the default endpoint for each service in an AWS Region. But you can specify an alternate endpoint for your API requests. Find more information on AWS service endpoints.
    • Profile Name: A named profile is a collection of settings and credentials that you can apply to an AWS CLI command. When you specify a profile to run a command, the settings and credentials are used to run that command. Multiple named profiles can be stored in the config and credentials files. You can inform this field if you’d like to use a profile other than default. Find more information about Named profiles for the AWS CLI.
    • Assume Role Arn: Typically, you use AssumeRole within your account or for cross-account access. In this field you’ll set the ARN (Amazon Resource Name) of the policy of the other account. A user who wants to access a role in a different account must also have permissions that are delegated from the account administrator. The administrator must attach a policy that allows the user to call AssumeRole for the ARN of the role in the other account. This is a required field if you’d like to AssumeRole. Find more information on AssumeRole.
    Tip: When using Assume Role authentication, ensure you provide the following details:

    • AWS Region: Specify the AWS region for your deployment.
    • Assume Role Session Name: An identifier for the assumed role session. Use the role session name to uniquely identify a session when the same role is assumed by different principals or for different reasons. By default, we’ll use the name OpenMetadataSession. Find more information about the Role Session Name.
    • Assume Role Source Identity: The source identity specified by the principal that is calling the AssumeRole operation. You can use source identity information in AWS CloudTrail logs to determine who took actions with a role. Find more information about Source Identity.
• IAM Policy Requirement: The principal used by ingestion must have rds-db:connect permission with the exact DB user resource ARN: arn:aws:rds-db:<aws_region>:<aws_account_number>:dbuser:<rds_db_resource_id>/openmetadata_iam.
• Credentials Source:
  • If ingestion runs on EC2/ECS/EKS, prefer runtime role credentials.
  • If ingestion runs locally, configure IAM user/profile credentials.
  • You can also provide AWS Access Key ID + AWS Secret Access Key + optional AWS Session Token.
  • If needed, use Assume Role (Assume Role Arn, Assume Role Session Name, optional Source Identity).
• Host and Port: Use the Aurora cluster endpoint and port 3306 that ingestion will use.
• databaseName: Optional name to give to the database in Collate. If left blank, Collate uses the default database name.
• databaseSchema: databaseSchema of the data source. This is optional parameter, if you would like to restrict the metadata reading to a single databaseSchema. When left blank, Collate ingestion attempts to scan all schemas.
• caCertificate: Provide the CA bundle path used by ingestion runtime (for example, global-bundle.pem).
• sslCertificate: Provide the path to ssl client certificate file (ssl_cert).
• sslKey: Provide the path to ssl client certificate file (ssl_key).

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Advanced Configuration

• Connection Options (Optional): Enter the details for any additional connection options that can be sent to database during the connection. These details must be added as Key-Value pairs.
• Connection Arguments (Optional): Enter the details for any additional connection arguments such as security or protocol configs that can be sent during the connection. These details must be added as Key-Value pairs.

password: secret:/my/database/password

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Test Connection

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Step 5: Configure Ingestion Options

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How Filter Patterns Work

• Include: Add one or more comma-separated regular expressions. Collate ingests only assets whose names match at least one expression. Leave blank to include all assets.
• Exclude: Add one or more comma-separated regular expressions. Collate skips any asset whose name matches an expression. Leave blank to exclude nothing.

• contains: matches any name containing the value. For example, sales matches my_sales_data and sales_2024.
• starts with: matches names beginning with the value. For example, prod_ matches prod_db and prod_schema.
• ends with: matches names ending with the value. For example, _raw matches events_raw and logs_raw.
• is exactly: matches the exact name only. For example, analytics matches only analytics.
• matches regex: matches names using a regular expression. For example, ^prod_.*_v\d+$ matches prod_events_v1.

• Database: Controls which databases Collate ingests from the source.
• Schema: Controls which schemas within the ingested databases are included.
• Table: Controls which tables and views within the ingested schemas are included.
• Stored Procedure: Controls which stored procedures are included in metadata ingestion.

• Scan Mode: You can choose between the following scan modes:
  • Scan all: Ingests every asset of that type the connector can access. This is the default.
  • Only specific: Enables include rules so only assets matching at least one rule are ingested.
• Exclude system toggle: Use this toggle to automatically filter out system-reserved names defined by the connector—for example, Exclude system databases for the Databases section.
• Always exclude: Add permanent exclusion rules (shown in red). Assets matching these rules are never ingested, regardless of include rules.
• Preview: Shows a real-time summary of what will be in scope based on your current rules.
• Include rules (available only in Only specific mode): Click + Add to define a rule. Added rules appear as chips. An asset is included if it matches any rule.

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Step 6: Create & Deploy

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Configure Metadata Agent and Schedule Ingestion

1. In the left navigation, click Connections and select your service.
2. Click the Agents tab.
3. Click Add Agent and select Metadata from the dropdown. For some services, the dropdown is not available and clicking Add Agent takes you directly to the agent configuration page.
4. On the Configure Ingestion page, do the following and click Next.
   • Name this Ingestion: Enter a unique recognizable name for this ingestion pipeline.
   • Agent Setup: Configure core parameters for metadata extraction. The following fields are available:

     Field	Default	Description
     Default Owner	—	Owner applied to all entities when no specific level owner is configured. Accepts a user or team name/email.
     Service Owner	—	Owner assigned to the service entity.
     Database Owner	—	Owner assigned to all ingested databases. Accepts a single owner or a per-database name mapping.
     Database Schema Owner	—	Owner assigned to all ingested schemas. Accepts a single owner or a per-schema name mapping.
     Table Owner	—	Owner assigned to all ingested tables. Accepts a single owner or a per-table name mapping.
     Enable Inheritance	On	When on, child entities inherit the owner from their parent when they have no owner configured.
     Query Log Duration	1	Number of days to look back in query logs when processing stored procedure results.
     Query Parsing Timeout Limit	300	Timeout in seconds for parsing a single query.
     Number of Threads	1	Number of threads to use for parallel table ingestion.
     Incremental Extraction	Off	When enabled, subsequent runs only extract entities changed since the last successful run.
     Successful Pipeline Run Lookback Days	7	Number of days to search back for a prior successful run to use as a baseline for incremental extraction.
     Safety Margin Days	1	Additional days added to the baseline timestamp as a buffer for incremental extraction.
     JSON Schema Sample Size	10	Number of rows sampled to infer JSON column schema. Only applies when Extract JSON Schema is enabled in Advanced Config.

     
   • Filter Patterns: Apply include or exclude rules to scope which databases, schemas, tables, and stored procedures this agent ingests. For more information about various filter options, see Step 5: Configure Ingestion Options.
   • Scope & Behaviour: Control how the agent handles metadata during ingestion. Toggle each option on or off based on your needs:

     Toggle	Default	Description
     Include Tables	On	Ingest table metadata from the source. Turn off to skip tables entirely.
     Include Tags	On	Ingest tags from the source.
     Include Stored Procedures	On	Ingest stored procedure metadata.
     Include DDL Statements	Off	Ingest DDL statements alongside table metadata.
     Include Owners	Off	Assign owners to ingested entities when the source owner’s email matches a user in Collate. Does not overwrite an existing owner.
     Include Custom Properties	Off	Ingest connector-specific custom properties onto entities.
     Mark Deleted Tables	On	Soft-delete tables in Collate when they are removed from the source. Applies only within the currently ingested schema.
     Mark Deleted Stored Procedures	On	Soft-delete stored procedures in Collate when they are removed from the source.
     Mark Deleted Schemas	Off	Soft-delete schemas and all their child assets when removed from the source.
     Mark Deleted Databases	Off	Soft-delete databases and all their child assets when removed from the source.
     Override Metadata	Off	When on, source values overwrite existing descriptions, tags, owners, and display names in Collate. When off, Collate only updates fields that have no existing value.
     Enable Debug Log	Off	Sets the ingestion log level to DEBUG. Useful for troubleshooting.

     Note: Available toggles vary by connector. Stored procedure options only appear for connectors that support stored procedures.
     
   • Advanced Config: Optional connector-specific settings such as Include Views and Extract JSON Schema.
5. On the Schedule Interval page, set when the agent runs:
   • Schedule: Choose a preset interval (Hourly, Daily, Weekly, Monthly) or enter a custom cron expression.
   • On-Demand: No automatic schedule; trigger the agent manually when needed.
   
6. Click Add to deploy the agent.

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Securing MySQL Connection with SSL in Collate

connectionArguments:
  ssl:
    ca: /path/in/runtime/global-bundle.pem

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Reverse Metadata

• Description Management: MySQL supports description updates at the following level:
  • Table level
• Owner Management: Owner management is not supported for MySQL.
• Tag Management: Tag management is not supported for MySQL.
• Custom SQL Template: MySQL supports custom SQL templates for metadata changes. The template is interpreted using python f-strings. Here are examples of custom SQL queries for metadata changes:
  -- Update table description
  ALTER TABLE {schema}.{table} COMMENT = {description};
  
  The list of variables for custom SQL can be found here.
• Requirements for Reverse Metadata: In addition to the basic ingestion requirements, for reverse metadata ingestion the user needs:
  • `

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Troubleshooting