Examples with RestResponseResult uk.ac.ebi.spot.goci.model.RestResponseResult used on opensource projects

Example 1 with RestResponseResult

use of uk.ac.ebi.spot.goci.model.RestResponseResult in project goci by EBISPOT.

the class GeneCheckingRestService method checkGeneSymbolIsValid.

/**
     * Check gene name returns a response
     *
     * @param gene Gene name to check
     * @return Error message
     */
public String checkGeneSymbolIsValid(String gene, String eRelease) {
    String error = null;
    try {
        RestResponseResult geneDataApiResult = ensemblRestcallHistoryService.getEnsemblRestCallByTypeAndParamAndVersion("lookup_symbol", gene, eRelease);
        if (geneDataApiResult == null) {
            geneDataApiResult = ensemblRestTemplateService.getRestCall(getEndpoint(), gene, "");
            ensemblRestcallHistoryService.create(geneDataApiResult, "lookup_symbol", gene, eRelease);
        }
        if (geneDataApiResult.hasErorr()) {
            error = geneDataApiResult.getError();
        } else {
            if (geneDataApiResult.getRestResult().getObject().has("object_type")) {
                String objectType = geneDataApiResult.getRestResult().getObject().get("object_type").toString();
                if (!(objectType.compareToIgnoreCase("gene") == 0)) {
                    error = "Gene symbol ".concat(gene).concat(" is not valid");
                }
            }
        }
    }// The query returns a 400 error if response returns an error
     catch (Exception e) {
        error = "Gene symbol ".concat(gene).concat(" was not retrieved by Ensembl Mapping. Contact Admin.");
        getLog().error("Gene Symbol".concat(gene).concat(" : was not retrieved. (exception)"), e);
    }
    return error;
}

Example 2 with RestResponseResult

use of uk.ac.ebi.spot.goci.model.RestResponseResult in project goci by EBISPOT.

the class EnsemblMappingPipeline method checkReportedGenes.

/**
     * Check that the reported gene symbols exist and that they are located in the same chromosome as the variant
     *
     * @param reportedGenes
     * @param locations
     */
private void checkReportedGenes(Collection<String> reportedGenes, Collection<Location> locations, String eRelease) throws EnsemblRestIOException {
    for (String reportedGene : reportedGenes) {
        // Remove extra spaces
        reportedGene = reportedGene.replaceAll(" ", "");
        // Skip the iteration if the gene name is in the "gene-to-ignore" list
        if (!getReportedGenesToIgnore().contains(reportedGene)) {
            String webservice = "lookup_symbol";
            RestResponseResult reportedGeneApiResult = ensemblRestcallHistoryService.getEnsemblRestCallByTypeAndParamAndVersion("lookup_symbol", reportedGene, eRelease);
            if (reportedGeneApiResult == null) {
                reportedGeneApiResult = ensemblRestTemplateService.getRestCall(webservice, reportedGene, "");
                ensemblRestcallHistoryService.create(reportedGeneApiResult, "lookup_symbol", reportedGene, eRelease);
            }
            // Check for errors
            if (reportedGeneApiResult.getError() != null && !reportedGeneApiResult.getError().isEmpty()) {
                getEnsemblMappingResult().addPipelineErrors(reportedGeneApiResult.getError());
            }
            if (reportedGeneApiResult.getRestResult() != null) {
                JSONObject reported_gene_result = reportedGeneApiResult.getRestResult().getObject();
                // Check if the gene is in the same chromosome as the variant
                if (reported_gene_result.has("seq_region_name")) {
                    if (locations.size() > 0) {
                        String gene_chromosome = reported_gene_result.getString("seq_region_name");
                        int same_chromosome = 0;
                        for (Location location : locations) {
                            String snp_chromosome = location.getChromosomeName();
                            if (gene_chromosome.equals(snp_chromosome)) {
                                same_chromosome = 1;
                                break;
                            }
                        }
                        if (same_chromosome == 0) {
                            getEnsemblMappingResult().addPipelineErrors("Reported gene " + reportedGene + " is on a different chromosome (chr" + gene_chromosome + ")");
                        }
                    } else {
                        getEnsemblMappingResult().addPipelineErrors("Can't compare the " + reportedGene + " location in Ensembl: no mapping available for the variant");
                    }
                } else // No gene location found
                {
                    getEnsemblMappingResult().addPipelineErrors("Can't find a location in Ensembl for the reported gene " + reportedGene);
                }
            } else {
                getLog().error("Reported gene check for " + reportedGene + " returned no result");
            }
        }
    }
}

Example 3 with RestResponseResult

use of uk.ac.ebi.spot.goci.model.RestResponseResult in project goci by EBISPOT.

the class EnsemblMappingPipeline method run_pipeline.

// Run the pipeline for a given SNP
public synchronized EnsemblMappingResult run_pipeline(String rsId, Collection<String> reportedGenes, String eRelease) throws EnsemblRestIOException {
    // Create our result object
    setEnsemblMappingResult(new EnsemblMappingResult());
    getEnsemblMappingResult().setRsId(rsId);
    // Variation call
    RestResponseResult variationDataApiResult = ensemblRestcallHistoryService.getEnsemblRestCallByTypeAndParamAndVersion("snp", rsId, eRelease);
    if (variationDataApiResult == null) {
        variationDataApiResult = ensemblRestTemplateService.getRestCall("variation", rsId, "");
        ensemblRestcallHistoryService.create(variationDataApiResult, "snp", rsId, eRelease);
    }
    String restApiError = variationDataApiResult.getError();
    // Check for any errors
    if (restApiError != null && !restApiError.isEmpty()) {
        getEnsemblMappingResult().addPipelineErrors(restApiError);
    }
    if (variationDataApiResult.getRestResult() != null) {
        JSONObject variationResult = variationDataApiResult.getRestResult().getObject();
        if (variationResult.has("error")) {
            checkError(variationResult, "variation", "Variant " + rsId + " is not found in Ensembl");
        } else if (variationResult.length() > 0) {
            // Merged SNP
            String currentRsId = variationResult.getString("name");
            getEnsemblMappingResult().setMerged((currentRsId.equals(rsId)) ? 0 : 1);
            if (getEnsemblMappingResult().getMerged() == 1) {
                getEnsemblMappingResult().setCurrentSnpId(currentRsId);
            }
            // Mapping errors
            if (variationResult.has("failed")) {
                getEnsemblMappingResult().addPipelineErrors(variationResult.getString("failed"));
            }
            // Mapping and genomic context calls
            JSONArray mappings = variationResult.getJSONArray("mappings");
            Collection<Location> locations = getMappings(mappings, eRelease);
            getEnsemblMappingResult().setLocations(locations);
            // Add genomic context
            if (locations.size() > 0) {
                // This implies there is at least one variant location.
                if (variationResult.has("most_severe_consequence")) {
                    getEnsemblMappingResult().setFunctionalClass(variationResult.getString("most_severe_consequence"));
                }
                // Genomic context (loop over the "locations" object)
                for (Location snp_location : locations) {
                    getAllGenomicContexts(snp_location, eRelease);
                }
            }
        }
    } else {
        getLog().error("Variation call for SNP " + rsId + " returned no result");
    }
    // Reported genes checks
    if (reportedGenes.size() > 0) {
        checkReportedGenes(reportedGenes, getEnsemblMappingResult().getLocations(), eRelease);
    }
    return getEnsemblMappingResult();
}

Example 4 with RestResponseResult

use of uk.ac.ebi.spot.goci.model.RestResponseResult in project goci by EBISPOT.

the class EnsemblRestTemplateService method getRestCall.

public RestResponseResult getRestCall(String endpoint_type, String data, String rest_parameters) {
    String endpoint = getEndpoints().get(endpoint_type);
    URL url = null;
    RestResponseResult restResponseResult = new RestResponseResult();
    try {
        // Build URL
        if (!Objects.equals(rest_parameters, "")) {
            Matcher matcher = Pattern.compile("^\\?").matcher(rest_parameters);
            if (!matcher.matches()) {
                rest_parameters = '?' + rest_parameters;
            }
        }
        url = new URL(getServer() + endpoint + data + rest_parameters);
        restResponseResult = fetch(url.toString());
    } catch (InterruptedException | MalformedURLException e) {
    //   getLog().error("Encountered a " + e.getClass().getSimpleName() +
    //           " whilst trying to run mapping of SNP", e);
    //    throw new EnsemblRestIOException("Encountered a " + e.getClass().getSimpleName() +
    //            " whilst trying to run mapping of SNP", e);
    }
    return restResponseResult;
}

Example 5 with RestResponseResult

use of uk.ac.ebi.spot.goci.model.RestResponseResult in project goci by EBISPOT.

the class EnsemblRestTemplateService method fetch.

public RestResponseResult fetch(String url) throws InterruptedException {
    ResponseEntity<String> out;
    Boolean ensemblDone = false;
    int maxTries = 0;
    RestResponseResult ensembl = new RestResponseResult();
    while ((!ensemblDone) && (maxTries < 5)) {
        ensembl = this.exec(url);
        if (ensembl.getStatus() == 429) {
            maxTries = maxTries + 1;
            Thread.sleep(ensembl.getWaitSeconds() * 1000);
        } else {
            ensemblDone = true;
        }
    }
    if (maxTries > 4) {
        getLog().debug("Failed to obtain a result from from '" + url + "' after after " + maxTries + " attempts");
        String extendedError = "Failed to obtain a result from from '" + url + "' after after " + maxTries + " attempts";
        ensembl.setError(extendedError);
    }
    return ensembl;
}