Examples with Registry org.icgc.dcc.song.client.register.Registry used on opensource projects

Example 1 with Registry

use of org.icgc.dcc.song.client.register.Registry in project SONG by overture-stack.

the class Benchmark method waitForStatus.

public void waitForStatus(PayloadFileVisitor payloadFileVisitor) {
    for (val studyId : payloadFileVisitor.getStudies()) {
        val registry = new Registry(createConfig(studyId), new RestClient());
        val uploadDatas = payloadFileVisitor.getDataForStudy(studyId);
        waitForStatusForStudy(studyId, registry, uploadDatas);
    }
}

Example 2 with Registry

use of org.icgc.dcc.song.client.register.Registry in project SONG by overture-stack.

the class Benchmark method upload.

public void upload(PayloadFileVisitor payloadFileVisitor) {
    for (val studyId : payloadFileVisitor.getStudies()) {
        setupStudy(studyId);
        val registry = new Registry(createConfig(studyId), new RestClient());
        checkState(registry.isAlive(), "The song server '%s' is not running", benchmarkConfig.getAccessToken());
        val uploadDatas = payloadFileVisitor.getDataForStudy(studyId);
        uploadStudy(studyId, registry, uploadDatas);
    }
}

Example 3 with Registry

use of org.icgc.dcc.song.client.register.Registry in project SONG by overture-stack.

the class Benchmark method save.

public void save(PayloadFileVisitor payloadFileVisitor) {
    for (val studyId : payloadFileVisitor.getStudies()) {
        val registry = new Registry(createConfig(studyId), new RestClient());
        val uploadDatas = payloadFileVisitor.getDataForStudy(studyId);
        saveForStudy(studyId, registry, uploadDatas);
    }
}

Example 4 with Registry

use of org.icgc.dcc.song.client.register.Registry in project SONG by overture-stack.

the class Benchmark method saveForStudy.

@SneakyThrows
private void saveForStudy(String studyId, Registry registry, List<UploadData> uploadDataList) {
    val modList = uploadDataList.stream().filter(x -> !x.getUploadState().equals("VALIDATION_ERROR")).collect(toList());
    val total = modList.size();
    val errored = uploadDataList.size() - total;
    log.warn("Num Errored Files: {}", errored);
    int count = 0;
    val saveMonitor = monitor.getStudyMonitor(studyId).getSaveMonitor();
    for (val uploadData : modList) {
        val submittedAnalysisId = uploadData.getAnalysisId();
        val idExists = doesIdExist(uploadData.getStudyId(), registry, submittedAnalysisId);
        log.info("ANALYSIS_ID {} existence: {}", submittedAnalysisId, idExists);
        val rawResponse = saveMonitor.callIncr(() -> registry.save(uploadData.getStudyId(), uploadData.getUploadId(), benchmarkConfig.isIgnoreIdCollisions()));
        val response = readTree(rawResponse.getOutputs());
        val status = response.path("status").textValue();
        val analysisId = response.path("analysisId").textValue();
        uploadData.setAnalysisId(analysisId);
        log.info("Saving {} file {} /{} : {}", uploadData.getStudyId(), ++count, total, uploadData.getFile().getFileName().toString());
    }
}