@Override
public QueryResult next(String chromosome, int position, QueryOptions options) {
String featureType = options.getString("featureType", null);
String featureClass = options.getString("featureClass", null);
BasicDBList chunksId = new BasicDBList();
String chunkId =
chromosome
+ "_"
+ getChunkId(position, regulatoryRegionChunkSize)
+ "_"
+ regulatoryRegionChunkSize / 1000
+ "k";
chunksId.add(chunkId);
// TODO: Add query to find next item considering next chunk
// db.regulatory_region.find({ "chromosome" : "19" , "start" : { "$gt" : 62005} , "featureType"
// : "TF_binding_site_motif"}).sort({start:1}).limit(1)
QueryBuilder builder;
if (options.getString("strand") == null
|| (options.getString("strand").equals("1") || options.getString("strand").equals("+"))) {
// db.core.find({chromosome: "1", start: {$gt: 1000000}}).sort({start: 1}).limit(1)
builder =
QueryBuilder.start("_chunkIds")
.in(chunksId)
.and("chromosome")
.is(chromosome)
.and("start")
.greaterThan(position);
options.put("sort", new BasicDBObject("start", 1));
options.put("limit", 1);
} else {
builder =
QueryBuilder.start("_chunkIds")
.in(chunksId)
.and("chromosome")
.is(chromosome)
.and("end")
.lessThan(position);
options.put("sort", new BasicDBObject("end", -1));
options.put("limit", 1);
}
if (featureType != null) {
builder.and("featureType").is(featureType);
}
if (featureClass != null) {
builder.and("featureClass").is(featureClass);
}
System.out.println(builder.get());
return executeQuery("result", builder.get(), options);
}
@GET
@Path("/{fileId}/fetch")
@Produces("application/json")
public Response fetch(
@PathParam("fileId") @DefaultValue("") String fileId,
@QueryParam("backend") String backend,
@QueryParam("dbName") String dbName,
@QueryParam("bioformat") @DefaultValue("") String bioformat,
@QueryParam("region") String region,
@QueryParam("path") @DefaultValue("") String path,
@QueryParam("view_as_pairs") @DefaultValue("false") boolean view_as_pairs,
@QueryParam("include_coverage") @DefaultValue("true") boolean include_coverage,
@QueryParam("process_differences") @DefaultValue("true") boolean process_differences,
@QueryParam("histogram") @DefaultValue("false") boolean histogram,
@QueryParam("interval") @DefaultValue("2000") int interval) {
try {
switch (bioformat) {
case "vcf":
break;
case "bam":
AlignmentStorageManager sm = StorageManagerFactory.getAlignmentStorageManager(backend);
ObjectMap params = new ObjectMap();
AlignmentDBAdaptor dbAdaptor = sm.getDBAdaptor(dbName, params);
QueryOptions options = new QueryOptions();
if (path != null && !path.isEmpty()) {
String rootDir =
OpenCGAStorageService.getInstance()
.getProperties()
.getProperty(
"OPENCGA.STORAGE.ROOTDIR",
"/home/cafetero/opencga/catalog/users/jcoll/projects/1/1/");
options.put(
AlignmentDBAdaptor.QO_BAM_PATH,
Paths.get(rootDir, path.replace(":", "/")).toString());
}
options.put(AlignmentDBAdaptor.QO_FILE_ID, fileId);
options.put(AlignmentDBAdaptor.QO_VIEW_AS_PAIRS, view_as_pairs);
options.put(AlignmentDBAdaptor.QO_INCLUDE_COVERAGE, include_coverage);
options.put(AlignmentDBAdaptor.QO_PROCESS_DIFFERENCES, process_differences);
options.put(AlignmentDBAdaptor.QO_INTERVAL_SIZE, interval);
options.put(AlignmentDBAdaptor.QO_HISTOGRAM, histogram);
// options.put(AlignmentDBAdaptor.QO_COVERAGE_CHUNK_SIZE, chunkSize);
QueryResult queryResult;
if (histogram) {
queryResult = dbAdaptor.getAllIntervalFrequencies(new Region(region), options);
} else {
queryResult =
dbAdaptor.getAllAlignmentsByRegion(Arrays.asList(new Region(region)), options);
}
return createOkResponse(queryResult);
default:
return createErrorResponse("Unknown bioformat " + bioformat);
}
} catch (Exception e) {
e.printStackTrace();
return createErrorResponse(e.toString());
}
return createErrorResponse("Unimplemented!");
}
