Skip to content

Latest commit

 

History

History
144 lines (123 loc) · 6.57 KB

README.md

File metadata and controls

144 lines (123 loc) · 6.57 KB

SIRIUS Java SDK

This is the SIRIUS Software development kit (SDK) for Java to connect to the generic Sirius Nightsky API. It provides models and clients to interact with the API as well as features to start/stop/locate the SIRIUS application.

This SDK is intended to be shipped with your software to connect to a SIRIUS installation on the user system. It does not contain the SIRIUS Software itself or any algorithms/methods.

The class SiriusSDK serves a single entry point to all features. It allows you to start SIRIUS and gives access all API endpoints.

Usage

Detailed documentation about the different endpoints can be found here.

Example Code

        // Search and Start SIRIUS installation in background.
        // If a compatible SIRIUS instance is already running this will be used instead
        // Closing the SiriusSDK shuts down SIRIUS depending on the ShutdownMode.
        try (SiriusSDK sirius = SiriusSDK.startAndConnectLocally(SiriusSDK.ShutdownMode.AUTO, false)) {
            // print some infos about the SIRIUS instance
            System.out.println(sirius.infos().getInfo(null, null));
            ProjectInfo project = sirius.projects().createProject("myProject", "/tmp/" + UUID.randomUUID(), null);

            // Import peak-list data from files.
            sirius.projects().importPreprocessedData(project.getProjectId(), true, true, List.of(
                    new File("/mydata/spectra1.mgf"),
                    new File("/mydata/spectra1.ms"),
                    new File("/mydata/spectra1.cef")
            ));
            
            //get default compute configuration/parameters from SIRIUS (optional)
            JobSubmission sub = sirius.jobs().getDefaultJobConfig(false);
            sub.getZodiacParams().setEnabled(false); //enable/disable tools

            //submit job to be computed in background
            Job job = sirius.jobs().startJob(project.getProjectId(), sub, null);
            job = sirius.awaitJob(project.getProjectId(), job.getId());

            // fetch results from the project
            sirius.features().getAlignedFeatures(project.getProjectId(), List.of(AlignedFeatureOptField.TOPANNOTATIONS))
                    .forEach(System.out::println);

        } catch (Exception e) {
            e.printStackTrace();
        }

Import Option 1:

Import peak-list data from files. Can be executed synchronously or asynchronously as a job

sirius.projects().importPreprocessedData(project.getProjectId(), true, true, List.of(
    new File("/mydata/spectra1.mgf"),
    new File("/mydata/spectra1.ms"),
    new File("/mydata/spectra1.cef")
));

Import Option 2:

Import LCMS Runs from file and Find and Align features during import. Can be executed synchronously or asynchronously as a job.

Job importJob = sirius.projects().importMsRunDataAsJob(project.getProjectId(), true, true, List.of(
    new File("/myRuns/run1a.mzml"),
    new File("/myRuns/run2a.mzml"),
    new File("/myRuns/run1b.mzml"),
    new File("/myRuns/run2b.mzml")
));

Import Option 3:

Direct data import. Synchronously only .

FeatureImport featureToImport = new FeatureImport()
                    .charge(1)
                    .addDetectedAdductsItem("[M+H]+")
                    .externalFeatureId("MyIdForMapping").ionMass(285.0787)
                    .mergedMs1(
                            new BasicSpectrum()
                                    .addPeaksItem(new SimplePeak().mz(285.0789).intensity(210252.13))
                                    .addPeaksItem(new SimplePeak().mz(286.0822).intensity(36264.31))
                                    .addPeaksItem(new SimplePeak().mz(287.0766).intensity(70364.01))
                                    .addPeaksItem(new SimplePeak().mz(288.0791).intensity(12274.46))
                                    .addPeaksItem(new SimplePeak().mz(289.0840).intensity(1037.72)))
                    .addMs2SpectraItem(
                            new BasicSpectrum()
                                    .precursorMz(285.07872)
                                    .addPeaksItem(new SimplePeak().mz(91.0545).intensity(317.62))
                                    .addPeaksItem(new SimplePeak().mz(105.0333).intensity(503.78))
                                    .addPeaksItem(new SimplePeak().mz(154.0415).intensity(3030.97))
                                    .addPeaksItem(new SimplePeak().mz(167.0116).intensity(240.42))
                                    .addPeaksItem(new SimplePeak().mz(172.0628).intensity(297.89))
                                    .addPeaksItem(new SimplePeak().mz(179.0369).intensity(207.02))
                                    .addPeaksItem(new SimplePeak().mz(180.0199).intensity(349.96))
                                    .addPeaksItem(new SimplePeak().mz(182.0367).intensity(780.00))
                                    .addPeaksItem(new SimplePeak().mz(193.0883).intensity(1824.38))
                                    .addPeaksItem(new SimplePeak().mz(221.1065).intensity(307.91))
                                    .addPeaksItem(new SimplePeak().mz(222.1147).intensity(2002.34))
                                    .addPeaksItem(new SimplePeak().mz(228.0573).intensity(1800.88))
                                    .addPeaksItem(new SimplePeak().mz(241.0527).intensity(301.77))
                                    .addPeaksItem(new SimplePeak().mz(255.0662).intensity(207.54))
                                    .addPeaksItem(new SimplePeak().mz(257.0839).intensity(3000.70))
                                    .addPeaksItem(new SimplePeak().mz(285.0787).intensity(18479.91))
                                    .addPeaksItem(new SimplePeak().mz(285.2895).intensity(268.90)));

List<AlignedFeature> importedFeatures = sirius.features()
    .addAlignedFeatures(project.getProjectId(), List.of(featureToImport), null, null);

Availability

The sirius-sdk is available as maven artifact.

Gradle

Insert following snippet into your build.gradle to add this package as dependency:

  repositories {
    maven {
        url 'https://gitlab.com/api/v4/projects/66031889/packages/maven'
    }
}

dependencies {
    implementation "io.sirius-ms:sirius-sdk:3.1+sirius6.1.1"
}

Maven

Insert following snippet into your project's POM to add this package as dependency:

<repositories>
  <repository>
    <id>gitlab-maven</id>
    <url>https://gitlab.com/api/v4/projects/66031889/packages/maven</url>
  </repository>
</repositories>

<dependency>
  <groupId>io.sirius-ms</groupId>
  <artifactId>sirius-sdk</artifactId>
  <version>3.1+sirius6.1.1</version>
  <scope>compile</scope>
</dependency>