public void removeWatcher(Run run, Long userId) throws IOException {
User user = securityManager.getUserById(userId);
if (user != null) {
Run clone = runs.get(run.getId());
if (clone == null) {
run.removeWatcher(user);
push(run);
} else {
clone.removeWatcher(user);
}
}
}
@Override
public boolean respondsTo(Event event) {
if (event instanceof RunEvent) {
RunEvent re = (RunEvent) event;
Run r = re.getEventObject();
if (re.getEventType().equals(MisoEventType.RUN_FAILED)
&& r.getStatus() != null
&& r.getStatus().getHealth().equals(HealthType.Failed)) {
log.info("Run " + r.getAlias() + ": " + re.getEventMessage());
return true;
}
}
return false;
}
public void pop(Run run) {
if (enabled) {
if (run != null) {
Run clone = runs.get(run.getId());
if (clone != null) {
removeListeners(clone);
clone = null;
runs.remove(run.getId());
log.debug("Dequeued " + run.getId());
}
}
} else {
log.warn("Alerting system disabled.");
}
}
public void updateGroupWatcher(Long userId) throws IOException {
User user = securityManager.getUserById(userId);
if (user != null) {
for (Run r : runs.values()) {
if (user.getGroups().contains(securityManager.getGroupByName("RunWatchers"))) {
addWatcher(r, userId);
} else {
if (r.getSecurityProfile() != null
&& r.getSecurityProfile().getOwner() != null
&& !r.getSecurityProfile().getOwner().equals(user)) {
removeWatcher(r, userId);
}
}
}
}
}
@Override
public void generateResponse(Event event) {
if (event instanceof RunEvent) {
RunEvent re = (RunEvent) event;
Run r = re.getEventObject();
for (User user : r.getWatchers()) {
Alert a = new DefaultAlert(user);
a.setAlertLevel(AlertLevel.CRITICAL);
a.setAlertTitle("Run Failed: " + r.getAlias());
StringBuilder at = new StringBuilder();
at.append(
"The following Run has been set to FAILED: "
+ r.getAlias()
+ " ("
+ event.getEventMessage()
+ "). Please view Run "
+ r.getId()
+ " in MISO for more information");
if (event.getEventContext().has("baseURL")) {
at.append(":\n\n" + event.getEventContext().getString("baseURL") + "/run/" + r.getId());
}
a.setAlertText(at.toString());
for (AlerterService as : alerterServices) {
try {
as.raiseAlert(a);
} catch (AlertingException e) {
log.error("Cannot raise user-level alert:" + e.getMessage());
e.printStackTrace();
}
}
}
if (getSaveSystemAlert()) {
raiseSystemAlert(event);
}
}
}
@Test
public void testRuns() {
try {
// get row count of experiments in the dataset
int expected = getDataSet().getTable("Run").getRowCount();
// get number of experiments from the DAO
int actual = getRunDAO().count();
// test data contains 2 experiments, check size of returned list
TestCase.assertEquals("Wrong number of Run", expected, actual);
System.out.println("Expected number of Run: " + expected + ", actual: " + actual);
for (Run d : random(getRunDAO(), actual, 5)) {
TestCase.assertNotNull(d);
TestCase.assertNotNull(d.getId());
}
} catch (Exception e) {
e.printStackTrace();
TestCase.fail();
}
}
public void push(Run run) {
if (enabled) {
if (run != null) {
Run clone = cloner.deepClone(run);
if (clone != null) {
applyListeners(clone);
if (runs.containsKey(run.getId())) {
if (clone.getStatus() != null) {
log.debug(
"Not replacing " + clone.getId() + ": " + clone.getStatus().getHealth().name());
}
} else {
runs.put(run.getId(), clone);
if (clone.getStatus() != null) {
log.debug("Queued " + clone.getId() + ": " + clone.getStatus().getHealth().name());
}
}
}
}
} else {
log.warn("Alerting system disabled.");
}
}
@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");
}
}
public void removeListeners(Run run) {
run.removeListener(getRunListener());
}
public void applyListeners(Run run) {
run.addListener(getRunListener());
}
private void update(Run r) throws IOException {
if (enabled) {
Run clone = runs.get(r.getId());
if (clone == null) {
log.debug("Update: no clone - pushing");
// new run - add all RunWatchers!
for (User u : securityManager.listUsersByGroupName("RunWatchers")) {
r.addWatcher(u);
}
push(r);
} else {
log.debug("Update: got clone of " + clone.getId());
if (r.getStatus() != null) {
clone.setStatus(r.getStatus());
}
// run QC added
if (r.getRunQCs().size() > clone.getRunQCs().size()) {
Set<RunQC> clonedQCs = new HashSet<RunQC>(clone.getRunQCs());
for (RunQC qc : r.getRunQCs()) {
if (!clonedQCs.contains(qc)) {
try {
clone.addQc(cloner.deepClone(qc));
} catch (MalformedRunQcException e) {
throw new IOException(e);
}
}
}
}
pop(clone);
push(r);
}
}
}
@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;
}