8bc46bda10949ec121c784fa0dd70deea12438f9,foreman/data_refinery_foreman/foreman/management/commands/rerun_salmon_old_samples.py,,update_salmon_versions,#Any#,37

Before Change

    latest_salmon_version = salmon_versions[0]

    // find the samples that were not processed with `latest_salmon_version` and trigger new processor jobs for them
    newest_computational_results = ComputationalResult.objects.all()\
        .filter(
            samples=OuterRef("id"),
            processor__name=ProcessorEnum.SALMON_QUANT.value["name"]
        )\
        .order_by("-created_at")
    
    samples = experiment.samples.all().annotate(
            salmon_version=Subquery(newest_computational_results.values("organism_index__salmon_version")[:1])
        )\

After Change

logger = get_and_configure_logger(__name__)

def update_salmon_versions(experiment: Experiment):
    quant_results = get_quant_results_for_experiment(experiment)\
                        .order_by("-organism_index__created_at")\
                        .prefetch_related("organism_index")\
                        .prefetch_related("samples__original_files")

    latest_salmon_version = None
    for quant_result in quant_results:
        if not latest_salmon_version:
            // we can safely ignore the latest salmon version, that will be the first
            // quant result. Note we are ordering by -organism_index__created_at
            latest_salmon_version = quant_result.organism_index.salmon_version
        elif latest_salmon_version != quant_result.organism_index.salmon_version:
            // we found a quant result associated with an experiment where we need to run salmon
            // hopefully each computational result is associated with a single sample
            for sample in quant_result.samples.all():
                original_files = list(sample.original_files.all())

                if not len(original_files): continue

                // Ensure that there"s no processor jobs for these original files that the foreman
                // might want to retry (failed | hung | lost)
                has_open_processor_job = ProcessorJob.objects.all()\
                                            .filter(original_files = original_files[0], pipeline_applied=ProcessorPipeline.SALMON)\
                                            .filter(
                                                Q(success=False, retried=False, no_retry=False) | 
                                                Q(success=None, retried=False, no_retry=False, start_time__isnull=False, end_time=None, nomad_job_id__isnull=False) |
                                                Q(success=None, retried=False, no_retry=False, start_time=None, end_time=None)
                                            )\
                                            .exists()
                if (has_open_processor_job):
                    continue

                create_processor_job_for_original_files(original_files)

def update_salmon_all_experiments():
    Creates a tximport job for all eligible experiments.
    eligible_experiments = Experiment.objects.all()\
        .filter(technology="RNA-SEQ", num_processed_samples=0)\

Instances