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Ena 6384 #185

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2d9d09e
Don't allow MAG assembly submission having associated samples with me…
dipayan1985 Sep 23, 2025
e3fa7f9
remove redundant test
dipayan1985 Sep 23, 2025
3ae6849
code cleanup
dipayan1985 Sep 23, 2025
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2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ plugins {
archivesBaseName = 'sequencetools'
group = 'uk.ac.ebi.ena.sequence'

version = '2.28.2'
version = '2.28.3'

sourceCompatibility = JavaVersion.VERSION_17
targetCompatibility = JavaVersion.VERSION_17
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30 changes: 29 additions & 1 deletion src/main/java/uk/ac/ebi/embl/api/validation/submission/SubmissionValidator.java
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Expand Up @@ -30,17 +30,22 @@
import uk.ac.ebi.ena.webin.cli.validator.api.Validator;
import uk.ac.ebi.ena.webin.cli.validator.manifest.*;
import uk.ac.ebi.ena.webin.cli.validator.reference.Attribute;
import uk.ac.ebi.ena.webin.cli.validator.reference.Sample;

public class SubmissionValidator implements Validator<Manifest, ValidationResponse> {

private SubmissionOptions options;
private static final int ERROR_MAX_LENGTH = 2000;
private static final Integer COVID_19_OUTBREAK_TAX_ID = 2697049;
private final TaxonomyClient taxonomyClient;

public SubmissionValidator() {}
public SubmissionValidator() {
this.taxonomyClient = new TaxonomyClient();
}

public SubmissionValidator(SubmissionOptions options) {
this.options = options;
this.taxonomyClient = new TaxonomyClient();
}

public void validate() throws ValidationEngineException {
Expand Down Expand Up @@ -181,6 +186,29 @@ SubmissionOptions mapManifestToSubmissionOptions(Manifest manifest)
msg, ValidationEngineException.ReportErrorType.VALIDATION_ERROR);
}

if (options.assemblyType.equals(AssemblyType.METAGENOME_ASSEMBLEDGENOME)) {
final Sample sample = manifest.getSample();
boolean isSampleOrganismMetagenome = false;

if (sample.getOrganism() != null) {
isSampleOrganismMetagenome = taxonomyClient.isOrganismMetagenome(sample.getOrganism());
} else if (sample.getTaxId() != null) {
isSampleOrganismMetagenome =
taxonomyClient.isMetagenomic(
taxonomyClient.getTaxonByTaxid(sample.getTaxId().longValue()));
}

if (isSampleOrganismMetagenome) {
final String msg =
"Assembly type: MAG (METAGENOME-ASSEMBLED GENOME) cannot reference a sample having a metagenome taxonomy";

reporter.writeToFile(manifest.getReportFile(), Severity.ERROR, msg);

throw new ValidationEngineException(
msg, ValidationEngineException.ReportErrorType.VALIDATION_ERROR);
}
}

options.context = Optional.of(Context.genome);
options.submissionFiles =
Optional.of(setGenomeOptions((GenomeManifest) manifest, assemblyInfo));
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