public JSONObject plateElementsDataTable(HttpSession session, JSONObject json) {
if (json.has("plateId")) {
try {
JSONObject j = new JSONObject();
JSONArray jsonArray = new JSONArray();
long plateId = json.getLong("plateId");
Plate<? extends List<? extends Plateable>, ? extends Plateable> plate =
requestManager.getPlateById(plateId);
if (plate != null) {
for (Plateable p : plate.getElements()) {
if (p instanceof Library) {
Library l = (Library) p;
String strategyName = "No barcode";
StringBuilder seqbuilder = new StringBuilder();
if (!l.getTagBarcodes().isEmpty()) {
int count = 1;
Collection<TagBarcode> barcodes = l.getTagBarcodes().values();
for (TagBarcode tb : barcodes) {
strategyName = tb.getStrategyName();
seqbuilder.append(tb.getSequence());
if (l.getTagBarcodes().values().size() > 1
&& count < l.getTagBarcodes().values().size()) {
seqbuilder.append("-");
}
count++;
}
} else {
log.info("No tag barcodes!");
}
jsonArray.add(
"['"
+ l.getName()
+ "','"
+ l.getAlias()
+ "','"
+ strategyName
+ "','"
+ seqbuilder.toString()
+ "','"
+ "<a href=\"/miso/library/"
+ l.getId()
+ "\"><span class=\"ui-icon ui-icon-pencil\"></span></a>"
+ "']");
}
}
}
j.put("elementsArray", jsonArray);
return j;
} catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed: " + e.getMessage());
}
} else {
return JSONUtils.SimpleJSONError("No plates to show");
}
}
@RequestMapping(value = "projects", method = RequestMethod.GET)
public @ResponseBody String jsonRest() throws IOException {
StringBuilder sb = new StringBuilder();
Collection<Project> lp = requestManager.listAllProjects();
int pi = 0;
for (Project p : lp) {
pi++;
sb.append(jsonRestProjectList(p.getProjectId()));
if (pi < lp.size()) {
sb.append(",");
}
}
return "[" + sb.toString() + "]";
}
public JSONObject getTagBarcodesForMaterialType(HttpSession session, JSONObject json) {
Map<String, Object> responseMap = new HashMap<String, Object>();
if (json.has("materialType") && !"".equals(json.getString("materialType"))) {
String materialType = json.getString("materialType");
StringBuilder srb = new StringBuilder();
srb.append("<select name='tagBarcode' id='tagBarcodes'>");
srb.append("<option value='0' selected='selected'>No barcode</option>");
// for (TagBarcode tb :
// requestManager.listPlateBarcodesByMaterialType(PlateMaterialType.get(materialType))) {
// srb.append("<option value='" + tb.getTagBarcodeId() + "'>" + tb.getName() + " ("+
// tb.getSequence()+")</option>");
// }
srb.append("</select>");
responseMap.put("plateBarcodes", srb.toString());
} else {
return JSONUtils.SimpleJSONError("Unrecognised MaterialType");
}
return JSONUtils.JSONObjectResponse(responseMap);
}
public String jsonRestProjectList(Long projectId) 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() + "'");
return "{" + sb.toString() + "}";
}
@Override
public Set<File> generateFilePath(SequencerPoolPartition partition, Dilution l)
throws SubmissionException {
Pool<? extends Poolable> pool = partition.getPool();
if (pool != null) {
if (pool.getExperiments() != null) {
Collection<Experiment> experiments = pool.getExperiments();
Experiment experiment = experiments.iterator().next();
StringBuilder filePath = new StringBuilder();
if (!"".equals(basePath)) {
filePath.append(
partition.getSequencerPartitionContainer().getRun().getFilePath()
+ "/Data/Intensities/BaseCalls/PAP/Project_"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
} else {
filePath.append(
basePath
+ "/"
+ experiment.getStudy().getProject().getAlias()
+ "/Sample_"
+ l.getLibrary().getName()
+ "/"
+ l.getLibrary().getName());
}
if (l.getLibrary().getTagBarcodes() != null && !l.getLibrary().getTagBarcodes().isEmpty()) {
filePath.append("_");
for (TagBarcode tb : l.getLibrary().getTagBarcodes().values()) {
filePath.append(tb.getSequence());
}
}
filePath.append("_L00" + partition.getPartitionNumber() + "*.fastq.gz");
Set<File> files = new HashSet<File>();
files.add(new File(filePath.toString()));
return files;
} else {
throw new SubmissionException("partition.getPool=null!");
}
} else {
throw new SubmissionException("Collection of experiments is empty");
}
}
@Override
public Set<File> generateFilePaths(SequencerPoolPartition partition) throws SubmissionException {
log.debug("Generating filepaths for partition " + partition.getId());
Set<File> filePaths = new HashSet<File>();
Pool pool = partition.getPool();
if (pool == null) {
throw new SubmissionException("partition.getPool=null!");
} else {
Collection<Experiment> experiments = pool.getExperiments();
if (experiments.isEmpty()) {
throw new SubmissionException("Collection or experiments is empty");
} else {
Collection<LibraryDilution> libraryDilutions = pool.getDilutions();
if (libraryDilutions.isEmpty()) {
throw new SubmissionException("Collection or libraryDilutions is empty");
} else {
for (Experiment e : experiments) {
StringBuilder filePath = new StringBuilder();
filePath.append(partition.getSequencerPartitionContainer().getRun().getFilePath());
filePath.append("/Data/Intensities/BaseCalls/PAP/Project_");
filePath.append(e.getStudy().getProject().getAlias());
filePath.append("/Sample_");
for (LibraryDilution l : libraryDilutions) {
// filePath.append(l.getLibrary().getName()+"/");
/*
+l.getLibrary().getName()+"_"+l.getLibrary().getTagBarcode().getSequence());
filePath.append("L00"+lane.getPartitionNumber())
*/
String folder = filePath.toString() + l.getLibrary().getName() + "/*.fastq.gz";
// System.out.println(folder);
File file = new File(folder);
filePaths.add(file);
}
}
}
}
}
return (filePaths);
}
@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() + "}";
}
private Map<String, Run> processRunJSON(
HealthType ht, JSONArray runs, RequestManager requestManager) {
Map<String, Run> updatedRuns = new HashMap<String, Run>();
List<Run> runsToSave = new ArrayList<Run>();
// 2011-01-25 15:37:27.093
DateFormat logDateFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS");
DateFormat simpleLogDateFormat = new SimpleDateFormat("yyyyMMdd");
Pattern simpleDateRegex = Pattern.compile("[0-9]{8}");
StringBuilder sb = new StringBuilder();
for (JSONObject run : (Iterable<JSONObject>) runs) {
String runName = run.getString("runName");
sb.append("Processing " + runName + "\n");
log.debug("Processing " + runName);
if (run.has("status")) {
String xml = run.getString("status");
Status is = new SolidStatus(xml);
is.setHealth(ht);
is.setRunName(runName);
Run r = null;
Matcher m = p.matcher(runName);
if (m.matches()) {
try {
r = requestManager.getRunByAlias(runName);
} catch (IOException ioe) {
log.warn(
"Cannot find run by this alias. This usually means the run hasn't been previously imported. If attemptRunPopulation is false, processing will not take place for this run!");
}
}
try {
if (attemptRunPopulation) {
if (r == null) {
log.debug("Saving new run and status: " + is.getRunName());
r = new SolidRun(xml);
r.getStatus().setHealth(ht);
if (run.has("fullPath")) {
r.setFilePath(run.getString("fullPath"));
}
SequencerReference sr = null;
if (run.has("sequencerName")) {
sr = requestManager.getSequencerReferenceByName(run.getString("sequencerName"));
r.getStatus().setInstrumentName(run.getString("sequencerName"));
r.setSequencerReference(sr);
}
if (r.getSequencerReference() == null) {
sr = requestManager.getSequencerReferenceByName(m.group(1));
r.getStatus().setInstrumentName(m.group(1));
r.setSequencerReference(sr);
}
if (r.getSequencerReference() == null) {
sr = requestManager.getSequencerReferenceByName(r.getStatus().getInstrumentName());
r.setSequencerReference(sr);
}
if (r.getSequencerReference() != null) {
if (run.has("startDate")) {
try {
log.debug("Updating start date:" + run.getString("startDate"));
Matcher m2 = simpleDateRegex.matcher(run.getString("startDate"));
if (m2.matches()) {
r.getStatus()
.setStartDate(simpleLogDateFormat.parse(run.getString("startDate")));
} else {
r.getStatus().setStartDate(logDateFormat.parse(run.getString("startDate")));
}
} catch (ParseException e) {
log.error(e.getMessage());
e.printStackTrace();
}
}
if (run.has("completionDate")) {
try {
if (run.get("completionDate") != null
&& !run.getString("completionDate").equals("null")) {
log.debug("Updating completion date:" + run.getString("completionDate"));
r.getStatus()
.setCompletionDate(logDateFormat.parse(run.getString("completionDate")));
} else {
r.getStatus().setCompletionDate(null);
}
} catch (ParseException e) {
log.error(e.getMessage());
e.printStackTrace();
}
}
}
} else {
log.debug("Updating existing run and status: " + is.getRunName());
r.setAlias(runName);
r.setPlatformType(PlatformType.SOLID);
if (r.getSequencerReference() == null) {
SequencerReference sr = null;
if (run.has("sequencerName")) {
sr = requestManager.getSequencerReferenceByName(run.getString("sequencerName"));
r.getStatus().setInstrumentName(run.getString("sequencerName"));
r.setSequencerReference(sr);
}
if (r.getSequencerReference() == null) {
sr = requestManager.getSequencerReferenceByName(m.group(1));
r.getStatus().setInstrumentName(m.group(1));
r.setSequencerReference(sr);
}
if (r.getSequencerReference() == null) {
sr =
requestManager.getSequencerReferenceByName(r.getStatus().getInstrumentName());
r.setSequencerReference(sr);
}
}
if (r.getSequencerReference() != null) {
if (run.has("startDate")) {
try {
log.debug("Updating start date:" + run.getString("startDate"));
Matcher m2 = simpleDateRegex.matcher(run.getString("startDate"));
if (m2.matches()) {
r.getStatus()
.setStartDate(simpleLogDateFormat.parse(run.getString("startDate")));
} else {
r.getStatus().setStartDate(logDateFormat.parse(run.getString("startDate")));
}
} catch (ParseException e) {
log.error(e.getMessage());
e.printStackTrace();
}
}
if (run.has("completionDate")) {
try {
if (run.get("completionDate") != null
&& !run.getString("completionDate").equals("null")) {
log.debug("Updating completion date:" + run.getString("completionDate"));
r.getStatus()
.setCompletionDate(logDateFormat.parse(run.getString("completionDate")));
} else {
r.getStatus().setCompletionDate(null);
}
} catch (ParseException e) {
log.error(e.getMessage());
e.printStackTrace();
}
}
// update path if changed
if (run.has("fullPath")
&& !"".equals(run.getString("fullPath"))
&& r.getFilePath() != null
&& !"".equals(r.getFilePath())) {
if (!run.getString("fullPath").equals(r.getFilePath())) {
log.debug(
"Updating run file path:"
+ r.getFilePath()
+ " -> "
+ run.getString("fullPath"));
r.setFilePath(run.getString("fullPath"));
}
}
// update status if run isn't completed or failed
if (!r.getStatus().getHealth().equals(HealthType.Completed)
&& !r.getStatus().getHealth().equals(HealthType.Failed)) {
log.debug(
"Saving previously saved status: "
+ is.getRunName()
+ " ("
+ r.getStatus().getHealth().getKey()
+ " -> "
+ is.getHealth().getKey()
+ ")");
r.setStatus(is);
}
}
}
if (r.getSequencerReference() != null) {
List<SequencerPartitionContainer<SequencerPoolPartition>> fs =
((SolidRun) r).getSequencerPartitionContainers();
if (fs.isEmpty()) {
if (run.has("containerId") && !"".equals(run.getString("containerId"))) {
Collection<SequencerPartitionContainer<SequencerPoolPartition>> pfs =
requestManager.listSequencerPartitionContainersByBarcode(
run.getString("containerId"));
if (!pfs.isEmpty()) {
if (pfs.size() == 1) {
SequencerPartitionContainer lf =
new ArrayList<SequencerPartitionContainer<SequencerPoolPartition>>(pfs)
.get(0);
if (lf.getSecurityProfile() != null && r.getSecurityProfile() == null) {
r.setSecurityProfile(lf.getSecurityProfile());
}
if (lf.getPlatform() == null
&& r.getSequencerReference().getPlatform() != null) {
lf.setPlatform(r.getSequencerReference().getPlatform());
}
// else {
// lf.setPlatformType(PlatformType.SOLID);
// }
((RunImpl) r).addSequencerPartitionContainer(lf);
}
} else {
log.debug("No containers linked to run " + r.getId() + ": creating...");
SequencerPartitionContainer f = new SequencerPartitionContainerImpl();
f.setSecurityProfile(r.getSecurityProfile());
f.initEmptyPartitions();
f.setIdentificationBarcode(run.getString("containerNum"));
if (f.getPlatform() == null
&& r.getSequencerReference().getPlatform() != null) {
f.setPlatform(r.getSequencerReference().getPlatform());
}
// else {
// f.setPlatformType(PlatformType.SOLID);
// }
// f.setPaired(r.getPairedEnd());
((RunImpl) r).addSequencerPartitionContainer(f);
}
}
} else {
SequencerPartitionContainer f = fs.iterator().next();
log.debug("Got container " + f.getId());
if (f.getSecurityProfile() == null) {
f.setSecurityProfile(r.getSecurityProfile());
}
if (f.getPlatform() == null && r.getSequencerReference().getPlatform() != null) {
f.setPlatform(r.getSequencerReference().getPlatform());
}
// else {
// f.setPlatformType(PlatformType.SOLID);
// }
if (run.has("containerId") && !"".equals(run.getString("containerId"))) {
f.setIdentificationBarcode(run.getString("containerId"));
}
long flowId = requestManager.saveSequencerPartitionContainer(f);
f.setId(flowId);
}
updatedRuns.put(r.getAlias(), r);
runsToSave.add(r);
}
}
} catch (IOException e) {
log.error(e.getMessage());
e.printStackTrace();
}
}
}
try {
if (runsToSave.size() > 0) {
int[] saved = requestManager.saveRuns(runsToSave);
log.info("Batch saved " + saved.length + " / " + runs.size() + " runs");
}
} catch (IOException e) {
log.error("Couldn't save run batch: " + e.getMessage());
e.printStackTrace();
}
return updatedRuns;
}