@Override
public String queryVariantRaw(
ExtendedFileInfo file, String chromosome, VariantFetchParams params) {
params.setFormat(ReturnFormat.vcf);
String rtn = queryVariantsInternal(file, chromosome, params);
logger.info(rtn);
return rtn;
}
@Override
public List<VariantRecord> queryVariantJSON(
ExtendedFileInfo file, String chromosome, VariantFetchParams params) {
try {
params.setFormat(ReturnFormat.json);
String rtn = queryVariantsInternal(file, chromosome, params);
logger.info(rtn);
JsonNode responseNode = mapper.readValue(rtn, JsonNode.class).findPath(ITEMS);
List<VariantRecord> records = new ArrayList<VariantRecord>();
for (int i = 0; i < responseNode.size(); i++) {
records.add(
(VariantRecord) mapper.readValue(responseNode.get(i).toString(), VariantRecord.class));
}
return records;
} catch (BaseSpaceException bs) {
throw bs;
} catch (Throwable t) {
throw new RuntimeException("Error during JSON query " + t);
}
}
protected String queryVariantsInternal(
ExtendedFileInfo file, String chromosome, VariantFetchParams params) {
if (file == null || file.getHrefVariants() == null) {
throw new IllegalArgumentException(
"null VariantFile or hrefVariants property for VariantFile object");
}
try {
MultivaluedMap<String, String> queryParams =
params == null ? new MultivaluedMapImpl() : params.toMap();
WebResource resource =
getClient()
.resource(
UriBuilder.fromUri(configuration.getApiRootUri())
.path(file.getHrefVariants())
.path("variants")
.path(chromosome)
.build())
.queryParams(queryParams);
ClientResponse response =
getClient()
.resource(resource.getURI())
.accept(MediaType.APPLICATION_XHTML_XML, MediaType.APPLICATION_JSON)
.get(ClientResponse.class);
switch (response.getClientResponseStatus()) {
case OK:
return response.getEntity(String.class);
default:
BasicResponse status =
mapper.readValue(response.getEntity(String.class), BasicResponse.class);
throw new IllegalArgumentException(status.getResponseStatus().getMessage());
}
} catch (BaseSpaceException bs) {
throw bs;
} catch (IllegalArgumentException iae) {
throw iae;
} catch (Throwable t) {
throw new RuntimeException(t);
}
}