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);
}
}
}
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;
}