submit-workflow-safely

Submitting Workflows Safely

This skill teaches you how to verify workflow configuration and safely submit workflows to Terra.

Pre-Submission Checklist

Before submitting a workflow, verify these three things:

1. Verify Method Configuration Points to Correct WDL Version

get_method_config(workspace_namespace, workspace_name, config_namespace, config_name)

Check the methodRepoMethod section for:

• methodNamespace: The WDL repository namespace
• methodName: The workflow name
• methodVersion: The snapshot/version number

Common issue: Configuration points to an old WDL version instead of the latest.

2. Verify Entity Data is Correct

get_entities returns one page (100 rows by default), so never use a bare call to decide whether an entity exists: on a table with more rows than one page, a real entity looks missing. Use entity_name, which is an exact lookup by the table's id, and ask only for the attributes you are about to check.

get_entities(
    workspace_namespace, workspace_name, entity_type,
    entity_name="<entity_name>",
    columns=["<attribute>", "<attribute>"],
)

Do not use filter_terms for this. It is a substring search over the row, so a miss does not mean the entity is absent. entity_name returns exactly 0 or 1 rows, and 0 is a real answer rather than an error.

Confirm from the response:

• count is 1, and the row is in entities
• The attributes you need are populated
• File paths (GCS URLs) look right

Attribute names come from get_workspace_data_tables, which lists each table's columns alongside its row count. Omitting columns returns every attribute and is refused outright above max_response_bytes on a wide table; see the manage-context-size skill.

3. Verify Input Mappings are Configured

In the method configuration (from step 1), check:

• inputs: Maps WDL input variables to entity attributes or literal values
• outputs: Maps WDL outputs to entity attributes for storage
• rootEntityType: Must match the entity type you're submitting