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"); } }
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() + "}"; }
@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() + "]"; }
@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); }
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); }
@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() + "}"; }