private List<Sample> generateSamples() {
List<Sample> samples = new ArrayList<Sample>();
DataObjectFactory dataObjectFactory = new TgacDataObjectFactory();
for (int i = 1; i < 6; i++) {
Sample s = dataObjectFactory.getSample();
s.setId(i);
s.setName("SAM" + i);
s.setAlias("MI_S" + i + "_TestSample");
s.setScientificName("F.bar");
s.setIdentificationBarcode(s.getName() + "::" + s.getAlias());
samples.add(s);
}
Collections.sort(samples);
return samples;
}
@Test
public void testSamples() {
try {
// get row count of experiments in the dataset
int expected = getDataSet().getTable("Sample").getRowCount();
// get number of experiments from the DAO
int actual = getSampleDAO().count();
// test data contains 2 experiments, check size of returned list
TestCase.assertEquals("Wrong number of Sample", expected, actual);
System.out.println("Expected number of Sample: " + expected + ", actual: " + actual);
for (Sample d : random(getSampleDAO(), actual, 5)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
@Deprecated
public JSONObject previewExperiment(HttpSession session, JSONObject json) {
String experimentId = (String) json.get("experimentId");
try {
Experiment e = requestManager.getExperimentById(Long.parseLong(experimentId));
Collection<Run> runs = requestManager.listRunsByExperimentId(e.getExperimentId());
session.setAttribute("experiment", e);
StringBuilder rb = new StringBuilder();
for (Run r : runs) {
rb.append("<li><a href='/miso/run/")
.append(r.getRunId())
.append("'>")
.append(r.getName())
.append("</a></li>");
}
StringBuilder sb = new StringBuilder();
if (e.getPool() != null) {
if (e.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
for (Object dil : e.getPool().getDilutions()) {
Sample s = ((LibraryDilution) dil).getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
} else {
for (Object dil : e.getPool().getDilutions()) {
Sample s =
((emPCRDilution) dil).getEmPCR().getLibraryDilution().getLibrary().getSample();
sb.append("<li><a href='/miso/sample/")
.append(s.getSampleId())
.append("'>")
.append(s.getName())
.append("</a></li>");
}
}
}
StringBuilder b = new StringBuilder();
b.append(
"<div onclick=\"Effect.toggle('preview"
+ experimentId
+ "','blind'); return false;\">"
+ "<img src=\"/styles/images/moreinfo.png\" class=\"previewimage\"/></div>");
b.append("<br/><div id=\"preview" + experimentId + "\" class='exppreview'>");
b.append("Title: <b>").append(e.getTitle()).append("</b><br/>");
b.append("Description: <b>").append(e.getDescription()).append("</b><br/>");
b.append("Samples: <ul class=\"bullets\">").append(sb.toString()).append("</ul>");
b.append("Runs: <ul class=\"bullets\">").append(rb.toString()).append("</ul>");
b.append("</div>");
return JSONUtils.SimpleJSONResponse(b.toString());
} catch (IOException e) {
log.debug("Failed", e);
return JSONUtils.SimpleJSONError("Failed");
}
}
@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() + "}";
}