@Override
public CoverageMongoDBWriter getDBWriter(String dbName) {
String fileId =
configuration
.getStorageEngine(STORAGE_ENGINE_ID)
.getAlignment()
.getOptions()
.getString(Options.FILE_ID.key());
return new CoverageMongoDBWriter(getMongoCredentials(dbName), fileId);
}
@Override
public URI load(URI inputUri) throws IOException {
checkUri(inputUri, "input uri");
Path input = Paths.get(inputUri.getPath());
// ObjectMapper objectMapper = new ObjectMapper();
// System.out.println("configuration = " +
// objectMapper.writerWithDefaultPrettyPrinter().writeValueAsString(configuration));
ObjectMap options =
configuration.getStorageEngine(STORAGE_ENGINE_ID).getAlignment().getOptions();
String fileId =
options.getString(Options.FILE_ID.key(), input.getFileName().toString().split("\\.")[0]);
String dbName = options.getString(Options.DB_NAME.key(), Options.DB_NAME.defaultValue());
// Reader
AlignmentCoverageJsonDataReader alignmentDataReader = getAlignmentCoverageJsonDataReader(input);
alignmentDataReader.setReadRegionCoverage(false); // Only load mean coverage
// Writer
CoverageMongoDBWriter dbWriter = this.getDBWriter(dbName);
// Runner
Runner<AlignmentRegion> runner =
new Runner<>(
alignmentDataReader,
Arrays.asList(dbWriter),
new LinkedList<Task<AlignmentRegion>>(),
1);
logger.info("Loading coverage...");
long start = System.currentTimeMillis();
runner.run();
long end = System.currentTimeMillis();
logger.info("end - start = " + (end - start) / 1000.0 + "s");
logger.info("Alignments loaded!");
return inputUri; // TODO: Return something like this: mongo://<host>/<dbName>/<collectionName>
}