public static VariantSource readVariantSource(
CatalogManager catalogManager, Study study, File file) throws CatalogException {
// TODO: Fix aggregate and studyType
VariantSource source =
new VariantSource(
file.getName(),
Integer.toString(file.getId()),
Integer.toString(study.getId()),
study.getName());
URI fileUri = catalogManager.getFileUri(file);
return VariantStorageManager.readVariantSource(Paths.get(fileUri.getPath()), source);
}
public QueryResult<File> index(
int fileId, int outDirId, String storageEngine, String sessionId, QueryOptions options)
throws IOException, CatalogException, AnalysisExecutionException {
if (options == null) {
options = new QueryOptions();
}
final boolean execute = options.getBoolean(AnalysisJobExecuter.EXECUTE);
final boolean simulate = options.getBoolean(AnalysisJobExecuter.SIMULATE);
final boolean recordOutput = options.getBoolean(AnalysisJobExecuter.RECORD_OUTPUT);
final long start = System.currentTimeMillis();
/** Query catalog for user data. * */
String userId = catalogManager.getUserIdBySessionId(sessionId);
File file = catalogManager.getFile(fileId, sessionId).first();
File outDir = catalogManager.getFile(outDirId, sessionId).first();
int studyIdByOutDirId = catalogManager.getStudyIdByFileId(outDirId);
Study study = catalogManager.getStudy(studyIdByOutDirId, sessionId).getResult().get(0);
if (file.getType() != File.Type.FILE) {
throw new CatalogException(
"Expected file type = " + File.Type.FILE + " instead of " + file.getType());
}
final String dbName;
if (options.containsKey(DB_NAME)) {
dbName = options.getString(DB_NAME);
} else {
if (study.getAttributes().containsKey(DB_NAME)
&& study.getAttributes().get(DB_NAME) != null) {
dbName = study.getAttributes().get(DB_NAME).toString();
} else {
int projectId = catalogManager.getProjectIdByStudyId(study.getId());
String alias =
catalogManager
.getProject(projectId, new QueryOptions("include", "alias"), sessionId)
.first()
.getAlias();
dbName =
Config.getAnalysisProperties()
.getProperty(OPENCGA_ANALYSIS_STORAGE_DATABASE_PREFIX, "opencga_")
+ userId
+ "_"
+ alias;
}
}
// TODO: Check if file can be indexed
// ObjectMap to fill with modifications over the indexed file (like new attributes or jobId)
ObjectMap indexFileModifyParams = new ObjectMap("attributes", new ObjectMap());
/** Create temporal Job Outdir * */
final URI temporalOutDirUri;
final String randomString = "I_" + StringUtils.randomString(10);
if (simulate) {
temporalOutDirUri = createSimulatedOutDirUri(randomString);
} else {
temporalOutDirUri =
catalogManager.createJobOutDir(studyIdByOutDirId, randomString, sessionId);
}
List<Sample> sampleList;
/** Create index file* */
final File index;
if (options.containsKey(INDEX_FILE_ID)) {
logger.debug("Using an existing indexedFile.");
int indexFileId = options.getInt(INDEX_FILE_ID);
index = catalogManager.getFile(indexFileId, sessionId).first();
if (index.getType() != File.Type.INDEX) {
throw new CatalogException("Expected {type: INDEX} in IndexedFile " + indexFileId);
}
if (index.getStatus() != File.Status.READY) {
throw new CatalogException("Expected {status: READY} in IndexedFile " + indexFileId);
}
if (simulate) {
index.setStatus(File.Status.INDEXING);
} else {
ObjectMap parameters = new ObjectMap("status", File.Status.INDEXING);
catalogManager.modifyFile(index.getId(), parameters, sessionId);
}
/** Get file samples * */
sampleList =
catalogManager
.getAllSamples(study.getId(), new QueryOptions("id", index.getSampleIds()), sessionId)
.getResult();
} else {
/** Get file samples * */
sampleList = getFileSamples(study, file, indexFileModifyParams, simulate, options, sessionId);
String indexedFileDescription = "Indexation of " + file.getName() + " (" + fileId + ")";
String indexedFileName = file.getName() + "." + storageEngine;
String indexedFilePath = Paths.get(outDir.getPath(), indexedFileName).toString();
if (simulate) {
index =
new File(
-10,
indexedFileName,
File.Type.INDEX,
file.getFormat(),
file.getBioformat(),
indexedFilePath,
userId,
TimeUtils.getTime(),
indexedFileDescription,
File.Status.INDEXING,
-1,
-1,
null,
-1,
null,
null,
new HashMap<String, Object>());
} else {
index =
catalogManager
.createFile(
studyIdByOutDirId,
File.Type.INDEX,
file.getFormat(),
file.getBioformat(),
indexedFilePath,
null,
null,
indexedFileDescription,
File.Status.INDEXING,
0,
-1,
null,
-1,
null,
null,
false,
null,
sessionId)
.first();
}
}
/** Create commandLine * */
String commandLine =
createCommandLine(
study,
file,
index,
sampleList,
storageEngine,
temporalOutDirUri,
indexFileModifyParams,
dbName,
options);
if (options.containsKey(PARAMETERS)) {
List<String> extraParams = options.getAsStringList(PARAMETERS);
for (String extraParam : extraParams) {
commandLine += " " + extraParam;
}
}
/** Create job * */
ObjectMap jobResourceManagerAttributes = new ObjectMap();
jobResourceManagerAttributes.put(Job.TYPE, Job.Type.INDEX);
jobResourceManagerAttributes.put(Job.INDEXED_FILE_ID, index.getId());
String jobName = "index";
String jobDescription = "Indexing file " + file.getName() + " (" + fileId + ")";
final Job job =
AnalysisJobExecuter.createJob(
catalogManager,
studyIdByOutDirId,
jobName,
OPENCGA_STORAGE_BIN_NAME,
jobDescription,
outDir,
Collections.<Integer>emptyList(),
sessionId,
randomString,
temporalOutDirUri,
commandLine,
execute,
simulate,
recordOutput,
jobResourceManagerAttributes)
.first();
if (simulate) {
index.getAttributes().put("job", job);
// index.getAttributes().putAll(indexFileModifyParams.getMap("attributes"));
index.setSampleIds(indexFileModifyParams.getAsIntegerList("sampleIds"));
// VariantSource variantSource = (VariantSource)
// index.getAttributes().get("variantSource");
// for (Map.Entry<String, Integer> entry :
// variantSource.getSamplesPosition().entrySet()) {
// System.out.println("entry.getKey() = " + entry.getKey());
// System.out.println("entry.getValue() = " + entry.getValue());
// }
// for (String s : variantSource.getSamples()) {
// System.out.println("sample = " + s);
// }
// variantSource.setSamplesPosition(new HashMap<String, Integer>());
return new QueryResult<>(
"indexFile",
(int) (System.currentTimeMillis() - start),
1,
1,
"",
"",
Collections.singletonList(index));
} else {
/** Update IndexFile to add extra information (jobId, sampleIds, attributes, ...) * */
indexFileModifyParams.put("jobId", job.getId());
Set<Integer> jobIds;
try {
jobIds = new HashSet<>(new ObjectMap(index.getAttributes()).getAsIntegerList("jobIds"));
} catch (Exception ignore) {
jobIds = new HashSet<>(1);
}
if (index.getJobId() > 0) {
jobIds.add(index.getJobId());
}
jobIds.add(job.getId());
indexFileModifyParams.getMap("attributes").put("jobIds", jobIds);
catalogManager.modifyFile(index.getId(), indexFileModifyParams, sessionId).getResult();
return new QueryResult<>(
"indexFile",
(int) (System.currentTimeMillis() - start),
1,
1,
"",
"",
catalogManager.getFile(index.getId(), sessionId).getResult());
}
}
private List<Sample> getFileSamples(
Study study,
File file,
ObjectMap indexFileModifyParams,
boolean simulate,
QueryOptions options,
String sessionId)
throws CatalogException {
List<Sample> sampleList;
QueryOptions queryOptions =
new QueryOptions(
"include",
Arrays.asList("projects.studies.samples.id", "projects.studies.samples.name"));
if (file.getSampleIds() == null || file.getSampleIds().isEmpty()) {
// Read samples from file
List<String> sampleNames = null;
switch (file.getBioformat()) {
case VARIANT:
{
if (file.getAttributes().containsKey("variantSource")) {
Object variantSource = file.getAttributes().get("variantSource");
if (variantSource instanceof VariantSource) {
sampleNames = ((VariantSource) variantSource).getSamples();
} else if (variantSource instanceof Map) {
sampleNames = new ObjectMap((Map) variantSource).getAsStringList("samples");
} else {
logger.warn(
"Unexpected object type of variantSource ({}) in file attributes. Expected {} or {}",
variantSource.getClass(),
VariantSource.class,
Map.class);
}
}
if (sampleNames == null) {
VariantSource variantSource = readVariantSource(catalogManager, study, file);
indexFileModifyParams
.get("attributes", ObjectMap.class)
.put("variantSource", variantSource);
sampleNames = variantSource.getSamples();
}
}
break;
default:
return new LinkedList<>();
// throw new CatalogException("Unknown to get samples names from
// bioformat " + file.getBioformat());
}
// Find matching samples in catalog with the sampleName from the VariantSource.
queryOptions.add("name", sampleNames);
sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();
// check if all file samples exists on Catalog
if (sampleList.size()
!= sampleNames.size()) { // Size does not match. Find the missing samples.
Set<String> set = new HashSet<>(sampleNames);
for (Sample sample : sampleList) {
set.remove(sample.getName());
}
logger.warn("Missing samples: m{}", set);
if (options.getBoolean(CREATE_MISSING_SAMPLES, true)) {
for (String sampleName : set) {
if (simulate) {
sampleList.add(new Sample(-1, sampleName, file.getName(), null, null));
} else {
sampleList.add(
catalogManager
.createSample(
study.getId(), sampleName, file.getName(), null, null, null, sessionId)
.first());
}
}
} else {
throw new CatalogException(
"Can not find samples " + set + " in catalog"); // FIXME: Create missing samples??
}
}
} else {
// Get samples from file.sampleIds
queryOptions.add("id", file.getSampleIds());
sampleList = catalogManager.getAllSamples(study.getId(), queryOptions, sessionId).getResult();
}
List<Integer> sampleIdsList = new ArrayList<>(sampleList.size());
for (Sample sample : sampleList) {
sampleIdsList.add(sample.getId());
//
// sampleIdsString.append(sample.getName()).append(":").append(sample.getId()).append(",");
}
indexFileModifyParams.put("sampleIds", sampleIdsList);
return sampleList;
}
/**
* @param study Study where file is located
* @param file File to be indexed
* @param indexFile Generated index file
* @param sampleList
* @param storageEngine StorageEngine to be used
* @param outDirUri Index outdir
* @param indexFileModifyParams This map will be used to modify the indexFile
* @param dbName
* @return CommandLine
* @throws org.opencb.opencga.catalog.db.CatalogDBException
* @throws CatalogIOManagerException
*/
private String createCommandLine(
Study study,
File file,
File indexFile,
List<Sample> sampleList,
String storageEngine,
URI outDirUri,
final ObjectMap indexFileModifyParams,
final String dbName,
QueryOptions options)
throws CatalogException {
// Create command line
String userId = file.getOwnerId();
String name = file.getName();
String commandLine;
ObjectMap indexAttributes = indexFileModifyParams.get("attributes", ObjectMap.class);
String opencgaStorageBin =
Paths.get(Config.getOpenCGAHome(), "bin", OPENCGA_STORAGE_BIN_NAME).toString();
if (file.getBioformat() == File.Bioformat.ALIGNMENT
|| name.endsWith(".bam")
|| name.endsWith(".sam")) {
int chunkSize = 200; // TODO: Read from properties.
commandLine =
new StringBuilder(opencgaStorageBin)
.append(" --storage-engine ")
.append(storageEngine)
.append(" index-alignments ")
.append(" --file-id ")
.append(indexFile.getId())
.append(" --database ")
.append(dbName)
.append(" --input ")
.append(catalogManager.getFileUri(file))
.append(" --calculate-coverage ")
.append(chunkSize)
.append(" --mean-coverage ")
.append(chunkSize)
.append(" --outdir ")
.append(outDirUri)
// .append(" --credentials ")
.toString();
indexAttributes.put("chunkSize", chunkSize);
} else if (name.endsWith(".fasta") || name.endsWith(".fasta.gz")) {
throw new UnsupportedOperationException();
} else if (file.getBioformat() == File.Bioformat.VARIANT
|| name.contains(".vcf")
|| name.contains(".vcf.gz")) {
StringBuilder sampleIdsString = new StringBuilder();
for (Sample sample : sampleList) {
sampleIdsString.append(sample.getName()).append(":").append(sample.getId()).append(",");
}
StringBuilder sb =
new StringBuilder(opencgaStorageBin)
.append(" --storage-engine ")
.append(storageEngine)
.append(" index-variants ")
.append(" --file-id ")
.append(indexFile.getId())
.append(" --study-name \'")
.append(study.getName())
.append("\'")
.append(" --study-id ")
.append(study.getId())
// .append(" --study-type ").append(study.getType())
.append(" --database ")
.append(dbName)
.append(" --input ")
.append(catalogManager.getFileUri(file))
.append(" --outdir ")
.append(outDirUri)
.append(" --include-genotypes ")
.append(" --compress-genotypes ")
.append(" --include-stats ")
// .append(" --sample-ids ").append(sampleIdsString)
// .append(" --credentials ")
;
if (options.getBoolean(VariantStorageManager.ANNOTATE, true)) {
sb.append(" --annotate ");
}
if (options.getBoolean(VariantStorageManager.INCLUDE_SRC, false)) {
sb.append(" --include-src ");
}
commandLine = sb.toString();
} else {
return null;
}
indexAttributes.put(INDEXED_FILE, file.getId());
indexAttributes.put(DB_NAME, dbName);
indexAttributes.put(STORAGE_ENGINE, storageEngine);
return commandLine;
}