@Override
public AlignmentDBAdaptor getDBAdaptor(String dbName) {
SequenceDBAdaptor adaptor;
if (dbName == null || dbName.isEmpty()) {
dbName =
configuration
.getStorageEngine(STORAGE_ENGINE_ID)
.getAlignment()
.getOptions()
.getString(Options.DB_NAME.key(), Options.DB_NAME.defaultValue());
logger.info(
"Using default dbName '{}' in MongoDBAlignmentStorageManager.getDBAdaptor()", dbName);
}
logger.debug("Using {} : '{}'", Options.DB_NAME.key(), dbName);
Path path =
Paths.get(
configuration
.getStorageEngine(STORAGE_ENGINE_ID)
.getAlignment()
.getOptions()
.getString(OPENCGA_STORAGE_SEQUENCE_DBADAPTOR, ""));
if (path == null
|| path.toString() == null
|| path.toString().isEmpty()
|| !path.toFile().exists()) {
adaptor = new CellBaseSequenceDBAdaptor();
} else {
if (path.toString().endsWith("sqlite.db")) {
adaptor = new SqliteSequenceDBAdaptor(path);
} else {
adaptor = new CellBaseSequenceDBAdaptor(path);
}
}
return new IndexedAlignmentDBAdaptor(adaptor, getMongoCredentials(dbName));
}
@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>
}