Examples with CivicApiWrapper com.hartwig.hmftools.apiclients.civic.api.CivicApiWrapper used on opensource projects

Example 1 with CivicApiWrapper

use of com.hartwig.hmftools.apiclients.civic.api.CivicApiWrapper in project hmftools by hartwigmedical.

the class CivicAnalyzer method civicVariantAlterations.

@NotNull
private static List<Alteration> civicVariantAlterations(@NotNull final List<VariantReport> reportedVariants, @NotNull final Collection<HmfGenomeRegion> geneRegions, @NotNull final Set<String> relevantDoids) {
    LOGGER.info("  Fetching civic variant alterations...");
    final List<Alteration> alterations = Lists.newArrayList();
    final CivicApiWrapper civicApi = new CivicApiWrapper();
    for (final HmfGenomeRegion region : geneRegions) {
        final List<VariantReport> reportedVariantsInGene = reportedVariants.stream().filter(variantReport -> region.gene().equals(variantReport.gene())).collect(Collectors.toList());
        if (!reportedVariantsInGene.isEmpty()) {
            for (final VariantReport variantReport : reportedVariantsInGene) {
                alterations.addAll(queryCivicAlteration(region.entrezId(), variantList -> Alteration.from(variantReport, variantList, relevantDoids), "  Failed to get civic variants for variant: " + variantReport.variant().chromosomePosition()));
            }
        }
    }
    civicApi.releaseResources();
    return alterations;
}

Example 2 with CivicApiWrapper

use of com.hartwig.hmftools.apiclients.civic.api.CivicApiWrapper in project hmftools by hartwigmedical.

the class CivicAnalyzer method civicWildTypeAlterations.

@NotNull
private static List<Alteration> civicWildTypeAlterations(@NotNull final List<HmfGenomeRegion> nonWildTypeGenes, @NotNull final Set<String> relevantDoids) {
    LOGGER.info("  Fetching civic wild type alterations...");
    final CivicApiWrapper civicApi = new CivicApiWrapper();
    final Set<String> nonWildTypeEntrezIds = nonWildTypeGenes.stream().flatMap(hmfGenomeRegion -> hmfGenomeRegion.entrezId().stream().map(Object::toString)).collect(Collectors.toSet());
    final List<Alteration> wildTypeAlterations = civicApi.getAllWildTypeVariants().filter(civicVariant -> !nonWildTypeEntrezIds.contains(civicVariant.entrezId())).groupBy(CivicVariantWithEvidence::gene).flatMap(pair -> pair.toList().map(variantList -> Alteration.fromWildType(pair.getKey(), variantList, relevantDoids)).filter(alteration -> !alteration.getMatches().isEmpty()).toObservable()).toList().blockingGet();
    civicApi.releaseResources();
    return wildTypeAlterations;
}

Example 3 with CivicApiWrapper

use of com.hartwig.hmftools.apiclients.civic.api.CivicApiWrapper in project hmftools by hartwigmedical.

the class CivicAnalyzer method queryCivicAlteration.

@NotNull
private static List<Alteration> queryCivicAlteration(@NotNull final List<Integer> entrezIds, io.reactivex.functions.Function<List<CivicVariantWithEvidence>, Alteration> alterationBuilder, @NotNull final String error) {
    final CivicApiWrapper civicApi = new CivicApiWrapper();
    final List<Alteration> result = Lists.newArrayList();
    try {
        result.addAll(Observable.fromIterable(entrezIds).flatMap(civicApi::getVariantsForGene).toList().map(alterationBuilder).filter(alteration -> !alteration.getMatches().isEmpty()).toObservable().toList().blockingGet());
    } catch (final Throwable throwable) {
        LOGGER.error("{}. Error message: {}", error, throwable.getMessage());
    }
    civicApi.releaseResources();
    return result;
}