Usage
The following usage docs provide instructions for common tasks and workflows in Song:
Metadata Submission
Submitting new metadata entries (Analyses) to Song.
Metadata Retrieval
Query & retrieval of metadata (Analyses) from Song.
Updating Metadata
Updating metadata for analyses in Songs database using various methods.
Publication Controls
Managing data release with publication controls.
Data Model Management
Creating & updating the data model using JSON schema.
Schema Strictness
Song's schema strictness determines whether analyses adhere strictly to the latest schema version or can use any version.
ID Management
Song provides two distinct approaches for managing primary keys across entities (Donors, Specimens, Samples, and Files):
Kafka Setup
Song can be configured to integrate with Kafka for event streaming. This page explains how to enable and configure the Kafka integration.
Configuring Keycloak
There are multiple methods of deploying Keycloak. Documentation on Keycloak deployment can be found on the Official Keycloak website.
API Reference
Songs API is a RESTful API that uses JSON for request and response bodies. It follows standard HTTP methods and status codes, providing a robust interface for managing song-related data in the Overture platform.
Client Reference
Commands and options supported by the Song client.
Song Terminology
Whether you're new to these tools or looking to refresh your understanding, this glossary is here as a reference of key terms and concepts.
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Analysis: A trackable unit of data in Song that combines metadata and associated data files. It's the main entity in a Song database.
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Analysis ID: A unique identifier (UUID) assigned to each analysis in Song. It's used to track, retrieve, and manage specific analyses throughout the Song and Score.
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Analysis State: The current status of an analysis in Song. States include PUBLISHED, UNPUBLISHED, and SUPPRESSED.
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Analysis Type: A category of analysis defined by Song administrators, which describes the structure and content of a particular kind of data submission.
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Dynamic Schema: A JSON-based schema that defines the structure and constraints of an analysis type in Song.
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Manifest: A file generated by Song that establishes a link between an analysis ID and the data files on your local system, used by Score for file uploads.
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Metadata: Data that describes other data. In the context of Song, it refers to the information about data files included in an analysis.
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Payload: A formatted set of metadata conforming to a specific analysis type schema, submitted to Song as part of the data submission process.
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Score: A file transfer and storage system designed to work alongside Song for managing large data files.
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Song: A metadata management system used to track and manage metadata related to files in a data repository. s
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Study: A collection of analyses in Song, typically representing a coherent set of data for a particular research project or data submission.
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Published Analysis: An analysis in Song that has been marked as ready for downstream processing and is searchable within the system.
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Unpublished Analysis: An analysis in Song that has been created but is not yet ready for downstream processing or searching.
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Suppressed Analysis: An analysis in Song that has been temporarily hidden or removed from active use, typically due to data quality issues or other concerns.