mars-repository-lib

Shared Java library for repository integrations in the MARS framework.

The library contains the common pieces that target repository services need when they translate repository-specific responses back into a MARS receipt:

• ISA-JSON model classes used by repository services
• MARS receipt model classes
• MarsReceiptProvider, the base class for building MARS-compatible receipts
• ReceiptAccessionsMap, a small mapping object for connecting ISA-JSON fields to repository accessions
• MarsReceiptException, a receipt-aware runtime exception for conversion errors

Repository service modules, such as ENA or BioSamples converters, should use this library instead of keeping local copies of the receipt and ISA model code.

Requirements

• Java 17
• Gradle wrapper included in this repository

Build

./gradlew build

Publish Locally

MARS services can consume a local development version from your Maven local repository:

./gradlew publishToMavenLocal

This publishes:

com.elixir.mars:mars-repository:0.0.2-SNAPSHOT

Then make sure the consuming service has mavenLocal() enabled and depends on the same version:

repositories {
    mavenLocal()
    mavenCentral()
}

dependencies {
    implementation 'com.elixir.mars:mars-repository:0.0.2-SNAPSHOT'
}

Releasing a New Version

To release a new library version:

1. Update the version in build.gradle from the current -SNAPSHOT value to the release version, for example 0.0.2.

2. Run the build to confirm the code still passes:

   ./gradlew build

3. Commit the version bump.

4. Create and push a git tag for the release, for example:

   git tag v0.0.2
   git push origin v0.0.2

5. After the release is published, bump build.gradle to the next -SNAPSHOT version, such as 0.0.3-SNAPSHOT, and commit that change.

6. Create a release based on the tag on Github to produce a changelog.

Creating a Receipt Provider

Target repository integrations typically extend MarsReceiptProvider, collect repository accessions, and let the base class build the MARS receipt paths.

public final class EnaReceiptProvider extends MarsReceiptProvider {

  public EnaReceiptProvider() {
    super("ena");
  }

  @Override
  public String convertMarsReceiptToJson() {
    return getMarsReceipt().toString();
  }
}

Use ReceiptAccessionsMap instances to describe which ISA-JSON field identifies each object and which repository accession belongs to each field value. The base provider can then produce MarsAccession entries pointing back to the relevant study, source, sample, other material, or data file in the ISA-JSON document.

Package Layout

com.elixir.mars.repository
com.elixir.mars.repository.models.isa
com.elixir.mars.repository.models.receipt

License

This project is licensed under the MIT License. See LICENSE.