Discover and call database APIs¶

Find and call database APIs by name or keyword.

1) Call a database operation by name and parameters¶

Purpose: Call a database operation by name and parameters.
Method: Validate the operation and arguments, then dispatch to its adapter and preserve the returned fields.
API： dnakit.databases.call(operation, arguments=None, *, max_result_bytes=20000000, verbose=True)
Input: Provide operation.
Output: Returns the selected operation's response; this example retrieves the Ensembl BRCA1 record.
Example code:

import dnakit

result = dnakit.databases.call(
    operation='ensembl_lookup_gene',
    arguments={'id': 'BRCA1', 'species': 'homo_sapiens'},
    verbose=False,
)
print(result)

Example output: Returns the selected operation's response; this example retrieves the Ensembl BRCA1 record.

Full parameters and usage notes

2) Inspect database input schemas and provenance¶

Purpose: Inspect database input schemas and provenance.
Method: Read parameter constraints and provenance from the local operation catalog, without network access.
API： dnakit.databases.describe(operation, *, verbose=True)
Input: Provide operation.
Output: Mapping with actual input_schema, provider config and upstream_name.
Example code:

import dnakit

result = dnakit.databases.describe(
    operation='gnomad_get_sv_by_region',
    verbose=False,
)
print(result)

Example output: Mapping with actual input_schema, provider config and upstream_name.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

{
  "name": "<str>",
  "upstream_name": "<str>",
  "input_schema": "<dict>",
  "config": "<dict>"
}

Full parameters and usage notes

3) Execute a structured database request¶

Purpose: Execute a structured database request.
Method: Parse an operation name or name/arguments request and dispatch to the database adapter.
API： dnakit.databases.execute(request, arguments=None, *, verbose=True)
Input: Provide request.
Output: Returns the requested operation's response; this example retrieves the Ensembl BRCA1 record.
Example code:

import dnakit

example_request = {'name': 'ensembl_lookup_gene',
 'arguments': {'id': 'BRCA1', 'species': 'homo_sapiens'}}

result = dnakit.databases.execute(
    request=example_request,
    verbose=False,
)
print(result)

Example output: Returns the requested operation's response; this example retrieves the Ensembl BRCA1 record.

Full parameters and usage notes

4) Dispatch a database operation using a compatible tool name¶

Purpose: Dispatch a tool name and arguments to a local DNAKit database operation; recursive self-calls are rejected.
Method: Use Execute to query or submit the supplied input and parse the response.
API： dnakit.databases.execute_tool(*, tool_name, arguments=None, verbose=True)
Input: Provide tool_name.
Output: Returns the result of the operation selected by tool_name, using that operation's fields.
Example code:

import dnakit

result = dnakit.databases.execute_tool(
    tool_name='list_tools',
    arguments={'mode': 'names', 'limit': '3'},
    verbose=False,
)
print(result)

Example output: Returns the result of the operation selected by tool_name, using that operation's fields.

Full parameters and usage notes

5) List database operations and aliases offline¶

Purpose: List database operations and aliases offline.
Method: List function names and upstream aliases from the local registry.
API： dnakit.databases.list_operations(*, verbose=True)
Input: Choose filters as shown in the example; omitted options use the operation defaults.
Output: List of name and upstream_name mappings.
Example code:

import dnakit

result = dnakit.databases.list_operations(
    verbose=False,
)
print(result)

Example output: List of name and upstream_name mappings.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "name": "<str>",
    "upstream_name": "<str>"
  }
]

Full parameters and usage notes

6) Discover database operations by task keywords offline¶

Purpose: Discover database operations by task keywords offline.
Method: Match keywords against local operation names and descriptions and rank by match count.
API： dnakit.databases.search(query, *, limit=10, verbose=True)
Input: Provide query.
Output: List of name, description and upstream_name mappings.
Example code:

import dnakit

result = dnakit.databases.search(
    query='gnomad',
    limit=5,
    verbose=False,
)
print(result)

Example output: List of name, description and upstream_name mappings.

Response-shape excerpt; <…> denotes type placeholders, not a captured query result.

[
  {
    "name": "<str>",
    "description": "<str>",
    "upstream_name": "<str>"
  }
]

Full parameters and usage notes