// this method depends on all of the Flow Cell's channel being sent in the doc, if an entire
// channel was deleted, this will not work!
// It depends on hibernate's cacade=all to delete the channel and all sequence lanes in
// SaveFlowCell
// now that we no longer use cascade=all, and in order to allow sequence lanes to move backward in
// the workflow
// we need to manage their work items individually and not just delete the sequence lanes when
// they are removed from a channel
public void parse(Session sess) throws Exception {
FlowCellChannel channel = new FlowCellChannel();
Element root = this.doc.getRootElement();
for (Iterator i = root.getChildren("FlowCellChannel").iterator(); i.hasNext(); ) {
Boolean isNewChannel = false;
Map sequenceLaneMap = new HashMap();
Element node = (Element) i.next();
String idFlowCellChannelString = node.getAttributeValue("idFlowCellChannel");
// Is this HISEQ or MISEQ?
String codeStepNext = "";
// What is the core?
Integer idCoreFacility = -1;
List workItems =
sess.createQuery(
"SELECT wi from WorkItem wi where idFlowCellChannel = " + idFlowCellChannelString)
.list();
for (Iterator i1 = workItems.iterator(); i1.hasNext(); ) {
WorkItem wi = (WorkItem) i1.next();
codeStepNext = wi.getCodeStepNext();
idCoreFacility = wi.getIdCoreFacility();
break;
}
if (idFlowCellChannelString.startsWith("FlowCellChannel")
|| idFlowCellChannelString.equals("")) {
isNewChannel = true;
channel = new FlowCellChannel();
channel.setSequenceLanes(new TreeSet(new LaneComparator()));
} else {
isNewChannel = false;
channel =
(FlowCellChannel)
sess.get(FlowCellChannel.class, Integer.parseInt(idFlowCellChannelString));
}
this.initializeFlowCellChannel(sess, node, channel);
if (node.getChild("sequenceLanes") != null
&& !node.getChild("sequenceLanes").getChildren("SequenceLane").isEmpty()) {
for (Iterator i1 = node.getChild("sequenceLanes").getChildren("SequenceLane").iterator();
i1.hasNext(); ) {
Boolean isNewLane = false;
SequenceLane sl = new SequenceLane();
Element sequenceLaneNode = (Element) i1.next();
String idSequenceLaneString = sequenceLaneNode.getAttributeValue("idSequenceLane");
if (idSequenceLaneString.startsWith("SequenceLane") || idSequenceLaneString.equals("")) {
isNewLane = true;
sl = new SequenceLane();
} else {
isNewLane = false;
sl =
(SequenceLane) sess.get(SequenceLane.class, Integer.parseInt(idSequenceLaneString));
}
sl.setIdFlowCellChannel(channel.getIdFlowCellChannel());
if (isNewLane) {
sess.save(sl);
idSequenceLaneString = sl.getIdSequenceLane().toString();
}
sequenceLaneMap.put(idSequenceLaneString, sl);
}
}
//
// Remove lanes which have been deleted by the user
//
if (channel.getSequenceLanes() != null || !channel.getSequenceLanes().isEmpty()) {
TreeSet lanesToDelete = new TreeSet(new LaneComparator());
for (Iterator i2 = channel.getSequenceLanes().iterator(); i2.hasNext(); ) {
SequenceLane existingLane = (SequenceLane) i2.next();
if (!sequenceLaneMap.containsKey(existingLane.getIdSequenceLane().toString())) {
lanesToDelete.add(
existingLane); // delete lane if it was stored in this channel but was not sent in
// the request (meaning the user deleted it from the channel)
}
}
for (Iterator i2 = lanesToDelete.iterator(); i2.hasNext(); ) {
SequenceLane laneToDelete = (SequenceLane) i2.next();
channel.getSequenceLanes().remove(laneToDelete);
laneToDelete.setIdFlowCellChannel(null);
// create a work item to move the sequence lane back to the assembly stage
WorkItem wi = new WorkItem();
wi.setIdRequest(laneToDelete.getIdRequest());
wi.setSequenceLane(laneToDelete);
wi.setCreateDate(new Date(System.currentTimeMillis()));
if (idCoreFacility > 0) {
wi.setIdCoreFacility(idCoreFacility);
}
if (codeStepNext.equals("HSEQFINFC") || codeStepNext.equals("HSEQPIPE")) {
wi.setCodeStepNext("HSEQASSEM");
} else if (codeStepNext.equals("MISEQFINFC") || codeStepNext.equals("MISEQPIPE")) {
wi.setCodeStepNext("MISEQASSEM");
}
sess.save(wi);
}
}
//
// Save newly added lanes to channel
//
for (Iterator i2 = sequenceLaneMap.keySet().iterator(); i2.hasNext(); ) {
String idLaneString = (String) i2.next();
SequenceLane sl = (SequenceLane) sequenceLaneMap.get(idLaneString);
boolean exists = false;
if (!isNewChannel) {
if (channel.getSequenceLanes() != null || !channel.getSequenceLanes().isEmpty()) {
for (Iterator i3 = channel.getSequenceLanes().iterator(); i3.hasNext(); ) {
SequenceLane existingLane = (SequenceLane) i3.next();
if (existingLane.getIdSequenceLane().equals(sl.getIdSequenceLane())) {
exists = true;
}
}
}
}
// New sequence lane -- add it to the list
if (!exists) {
channel.getSequenceLanes().add(sl);
// delete the work item for the sequence lane
workItems =
sess.createQuery(
"SELECT wi from WorkItem wi where idSequenceLane = " + sl.getIdSequenceLane())
.list();
for (Iterator i1 = workItems.iterator(); i1.hasNext(); ) {
WorkItem wi = (WorkItem) i1.next();
sess.delete(wi);
break;
}
}
}
sess.flush();
if (isNewChannel) {
sess.save(channel);
idFlowCellChannelString = channel.getIdFlowCellChannel().toString();
}
channelMap.put(idFlowCellChannelString, channel);
}
}
protected void initializeFlowCellChannel(Session sess, Element n, FlowCellChannel channel)
throws Exception {
if (n.getAttributeValue("number") != null && !n.getAttributeValue("number").equals("")) {
channel.setNumber(new Integer(n.getAttributeValue("number")));
} else {
channel.setNumber(null);
}
if (n.getAttributeValue("idFlowCell") != null
&& !n.getAttributeValue("idFlowCell").equals("")) {
channel.setIdFlowCell(new Integer(n.getAttributeValue("idFlowCell")));
}
if (n.getAttributeValue("idSequencingControl") != null
&& !n.getAttributeValue("idSequencingControl").equals("")) {
channel.setIdSequencingControl(new Integer(n.getAttributeValue("idSequencingControl")));
} else {
channel.setIdSequencingControl(null);
}
if (n.getAttributeValue("startDate") != null && !n.getAttributeValue("startDate").equals("")) {
channel.setStartDate(this.parseDate(n.getAttributeValue("startDate")));
} else {
channel.setStartDate(null);
}
if (n.getAttributeValue("firstCycleDate") != null
&& !n.getAttributeValue("firstCycleDate").equals("")) {
channel.setFirstCycleDate(this.parseDate(n.getAttributeValue("firstCycleDate")));
} else {
channel.setFirstCycleDate(null);
}
if (n.getAttributeValue("firstCycleDate") != null
&& !n.getAttributeValue("firstCycleDate").equals("")) {
channel.setFirstCycleDate(this.parseDate(n.getAttributeValue("firstCycleDate")));
} else {
channel.setFirstCycleDate(null);
}
if (n.getAttributeValue("firstCycleFailed") != null
&& !n.getAttributeValue("firstCycleFailed").equals("")) {
channel.setFirstCycleFailed(n.getAttributeValue("firstCycleFailed"));
}
if (n.getAttributeValue("lastCycleDate") != null
&& !n.getAttributeValue("lastCycleDate").equals("")) {
channel.setLastCycleDate(this.parseDate(n.getAttributeValue("lastCycleDate")));
} else {
channel.setLastCycleDate(null);
}
if (n.getAttributeValue("lastCycleFailed") != null
&& !n.getAttributeValue("lastCycleFailed").equals("")) {
channel.setLastCycleFailed(n.getAttributeValue("lastCycleFailed"));
}
if (n.getAttributeValue("clustersPerTile") != null
&& !n.getAttributeValue("clustersPerTile").equals("")) {
channel.setClustersPerTile(new Integer(n.getAttributeValue("clustersPerTile")));
} else {
channel.setClustersPerTile(null);
}
if (n.getAttributeValue("fileName") != null && !n.getAttributeValue("fileName").equals("")) {
channel.setFileName(n.getAttributeValue("fileName"));
}
if (n.getAttributeValue("sampleConcentrationpM") != null
&& !n.getAttributeValue("sampleConcentrationpM").equals("")) {
channel.setSampleConcentrationpM(
new BigDecimal(n.getAttributeValue("sampleConcentrationpM")));
} else {
channel.setSampleConcentrationpM(null);
}
if (n.getAttributeValue("numberSequencingCyclesActual") != null
&& !n.getAttributeValue("numberSequencingCyclesActual").equals("")) {
channel.setNumberSequencingCyclesActual(
new Integer(n.getAttributeValue("numberSequencingCyclesActual")));
} else {
channel.setNumberSequencingCyclesActual(null);
}
if (n.getAttributeValue("pipelineDate") != null
&& !n.getAttributeValue("pipelineDate").equals("")) {
channel.setPipelineDate(this.parseDate(n.getAttributeValue("pipelineDate")));
} else {
channel.setPipelineDate(null);
}
if (n.getAttributeValue("pipelineFailed") != null
&& !n.getAttributeValue("pipelineFailed").equals("")) {
channel.setPipelineFailed(n.getAttributeValue("pipelineFailed"));
}
if (n.getAttributeValue("isControl") != null && !n.getAttributeValue("isControl").equals("")) {
channel.setIsControl(n.getAttributeValue("isControl"));
}
if (n.getAttributeValue("phiXErrorRate") != null
&& !n.getAttributeValue("phiXErrorRate").equals("")) {
channel.setPhiXErrorRate(new BigDecimal(n.getAttributeValue("phiXErrorRate")));
} else {
channel.setPhiXErrorRate(null);
}
if (n.getAttributeValue("read1ClustersPassedFilterM") != null
&& !n.getAttributeValue("read1ClustersPassedFilterM").equals("")) {
channel.setRead1ClustersPassedFilterM(
new BigDecimal(n.getAttributeValue("read1ClustersPassedFilterM")));
} else {
channel.setRead1ClustersPassedFilterM(null);
}
if (n.getAttributeValue("q30PercentForDisplay") != null
&& !n.getAttributeValue("q30PercentForDisplay").equals("")) {
channel.setQ30Percent(
new BigDecimal(n.getAttributeValue("q30PercentForDisplay")).movePointLeft(2));
} else {
channel.setQ30Percent(null);
}
if (n.getAttributeValue("sampleConcentrationpM") != null
&& !n.getAttributeValue("sampleConcentrationpM").equals("")) {
channel.setSampleConcentrationpM(
new BigDecimal(n.getAttributeValue("sampleConcentrationpM")));
} else {
channel.setSampleConcentrationpM(null);
}
}