public void parseStatsMessage(Message<Map<String, Map<String, byte[]>>> message)
throws IOException {
Map<String, Map<String, byte[]>> a = message.getPayload();
for (String type : a.keySet()) {
Map<String, byte[]> b = a.get(type);
for (String filename : b.keySet()) {
log.info("Processing stats for: " + filename);
BufferedInputStream bis =
new BufferedInputStream(new ByteArrayInputStream(b.get(filename)));
File outFile = null;
OutputStream out = null;
try {
outFile = new File(new File("/tmp/"), filename);
try {
out = new FileOutputStream(outFile);
byte[] buf = new byte[16884];
int len;
while ((len = bis.read(buf)) > 0) {
out.write(buf, 0, len);
}
} catch (IOException e) {
log.error("Could not write temporary file: " + outFile.getAbsolutePath());
e.printStackTrace();
} finally {
try {
bis.close();
} catch (IOException e) {
// ignore
}
}
} finally {
if (out != null) {
out.close();
}
if (outFile != null) {
File newFile = misoFileManager.storeFile(Run.class, "stats", outFile);
if (newFile != null && outFile.delete()) {
File destination = new File(newFile.getParentFile(), newFile.getName().split("-")[0]);
if (LimsUtils.checkDirectory(destination, true)) {
if (LimsUtils.unzipFile(newFile, destination)) {
newFile.delete();
}
}
}
}
}
}
}
}
public JSONObject changePlateLocation(HttpSession session, JSONObject json) {
Long plateId = json.getLong("plateId");
String locationBarcode = json.getString("locationBarcode");
try {
String newLocation = LimsUtils.lookupLocation(locationBarcode);
if (newLocation != null) {
User user =
securityManager.getUserByLoginName(
SecurityContextHolder.getContext().getAuthentication().getName());
// Plate<LinkedList<Plateable>, Plateable> plate = requestManager.<LinkedList<Plateable>,
// Plateable> getPlateById(plateId);
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
plate.setLocationBarcode(locationBarcode);
/*
Note note = new Note();
note.setInternalOnly(true);
note.setText("Location changed to " + newLocation + " by " + user.getLoginName() + " on " + new Date());
note.setOwner(user);
note.setCreationDate(new Date());
plate.getNotes().add(note);
requestManager.saveSampleNote(sample, note);
*/
requestManager.savePlate(plate);
} else {
return JSONUtils.SimpleJSONError("New location barcode not recognised");
}
} catch (IOException e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError(e.getMessage());
}
return JSONUtils.SimpleJSONResponse("Plate saved successfully");
}
@Test
public void testImportBulkInputXLS() {
try {
InputStream in =
FormUtilsTests.class.getClassLoader().getResourceAsStream("test-bulk_input.xlsx");
LimsUtils.writeFile(in, testSampleBulkInputXlsFile);
User u = new UserImpl();
u.setLoginName("testBulkImportUser");
List<Sample> samples =
FormUtils.importSampleInputSpreadsheet(
testSampleBulkInputXlsFile,
u,
new MockFormTestRequestManager(),
new DefaultLibraryNamingScheme());
log.info("Imported :: " + LimsUtils.join(samples, " | "));
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
} finally {
testSampleBulkInputXlsFile.delete();
}
}
public JSONObject downloadPlateInputForm(HttpSession session, JSONObject json) {
if (json.has("documentFormat")) {
String documentFormat = json.getString("documentFormat");
try {
File f =
misoFileManager.getNewFile(
Plate.class,
"forms",
"PlateInputForm-" + LimsUtils.getCurrentDateAsString() + "." + documentFormat);
FormUtils.createPlateInputSpreadsheet(f);
return JSONUtils.SimpleJSONResponse("" + f.getName().hashCode());
} catch (Exception e) {
e.printStackTrace();
return JSONUtils.SimpleJSONError("Failed to get plate input form: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("Missing project ID or document format supplied.");
}
}
@Transactional(readOnly = false, rollbackFor = IOException.class)
@TriggersRemove(
cacheName = {"userCache", "lazyUserCache"},
keyGenerator =
@KeyGenerator(
name = "HashCodeCacheKeyGenerator",
properties = {
@Property(name = "includeMethod", value = "false"),
@Property(name = "includeParameterTypes", value = "false")
}))
public long saveUser(User user) throws IOException {
Blob roleBlob = null;
if (user.getRoles() != null) {
List<String> roles = new ArrayList<String>(Arrays.asList(user.getRoles()));
if (user.isExternal() && !roles.contains("ROLE_EXTERNAL")) roles.add("ROLE_EXTERNAL");
if (user.isInternal() && !roles.contains("ROLE_INTERNAL")) roles.add("ROLE_INTERNAL");
if (user.isAdmin() && !roles.contains("ROLE_ADMIN")) roles.add("ROLE_ADMIN");
user.setRoles(roles.toArray(new String[user.getRoles().length]));
try {
if (user.getRoles().length > 0) {
byte[] rbytes = LimsUtils.join(user.getRoles(), ",").getBytes();
roleBlob = new SerialBlob(rbytes);
}
} catch (SerialException e) {
e.printStackTrace();
} catch (SQLException e) {
e.printStackTrace();
}
}
MapSqlParameterSource params = new MapSqlParameterSource();
params
.addValue("active", user.isActive())
.addValue("admin", user.isAdmin())
.addValue("external", user.isExternal())
.addValue("fullName", user.getFullName())
.addValue("internal", user.isInternal())
.addValue("loginName", user.getLoginName())
.addValue("roles", roleBlob)
.addValue("email", user.getEmail());
if (passwordCodecService != null) {
params.addValue("password", passwordCodecService.encrypt(user.getPassword()));
} else {
log.warn(
"No PasswordCodecService has been wired to this SQLSecurityDAO. This means your passwords may be being "
+ "stored in plaintext, if not already encrypted. Please specify a PasswordCodecService in your Spring config and (auto)wire it "
+ "to this DAO.");
params.addValue("password", user.getPassword());
}
if (user.getUserId() == UserImpl.UNSAVED_ID) {
SimpleJdbcInsert insert =
new SimpleJdbcInsert(template).withTableName("User").usingGeneratedKeyColumns("userId");
Number newId = insert.executeAndReturnKey(params);
user.setUserId(newId.longValue());
} else {
params.addValue("userId", user.getUserId());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(USER_UPDATE, params);
}
// sort User_Group
// delete existing joins
MapSqlParameterSource delparams = new MapSqlParameterSource();
delparams.addValue("userId", user.getUserId());
NamedParameterJdbcTemplate namedTemplate = new NamedParameterJdbcTemplate(template);
namedTemplate.update(USER_GROUP_DELETE_BY_USER_ID, delparams);
if (user.getGroups() != null && !user.getGroups().isEmpty()) {
SimpleJdbcInsert eInsert = new SimpleJdbcInsert(template).withTableName("User_Group");
for (Group g : user.getGroups()) {
MapSqlParameterSource ugParams = new MapSqlParameterSource();
ugParams
.addValue("users_userId", user.getUserId())
.addValue("groups_groupId", g.getGroupId());
eInsert.execute(ugParams);
}
}
return user.getUserId();
}
@RequestMapping(value = "project/{projectId}", method = RequestMethod.GET)
public @ResponseBody String jsonRestProject(@PathVariable Long projectId, ModelMap model)
throws IOException {
StringBuilder sb = new StringBuilder();
Project p = requestManager.getProjectById(projectId);
sb.append("'id':'" + projectId + "'");
sb.append(",");
sb.append("'name':'" + p.getName() + "'");
sb.append(",");
sb.append("'alias':'" + p.getAlias() + "'");
sb.append(",");
sb.append("'progress':'" + p.getProgress().name() + "'");
sb.append(",");
sb.append("'description':'" + p.getDescription() + "'");
sb.append(",");
sb.append("'overviews':[");
if (p.getOverviews().size() > 0) {
int oi = 0;
for (ProjectOverview overview : p.getOverviews()) {
oi++;
sb.append("{");
sb.append("'allSampleQcPassed':" + overview.getAllSampleQcPassed());
sb.append(",");
sb.append("'libraryPreparationComplete':" + overview.getLibraryPreparationComplete());
sb.append(",");
sb.append("'allLibrariesQcPassed':" + overview.getAllLibrariesQcPassed());
sb.append(",");
sb.append("'allPoolsConstructed':" + overview.getAllPoolsConstructed());
sb.append(",");
sb.append("'allRunsCompleted':" + overview.getAllRunsCompleted());
sb.append(",");
sb.append("'primaryAnalysisCompleted':" + overview.getPrimaryAnalysisCompleted());
sb.append("}");
if (oi < p.getOverviews().size()) {
sb.append(",");
}
}
}
sb.append("]");
sb.append(",");
sb.append("'samples':[");
Collection<Sample> samples = requestManager.listAllSamplesByProjectId(projectId);
if (samples.size() > 0) {
int si = 0;
for (Sample sample : samples) {
si++;
String sampleQubit = "not available";
if (requestManager.listAllSampleQCsBySampleId(sample.getId()).size() > 0) {
ArrayList<SampleQC> sampleQcList =
new ArrayList(requestManager.listAllSampleQCsBySampleId(sample.getId()));
SampleQC lastQc = sampleQcList.get(sampleQcList.size() - 1);
sampleQubit = (lastQc.getResults() != null ? lastQc.getResults().toString() : "");
}
sb.append("{");
sb.append("'alias':'" + sample.getAlias() + "'");
sb.append(",");
sb.append(
"'qcPassed':'"
+ (sample.getQcPassed() != null ? sample.getQcPassed().toString() : "")
+ "'");
sb.append(",");
sb.append(
"'receivedDate':'"
+ (sample.getReceivedDate() != null
? LimsUtils.getDateAsString(sample.getReceivedDate())
: "not available")
+ "'");
sb.append(",");
sb.append(
"'sampleType':'"
+ (sample.getSampleType() != null ? sample.getSampleType() : "")
+ "'");
sb.append(",");
sb.append("'sampleQubit':'" + sampleQubit + "'");
sb.append("}");
if (si < samples.size()) {
sb.append(",");
}
}
}
sb.append("]");
sb.append(",");
sb.append("'runs':[");
Collection<Run> runs = requestManager.listAllRunsByProjectId(projectId);
if (runs.size() > 0) {
int ri = 0;
for (Run run : runs) {
ri++;
if (!run.getStatus().getHealth().getKey().equals("Failed")) {
ArrayList<String> runSamples = new ArrayList();
Collection<SequencerPartitionContainer<SequencerPoolPartition>> spcs =
requestManager.listSequencerPartitionContainersByRunId(run.getId());
if (spcs.size() > 0) {
for (SequencerPartitionContainer<SequencerPoolPartition> spc : spcs) {
if (spc.getPartitions().size() > 0) {
for (SequencerPoolPartition spp : spc.getPartitions()) {
if (spp.getPool() != null) {
if (spp.getPool().getDilutions().size() > 0) {
for (Dilution dilution : spp.getPool().getDilutions()) {
Sample sample = dilution.getLibrary().getSample();
if (sample.getProject().equals(p)) {
runSamples.add(sample.getAlias());
}
}
}
}
}
}
}
}
sb.append("{");
sb.append("'name':'" + run.getName() + "'");
sb.append(",");
sb.append(
"'status':'"
+ (run.getStatus() != null && run.getStatus().getHealth() != null
? run.getStatus().getHealth().getKey()
: "")
+ "'");
sb.append(",");
sb.append(
"'startDate':'"
+ (run.getStatus() != null && run.getStatus().getStartDate() != null
? run.getStatus().getStartDate().toString()
: "")
+ "'");
sb.append(",");
sb.append(
"'completionDate':'"
+ (run.getStatus() != null && run.getStatus().getCompletionDate() != null
? run.getStatus().getCompletionDate().toString()
: "")
+ "'");
sb.append(",");
sb.append(
"'platformType':'"
+ (run.getPlatformType() != null ? run.getPlatformType().getKey() : "")
+ "'");
sb.append(",");
sb.append("'samples':[");
if (runSamples.size() > 0) {
int rsi = 0;
for (String alias : runSamples) {
rsi++;
sb.append("{'sampleAlias':'" + alias + "'}");
if (rsi < runSamples.size()) {
sb.append(",");
}
}
}
sb.append("]");
sb.append("}");
if (ri < runs.size()) {
sb.append(",");
}
}
}
}
sb.append("]");
return "{" + sb.toString() + "}";
}