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package net.sf.basedb.meludi.servlet; |
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import java.io.IOException; |
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import java.io.PrintWriter; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.Collections; |
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import java.util.Date; |
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import java.util.List; |
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|
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import javax.servlet.ServletException; |
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import javax.servlet.http.HttpServlet; |
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import javax.servlet.http.HttpServletRequest; |
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import javax.servlet.http.HttpServletResponse; |
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|
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import org.json.simple.JSONArray; |
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import org.json.simple.JSONObject; |
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import org.json.simple.parser.JSONParser; |
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|
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import net.sf.basedb.core.Application; |
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import net.sf.basedb.core.BasicItem; |
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import net.sf.basedb.core.BioMaterialEvent; |
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import net.sf.basedb.core.BioMaterialEventSource; |
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import net.sf.basedb.core.BioPlate; |
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import net.sf.basedb.core.BioPlateType; |
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import net.sf.basedb.core.BioWell; |
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import net.sf.basedb.core.DbControl; |
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import net.sf.basedb.core.Extract; |
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import net.sf.basedb.core.Include; |
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import net.sf.basedb.core.InvalidDataException; |
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import net.sf.basedb.core.Item; |
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import net.sf.basedb.core.ItemList; |
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import net.sf.basedb.core.ItemQuery; |
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import net.sf.basedb.core.ItemSubtype; |
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import net.sf.basedb.core.Permission; |
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import net.sf.basedb.core.PlateGeometry; |
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import net.sf.basedb.core.Protocol; |
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import net.sf.basedb.core.Sample; |
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import net.sf.basedb.core.SessionControl; |
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import net.sf.basedb.core.Type; |
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import net.sf.basedb.core.query.Annotations; |
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import net.sf.basedb.core.query.Expressions; |
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import net.sf.basedb.core.query.Hql; |
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import net.sf.basedb.core.query.Orders; |
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import net.sf.basedb.core.query.Restrictions; |
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import net.sf.basedb.core.snapshot.SnapshotManager; |
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import net.sf.basedb.meludi.JsonUtil; |
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import net.sf.basedb.meludi.Meludi; |
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import net.sf.basedb.meludi.converter.ValueConverter; |
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import net.sf.basedb.meludi.counter.CounterService; |
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import net.sf.basedb.meludi.dao.Annotationtype; |
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import net.sf.basedb.meludi.dao.BiomaterialList; |
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import net.sf.basedb.meludi.dao.BioplateType; |
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import net.sf.basedb.meludi.dao.Case; |
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import net.sf.basedb.meludi.dao.FfpeBlock; |
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import net.sf.basedb.meludi.dao.Histology; |
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import net.sf.basedb.meludi.dao.MeludiRole; |
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import net.sf.basedb.meludi.dao.Patient; |
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import net.sf.basedb.meludi.dao.Dna; |
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import net.sf.basedb.meludi.dao.ReactionPlate; |
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import net.sf.basedb.meludi.dao.Rna; |
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import net.sf.basedb.meludi.dao.SpecimenTube; |
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import net.sf.basedb.meludi.dao.StartList; |
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import net.sf.basedb.meludi.dao.StoragePlate; |
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import net.sf.basedb.meludi.dao.Subtype; |
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import net.sf.basedb.util.Values; |
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import net.sf.basedb.util.error.ThrowableUtil; |
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import net.sf.basedb.util.export.TableWriter; |
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public class ExtractionServlet |
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extends HttpServlet |
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{ |
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|
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|
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private static final long serialVersionUID = 5374097270488331091L; |
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|
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public ExtractionServlet() |
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{} |
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|
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@SuppressWarnings("unchecked") |
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@Override |
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protected void doGet(HttpServletRequest req, HttpServletResponse resp) |
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throws ServletException, IOException |
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{ |
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|
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String ID = req.getParameter("ID"); |
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String cmd = req.getParameter("cmd"); |
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JsonUtil.setJsonResponseHeaders(resp); |
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|
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JSONObject json = new JSONObject(); |
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json.put("status", "ok"); |
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|
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//final SessionControl sc = Application.getSessionControl(ID, req.getRemoteAddr()); |
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//final SessionControl sc = Application.getSessionControl(ID, "", req.getRemoteAddr(), true); |
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final SessionControl sc = Application.getSessionControl(ID, null, req.getRemoteAddr(), true); |
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DbControl dc = null; |
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try |
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{ |
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if ("GetUnprocessedSpecimens".equals(cmd)) |
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{ |
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Boolean withExtracts = Values.getBoolean(req.getParameter("withExtracts"), true); |
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/* |
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Find SpecimenTube items that have no created date. Order by |
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bioplate position. |
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*/ |
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dc = sc.newDbControl(); |
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List<SpecimenTube> specimenTubes = SpecimenTube.findUnProcessedTubes(dc, withExtracts); |
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|
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JSONArray jsonSpecimen = new JSONArray(); |
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|
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for (SpecimenTube s : specimenTubes) |
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{ |
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s.loadBioPlateLocation(); |
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jsonSpecimen.add(s.asJSONObject()); |
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} |
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|
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json.put("specimens", jsonSpecimen); |
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} |
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else if ("GetUnprocessedItems".equals(cmd)) |
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{ |
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JSONObject jsonItemsByName = new JSONObject(); |
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List<String> itemNameList = new ArrayList<String>(); |
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List<String> meludiItemNameList = new ArrayList<String>(); |
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List<String> extraItemNameList = new ArrayList<String>(); |
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|
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/* |
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Find SpecimenTube items that have no created date. Order by |
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bioplate position. |
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*/ |
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dc = sc.newDbControl(); |
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List<SpecimenTube> specimenTubes = SpecimenTube.findUnProcessedTubes(dc); |
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|
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JSONArray jsonSpecimen = new JSONArray(); |
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|
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String itemNamePrefix = Meludi.fetchSampleItemPrefix(sc.getActiveProjectId()); |
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for (SpecimenTube s : specimenTubes) |
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{ |
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s.loadBioPlateLocation(); |
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s.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT, null); |
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JSONObject jsonSpec = s.asJSONObject(); |
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// Get DNA extract plate position |
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String specDnaName = s.getName() + ".d"; |
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Dna dna = Dna.findByName(dc, specDnaName); |
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if (dna != null) |
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{ |
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dna.loadBioPlateLocation(); |
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jsonSpec.put("dna", dna.asJSONObject()); |
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} |
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// Get RNA extract plate position |
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String specRnaName = s.getName() + ".r"; |
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Rna rna = Rna.findByName(dc, specRnaName); |
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if (rna != null) |
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{ |
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rna.loadBioPlateLocation(); |
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jsonSpec.put("rna", rna.asJSONObject()); |
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} |
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// Get histology info |
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String histologyName = s.getName() + ".his"; |
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List<Histology> histology = Histology.findByName(dc, histologyName); |
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if (histology.size() > 0) |
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{ |
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JSONArray jsonHistology = new JSONArray(); |
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for (Histology his : histology) |
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{ |
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loadHistologyInfo(dc, his); |
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//jsonHistology.add(his.asJSONObject()); |
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jsonSpec.put("histology", his.asJSONObject()); |
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} |
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//jsonSections.add(loadSectionInfo(sc, "histology")); |
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//json.put("histology", jsonHistology); |
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} |
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|
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// Add JSON data for specimen |
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jsonSpecimen.add(jsonSpec); |
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String itemName = s.getName(); |
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jsonItemsByName.put(itemName, jsonSpec); |
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itemNameList.add(itemName); |
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if (itemName.startsWith(itemNamePrefix)) |
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{ |
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meludiItemNameList.add(itemName); |
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} |
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else |
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{ |
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extraItemNameList.add(itemName); |
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} |
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} |
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json.put("specimens", jsonSpecimen); |
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|
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/* |
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Find RNA items that have no original quantity. Order by |
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bioplate position. |
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*/ |
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List<Rna> rnas = Rna.findUnquantifiedRna(dc); |
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|
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JSONArray jsonRna = new JSONArray(); |
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|
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for (Rna r : rnas) |
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{ |
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String itemName = r.getName(); |
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if (Meludi.itemIsExtractSourceItem(itemName)) |
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{ |
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r.loadBioPlateLocation(); |
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r.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT_EXTRACT, null); |
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jsonRna.add(r.asJSONObject()); |
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jsonItemsByName.put(itemName, r.asJSONObject()); |
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itemNameList.add(itemName); |
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if (itemName.startsWith(itemNamePrefix)) |
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{ |
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meludiItemNameList.add(itemName); |
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} |
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else |
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{ |
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extraItemNameList.add(itemName); |
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} |
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} |
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} |
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json.put("rnas", jsonRna); |
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|
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/* |
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Find DNA items that have no original quantity. Order by |
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bioplate position. |
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*/ |
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List<Dna> dnas = Dna.findUnquantifiedDna(dc); |
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|
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JSONArray jsonDna = new JSONArray(); |
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|
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for (Dna d : dnas) |
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{ |
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String itemName = d.getName(); |
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if (Meludi.itemIsExtractSourceItem(itemName)) |
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{ |
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d.loadBioPlateLocation(); |
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d.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT_EXTRACT, null); |
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jsonDna.add(d.asJSONObject()); |
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jsonItemsByName.put(itemName, d.asJSONObject()); |
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itemNameList.add(itemName); |
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if (itemName.startsWith(itemNamePrefix)) |
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{ |
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meludiItemNameList.add(itemName); |
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} |
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else |
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{ |
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extraItemNameList.add(itemName); |
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} |
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} |
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} |
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json.put("dnas", jsonDna); |
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|
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// Sort item name list |
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Collections.sort(itemNameList); |
| 3413 |
23 Jun 15 |
olle |
252 |
Collections.sort(meludiItemNameList); |
| 3413 |
23 Jun 15 |
olle |
253 |
Collections.sort(extraItemNameList); |
| 3212 |
27 Mar 15 |
olle |
// Create JSON array of items sorted after name |
| 3212 |
27 Mar 15 |
olle |
255 |
JSONArray jsonItems = new JSONArray(); |
| 3413 |
23 Jun 15 |
olle |
// List MeLuDI items first, then extra material, each sorted alphabetically in its group |
| 3413 |
23 Jun 15 |
olle |
257 |
for (int i = 0; i < meludiItemNameList.size(); i++) |
| 3413 |
23 Jun 15 |
olle |
258 |
{ |
| 3413 |
23 Jun 15 |
olle |
259 |
String itemName = (String) meludiItemNameList.get(i); |
| 3413 |
23 Jun 15 |
olle |
260 |
JSONObject jsonItem = (JSONObject) jsonItemsByName.get(itemName); |
| 3413 |
23 Jun 15 |
olle |
261 |
jsonItems.add(jsonItem); |
| 3413 |
23 Jun 15 |
olle |
262 |
} |
| 3413 |
23 Jun 15 |
olle |
263 |
for (int i = 0; i < extraItemNameList.size(); i++) |
| 3413 |
23 Jun 15 |
olle |
264 |
{ |
| 3413 |
23 Jun 15 |
olle |
265 |
String itemName = (String) extraItemNameList.get(i); |
| 3413 |
23 Jun 15 |
olle |
266 |
JSONObject jsonItem = (JSONObject) jsonItemsByName.get(itemName); |
| 3413 |
23 Jun 15 |
olle |
267 |
jsonItems.add(jsonItem); |
| 3413 |
23 Jun 15 |
olle |
268 |
} |
| 3212 |
27 Mar 15 |
olle |
269 |
json.put("items", jsonItems); |
| 3176 |
06 Mar 15 |
olle |
270 |
} |
| 3206 |
20 Mar 15 |
olle |
271 |
else if ("GetStartPlates".equals(cmd)) |
| 3206 |
20 Mar 15 |
olle |
272 |
{ |
| 3206 |
20 Mar 15 |
olle |
273 |
/* |
| 3206 |
20 Mar 15 |
olle |
Find start DNA plates. Order by bioplate name. |
| 3206 |
20 Mar 15 |
olle |
275 |
*/ |
| 3206 |
20 Mar 15 |
olle |
276 |
dc = sc.newDbControl(); |
| 3206 |
20 Mar 15 |
olle |
277 |
Subtype subtype = null; |
| 4200 |
01 Nov 16 |
olle |
278 |
String prefix = Meludi.fetchStartPlateItemPrefix(sc.getActiveProjectId()); |
| 3206 |
20 Mar 15 |
olle |
279 |
int numFreeWells = 0; |
| 3206 |
20 Mar 15 |
olle |
280 |
Annotationtype runDateAnnotation = null; |
| 3254 |
17 Apr 15 |
olle |
281 |
Boolean destroyed = false; |
| 3255 |
17 Apr 15 |
olle |
282 |
Boolean orderDesc = Boolean.valueOf(req.getParameter("orderDesc")); |
| 3255 |
17 Apr 15 |
olle |
283 |
if (orderDesc == null) |
| 3254 |
17 Apr 15 |
olle |
284 |
{ |
| 3255 |
17 Apr 15 |
olle |
285 |
orderDesc = false; |
| 3254 |
17 Apr 15 |
olle |
286 |
} |
| 3206 |
20 Mar 15 |
olle |
287 |
List<ReactionPlate> startPlates = ReactionPlate.findByBioPlateType(dc, |
| 3254 |
17 Apr 15 |
olle |
288 |
BioplateType.DNA, subtype, prefix, numFreeWells, runDateAnnotation, destroyed, orderDesc); |
| 3206 |
20 Mar 15 |
olle |
289 |
|
| 3206 |
20 Mar 15 |
olle |
290 |
JSONArray jsonPlates = new JSONArray(); |
| 3206 |
20 Mar 15 |
olle |
291 |
|
| 3440 |
17 Jul 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3440 |
17 Jul 15 |
olle |
293 |
SnapshotManager manager = new SnapshotManager(); |
| 3440 |
17 Jul 15 |
olle |
294 |
|
| 3206 |
20 Mar 15 |
olle |
295 |
for (ReactionPlate p : startPlates) |
| 3206 |
20 Mar 15 |
olle |
296 |
{ |
| 3225 |
02 Apr 15 |
olle |
297 |
Date extractionDate = null; |
| 3225 |
02 Apr 15 |
olle |
298 |
BioPlate bioPlate = p.getBioPlate(); |
| 3225 |
02 Apr 15 |
olle |
299 |
if (bioPlate != null) |
| 3225 |
02 Apr 15 |
olle |
300 |
{ |
| 3225 |
02 Apr 15 |
olle |
301 |
extractionDate = bioPlate.getEventDate(); |
| 3225 |
02 Apr 15 |
olle |
302 |
} |
| 3233 |
09 Apr 15 |
olle |
//p.loadAnnotations(dc, "sourceItemNames", Annotationtype.SOURCE_ITEM_NAMES, null); |
| 3440 |
17 Jul 15 |
olle |
304 |
p.loadAnnotations(dc, manager, "sourceItemNames", Annotationtype.SOURCE_ITEM_NAMES_LIST_STRING, null, true, true); |
| 3440 |
17 Jul 15 |
olle |
305 |
p.loadAnnotations(dc, manager, "numberExtraQiacubeItems", Annotationtype.BATCH_NUMBER_EXTRA_QIACUBE_ITEMS, null); |
| 3440 |
17 Jul 15 |
olle |
306 |
p.loadAnnotations(dc, manager, "extraItemNames", Annotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING, null, true, true); |
| 3225 |
02 Apr 15 |
olle |
307 |
JSONObject jsonPlate = p.asJSONObject(); |
| 3225 |
02 Apr 15 |
olle |
308 |
jsonPlate.put("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(extractionDate)); |
| 3225 |
02 Apr 15 |
olle |
309 |
jsonPlates.add(jsonPlate); |
| 3206 |
20 Mar 15 |
olle |
310 |
} |
| 3206 |
20 Mar 15 |
olle |
311 |
|
| 3206 |
20 Mar 15 |
olle |
312 |
json.put("plates", jsonPlates); |
| 3206 |
20 Mar 15 |
olle |
313 |
} |
| 3180 |
17 Mar 15 |
olle |
314 |
else if ("GetUnprocessedStartPlates".equals(cmd)) |
| 3180 |
17 Mar 15 |
olle |
315 |
{ |
| 3180 |
17 Mar 15 |
olle |
316 |
/* |
| 3180 |
17 Mar 15 |
olle |
Find start DNA plates that have no created date. Order by |
| 3180 |
17 Mar 15 |
olle |
bioplate name. |
| 3180 |
17 Mar 15 |
olle |
319 |
*/ |
| 3180 |
17 Mar 15 |
olle |
320 |
dc = sc.newDbControl(); |
| 3180 |
17 Mar 15 |
olle |
321 |
Subtype subtype = null; |
| 4200 |
01 Nov 16 |
olle |
322 |
String prefix = Meludi.fetchStartPlateItemPrefix(sc.getActiveProjectId()); |
| 3180 |
17 Mar 15 |
olle |
323 |
int numFreeWells = 0; |
| 3180 |
17 Mar 15 |
olle |
324 |
Annotationtype runDateAnnotation = null; |
| 3180 |
17 Mar 15 |
olle |
325 |
List<ReactionPlate> startPlates = ReactionPlate.findActiveByBioPlateType(dc, |
| 3180 |
17 Mar 15 |
olle |
326 |
BioplateType.DNA, subtype, prefix, numFreeWells, runDateAnnotation); |
| 3180 |
17 Mar 15 |
olle |
327 |
|
| 3180 |
17 Mar 15 |
olle |
328 |
JSONArray jsonPlates = new JSONArray(); |
| 3180 |
17 Mar 15 |
olle |
329 |
|
| 3440 |
17 Jul 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3440 |
17 Jul 15 |
olle |
331 |
SnapshotManager manager = new SnapshotManager(); |
| 3180 |
17 Mar 15 |
olle |
332 |
for (ReactionPlate p : startPlates) |
| 3180 |
17 Mar 15 |
olle |
333 |
{ |
| 3440 |
17 Jul 15 |
olle |
334 |
p.loadAnnotations(dc, manager, "sourceItemNames", Annotationtype.SOURCE_ITEM_NAMES_LIST_STRING, null, true, true); |
| 3440 |
17 Jul 15 |
olle |
335 |
p.loadAnnotations(dc, manager, "numberExtraQiacubeItems", Annotationtype.BATCH_NUMBER_EXTRA_QIACUBE_ITEMS, null); |
| 3440 |
17 Jul 15 |
olle |
336 |
p.loadAnnotations(dc, manager, "extraItemNames", Annotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING, null, true, true); |
| 3180 |
17 Mar 15 |
olle |
337 |
jsonPlates.add(p.asJSONObject()); |
| 3180 |
17 Mar 15 |
olle |
338 |
} |
| 3180 |
17 Mar 15 |
olle |
339 |
|
| 3180 |
17 Mar 15 |
olle |
340 |
json.put("plates", jsonPlates); |
| 3180 |
17 Mar 15 |
olle |
341 |
} |
| 3447 |
27 Jul 15 |
olle |
342 |
else if ("CheckIfStartPlateNameUsed".equals(cmd)) |
| 3447 |
27 Jul 15 |
olle |
343 |
{ |
| 3447 |
27 Jul 15 |
olle |
344 |
dc = sc.newDbControl(); |
| 3447 |
27 Jul 15 |
olle |
345 |
String startPlateName = req.getParameter("startPlateName"); |
| 3447 |
27 Jul 15 |
olle |
346 |
|
| 3447 |
27 Jul 15 |
olle |
347 |
Integer bioPlateId = null; |
| 3447 |
27 Jul 15 |
olle |
348 |
if (startPlateName != null && !startPlateName.equals("")) |
| 3447 |
27 Jul 15 |
olle |
349 |
{ |
| 3447 |
27 Jul 15 |
olle |
350 |
ItemQuery<BioPlate> query = BioPlate.getQuery(); |
| 3447 |
27 Jul 15 |
olle |
351 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 3447 |
27 Jul 15 |
olle |
352 |
query.restrict(Restrictions.eq(Hql.property("name"), Expressions.string(startPlateName))); |
| 3447 |
27 Jul 15 |
olle |
353 |
query.order(Orders.asc(Hql.property("name"))); |
| 3447 |
27 Jul 15 |
olle |
354 |
List<BioPlate> plates = query.list(dc); |
| 3447 |
27 Jul 15 |
olle |
355 |
|
| 3447 |
27 Jul 15 |
olle |
356 |
if (plates.size() > 0) |
| 3447 |
27 Jul 15 |
olle |
357 |
{ |
| 3447 |
27 Jul 15 |
olle |
358 |
BioPlate bioPlate = (BioPlate) plates.get(0); |
| 3447 |
27 Jul 15 |
olle |
359 |
bioPlateId = bioPlate.getId(); |
| 3447 |
27 Jul 15 |
olle |
360 |
} |
| 3447 |
27 Jul 15 |
olle |
361 |
} |
| 3447 |
27 Jul 15 |
olle |
362 |
JSONObject jsonPlate = new JSONObject(); |
| 3447 |
27 Jul 15 |
olle |
363 |
jsonPlate.put("name", startPlateName); |
| 3447 |
27 Jul 15 |
olle |
364 |
jsonPlate.put("id", bioPlateId); |
| 3447 |
27 Jul 15 |
olle |
365 |
json.put("startplate", jsonPlate); |
| 3447 |
27 Jul 15 |
olle |
366 |
} |
| 3180 |
17 Mar 15 |
olle |
367 |
else if ("GetSourceItemListFromStartPlate".equals(cmd)) |
| 3180 |
17 Mar 15 |
olle |
368 |
{ |
| 3180 |
17 Mar 15 |
olle |
369 |
/* |
| 3180 |
17 Mar 15 |
olle |
Find source items on start DNA plate from "SourceItemNames" annotation. |
| 3180 |
17 Mar 15 |
olle |
371 |
*/ |
| 3180 |
17 Mar 15 |
olle |
372 |
dc = sc.newDbControl(); |
| 3180 |
17 Mar 15 |
olle |
373 |
Integer startPlateId = Values.getInteger(req.getParameter("startPlateId"), null); |
| 3225 |
02 Apr 15 |
olle |
374 |
Boolean includeSpecimenExtracts = Boolean.valueOf(req.getParameter("includeSpecimenExtracts")); |
| 3225 |
02 Apr 15 |
olle |
375 |
if (includeSpecimenExtracts == null) |
| 3225 |
02 Apr 15 |
olle |
376 |
{ |
| 3225 |
02 Apr 15 |
olle |
377 |
includeSpecimenExtracts = false; |
| 3225 |
02 Apr 15 |
olle |
378 |
} |
| 3180 |
17 Mar 15 |
olle |
379 |
|
| 3180 |
17 Mar 15 |
olle |
380 |
JSONObject jsonStartPlate = new JSONObject(); |
| 3180 |
17 Mar 15 |
olle |
381 |
JSONArray jsonSpecimen = new JSONArray(); |
| 3180 |
17 Mar 15 |
olle |
382 |
JSONArray jsonRna = new JSONArray(); |
| 3180 |
17 Mar 15 |
olle |
383 |
JSONArray jsonDna = new JSONArray(); |
| 3212 |
27 Mar 15 |
olle |
384 |
JSONArray jsonItems = new JSONArray(); |
| 3245 |
14 Apr 15 |
olle |
385 |
JSONArray jsonExtraItems = new JSONArray(); |
| 3180 |
17 Mar 15 |
olle |
386 |
|
| 3225 |
02 Apr 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3225 |
02 Apr 15 |
olle |
388 |
SnapshotManager manager = new SnapshotManager(); |
| 3245 |
14 Apr 15 |
olle |
389 |
Integer numExtraQiacubeItems = 0; |
| 3180 |
17 Mar 15 |
olle |
390 |
List<String> itemNameList = null; |
| 3245 |
14 Apr 15 |
olle |
391 |
List<String> extraItemNameList = null; |
| 3180 |
17 Mar 15 |
olle |
392 |
if (startPlateId != null) |
| 3180 |
17 Mar 15 |
olle |
393 |
{ |
| 3180 |
17 Mar 15 |
olle |
//ReactionPlate startPlate = ReactionPlate.getById(dc, startPlateId, BioplateType.DNA); |
| 3180 |
17 Mar 15 |
olle |
395 |
BioPlate startPlate = BioPlate.getById(dc, startPlateId); |
| 3180 |
17 Mar 15 |
olle |
396 |
if (startPlate != null) |
| 3180 |
17 Mar 15 |
olle |
397 |
{ |
| 3233 |
09 Apr 15 |
olle |
//itemNameList = (List<String>) Annotationtype.SOURCE_ITEM_NAMES.getAnnotationValues(dc, startPlate); |
| 3233 |
09 Apr 15 |
olle |
399 |
itemNameList = (List<String>) Annotationtype.SOURCE_ITEM_NAMES_LIST_STRING.getAnnotationValues(dc, startPlate, true, true); |
| 3245 |
14 Apr 15 |
olle |
400 |
extraItemNameList = (List<String>) Annotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING.getAnnotationValues(dc, startPlate, true, true); |
| 3180 |
17 Mar 15 |
olle |
401 |
jsonStartPlate.put("id", startPlate.getId()); |
| 3180 |
17 Mar 15 |
olle |
402 |
jsonStartPlate.put("name", (String) startPlate.getName()); |
| 3225 |
02 Apr 15 |
olle |
403 |
Date extractionDate = startPlate.getEventDate(); |
| 3225 |
02 Apr 15 |
olle |
404 |
jsonStartPlate.put("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(extractionDate)); |
| 3245 |
14 Apr 15 |
olle |
405 |
numExtraQiacubeItems = (Integer)Annotationtype.BATCH_NUMBER_EXTRA_QIACUBE_ITEMS.getAnnotationValue(dc, manager, startPlate); |
| 3180 |
17 Mar 15 |
olle |
// Get start plate extraction annotations |
| 3180 |
17 Mar 15 |
olle |
407 |
Date isolationDate = (Date) Annotationtype.BATCH_ISOLATION_DATE.getAnnotationValue(dc, startPlate); |
| 3225 |
02 Apr 15 |
olle |
408 |
Number extractionProtocolId = (Number) Annotationtype.BATCH_EXTRACTION_PROTOCOL_ID.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
409 |
String extractionProtocolName = (String)Annotationtype.BATCH_EXTRACTION_PROTOCOL_NAME.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
410 |
Float rnaDefaultVolume = (Float)Annotationtype.BATCH_RNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
411 |
Float dnaDefaultVolume = (Float)Annotationtype.BATCH_DNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startPlate); |
| 3180 |
17 Mar 15 |
olle |
// Get start plate QIAcube annotations |
| 3225 |
02 Apr 15 |
olle |
413 |
Date qiacubeDate = (Date) Annotationtype.BATCH_QIACUBE_DATE.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
414 |
String qiacubePrimaryPrefix = (String)Annotationtype.BATCH_QIACUBE_PRIMARY_PREFIX.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
415 |
String qiacubeSecondaryPrefix = (String)Annotationtype.BATCH_QIACUBE_SECONDARY_PREFIX.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
416 |
Integer qiacubeRunNo = (Integer)Annotationtype.BATCH_QIACUBE_RUN_NO.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
417 |
String qiacubeOperator = (String)Annotationtype.BATCH_QIACUBE_OPERATOR.getAnnotationValue(dc, manager, startPlate); |
| 3225 |
02 Apr 15 |
olle |
418 |
String allPrepFfpeKit = (String)Annotationtype.BATCH_ALLPREP_FFPE_KIT.getAnnotationValue(dc, manager, startPlate); |
| 3180 |
17 Mar 15 |
olle |
419 |
|
| 3180 |
17 Mar 15 |
olle |
420 |
jsonStartPlate.put("numExtraQiacubeItems", numExtraQiacubeItems); |
| 3180 |
17 Mar 15 |
olle |
421 |
jsonStartPlate.put("isolationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(isolationDate)); |
| 3180 |
17 Mar 15 |
olle |
422 |
jsonStartPlate.put("extractionProtocolId", extractionProtocolId); |
| 3180 |
17 Mar 15 |
olle |
423 |
jsonStartPlate.put("extractionProtocolName", extractionProtocolName); |
| 3180 |
17 Mar 15 |
olle |
424 |
jsonStartPlate.put("rnaDefaultVolume", rnaDefaultVolume); |
| 3180 |
17 Mar 15 |
olle |
425 |
jsonStartPlate.put("dnaDefaultVolume", dnaDefaultVolume); |
| 3180 |
17 Mar 15 |
olle |
426 |
jsonStartPlate.put("qiacubeDate", Meludi.CONVERTER_DATE_TO_STRING.convert(qiacubeDate)); |
| 3180 |
17 Mar 15 |
olle |
427 |
jsonStartPlate.put("qiacubePrimaryPrefix", qiacubePrimaryPrefix); |
| 3180 |
17 Mar 15 |
olle |
428 |
jsonStartPlate.put("qiacubeSecondaryPrefix", qiacubeSecondaryPrefix); |
| 3180 |
17 Mar 15 |
olle |
429 |
jsonStartPlate.put("qiacubeRunNo", qiacubeRunNo); |
| 3180 |
17 Mar 15 |
olle |
430 |
jsonStartPlate.put("qiacubeOperator", qiacubeOperator); |
| 3180 |
17 Mar 15 |
olle |
431 |
jsonStartPlate.put("allPrepFfpeKit", allPrepFfpeKit); |
| 3180 |
17 Mar 15 |
olle |
432 |
} |
| 3180 |
17 Mar 15 |
olle |
433 |
} |
| 3180 |
17 Mar 15 |
olle |
434 |
|
| 3180 |
17 Mar 15 |
olle |
// Convert item names to items |
| 3180 |
17 Mar 15 |
olle |
436 |
if (itemNameList != null) |
| 3180 |
17 Mar 15 |
olle |
437 |
{ |
| 3180 |
17 Mar 15 |
olle |
438 |
for (String itemName : itemNameList) |
| 3180 |
17 Mar 15 |
olle |
439 |
{ |
| 3433 |
29 Jun 15 |
olle |
440 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3180 |
17 Mar 15 |
olle |
441 |
{ |
| 3180 |
17 Mar 15 |
olle |
442 |
SpecimenTube s = SpecimenTube.findByTubeName(dc, itemName); |
| 5823 |
04 Feb 20 |
olle |
443 |
if (s != null) |
| 3225 |
02 Apr 15 |
olle |
444 |
{ |
| 5823 |
04 Feb 20 |
olle |
445 |
s.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
446 |
loadSpecimenInfo(dc, manager, s); |
| 5823 |
04 Feb 20 |
olle |
447 |
jsonSpecimen.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
448 |
JSONObject jsonSpec = s.asJSONObject(); |
| 5823 |
04 Feb 20 |
olle |
//jsonItems.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
// Loading specimen extract data might decrease performance, only use when needed |
| 5823 |
04 Feb 20 |
olle |
451 |
if (includeSpecimenExtracts) |
| 3225 |
02 Apr 15 |
olle |
452 |
{ |
| 5823 |
04 Feb 20 |
olle |
453 |
String specQiacubePosition = null; |
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Rna for specimen |
| 5823 |
04 Feb 20 |
olle |
455 |
String rnaName = itemName + ".r"; |
| 5823 |
04 Feb 20 |
olle |
456 |
Rna r = Rna.findByName(dc, rnaName); |
| 5823 |
04 Feb 20 |
olle |
457 |
if (r != null) |
| 5823 |
04 Feb 20 |
olle |
458 |
{ |
| 5823 |
04 Feb 20 |
olle |
459 |
r.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
460 |
loadRnaInfo(dc, manager, r); |
| 5823 |
04 Feb 20 |
olle |
461 |
jsonRna.add(r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
462 |
jsonSpec.put("rna", r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
463 |
} |
| 5823 |
04 Feb 20 |
olle |
464 |
|
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Dna for specimen |
| 5823 |
04 Feb 20 |
olle |
466 |
String dnaName = itemName + ".d"; |
| 5823 |
04 Feb 20 |
olle |
467 |
Dna d = Dna.findByName(dc, dnaName); |
| 5823 |
04 Feb 20 |
olle |
468 |
if (d != null) |
| 5823 |
04 Feb 20 |
olle |
469 |
{ |
| 5823 |
04 Feb 20 |
olle |
470 |
d.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
471 |
loadDnaInfo(dc, manager, d); |
| 5823 |
04 Feb 20 |
olle |
472 |
jsonDna.add(d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
473 |
jsonSpec.put("dna", d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
474 |
} |
| 3225 |
02 Apr 15 |
olle |
475 |
} |
| 5823 |
04 Feb 20 |
olle |
476 |
jsonItems.add(jsonSpec); |
| 3225 |
02 Apr 15 |
olle |
477 |
} |
| 5823 |
04 Feb 20 |
olle |
478 |
else |
| 5823 |
04 Feb 20 |
olle |
479 |
{ |
| 5823 |
04 Feb 20 |
olle |
480 |
System.out.println(new Date() + " ExtractionServlet::doGet(): cmd = \"" + cmd + "\" itemName = \"" + itemName + "\" SpecimenTube s = null."); |
| 5823 |
04 Feb 20 |
olle |
481 |
} |
| 3180 |
17 Mar 15 |
olle |
482 |
} |
| 3433 |
29 Jun 15 |
olle |
483 |
else if (Meludi.itemIsRna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
484 |
{ |
| 3180 |
17 Mar 15 |
olle |
485 |
Rna r = Rna.findByName(dc, itemName); |
| 3180 |
17 Mar 15 |
olle |
486 |
r.loadBioPlateLocation(); |
| 3318 |
08 May 15 |
olle |
487 |
loadRnaInfo(dc, manager, r); |
| 3180 |
17 Mar 15 |
olle |
488 |
jsonRna.add(r.asJSONObject()); |
| 3225 |
02 Apr 15 |
olle |
489 |
JSONObject jsonR = r.asJSONObject(); |
| 3225 |
02 Apr 15 |
olle |
490 |
jsonItems.add(jsonR); |
| 3180 |
17 Mar 15 |
olle |
491 |
} |
| 3433 |
29 Jun 15 |
olle |
492 |
else if (Meludi.itemIsDna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
493 |
{ |
| 3180 |
17 Mar 15 |
olle |
494 |
Dna d = Dna.findByName(dc, itemName); |
| 3180 |
17 Mar 15 |
olle |
495 |
d.loadBioPlateLocation(); |
| 3318 |
08 May 15 |
olle |
496 |
loadDnaInfo(dc, manager, d); |
| 3180 |
17 Mar 15 |
olle |
497 |
jsonDna.add(d.asJSONObject()); |
| 3225 |
02 Apr 15 |
olle |
498 |
JSONObject jsonD = d.asJSONObject(); |
| 3225 |
02 Apr 15 |
olle |
499 |
jsonItems.add(jsonD); |
| 3180 |
17 Mar 15 |
olle |
500 |
} |
| 3180 |
17 Mar 15 |
olle |
501 |
} |
| 3180 |
17 Mar 15 |
olle |
502 |
} |
| 3180 |
17 Mar 15 |
olle |
503 |
|
| 3245 |
14 Apr 15 |
olle |
// Convert extra QIAcube item names to items |
| 3245 |
14 Apr 15 |
olle |
505 |
if (extraItemNameList != null && extraItemNameList.size() > 0) |
| 3245 |
14 Apr 15 |
olle |
506 |
{ |
| 3245 |
14 Apr 15 |
olle |
507 |
for (String itemName : extraItemNameList) |
| 3245 |
14 Apr 15 |
olle |
508 |
{ |
| 3245 |
14 Apr 15 |
olle |
509 |
JSONObject jsonExtra = new JSONObject(); |
| 3245 |
14 Apr 15 |
olle |
510 |
jsonExtra.put("name", itemName); |
| 3245 |
14 Apr 15 |
olle |
511 |
jsonExtraItems.add(jsonExtra); |
| 3245 |
14 Apr 15 |
olle |
512 |
} |
| 3245 |
14 Apr 15 |
olle |
513 |
} |
| 3245 |
14 Apr 15 |
olle |
514 |
else if (numExtraQiacubeItems != null) |
| 3245 |
14 Apr 15 |
olle |
515 |
{ |
| 3245 |
14 Apr 15 |
olle |
516 |
for (int i = 1; i <= numExtraQiacubeItems; i++) |
| 3245 |
14 Apr 15 |
olle |
517 |
{ |
| 3245 |
14 Apr 15 |
olle |
// Create extra item names as E01, E02, ... ,E09, E10, E11, ... |
| 3245 |
14 Apr 15 |
olle |
519 |
String itemName = "E"; |
| 3245 |
14 Apr 15 |
olle |
520 |
if (i < 10) |
| 3245 |
14 Apr 15 |
olle |
521 |
{ |
| 3245 |
14 Apr 15 |
olle |
522 |
itemName += "0"; |
| 3245 |
14 Apr 15 |
olle |
523 |
} |
| 3245 |
14 Apr 15 |
olle |
524 |
itemName += "" + i; |
| 3245 |
14 Apr 15 |
olle |
525 |
JSONObject jsonExtra = new JSONObject(); |
| 3245 |
14 Apr 15 |
olle |
526 |
jsonExtra.put("name", itemName); |
| 3245 |
14 Apr 15 |
olle |
527 |
jsonExtraItems.add(jsonExtra); |
| 3245 |
14 Apr 15 |
olle |
528 |
} |
| 3245 |
14 Apr 15 |
olle |
529 |
} |
| 3245 |
14 Apr 15 |
olle |
530 |
|
| 3180 |
17 Mar 15 |
olle |
531 |
json.put("startplate", jsonStartPlate); |
| 3180 |
17 Mar 15 |
olle |
532 |
json.put("specimens", jsonSpecimen); |
| 3180 |
17 Mar 15 |
olle |
533 |
json.put("rnas", jsonRna); |
| 3180 |
17 Mar 15 |
olle |
534 |
json.put("dnas", jsonDna); |
| 3212 |
27 Mar 15 |
olle |
535 |
json.put("items", jsonItems); |
| 3245 |
14 Apr 15 |
olle |
536 |
json.put("extraitems", jsonExtraItems); |
| 3180 |
17 Mar 15 |
olle |
537 |
} |
| 3432 |
29 Jun 15 |
olle |
538 |
else if ("GetStartItemLists".equals(cmd)) |
| 3432 |
29 Jun 15 |
olle |
539 |
{ |
| 3432 |
29 Jun 15 |
olle |
540 |
/* |
| 3432 |
29 Jun 15 |
olle |
Find start item lists. Order by item list name. |
| 3432 |
29 Jun 15 |
olle |
542 |
*/ |
| 3432 |
29 Jun 15 |
olle |
543 |
dc = sc.newDbControl(); |
| 3440 |
17 Jul 15 |
olle |
544 |
Boolean processed = null; |
| 3432 |
29 Jun 15 |
olle |
545 |
Boolean orderDesc = Boolean.valueOf(req.getParameter("orderDesc")); |
| 3644 |
03 Dec 15 |
olle |
546 |
Boolean anItemNotOnLibPlate = Boolean.valueOf(req.getParameter("anItemNotOnLibPlate")); |
| 3719 |
22 Jan 16 |
olle |
547 |
Boolean ignoreQpcrBranch = Boolean.valueOf(req.getParameter("ignoreQpcrBranch")); |
| 3432 |
29 Jun 15 |
olle |
548 |
|
| 3719 |
22 Jan 16 |
olle |
549 |
JSONArray jsonItemLists = fetchStartItemLists(dc, processed, orderDesc, anItemNotOnLibPlate, ignoreQpcrBranch); |
| 3432 |
29 Jun 15 |
olle |
550 |
|
| 3432 |
29 Jun 15 |
olle |
551 |
json.put("itemLists", jsonItemLists); |
| 3432 |
29 Jun 15 |
olle |
552 |
} |
| 3432 |
29 Jun 15 |
olle |
553 |
else if ("GetUnprocessedStartItemLists".equals(cmd)) |
| 3432 |
29 Jun 15 |
olle |
554 |
{ |
| 3432 |
29 Jun 15 |
olle |
555 |
/* |
| 3432 |
29 Jun 15 |
olle |
Find unprocessed start item lists. Order by item list name. |
| 3432 |
29 Jun 15 |
olle |
557 |
*/ |
| 3432 |
29 Jun 15 |
olle |
558 |
dc = sc.newDbControl(); |
| 3440 |
17 Jul 15 |
olle |
559 |
Boolean processed = false; |
| 3432 |
29 Jun 15 |
olle |
560 |
Boolean orderDesc = Boolean.valueOf(req.getParameter("orderDesc")); |
| 3644 |
03 Dec 15 |
olle |
561 |
Boolean anItemNotOnLibPlate = Boolean.valueOf(req.getParameter("anItemNotOnLibPlate")); |
| 3719 |
22 Jan 16 |
olle |
562 |
Boolean ignoreQpcrBranch = Boolean.valueOf(req.getParameter("ignoreQpcrBranch")); |
| 3432 |
29 Jun 15 |
olle |
563 |
|
| 3719 |
22 Jan 16 |
olle |
564 |
JSONArray jsonItemLists = fetchStartItemLists(dc, processed, orderDesc, anItemNotOnLibPlate, ignoreQpcrBranch); |
| 3432 |
29 Jun 15 |
olle |
565 |
|
| 3440 |
17 Jul 15 |
olle |
566 |
json.put("itemLists", jsonItemLists); |
| 3440 |
17 Jul 15 |
olle |
567 |
} |
| 3440 |
17 Jul 15 |
olle |
568 |
else if ("GetProcessedStartItemLists".equals(cmd)) |
| 3440 |
17 Jul 15 |
olle |
569 |
{ |
| 3440 |
17 Jul 15 |
olle |
570 |
/* |
| 3440 |
17 Jul 15 |
olle |
Find processed start item lists. Order by item list name. |
| 3440 |
17 Jul 15 |
olle |
572 |
*/ |
| 3440 |
17 Jul 15 |
olle |
573 |
dc = sc.newDbControl(); |
| 3440 |
17 Jul 15 |
olle |
574 |
Boolean processed = true; |
| 3440 |
17 Jul 15 |
olle |
575 |
Boolean orderDesc = Boolean.valueOf(req.getParameter("orderDesc")); |
| 3644 |
03 Dec 15 |
olle |
576 |
Boolean anItemNotOnLibPlate = Boolean.valueOf(req.getParameter("anItemNotOnLibPlate")); |
| 3719 |
22 Jan 16 |
olle |
577 |
Boolean ignoreQpcrBranch = Boolean.valueOf(req.getParameter("ignoreQpcrBranch")); |
| 3440 |
17 Jul 15 |
olle |
578 |
|
| 3719 |
22 Jan 16 |
olle |
579 |
JSONArray jsonItemLists = fetchStartItemLists(dc, processed, orderDesc, anItemNotOnLibPlate, ignoreQpcrBranch); |
| 3432 |
29 Jun 15 |
olle |
580 |
|
| 3432 |
29 Jun 15 |
olle |
581 |
json.put("itemLists", jsonItemLists); |
| 3432 |
29 Jun 15 |
olle |
582 |
} |
| 3432 |
29 Jun 15 |
olle |
583 |
else if ("GetSourceItemListFromStartItemList".equals(cmd)) |
| 3432 |
29 Jun 15 |
olle |
584 |
{ |
| 3432 |
29 Jun 15 |
olle |
585 |
/* |
| 3432 |
29 Jun 15 |
olle |
Find extract source items from start item list members. |
| 3432 |
29 Jun 15 |
olle |
587 |
*/ |
| 3432 |
29 Jun 15 |
olle |
588 |
dc = sc.newDbControl(); |
| 3432 |
29 Jun 15 |
olle |
589 |
Integer startItemListId = Values.getInteger(req.getParameter("startItemListId"), null); |
| 3432 |
29 Jun 15 |
olle |
590 |
Boolean includeSpecimenExtracts = Boolean.valueOf(req.getParameter("includeSpecimenExtracts")); |
| 3432 |
29 Jun 15 |
olle |
591 |
if (includeSpecimenExtracts == null) |
| 3432 |
29 Jun 15 |
olle |
592 |
{ |
| 3432 |
29 Jun 15 |
olle |
593 |
includeSpecimenExtracts = false; |
| 3432 |
29 Jun 15 |
olle |
594 |
} |
| 3432 |
29 Jun 15 |
olle |
595 |
|
| 3432 |
29 Jun 15 |
olle |
596 |
JSONObject jsonStartItemList = new JSONObject(); |
| 3432 |
29 Jun 15 |
olle |
597 |
JSONArray jsonSpecimen = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
598 |
JSONArray jsonRna = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
599 |
JSONArray jsonDna = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
600 |
JSONArray jsonItems = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
601 |
JSONArray jsonExtraItems = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
602 |
|
| 3432 |
29 Jun 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3432 |
29 Jun 15 |
olle |
604 |
SnapshotManager manager = new SnapshotManager(); |
| 3432 |
29 Jun 15 |
olle |
605 |
List<String> itemNameList = null; |
| 3432 |
29 Jun 15 |
olle |
606 |
if (startItemListId != null) |
| 3432 |
29 Jun 15 |
olle |
607 |
{ |
| 3432 |
29 Jun 15 |
olle |
608 |
ItemList startItemList = ItemList.getById(dc, startItemListId); |
| 3432 |
29 Jun 15 |
olle |
609 |
if (startItemList != null) |
| 3432 |
29 Jun 15 |
olle |
610 |
{ |
| 3433 |
29 Jun 15 |
olle |
611 |
StartList sl = new StartList(startItemList); |
| 3433 |
29 Jun 15 |
olle |
612 |
itemNameList = sl.fetchExtractSourceNameListFromItemList(dc); |
| 3432 |
29 Jun 15 |
olle |
613 |
jsonStartItemList.put("id", startItemList.getId()); |
| 3432 |
29 Jun 15 |
olle |
614 |
jsonStartItemList.put("name", (String) startItemList.getName()); |
| 3432 |
29 Jun 15 |
olle |
615 |
Date extractionDate = (Date) Annotationtype.LIST_EXTRACTION_DATE.getAnnotationValue(dc, startItemList); |
| 3432 |
29 Jun 15 |
olle |
616 |
jsonStartItemList.put("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(extractionDate)); |
| 3432 |
29 Jun 15 |
olle |
// Get start item list extraction annotations |
| 3432 |
29 Jun 15 |
olle |
618 |
Date isolationDate = (Date) Annotationtype.LIST_ISOLATION_DATE.getAnnotationValue(dc, startItemList); |
| 3501 |
21 Sep 15 |
olle |
619 |
String extractionOperator = (String)Annotationtype.LIST_EXTRACTION_OPERATOR.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
620 |
Number extractionProtocolId = (Number) Annotationtype.LIST_EXTRACTION_PROTOCOL_ID.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
621 |
String extractionProtocolName = (String)Annotationtype.LIST_EXTRACTION_PROTOCOL_NAME.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
622 |
Float rnaDefaultVolume = (Float)Annotationtype.LIST_RNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
623 |
Float dnaDefaultVolume = (Float)Annotationtype.LIST_DNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
// Get start item list QIAcube annotations |
| 3432 |
29 Jun 15 |
olle |
625 |
Date qiacubeDate = (Date) Annotationtype.LIST_QIACUBE_DATE.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
626 |
String qiacubeOperator = (String)Annotationtype.LIST_QIACUBE_OPERATOR.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
627 |
String qiacubePrimaryPrefix = (String)Annotationtype.LIST_QIACUBE_PRIMARY_PREFIX.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
628 |
String qiacubeSecondaryPrefix = (String)Annotationtype.LIST_QIACUBE_SECONDARY_PREFIX.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
629 |
Integer qiacubeRunNo = (Integer)Annotationtype.LIST_QIACUBE_RUN_NO.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
630 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3432 |
29 Jun 15 |
olle |
632 |
String allPrepFfpeKit = (String)Annotationtype.LIST_ALLPREP_FFPE_KIT.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
633 |
String xyleneSpecimen = (String)Annotationtype.LIST_XYLENE_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
634 |
String etoh995Specimen = (String)Annotationtype.LIST_ETOH995_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
635 |
String bufferPkdSpecimen = (String)Annotationtype.LIST_BUFFER_PKD_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
636 |
String bufferAtlSpecimen = (String)Annotationtype.LIST_BUFFER_ATL_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
637 |
String proteinaseKSpecimen = (String)Annotationtype.LIST_PROTEINASE_K_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
638 |
String rnaseASpecimen = (String)Annotationtype.LIST_RNASE_A_SPECIMEN.getAnnotationValue(dc, manager, startItemList); |
| 3432 |
29 Jun 15 |
olle |
639 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
641 |
String etoh995 = (String)Annotationtype.LIST_ETOH995.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
642 |
String bufferRlt = (String)Annotationtype.LIST_BUFFER_RLT.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
643 |
String bufferFrn = (String)Annotationtype.LIST_BUFFER_FRN.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
644 |
String bufferRpe = (String)Annotationtype.LIST_BUFFER_RPE.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
645 |
String bufferAl = (String)Annotationtype.LIST_BUFFER_AL.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
646 |
String bufferAw1 = (String)Annotationtype.LIST_BUFFER_AW1.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
647 |
String bufferAw2 = (String)Annotationtype.LIST_BUFFER_AW2.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
648 |
String bufferAte = (String)Annotationtype.LIST_BUFFER_ATE.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
649 |
String bufferRdd = (String)Annotationtype.LIST_BUFFER_RDD.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
650 |
String rnaseFreeWater = (String)Annotationtype.LIST_RNASE_FREE_WATER.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
651 |
String dnaseMix = (String)Annotationtype.LIST_DNASE_MIX.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
652 |
String rneasyMinEluteSpinColumn = (String)Annotationtype.LIST_RNEASY_MIN_ELUTE_SPIN_COL.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
653 |
String qiaampMinEluteSpinColumn = (String)Annotationtype.LIST_QIAAMP_MIN_ELUTE_SPIN_COL.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
654 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
656 |
String kapaSybrFast = (String)Annotationtype.LIST_KAPA_SYBR_FAST.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
657 |
String qualityControlPrimersQcpRgt = (String)Annotationtype.LIST_QUALITY_CONTROL_PRIMERS_QCP_RGT.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
658 |
String qualityControlTemplateQct = (String)Annotationtype.LIST_QUALITY_CONTROL_TEMPLATE_QCT.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
659 |
String qubitDnaHighSens = (String)Annotationtype.LIST_QUBIT_DNA_HIGH_SENS.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
660 |
String qubitDnaBroadRange = (String)Annotationtype.LIST_QUBIT_DNA_BROAD_RANGE.getAnnotationValue(dc, manager, startItemList); |
| 3501 |
21 Sep 15 |
olle |
661 |
|
| 3432 |
29 Jun 15 |
olle |
662 |
jsonStartItemList.put("isolationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(isolationDate)); |
| 3501 |
21 Sep 15 |
olle |
663 |
jsonStartItemList.put("extractionOperator", extractionOperator); |
| 3432 |
29 Jun 15 |
olle |
664 |
jsonStartItemList.put("extractionProtocolId", extractionProtocolId); |
| 3432 |
29 Jun 15 |
olle |
665 |
jsonStartItemList.put("extractionProtocolName", extractionProtocolName); |
| 3432 |
29 Jun 15 |
olle |
666 |
jsonStartItemList.put("rnaDefaultVolume", rnaDefaultVolume); |
| 3432 |
29 Jun 15 |
olle |
667 |
jsonStartItemList.put("dnaDefaultVolume", dnaDefaultVolume); |
| 3432 |
29 Jun 15 |
olle |
668 |
jsonStartItemList.put("qiacubeDate", Meludi.CONVERTER_DATE_TO_STRING.convert(qiacubeDate)); |
| 3501 |
21 Sep 15 |
olle |
669 |
jsonStartItemList.put("qiacubeOperator", qiacubeOperator); |
| 3432 |
29 Jun 15 |
olle |
670 |
jsonStartItemList.put("qiacubePrimaryPrefix", qiacubePrimaryPrefix); |
| 3432 |
29 Jun 15 |
olle |
671 |
jsonStartItemList.put("qiacubeSecondaryPrefix", qiacubeSecondaryPrefix); |
| 3432 |
29 Jun 15 |
olle |
672 |
jsonStartItemList.put("qiacubeRunNo", qiacubeRunNo); |
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3432 |
29 Jun 15 |
olle |
674 |
jsonStartItemList.put("allPrepFfpeKit", allPrepFfpeKit); |
| 3501 |
21 Sep 15 |
olle |
675 |
jsonStartItemList.put("xyleneSpecimen", xyleneSpecimen); |
| 3501 |
21 Sep 15 |
olle |
676 |
jsonStartItemList.put("etoh995Specimen", etoh995Specimen); |
| 3501 |
21 Sep 15 |
olle |
677 |
jsonStartItemList.put("bufferPkdSpecimen", bufferPkdSpecimen); |
| 3501 |
21 Sep 15 |
olle |
678 |
jsonStartItemList.put("bufferAtlSpecimen", bufferAtlSpecimen); |
| 3501 |
21 Sep 15 |
olle |
679 |
jsonStartItemList.put("proteinaseKSpecimen", proteinaseKSpecimen); |
| 3501 |
21 Sep 15 |
olle |
680 |
jsonStartItemList.put("rnaseASpecimen", rnaseASpecimen); |
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
682 |
jsonStartItemList.put("etoh995", etoh995); |
| 3501 |
21 Sep 15 |
olle |
683 |
jsonStartItemList.put("bufferRlt", bufferRlt); |
| 3501 |
21 Sep 15 |
olle |
684 |
jsonStartItemList.put("bufferFrn", bufferFrn); |
| 3501 |
21 Sep 15 |
olle |
685 |
jsonStartItemList.put("bufferRpe", bufferRpe); |
| 3501 |
21 Sep 15 |
olle |
686 |
jsonStartItemList.put("bufferAl", bufferAl); |
| 3501 |
21 Sep 15 |
olle |
687 |
jsonStartItemList.put("bufferAw1", bufferAw1); |
| 3501 |
21 Sep 15 |
olle |
688 |
jsonStartItemList.put("bufferAw2", bufferAw2); |
| 3501 |
21 Sep 15 |
olle |
689 |
jsonStartItemList.put("bufferAte", bufferAte); |
| 3501 |
21 Sep 15 |
olle |
690 |
jsonStartItemList.put("bufferRdd", bufferRdd); |
| 3501 |
21 Sep 15 |
olle |
691 |
jsonStartItemList.put("rnaseFreeWater", rnaseFreeWater); |
| 3501 |
21 Sep 15 |
olle |
692 |
jsonStartItemList.put("dnaseMix", dnaseMix); |
| 3501 |
21 Sep 15 |
olle |
693 |
jsonStartItemList.put("rneasyMinEluteSpinColumn", rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
694 |
jsonStartItemList.put("qiaampMinEluteSpinColumn", qiaampMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
696 |
jsonStartItemList.put("kapaSybrFast", kapaSybrFast); |
| 3501 |
21 Sep 15 |
olle |
697 |
jsonStartItemList.put("qualityControlPrimersQcpRgt", qualityControlPrimersQcpRgt); |
| 3501 |
21 Sep 15 |
olle |
698 |
jsonStartItemList.put("qualityControlTemplateQct", qualityControlTemplateQct); |
| 3501 |
21 Sep 15 |
olle |
699 |
jsonStartItemList.put("qubitDnaHighSens", qubitDnaHighSens); |
| 3501 |
21 Sep 15 |
olle |
700 |
jsonStartItemList.put("qubitDnaBroadRange", qubitDnaBroadRange); |
| 3432 |
29 Jun 15 |
olle |
701 |
} |
| 3432 |
29 Jun 15 |
olle |
702 |
} |
| 3432 |
29 Jun 15 |
olle |
703 |
|
| 3432 |
29 Jun 15 |
olle |
// Convert item names to items |
| 3432 |
29 Jun 15 |
olle |
705 |
if (itemNameList != null) |
| 3432 |
29 Jun 15 |
olle |
706 |
{ |
| 3432 |
29 Jun 15 |
olle |
707 |
for (String itemName : itemNameList) |
| 3432 |
29 Jun 15 |
olle |
708 |
{ |
| 3433 |
29 Jun 15 |
olle |
709 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3432 |
29 Jun 15 |
olle |
710 |
{ |
| 3432 |
29 Jun 15 |
olle |
711 |
SpecimenTube s = SpecimenTube.findByTubeName(dc, itemName); |
| 5823 |
04 Feb 20 |
olle |
712 |
if (s != null) |
| 3432 |
29 Jun 15 |
olle |
713 |
{ |
| 5823 |
04 Feb 20 |
olle |
714 |
s.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
715 |
loadSpecimenInfo(dc, manager, s); |
| 5823 |
04 Feb 20 |
olle |
716 |
jsonSpecimen.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
717 |
JSONObject jsonSpec = s.asJSONObject(); |
| 5823 |
04 Feb 20 |
olle |
//jsonItems.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
// Loading specimen extract data might decrease performance, only use when needed |
| 5823 |
04 Feb 20 |
olle |
720 |
if (includeSpecimenExtracts) |
| 3432 |
29 Jun 15 |
olle |
721 |
{ |
| 5823 |
04 Feb 20 |
olle |
722 |
String specQiacubePosition = null; |
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Rna for specimen |
| 5823 |
04 Feb 20 |
olle |
724 |
String rnaName = itemName + ".r"; |
| 5823 |
04 Feb 20 |
olle |
725 |
Rna r = Rna.findByName(dc, rnaName); |
| 5823 |
04 Feb 20 |
olle |
726 |
if (r != null) |
| 5823 |
04 Feb 20 |
olle |
727 |
{ |
| 5823 |
04 Feb 20 |
olle |
728 |
r.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
729 |
loadRnaInfo(dc, manager, r); |
| 5823 |
04 Feb 20 |
olle |
730 |
jsonRna.add(r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
731 |
jsonSpec.put("rna", r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
732 |
} |
| 5823 |
04 Feb 20 |
olle |
733 |
|
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Dna for specimen |
| 5823 |
04 Feb 20 |
olle |
735 |
String dnaName = itemName + ".d"; |
| 5823 |
04 Feb 20 |
olle |
736 |
Dna d = Dna.findByName(dc, dnaName); |
| 5823 |
04 Feb 20 |
olle |
737 |
if (d != null) |
| 5823 |
04 Feb 20 |
olle |
738 |
{ |
| 5823 |
04 Feb 20 |
olle |
739 |
d.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
740 |
loadDnaInfo(dc, manager, d); |
| 5823 |
04 Feb 20 |
olle |
741 |
jsonDna.add(d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
742 |
jsonSpec.put("dna", d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
743 |
} |
| 3432 |
29 Jun 15 |
olle |
744 |
} |
| 5823 |
04 Feb 20 |
olle |
745 |
jsonItems.add(jsonSpec); |
| 3432 |
29 Jun 15 |
olle |
746 |
} |
| 5823 |
04 Feb 20 |
olle |
747 |
else |
| 5823 |
04 Feb 20 |
olle |
748 |
{ |
| 5823 |
04 Feb 20 |
olle |
749 |
System.out.println(new Date() + " ExtractionServlet::doGet(): cmd = \"" + cmd + "\" itemName = \"" + itemName + "\" SpecimenTube s = null."); |
| 5823 |
04 Feb 20 |
olle |
750 |
} |
| 3432 |
29 Jun 15 |
olle |
751 |
} |
| 3433 |
29 Jun 15 |
olle |
752 |
else if (Meludi.itemIsRna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
753 |
{ |
| 3432 |
29 Jun 15 |
olle |
754 |
Rna r = Rna.findByName(dc, itemName); |
| 3432 |
29 Jun 15 |
olle |
755 |
r.loadBioPlateLocation(); |
| 3432 |
29 Jun 15 |
olle |
756 |
loadRnaInfo(dc, manager, r); |
| 3432 |
29 Jun 15 |
olle |
757 |
jsonRna.add(r.asJSONObject()); |
| 3432 |
29 Jun 15 |
olle |
758 |
JSONObject jsonR = r.asJSONObject(); |
| 3432 |
29 Jun 15 |
olle |
759 |
jsonItems.add(jsonR); |
| 3432 |
29 Jun 15 |
olle |
760 |
} |
| 3433 |
29 Jun 15 |
olle |
761 |
else if (Meludi.itemIsDna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
762 |
{ |
| 3432 |
29 Jun 15 |
olle |
763 |
Dna d = Dna.findByName(dc, itemName); |
| 3432 |
29 Jun 15 |
olle |
764 |
d.loadBioPlateLocation(); |
| 3432 |
29 Jun 15 |
olle |
765 |
loadDnaInfo(dc, manager, d); |
| 3432 |
29 Jun 15 |
olle |
766 |
jsonDna.add(d.asJSONObject()); |
| 3432 |
29 Jun 15 |
olle |
767 |
JSONObject jsonD = d.asJSONObject(); |
| 3432 |
29 Jun 15 |
olle |
768 |
jsonItems.add(jsonD); |
| 3432 |
29 Jun 15 |
olle |
769 |
} |
| 3432 |
29 Jun 15 |
olle |
770 |
} |
| 3432 |
29 Jun 15 |
olle |
771 |
} |
| 3432 |
29 Jun 15 |
olle |
772 |
|
| 3432 |
29 Jun 15 |
olle |
773 |
json.put("startitemlist", jsonStartItemList); |
| 3432 |
29 Jun 15 |
olle |
774 |
json.put("specimens", jsonSpecimen); |
| 3432 |
29 Jun 15 |
olle |
775 |
json.put("rnas", jsonRna); |
| 3432 |
29 Jun 15 |
olle |
776 |
json.put("dnas", jsonDna); |
| 3432 |
29 Jun 15 |
olle |
777 |
json.put("items", jsonItems); |
| 3432 |
29 Jun 15 |
olle |
778 |
} |
| 3440 |
17 Jul 15 |
olle |
779 |
else if ("GetListOfItemsFromStartItemLists".equals(cmd)) |
| 3440 |
17 Jul 15 |
olle |
780 |
{ |
| 3440 |
17 Jul 15 |
olle |
781 |
/* |
| 3440 |
17 Jul 15 |
olle |
Find items from members of start item lists. |
| 3440 |
17 Jul 15 |
olle |
783 |
*/ |
| 3440 |
17 Jul 15 |
olle |
784 |
dc = sc.newDbControl(); |
| 3440 |
17 Jul 15 |
olle |
785 |
List<Integer> startItemListIds = new ArrayList<Integer>(); |
| 3440 |
17 Jul 15 |
olle |
786 |
String startListInfoStr = req.getParameter("startListIds"); |
| 3440 |
17 Jul 15 |
olle |
787 |
JSONArray jsonStartItemListIds = (JSONArray)new JSONParser().parse(startListInfoStr); |
| 3644 |
03 Dec 15 |
olle |
788 |
Boolean itemNotOnLibPlate = Boolean.valueOf(req.getParameter("itemNotOnLibPlate")); |
| 3644 |
03 Dec 15 |
olle |
789 |
if (itemNotOnLibPlate == null) |
| 3644 |
03 Dec 15 |
olle |
790 |
{ |
| 3644 |
03 Dec 15 |
olle |
791 |
itemNotOnLibPlate = false; |
| 3644 |
03 Dec 15 |
olle |
792 |
} |
| 3719 |
22 Jan 16 |
olle |
793 |
Boolean ignoreQpcrBranch = Boolean.valueOf(req.getParameter("ignoreQpcrBranch")); |
| 3719 |
22 Jan 16 |
olle |
794 |
if (ignoreQpcrBranch == null) |
| 3719 |
22 Jan 16 |
olle |
795 |
{ |
| 3719 |
22 Jan 16 |
olle |
796 |
ignoreQpcrBranch = false; |
| 3719 |
22 Jan 16 |
olle |
797 |
} |
| 3440 |
17 Jul 15 |
olle |
798 |
int numSpecimen = 0; |
| 3440 |
17 Jul 15 |
olle |
799 |
int numRna = 0; |
| 3440 |
17 Jul 15 |
olle |
800 |
int numDna = 0; |
| 3440 |
17 Jul 15 |
olle |
801 |
for (int i = 0; i < jsonStartItemListIds.size(); i++) |
| 3440 |
17 Jul 15 |
olle |
802 |
{ |
| 3440 |
17 Jul 15 |
olle |
803 |
JSONObject jsonStartItemListId = (JSONObject)jsonStartItemListIds.get(i); |
| 3440 |
17 Jul 15 |
olle |
804 |
String startItemListIdStr = (String)jsonStartItemListId.get("id"); |
| 3440 |
17 Jul 15 |
olle |
805 |
Integer startItemListId = Values.getInteger(startItemListIdStr, null); |
| 3440 |
17 Jul 15 |
olle |
806 |
if (startItemListId != null) |
| 3440 |
17 Jul 15 |
olle |
807 |
{ |
| 3440 |
17 Jul 15 |
olle |
808 |
startItemListIds.add(startItemListId); |
| 3440 |
17 Jul 15 |
olle |
809 |
} |
| 3440 |
17 Jul 15 |
olle |
810 |
} |
| 3448 |
28 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doGet(): cmd = \"" + cmd + "\" startItemListIds = " + startItemListIds); |
| 3440 |
17 Jul 15 |
olle |
812 |
String itemType = req.getParameter("itemType"); |
| 3440 |
17 Jul 15 |
olle |
//String itemType = (String)jsonReq.get("itemType"); |
| 3446 |
27 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doGet(): cmd = \"" + cmd + "\" itemType = " + itemType); |
| 3440 |
17 Jul 15 |
olle |
815 |
if (itemType == null || !(itemType.equals("Specimen") || itemType.equals("DNA") || itemType.equals("RNA"))) |
| 3440 |
17 Jul 15 |
olle |
816 |
{ |
| 3440 |
17 Jul 15 |
olle |
817 |
itemType = "DNA"; |
| 3440 |
17 Jul 15 |
olle |
818 |
} |
| 3440 |
17 Jul 15 |
olle |
819 |
Boolean includeSpecimenExtracts = Boolean.valueOf(req.getParameter("includeSpecimenExtracts")); |
| 3440 |
17 Jul 15 |
olle |
820 |
if (includeSpecimenExtracts == null) |
| 3440 |
17 Jul 15 |
olle |
821 |
{ |
| 3440 |
17 Jul 15 |
olle |
822 |
includeSpecimenExtracts = false; |
| 3440 |
17 Jul 15 |
olle |
823 |
} |
| 3440 |
17 Jul 15 |
olle |
824 |
|
| 3440 |
17 Jul 15 |
olle |
825 |
JSONObject jsonStartItemList = new JSONObject(); |
| 3440 |
17 Jul 15 |
olle |
826 |
JSONArray jsonSpecimen = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
827 |
JSONArray jsonRna = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
828 |
JSONArray jsonDna = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
829 |
JSONArray jsonItems = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
830 |
JSONArray jsonExtraItems = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
831 |
|
| 3440 |
17 Jul 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3440 |
17 Jul 15 |
olle |
833 |
SnapshotManager manager = new SnapshotManager(); |
| 3440 |
17 Jul 15 |
olle |
// Store item names from start lists in lists of MeLuDI-items and extra items |
| 4150 |
03 Oct 16 |
olle |
835 |
int activeProjectId = sc.getActiveProjectId(); |
| 3440 |
17 Jul 15 |
olle |
836 |
List<String> meludiItemNameList = new ArrayList<String>(); |
| 3440 |
17 Jul 15 |
olle |
837 |
List<String> extraItemNameList = new ArrayList<String>(); |
| 3440 |
17 Jul 15 |
olle |
838 |
for (Integer startItemListId: startItemListIds) |
| 3440 |
17 Jul 15 |
olle |
839 |
{ |
| 3440 |
17 Jul 15 |
olle |
840 |
List<String> tmpItemNameList = null; |
| 3440 |
17 Jul 15 |
olle |
841 |
ItemList startItemList = ItemList.getById(dc, startItemListId); |
| 3440 |
17 Jul 15 |
olle |
842 |
if (startItemList != null) |
| 3440 |
17 Jul 15 |
olle |
843 |
{ |
| 3440 |
17 Jul 15 |
olle |
844 |
StartList sl = new StartList(startItemList); |
| 3440 |
17 Jul 15 |
olle |
845 |
tmpItemNameList = sl.fetchItemNameListFromItemList(dc, itemType); |
| 3440 |
17 Jul 15 |
olle |
846 |
if (tmpItemNameList != null) |
| 3440 |
17 Jul 15 |
olle |
847 |
{ |
| 3440 |
17 Jul 15 |
olle |
848 |
for (String itemName: tmpItemNameList) |
| 3440 |
17 Jul 15 |
olle |
849 |
{ |
| 4150 |
03 Oct 16 |
olle |
850 |
if (Meludi.itemIsMeludiItem(itemName, activeProjectId)) |
| 3440 |
17 Jul 15 |
olle |
851 |
{ |
| 3440 |
17 Jul 15 |
olle |
852 |
meludiItemNameList.add(itemName); |
| 3440 |
17 Jul 15 |
olle |
853 |
} |
| 3440 |
17 Jul 15 |
olle |
854 |
else |
| 3440 |
17 Jul 15 |
olle |
855 |
{ |
| 3440 |
17 Jul 15 |
olle |
856 |
extraItemNameList.add(itemName); |
| 3440 |
17 Jul 15 |
olle |
857 |
} |
| 3440 |
17 Jul 15 |
olle |
858 |
} |
| 3440 |
17 Jul 15 |
olle |
859 |
} |
| 3440 |
17 Jul 15 |
olle |
860 |
jsonStartItemList.put("id", startItemList.getId()); |
| 3440 |
17 Jul 15 |
olle |
861 |
jsonStartItemList.put("name", (String) startItemList.getName()); |
| 3440 |
17 Jul 15 |
olle |
862 |
} |
| 3440 |
17 Jul 15 |
olle |
863 |
} |
| 3462 |
31 Jul 15 |
olle |
// Sort each item name list |
| 3462 |
31 Jul 15 |
olle |
865 |
Collections.sort(meludiItemNameList); |
| 3462 |
31 Jul 15 |
olle |
866 |
Collections.sort(extraItemNameList); |
| 3462 |
31 Jul 15 |
olle |
867 |
|
| 3440 |
17 Jul 15 |
olle |
// Store item names from start lists in list with MeLuDI-items before extra items |
| 3440 |
17 Jul 15 |
olle |
869 |
List<String> itemNameList = new ArrayList<String>(); |
| 3440 |
17 Jul 15 |
olle |
870 |
for (String itemName: meludiItemNameList) |
| 3440 |
17 Jul 15 |
olle |
871 |
{ |
| 3440 |
17 Jul 15 |
olle |
872 |
itemNameList.add(itemName); |
| 3440 |
17 Jul 15 |
olle |
873 |
} |
| 3440 |
17 Jul 15 |
olle |
874 |
for (String itemName: extraItemNameList) |
| 3440 |
17 Jul 15 |
olle |
875 |
{ |
| 3440 |
17 Jul 15 |
olle |
876 |
itemNameList.add(itemName); |
| 3440 |
17 Jul 15 |
olle |
877 |
} |
| 3440 |
17 Jul 15 |
olle |
// Convert item names to items |
| 3440 |
17 Jul 15 |
olle |
879 |
if (itemNameList != null) |
| 3440 |
17 Jul 15 |
olle |
880 |
{ |
| 3440 |
17 Jul 15 |
olle |
881 |
for (String itemName : itemNameList) |
| 3440 |
17 Jul 15 |
olle |
882 |
{ |
| 3440 |
17 Jul 15 |
olle |
883 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3440 |
17 Jul 15 |
olle |
884 |
{ |
| 3440 |
17 Jul 15 |
olle |
885 |
SpecimenTube s = SpecimenTube.findByTubeName(dc, itemName); |
| 5823 |
04 Feb 20 |
olle |
886 |
if (s != null) |
| 3440 |
17 Jul 15 |
olle |
887 |
{ |
| 5823 |
04 Feb 20 |
olle |
888 |
s.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
889 |
loadSpecimenInfo(dc, manager, s); |
| 5823 |
04 Feb 20 |
olle |
890 |
jsonSpecimen.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
891 |
JSONObject jsonSpec = s.asJSONObject(); |
| 5823 |
04 Feb 20 |
olle |
//jsonItems.add(s.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
// Loading specimen extract data might decrease performance, only use when needed |
| 5823 |
04 Feb 20 |
olle |
894 |
if (includeSpecimenExtracts) |
| 3440 |
17 Jul 15 |
olle |
895 |
{ |
| 5823 |
04 Feb 20 |
olle |
896 |
String specQiacubePosition = null; |
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Rna for specimen |
| 5823 |
04 Feb 20 |
olle |
898 |
String rnaName = itemName + ".r"; |
| 5823 |
04 Feb 20 |
olle |
899 |
Rna r = Rna.findByName(dc, rnaName); |
| 5823 |
04 Feb 20 |
olle |
900 |
if (r != null) |
| 3644 |
03 Dec 15 |
olle |
901 |
{ |
| 5823 |
04 Feb 20 |
olle |
902 |
r.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
903 |
loadRnaInfo(dc, manager, r); |
| 5823 |
04 Feb 20 |
olle |
904 |
jsonRna.add(r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
905 |
jsonSpec.put("rna", r.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
906 |
} |
| 5823 |
04 Feb 20 |
olle |
907 |
|
| 5823 |
04 Feb 20 |
olle |
// Load optional data for Dna for specimen |
| 5823 |
04 Feb 20 |
olle |
909 |
String dnaName = itemName + ".d"; |
| 5823 |
04 Feb 20 |
olle |
910 |
Dna d = Dna.findByName(dc, dnaName); |
| 5823 |
04 Feb 20 |
olle |
911 |
if (d != null) |
| 5823 |
04 Feb 20 |
olle |
912 |
{ |
| 5823 |
04 Feb 20 |
olle |
913 |
boolean includeDna = true; |
| 5823 |
04 Feb 20 |
olle |
914 |
if (itemNotOnLibPlate) |
| 3719 |
22 Jan 16 |
olle |
915 |
{ |
| 5823 |
04 Feb 20 |
olle |
// Check if DNA extract has FPA child extracts |
| 5823 |
04 Feb 20 |
olle |
917 |
includeDna = dnaHasNoFpaChild(dc, d.getExtract()); |
| 5823 |
04 Feb 20 |
olle |
// Check if DNA extracts marked for qPCR processing should be ignored |
| 5823 |
04 Feb 20 |
olle |
919 |
if (includeDna && ignoreQpcrBranch) |
| 3719 |
22 Jan 16 |
olle |
920 |
{ |
| 5823 |
04 Feb 20 |
olle |
// Ignore DNA extracts marked for qPCR processing |
| 5823 |
04 Feb 20 |
olle |
922 |
Boolean markedForQPcr = (Boolean) Annotationtype.QPCR_BRANCH.getAnnotationValue(dc, d.getExtract()); |
| 5823 |
04 Feb 20 |
olle |
923 |
if (markedForQPcr != null && markedForQPcr) |
| 5823 |
04 Feb 20 |
olle |
924 |
{ |
| 5823 |
04 Feb 20 |
olle |
925 |
includeDna = false; |
| 5823 |
04 Feb 20 |
olle |
926 |
} |
| 3719 |
22 Jan 16 |
olle |
927 |
} |
| 3719 |
22 Jan 16 |
olle |
928 |
} |
| 5823 |
04 Feb 20 |
olle |
929 |
if (includeDna) |
| 5823 |
04 Feb 20 |
olle |
930 |
{ |
| 5823 |
04 Feb 20 |
olle |
931 |
d.loadBioPlateLocation(); |
| 5823 |
04 Feb 20 |
olle |
932 |
loadDnaInfo(dc, manager, d); |
| 5823 |
04 Feb 20 |
olle |
933 |
jsonDna.add(d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
934 |
jsonSpec.put("dna", d.asJSONObject()); |
| 5823 |
04 Feb 20 |
olle |
935 |
} |
| 3644 |
03 Dec 15 |
olle |
936 |
} |
| 3440 |
17 Jul 15 |
olle |
937 |
} |
| 5823 |
04 Feb 20 |
olle |
938 |
jsonItems.add(jsonSpec); |
| 3440 |
17 Jul 15 |
olle |
939 |
} |
| 5823 |
04 Feb 20 |
olle |
940 |
else |
| 5823 |
04 Feb 20 |
olle |
941 |
{ |
| 5823 |
04 Feb 20 |
olle |
942 |
System.out.println(new Date() + " ExtractionServlet::doGet(): cmd = \"" + cmd + "\" itemName = \"" + itemName + "\" SpecimenTube s = null."); |
| 5823 |
04 Feb 20 |
olle |
943 |
} |
| 3440 |
17 Jul 15 |
olle |
944 |
} |
| 3440 |
17 Jul 15 |
olle |
945 |
else if (Meludi.itemIsRna(itemName)) |
| 3440 |
17 Jul 15 |
olle |
946 |
{ |
| 3440 |
17 Jul 15 |
olle |
947 |
Rna r = Rna.findByName(dc, itemName); |
| 3440 |
17 Jul 15 |
olle |
948 |
r.loadBioPlateLocation(); |
| 3440 |
17 Jul 15 |
olle |
949 |
loadRnaInfo(dc, manager, r); |
| 3440 |
17 Jul 15 |
olle |
950 |
jsonRna.add(r.asJSONObject()); |
| 3440 |
17 Jul 15 |
olle |
951 |
JSONObject jsonR = r.asJSONObject(); |
| 3440 |
17 Jul 15 |
olle |
952 |
jsonItems.add(jsonR); |
| 3440 |
17 Jul 15 |
olle |
953 |
} |
| 3440 |
17 Jul 15 |
olle |
954 |
else if (Meludi.itemIsDna(itemName)) |
| 3440 |
17 Jul 15 |
olle |
955 |
{ |
| 3440 |
17 Jul 15 |
olle |
956 |
Dna d = Dna.findByName(dc, itemName); |
| 3644 |
03 Dec 15 |
olle |
957 |
boolean includeDna = true; |
| 3644 |
03 Dec 15 |
olle |
958 |
if (itemNotOnLibPlate) |
| 3644 |
03 Dec 15 |
olle |
959 |
{ |
| 3644 |
03 Dec 15 |
olle |
// Check if DNA extract has FPA child extracts |
| 3644 |
03 Dec 15 |
olle |
961 |
includeDna = dnaHasNoFpaChild(dc, d.getExtract()); |
| 3719 |
22 Jan 16 |
olle |
// Check if DNA extracts marked for qPCR processing should be ignored |
| 3719 |
22 Jan 16 |
olle |
963 |
if (includeDna && ignoreQpcrBranch) |
| 3719 |
22 Jan 16 |
olle |
964 |
{ |
| 3719 |
22 Jan 16 |
olle |
// Ignore DNA extracts marked for qPCR processing |
| 3719 |
22 Jan 16 |
olle |
966 |
Boolean markedForQPcr = (Boolean) Annotationtype.QPCR_BRANCH.getAnnotationValue(dc, d.getExtract()); |
| 3719 |
22 Jan 16 |
olle |
967 |
if (markedForQPcr != null && markedForQPcr) |
| 3719 |
22 Jan 16 |
olle |
968 |
{ |
| 3719 |
22 Jan 16 |
olle |
969 |
includeDna = false; |
| 3719 |
22 Jan 16 |
olle |
970 |
} |
| 3719 |
22 Jan 16 |
olle |
971 |
} |
| 3644 |
03 Dec 15 |
olle |
972 |
} |
| 3644 |
03 Dec 15 |
olle |
973 |
if (includeDna) |
| 3644 |
03 Dec 15 |
olle |
974 |
{ |
| 3644 |
03 Dec 15 |
olle |
975 |
d.loadBioPlateLocation(); |
| 3644 |
03 Dec 15 |
olle |
976 |
loadDnaInfo(dc, manager, d); |
| 3644 |
03 Dec 15 |
olle |
977 |
jsonDna.add(d.asJSONObject()); |
| 3644 |
03 Dec 15 |
olle |
978 |
JSONObject jsonD = d.asJSONObject(); |
| 3644 |
03 Dec 15 |
olle |
979 |
jsonItems.add(jsonD); |
| 3644 |
03 Dec 15 |
olle |
980 |
} |
| 3440 |
17 Jul 15 |
olle |
981 |
} |
| 3440 |
17 Jul 15 |
olle |
982 |
} |
| 3440 |
17 Jul 15 |
olle |
983 |
} |
| 3446 |
27 Jul 15 |
olle |
984 |
|
| 3446 |
27 Jul 15 |
olle |
985 |
/* |
| 3440 |
17 Jul 15 |
olle |
json.put("startitemlist", jsonStartItemList); |
| 3440 |
17 Jul 15 |
olle |
json.put("specimens", jsonSpecimen); |
| 3440 |
17 Jul 15 |
olle |
json.put("rnas", jsonRna); |
| 3440 |
17 Jul 15 |
olle |
json.put("dnas", jsonDna); |
| 3446 |
27 Jul 15 |
olle |
990 |
*/ |
| 3446 |
27 Jul 15 |
olle |
991 |
json.put("startListIds", jsonStartItemListIds); |
| 3440 |
17 Jul 15 |
olle |
992 |
json.put("items", jsonItems); |
| 3440 |
17 Jul 15 |
olle |
993 |
} |
| 5162 |
03 Dec 18 |
olle |
994 |
else if ("GetCases".equals(cmd)) |
| 5162 |
03 Dec 18 |
olle |
995 |
{ |
| 5162 |
03 Dec 18 |
olle |
996 |
/* |
| 5162 |
03 Dec 18 |
olle |
All cases |
| 5162 |
03 Dec 18 |
olle |
998 |
*/ |
| 5162 |
03 Dec 18 |
olle |
999 |
dc = sc.newDbControl(); |
| 5162 |
03 Dec 18 |
olle |
1000 |
|
| 5162 |
03 Dec 18 |
olle |
1001 |
JSONArray jsonCases = new JSONArray(); |
| 5162 |
03 Dec 18 |
olle |
1002 |
|
| 5162 |
03 Dec 18 |
olle |
1003 |
ItemQuery<Sample> query = Sample.getQuery(); |
| 5162 |
03 Dec 18 |
olle |
1004 |
Subtype.CASE.addFilter(dc, query); |
| 5162 |
03 Dec 18 |
olle |
1005 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 5162 |
03 Dec 18 |
olle |
1006 |
query.order(Orders.desc(Hql.property("name"))); |
| 5162 |
03 Dec 18 |
olle |
1007 |
query.setCacheResult(true); |
| 5162 |
03 Dec 18 |
olle |
1008 |
List<Sample> cases = query.list(dc); |
| 5162 |
03 Dec 18 |
olle |
1009 |
for (int i = 0; i < cases.size(); i++) |
| 5162 |
03 Dec 18 |
olle |
1010 |
{ |
| 5162 |
03 Dec 18 |
olle |
1011 |
Sample caseSample = (Sample) cases.get(i); |
| 5162 |
03 Dec 18 |
olle |
1012 |
Case theCase = Case.findByName(dc, caseSample.getName()); |
| 5162 |
03 Dec 18 |
olle |
1013 |
String personalNumber = ""; |
| 5162 |
03 Dec 18 |
olle |
1014 |
Patient patient = Patient.findByCase(dc, theCase); |
| 5162 |
03 Dec 18 |
olle |
1015 |
if (patient != null) |
| 5162 |
03 Dec 18 |
olle |
1016 |
{ |
| 5162 |
03 Dec 18 |
olle |
1017 |
try |
| 5162 |
03 Dec 18 |
olle |
1018 |
{ |
| 5162 |
03 Dec 18 |
olle |
1019 |
patient.loadDefaultAnnotations(dc); |
| 5162 |
03 Dec 18 |
olle |
1020 |
personalNumber = (String) Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, patient.getBioSource()); |
| 5162 |
03 Dec 18 |
olle |
1021 |
} |
| 5162 |
03 Dec 18 |
olle |
1022 |
catch (Exception e) |
| 5162 |
03 Dec 18 |
olle |
1023 |
{} |
| 5162 |
03 Dec 18 |
olle |
1024 |
} |
| 5162 |
03 Dec 18 |
olle |
1025 |
String referralId = ""; |
| 5162 |
03 Dec 18 |
olle |
1026 |
try |
| 5162 |
03 Dec 18 |
olle |
1027 |
{ |
| 5162 |
03 Dec 18 |
olle |
1028 |
theCase.loadAnnotations(dc, "referralId", Annotationtype.REFERRAL_ID, null); |
| 5162 |
03 Dec 18 |
olle |
1029 |
referralId = (String) Annotationtype.REFERRAL_ID.getAnnotationValue(dc, caseSample); |
| 5162 |
03 Dec 18 |
olle |
1030 |
} |
| 5162 |
03 Dec 18 |
olle |
1031 |
catch (Exception e) |
| 5162 |
03 Dec 18 |
olle |
1032 |
{} |
| 5325 |
05 Mar 19 |
olle |
1033 |
try |
| 5325 |
05 Mar 19 |
olle |
1034 |
{ |
| 5325 |
05 Mar 19 |
olle |
1035 |
theCase.setAnnotation("registrationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(caseSample.getEntryDate())); |
| 5325 |
05 Mar 19 |
olle |
1036 |
} |
| 5325 |
05 Mar 19 |
olle |
1037 |
catch (Exception e) |
| 5325 |
05 Mar 19 |
olle |
1038 |
{} |
| 5325 |
05 Mar 19 |
olle |
1039 |
if (theCase != null) |
| 5325 |
05 Mar 19 |
olle |
1040 |
{ |
| 5325 |
05 Mar 19 |
olle |
1041 |
JSONObject jsonCase = new JSONObject(); |
| 5325 |
05 Mar 19 |
olle |
1042 |
jsonCase = theCase.asJSONObject(); |
| 5325 |
05 Mar 19 |
olle |
1043 |
jsonCase.put("personalNumber", personalNumber); |
| 5325 |
05 Mar 19 |
olle |
1044 |
jsonCases.add(jsonCase); |
| 5325 |
05 Mar 19 |
olle |
1045 |
} |
| 5162 |
03 Dec 18 |
olle |
1046 |
} |
| 5162 |
03 Dec 18 |
olle |
1047 |
|
| 5162 |
03 Dec 18 |
olle |
1048 |
json.put("items", jsonCases); |
| 5162 |
03 Dec 18 |
olle |
1049 |
} |
| 5158 |
30 Nov 18 |
olle |
1050 |
else if ("GetCasesUnusedForFfpeBlockOrderForm".equals(cmd)) |
| 5158 |
30 Nov 18 |
olle |
1051 |
{ |
| 5158 |
30 Nov 18 |
olle |
1052 |
/* |
| 5158 |
30 Nov 18 |
olle |
All cases with consent not used for FFPE block order forms |
| 5158 |
30 Nov 18 |
olle |
1054 |
*/ |
| 5158 |
30 Nov 18 |
olle |
1055 |
dc = sc.newDbControl(); |
| 5158 |
30 Nov 18 |
olle |
1056 |
|
| 5158 |
30 Nov 18 |
olle |
1057 |
JSONArray jsonCases = new JSONArray(); |
| 5158 |
30 Nov 18 |
olle |
1058 |
|
| 5158 |
30 Nov 18 |
olle |
1059 |
ItemQuery<Sample> query = Sample.getQuery(); |
| 5158 |
30 Nov 18 |
olle |
1060 |
Subtype.CASE.addFilter(dc, query); |
| 5158 |
30 Nov 18 |
olle |
1061 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 5158 |
30 Nov 18 |
olle |
1062 |
query.setCacheResult(true); |
| 5158 |
30 Nov 18 |
olle |
1063 |
List<Sample> cases = query.list(dc); |
| 5158 |
30 Nov 18 |
olle |
// Case items unused for FFPE block order form |
| 5158 |
30 Nov 18 |
olle |
1065 |
for (int i = 0; i < cases.size(); i++) |
| 5158 |
30 Nov 18 |
olle |
1066 |
{ |
| 5158 |
30 Nov 18 |
olle |
1067 |
Sample caseSample = (Sample) cases.get(i); |
| 5158 |
30 Nov 18 |
olle |
1068 |
Case theCase = Case.findByName(dc, caseSample.getName()); |
| 5158 |
30 Nov 18 |
olle |
1069 |
Date consentDate = null; |
| 5158 |
30 Nov 18 |
olle |
1070 |
if (theCase != null) |
| 5158 |
30 Nov 18 |
olle |
1071 |
{ |
| 5158 |
30 Nov 18 |
olle |
1072 |
theCase.loadAnnotations(dc, "consentDate", Annotationtype.CONSENT_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 5158 |
30 Nov 18 |
olle |
1073 |
consentDate = (Date) Annotationtype.CONSENT_DATE.getAnnotationValue(dc, theCase.getSample()); |
| 5158 |
30 Nov 18 |
olle |
1074 |
} |
| 5158 |
30 Nov 18 |
olle |
1075 |
if (consentDate != null) |
| 5158 |
30 Nov 18 |
olle |
1076 |
{ |
| 5243 |
17 Jan 19 |
olle |
1077 |
Date ffpeBlockOrderDate = (Date) Annotationtype.FFPE_BLOCK_ORDER_DATE.getAnnotationValue(dc, caseSample); |
| 5243 |
17 Jan 19 |
olle |
1078 |
if (ffpeBlockOrderDate == null) |
| 5158 |
30 Nov 18 |
olle |
1079 |
{ |
| 5158 |
30 Nov 18 |
olle |
1080 |
String personalNumber = ""; |
| 5158 |
30 Nov 18 |
olle |
1081 |
Patient patient = Patient.findByCase(dc, theCase); |
| 5158 |
30 Nov 18 |
olle |
1082 |
if (patient != null) |
| 5158 |
30 Nov 18 |
olle |
1083 |
{ |
| 5158 |
30 Nov 18 |
olle |
1084 |
patient.loadDefaultAnnotations(dc); |
| 5158 |
30 Nov 18 |
olle |
1085 |
personalNumber = (String) Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, patient.getBioSource()); |
| 5158 |
30 Nov 18 |
olle |
1086 |
} |
| 5158 |
30 Nov 18 |
olle |
1087 |
theCase.loadAnnotations(dc, "referralId", Annotationtype.REFERRAL_ID, null); |
| 5158 |
30 Nov 18 |
olle |
1088 |
String referralId = (String) Annotationtype.REFERRAL_ID.getAnnotationValue(dc, caseSample); |
| 5158 |
30 Nov 18 |
olle |
1089 |
if (referralId != null && !referralId.equals("")) |
| 5158 |
30 Nov 18 |
olle |
1090 |
{ |
| 5158 |
30 Nov 18 |
olle |
1091 |
JSONObject jsonCase = new JSONObject(); |
| 5158 |
30 Nov 18 |
olle |
1092 |
jsonCase = theCase.asJSONObject(); |
| 5158 |
30 Nov 18 |
olle |
1093 |
jsonCase.put("personalNumber", personalNumber); |
| 5158 |
30 Nov 18 |
olle |
1094 |
jsonCases.add(jsonCase); |
| 5158 |
30 Nov 18 |
olle |
1095 |
} |
| 5158 |
30 Nov 18 |
olle |
1096 |
} |
| 5158 |
30 Nov 18 |
olle |
1097 |
} |
| 5158 |
30 Nov 18 |
olle |
1098 |
} |
| 5158 |
30 Nov 18 |
olle |
1099 |
|
| 5158 |
30 Nov 18 |
olle |
1100 |
json.put("items", jsonCases); |
| 5158 |
30 Nov 18 |
olle |
1101 |
} |
| 5237 |
16 Jan 19 |
olle |
1102 |
else if ("GetCasesWithUnprocessedFfpeBlockOrders".equals(cmd)) |
| 5237 |
16 Jan 19 |
olle |
1103 |
{ |
| 5237 |
16 Jan 19 |
olle |
1104 |
/* |
| 5237 |
16 Jan 19 |
olle |
All cases with consent used for FFPE block order forms |
| 5237 |
16 Jan 19 |
olle |
1106 |
*/ |
| 5237 |
16 Jan 19 |
olle |
1107 |
dc = sc.newDbControl(); |
| 5237 |
16 Jan 19 |
olle |
1108 |
|
| 5237 |
16 Jan 19 |
olle |
1109 |
JSONArray jsonCases = new JSONArray(); |
| 5237 |
16 Jan 19 |
olle |
1110 |
|
| 5237 |
16 Jan 19 |
olle |
1111 |
ItemQuery<Sample> query = Sample.getQuery(); |
| 5237 |
16 Jan 19 |
olle |
1112 |
Subtype.CASE.addFilter(dc, query); |
| 5237 |
16 Jan 19 |
olle |
1113 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 5237 |
16 Jan 19 |
olle |
1114 |
query.setCacheResult(true); |
| 5237 |
16 Jan 19 |
olle |
1115 |
List<Sample> cases = query.list(dc); |
| 5237 |
16 Jan 19 |
olle |
// Case items unused for FFPE block order form |
| 5237 |
16 Jan 19 |
olle |
1117 |
for (int i = 0; i < cases.size(); i++) |
| 5237 |
16 Jan 19 |
olle |
1118 |
{ |
| 5237 |
16 Jan 19 |
olle |
1119 |
Sample caseSample = (Sample) cases.get(i); |
| 5237 |
16 Jan 19 |
olle |
1120 |
Case theCase = Case.findByName(dc, caseSample.getName()); |
| 5237 |
16 Jan 19 |
olle |
1121 |
Date consentDate = null; |
| 5237 |
16 Jan 19 |
olle |
1122 |
if (theCase != null) |
| 5237 |
16 Jan 19 |
olle |
1123 |
{ |
| 5237 |
16 Jan 19 |
olle |
1124 |
theCase.loadAnnotations(dc, "consentDate", Annotationtype.CONSENT_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 5237 |
16 Jan 19 |
olle |
1125 |
consentDate = (Date) Annotationtype.CONSENT_DATE.getAnnotationValue(dc, theCase.getSample()); |
| 5237 |
16 Jan 19 |
olle |
1126 |
} |
| 5237 |
16 Jan 19 |
olle |
1127 |
if (consentDate != null) |
| 5237 |
16 Jan 19 |
olle |
1128 |
{ |
| 5243 |
17 Jan 19 |
olle |
1129 |
Date ffpeBlockOrderDate = (Date) Annotationtype.FFPE_BLOCK_ORDER_DATE.getAnnotationValue(dc, caseSample); |
| 5243 |
17 Jan 19 |
olle |
1130 |
String ffpeBlockOrderDateStr = Meludi.CONVERTER_DATE_TO_STRING.convert(ffpeBlockOrderDate); |
| 5243 |
17 Jan 19 |
olle |
1131 |
|
| 5243 |
17 Jan 19 |
olle |
1132 |
if (ffpeBlockOrderDate != null) |
| 5237 |
16 Jan 19 |
olle |
1133 |
{ |
| 5237 |
16 Jan 19 |
olle |
1134 |
String personalNumber = ""; |
| 5237 |
16 Jan 19 |
olle |
1135 |
Patient patient = Patient.findByCase(dc, theCase); |
| 5237 |
16 Jan 19 |
olle |
1136 |
if (patient != null) |
| 5237 |
16 Jan 19 |
olle |
1137 |
{ |
| 5237 |
16 Jan 19 |
olle |
1138 |
patient.loadDefaultAnnotations(dc); |
| 5237 |
16 Jan 19 |
olle |
1139 |
personalNumber = (String) Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, patient.getBioSource()); |
| 5237 |
16 Jan 19 |
olle |
1140 |
} |
| 5237 |
16 Jan 19 |
olle |
// Case is used for FFPE block order form |
| 5237 |
16 Jan 19 |
olle |
1142 |
boolean ffpeBlockExistsForCase = false; |
| 5237 |
16 Jan 19 |
olle |
1143 |
theCase.loadAnnotations(dc, "referralId", Annotationtype.REFERRAL_ID, null); |
| 5237 |
16 Jan 19 |
olle |
1144 |
String referralId = (String) Annotationtype.REFERRAL_ID.getAnnotationValue(dc, caseSample); |
| 5237 |
16 Jan 19 |
olle |
1145 |
if (referralId != null && !referralId.equals("")) |
| 5237 |
16 Jan 19 |
olle |
1146 |
{ |
| 5237 |
16 Jan 19 |
olle |
// Check if FFPE block item exists for case |
| 5237 |
16 Jan 19 |
olle |
1148 |
String caseName = theCase.getName(); |
| 5237 |
16 Jan 19 |
olle |
1149 |
query = Sample.getQuery(); |
| 5237 |
16 Jan 19 |
olle |
1150 |
Subtype.FFPE_BLOCK.addFilter(dc, query); |
| 5237 |
16 Jan 19 |
olle |
1151 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 5237 |
16 Jan 19 |
olle |
1152 |
query.setCacheResult(true); |
| 5237 |
16 Jan 19 |
olle |
1153 |
List<Sample> ffpeBlocks = query.list(dc); |
| 5237 |
16 Jan 19 |
olle |
1154 |
for (int j = 0; j < ffpeBlocks.size(); j++) |
| 5237 |
16 Jan 19 |
olle |
1155 |
{ |
| 5237 |
16 Jan 19 |
olle |
1156 |
Sample ffpeBlockSample = (Sample) ffpeBlocks.get(j); |
| 5237 |
16 Jan 19 |
olle |
1157 |
FfpeBlock ffpeBlock = FfpeBlock.getByName(dc, ffpeBlockSample.getName()); |
| 5237 |
16 Jan 19 |
olle |
1158 |
ffpeBlock.loadAnnotations(dc, "caseId", Annotationtype.CASE_ID, null); |
| 5237 |
16 Jan 19 |
olle |
1159 |
String caseId = (String) Annotationtype.CASE_ID.getAnnotationValue(dc, ffpeBlockSample); |
| 5237 |
16 Jan 19 |
olle |
1160 |
if (caseId != null && caseId.equals(caseName)) |
| 5237 |
16 Jan 19 |
olle |
1161 |
{ |
| 5237 |
16 Jan 19 |
olle |
1162 |
ffpeBlockExistsForCase = true; |
| 5237 |
16 Jan 19 |
olle |
1163 |
break; |
| 5237 |
16 Jan 19 |
olle |
1164 |
} |
| 5237 |
16 Jan 19 |
olle |
1165 |
} |
| 5237 |
16 Jan 19 |
olle |
1166 |
if (!ffpeBlockExistsForCase) |
| 5237 |
16 Jan 19 |
olle |
1167 |
{ |
| 5237 |
16 Jan 19 |
olle |
1168 |
JSONObject jsonCase = new JSONObject(); |
| 5237 |
16 Jan 19 |
olle |
1169 |
jsonCase = theCase.asJSONObject(); |
| 5237 |
16 Jan 19 |
olle |
1170 |
jsonCase.put("personalNumber", personalNumber); |
| 5243 |
17 Jan 19 |
olle |
1171 |
jsonCase.put("ffpeBlockOrderDate", ffpeBlockOrderDateStr); |
| 5237 |
16 Jan 19 |
olle |
1172 |
jsonCases.add(jsonCase); |
| 5237 |
16 Jan 19 |
olle |
1173 |
} |
| 5237 |
16 Jan 19 |
olle |
1174 |
} |
| 5237 |
16 Jan 19 |
olle |
1175 |
} |
| 5237 |
16 Jan 19 |
olle |
1176 |
} |
| 5237 |
16 Jan 19 |
olle |
1177 |
} |
| 5237 |
16 Jan 19 |
olle |
1178 |
|
| 5237 |
16 Jan 19 |
olle |
1179 |
json.put("items", jsonCases); |
| 5237 |
16 Jan 19 |
olle |
1180 |
} |
| 4954 |
31 Aug 18 |
olle |
1181 |
else if ("GetFfpeBlocks".equals(cmd)) |
| 4954 |
31 Aug 18 |
olle |
1182 |
{ |
| 4954 |
31 Aug 18 |
olle |
1183 |
/* |
| 4954 |
31 Aug 18 |
olle |
All free FFPE blocks items |
| 4954 |
31 Aug 18 |
olle |
1185 |
*/ |
| 4954 |
31 Aug 18 |
olle |
1186 |
dc = sc.newDbControl(); |
| 4954 |
31 Aug 18 |
olle |
1187 |
List<FfpeBlock> ffpeBlocks = FfpeBlock.findAll(dc); |
| 4954 |
31 Aug 18 |
olle |
1188 |
|
| 4954 |
31 Aug 18 |
olle |
1189 |
JSONArray jsonFfpeBlock = new JSONArray(); |
| 4954 |
31 Aug 18 |
olle |
1190 |
|
| 4954 |
31 Aug 18 |
olle |
1191 |
for (FfpeBlock f : ffpeBlocks) |
| 4954 |
31 Aug 18 |
olle |
1192 |
{ |
| 5048 |
22 Oct 18 |
olle |
1193 |
f.loadAnnotations(dc, "pad", Annotationtype.PAD, null); |
| 5095 |
14 Nov 18 |
olle |
1194 |
f.loadAnnotations(dc, "materialNumber", Annotationtype.MATERIAL_NUMBER, null); |
| 5048 |
22 Oct 18 |
olle |
1195 |
f.loadAnnotations(dc, "yellowLabel", Annotationtype.YELLOW_LABEL, null); |
| 4954 |
31 Aug 18 |
olle |
1196 |
jsonFfpeBlock.add(f.asJSONObject()); |
| 4954 |
31 Aug 18 |
olle |
1197 |
} |
| 4954 |
31 Aug 18 |
olle |
1198 |
|
| 4954 |
31 Aug 18 |
olle |
1199 |
json.put("items", jsonFfpeBlock); |
| 4954 |
31 Aug 18 |
olle |
1200 |
} |
| 5061 |
30 Oct 18 |
olle |
1201 |
else if ("GetFfpeBlocksUnusedForSectionOrderForm".equals(cmd)) |
| 5052 |
25 Oct 18 |
olle |
1202 |
{ |
| 5052 |
25 Oct 18 |
olle |
1203 |
/* |
| 5061 |
30 Oct 18 |
olle |
All free FFPE block items unused for FFPE section order forms |
| 5052 |
25 Oct 18 |
olle |
1205 |
*/ |
| 5052 |
25 Oct 18 |
olle |
1206 |
dc = sc.newDbControl(); |
| 5052 |
25 Oct 18 |
olle |
1207 |
List<FfpeBlock> ffpeBlocks = FfpeBlock.findAll(dc); |
| 5052 |
25 Oct 18 |
olle |
1208 |
|
| 5052 |
25 Oct 18 |
olle |
1209 |
JSONArray jsonFfpeBlock = new JSONArray(); |
| 5052 |
25 Oct 18 |
olle |
1210 |
|
| 5052 |
25 Oct 18 |
olle |
1211 |
for (FfpeBlock f : ffpeBlocks) |
| 5052 |
25 Oct 18 |
olle |
1212 |
{ |
| 5060 |
29 Oct 18 |
olle |
// Only include unreturned FFPE blocks |
| 5060 |
29 Oct 18 |
olle |
1214 |
f.loadAnnotations(dc, "returnedDate", Annotationtype.RETURNED_DATE, null); |
| 5060 |
29 Oct 18 |
olle |
1215 |
Date returnedDate = (Date)f.asJSONObject().get("returnedDate"); |
| 5060 |
29 Oct 18 |
olle |
1216 |
if (returnedDate == null) |
| 5052 |
25 Oct 18 |
olle |
1217 |
{ |
| 5061 |
30 Oct 18 |
olle |
// Only include FFPE blocks not used for FFPE section order forms |
| 5061 |
30 Oct 18 |
olle |
1219 |
f.loadAnnotations(dc, "usedForFfpeSectionOrderForm", Annotationtype.USED_FOR_FFPE_SECTION_ORDER_FORM, null); |
| 5061 |
30 Oct 18 |
olle |
1220 |
Boolean usedFfpeBlockValue = (Boolean)f.asJSONObject().get("usedForFfpeSectionOrderForm"); |
| 5060 |
29 Oct 18 |
olle |
1221 |
if (usedFfpeBlockValue == null || !usedFfpeBlockValue) |
| 5060 |
29 Oct 18 |
olle |
1222 |
{ |
| 5060 |
29 Oct 18 |
olle |
1223 |
f.loadAnnotations(dc, "pad", Annotationtype.PAD, null); |
| 5095 |
14 Nov 18 |
olle |
1224 |
f.loadAnnotations(dc, "materialNumber", Annotationtype.MATERIAL_NUMBER, null); |
| 5060 |
29 Oct 18 |
olle |
1225 |
f.loadAnnotations(dc, "yellowLabel", Annotationtype.YELLOW_LABEL, null); |
| 5060 |
29 Oct 18 |
olle |
1226 |
f.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT, null); |
| 5060 |
29 Oct 18 |
olle |
1227 |
jsonFfpeBlock.add(f.asJSONObject()); |
| 5060 |
29 Oct 18 |
olle |
1228 |
} |
| 5060 |
29 Oct 18 |
olle |
1229 |
} |
| 5060 |
29 Oct 18 |
olle |
1230 |
} |
| 5060 |
29 Oct 18 |
olle |
1231 |
|
| 5060 |
29 Oct 18 |
olle |
1232 |
json.put("items", jsonFfpeBlock); |
| 5060 |
29 Oct 18 |
olle |
1233 |
} |
| 5061 |
30 Oct 18 |
olle |
1234 |
else if ("GetFfpeBlocksUnusedForSection".equals(cmd)) |
| 5060 |
29 Oct 18 |
olle |
1235 |
{ |
| 5060 |
29 Oct 18 |
olle |
1236 |
/* |
| 5061 |
30 Oct 18 |
olle |
All free FFPE block items unused for FFPE section |
| 5060 |
29 Oct 18 |
olle |
1238 |
*/ |
| 5060 |
29 Oct 18 |
olle |
1239 |
dc = sc.newDbControl(); |
| 5060 |
29 Oct 18 |
olle |
1240 |
List<FfpeBlock> ffpeBlocks = FfpeBlock.findAll(dc); |
| 5060 |
29 Oct 18 |
olle |
1241 |
|
| 5060 |
29 Oct 18 |
olle |
1242 |
JSONArray jsonFfpeBlock = new JSONArray(); |
| 5060 |
29 Oct 18 |
olle |
1243 |
|
| 5060 |
29 Oct 18 |
olle |
1244 |
for (FfpeBlock f : ffpeBlocks) |
| 5060 |
29 Oct 18 |
olle |
1245 |
{ |
| 5060 |
29 Oct 18 |
olle |
// Only include unreturned FFPE blocks |
| 5060 |
29 Oct 18 |
olle |
1247 |
f.loadAnnotations(dc, "returnedDate", Annotationtype.RETURNED_DATE, null); |
| 5060 |
29 Oct 18 |
olle |
1248 |
Date returnedDate = (Date)f.asJSONObject().get("returnedDate"); |
| 5060 |
29 Oct 18 |
olle |
1249 |
if (returnedDate == null) |
| 5060 |
29 Oct 18 |
olle |
1250 |
{ |
| 5824 |
04 Feb 20 |
olle |
// Only include FFPE blocks with approved FFPE section order forms |
| 5824 |
04 Feb 20 |
olle |
1252 |
f.loadAnnotations(dc, "usedForFfpeSectionOrderForm", Annotationtype.USED_FOR_FFPE_SECTION_ORDER_FORM, null); |
| 5824 |
04 Feb 20 |
olle |
1253 |
Boolean usedForFfpeSectionOrderFormValue = (Boolean)f.asJSONObject().get("usedForFfpeSectionOrderForm"); |
| 5824 |
04 Feb 20 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doGet() cmd = \"" + cmd + "\" f.getName() = \"" + f.getName() + "\" usedForFfpeSectionOrderFormValue = \"" + usedForFfpeSectionOrderFormValue + "\""); |
| 5824 |
04 Feb 20 |
olle |
1255 |
if (usedForFfpeSectionOrderFormValue != null && usedForFfpeSectionOrderFormValue) |
| 5060 |
29 Oct 18 |
olle |
1256 |
{ |
| 5824 |
04 Feb 20 |
olle |
// Only include FFPE blocks not used for FFPE section |
| 5824 |
04 Feb 20 |
olle |
1258 |
f.loadAnnotations(dc, "usedForFfpeSection", Annotationtype.USED_FOR_FFPE_SECTION, null); |
| 5824 |
04 Feb 20 |
olle |
1259 |
Boolean usedFfpeBlockValue = (Boolean)f.asJSONObject().get("usedForFfpeSection"); |
| 5824 |
04 Feb 20 |
olle |
1260 |
if (usedFfpeBlockValue == null || !usedFfpeBlockValue) |
| 5824 |
04 Feb 20 |
olle |
1261 |
{ |
| 5824 |
04 Feb 20 |
olle |
1262 |
f.loadAnnotations(dc, "pad", Annotationtype.PAD, null); |
| 5824 |
04 Feb 20 |
olle |
1263 |
f.loadAnnotations(dc, "materialNumber", Annotationtype.MATERIAL_NUMBER, null); |
| 5824 |
04 Feb 20 |
olle |
1264 |
f.loadAnnotations(dc, "yellowLabel", Annotationtype.YELLOW_LABEL, null); |
| 5824 |
04 Feb 20 |
olle |
1265 |
f.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT, null); |
| 5824 |
04 Feb 20 |
olle |
1266 |
jsonFfpeBlock.add(f.asJSONObject()); |
| 5824 |
04 Feb 20 |
olle |
1267 |
} |
| 5060 |
29 Oct 18 |
olle |
1268 |
} |
| 5060 |
29 Oct 18 |
olle |
1269 |
} |
| 5060 |
29 Oct 18 |
olle |
1270 |
} |
| 5060 |
29 Oct 18 |
olle |
1271 |
|
| 5060 |
29 Oct 18 |
olle |
1272 |
json.put("items", jsonFfpeBlock); |
| 5060 |
29 Oct 18 |
olle |
1273 |
} |
| 5060 |
29 Oct 18 |
olle |
1274 |
else if ("GetUnreturnedFfpeBlocks".equals(cmd)) |
| 5060 |
29 Oct 18 |
olle |
1275 |
{ |
| 5060 |
29 Oct 18 |
olle |
1276 |
/* |
| 5060 |
29 Oct 18 |
olle |
All free unreturned FFPE block items |
| 5060 |
29 Oct 18 |
olle |
1278 |
*/ |
| 5060 |
29 Oct 18 |
olle |
1279 |
dc = sc.newDbControl(); |
| 5060 |
29 Oct 18 |
olle |
1280 |
List<FfpeBlock> ffpeBlocks = FfpeBlock.findAll(dc); |
| 5060 |
29 Oct 18 |
olle |
1281 |
|
| 5060 |
29 Oct 18 |
olle |
1282 |
JSONArray jsonFfpeBlock = new JSONArray(); |
| 5060 |
29 Oct 18 |
olle |
1283 |
|
| 5060 |
29 Oct 18 |
olle |
1284 |
for (FfpeBlock f : ffpeBlocks) |
| 5060 |
29 Oct 18 |
olle |
1285 |
{ |
| 5060 |
29 Oct 18 |
olle |
// Only include unreturned FFPE blocks |
| 5060 |
29 Oct 18 |
olle |
1287 |
f.loadAnnotations(dc, "returnedDate", Annotationtype.RETURNED_DATE, null); |
| 5060 |
29 Oct 18 |
olle |
1288 |
Date returnedDate = (Date)f.asJSONObject().get("returnedDate"); |
| 5060 |
29 Oct 18 |
olle |
1289 |
if (returnedDate == null) |
| 5060 |
29 Oct 18 |
olle |
1290 |
{ |
| 5061 |
30 Oct 18 |
olle |
1291 |
f.loadAnnotations(dc, "usedForFfpeSection", Annotationtype.USED_FOR_FFPE_SECTION, null); |
| 5052 |
25 Oct 18 |
olle |
1292 |
f.loadAnnotations(dc, "pad", Annotationtype.PAD, null); |
| 5095 |
14 Nov 18 |
olle |
1293 |
f.loadAnnotations(dc, "materialNumber", Annotationtype.MATERIAL_NUMBER, null); |
| 5052 |
25 Oct 18 |
olle |
1294 |
f.loadAnnotations(dc, "yellowLabel", Annotationtype.YELLOW_LABEL, null); |
| 5052 |
25 Oct 18 |
olle |
1295 |
jsonFfpeBlock.add(f.asJSONObject()); |
| 5052 |
25 Oct 18 |
olle |
1296 |
} |
| 5052 |
25 Oct 18 |
olle |
1297 |
} |
| 5052 |
25 Oct 18 |
olle |
1298 |
|
| 5052 |
25 Oct 18 |
olle |
1299 |
json.put("items", jsonFfpeBlock); |
| 5052 |
25 Oct 18 |
olle |
1300 |
} |
| 5060 |
29 Oct 18 |
olle |
1301 |
else if ("GetReturnedFfpeBlocks".equals(cmd)) |
| 5060 |
29 Oct 18 |
olle |
1302 |
{ |
| 5060 |
29 Oct 18 |
olle |
1303 |
/* |
| 5060 |
29 Oct 18 |
olle |
All free returned FFPE block items |
| 5060 |
29 Oct 18 |
olle |
1305 |
*/ |
| 5060 |
29 Oct 18 |
olle |
1306 |
dc = sc.newDbControl(); |
| 5060 |
29 Oct 18 |
olle |
1307 |
List<FfpeBlock> ffpeBlocks = FfpeBlock.findAll(dc); |
| 5060 |
29 Oct 18 |
olle |
1308 |
|
| 5060 |
29 Oct 18 |
olle |
1309 |
JSONArray jsonFfpeBlock = new JSONArray(); |
| 5060 |
29 Oct 18 |
olle |
1310 |
|
| 5060 |
29 Oct 18 |
olle |
1311 |
for (FfpeBlock f : ffpeBlocks) |
| 5060 |
29 Oct 18 |
olle |
1312 |
{ |
| 5060 |
29 Oct 18 |
olle |
// Only include unreturned FFPE blocks |
| 5060 |
29 Oct 18 |
olle |
1314 |
f.loadAnnotations(dc, "returnedDate", Annotationtype.RETURNED_DATE, null); |
| 5060 |
29 Oct 18 |
olle |
1315 |
Date returnedDate = (Date)f.asJSONObject().get("returnedDate"); |
| 5060 |
29 Oct 18 |
olle |
1316 |
if (returnedDate != null) |
| 5060 |
29 Oct 18 |
olle |
1317 |
{ |
| 5061 |
30 Oct 18 |
olle |
1318 |
f.loadAnnotations(dc, "usedForFfpeSection", Annotationtype.USED_FOR_FFPE_SECTION, null); |
| 5060 |
29 Oct 18 |
olle |
1319 |
f.loadAnnotations(dc, "pad", Annotationtype.PAD, null); |
| 5095 |
14 Nov 18 |
olle |
1320 |
f.loadAnnotations(dc, "materialNumber", Annotationtype.MATERIAL_NUMBER, null); |
| 5060 |
29 Oct 18 |
olle |
1321 |
f.loadAnnotations(dc, "yellowLabel", Annotationtype.YELLOW_LABEL, null); |
| 5060 |
29 Oct 18 |
olle |
1322 |
jsonFfpeBlock.add(f.asJSONObject()); |
| 5060 |
29 Oct 18 |
olle |
1323 |
} |
| 5060 |
29 Oct 18 |
olle |
1324 |
} |
| 5060 |
29 Oct 18 |
olle |
1325 |
|
| 5060 |
29 Oct 18 |
olle |
1326 |
json.put("items", jsonFfpeBlock); |
| 5060 |
29 Oct 18 |
olle |
1327 |
} |
| 3225 |
02 Apr 15 |
olle |
1328 |
else if ("GetDna".equals(cmd)) |
| 3225 |
02 Apr 15 |
olle |
1329 |
{ |
| 3225 |
02 Apr 15 |
olle |
1330 |
/* |
| 3225 |
02 Apr 15 |
olle |
Find DNA extract from name. |
| 3225 |
02 Apr 15 |
olle |
1332 |
*/ |
| 3225 |
02 Apr 15 |
olle |
1333 |
dc = sc.newDbControl(); |
| 3225 |
02 Apr 15 |
olle |
1334 |
String name = req.getParameter("name"); |
| 3225 |
02 Apr 15 |
olle |
1335 |
|
| 3318 |
08 May 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3318 |
08 May 15 |
olle |
1337 |
SnapshotManager manager = new SnapshotManager(); |
| 3318 |
08 May 15 |
olle |
1338 |
|
| 3225 |
02 Apr 15 |
olle |
1339 |
Dna dna = Dna.findByName(dc, name); |
| 3225 |
02 Apr 15 |
olle |
1340 |
JSONObject jsonDna = new JSONObject(); |
| 3225 |
02 Apr 15 |
olle |
1341 |
if (dna != null) |
| 3225 |
02 Apr 15 |
olle |
1342 |
{ |
| 3318 |
08 May 15 |
olle |
1343 |
loadDnaInfo(dc, manager, dna); |
| 3225 |
02 Apr 15 |
olle |
1344 |
jsonDna = dna.asJSONObject(); |
| 3225 |
02 Apr 15 |
olle |
1345 |
} |
| 3225 |
02 Apr 15 |
olle |
1346 |
json.put("dna", jsonDna); |
| 3225 |
02 Apr 15 |
olle |
1347 |
} |
| 3176 |
06 Mar 15 |
olle |
1348 |
else if ("GetLastProcessedDna".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1349 |
{ |
| 3176 |
06 Mar 15 |
olle |
1350 |
/* |
| 3176 |
06 Mar 15 |
olle |
Find SpecimenTube items that have extracts. |
| 3176 |
06 Mar 15 |
olle |
1352 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1353 |
dc = sc.newDbControl(); |
| 3176 |
06 Mar 15 |
olle |
1354 |
List<SpecimenTube> specimenTubes = SpecimenTube.findProcessedTubes(dc); |
| 3176 |
06 Mar 15 |
olle |
1355 |
|
| 3176 |
06 Mar 15 |
olle |
1356 |
JSONArray jsonDna = new JSONArray(); |
| 3176 |
06 Mar 15 |
olle |
1357 |
|
| 3176 |
06 Mar 15 |
olle |
1358 |
Dna lastExtractedDna = null; |
| 3176 |
06 Mar 15 |
olle |
1359 |
Date lastExtractionDate = null; |
| 3176 |
06 Mar 15 |
olle |
1360 |
|
| 3176 |
06 Mar 15 |
olle |
1361 |
for (SpecimenTube tube : specimenTubes) |
| 3176 |
06 Mar 15 |
olle |
1362 |
{ |
| 3176 |
06 Mar 15 |
olle |
1363 |
Sample s = tube.getSample(); |
| 3176 |
06 Mar 15 |
olle |
1364 |
String specimenName = s.getName(); |
| 3176 |
06 Mar 15 |
olle |
1365 |
if (specimenName != null && !specimenName.equals("")) |
| 3176 |
06 Mar 15 |
olle |
1366 |
{ |
| 3176 |
06 Mar 15 |
olle |
1367 |
int dotIndex = specimenName.indexOf("."); |
| 3176 |
06 Mar 15 |
olle |
1368 |
if (dotIndex >= 0) |
| 3176 |
06 Mar 15 |
olle |
1369 |
{ |
| 3176 |
06 Mar 15 |
olle |
1370 |
String caseName = specimenName.substring(0,dotIndex); |
| 3176 |
06 Mar 15 |
olle |
1371 |
List<Dna> dnas = Dna.findByCaseName(dc, caseName); |
| 3176 |
06 Mar 15 |
olle |
1372 |
if (dnas.size() > 0) |
| 3176 |
06 Mar 15 |
olle |
1373 |
{ |
| 3176 |
06 Mar 15 |
olle |
1374 |
Dna dna = (Dna) dnas.get(0); |
| 3176 |
06 Mar 15 |
olle |
1375 |
Extract e = dna.getExtract(); |
| 3176 |
06 Mar 15 |
olle |
1376 |
BioMaterialEvent created = e.getCreationEvent(); |
| 3176 |
06 Mar 15 |
olle |
1377 |
Date extractionDate = created.getEventDate(); |
| 3176 |
06 Mar 15 |
olle |
1378 |
if (lastExtractionDate != null) |
| 3176 |
06 Mar 15 |
olle |
1379 |
{ |
| 3176 |
06 Mar 15 |
olle |
1380 |
if (extractionDate != null && (extractionDate.after(lastExtractionDate) || extractionDate.equals(lastExtractionDate))) |
| 3176 |
06 Mar 15 |
olle |
1381 |
{ |
| 3176 |
06 Mar 15 |
olle |
1382 |
lastExtractedDna = dna; |
| 3176 |
06 Mar 15 |
olle |
1383 |
lastExtractionDate = extractionDate; |
| 3176 |
06 Mar 15 |
olle |
1384 |
} |
| 3176 |
06 Mar 15 |
olle |
1385 |
} |
| 3176 |
06 Mar 15 |
olle |
1386 |
else |
| 3176 |
06 Mar 15 |
olle |
1387 |
{ |
| 3176 |
06 Mar 15 |
olle |
1388 |
if (extractionDate != null) |
| 3176 |
06 Mar 15 |
olle |
1389 |
{ |
| 3176 |
06 Mar 15 |
olle |
1390 |
lastExtractedDna = dna; |
| 3176 |
06 Mar 15 |
olle |
1391 |
lastExtractionDate = extractionDate; |
| 3176 |
06 Mar 15 |
olle |
1392 |
} |
| 3176 |
06 Mar 15 |
olle |
1393 |
} |
| 3176 |
06 Mar 15 |
olle |
1394 |
} |
| 3176 |
06 Mar 15 |
olle |
1395 |
} |
| 3176 |
06 Mar 15 |
olle |
1396 |
} |
| 3176 |
06 Mar 15 |
olle |
1397 |
} |
| 3176 |
06 Mar 15 |
olle |
1398 |
if (lastExtractedDna != null) |
| 3176 |
06 Mar 15 |
olle |
1399 |
{ |
| 3318 |
08 May 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3318 |
08 May 15 |
olle |
1401 |
SnapshotManager manager = new SnapshotManager(); |
| 3318 |
08 May 15 |
olle |
1402 |
|
| 3318 |
08 May 15 |
olle |
1403 |
loadDnaInfo(dc, manager, lastExtractedDna); |
| 3176 |
06 Mar 15 |
olle |
1404 |
jsonDna.add(lastExtractedDna.asJSONObject()); |
| 3176 |
06 Mar 15 |
olle |
1405 |
} |
| 3176 |
06 Mar 15 |
olle |
1406 |
json.put("dnas", jsonDna); |
| 3176 |
06 Mar 15 |
olle |
1407 |
} |
| 3176 |
06 Mar 15 |
olle |
1408 |
else if ("GetNextQiacubeRunNo".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1409 |
{ |
| 3176 |
06 Mar 15 |
olle |
1410 |
/* |
| 3176 |
06 Mar 15 |
olle |
Get the next qiacube run number for the given date |
| 3176 |
06 Mar 15 |
olle |
1412 |
*/ |
| 5823 |
04 Feb 20 |
olle |
1413 |
String qiacubeDateStr = req.getParameter("qiacubeDate"); |
| 5823 |
04 Feb 20 |
olle |
1414 |
System.out.println("ExtractionServlet::doGet(): cmd = \"" + cmd + "\" qiacubeDateStr = \"" + qiacubeDateStr + "\"."); |
| 3176 |
06 Mar 15 |
olle |
1415 |
Date date = Meludi.CONVERTER_STRING_TO_DATE.convert(req.getParameter("qiacubeDate")); |
| 3176 |
06 Mar 15 |
olle |
1416 |
dc = sc.newDbControl(); |
| 3176 |
06 Mar 15 |
olle |
1417 |
|
| 3176 |
06 Mar 15 |
olle |
// Find existing RNA with QiacubeDate |
| 3176 |
06 Mar 15 |
olle |
1419 |
ItemQuery<Extract> query = Extract.getQuery(); |
| 3176 |
06 Mar 15 |
olle |
1420 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 3176 |
06 Mar 15 |
olle |
// Filter on RNA subtype |
| 3176 |
06 Mar 15 |
olle |
1422 |
Subtype.RNA.addFilter(dc, query); |
| 3176 |
06 Mar 15 |
olle |
1423 |
|
| 3176 |
06 Mar 15 |
olle |
// Filter on given date |
| 3176 |
06 Mar 15 |
olle |
1425 |
query.join(Hql.innerJoin("creationEvent", "ce")); |
| 3176 |
06 Mar 15 |
olle |
1426 |
query.restrict(Restrictions.eq(Hql.property("ce", "eventDate"), Expressions.parameter("created", date, Type.DATE))); |
| 3176 |
06 Mar 15 |
olle |
1427 |
|
| 3176 |
06 Mar 15 |
olle |
1428 |
int nextQiacubeRunNumber = 1; |
| 3176 |
06 Mar 15 |
olle |
1429 |
/* |
| 3176 |
06 Mar 15 |
olle |
for (Extract e : query.list(dc)) |
| 3176 |
06 Mar 15 |
olle |
1431 |
{ |
| 3176 |
06 Mar 15 |
olle |
Integer qiacubeRunNumber = (Integer)Annotationtype.QIACUBE_RUN_NO.getAnnotationValue(dc, e); |
| 3176 |
06 Mar 15 |
olle |
if (qiacubeRunNumber != null && qiacubeRunNumber >= nextQiacubeRunNumber) |
| 3176 |
06 Mar 15 |
olle |
1434 |
{ |
| 3176 |
06 Mar 15 |
olle |
nextQiacubeRunNumber = qiacubeRunNumber + 1; |
| 3176 |
06 Mar 15 |
olle |
1436 |
} |
| 3176 |
06 Mar 15 |
olle |
1437 |
|
| 3176 |
06 Mar 15 |
olle |
1438 |
} |
| 3176 |
06 Mar 15 |
olle |
1439 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1440 |
json.put("nextQiacubeRunNo", nextQiacubeRunNumber); |
| 3176 |
06 Mar 15 |
olle |
1441 |
} |
| 3176 |
06 Mar 15 |
olle |
1442 |
else if ("DownloadNanoDropSampleIdFile".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1443 |
{ |
| 3176 |
06 Mar 15 |
olle |
1444 |
json = null; // No JSON output |
| 3432 |
29 Jun 15 |
olle |
1445 |
|
| 3432 |
29 Jun 15 |
olle |
1446 |
String startListName = req.getParameter("startListName"); |
| 3176 |
06 Mar 15 |
olle |
1447 |
String qiacubeDate = req.getParameter("qiacubeDate"); |
| 3176 |
06 Mar 15 |
olle |
1448 |
String qiacubeRunNo = req.getParameter("qiacubeRunNo"); |
| 3176 |
06 Mar 15 |
olle |
1449 |
String[] itemNames = req.getParameter("itemNames").split(","); |
| 3255 |
17 Apr 15 |
olle |
1450 |
Boolean useBlankControlColumn = Boolean.valueOf(req.getParameter("blankControlColumn")); |
| 3255 |
17 Apr 15 |
olle |
1451 |
if (useBlankControlColumn == null) |
| 3255 |
17 Apr 15 |
olle |
1452 |
{ |
| 3255 |
17 Apr 15 |
olle |
1453 |
useBlankControlColumn = true; |
| 3255 |
17 Apr 15 |
olle |
1454 |
} |
| 3176 |
06 Mar 15 |
olle |
1455 |
|
| 3432 |
29 Jun 15 |
olle |
1456 |
resp.setHeader("Content-Disposition", "attachment; filename=nd-sample-id-" + startListName + "-" + qiacubeDate + "-" + qiacubeRunNo + ".csv"); |
| 3176 |
06 Mar 15 |
olle |
1457 |
resp.setContentType("text/plain"); |
| 3176 |
06 Mar 15 |
olle |
1458 |
resp.setCharacterEncoding("UTF-8"); |
| 3176 |
06 Mar 15 |
olle |
1459 |
|
| 3176 |
06 Mar 15 |
olle |
1460 |
PrintWriter out = resp.getWriter(); |
| 3176 |
06 Mar 15 |
olle |
1461 |
TableWriter tw = new TableWriter(out); |
| 3176 |
06 Mar 15 |
olle |
1462 |
|
| 3275 |
24 Apr 15 |
olle |
1463 |
String[] cols = new String[12]; |
| 3176 |
06 Mar 15 |
olle |
1464 |
String[] itemNamesNonNull = new String[24]; |
| 3176 |
06 Mar 15 |
olle |
1465 |
|
| 3176 |
06 Mar 15 |
olle |
1466 |
int numItems = 0; |
| 3176 |
06 Mar 15 |
olle |
1467 |
for (int i = 0; i < itemNames.length; i++) |
| 3176 |
06 Mar 15 |
olle |
1468 |
{ |
| 3176 |
06 Mar 15 |
olle |
1469 |
String itemName = itemNames[i]; |
| 3176 |
06 Mar 15 |
olle |
1470 |
if (itemName != null && !itemName.equals("")) |
| 3176 |
06 Mar 15 |
olle |
1471 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Only add newly created and input RNA items |
| 3433 |
29 Jun 15 |
olle |
1473 |
if (Meludi.itemIsSpecimen(itemName) || Meludi.itemIsRna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
1474 |
{ |
| 3176 |
06 Mar 15 |
olle |
1475 |
if (numItems < 24) |
| 3176 |
06 Mar 15 |
olle |
1476 |
{ |
| 3176 |
06 Mar 15 |
olle |
1477 |
itemNamesNonNull[numItems] = itemName; |
| 3176 |
06 Mar 15 |
olle |
1478 |
numItems++; |
| 3176 |
06 Mar 15 |
olle |
1479 |
} |
| 3176 |
06 Mar 15 |
olle |
1480 |
} |
| 3176 |
06 Mar 15 |
olle |
1481 |
} |
| 3176 |
06 Mar 15 |
olle |
1482 |
} |
| 3176 |
06 Mar 15 |
olle |
1483 |
|
| 3176 |
06 Mar 15 |
olle |
// NanoDrop sample id file for RNA extracts from 1-24 specimens |
| 3176 |
06 Mar 15 |
olle |
1485 |
for (int row = 0; row < 8; ++row) |
| 3176 |
06 Mar 15 |
olle |
1486 |
{ |
| 3176 |
06 Mar 15 |
olle |
1487 |
for (int col = 0; col < 4; ++col) |
| 3176 |
06 Mar 15 |
olle |
1488 |
{ |
| 3255 |
17 Apr 15 |
olle |
// Column to the right of last column with sample, should be filled with blank controls |
| 3255 |
17 Apr 15 |
olle |
1490 |
int blankColumn = (numItems - 1)/8 + 1; |
| 3255 |
17 Apr 15 |
olle |
1491 |
int firstNonSampleColumnPos = numItems - 8*col; |
| 3255 |
17 Apr 15 |
olle |
// Note: firstNonSampleColumnPos < 0 => cols[col] is set to null for all rows |
| 3176 |
06 Mar 15 |
olle |
1493 |
|
| 3255 |
17 Apr 15 |
olle |
1494 |
if (row < firstNonSampleColumnPos) |
| 3176 |
06 Mar 15 |
olle |
1495 |
{ |
| 3176 |
06 Mar 15 |
olle |
1496 |
String itemName = itemNamesNonNull[row+8*col]; |
| 3433 |
29 Jun 15 |
olle |
1497 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
1498 |
{ |
| 3176 |
06 Mar 15 |
olle |
1499 |
cols[col] = itemName + ".r"; |
| 3176 |
06 Mar 15 |
olle |
1500 |
} |
| 3176 |
06 Mar 15 |
olle |
1501 |
else |
| 3176 |
06 Mar 15 |
olle |
1502 |
{ |
| 3176 |
06 Mar 15 |
olle |
1503 |
cols[col] = itemName; |
| 3176 |
06 Mar 15 |
olle |
1504 |
} |
| 3176 |
06 Mar 15 |
olle |
1505 |
} |
| 3255 |
17 Apr 15 |
olle |
1506 |
else if ((useBlankControlColumn && col == blankColumn) || |
| 3255 |
17 Apr 15 |
olle |
1507 |
(!useBlankControlColumn && row == firstNonSampleColumnPos)) |
| 3176 |
06 Mar 15 |
olle |
1508 |
{ |
| 3176 |
06 Mar 15 |
olle |
1509 |
cols[col] = "blank"; |
| 3176 |
06 Mar 15 |
olle |
1510 |
} |
| 3176 |
06 Mar 15 |
olle |
1511 |
else |
| 3255 |
17 Apr 15 |
olle |
1512 |
{ |
| 3176 |
06 Mar 15 |
olle |
1513 |
cols[col] = null; |
| 3176 |
06 Mar 15 |
olle |
1514 |
} |
| 3176 |
06 Mar 15 |
olle |
1515 |
} |
| 3176 |
06 Mar 15 |
olle |
1516 |
tw.tablePrintData((Object[])cols); |
| 3176 |
06 Mar 15 |
olle |
1517 |
} |
| 3176 |
06 Mar 15 |
olle |
1518 |
|
| 3176 |
06 Mar 15 |
olle |
1519 |
out.flush(); |
| 3176 |
06 Mar 15 |
olle |
1520 |
out.close(); |
| 3176 |
06 Mar 15 |
olle |
1521 |
|
| 3176 |
06 Mar 15 |
olle |
1522 |
} |
| 3176 |
06 Mar 15 |
olle |
1523 |
else if ("DownloadQPcrSampleIdFile".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1524 |
{ |
| 3176 |
06 Mar 15 |
olle |
1525 |
json = null; // No JSON output |
| 3176 |
06 Mar 15 |
olle |
1526 |
|
| 3432 |
29 Jun 15 |
olle |
1527 |
String startListName = req.getParameter("startListName"); |
| 3176 |
06 Mar 15 |
olle |
1528 |
String qiacubeDate = req.getParameter("qiacubeDate"); |
| 3176 |
06 Mar 15 |
olle |
1529 |
String qiacubeRunNo = req.getParameter("qiacubeRunNo"); |
| 3176 |
06 Mar 15 |
olle |
1530 |
String[] itemNames = req.getParameter("itemNames").split(","); |
| 3176 |
06 Mar 15 |
olle |
1531 |
|
| 3432 |
29 Jun 15 |
olle |
1532 |
resp.setHeader("Content-Disposition", "attachment; filename=qpcr-sample-id-" + startListName + "-" + qiacubeDate + "-" + qiacubeRunNo+ ".csv"); |
| 3176 |
06 Mar 15 |
olle |
1533 |
resp.setContentType("text/plain"); |
| 3176 |
06 Mar 15 |
olle |
1534 |
resp.setCharacterEncoding("UTF-8"); |
| 3176 |
06 Mar 15 |
olle |
1535 |
|
| 3176 |
06 Mar 15 |
olle |
1536 |
PrintWriter out = resp.getWriter(); |
| 3176 |
06 Mar 15 |
olle |
1537 |
TableWriter tw = new TableWriter(out); |
| 3176 |
06 Mar 15 |
olle |
1538 |
|
| 3176 |
06 Mar 15 |
olle |
1539 |
String[] cols = new String[1]; |
| 3176 |
06 Mar 15 |
olle |
1540 |
String[] itemNamesNonNull = new String[24]; |
| 3176 |
06 Mar 15 |
olle |
1541 |
|
| 3176 |
06 Mar 15 |
olle |
1542 |
int numItems = 0; |
| 3176 |
06 Mar 15 |
olle |
1543 |
for (int i = 0; i < itemNames.length; i++) |
| 3176 |
06 Mar 15 |
olle |
1544 |
{ |
| 3176 |
06 Mar 15 |
olle |
1545 |
String itemName = itemNames[i]; |
| 3176 |
06 Mar 15 |
olle |
1546 |
if (itemName != null && !itemName.equals("")) |
| 3176 |
06 Mar 15 |
olle |
1547 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Only add newly created and input DNA items |
| 3433 |
29 Jun 15 |
olle |
1549 |
if (Meludi.itemIsSpecimen(itemName) || Meludi.itemIsDna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
1550 |
{ |
| 3433 |
29 Jun 15 |
olle |
1551 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3230 |
08 Apr 15 |
olle |
1552 |
{ |
| 3230 |
08 Apr 15 |
olle |
1553 |
itemName += ".d"; |
| 3230 |
08 Apr 15 |
olle |
1554 |
} |
| 3176 |
06 Mar 15 |
olle |
1555 |
if (numItems < 24) |
| 3176 |
06 Mar 15 |
olle |
1556 |
{ |
| 3176 |
06 Mar 15 |
olle |
1557 |
itemNamesNonNull[numItems] = itemName; |
| 3176 |
06 Mar 15 |
olle |
1558 |
numItems++; |
| 3176 |
06 Mar 15 |
olle |
1559 |
} |
| 3176 |
06 Mar 15 |
olle |
1560 |
} |
| 3176 |
06 Mar 15 |
olle |
1561 |
} |
| 3176 |
06 Mar 15 |
olle |
1562 |
} |
| 3176 |
06 Mar 15 |
olle |
1563 |
|
| 3205 |
20 Mar 15 |
olle |
// qPCR sample id file header |
| 3205 |
20 Mar 15 |
olle |
1565 |
String[] headerCols = new String[1]; |
| 3205 |
20 Mar 15 |
olle |
1566 |
headerCols[0] = "Row,Column,*Target Name,*Sample Name"; |
| 3205 |
20 Mar 15 |
olle |
1567 |
tw.tablePrintData((Object[])headerCols); |
| 3205 |
20 Mar 15 |
olle |
1568 |
|
| 3176 |
06 Mar 15 |
olle |
// qPCR sample id file for DNA extracts from 1-24 specimens |
| 3213 |
27 Mar 15 |
olle |
1570 |
int sampleNo = 0; |
| 3176 |
06 Mar 15 |
olle |
1571 |
for (int row = 0; row < 8; ++row) |
| 3176 |
06 Mar 15 |
olle |
1572 |
{ |
| 3176 |
06 Mar 15 |
olle |
1573 |
for (int col = 0; col < 12; ++col) |
| 3176 |
06 Mar 15 |
olle |
1574 |
{ |
| 3213 |
27 Mar 15 |
olle |
1575 |
int tripletColNo = col/3; |
| 3213 |
27 Mar 15 |
olle |
1576 |
sampleNo = 8*tripletColNo + row + 1; |
| 3213 |
27 Mar 15 |
olle |
1577 |
if (sampleNo <= (numItems + 2)) |
| 3176 |
06 Mar 15 |
olle |
1578 |
{ |
| 3176 |
06 Mar 15 |
olle |
1579 |
String rowId = getPlateRowId(row); |
| 3176 |
06 Mar 15 |
olle |
1580 |
int colId = col+1; |
| 3176 |
06 Mar 15 |
olle |
1581 |
String targetName = ""; |
| 3176 |
06 Mar 15 |
olle |
1582 |
String sampleName = ""; |
| 3591 |
11 Nov 15 |
olle |
1583 |
if (sampleNo == 1) |
| 3176 |
06 Mar 15 |
olle |
1584 |
{ |
| 3591 |
11 Nov 15 |
olle |
// QCT (Quality Control Template) |
| 3230 |
08 Apr 15 |
olle |
1586 |
targetName = "UNKN"; |
| 3591 |
11 Nov 15 |
olle |
1587 |
sampleName = "QCT"; |
| 3176 |
06 Mar 15 |
olle |
1588 |
} |
| 3591 |
11 Nov 15 |
olle |
1589 |
else if (sampleNo <= (numItems + 1)) |
| 3176 |
06 Mar 15 |
olle |
1590 |
{ |
| 3230 |
08 Apr 15 |
olle |
1591 |
targetName = "UNKN"; |
| 3591 |
11 Nov 15 |
olle |
1592 |
sampleName = itemNamesNonNull[sampleNo - 2]; |
| 3176 |
06 Mar 15 |
olle |
1593 |
} |
| 3213 |
27 Mar 15 |
olle |
1594 |
else if (sampleNo == (numItems + 2)) |
| 3176 |
06 Mar 15 |
olle |
1595 |
{ |
| 3213 |
27 Mar 15 |
olle |
// NTC (Non Template Control) |
| 3230 |
08 Apr 15 |
olle |
1597 |
targetName = "NTC"; |
| 3176 |
06 Mar 15 |
olle |
1598 |
sampleName = ""; |
| 3176 |
06 Mar 15 |
olle |
1599 |
} |
| 3176 |
06 Mar 15 |
olle |
1600 |
cols[0] = rowId + "," + colId + "," + targetName + "," + sampleName; |
| 3176 |
06 Mar 15 |
olle |
1601 |
tw.tablePrintData((Object[])cols); |
| 3176 |
06 Mar 15 |
olle |
1602 |
} |
| 3176 |
06 Mar 15 |
olle |
1603 |
} |
| 3176 |
06 Mar 15 |
olle |
1604 |
} |
| 3176 |
06 Mar 15 |
olle |
1605 |
|
| 3176 |
06 Mar 15 |
olle |
1606 |
out.flush(); |
| 3176 |
06 Mar 15 |
olle |
1607 |
out.close(); |
| 3176 |
06 Mar 15 |
olle |
1608 |
|
| 3176 |
06 Mar 15 |
olle |
1609 |
} |
| 3332 |
12 May 15 |
olle |
1610 |
else if ("DownloadReagentLotNoFile".equals(cmd)) |
| 3332 |
12 May 15 |
olle |
1611 |
{ |
| 3332 |
12 May 15 |
olle |
1612 |
json = null; // No JSON output |
| 3332 |
12 May 15 |
olle |
1613 |
|
| 3432 |
29 Jun 15 |
olle |
1614 |
String startListName = req.getParameter("startListName"); |
| 3332 |
12 May 15 |
olle |
1615 |
String isolationDate = req.getParameter("isolationDate"); |
| 3332 |
12 May 15 |
olle |
1616 |
String reagentInfoStr = req.getParameter("reagentInfo"); |
| 3332 |
12 May 15 |
olle |
1617 |
JSONObject reagentInfo = (JSONObject)new JSONParser().parse(reagentInfoStr); |
| 3332 |
12 May 15 |
olle |
1618 |
|
| 3432 |
29 Jun 15 |
olle |
1619 |
resp.setHeader("Content-Disposition", "attachment; filename=extraction-reagents-" + startListName + "-" + isolationDate + ".csv"); |
| 3332 |
12 May 15 |
olle |
1620 |
resp.setContentType("text/plain"); |
| 3332 |
12 May 15 |
olle |
1621 |
resp.setCharacterEncoding("UTF-8"); |
| 3332 |
12 May 15 |
olle |
1622 |
|
| 3332 |
12 May 15 |
olle |
1623 |
PrintWriter out = resp.getWriter(); |
| 3332 |
12 May 15 |
olle |
1624 |
out.println("MeLuDI Extraction Reagents;"); |
| 3332 |
12 May 15 |
olle |
1625 |
out.println(";"); |
| 3332 |
12 May 15 |
olle |
1626 |
out.println("Specimen Reagents;"); |
| 3332 |
12 May 15 |
olle |
1627 |
out.println("Xylen;" + reagentInfo.get("xyleneSpecimen")); |
| 3332 |
12 May 15 |
olle |
1628 |
out.println("ETOH 99,5%;" + reagentInfo.get("etoh995Specimen")); |
| 3332 |
12 May 15 |
olle |
1629 |
out.println("Buffer PKD;" + reagentInfo.get("bufferPkdSpecimen")); |
| 3332 |
12 May 15 |
olle |
1630 |
out.println("Buffer ATL;" + reagentInfo.get("bufferAtlSpecimen")); |
| 3332 |
12 May 15 |
olle |
1631 |
out.println("Proteinase K;" + reagentInfo.get("proteinaseKSpecimen")); |
| 3332 |
12 May 15 |
olle |
1632 |
out.println("Rnase A;" + reagentInfo.get("rnaseASpecimen")); |
| 3332 |
12 May 15 |
olle |
1633 |
out.println(";"); |
| 3332 |
12 May 15 |
olle |
1634 |
out.println("Qiacube Reagents;"); |
| 3332 |
12 May 15 |
olle |
1635 |
out.println("AllPrep DNA/RNA FFPE kit;" + reagentInfo.get("allPrepFfpeKit")); |
| 3332 |
12 May 15 |
olle |
1636 |
out.println("ETOH 99,5%;" + reagentInfo.get("etoh995")); |
| 3332 |
12 May 15 |
olle |
1637 |
out.println("Buffer RLT;" + reagentInfo.get("bufferRlt")); |
| 3332 |
12 May 15 |
olle |
1638 |
out.println("Buffer FRN;" + reagentInfo.get("bufferFrn")); |
| 3332 |
12 May 15 |
olle |
1639 |
out.println("Buffer RPE;" + reagentInfo.get("bufferRpe")); |
| 3332 |
12 May 15 |
olle |
1640 |
out.println("Buffer AL;" + reagentInfo.get("bufferAl")); |
| 3332 |
12 May 15 |
olle |
1641 |
out.println("Buffer AW1;" + reagentInfo.get("bufferAw1")); |
| 3332 |
12 May 15 |
olle |
1642 |
out.println("Buffer AW2;" + reagentInfo.get("bufferAw2")); |
| 3332 |
12 May 15 |
olle |
1643 |
out.println("Buffer ATE;" + reagentInfo.get("bufferAte")); |
| 3332 |
12 May 15 |
olle |
1644 |
out.println("RDD;" + reagentInfo.get("bufferRdd")); |
| 3332 |
12 May 15 |
olle |
1645 |
out.println("Rnase-free Water;" + reagentInfo.get("rnaseFreeWater")); |
| 3332 |
12 May 15 |
olle |
1646 |
out.println("DNAse mix;" + reagentInfo.get("dnaseMix")); |
| 3332 |
12 May 15 |
olle |
1647 |
out.println("Rneasy MinElute Spin Column;" + reagentInfo.get("rneasyMinEluteSpinColumn")); |
| 3332 |
12 May 15 |
olle |
1648 |
out.println("QIAamp MinElute Spin Column;" + reagentInfo.get("qiaampMinEluteSpinColumn")); |
| 3332 |
12 May 15 |
olle |
1649 |
out.println(";"); |
| 3332 |
12 May 15 |
olle |
1650 |
out.println("Quality Control Reagents;"); |
| 3332 |
12 May 15 |
olle |
1651 |
out.println("Kapa SYBR Fast;" + reagentInfo.get("kapaSybrFast")); |
| 3332 |
12 May 15 |
olle |
1652 |
out.println("Quality Control Primers (QCP) RGT;" + reagentInfo.get("qualityControlPrimersQcpRgt")); |
| 3438 |
03 Jul 15 |
olle |
1653 |
out.println("Quality Control Template (QCT);" + reagentInfo.get("qualityControlTemplateQct")); |
| 3332 |
12 May 15 |
olle |
1654 |
out.println("QUBIT DNA High Sens;" + reagentInfo.get("qubitDnaHighSens")); |
| 3332 |
12 May 15 |
olle |
1655 |
out.println("QUBIT DNA Broad Range;" + reagentInfo.get("qubitDnaBroadRange")); |
| 3332 |
12 May 15 |
olle |
1656 |
|
| 3332 |
12 May 15 |
olle |
1657 |
out.flush(); |
| 3332 |
12 May 15 |
olle |
1658 |
out.close(); |
| 3332 |
12 May 15 |
olle |
1659 |
} |
| 3176 |
06 Mar 15 |
olle |
1660 |
else if ("GetRNAToNormalize".equals(cmd) || "GetRNAInfoForNormalize".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1661 |
{ |
| 3176 |
06 Mar 15 |
olle |
1662 |
/* |
| 3176 |
06 Mar 15 |
olle |
Find RNA items that have been selected for pre-normalization. |
| 3176 |
06 Mar 15 |
olle |
1664 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1665 |
dc = sc.newDbControl(); |
| 3176 |
06 Mar 15 |
olle |
// Create a query that load all Lysate extracts without created date |
| 3176 |
06 Mar 15 |
olle |
1667 |
ItemQuery<Extract> query = Extract.getQuery(); |
| 3176 |
06 Mar 15 |
olle |
1668 |
query.setIncludes(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 3176 |
06 Mar 15 |
olle |
// Filter on RNA subtype |
| 3176 |
06 Mar 15 |
olle |
1670 |
Subtype.RNA.addFilter(dc, query); |
| 3176 |
06 Mar 15 |
olle |
1671 |
|
| 3176 |
06 Mar 15 |
olle |
1672 |
/* |
| 3176 |
06 Mar 15 |
olle |
if ("GetRNAToNormalize".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1674 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Join AutoProcessing annotation |
| 3176 |
06 Mar 15 |
olle |
query.join(Annotations.leftJoin(null, Annotationtype.AUTO_PROCESSING.load(dc), "ap")); |
| 3176 |
06 Mar 15 |
olle |
query.restrict(Restrictions.eq(Hql.alias("ap"), Expressions.string(Rna.AUTO_PROCESSING_PRE_NORMALIZE))); |
| 3176 |
06 Mar 15 |
olle |
1678 |
} |
| 3176 |
06 Mar 15 |
olle |
else |
| 3176 |
06 Mar 15 |
olle |
1680 |
{ |
| 3176 |
06 Mar 15 |
olle |
1681 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1682 |
String[] selected = req.getParameter("rnaIds").split(","); |
| 3176 |
06 Mar 15 |
olle |
1683 |
query.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected"))); |
| 3176 |
06 Mar 15 |
olle |
1684 |
query.setParameter("selected", Arrays.asList(Values.getInt(selected)), Type.INT); |
| 3176 |
06 Mar 15 |
olle |
1685 |
/* |
| 3176 |
06 Mar 15 |
olle |
1686 |
} |
| 3176 |
06 Mar 15 |
olle |
1687 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1688 |
|
| 3176 |
06 Mar 15 |
olle |
1689 |
JSONArray jsonRna = new JSONArray(); |
| 3176 |
06 Mar 15 |
olle |
1690 |
List<Rna> rna = Rna.toRna(query.list(dc)); |
| 3176 |
06 Mar 15 |
olle |
1691 |
|
| 3176 |
06 Mar 15 |
olle |
1692 |
for (Rna r : rna) |
| 3176 |
06 Mar 15 |
olle |
1693 |
{ |
| 3176 |
06 Mar 15 |
olle |
1694 |
r.loadBioPlateLocation(); |
| 3176 |
06 Mar 15 |
olle |
1695 |
r.setAnnotation("remainingQuantity", r.getItem().getRemainingQuantity()); |
| 3176 |
06 Mar 15 |
olle |
1696 |
/* |
| 3176 |
06 Mar 15 |
olle |
r.setAnnotation("nextAliquotName", r.getNextNormalizedAliquotName(dc)); |
| 3176 |
06 Mar 15 |
olle |
r.loadAnnotations(dc, "NDConc", Annotationtype.ND_CONC, null); |
| 3176 |
06 Mar 15 |
olle |
r.loadAnnotations(dc, "QiacubeDate", Annotationtype.QIACUBE_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3176 |
06 Mar 15 |
olle |
r.loadAnnotations(dc, "QiacubeRunNo", Annotationtype.QIACUBE_RUN_NO, null); |
| 3176 |
06 Mar 15 |
olle |
r.loadAnnotations(dc, "QiacubePosition", Annotationtype.QIACUBE_POSITION, null); |
| 3176 |
06 Mar 15 |
olle |
1702 |
*/ |
| 3176 |
06 Mar 15 |
olle |
1703 |
|
| 3176 |
06 Mar 15 |
olle |
1704 |
jsonRna.add(r.asJSONObject()); |
| 3176 |
06 Mar 15 |
olle |
1705 |
} |
| 3176 |
06 Mar 15 |
olle |
1706 |
|
| 3176 |
06 Mar 15 |
olle |
1707 |
json.put("rnaExtracts", jsonRna); |
| 3176 |
06 Mar 15 |
olle |
1708 |
} |
| 3180 |
17 Mar 15 |
olle |
1709 |
else if ("GetNextStartPlateName".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
1710 |
{ |
| 3176 |
06 Mar 15 |
olle |
1711 |
dc = sc.newDbControl(); |
| 4200 |
01 Nov 16 |
olle |
1712 |
String startPlatePrefix = Meludi.fetchStartPlateItemPrefix(sc.getActiveProjectId()); |
| 4225 |
10 Nov 16 |
olle |
1713 |
Integer startPlateNumDigits = Meludi.fetchStartPlateItemNumDigits(sc.getActiveProjectId()); |
| 3180 |
17 Mar 15 |
olle |
1714 |
BioPlate highestPlate = findPlateWithHighestNumber(dc, startPlatePrefix); |
| 3180 |
17 Mar 15 |
olle |
1715 |
long highestPlateNum = 0; |
| 3180 |
17 Mar 15 |
olle |
1716 |
if (highestPlate != null) |
| 3176 |
06 Mar 15 |
olle |
1717 |
{ |
| 3180 |
17 Mar 15 |
olle |
1718 |
String highestPlateName = highestPlate.getName(); |
| 3180 |
17 Mar 15 |
olle |
// Remove library plate prefix |
| 3180 |
17 Mar 15 |
olle |
1720 |
if (highestPlateName.indexOf(startPlatePrefix) >= 0) |
| 3180 |
17 Mar 15 |
olle |
1721 |
{ |
| 3180 |
17 Mar 15 |
olle |
1722 |
highestPlateName = highestPlateName.substring(startPlatePrefix.length()); |
| 3180 |
17 Mar 15 |
olle |
1723 |
} |
| 3180 |
17 Mar 15 |
olle |
// Remove initial zeroes |
| 3180 |
17 Mar 15 |
olle |
1725 |
while (highestPlateName.indexOf("0") == 0) |
| 3180 |
17 Mar 15 |
olle |
1726 |
{ |
| 3180 |
17 Mar 15 |
olle |
1727 |
highestPlateName = highestPlateName.substring(1); |
| 3180 |
17 Mar 15 |
olle |
1728 |
} |
| 3180 |
17 Mar 15 |
olle |
1729 |
if (!highestPlateName.equals("")) |
| 3180 |
17 Mar 15 |
olle |
1730 |
{ |
| 3180 |
17 Mar 15 |
olle |
1731 |
highestPlateNum = Long.parseLong(highestPlateName); |
| 3180 |
17 Mar 15 |
olle |
1732 |
} |
| 3176 |
06 Mar 15 |
olle |
1733 |
} |
| 3180 |
17 Mar 15 |
olle |
1734 |
long nextStartPlateNumber = highestPlateNum + 1; |
| 3180 |
17 Mar 15 |
olle |
1735 |
String nextStartPlateNumberStr = "" + nextStartPlateNumber; |
| 4225 |
10 Nov 16 |
olle |
// Pad with initial zeros to get right number of digits |
| 4225 |
10 Nov 16 |
olle |
1737 |
while (nextStartPlateNumberStr.length() < startPlateNumDigits) |
| 3176 |
06 Mar 15 |
olle |
1738 |
{ |
| 3180 |
17 Mar 15 |
olle |
1739 |
nextStartPlateNumberStr = "0" + nextStartPlateNumberStr; |
| 3180 |
17 Mar 15 |
olle |
1740 |
} |
| 3180 |
17 Mar 15 |
olle |
1741 |
String nextStartPlateName = startPlatePrefix + nextStartPlateNumberStr; |
| 3180 |
17 Mar 15 |
olle |
1742 |
json.put("nextStartPlateName", nextStartPlateName); |
| 3176 |
06 Mar 15 |
olle |
1743 |
} |
| 3432 |
29 Jun 15 |
olle |
1744 |
else if ("GetNextStartListName".equals(cmd)) |
| 3432 |
29 Jun 15 |
olle |
1745 |
{ |
| 3432 |
29 Jun 15 |
olle |
1746 |
dc = sc.newDbControl(); |
| 4150 |
03 Oct 16 |
olle |
1747 |
String startListPrefix = Meludi.fetchStartListItemPrefix(sc.getActiveProjectId()); |
| 4225 |
10 Nov 16 |
olle |
1748 |
Integer startListNumDigits = Meludi.fetchStartListItemNumDigits(sc.getActiveProjectId()); |
| 3432 |
29 Jun 15 |
olle |
1749 |
ItemList highestItemList = findItemListWithHighestNumber(dc, startListPrefix); |
| 3432 |
29 Jun 15 |
olle |
1750 |
long highestItemListNum = 0; |
| 3432 |
29 Jun 15 |
olle |
1751 |
if (highestItemList != null) |
| 3432 |
29 Jun 15 |
olle |
1752 |
{ |
| 3432 |
29 Jun 15 |
olle |
1753 |
String highestItemListName = highestItemList.getName(); |
| 3432 |
29 Jun 15 |
olle |
// Remove item list prefix |
| 3432 |
29 Jun 15 |
olle |
1755 |
if (highestItemListName.indexOf(startListPrefix) >= 0) |
| 3432 |
29 Jun 15 |
olle |
1756 |
{ |
| 3432 |
29 Jun 15 |
olle |
1757 |
highestItemListName = highestItemListName.substring(startListPrefix.length()); |
| 3432 |
29 Jun 15 |
olle |
1758 |
} |
| 3432 |
29 Jun 15 |
olle |
// Remove initial zeroes |
| 3432 |
29 Jun 15 |
olle |
1760 |
while (highestItemListName.indexOf("0") == 0) |
| 3432 |
29 Jun 15 |
olle |
1761 |
{ |
| 3432 |
29 Jun 15 |
olle |
1762 |
highestItemListName = highestItemListName.substring(1); |
| 3432 |
29 Jun 15 |
olle |
1763 |
} |
| 3432 |
29 Jun 15 |
olle |
1764 |
if (!highestItemListName.equals("")) |
| 3432 |
29 Jun 15 |
olle |
1765 |
{ |
| 3432 |
29 Jun 15 |
olle |
1766 |
highestItemListNum = Long.parseLong(highestItemListName); |
| 3432 |
29 Jun 15 |
olle |
1767 |
} |
| 3432 |
29 Jun 15 |
olle |
1768 |
} |
| 3432 |
29 Jun 15 |
olle |
1769 |
long nextStartListNumber = highestItemListNum + 1; |
| 3432 |
29 Jun 15 |
olle |
1770 |
String nextStartListNumberStr = "" + nextStartListNumber; |
| 4225 |
10 Nov 16 |
olle |
// Pad with initial zeros to get right number of digits |
| 4225 |
10 Nov 16 |
olle |
1772 |
while (nextStartListNumberStr.length() < startListNumDigits) |
| 3432 |
29 Jun 15 |
olle |
1773 |
{ |
| 3432 |
29 Jun 15 |
olle |
1774 |
nextStartListNumberStr = "0" + nextStartListNumberStr; |
| 3432 |
29 Jun 15 |
olle |
1775 |
} |
| 3432 |
29 Jun 15 |
olle |
1776 |
String nextStartListName = startListPrefix + nextStartListNumberStr; |
| 3432 |
29 Jun 15 |
olle |
1777 |
json.put("nextStartListName", nextStartListName); |
| 3432 |
29 Jun 15 |
olle |
1778 |
} |
| 3176 |
06 Mar 15 |
olle |
1779 |
} |
| 3176 |
06 Mar 15 |
olle |
1780 |
catch (Throwable t) |
| 3176 |
06 Mar 15 |
olle |
1781 |
{ |
| 3176 |
06 Mar 15 |
olle |
1782 |
t.printStackTrace(); |
| 3176 |
06 Mar 15 |
olle |
1783 |
if (json != null) |
| 3176 |
06 Mar 15 |
olle |
1784 |
{ |
| 3176 |
06 Mar 15 |
olle |
1785 |
json.clear(); |
| 3176 |
06 Mar 15 |
olle |
1786 |
json.put("status", "error"); |
| 3176 |
06 Mar 15 |
olle |
1787 |
json.put("message", t.getMessage()); |
| 3176 |
06 Mar 15 |
olle |
1788 |
json.put("stacktrace", ThrowableUtil.stackTraceToString(t)); |
| 3176 |
06 Mar 15 |
olle |
1789 |
} |
| 3176 |
06 Mar 15 |
olle |
1790 |
else |
| 3176 |
06 Mar 15 |
olle |
1791 |
{ |
| 3176 |
06 Mar 15 |
olle |
1792 |
resp.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR, t.getMessage()); |
| 3176 |
06 Mar 15 |
olle |
1793 |
} |
| 3176 |
06 Mar 15 |
olle |
1794 |
} |
| 3176 |
06 Mar 15 |
olle |
1795 |
finally |
| 3176 |
06 Mar 15 |
olle |
1796 |
{ |
| 3176 |
06 Mar 15 |
olle |
1797 |
if (dc != null) dc.close(); |
| 3176 |
06 Mar 15 |
olle |
1798 |
if (json != null) |
| 3176 |
06 Mar 15 |
olle |
1799 |
{ |
| 3176 |
06 Mar 15 |
olle |
1800 |
json.writeJSONString(resp.getWriter()); |
| 3176 |
06 Mar 15 |
olle |
1801 |
} |
| 3176 |
06 Mar 15 |
olle |
1802 |
} |
| 3176 |
06 Mar 15 |
olle |
1803 |
|
| 3176 |
06 Mar 15 |
olle |
1804 |
} |
| 3176 |
06 Mar 15 |
olle |
1805 |
|
| 3440 |
17 Jul 15 |
olle |
1806 |
/** |
| 3440 |
17 Jul 15 |
olle |
* Returns a JSONArray of item lists. |
| 3440 |
17 Jul 15 |
olle |
1808 |
* |
| 3440 |
17 Jul 15 |
olle |
* @param dc DbControl The DbControl to use. |
| 3440 |
17 Jul 15 |
olle |
* @param processed Boolean Flag indicating whether only processed or unprocessed item lists should be included. `null` gets both types. |
| 3440 |
17 Jul 15 |
olle |
* @param orderDesc Boolean Flag indicating whether ordering should be descendant. Default is `false`. |
| 3644 |
03 Dec 15 |
olle |
* @param anItemNotOnLibPlate Boolean Flag indicating that item list should be included if one item is without FPA child. |
| 3719 |
22 Jan 16 |
olle |
* @param ignoreQpcrBranch Boolean Flag indicating that DNA extracts marked for qPCR should be ignored when checking if one item is without FPA child. |
| 3440 |
17 Jul 15 |
olle |
* @return JSONArray A JSONArray with item lists. |
| 3440 |
17 Jul 15 |
olle |
1815 |
*/ |
| 3719 |
22 Jan 16 |
olle |
1816 |
private JSONArray fetchStartItemLists(DbControl dc, Boolean processed, Boolean orderDesc, Boolean anItemNotOnLibPlate, Boolean ignoreQpcrBranch) |
| 3440 |
17 Jul 15 |
olle |
1817 |
{ |
| 3440 |
17 Jul 15 |
olle |
1818 |
/* |
| 3440 |
17 Jul 15 |
olle |
Find start item lists. Order by item list name. |
| 3440 |
17 Jul 15 |
olle |
1820 |
*/ |
| 4150 |
03 Oct 16 |
olle |
1821 |
int activeProjectId = dc.getSessionControl().getActiveProjectId(); |
| 4150 |
03 Oct 16 |
olle |
1822 |
String prefix = Meludi.fetchStartListItemPrefix(activeProjectId); |
| 3440 |
17 Jul 15 |
olle |
// Default ordering is ascending |
| 3440 |
17 Jul 15 |
olle |
1824 |
if (orderDesc == null) |
| 3440 |
17 Jul 15 |
olle |
1825 |
{ |
| 3440 |
17 Jul 15 |
olle |
1826 |
orderDesc = false; |
| 3440 |
17 Jul 15 |
olle |
1827 |
} |
| 3644 |
03 Dec 15 |
olle |
1828 |
if (anItemNotOnLibPlate == null) |
| 3644 |
03 Dec 15 |
olle |
1829 |
{ |
| 3644 |
03 Dec 15 |
olle |
1830 |
anItemNotOnLibPlate = false; |
| 3644 |
03 Dec 15 |
olle |
1831 |
} |
| 3719 |
22 Jan 16 |
olle |
1832 |
if (ignoreQpcrBranch == null) |
| 3719 |
22 Jan 16 |
olle |
1833 |
{ |
| 3719 |
22 Jan 16 |
olle |
1834 |
ignoreQpcrBranch = false; |
| 3719 |
22 Jan 16 |
olle |
1835 |
} |
| 3440 |
17 Jul 15 |
olle |
1836 |
List<ItemList> startItemLists = null; |
| 3440 |
17 Jul 15 |
olle |
1837 |
if (processed == null) |
| 3440 |
17 Jul 15 |
olle |
1838 |
{ |
| 3440 |
17 Jul 15 |
olle |
1839 |
startItemLists = StartList.findByPrefix(dc, |
| 3440 |
17 Jul 15 |
olle |
1840 |
prefix, orderDesc); |
| 3440 |
17 Jul 15 |
olle |
1841 |
} |
| 3440 |
17 Jul 15 |
olle |
1842 |
else |
| 3440 |
17 Jul 15 |
olle |
1843 |
{ |
| 3440 |
17 Jul 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3440 |
17 Jul 15 |
olle |
1845 |
SnapshotManager manager = new SnapshotManager(); |
| 3440 |
17 Jul 15 |
olle |
1846 |
startItemLists = StartList.findActiveByPrefix(dc, |
| 3440 |
17 Jul 15 |
olle |
1847 |
manager, prefix, orderDesc); |
| 3440 |
17 Jul 15 |
olle |
1848 |
} |
| 3440 |
17 Jul 15 |
olle |
1849 |
|
| 3440 |
17 Jul 15 |
olle |
1850 |
JSONArray jsonItemLists = new JSONArray(); |
| 3440 |
17 Jul 15 |
olle |
1851 |
|
| 3440 |
17 Jul 15 |
olle |
1852 |
for (ItemList itemList : startItemLists) |
| 3440 |
17 Jul 15 |
olle |
1853 |
{ |
| 3440 |
17 Jul 15 |
olle |
1854 |
Date extractionDate = null; |
| 3440 |
17 Jul 15 |
olle |
1855 |
if (itemList != null) |
| 3440 |
17 Jul 15 |
olle |
1856 |
{ |
| 3440 |
17 Jul 15 |
olle |
// Check if item list should be included |
| 3440 |
17 Jul 15 |
olle |
1858 |
boolean includeItemList = false; |
| 3440 |
17 Jul 15 |
olle |
1859 |
if (processed == null) |
| 3440 |
17 Jul 15 |
olle |
1860 |
{ |
| 3440 |
17 Jul 15 |
olle |
1861 |
includeItemList = true; |
| 3440 |
17 Jul 15 |
olle |
1862 |
} |
| 3440 |
17 Jul 15 |
olle |
1863 |
else |
| 3440 |
17 Jul 15 |
olle |
1864 |
{ |
| 3440 |
17 Jul 15 |
olle |
1865 |
Boolean isProcessed = (Boolean) Annotationtype.SAMPLE_PREP_LIST_IS_PROCESSED.getAnnotationValue(dc, itemList); |
| 3440 |
17 Jul 15 |
olle |
1866 |
if (processed) |
| 3440 |
17 Jul 15 |
olle |
1867 |
{ |
| 3440 |
17 Jul 15 |
olle |
1868 |
if (isProcessed != null && isProcessed) |
| 3440 |
17 Jul 15 |
olle |
1869 |
{ |
| 3440 |
17 Jul 15 |
olle |
1870 |
includeItemList = true; |
| 3440 |
17 Jul 15 |
olle |
1871 |
} |
| 3440 |
17 Jul 15 |
olle |
1872 |
} |
| 3440 |
17 Jul 15 |
olle |
1873 |
else |
| 3440 |
17 Jul 15 |
olle |
1874 |
{ |
| 3440 |
17 Jul 15 |
olle |
1875 |
if (isProcessed == null || !isProcessed) |
| 3440 |
17 Jul 15 |
olle |
1876 |
{ |
| 3440 |
17 Jul 15 |
olle |
1877 |
includeItemList = true; |
| 3440 |
17 Jul 15 |
olle |
1878 |
} |
| 3440 |
17 Jul 15 |
olle |
1879 |
} |
| 3440 |
17 Jul 15 |
olle |
1880 |
} |
| 3644 |
03 Dec 15 |
olle |
1881 |
if (includeItemList && anItemNotOnLibPlate) |
| 3644 |
03 Dec 15 |
olle |
1882 |
{ |
| 3644 |
03 Dec 15 |
olle |
// Check if all DNA extract items in list have FPA child extracts |
| 3644 |
03 Dec 15 |
olle |
1884 |
boolean oneItemWithoutFpaChild = false; |
| 3644 |
03 Dec 15 |
olle |
// Construct a query to get all member extract items in the item list, sorted alphabetically after name |
| 3644 |
03 Dec 15 |
olle |
1886 |
ItemQuery<Extract> query = (ItemQuery<Extract>)itemList.getMembers(); |
| 3644 |
03 Dec 15 |
olle |
1887 |
query.include(Include.ALL); |
| 3644 |
03 Dec 15 |
olle |
1888 |
query.order(Orders.asc(Hql.property("name"))); |
| 3644 |
03 Dec 15 |
olle |
1889 |
List<Extract> extractList = query.list(dc); |
| 3644 |
03 Dec 15 |
olle |
1890 |
for (int i = 0; i < extractList.size() && !oneItemWithoutFpaChild; i++) |
| 3644 |
03 Dec 15 |
olle |
1891 |
{ |
| 3644 |
03 Dec 15 |
olle |
1892 |
Extract e = (Extract) extractList.get(i); |
| 3719 |
22 Jan 16 |
olle |
1893 |
|
| 3719 |
22 Jan 16 |
olle |
// Check if DNA extracts marked for qPCR processing should be ignored |
| 3719 |
22 Jan 16 |
olle |
1895 |
if (ignoreQpcrBranch) |
| 3719 |
22 Jan 16 |
olle |
1896 |
{ |
| 3719 |
22 Jan 16 |
olle |
// Ignore DNA extracts marked for qPCR processing |
| 3719 |
22 Jan 16 |
olle |
1898 |
Boolean markedForQPcr = (Boolean) Annotationtype.QPCR_BRANCH.getAnnotationValue(dc, e); |
| 3719 |
22 Jan 16 |
olle |
1899 |
if (markedForQPcr == null || !markedForQPcr) |
| 3719 |
22 Jan 16 |
olle |
1900 |
{ |
| 3719 |
22 Jan 16 |
olle |
1901 |
oneItemWithoutFpaChild = dnaHasNoFpaChild(dc, e); |
| 3719 |
22 Jan 16 |
olle |
1902 |
} |
| 3719 |
22 Jan 16 |
olle |
1903 |
} |
| 3719 |
22 Jan 16 |
olle |
1904 |
else |
| 3719 |
22 Jan 16 |
olle |
1905 |
{ |
| 3719 |
22 Jan 16 |
olle |
1906 |
oneItemWithoutFpaChild = dnaHasNoFpaChild(dc, e); |
| 3719 |
22 Jan 16 |
olle |
1907 |
} |
| 3644 |
03 Dec 15 |
olle |
1908 |
} |
| 3644 |
03 Dec 15 |
olle |
1909 |
if (!oneItemWithoutFpaChild) |
| 3644 |
03 Dec 15 |
olle |
1910 |
{ |
| 3644 |
03 Dec 15 |
olle |
1911 |
includeItemList = false; |
| 3644 |
03 Dec 15 |
olle |
1912 |
} |
| 3644 |
03 Dec 15 |
olle |
1913 |
} |
| 3440 |
17 Jul 15 |
olle |
1914 |
if (includeItemList) |
| 3440 |
17 Jul 15 |
olle |
1915 |
{ |
| 3440 |
17 Jul 15 |
olle |
1916 |
extractionDate = (Date) Annotationtype.LIST_EXTRACTION_DATE.getAnnotationValue(dc, itemList); |
| 3440 |
17 Jul 15 |
olle |
1917 |
StartList sl = new StartList(itemList); |
| 3440 |
17 Jul 15 |
olle |
1918 |
List<String> itemNameList = sl.fetchExtractSourceNameListFromItemList(dc); |
| 3440 |
17 Jul 15 |
olle |
1919 |
JSONObject jsonItemList = sl.asJSONObject(); |
| 3440 |
17 Jul 15 |
olle |
1920 |
jsonItemList.put("sourceItemNames", itemNameList); |
| 3440 |
17 Jul 15 |
olle |
1921 |
jsonItemList.put("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(extractionDate)); |
| 3440 |
17 Jul 15 |
olle |
// Get number of MeLuDI and extra material items in source extract item list |
| 3440 |
17 Jul 15 |
olle |
1923 |
int numMeludiItems = 0; |
| 3440 |
17 Jul 15 |
olle |
1924 |
int numExtraItems = 0; |
| 3440 |
17 Jul 15 |
olle |
1925 |
for (String itemName: itemNameList) |
| 3440 |
17 Jul 15 |
olle |
1926 |
{ |
| 4150 |
03 Oct 16 |
olle |
1927 |
if (Meludi.itemIsMeludiItem(itemName, activeProjectId)) |
| 3440 |
17 Jul 15 |
olle |
1928 |
{ |
| 3440 |
17 Jul 15 |
olle |
1929 |
numMeludiItems++; |
| 3440 |
17 Jul 15 |
olle |
1930 |
} |
| 3440 |
17 Jul 15 |
olle |
1931 |
else |
| 3440 |
17 Jul 15 |
olle |
1932 |
{ |
| 3440 |
17 Jul 15 |
olle |
1933 |
numExtraItems++; |
| 3440 |
17 Jul 15 |
olle |
1934 |
} |
| 3440 |
17 Jul 15 |
olle |
1935 |
} |
| 3440 |
17 Jul 15 |
olle |
1936 |
jsonItemList.put("numMeludiItems", numMeludiItems); |
| 3440 |
17 Jul 15 |
olle |
1937 |
jsonItemList.put("numExtraItems", numExtraItems); |
| 3440 |
17 Jul 15 |
olle |
1938 |
// |
| 3440 |
17 Jul 15 |
olle |
1939 |
jsonItemLists.add(jsonItemList); |
| 3440 |
17 Jul 15 |
olle |
1940 |
} |
| 3440 |
17 Jul 15 |
olle |
1941 |
} |
| 3440 |
17 Jul 15 |
olle |
1942 |
} |
| 3440 |
17 Jul 15 |
olle |
1943 |
|
| 3440 |
17 Jul 15 |
olle |
1944 |
return jsonItemLists; |
| 3440 |
17 Jul 15 |
olle |
1945 |
} |
| 3440 |
17 Jul 15 |
olle |
1946 |
|
| 3644 |
03 Dec 15 |
olle |
1947 |
/** |
| 3644 |
03 Dec 15 |
olle |
* Checks whether an extract is of type DNA and has no FPA child items. |
| 3644 |
03 Dec 15 |
olle |
1949 |
* |
| 3644 |
03 Dec 15 |
olle |
* @param dc DbControl The DbControl to use. |
| 3644 |
03 Dec 15 |
olle |
* @param e Extract The extract to check. |
| 3644 |
03 Dec 15 |
olle |
* @return boolean Returns `true` if the extract is of type DNA and has no FPA child items, else false |
| 3644 |
03 Dec 15 |
olle |
1953 |
*/ |
| 3644 |
03 Dec 15 |
olle |
1954 |
private boolean dnaHasNoFpaChild(DbControl dc, Extract e) |
| 3644 |
03 Dec 15 |
olle |
1955 |
{ |
| 3644 |
03 Dec 15 |
olle |
1956 |
boolean hasNoFpaChild = false; |
| 3644 |
03 Dec 15 |
olle |
1957 |
if (e != null) |
| 3644 |
03 Dec 15 |
olle |
1958 |
{ |
| 3644 |
03 Dec 15 |
olle |
1959 |
if (Meludi.itemIsDna(e.getName())) |
| 3644 |
03 Dec 15 |
olle |
1960 |
{ |
| 3644 |
03 Dec 15 |
olle |
1961 |
ItemQuery<Extract> childQuery = e.getChildExtracts(); |
| 3644 |
03 Dec 15 |
olle |
1962 |
List<Extract> childExtracts = childQuery.list(dc); |
| 3644 |
03 Dec 15 |
olle |
1963 |
if (childExtracts == null) |
| 3644 |
03 Dec 15 |
olle |
1964 |
{ |
| 3644 |
03 Dec 15 |
olle |
1965 |
hasNoFpaChild = true; |
| 3644 |
03 Dec 15 |
olle |
1966 |
} |
| 3644 |
03 Dec 15 |
olle |
1967 |
else |
| 3644 |
03 Dec 15 |
olle |
1968 |
{ |
| 3644 |
03 Dec 15 |
olle |
// Search for FPA aliquot child extracts |
| 3644 |
03 Dec 15 |
olle |
1970 |
boolean fpaAliquotFound = false; |
| 3644 |
03 Dec 15 |
olle |
1971 |
for (int j = 0; j < childExtracts.size() && !fpaAliquotFound; j++) |
| 3644 |
03 Dec 15 |
olle |
1972 |
{ |
| 3644 |
03 Dec 15 |
olle |
1973 |
Extract childExtract = (Extract) childExtracts.get(j); |
| 3644 |
03 Dec 15 |
olle |
1974 |
String childName = childExtract.getName(); |
| 3644 |
03 Dec 15 |
olle |
1975 |
if (childName.endsWith(".fpa")) |
| 3644 |
03 Dec 15 |
olle |
1976 |
{ |
| 3644 |
03 Dec 15 |
olle |
1977 |
fpaAliquotFound = true; |
| 3644 |
03 Dec 15 |
olle |
1978 |
} |
| 3644 |
03 Dec 15 |
olle |
1979 |
} |
| 3644 |
03 Dec 15 |
olle |
1980 |
if (!fpaAliquotFound) |
| 3644 |
03 Dec 15 |
olle |
1981 |
{ |
| 3644 |
03 Dec 15 |
olle |
1982 |
hasNoFpaChild = true; |
| 3644 |
03 Dec 15 |
olle |
1983 |
} |
| 3644 |
03 Dec 15 |
olle |
1984 |
} |
| 3644 |
03 Dec 15 |
olle |
1985 |
} |
| 3644 |
03 Dec 15 |
olle |
1986 |
} |
| 3644 |
03 Dec 15 |
olle |
1987 |
return hasNoFpaChild; |
| 3644 |
03 Dec 15 |
olle |
1988 |
} |
| 3644 |
03 Dec 15 |
olle |
1989 |
|
| 3176 |
06 Mar 15 |
olle |
1990 |
private String getPlateRowId(int row) |
| 3176 |
06 Mar 15 |
olle |
1991 |
{ |
| 3176 |
06 Mar 15 |
olle |
1992 |
String[] idArr = {"A","B","C","D","E","F","G","H"}; |
| 3176 |
06 Mar 15 |
olle |
1993 |
String rowId = null; |
| 3176 |
06 Mar 15 |
olle |
1994 |
if (row >= 0 && row < 8) |
| 3176 |
06 Mar 15 |
olle |
1995 |
{ |
| 3176 |
06 Mar 15 |
olle |
1996 |
rowId = idArr[row]; |
| 3176 |
06 Mar 15 |
olle |
1997 |
} |
| 3176 |
06 Mar 15 |
olle |
1998 |
return rowId; |
| 3176 |
06 Mar 15 |
olle |
1999 |
} |
| 3176 |
06 Mar 15 |
olle |
2000 |
|
| 3318 |
08 May 15 |
olle |
2001 |
private void loadSpecimenInfo(DbControl dc, SnapshotManager manager, SpecimenTube sp) |
| 3225 |
02 Apr 15 |
olle |
2002 |
{ |
| 3225 |
02 Apr 15 |
olle |
2003 |
Sample s = sp.getSample(); |
| 3225 |
02 Apr 15 |
olle |
2004 |
BioMaterialEvent created = s.getCreationEvent(); |
| 3225 |
02 Apr 15 |
olle |
2005 |
|
| 3225 |
02 Apr 15 |
olle |
2006 |
sp.loadBioPlateLocation(); |
| 3225 |
02 Apr 15 |
olle |
2007 |
sp.setAnnotation("registrationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(s.getEntryDate())); |
| 3225 |
02 Apr 15 |
olle |
2008 |
sp.setAnnotation("editable", s.hasPermission(Permission.WRITE)); |
| 3318 |
08 May 15 |
olle |
2009 |
sp.setAnnotation("specimenType", fetchSpecimenType(dc, manager, s)); |
| 3225 |
02 Apr 15 |
olle |
2010 |
Float usedQuantity = null; |
| 3225 |
02 Apr 15 |
olle |
2011 |
if (s.getParent() instanceof Sample) |
| 3225 |
02 Apr 15 |
olle |
2012 |
{ |
| 3225 |
02 Apr 15 |
olle |
2013 |
usedQuantity = created.getUsedQuantity(s); |
| 3225 |
02 Apr 15 |
olle |
2014 |
} |
| 3225 |
02 Apr 15 |
olle |
2015 |
sp.setAnnotation("usedQuantity", usedQuantity); |
| 3225 |
02 Apr 15 |
olle |
2016 |
sp.setAnnotation("originalQuantity", s.getOriginalQuantity()); |
| 3225 |
02 Apr 15 |
olle |
2017 |
sp.setAnnotation("remainingQuantity", s.getRemainingQuantity()); |
| 3225 |
02 Apr 15 |
olle |
2018 |
sp.setAnnotation("description", s.getDescription()); |
| 3225 |
02 Apr 15 |
olle |
2019 |
|
| 3225 |
02 Apr 15 |
olle |
2020 |
sp.loadAnnotations(dc, "arrivalDate", Annotationtype.ARRIVAL_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3225 |
02 Apr 15 |
olle |
2021 |
sp.loadAnnotations(dc, "samplingDate", Annotationtype.SAMPLING_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3225 |
02 Apr 15 |
olle |
2022 |
sp.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT, null); |
| 3225 |
02 Apr 15 |
olle |
2023 |
sp.loadAnnotations(dc, "otherPathNote", Annotationtype.OTHER_PATH_NOTE, null); |
| 3225 |
02 Apr 15 |
olle |
2024 |
sp.loadAnnotations(dc, "viableTumourCellsPercent", Annotationtype.VIABLE_TUMOUR_CELLS_PERCENT, null); |
| 3225 |
02 Apr 15 |
olle |
2025 |
sp.loadAnnotations(dc, "nofSections", Annotationtype.NOF_SECTIONS, null); |
| 3225 |
02 Apr 15 |
olle |
2026 |
} |
| 3225 |
02 Apr 15 |
olle |
2027 |
|
| 3318 |
08 May 15 |
olle |
2028 |
private void loadRnaInfo(DbControl dc, SnapshotManager manager, Rna rna) |
| 3225 |
02 Apr 15 |
olle |
2029 |
{ |
| 3225 |
02 Apr 15 |
olle |
2030 |
Extract e = rna.getExtract(); |
| 3225 |
02 Apr 15 |
olle |
2031 |
BioMaterialEvent created = e.getCreationEvent(); |
| 3225 |
02 Apr 15 |
olle |
2032 |
|
| 3225 |
02 Apr 15 |
olle |
2033 |
rna.loadBioPlateLocation(); |
| 3225 |
02 Apr 15 |
olle |
2034 |
rna.setAnnotation("registrationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate())); |
| 3225 |
02 Apr 15 |
olle |
2035 |
rna.setAnnotation("editable", e.hasPermission(Permission.WRITE)); |
| 3318 |
08 May 15 |
olle |
2036 |
rna.setAnnotation("specimenType", fetchSpecimenTypeExtract(dc, manager, e)); |
| 3225 |
02 Apr 15 |
olle |
2037 |
Float usedQuantity = null; |
| 3225 |
02 Apr 15 |
olle |
2038 |
if (e.getParent() instanceof Sample) |
| 3225 |
02 Apr 15 |
olle |
2039 |
{ |
| 3225 |
02 Apr 15 |
olle |
2040 |
usedQuantity = created.getUsedQuantity((Sample)e.getParent()); |
| 3225 |
02 Apr 15 |
olle |
2041 |
} |
| 3225 |
02 Apr 15 |
olle |
2042 |
else if (e.getParent() instanceof Extract) |
| 3225 |
02 Apr 15 |
olle |
2043 |
{ |
| 3225 |
02 Apr 15 |
olle |
2044 |
usedQuantity = created.getUsedQuantity((Extract)e.getParent()); |
| 3225 |
02 Apr 15 |
olle |
2045 |
} |
| 3225 |
02 Apr 15 |
olle |
2046 |
rna.setAnnotation("usedQuantity", usedQuantity); |
| 3225 |
02 Apr 15 |
olle |
2047 |
rna.setAnnotation("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(created.getEventDate())); |
| 3225 |
02 Apr 15 |
olle |
2048 |
rna.setAnnotation("extractionProtocol", JsonUtil.getProtocolAsJSON(created.getProtocol())); |
| 3225 |
02 Apr 15 |
olle |
2049 |
rna.setAnnotation("originalQuantity", e.getOriginalQuantity()); |
| 3225 |
02 Apr 15 |
olle |
2050 |
rna.setAnnotation("remainingQuantity", e.getRemainingQuantity()); |
| 3225 |
02 Apr 15 |
olle |
2051 |
rna.setAnnotation("description", e.getDescription()); |
| 3225 |
02 Apr 15 |
olle |
2052 |
|
| 3318 |
08 May 15 |
olle |
2053 |
rna.loadAnnotations(dc, "arrivalDate", Annotationtype.ARRIVAL_DATE_EXTRACT, Meludi.CONVERTER_DATE_TO_STRING); |
| 3318 |
08 May 15 |
olle |
2054 |
rna.loadAnnotations(dc, "samplingDate", Annotationtype.SAMPLING_DATE_EXTRACT, Meludi.CONVERTER_DATE_TO_STRING); |
| 3318 |
08 May 15 |
olle |
2055 |
rna.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT_EXTRACT, null); |
| 3318 |
08 May 15 |
olle |
2056 |
rna.loadAnnotations(dc, "viableTumourCellsPercent", Annotationtype.VIABLE_TUMOUR_CELLS_PERCENT_EXTRACT, null); |
| 3318 |
08 May 15 |
olle |
2057 |
|
| 3225 |
02 Apr 15 |
olle |
2058 |
rna.loadAnnotations(dc, "isolationDate", Annotationtype.ISOLATION_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3501 |
21 Sep 15 |
olle |
2059 |
rna.loadAnnotations(dc, "extractionOperator", Annotationtype.EXTRACTION_OPERATOR, null); |
| 3225 |
02 Apr 15 |
olle |
2060 |
rna.loadAnnotations(dc, "qiacubeDate", Annotationtype.QIACUBE_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3501 |
21 Sep 15 |
olle |
2061 |
rna.loadAnnotations(dc, "qiacubeOperator", Annotationtype.QIACUBE_OPERATOR, null); |
| 3225 |
02 Apr 15 |
olle |
2062 |
rna.loadAnnotations(dc, "qiacubeInstrumentPrefix", Annotationtype.QIACUBE_INSTRUMENT_PREFIX, null); |
| 3225 |
02 Apr 15 |
olle |
2063 |
rna.loadAnnotations(dc, "qiacubePosition", Annotationtype.QIACUBE_POSITION, null); |
| 3225 |
02 Apr 15 |
olle |
2064 |
rna.loadAnnotations(dc, "qiacubeRunNo", Annotationtype.QIACUBE_RUN_NO, null); |
| 3225 |
02 Apr 15 |
olle |
2065 |
rna.loadAnnotations(dc, "ndConc", Annotationtype.ND_CONC, null); |
| 3225 |
02 Apr 15 |
olle |
2066 |
rna.loadAnnotations(dc, "nd260by230", Annotationtype.ND_260_BY_230, null); |
| 3225 |
02 Apr 15 |
olle |
2067 |
rna.loadAnnotations(dc, "nd260by280", Annotationtype.ND_260_BY_280, null); |
| 3225 |
02 Apr 15 |
olle |
2068 |
rna.loadAnnotations(dc, "qubitConc", Annotationtype.QUBIT_CONC, null); |
| 3225 |
02 Apr 15 |
olle |
2069 |
rna.loadAnnotations(dc, "deltaCt", Annotationtype.DELTA_CT, null); |
| 3225 |
02 Apr 15 |
olle |
// Specimen reagents |
| 3225 |
02 Apr 15 |
olle |
2071 |
rna.loadAnnotations(dc, "xyleneSpecimen", Annotationtype.XYLENE_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
2072 |
rna.loadAnnotations(dc, "etoh995Specimen", Annotationtype.ETOH995_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
2073 |
rna.loadAnnotations(dc, "bufferPkdSpecimen", Annotationtype.BUFFER_PKD_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
2074 |
rna.loadAnnotations(dc, "bufferAtlSpecimen", Annotationtype.BUFFER_ATL_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
2075 |
rna.loadAnnotations(dc, "proteinaseKSpecimen", Annotationtype.PROTEINASE_K_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
2076 |
rna.loadAnnotations(dc, "rnaseASpecimen", Annotationtype.RNASE_A_SPECIMEN, null); |
| 3225 |
02 Apr 15 |
olle |
// QIAcube reagents |
| 3225 |
02 Apr 15 |
olle |
2078 |
rna.loadAnnotations(dc, "allPrepFfpeKit", Annotationtype.ALLPREP_FFPE_KIT, null); |
| 3225 |
02 Apr 15 |
olle |
2079 |
rna.loadAnnotations(dc, "etoh995", Annotationtype.ETOH995, null); |
| 3225 |
02 Apr 15 |
olle |
2080 |
rna.loadAnnotations(dc, "bufferRlt", Annotationtype.BUFFER_RLT, null); |
| 3225 |
02 Apr 15 |
olle |
2081 |
rna.loadAnnotations(dc, "bufferFrn", Annotationtype.BUFFER_FRN, null); |
| 3225 |
02 Apr 15 |
olle |
2082 |
rna.loadAnnotations(dc, "bufferRpe", Annotationtype.BUFFER_RPE, null); |
| 3225 |
02 Apr 15 |
olle |
2083 |
rna.loadAnnotations(dc, "bufferAl", Annotationtype.BUFFER_AL, null); |
| 3225 |
02 Apr 15 |
olle |
2084 |
rna.loadAnnotations(dc, "bufferAw1", Annotationtype.BUFFER_AW1, null); |
| 3225 |
02 Apr 15 |
olle |
2085 |
rna.loadAnnotations(dc, "bufferAw2", Annotationtype.BUFFER_AW2, null); |
| 3225 |
02 Apr 15 |
olle |
2086 |
rna.loadAnnotations(dc, "bufferAte", Annotationtype.BUFFER_ATE, null); |
| 3225 |
02 Apr 15 |
olle |
2087 |
rna.loadAnnotations(dc, "bufferRdd", Annotationtype.BUFFER_RDD, null); |
| 3225 |
02 Apr 15 |
olle |
2088 |
rna.loadAnnotations(dc, "rnaseFreeWater", Annotationtype.RNASE_FREE_WATER, null); |
| 3225 |
02 Apr 15 |
olle |
2089 |
rna.loadAnnotations(dc, "dnaseMix", Annotationtype.DNASE_MIX, null); |
| 3225 |
02 Apr 15 |
olle |
2090 |
rna.loadAnnotations(dc, "rneasyMinEluteSpinColumn", Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL, null); |
| 3324 |
11 May 15 |
olle |
2091 |
rna.loadAnnotations(dc, "qiaampMinEluteSpinColumn", Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL, null); |
| 3324 |
11 May 15 |
olle |
2092 |
rna.loadAnnotations(dc, "kapaSybrFast", Annotationtype.KAPA_SYBR_FAST, null); |
| 3324 |
11 May 15 |
olle |
2093 |
rna.loadAnnotations(dc, "qualityControlPrimersQcpRgt", Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT, null); |
| 3438 |
03 Jul 15 |
olle |
2094 |
rna.loadAnnotations(dc, "qualityControlTemplateQct", Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT, null); |
| 3324 |
11 May 15 |
olle |
2095 |
rna.loadAnnotations(dc, "qubitDnaHighSens", Annotationtype.QUBIT_DNA_HIGH_SENS, null); |
| 3324 |
11 May 15 |
olle |
2096 |
rna.loadAnnotations(dc, "qubitDnaBroadRange", Annotationtype.QUBIT_DNA_BROAD_RANGE, null); |
| 3225 |
02 Apr 15 |
olle |
2097 |
} |
| 3225 |
02 Apr 15 |
olle |
2098 |
|
| 3318 |
08 May 15 |
olle |
2099 |
private void loadDnaInfo(DbControl dc, SnapshotManager manager, Dna dna) |
| 3176 |
06 Mar 15 |
olle |
2100 |
{ |
| 3176 |
06 Mar 15 |
olle |
2101 |
Extract e = dna.getExtract(); |
| 3176 |
06 Mar 15 |
olle |
2102 |
BioMaterialEvent created = e.getCreationEvent(); |
| 3176 |
06 Mar 15 |
olle |
2103 |
|
| 3176 |
06 Mar 15 |
olle |
2104 |
dna.loadBioPlateLocation(); |
| 3176 |
06 Mar 15 |
olle |
2105 |
dna.setAnnotation("registrationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate())); |
| 3176 |
06 Mar 15 |
olle |
2106 |
dna.setAnnotation("editable", e.hasPermission(Permission.WRITE)); |
| 3318 |
08 May 15 |
olle |
2107 |
dna.setAnnotation("specimenType", fetchSpecimenTypeExtract(dc, manager, e)); |
| 3176 |
06 Mar 15 |
olle |
2108 |
Float usedQuantity = null; |
| 3176 |
06 Mar 15 |
olle |
2109 |
if (e.getParent() instanceof Sample) |
| 3176 |
06 Mar 15 |
olle |
2110 |
{ |
| 3176 |
06 Mar 15 |
olle |
2111 |
usedQuantity = created.getUsedQuantity((Sample)e.getParent()); |
| 3176 |
06 Mar 15 |
olle |
2112 |
} |
| 3176 |
06 Mar 15 |
olle |
2113 |
else if (e.getParent() instanceof Extract) |
| 3176 |
06 Mar 15 |
olle |
2114 |
{ |
| 3176 |
06 Mar 15 |
olle |
2115 |
usedQuantity = created.getUsedQuantity((Extract)e.getParent()); |
| 3176 |
06 Mar 15 |
olle |
2116 |
} |
| 3176 |
06 Mar 15 |
olle |
2117 |
dna.setAnnotation("usedQuantity", usedQuantity); |
| 3176 |
06 Mar 15 |
olle |
2118 |
dna.setAnnotation("extractionDate", Meludi.CONVERTER_DATE_TO_STRING.convert(created.getEventDate())); |
| 3176 |
06 Mar 15 |
olle |
2119 |
dna.setAnnotation("extractionProtocol", JsonUtil.getProtocolAsJSON(created.getProtocol())); |
| 3176 |
06 Mar 15 |
olle |
2120 |
dna.setAnnotation("originalQuantity", e.getOriginalQuantity()); |
| 3176 |
06 Mar 15 |
olle |
2121 |
dna.setAnnotation("remainingQuantity", e.getRemainingQuantity()); |
| 3176 |
06 Mar 15 |
olle |
2122 |
dna.setAnnotation("description", e.getDescription()); |
| 3176 |
06 Mar 15 |
olle |
2123 |
|
| 3318 |
08 May 15 |
olle |
2124 |
dna.loadAnnotations(dc, "arrivalDate", Annotationtype.ARRIVAL_DATE_EXTRACT, Meludi.CONVERTER_DATE_TO_STRING); |
| 3318 |
08 May 15 |
olle |
2125 |
dna.loadAnnotations(dc, "samplingDate", Annotationtype.SAMPLING_DATE_EXTRACT, Meludi.CONVERTER_DATE_TO_STRING); |
| 3318 |
08 May 15 |
olle |
2126 |
dna.loadAnnotations(dc, "operatorDeliveryComment", Annotationtype.OPERATOR_DELIVERY_COMMENT_EXTRACT, null); |
| 3318 |
08 May 15 |
olle |
2127 |
dna.loadAnnotations(dc, "viableTumourCellsPercent", Annotationtype.VIABLE_TUMOUR_CELLS_PERCENT_EXTRACT, null); |
| 3318 |
08 May 15 |
olle |
2128 |
|
| 3225 |
02 Apr 15 |
olle |
2129 |
dna.loadAnnotations(dc, "isolationDate", Annotationtype.ISOLATION_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3501 |
21 Sep 15 |
olle |
2130 |
dna.loadAnnotations(dc, "extractionOperator", Annotationtype.EXTRACTION_OPERATOR, null); |
| 3225 |
02 Apr 15 |
olle |
2131 |
dna.loadAnnotations(dc, "qiacubeDate", Annotationtype.QIACUBE_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 3501 |
21 Sep 15 |
olle |
2132 |
dna.loadAnnotations(dc, "qiacubeOperator", Annotationtype.QIACUBE_OPERATOR, null); |
| 3225 |
02 Apr 15 |
olle |
2133 |
dna.loadAnnotations(dc, "qiacubeInstrumentPrefix", Annotationtype.QIACUBE_INSTRUMENT_PREFIX, null); |
| 3225 |
02 Apr 15 |
olle |
2134 |
dna.loadAnnotations(dc, "qiacubePosition", Annotationtype.QIACUBE_POSITION, null); |
| 3225 |
02 Apr 15 |
olle |
2135 |
dna.loadAnnotations(dc, "qiacubeRunNo", Annotationtype.QIACUBE_RUN_NO, null); |
| 3225 |
02 Apr 15 |
olle |
2136 |
dna.loadAnnotations(dc, "ndConc", Annotationtype.ND_CONC, null); |
| 3225 |
02 Apr 15 |
olle |
2137 |
dna.loadAnnotations(dc, "nd260by230", Annotationtype.ND_260_BY_230, null); |
| 3225 |
02 Apr 15 |
olle |
2138 |
dna.loadAnnotations(dc, "nd260by280", Annotationtype.ND_260_BY_280, null); |
| 3176 |
06 Mar 15 |
olle |
2139 |
dna.loadAnnotations(dc, "qubitConc", Annotationtype.QUBIT_CONC, null); |
| 3176 |
06 Mar 15 |
olle |
2140 |
dna.loadAnnotations(dc, "deltaCt", Annotationtype.DELTA_CT, null); |
| 3176 |
06 Mar 15 |
olle |
// Specimen reagents |
| 3176 |
06 Mar 15 |
olle |
2142 |
dna.loadAnnotations(dc, "xyleneSpecimen", Annotationtype.XYLENE_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
2143 |
dna.loadAnnotations(dc, "etoh995Specimen", Annotationtype.ETOH995_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
2144 |
dna.loadAnnotations(dc, "bufferPkdSpecimen", Annotationtype.BUFFER_PKD_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
2145 |
dna.loadAnnotations(dc, "bufferAtlSpecimen", Annotationtype.BUFFER_ATL_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
2146 |
dna.loadAnnotations(dc, "proteinaseKSpecimen", Annotationtype.PROTEINASE_K_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
2147 |
dna.loadAnnotations(dc, "rnaseASpecimen", Annotationtype.RNASE_A_SPECIMEN, null); |
| 3176 |
06 Mar 15 |
olle |
// QIAcube reagents |
| 3176 |
06 Mar 15 |
olle |
2149 |
dna.loadAnnotations(dc, "allPrepFfpeKit", Annotationtype.ALLPREP_FFPE_KIT, null); |
| 3176 |
06 Mar 15 |
olle |
2150 |
dna.loadAnnotations(dc, "etoh995", Annotationtype.ETOH995, null); |
| 3176 |
06 Mar 15 |
olle |
2151 |
dna.loadAnnotations(dc, "bufferRlt", Annotationtype.BUFFER_RLT, null); |
| 3176 |
06 Mar 15 |
olle |
2152 |
dna.loadAnnotations(dc, "bufferFrn", Annotationtype.BUFFER_FRN, null); |
| 3176 |
06 Mar 15 |
olle |
2153 |
dna.loadAnnotations(dc, "bufferRpe", Annotationtype.BUFFER_RPE, null); |
| 3176 |
06 Mar 15 |
olle |
2154 |
dna.loadAnnotations(dc, "bufferAl", Annotationtype.BUFFER_AL, null); |
| 3176 |
06 Mar 15 |
olle |
2155 |
dna.loadAnnotations(dc, "bufferAw1", Annotationtype.BUFFER_AW1, null); |
| 3176 |
06 Mar 15 |
olle |
2156 |
dna.loadAnnotations(dc, "bufferAw2", Annotationtype.BUFFER_AW2, null); |
| 3176 |
06 Mar 15 |
olle |
2157 |
dna.loadAnnotations(dc, "bufferAte", Annotationtype.BUFFER_ATE, null); |
| 3176 |
06 Mar 15 |
olle |
2158 |
dna.loadAnnotations(dc, "bufferRdd", Annotationtype.BUFFER_RDD, null); |
| 3176 |
06 Mar 15 |
olle |
2159 |
dna.loadAnnotations(dc, "rnaseFreeWater", Annotationtype.RNASE_FREE_WATER, null); |
| 3176 |
06 Mar 15 |
olle |
2160 |
dna.loadAnnotations(dc, "dnaseMix", Annotationtype.DNASE_MIX, null); |
| 3176 |
06 Mar 15 |
olle |
2161 |
dna.loadAnnotations(dc, "rneasyMinEluteSpinColumn", Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL, null); |
| 3324 |
11 May 15 |
olle |
2162 |
dna.loadAnnotations(dc, "qiaampMinEluteSpinColumn", Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL, null); |
| 3324 |
11 May 15 |
olle |
2163 |
dna.loadAnnotations(dc, "kapaSybrFast", Annotationtype.KAPA_SYBR_FAST, null); |
| 3324 |
11 May 15 |
olle |
2164 |
dna.loadAnnotations(dc, "qualityControlPrimersQcpRgt", Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT, null); |
| 3438 |
03 Jul 15 |
olle |
2165 |
dna.loadAnnotations(dc, "qualityControlTemplateQct", Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT, null); |
| 3324 |
11 May 15 |
olle |
2166 |
dna.loadAnnotations(dc, "qubitDnaHighSens", Annotationtype.QUBIT_DNA_HIGH_SENS, null); |
| 3324 |
11 May 15 |
olle |
2167 |
dna.loadAnnotations(dc, "qubitDnaBroadRange", Annotationtype.QUBIT_DNA_BROAD_RANGE, null); |
| 3719 |
22 Jan 16 |
olle |
// qPCR branch |
| 3719 |
22 Jan 16 |
olle |
2169 |
dna.loadAnnotations(dc, "qpcrBranch", Annotationtype.QPCR_BRANCH, null); |
| 3176 |
06 Mar 15 |
olle |
2170 |
} |
| 3176 |
06 Mar 15 |
olle |
2171 |
|
| 3176 |
06 Mar 15 |
olle |
2172 |
@SuppressWarnings("unchecked") |
| 3176 |
06 Mar 15 |
olle |
2173 |
@Override |
| 3176 |
06 Mar 15 |
olle |
2174 |
protected void doPost(HttpServletRequest req, HttpServletResponse resp) |
| 3176 |
06 Mar 15 |
olle |
2175 |
throws ServletException, IOException |
| 3176 |
06 Mar 15 |
olle |
2176 |
{ |
| 3176 |
06 Mar 15 |
olle |
2177 |
String ID = req.getParameter("ID"); |
| 3176 |
06 Mar 15 |
olle |
2178 |
String cmd = req.getParameter("cmd"); |
| 3176 |
06 Mar 15 |
olle |
2179 |
JsonUtil.setJsonResponseHeaders(resp); |
| 3176 |
06 Mar 15 |
olle |
2180 |
|
| 3176 |
06 Mar 15 |
olle |
2181 |
JSONObject json = new JSONObject(); |
| 3176 |
06 Mar 15 |
olle |
2182 |
json.put("status", "ok"); |
| 3176 |
06 Mar 15 |
olle |
2183 |
|
| 3176 |
06 Mar 15 |
olle |
2184 |
JSONArray jsonMessages = new JSONArray(); |
| 3176 |
06 Mar 15 |
olle |
2185 |
|
| 5468 |
04 Jun 19 |
olle |
//final SessionControl sc = Application.getSessionControl(ID, req.getRemoteAddr()); |
| 5744 |
20 Nov 19 |
olle |
//final SessionControl sc = Application.getSessionControl(ID, "", req.getRemoteAddr(), true); |
| 5744 |
20 Nov 19 |
olle |
2188 |
final SessionControl sc = Application.getSessionControl(ID, null, req.getRemoteAddr(), true); |
| 3176 |
06 Mar 15 |
olle |
2189 |
DbControl dc = null; |
| 3176 |
06 Mar 15 |
olle |
2190 |
try |
| 3176 |
06 Mar 15 |
olle |
2191 |
{ |
| 3180 |
17 Mar 15 |
olle |
2192 |
if ("RegisterStartPlate".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
2193 |
{ |
| 3176 |
06 Mar 15 |
olle |
2194 |
dc = sc.newDbControl(); |
| 3180 |
17 Mar 15 |
olle |
2195 |
|
| 3180 |
17 Mar 15 |
olle |
2196 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3180 |
17 Mar 15 |
olle |
2197 |
|
| 3180 |
17 Mar 15 |
olle |
2198 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3180 |
17 Mar 15 |
olle |
2199 |
String plateName = (String)jsonReq.get("startPlateName"); |
| 3180 |
17 Mar 15 |
olle |
2200 |
|
| 3180 |
17 Mar 15 |
olle |
// Get parameter values |
| 3180 |
17 Mar 15 |
olle |
2202 |
Date isolationDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("isolationDate")); |
| 3180 |
17 Mar 15 |
olle |
2203 |
Number extractionProtocolId = (Number)jsonReq.get("extractionProtocol"); |
| 3180 |
17 Mar 15 |
olle |
2204 |
Protocol extractionProtocol = extractionProtocolId != null ? Protocol.getById(dc, extractionProtocolId.intValue()) : null; |
| 3180 |
17 Mar 15 |
olle |
2205 |
String extractionProtocolName = (String)jsonReq.get("extractionProtocolName"); |
| 3180 |
17 Mar 15 |
olle |
2206 |
Number numExtraQiacubeItems = (Number)jsonReq.get("numExtraQiacubeItems"); |
| 3180 |
17 Mar 15 |
olle |
2207 |
Date qiacubeDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("qiacubeDate")); |
| 3180 |
17 Mar 15 |
olle |
2208 |
String qiacubePrimaryPrefix = (String)jsonReq.get("qiacubePrimaryPrefix"); |
| 3180 |
17 Mar 15 |
olle |
2209 |
String qiacubeSecondaryPrefix = (String)jsonReq.get("qiacubeSecondaryPrefix"); |
| 3180 |
17 Mar 15 |
olle |
2210 |
Number qiacubeRunNo = (Number)jsonReq.get("qiacubeRunNo"); |
| 3180 |
17 Mar 15 |
olle |
2211 |
String qiacubeOperator = (String)jsonReq.get("qiacubeOperator"); |
| 3180 |
17 Mar 15 |
olle |
2212 |
String allPrepFfpeKit = Values.getStringOrNull((String)jsonReq.get("allPrepFfpeKit")); |
| 3176 |
06 Mar 15 |
olle |
2213 |
|
| 3180 |
17 Mar 15 |
olle |
// Get list of extract source item names |
| 3180 |
17 Mar 15 |
olle |
2215 |
List<String> itemNameList = new ArrayList<String>(); |
| 3180 |
17 Mar 15 |
olle |
2216 |
JSONArray jsonItems = (JSONArray)jsonReq.get("items"); |
| 3180 |
17 Mar 15 |
olle |
2217 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3180 |
17 Mar 15 |
olle |
2218 |
{ |
| 3180 |
17 Mar 15 |
olle |
2219 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3180 |
17 Mar 15 |
olle |
2220 |
String itemName = (String)jsonItem.get("name"); |
| 3180 |
17 Mar 15 |
olle |
2221 |
itemNameList.add(itemName); |
| 3180 |
17 Mar 15 |
olle |
2222 |
} |
| 3180 |
17 Mar 15 |
olle |
2223 |
|
| 3245 |
14 Apr 15 |
olle |
// Get list of extra QIAcube item names |
| 3245 |
14 Apr 15 |
olle |
2225 |
List<String> extraItemNameList = new ArrayList<String>(); |
| 3245 |
14 Apr 15 |
olle |
2226 |
JSONArray jsonExtraItems = (JSONArray)jsonReq.get("extraItems"); |
| 3245 |
14 Apr 15 |
olle |
2227 |
for (int i = 0; i < jsonExtraItems.size(); ++i) |
| 3245 |
14 Apr 15 |
olle |
2228 |
{ |
| 3245 |
14 Apr 15 |
olle |
2229 |
JSONObject jsonItem = (JSONObject)jsonExtraItems.get(i); |
| 3245 |
14 Apr 15 |
olle |
2230 |
String itemName = (String)jsonItem.get("name"); |
| 3245 |
14 Apr 15 |
olle |
2231 |
extraItemNameList.add(itemName); |
| 3245 |
14 Apr 15 |
olle |
2232 |
} |
| 3245 |
14 Apr 15 |
olle |
2233 |
|
| 3180 |
17 Mar 15 |
olle |
// Create start DNA reaction plate |
| 3180 |
17 Mar 15 |
olle |
2235 |
JSONArray jsonCreatedDnaPlate = new JSONArray(); |
| 3180 |
17 Mar 15 |
olle |
2236 |
if (plateName != null && !plateName.equals("")) |
| 3180 |
17 Mar 15 |
olle |
2237 |
{ |
| 3180 |
17 Mar 15 |
olle |
2238 |
PlateGeometry geometry = BioplateType.DNA.getPlateGeometry(dc); |
| 3180 |
17 Mar 15 |
olle |
2239 |
BioPlateType plateType = BioplateType.DNA.load(dc); |
| 3180 |
17 Mar 15 |
olle |
2240 |
|
| 3180 |
17 Mar 15 |
olle |
2241 |
BioPlate dnaPlate = BioPlate.getNew(dc, geometry, plateType); |
| 3180 |
17 Mar 15 |
olle |
2242 |
dnaPlate.setName(plateName); |
| 3180 |
17 Mar 15 |
olle |
//dnaPlate.setDescription(Values.getStringOrNull((String)jsonPlate.get("comments"))); |
| 3180 |
17 Mar 15 |
olle |
//Annotationtype.POOL_SCHEMA.setAnnotationValue(dc, dnaPlate, jsonPlate.get("poolSchema")); |
| 3180 |
17 Mar 15 |
olle |
2245 |
jsonMessages.add("Created '" + dnaPlate.getName() + "' DNA reaction plate"); |
| 3233 |
09 Apr 15 |
olle |
//Annotationtype.SOURCE_ITEM_NAMES.setAnnotationValues(dc, dnaPlate, itemNameList); |
| 3233 |
09 Apr 15 |
olle |
2247 |
Annotationtype.SOURCE_ITEM_NAMES_LIST_STRING.setAnnotationValues(dc, dnaPlate, itemNameList); |
| 3180 |
17 Mar 15 |
olle |
2248 |
Annotationtype.BATCH_NUMBER_EXTRA_QIACUBE_ITEMS.setAnnotationValue(dc, dnaPlate, numExtraQiacubeItems); |
| 3245 |
14 Apr 15 |
olle |
2249 |
Annotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING.setAnnotationValues(dc, dnaPlate, extraItemNameList); |
| 3180 |
17 Mar 15 |
olle |
2250 |
Annotationtype.BATCH_ISOLATION_DATE.setAnnotationValue(dc, dnaPlate, isolationDate); |
| 3180 |
17 Mar 15 |
olle |
2251 |
Annotationtype.BATCH_EXTRACTION_PROTOCOL_ID.setAnnotationValue(dc, dnaPlate, extractionProtocolId); |
| 3180 |
17 Mar 15 |
olle |
2252 |
Annotationtype.BATCH_EXTRACTION_PROTOCOL_NAME.setAnnotationValue(dc, dnaPlate, extractionProtocolName); |
| 3180 |
17 Mar 15 |
olle |
2253 |
Annotationtype.BATCH_QIACUBE_DATE.setAnnotationValue(dc, dnaPlate, qiacubeDate); |
| 3180 |
17 Mar 15 |
olle |
2254 |
Annotationtype.BATCH_QIACUBE_PRIMARY_PREFIX.setAnnotationValue(dc, dnaPlate, qiacubePrimaryPrefix); |
| 3180 |
17 Mar 15 |
olle |
2255 |
Annotationtype.BATCH_QIACUBE_SECONDARY_PREFIX.setAnnotationValue(dc, dnaPlate, qiacubeSecondaryPrefix); |
| 3180 |
17 Mar 15 |
olle |
2256 |
Annotationtype.BATCH_QIACUBE_RUN_NO.setAnnotationValue(dc, dnaPlate, qiacubeRunNo); |
| 3180 |
17 Mar 15 |
olle |
2257 |
Annotationtype.BATCH_QIACUBE_OPERATOR.setAnnotationValue(dc, dnaPlate, qiacubeOperator); |
| 3180 |
17 Mar 15 |
olle |
2258 |
Annotationtype.BATCH_ALLPREP_FFPE_KIT.setAnnotationValue(dc, dnaPlate, allPrepFfpeKit); |
| 3180 |
17 Mar 15 |
olle |
2259 |
dc.saveItem(dnaPlate); |
| 3180 |
17 Mar 15 |
olle |
2260 |
jsonCreatedDnaPlate.add(dnaPlate.getId()); |
| 3180 |
17 Mar 15 |
olle |
2261 |
} |
| 3180 |
17 Mar 15 |
olle |
2262 |
|
| 3180 |
17 Mar 15 |
olle |
// Set original quantity for extract source item to 0,0, in order to mark them as processed |
| 3180 |
17 Mar 15 |
olle |
2264 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3180 |
17 Mar 15 |
olle |
2265 |
{ |
| 3180 |
17 Mar 15 |
olle |
2266 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3180 |
17 Mar 15 |
olle |
2267 |
String itemName = (String)jsonItem.get("name"); |
| 3180 |
17 Mar 15 |
olle |
2268 |
Number itemId = (Number)jsonItem.get("id"); |
| 3180 |
17 Mar 15 |
olle |
2269 |
Sample specimen = null; |
| 3180 |
17 Mar 15 |
olle |
2270 |
Extract dna = null; |
| 3180 |
17 Mar 15 |
olle |
2271 |
Extract rna = null; |
| 3180 |
17 Mar 15 |
olle |
2272 |
|
| 3433 |
29 Jun 15 |
olle |
2273 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2274 |
{ |
| 3180 |
17 Mar 15 |
olle |
2275 |
specimen = Sample.getById(dc, itemId.intValue()); |
| 3180 |
17 Mar 15 |
olle |
2276 |
specimen.setItemSubtype(Subtype.SPECIMEN.load(dc)); |
| 3180 |
17 Mar 15 |
olle |
2277 |
specimen.setOriginalQuantity(0.0f); |
| 3180 |
17 Mar 15 |
olle |
2278 |
} |
| 3180 |
17 Mar 15 |
olle |
2279 |
|
| 3180 |
17 Mar 15 |
olle |
// DNA |
| 3433 |
29 Jun 15 |
olle |
2281 |
if (Meludi.itemIsDna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2282 |
{ |
| 3180 |
17 Mar 15 |
olle |
2283 |
JSONObject jsonDna = (JSONObject)jsonItem.get("dna"); |
| 3180 |
17 Mar 15 |
olle |
2284 |
dna = Extract.getById(dc, itemId.intValue()); |
| 3180 |
17 Mar 15 |
olle |
2285 |
dna.setItemSubtype(Subtype.DNA.load(dc)); |
| 3180 |
17 Mar 15 |
olle |
2286 |
dna.setOriginalQuantity(0.0f); |
| 3180 |
17 Mar 15 |
olle |
2287 |
} |
| 3180 |
17 Mar 15 |
olle |
2288 |
|
| 3180 |
17 Mar 15 |
olle |
// RNA |
| 3433 |
29 Jun 15 |
olle |
2290 |
if (Meludi.itemIsRna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2291 |
{ |
| 3180 |
17 Mar 15 |
olle |
2292 |
JSONObject jsonRna = (JSONObject)jsonItem.get("rna"); |
| 3180 |
17 Mar 15 |
olle |
2293 |
rna = Extract.getById(dc, itemId.intValue()); |
| 3180 |
17 Mar 15 |
olle |
2294 |
rna.setItemSubtype(Subtype.RNA.load(dc)); |
| 3180 |
17 Mar 15 |
olle |
2295 |
rna.setOriginalQuantity(0.0f); |
| 3180 |
17 Mar 15 |
olle |
2296 |
} |
| 3180 |
17 Mar 15 |
olle |
2297 |
|
| 3180 |
17 Mar 15 |
olle |
2298 |
String msg = ""; |
| 3433 |
29 Jun 15 |
olle |
2299 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2300 |
{ |
| 3180 |
17 Mar 15 |
olle |
2301 |
msg += "Original quantity set to 0.0 for specimen " + itemName; |
| 3180 |
17 Mar 15 |
olle |
2302 |
} |
| 3433 |
29 Jun 15 |
olle |
2303 |
else if (Meludi.itemIsRna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2304 |
{ |
| 3180 |
17 Mar 15 |
olle |
2305 |
msg += "Original quantity set to 0.0 for RNA " + itemName; |
| 3180 |
17 Mar 15 |
olle |
2306 |
} |
| 3433 |
29 Jun 15 |
olle |
2307 |
else if (Meludi.itemIsDna(itemName)) |
| 3180 |
17 Mar 15 |
olle |
2308 |
{ |
| 3180 |
17 Mar 15 |
olle |
2309 |
msg += "Original quantity set to 0.0 for DNA " + itemName; |
| 3180 |
17 Mar 15 |
olle |
2310 |
} |
| 3180 |
17 Mar 15 |
olle |
2311 |
|
| 3180 |
17 Mar 15 |
olle |
2312 |
jsonMessages.add(msg); |
| 3180 |
17 Mar 15 |
olle |
2313 |
} |
| 3180 |
17 Mar 15 |
olle |
2314 |
dc.commit(); |
| 3180 |
17 Mar 15 |
olle |
2315 |
|
| 3180 |
17 Mar 15 |
olle |
2316 |
json.put("createdDnaPlate", jsonCreatedDnaPlate); |
| 3180 |
17 Mar 15 |
olle |
2317 |
} |
| 3432 |
29 Jun 15 |
olle |
2318 |
else if ("RegisterStartItemList".equals(cmd)) |
| 3432 |
29 Jun 15 |
olle |
2319 |
{ |
| 3432 |
29 Jun 15 |
olle |
2320 |
dc = sc.newDbControl(); |
| 3432 |
29 Jun 15 |
olle |
2321 |
|
| 3432 |
29 Jun 15 |
olle |
2322 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3432 |
29 Jun 15 |
olle |
2323 |
|
| 3432 |
29 Jun 15 |
olle |
2324 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3432 |
29 Jun 15 |
olle |
2325 |
String itemListName = (String)jsonReq.get("startListName"); |
| 3432 |
29 Jun 15 |
olle |
2326 |
|
| 3432 |
29 Jun 15 |
olle |
// Get parameter values |
| 3432 |
29 Jun 15 |
olle |
2328 |
Date isolationDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("isolationDate")); |
| 3501 |
21 Sep 15 |
olle |
2329 |
String extractionOperator = (String)jsonReq.get("extractionOperator"); |
| 3432 |
29 Jun 15 |
olle |
2330 |
Number extractionProtocolId = (Number)jsonReq.get("extractionProtocol"); |
| 3432 |
29 Jun 15 |
olle |
2331 |
Protocol extractionProtocol = extractionProtocolId != null ? Protocol.getById(dc, extractionProtocolId.intValue()) : null; |
| 3432 |
29 Jun 15 |
olle |
2332 |
String extractionProtocolName = (String)jsonReq.get("extractionProtocolName"); |
| 3432 |
29 Jun 15 |
olle |
2333 |
Number numExtraQiacubeItems = (Number)jsonReq.get("numExtraQiacubeItems"); |
| 3432 |
29 Jun 15 |
olle |
2334 |
Date qiacubeDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("qiacubeDate")); |
| 3501 |
21 Sep 15 |
olle |
2335 |
String qiacubeOperator = (String)jsonReq.get("qiacubeOperator"); |
| 3432 |
29 Jun 15 |
olle |
2336 |
String qiacubePrimaryPrefix = (String)jsonReq.get("qiacubePrimaryPrefix"); |
| 3432 |
29 Jun 15 |
olle |
2337 |
String qiacubeSecondaryPrefix = (String)jsonReq.get("qiacubeSecondaryPrefix"); |
| 3432 |
29 Jun 15 |
olle |
2338 |
Number qiacubeRunNo = (Number)jsonReq.get("qiacubeRunNo"); |
| 3501 |
21 Sep 15 |
olle |
2339 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2341 |
String xyleneSpecimen = Values.getStringOrNull((String)jsonReq.get("xyleneSpecimen")); |
| 3501 |
21 Sep 15 |
olle |
2342 |
String etoh995Specimen = Values.getStringOrNull((String)jsonReq.get("etoh995Specimen")); |
| 3432 |
29 Jun 15 |
olle |
2343 |
String allPrepFfpeKit = Values.getStringOrNull((String)jsonReq.get("allPrepFfpeKit")); |
| 3501 |
21 Sep 15 |
olle |
2344 |
String bufferPkdSpecimen = Values.getStringOrNull((String)jsonReq.get("bufferPkdSpecimen")); |
| 3501 |
21 Sep 15 |
olle |
2345 |
String bufferAtlSpecimen = Values.getStringOrNull((String)jsonReq.get("bufferAtlSpecimen")); |
| 3501 |
21 Sep 15 |
olle |
2346 |
String proteinaseKSpecimen = Values.getStringOrNull((String)jsonReq.get("proteinaseKSpecimen")); |
| 3501 |
21 Sep 15 |
olle |
2347 |
String rnaseASpecimen = Values.getStringOrNull((String)jsonReq.get("rnaseASpecimen")); |
| 3501 |
21 Sep 15 |
olle |
2348 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
2350 |
String etoh995 = Values.getStringOrNull((String)jsonReq.get("etoh995")); |
| 3501 |
21 Sep 15 |
olle |
2351 |
String bufferRlt = Values.getStringOrNull((String)jsonReq.get("bufferRlt")); |
| 3501 |
21 Sep 15 |
olle |
2352 |
String bufferFrn = Values.getStringOrNull((String)jsonReq.get("bufferFrn")); |
| 3501 |
21 Sep 15 |
olle |
2353 |
String bufferRpe = Values.getStringOrNull((String)jsonReq.get("bufferRpe")); |
| 3501 |
21 Sep 15 |
olle |
2354 |
String bufferAl = Values.getStringOrNull((String)jsonReq.get("bufferAl")); |
| 3501 |
21 Sep 15 |
olle |
2355 |
String bufferAw1 = Values.getStringOrNull((String)jsonReq.get("bufferAw1")); |
| 3501 |
21 Sep 15 |
olle |
2356 |
String bufferAw2 = Values.getStringOrNull((String)jsonReq.get("bufferAw2")); |
| 3501 |
21 Sep 15 |
olle |
2357 |
String bufferAte = Values.getStringOrNull((String)jsonReq.get("bufferAte")); |
| 3501 |
21 Sep 15 |
olle |
2358 |
String bufferRdd = Values.getStringOrNull((String)jsonReq.get("bufferRdd")); |
| 3501 |
21 Sep 15 |
olle |
2359 |
String rnaseFreeWater = Values.getStringOrNull((String)jsonReq.get("rnaseFreeWater")); |
| 3501 |
21 Sep 15 |
olle |
2360 |
String dnaseMix = Values.getStringOrNull((String)jsonReq.get("dnaseMix")); |
| 3501 |
21 Sep 15 |
olle |
2361 |
String rneasyMinEluteSpinColumn = Values.getStringOrNull((String)jsonReq.get("rneasyMinEluteSpinColumn")); |
| 3501 |
21 Sep 15 |
olle |
2362 |
String qiaampMinEluteSpinColumn = Values.getStringOrNull((String)jsonReq.get("qiaampMinEluteSpinColumn")); |
| 3501 |
21 Sep 15 |
olle |
2363 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
2365 |
String kapaSybrFast = Values.getStringOrNull((String)jsonReq.get("kapaSybrFast")); |
| 3501 |
21 Sep 15 |
olle |
2366 |
String qualityControlPrimersQcpRgt = Values.getStringOrNull((String)jsonReq.get("qualityControlPrimersQcpRgt")); |
| 3501 |
21 Sep 15 |
olle |
2367 |
String qualityControlTemplateQct = Values.getStringOrNull((String)jsonReq.get("qualityControlTemplateQct")); |
| 3501 |
21 Sep 15 |
olle |
2368 |
String qubitDnaHighSens = Values.getStringOrNull((String)jsonReq.get("qubitDnaHighSens")); |
| 3501 |
21 Sep 15 |
olle |
2369 |
String qubitDnaBroadRange = Values.getStringOrNull((String)jsonReq.get("qubitDnaBroadRange")); |
| 3501 |
21 Sep 15 |
olle |
2370 |
|
| 3432 |
29 Jun 15 |
olle |
// Get list of extract source item names |
| 3432 |
29 Jun 15 |
olle |
2372 |
List<String> itemNameList = new ArrayList<String>(); |
| 3432 |
29 Jun 15 |
olle |
2373 |
JSONArray jsonItems = (JSONArray)jsonReq.get("items"); |
| 3432 |
29 Jun 15 |
olle |
2374 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3432 |
29 Jun 15 |
olle |
2375 |
{ |
| 3432 |
29 Jun 15 |
olle |
2376 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3432 |
29 Jun 15 |
olle |
2377 |
String itemName = (String)jsonItem.get("name"); |
| 3432 |
29 Jun 15 |
olle |
2378 |
itemNameList.add(itemName); |
| 3432 |
29 Jun 15 |
olle |
2379 |
} |
| 3432 |
29 Jun 15 |
olle |
2380 |
|
| 3432 |
29 Jun 15 |
olle |
// Create start item list |
| 3432 |
29 Jun 15 |
olle |
2382 |
ItemList startItemList = null; |
| 3432 |
29 Jun 15 |
olle |
2383 |
JSONArray jsonCreatedStartItemList = new JSONArray(); |
| 3432 |
29 Jun 15 |
olle |
2384 |
if (itemListName != null && !itemListName.equals("")) |
| 3432 |
29 Jun 15 |
olle |
2385 |
{ |
| 3432 |
29 Jun 15 |
olle |
2386 |
startItemList = ItemList.getNew(dc, Item.EXTRACT); |
| 3432 |
29 Jun 15 |
olle |
2387 |
startItemList.setName(itemListName); |
| 3432 |
29 Jun 15 |
olle |
2388 |
jsonMessages.add("Created '" + startItemList.getName() + "' Start item list"); |
| 3432 |
29 Jun 15 |
olle |
2389 |
Annotationtype.LIST_ISOLATION_DATE.setAnnotationValue(dc, startItemList, isolationDate); |
| 3501 |
21 Sep 15 |
olle |
2390 |
Annotationtype.LIST_EXTRACTION_OPERATOR.setAnnotationValue(dc, startItemList, extractionOperator); |
| 3432 |
29 Jun 15 |
olle |
2391 |
Annotationtype.LIST_EXTRACTION_PROTOCOL_ID.setAnnotationValue(dc, startItemList, extractionProtocolId); |
| 3432 |
29 Jun 15 |
olle |
2392 |
Annotationtype.LIST_EXTRACTION_PROTOCOL_NAME.setAnnotationValue(dc, startItemList, extractionProtocolName); |
| 3432 |
29 Jun 15 |
olle |
2393 |
Annotationtype.LIST_QIACUBE_DATE.setAnnotationValue(dc, startItemList, qiacubeDate); |
| 3501 |
21 Sep 15 |
olle |
2394 |
Annotationtype.LIST_QIACUBE_OPERATOR.setAnnotationValue(dc, startItemList, qiacubeOperator); |
| 3432 |
29 Jun 15 |
olle |
2395 |
Annotationtype.LIST_QIACUBE_PRIMARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubePrimaryPrefix); |
| 3432 |
29 Jun 15 |
olle |
2396 |
Annotationtype.LIST_QIACUBE_SECONDARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubeSecondaryPrefix); |
| 3432 |
29 Jun 15 |
olle |
2397 |
Annotationtype.LIST_QIACUBE_RUN_NO.setAnnotationValue(dc, startItemList, qiacubeRunNo); |
| 3501 |
21 Sep 15 |
olle |
2398 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3432 |
29 Jun 15 |
olle |
2400 |
Annotationtype.LIST_ALLPREP_FFPE_KIT.setAnnotationValue(dc, startItemList, allPrepFfpeKit); |
| 3501 |
21 Sep 15 |
olle |
2401 |
Annotationtype.LIST_XYLENE_SPECIMEN.setAnnotationValue(dc, startItemList, xyleneSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2402 |
Annotationtype.LIST_ETOH995_SPECIMEN.setAnnotationValue(dc, startItemList, etoh995Specimen); |
| 3501 |
21 Sep 15 |
olle |
2403 |
Annotationtype.LIST_BUFFER_PKD_SPECIMEN.setAnnotationValue(dc, startItemList, bufferPkdSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2404 |
Annotationtype.LIST_BUFFER_ATL_SPECIMEN.setAnnotationValue(dc, startItemList, bufferAtlSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2405 |
Annotationtype.LIST_PROTEINASE_K_SPECIMEN.setAnnotationValue(dc, startItemList, proteinaseKSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2406 |
Annotationtype.LIST_RNASE_A_SPECIMEN.setAnnotationValue(dc, startItemList, rnaseASpecimen); |
| 3501 |
21 Sep 15 |
olle |
2407 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
2409 |
Annotationtype.LIST_ETOH995.setAnnotationValue(dc, startItemList, etoh995); |
| 3501 |
21 Sep 15 |
olle |
2410 |
Annotationtype.LIST_BUFFER_RLT.setAnnotationValue(dc, startItemList, bufferRlt); |
| 3501 |
21 Sep 15 |
olle |
2411 |
Annotationtype.LIST_BUFFER_FRN.setAnnotationValue(dc, startItemList, bufferFrn); |
| 3501 |
21 Sep 15 |
olle |
2412 |
Annotationtype.LIST_BUFFER_RPE.setAnnotationValue(dc, startItemList, bufferRpe); |
| 3501 |
21 Sep 15 |
olle |
2413 |
Annotationtype.LIST_BUFFER_AL.setAnnotationValue(dc, startItemList, bufferAl); |
| 3501 |
21 Sep 15 |
olle |
2414 |
Annotationtype.LIST_BUFFER_AW1.setAnnotationValue(dc, startItemList, bufferAw1); |
| 3501 |
21 Sep 15 |
olle |
2415 |
Annotationtype.LIST_BUFFER_AW2.setAnnotationValue(dc, startItemList, bufferAw2); |
| 3501 |
21 Sep 15 |
olle |
2416 |
Annotationtype.LIST_BUFFER_ATE.setAnnotationValue(dc, startItemList, bufferAte); |
| 3501 |
21 Sep 15 |
olle |
2417 |
Annotationtype.LIST_BUFFER_RDD.setAnnotationValue(dc, startItemList, bufferRdd); |
| 3501 |
21 Sep 15 |
olle |
2418 |
Annotationtype.LIST_RNASE_FREE_WATER.setAnnotationValue(dc, startItemList, rnaseFreeWater); |
| 3501 |
21 Sep 15 |
olle |
2419 |
Annotationtype.LIST_DNASE_MIX.setAnnotationValue(dc, startItemList, dnaseMix); |
| 3501 |
21 Sep 15 |
olle |
2420 |
Annotationtype.LIST_RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
2421 |
Annotationtype.LIST_QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, qiaampMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
2422 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
2424 |
Annotationtype.LIST_KAPA_SYBR_FAST.setAnnotationValue(dc, startItemList, kapaSybrFast); |
| 3501 |
21 Sep 15 |
olle |
2425 |
Annotationtype.LIST_QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, startItemList, qualityControlPrimersQcpRgt); |
| 3501 |
21 Sep 15 |
olle |
2426 |
Annotationtype.LIST_QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, startItemList, qualityControlTemplateQct); |
| 3501 |
21 Sep 15 |
olle |
2427 |
Annotationtype.LIST_QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, startItemList, qubitDnaHighSens); |
| 3501 |
21 Sep 15 |
olle |
2428 |
Annotationtype.LIST_QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, startItemList, qubitDnaBroadRange); |
| 3501 |
21 Sep 15 |
olle |
2429 |
|
| 3432 |
29 Jun 15 |
olle |
2430 |
dc.saveItem(startItemList); |
| 3432 |
29 Jun 15 |
olle |
2431 |
jsonCreatedStartItemList.add(startItemList.getId()); |
| 3432 |
29 Jun 15 |
olle |
2432 |
} |
| 3432 |
29 Jun 15 |
olle |
2433 |
|
| 3432 |
29 Jun 15 |
olle |
// Add input DNA/RNA extracts to start item list, and child DNA extract for specimen |
| 3432 |
29 Jun 15 |
olle |
// Set original quantity for extract source item to 0,0, in order to mark them as processed |
| 3432 |
29 Jun 15 |
olle |
2436 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3432 |
29 Jun 15 |
olle |
2437 |
{ |
| 3432 |
29 Jun 15 |
olle |
2438 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3432 |
29 Jun 15 |
olle |
2439 |
String itemName = (String)jsonItem.get("name"); |
| 3432 |
29 Jun 15 |
olle |
2440 |
Number itemId = (Number)jsonItem.get("id"); |
| 3432 |
29 Jun 15 |
olle |
2441 |
Sample specimen = null; |
| 3432 |
29 Jun 15 |
olle |
2442 |
Extract dna = null; |
| 3432 |
29 Jun 15 |
olle |
2443 |
Extract rna = null; |
| 3432 |
29 Jun 15 |
olle |
2444 |
|
| 3433 |
29 Jun 15 |
olle |
2445 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2446 |
{ |
| 3432 |
29 Jun 15 |
olle |
2447 |
specimen = Sample.getById(dc, itemId.intValue()); |
| 3432 |
29 Jun 15 |
olle |
2448 |
specimen.setItemSubtype(Subtype.SPECIMEN.load(dc)); |
| 3432 |
29 Jun 15 |
olle |
2449 |
specimen.setOriginalQuantity(0.0f); |
| 3432 |
29 Jun 15 |
olle |
// Add child DNA extract to start item list |
| 3432 |
29 Jun 15 |
olle |
2451 |
if (startItemList != null) |
| 3432 |
29 Jun 15 |
olle |
2452 |
{ |
| 3432 |
29 Jun 15 |
olle |
2453 |
Dna d = Dna.findByName(dc, itemName + ".d"); |
| 3432 |
29 Jun 15 |
olle |
2454 |
if (d == null) |
| 3432 |
29 Jun 15 |
olle |
2455 |
{ |
| 3432 |
29 Jun 15 |
olle |
2456 |
throw new InvalidDataException("Extract " + itemName + ".d" + " not found in database."); |
| 3432 |
29 Jun 15 |
olle |
2457 |
} |
| 3432 |
29 Jun 15 |
olle |
2458 |
dna = d.getExtract(); |
| 3432 |
29 Jun 15 |
olle |
2459 |
startItemList.add(dna); |
| 3432 |
29 Jun 15 |
olle |
2460 |
} |
| 3432 |
29 Jun 15 |
olle |
2461 |
} |
| 3432 |
29 Jun 15 |
olle |
2462 |
|
| 3432 |
29 Jun 15 |
olle |
// DNA |
| 3433 |
29 Jun 15 |
olle |
2464 |
if (Meludi.itemIsDna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2465 |
{ |
| 3432 |
29 Jun 15 |
olle |
2466 |
JSONObject jsonDna = (JSONObject)jsonItem.get("dna"); |
| 3432 |
29 Jun 15 |
olle |
2467 |
dna = Extract.getById(dc, itemId.intValue()); |
| 3432 |
29 Jun 15 |
olle |
2468 |
dna.setItemSubtype(Subtype.DNA.load(dc)); |
| 3432 |
29 Jun 15 |
olle |
2469 |
dna.setOriginalQuantity(0.0f); |
| 3432 |
29 Jun 15 |
olle |
// Add to start item list |
| 3432 |
29 Jun 15 |
olle |
2471 |
if (startItemList != null) |
| 3432 |
29 Jun 15 |
olle |
2472 |
{ |
| 3432 |
29 Jun 15 |
olle |
2473 |
startItemList.add(dna); |
| 3432 |
29 Jun 15 |
olle |
2474 |
} |
| 3432 |
29 Jun 15 |
olle |
2475 |
} |
| 3432 |
29 Jun 15 |
olle |
2476 |
|
| 3432 |
29 Jun 15 |
olle |
// RNA |
| 3433 |
29 Jun 15 |
olle |
2478 |
if (Meludi.itemIsRna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2479 |
{ |
| 3432 |
29 Jun 15 |
olle |
2480 |
JSONObject jsonRna = (JSONObject)jsonItem.get("rna"); |
| 3432 |
29 Jun 15 |
olle |
2481 |
rna = Extract.getById(dc, itemId.intValue()); |
| 3432 |
29 Jun 15 |
olle |
2482 |
rna.setItemSubtype(Subtype.RNA.load(dc)); |
| 3432 |
29 Jun 15 |
olle |
2483 |
rna.setOriginalQuantity(0.0f); |
| 3432 |
29 Jun 15 |
olle |
// Add to start item list |
| 3432 |
29 Jun 15 |
olle |
2485 |
if (startItemList != null) |
| 3432 |
29 Jun 15 |
olle |
2486 |
{ |
| 3432 |
29 Jun 15 |
olle |
2487 |
startItemList.add(rna); |
| 3432 |
29 Jun 15 |
olle |
2488 |
} |
| 3432 |
29 Jun 15 |
olle |
2489 |
} |
| 3432 |
29 Jun 15 |
olle |
2490 |
|
| 3432 |
29 Jun 15 |
olle |
2491 |
String msg = ""; |
| 3433 |
29 Jun 15 |
olle |
2492 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2493 |
{ |
| 3432 |
29 Jun 15 |
olle |
2494 |
msg += "Original quantity set to 0.0 for specimen " + itemName; |
| 3432 |
29 Jun 15 |
olle |
2495 |
} |
| 3433 |
29 Jun 15 |
olle |
2496 |
else if (Meludi.itemIsRna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2497 |
{ |
| 3432 |
29 Jun 15 |
olle |
2498 |
msg += "Original quantity set to 0.0 for RNA " + itemName; |
| 3432 |
29 Jun 15 |
olle |
2499 |
} |
| 3433 |
29 Jun 15 |
olle |
2500 |
else if (Meludi.itemIsDna(itemName)) |
| 3432 |
29 Jun 15 |
olle |
2501 |
{ |
| 3432 |
29 Jun 15 |
olle |
2502 |
msg += "Original quantity set to 0.0 for DNA " + itemName; |
| 3432 |
29 Jun 15 |
olle |
2503 |
} |
| 3432 |
29 Jun 15 |
olle |
2504 |
jsonMessages.add(msg); |
| 3432 |
29 Jun 15 |
olle |
2505 |
} |
| 3432 |
29 Jun 15 |
olle |
2506 |
dc.commit(); |
| 3432 |
29 Jun 15 |
olle |
2507 |
|
| 3432 |
29 Jun 15 |
olle |
2508 |
json.put("createdStartItemList", jsonCreatedStartItemList); |
| 3502 |
22 Sep 15 |
olle |
2509 |
CounterService.getInstance().setForceCount(); |
| 3432 |
29 Jun 15 |
olle |
2510 |
} |
| 3502 |
22 Sep 15 |
olle |
2511 |
else if ("RemoveStartItemList".equals(cmd)) |
| 3502 |
22 Sep 15 |
olle |
2512 |
{ |
| 3502 |
22 Sep 15 |
olle |
2513 |
dc = sc.newDbControl(); |
| 3502 |
22 Sep 15 |
olle |
2514 |
|
| 3502 |
22 Sep 15 |
olle |
2515 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3502 |
22 Sep 15 |
olle |
2516 |
|
| 3502 |
22 Sep 15 |
olle |
2517 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3502 |
22 Sep 15 |
olle |
2518 |
Integer startItemListId = Values.getInteger(req.getParameter("startItemListId"), null); |
| 3502 |
22 Sep 15 |
olle |
2519 |
JSONArray jsonRemovedStartItemList = new JSONArray(); |
| 3502 |
22 Sep 15 |
olle |
2520 |
JSONObject jsonStartItemList = new JSONObject(); |
| 3502 |
22 Sep 15 |
olle |
2521 |
|
| 3502 |
22 Sep 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3502 |
22 Sep 15 |
olle |
2523 |
SnapshotManager manager = new SnapshotManager(); |
| 3502 |
22 Sep 15 |
olle |
2524 |
List<String> extractSourceItemNameList = null; |
| 3502 |
22 Sep 15 |
olle |
// Remove start item list |
| 3502 |
22 Sep 15 |
olle |
2526 |
if (startItemListId != null) |
| 3502 |
22 Sep 15 |
olle |
2527 |
{ |
| 3502 |
22 Sep 15 |
olle |
2528 |
ItemList startItemList = ItemList.getById(dc, startItemListId); |
| 3502 |
22 Sep 15 |
olle |
2529 |
if (startItemList != null) |
| 3502 |
22 Sep 15 |
olle |
2530 |
{ |
| 3502 |
22 Sep 15 |
olle |
2531 |
StartList sl = new StartList(startItemList); |
| 3502 |
22 Sep 15 |
olle |
2532 |
extractSourceItemNameList = sl.fetchExtractSourceNameListFromItemList(dc); |
| 3502 |
22 Sep 15 |
olle |
// Construct a query to get all member extract items in the item list, sorted alphabetically after name |
| 3502 |
22 Sep 15 |
olle |
2534 |
ItemQuery<Extract> query = (ItemQuery<Extract>)startItemList.getMembers(); |
| 3502 |
22 Sep 15 |
olle |
2535 |
query.include(Include.ALL); |
| 3502 |
22 Sep 15 |
olle |
2536 |
query.order(Orders.asc(Hql.property("name"))); |
| 3502 |
22 Sep 15 |
olle |
2537 |
List<Extract> extractList = query.list(dc); |
| 3502 |
22 Sep 15 |
olle |
2538 |
if (extractList != null) |
| 3502 |
22 Sep 15 |
olle |
2539 |
{ |
| 3502 |
22 Sep 15 |
olle |
2540 |
for (Extract extract: extractList) |
| 3502 |
22 Sep 15 |
olle |
2541 |
{ |
| 3502 |
22 Sep 15 |
olle |
2542 |
startItemList.remove(extract); |
| 3502 |
22 Sep 15 |
olle |
2543 |
} |
| 3502 |
22 Sep 15 |
olle |
2544 |
} |
| 3502 |
22 Sep 15 |
olle |
2545 |
startItemList.setRemoved(true); |
| 3502 |
22 Sep 15 |
olle |
2546 |
String msg = "Removed start item list " + startItemList.getName(); |
| 3502 |
22 Sep 15 |
olle |
2547 |
jsonMessages.add(msg); |
| 3502 |
22 Sep 15 |
olle |
2548 |
jsonRemovedStartItemList.add(startItemList.getId()); |
| 3502 |
22 Sep 15 |
olle |
2549 |
dc.deleteItem(startItemList); |
| 3502 |
22 Sep 15 |
olle |
2550 |
List<String> itemNameList = null; |
| 3502 |
22 Sep 15 |
olle |
2551 |
} |
| 3502 |
22 Sep 15 |
olle |
2552 |
} |
| 3502 |
22 Sep 15 |
olle |
// Get list of extract source item names |
| 3502 |
22 Sep 15 |
olle |
2554 |
List<String> itemNameList = new ArrayList<String>(); |
| 3502 |
22 Sep 15 |
olle |
2555 |
JSONArray jsonItems = (JSONArray)jsonReq.get("items"); |
| 3502 |
22 Sep 15 |
olle |
2556 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3502 |
22 Sep 15 |
olle |
2557 |
{ |
| 3502 |
22 Sep 15 |
olle |
2558 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3502 |
22 Sep 15 |
olle |
2559 |
String itemName = (String)jsonItem.get("name"); |
| 3502 |
22 Sep 15 |
olle |
2560 |
itemNameList.add(itemName); |
| 3502 |
22 Sep 15 |
olle |
2561 |
} |
| 3502 |
22 Sep 15 |
olle |
2562 |
|
| 3502 |
22 Sep 15 |
olle |
// Set original quantity for extract source item to null, in order to mark them as unprocessed |
| 3502 |
22 Sep 15 |
olle |
2564 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3502 |
22 Sep 15 |
olle |
2565 |
{ |
| 3502 |
22 Sep 15 |
olle |
2566 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3502 |
22 Sep 15 |
olle |
2567 |
String itemName = (String)jsonItem.get("name"); |
| 3502 |
22 Sep 15 |
olle |
2568 |
Number itemId = (Number)jsonItem.get("id"); |
| 3502 |
22 Sep 15 |
olle |
2569 |
Sample specimen = null; |
| 3502 |
22 Sep 15 |
olle |
2570 |
Extract dna = null; |
| 3502 |
22 Sep 15 |
olle |
2571 |
Extract rna = null; |
| 3502 |
22 Sep 15 |
olle |
2572 |
|
| 3502 |
22 Sep 15 |
olle |
2573 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2574 |
{ |
| 3502 |
22 Sep 15 |
olle |
2575 |
specimen = Sample.getById(dc, itemId.intValue()); |
| 3502 |
22 Sep 15 |
olle |
2576 |
specimen.setItemSubtype(Subtype.SPECIMEN.load(dc)); |
| 3502 |
22 Sep 15 |
olle |
2577 |
specimen.setOriginalQuantity(null); |
| 3502 |
22 Sep 15 |
olle |
2578 |
} |
| 3502 |
22 Sep 15 |
olle |
2579 |
|
| 3502 |
22 Sep 15 |
olle |
// DNA |
| 3502 |
22 Sep 15 |
olle |
2581 |
if (Meludi.itemIsDna(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2582 |
{ |
| 3502 |
22 Sep 15 |
olle |
2583 |
dna = Extract.getById(dc, itemId.intValue()); |
| 3502 |
22 Sep 15 |
olle |
2584 |
dna.setItemSubtype(Subtype.DNA.load(dc)); |
| 3502 |
22 Sep 15 |
olle |
2585 |
dna.setOriginalQuantity(null); |
| 3502 |
22 Sep 15 |
olle |
2586 |
} |
| 3502 |
22 Sep 15 |
olle |
2587 |
|
| 3502 |
22 Sep 15 |
olle |
// RNA |
| 3502 |
22 Sep 15 |
olle |
2589 |
if (Meludi.itemIsRna(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2590 |
{ |
| 3502 |
22 Sep 15 |
olle |
2591 |
rna = Extract.getById(dc, itemId.intValue()); |
| 3502 |
22 Sep 15 |
olle |
2592 |
rna.setItemSubtype(Subtype.RNA.load(dc)); |
| 3502 |
22 Sep 15 |
olle |
2593 |
rna.setOriginalQuantity(null); |
| 3502 |
22 Sep 15 |
olle |
2594 |
} |
| 3502 |
22 Sep 15 |
olle |
2595 |
|
| 3502 |
22 Sep 15 |
olle |
2596 |
String msg = ""; |
| 3502 |
22 Sep 15 |
olle |
2597 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2598 |
{ |
| 3502 |
22 Sep 15 |
olle |
2599 |
msg += "Original quantity set to null for specimen " + itemName; |
| 3502 |
22 Sep 15 |
olle |
2600 |
} |
| 3502 |
22 Sep 15 |
olle |
2601 |
else if (Meludi.itemIsRna(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2602 |
{ |
| 3502 |
22 Sep 15 |
olle |
2603 |
msg += "Original quantity set to null for RNA " + itemName; |
| 3502 |
22 Sep 15 |
olle |
2604 |
} |
| 3502 |
22 Sep 15 |
olle |
2605 |
else if (Meludi.itemIsDna(itemName)) |
| 3502 |
22 Sep 15 |
olle |
2606 |
{ |
| 3502 |
22 Sep 15 |
olle |
2607 |
msg += "Original quantity set to null for DNA " + itemName; |
| 3502 |
22 Sep 15 |
olle |
2608 |
} |
| 3502 |
22 Sep 15 |
olle |
2609 |
jsonMessages.add(msg); |
| 3502 |
22 Sep 15 |
olle |
2610 |
} |
| 3502 |
22 Sep 15 |
olle |
2611 |
dc.commit(); |
| 3502 |
22 Sep 15 |
olle |
2612 |
|
| 3502 |
22 Sep 15 |
olle |
2613 |
json.put("removedStartItemList", jsonRemovedStartItemList); |
| 3502 |
22 Sep 15 |
olle |
2614 |
CounterService.getInstance().setForceCount(); |
| 3502 |
22 Sep 15 |
olle |
2615 |
} |
| 3180 |
17 Mar 15 |
olle |
2616 |
else if ("RegisterDnaRna".equals(cmd)) |
| 3180 |
17 Mar 15 |
olle |
2617 |
{ |
| 3180 |
17 Mar 15 |
olle |
2618 |
dc = sc.newDbControl(); |
| 3180 |
17 Mar 15 |
olle |
2619 |
|
| 3176 |
06 Mar 15 |
olle |
2620 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3176 |
06 Mar 15 |
olle |
2621 |
|
| 3176 |
06 Mar 15 |
olle |
2622 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3176 |
06 Mar 15 |
olle |
2623 |
JSONArray jsonItems = (JSONArray)jsonReq.get("items"); |
| 3176 |
06 Mar 15 |
olle |
2624 |
int numSpecimen = 0; |
| 3176 |
06 Mar 15 |
olle |
2625 |
int numRna = 0; |
| 3176 |
06 Mar 15 |
olle |
2626 |
int numDna = 0; |
| 3176 |
06 Mar 15 |
olle |
2627 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3176 |
06 Mar 15 |
olle |
2628 |
{ |
| 3176 |
06 Mar 15 |
olle |
2629 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3176 |
06 Mar 15 |
olle |
2630 |
String itemName = (String)jsonItem.get("name"); |
| 3433 |
29 Jun 15 |
olle |
2631 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2632 |
{ |
| 3176 |
06 Mar 15 |
olle |
2633 |
numSpecimen++; |
| 3176 |
06 Mar 15 |
olle |
2634 |
numRna++; |
| 3176 |
06 Mar 15 |
olle |
2635 |
numDna++; |
| 3176 |
06 Mar 15 |
olle |
2636 |
} |
| 3433 |
29 Jun 15 |
olle |
2637 |
else if (Meludi.itemIsRna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2638 |
{ |
| 3176 |
06 Mar 15 |
olle |
2639 |
numRna++; |
| 3176 |
06 Mar 15 |
olle |
2640 |
} |
| 3433 |
29 Jun 15 |
olle |
2641 |
else if (Meludi.itemIsDna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2642 |
{ |
| 3176 |
06 Mar 15 |
olle |
2643 |
numDna++; |
| 3176 |
06 Mar 15 |
olle |
2644 |
} |
| 3176 |
06 Mar 15 |
olle |
2645 |
} |
| 3176 |
06 Mar 15 |
olle |
2646 |
JSONArray jsonCreatedRna = new JSONArray(); |
| 3176 |
06 Mar 15 |
olle |
2647 |
JSONArray jsonCreatedDna = new JSONArray(); |
| 3176 |
06 Mar 15 |
olle |
2648 |
List<Extract> newRna = new ArrayList<Extract>(numRna); |
| 3176 |
06 Mar 15 |
olle |
2649 |
List<Extract> newDna = new ArrayList<Extract>(numDna); |
| 3276 |
29 Apr 15 |
olle |
2650 |
/* |
| 3176 |
06 Mar 15 |
olle |
SpecimenTubeServlet specimenTubeServlet = new SpecimenTubeServlet(); |
| 3253 |
17 Apr 15 |
olle |
List<BioWell> freeRnaWells = specimenTubeServlet.findFreeWells2(dc, numSpecimen, "_rna"); |
| 3253 |
17 Apr 15 |
olle |
List<BioWell> freeDnaWells = specimenTubeServlet.findFreeWells2(dc, numSpecimen, "_dna"); |
| 3276 |
29 Apr 15 |
olle |
2654 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2655 |
|
| 3180 |
17 Mar 15 |
olle |
2656 |
Date isolationDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("isolationDate")); |
| 3501 |
21 Sep 15 |
olle |
2657 |
String extractionOperator = (String)jsonReq.get("extractionOperator"); |
| 3176 |
06 Mar 15 |
olle |
2658 |
Number extractionProtocolId = (Number)jsonReq.get("extractionProtocol"); |
| 3176 |
06 Mar 15 |
olle |
2659 |
Protocol extractionProtocol = extractionProtocolId != null ? Protocol.getById(dc, extractionProtocolId.intValue()) : null; |
| 3180 |
17 Mar 15 |
olle |
2660 |
Number rnaDefaultVolume = (Number)jsonReq.get("rnaDefaultVolume"); |
| 3180 |
17 Mar 15 |
olle |
2661 |
Number dnaDefaultVolume = (Number)jsonReq.get("dnaDefaultVolume"); |
| 3176 |
06 Mar 15 |
olle |
2662 |
|
| 3176 |
06 Mar 15 |
olle |
// QIAcube properties |
| 3176 |
06 Mar 15 |
olle |
2664 |
Date qiacubeDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("qiacubeDate")); |
| 3501 |
21 Sep 15 |
olle |
2665 |
String qiacubeOperator = (String)jsonReq.get("qiacubeOperator"); |
| 3176 |
06 Mar 15 |
olle |
2666 |
Number qiacubeRunNo = (Number)jsonReq.get("qiacubeRunNo"); |
| 3180 |
17 Mar 15 |
olle |
2667 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2669 |
String d_allPrepFfpeKit = Values.getStringOrNull((String)jsonReq.get("allPrepFfpeKit")); |
| 3176 |
06 Mar 15 |
olle |
2670 |
String d_xyleneSpecimen = Values.getStringOrNull((String)jsonReq.get("xyleneSpecimen")); |
| 3176 |
06 Mar 15 |
olle |
2671 |
String d_etoh995Specimen = Values.getStringOrNull((String)jsonReq.get("etoh995Specimen")); |
| 3176 |
06 Mar 15 |
olle |
2672 |
String d_bufferPkdSpecimen = Values.getStringOrNull((String)jsonReq.get("bufferPkdSpecimen")); |
| 3176 |
06 Mar 15 |
olle |
2673 |
String d_bufferAtlSpecimen = Values.getStringOrNull((String)jsonReq.get("bufferAtlSpecimen")); |
| 3176 |
06 Mar 15 |
olle |
2674 |
String d_proteinaseKSpecimen = Values.getStringOrNull((String)jsonReq.get("proteinaseKSpecimen")); |
| 3176 |
06 Mar 15 |
olle |
2675 |
String d_rnaseASpecimen = Values.getStringOrNull((String)jsonReq.get("rnaseASpecimen")); |
| 3176 |
06 Mar 15 |
olle |
2676 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3176 |
06 Mar 15 |
olle |
2678 |
String d_etoh995 = Values.getStringOrNull((String)jsonReq.get("etoh995")); |
| 3176 |
06 Mar 15 |
olle |
2679 |
String d_bufferRlt = Values.getStringOrNull((String)jsonReq.get("bufferRlt")); |
| 3176 |
06 Mar 15 |
olle |
2680 |
String d_bufferFrn = Values.getStringOrNull((String)jsonReq.get("bufferFrn")); |
| 3176 |
06 Mar 15 |
olle |
2681 |
String d_bufferRpe = Values.getStringOrNull((String)jsonReq.get("bufferRpe")); |
| 3176 |
06 Mar 15 |
olle |
2682 |
String d_bufferAl = Values.getStringOrNull((String)jsonReq.get("bufferAl")); |
| 3176 |
06 Mar 15 |
olle |
2683 |
String d_bufferAw1 = Values.getStringOrNull((String)jsonReq.get("bufferAw1")); |
| 3176 |
06 Mar 15 |
olle |
2684 |
String d_bufferAw2 = Values.getStringOrNull((String)jsonReq.get("bufferAw2")); |
| 3176 |
06 Mar 15 |
olle |
2685 |
String d_bufferAte = Values.getStringOrNull((String)jsonReq.get("bufferAte")); |
| 3176 |
06 Mar 15 |
olle |
2686 |
String d_bufferRdd = Values.getStringOrNull((String)jsonReq.get("bufferRdd")); |
| 3176 |
06 Mar 15 |
olle |
2687 |
String d_rnaseFreeWater = Values.getStringOrNull((String)jsonReq.get("rnaseFreeWater")); |
| 3176 |
06 Mar 15 |
olle |
2688 |
String d_dnaseMix = Values.getStringOrNull((String)jsonReq.get("dnaseMix")); |
| 3176 |
06 Mar 15 |
olle |
2689 |
String d_rneasyMinEluteSpinColumn = Values.getStringOrNull((String)jsonReq.get("rneasyMinEluteSpinColumn")); |
| 3176 |
06 Mar 15 |
olle |
2690 |
String d_qiaampMinEluteSpinColumn = Values.getStringOrNull((String)jsonReq.get("qiaampMinEluteSpinColumn")); |
| 3176 |
06 Mar 15 |
olle |
2691 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3324 |
11 May 15 |
olle |
2693 |
String d_kapaSybrFast = Values.getStringOrNull((String)jsonReq.get("kapaSybrFast")); |
| 3324 |
11 May 15 |
olle |
2694 |
String d_qualityControlPrimersQcpRgt = Values.getStringOrNull((String)jsonReq.get("qualityControlPrimersQcpRgt")); |
| 3438 |
03 Jul 15 |
olle |
2695 |
String d_qualityControlTemplateQct = Values.getStringOrNull((String)jsonReq.get("qualityControlTemplateQct")); |
| 3324 |
11 May 15 |
olle |
2696 |
String d_qubitDnaHighSens = Values.getStringOrNull((String)jsonReq.get("qubitDnaHighSens")); |
| 3324 |
11 May 15 |
olle |
2697 |
String d_qubitDnaBroadRange = Values.getStringOrNull((String)jsonReq.get("qubitDnaBroadRange")); |
| 3324 |
11 May 15 |
olle |
2698 |
|
| 3501 |
21 Sep 15 |
olle |
// Set start item list extraction date annotation |
| 3501 |
21 Sep 15 |
olle |
2700 |
Integer startItemListId = Values.getInteger((String)jsonReq.get("startListId"),1); |
| 3501 |
21 Sep 15 |
olle |
2701 |
ItemList startItemList = null; |
| 3501 |
21 Sep 15 |
olle |
2702 |
if (startItemListId != null) |
| 3501 |
21 Sep 15 |
olle |
2703 |
{ |
| 3501 |
21 Sep 15 |
olle |
2704 |
startItemList = ItemList.getById(dc, startItemListId); |
| 3501 |
21 Sep 15 |
olle |
2705 |
if (startItemList != null) |
| 3501 |
21 Sep 15 |
olle |
2706 |
{ |
| 3501 |
21 Sep 15 |
olle |
// Set start item list extraction date annotation to QIAcube date and mark the item list as processed |
| 3501 |
21 Sep 15 |
olle |
2708 |
Annotationtype.LIST_EXTRACTION_DATE.setAnnotationValue(dc, startItemList, qiacubeDate); |
| 3501 |
21 Sep 15 |
olle |
2709 |
Annotationtype.LIST_EXTRACTION_OPERATOR.setAnnotationValue(dc, startItemList, extractionOperator); |
| 3501 |
21 Sep 15 |
olle |
2710 |
Annotationtype.SAMPLE_PREP_LIST_IS_PROCESSED.setAnnotationValue(dc, startItemList, true); |
| 3501 |
21 Sep 15 |
olle |
2711 |
jsonMessages.add("Extraction date updated for start item list " + startItemList.getName()); |
| 3501 |
21 Sep 15 |
olle |
2712 |
|
| 3501 |
21 Sep 15 |
olle |
// Set start list QIAcube annotations |
| 3501 |
21 Sep 15 |
olle |
2714 |
Annotationtype.LIST_QIACUBE_DATE.setAnnotationValue(dc, startItemList, qiacubeDate); |
| 3501 |
21 Sep 15 |
olle |
2715 |
Annotationtype.LIST_QIACUBE_OPERATOR.setAnnotationValue(dc, startItemList, qiacubeOperator); |
| 3501 |
21 Sep 15 |
olle |
//Annotationtype.LIST_QIACUBE_PRIMARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubePrimaryPrefix); |
| 3501 |
21 Sep 15 |
olle |
//Annotationtype.LIST_QIACUBE_SECONDARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubeSecondaryPrefix); |
| 3501 |
21 Sep 15 |
olle |
2718 |
Annotationtype.LIST_QIACUBE_RUN_NO.setAnnotationValue(dc, startItemList, qiacubeRunNo); |
| 3501 |
21 Sep 15 |
olle |
2719 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2721 |
Annotationtype.LIST_ALLPREP_FFPE_KIT.setAnnotationValue(dc, startItemList, d_allPrepFfpeKit); |
| 3501 |
21 Sep 15 |
olle |
2722 |
Annotationtype.LIST_XYLENE_SPECIMEN.setAnnotationValue(dc, startItemList, d_xyleneSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2723 |
Annotationtype.LIST_ETOH995_SPECIMEN.setAnnotationValue(dc, startItemList, d_etoh995Specimen); |
| 3501 |
21 Sep 15 |
olle |
2724 |
Annotationtype.LIST_BUFFER_PKD_SPECIMEN.setAnnotationValue(dc, startItemList, d_bufferPkdSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2725 |
Annotationtype.LIST_BUFFER_ATL_SPECIMEN.setAnnotationValue(dc, startItemList, d_bufferAtlSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2726 |
Annotationtype.LIST_PROTEINASE_K_SPECIMEN.setAnnotationValue(dc, startItemList, d_proteinaseKSpecimen); |
| 3501 |
21 Sep 15 |
olle |
2727 |
Annotationtype.LIST_RNASE_A_SPECIMEN.setAnnotationValue(dc, startItemList, d_rnaseASpecimen); |
| 3501 |
21 Sep 15 |
olle |
2728 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
2730 |
Annotationtype.LIST_ETOH995.setAnnotationValue(dc, startItemList, d_etoh995); |
| 3501 |
21 Sep 15 |
olle |
2731 |
Annotationtype.LIST_BUFFER_RLT.setAnnotationValue(dc, startItemList, d_bufferRlt); |
| 3501 |
21 Sep 15 |
olle |
2732 |
Annotationtype.LIST_BUFFER_FRN.setAnnotationValue(dc, startItemList, d_bufferFrn); |
| 3501 |
21 Sep 15 |
olle |
2733 |
Annotationtype.LIST_BUFFER_RPE.setAnnotationValue(dc, startItemList, d_bufferRpe); |
| 3501 |
21 Sep 15 |
olle |
2734 |
Annotationtype.LIST_BUFFER_AL.setAnnotationValue(dc, startItemList, d_bufferAl); |
| 3501 |
21 Sep 15 |
olle |
2735 |
Annotationtype.LIST_BUFFER_AW1.setAnnotationValue(dc, startItemList, d_bufferAw1); |
| 3501 |
21 Sep 15 |
olle |
2736 |
Annotationtype.LIST_BUFFER_AW2.setAnnotationValue(dc, startItemList, d_bufferAw2); |
| 3501 |
21 Sep 15 |
olle |
2737 |
Annotationtype.LIST_BUFFER_ATE.setAnnotationValue(dc, startItemList, d_bufferAte); |
| 3501 |
21 Sep 15 |
olle |
2738 |
Annotationtype.LIST_BUFFER_RDD.setAnnotationValue(dc, startItemList, d_bufferRdd); |
| 3501 |
21 Sep 15 |
olle |
2739 |
Annotationtype.LIST_RNASE_FREE_WATER.setAnnotationValue(dc, startItemList, d_rnaseFreeWater); |
| 3501 |
21 Sep 15 |
olle |
2740 |
Annotationtype.LIST_DNASE_MIX.setAnnotationValue(dc, startItemList, d_dnaseMix); |
| 3501 |
21 Sep 15 |
olle |
2741 |
Annotationtype.LIST_RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, d_rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
2742 |
Annotationtype.LIST_QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, d_qiaampMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
2743 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
2745 |
Annotationtype.LIST_KAPA_SYBR_FAST.setAnnotationValue(dc, startItemList, d_kapaSybrFast); |
| 3501 |
21 Sep 15 |
olle |
2746 |
Annotationtype.LIST_QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, startItemList, d_qualityControlPrimersQcpRgt); |
| 3501 |
21 Sep 15 |
olle |
2747 |
Annotationtype.LIST_QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, startItemList, d_qualityControlTemplateQct); |
| 3501 |
21 Sep 15 |
olle |
2748 |
Annotationtype.LIST_QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, startItemList, d_qubitDnaHighSens); |
| 3501 |
21 Sep 15 |
olle |
2749 |
Annotationtype.LIST_QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, startItemList, d_qubitDnaBroadRange); |
| 3501 |
21 Sep 15 |
olle |
2750 |
|
| 3501 |
21 Sep 15 |
olle |
// Set annotation values for new properties |
| 3501 |
21 Sep 15 |
olle |
2752 |
Annotationtype.LIST_RNA_DEFAULT_VOLUME_IN_MICROLITRE.setAnnotationValue(dc, startItemList, rnaDefaultVolume); |
| 3501 |
21 Sep 15 |
olle |
2753 |
Annotationtype.LIST_DNA_DEFAULT_VOLUME_IN_MICROLITRE.setAnnotationValue(dc, startItemList, dnaDefaultVolume); |
| 3501 |
21 Sep 15 |
olle |
2754 |
} |
| 3501 |
21 Sep 15 |
olle |
2755 |
} |
| 3501 |
21 Sep 15 |
olle |
2756 |
|
| 3176 |
06 Mar 15 |
olle |
2757 |
/* |
| 3176 |
06 Mar 15 |
olle |
BioMaterialList flaggedRna = BiomaterialList.FLAGGED_RNA.load(dc); |
| 3176 |
06 Mar 15 |
olle |
2759 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2760 |
boolean preNormalize = false; |
| 3176 |
06 Mar 15 |
olle |
2761 |
boolean flagged = false; |
| 3176 |
06 Mar 15 |
olle |
2762 |
int numFlagged = 0; |
| 3253 |
17 Apr 15 |
olle |
2763 |
int numStoredDna = 0; |
| 3176 |
06 Mar 15 |
olle |
2764 |
int numStoredRna = 0; |
| 3176 |
06 Mar 15 |
olle |
2765 |
|
| 3176 |
06 Mar 15 |
olle |
2766 |
for (int i = 0; i < jsonItems.size(); ++i) |
| 3176 |
06 Mar 15 |
olle |
2767 |
{ |
| 3176 |
06 Mar 15 |
olle |
2768 |
JSONObject jsonItem = (JSONObject)jsonItems.get(i); |
| 3176 |
06 Mar 15 |
olle |
2769 |
String itemName = (String)jsonItem.get("name"); |
| 3176 |
06 Mar 15 |
olle |
2770 |
Number itemId = (Number)jsonItem.get("id"); |
| 3176 |
06 Mar 15 |
olle |
2771 |
/* |
| 3176 |
06 Mar 15 |
olle |
float itemOriginalQuantity = ((Number)jsonItem.get("originalQuantity")).floatValue(); |
| 3176 |
06 Mar 15 |
olle |
float itemProcessedQuantity = ((Number)jsonItem.get("processedQuantity")).floatValue(); |
| 3176 |
06 Mar 15 |
olle |
2774 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2775 |
float itemOriginalQuantity = fetchFloatValue(jsonItem.get("originalQuantity")); |
| 3176 |
06 Mar 15 |
olle |
2776 |
float itemProcessedQuantity = fetchFloatValue(jsonItem.get("processedQuantity")); |
| 3176 |
06 Mar 15 |
olle |
2777 |
BioWell specimenWell = null; |
| 3176 |
06 Mar 15 |
olle |
2778 |
Sample specimen = null; |
| 3176 |
06 Mar 15 |
olle |
2779 |
|
| 3433 |
29 Jun 15 |
olle |
2780 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2781 |
{ |
| 3176 |
06 Mar 15 |
olle |
2782 |
specimen = Sample.getById(dc, itemId.intValue()); |
| 3176 |
06 Mar 15 |
olle |
2783 |
specimen.setItemSubtype(Subtype.SPECIMEN.load(dc)); |
| 3176 |
06 Mar 15 |
olle |
2784 |
/* |
| 3176 |
06 Mar 15 |
olle |
BioMaterialEvent specimenEvent = specimen.getCreationEvent(); |
| 3176 |
06 Mar 15 |
olle |
specimenEvent.setEventDate(samplingDate); |
| 3176 |
06 Mar 15 |
olle |
specimenEvent.setProtocol(specimenProtocol); |
| 3176 |
06 Mar 15 |
olle |
2788 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2789 |
specimen.setOriginalQuantity(itemOriginalQuantity); |
| 3176 |
06 Mar 15 |
olle |
2790 |
specimen.setDescription((String)jsonItem.get("comment")); |
| 3176 |
06 Mar 15 |
olle |
2791 |
specimenWell = specimen.getBioWell(); |
| 3176 |
06 Mar 15 |
olle |
2792 |
} |
| 3176 |
06 Mar 15 |
olle |
2793 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2795 |
String allPrepFfpeKit = Values.getString((String)jsonItem.get("allPrepFfpeKit"), d_allPrepFfpeKit); |
| 3176 |
06 Mar 15 |
olle |
2796 |
String xyleneSpecimen = Values.getString((String)jsonItem.get("xyleneSpecimen"), d_xyleneSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2797 |
String etoh995Specimen = Values.getString((String)jsonItem.get("etoh995Specimen"), d_etoh995Specimen); |
| 3176 |
06 Mar 15 |
olle |
2798 |
String bufferPkdSpecimen = Values.getString((String)jsonItem.get("bufferPkdSpecimen"), d_bufferPkdSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2799 |
String bufferAtlSpecimen = Values.getString((String)jsonItem.get("bufferAtlSpecimen"), d_bufferAtlSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2800 |
String proteinaseKSpecimen = Values.getString((String)jsonItem.get("proteinaseKSpecimen"), d_proteinaseKSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2801 |
String rnaseASpecimen = Values.getString((String)jsonItem.get("rnaseASpecimen"), d_rnaseASpecimen); |
| 3176 |
06 Mar 15 |
olle |
2802 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3176 |
06 Mar 15 |
olle |
2804 |
String etoh995 = Values.getString((String)jsonItem.get("etoh995"), d_etoh995); |
| 3176 |
06 Mar 15 |
olle |
2805 |
String bufferRlt = Values.getString((String)jsonItem.get("bufferRlt"), d_bufferRlt); |
| 3176 |
06 Mar 15 |
olle |
2806 |
String bufferFrn = Values.getString((String)jsonItem.get("bufferFrn"), d_bufferFrn); |
| 3176 |
06 Mar 15 |
olle |
2807 |
String bufferRpe = Values.getString((String)jsonItem.get("bufferRpe"), d_bufferRpe); |
| 3176 |
06 Mar 15 |
olle |
2808 |
String bufferAl = Values.getString((String)jsonItem.get("bufferAl"), d_bufferAl); |
| 3176 |
06 Mar 15 |
olle |
2809 |
String bufferAw1 = Values.getString((String)jsonItem.get("bufferAw1"), d_bufferAw1); |
| 3176 |
06 Mar 15 |
olle |
2810 |
String bufferAw2 = Values.getString((String)jsonItem.get("bufferAw2"), d_bufferAw2); |
| 3176 |
06 Mar 15 |
olle |
2811 |
String bufferAte = Values.getString((String)jsonItem.get("bufferAte"), d_bufferAte); |
| 3176 |
06 Mar 15 |
olle |
2812 |
String bufferRdd = Values.getString((String)jsonItem.get("bufferRdd"), d_bufferRdd); |
| 3176 |
06 Mar 15 |
olle |
2813 |
String rnaseFreeWater = Values.getString((String)jsonItem.get("rnaseFreeWater"), d_rnaseFreeWater); |
| 3176 |
06 Mar 15 |
olle |
2814 |
String dnaseMix = Values.getString((String)jsonItem.get("dnaseMix"), d_dnaseMix); |
| 3176 |
06 Mar 15 |
olle |
2815 |
String rneasyMinEluteSpinColumn = Values.getString((String)jsonItem.get("rneasyMinEluteSpinColumn"), d_rneasyMinEluteSpinColumn); |
| 3324 |
11 May 15 |
olle |
2816 |
String qiaampMinEluteSpinColumn = Values.getString((String)jsonItem.get("qiaampMinEluteSpinColumn"), d_qiaampMinEluteSpinColumn); |
| 3176 |
06 Mar 15 |
olle |
2817 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3324 |
11 May 15 |
olle |
2819 |
String kapaSybrFast = Values.getString((String)jsonItem.get("kapaSybrFast"), d_kapaSybrFast); |
| 3324 |
11 May 15 |
olle |
2820 |
String qualityControlPrimersQcpRgt = Values.getString((String)jsonItem.get("qualityControlPrimersQcpRgt"), d_qualityControlPrimersQcpRgt); |
| 3438 |
03 Jul 15 |
olle |
2821 |
String qualityControlTemplateQct = Values.getString((String)jsonItem.get("qualityControlTemplateQct"), d_qualityControlTemplateQct); |
| 3324 |
11 May 15 |
olle |
2822 |
String qubitDnaHighSens = Values.getString((String)jsonItem.get("qubitDnaHighSens"), d_qubitDnaHighSens); |
| 3324 |
11 May 15 |
olle |
2823 |
String qubitDnaBroadRange = Values.getString((String)jsonItem.get("qubitDnaBroadRange"), d_qubitDnaBroadRange); |
| 3324 |
11 May 15 |
olle |
2824 |
|
| 3176 |
06 Mar 15 |
olle |
// Qiacube |
| 3176 |
06 Mar 15 |
olle |
//Number qiacubePosition = (Number)jsonItem.get("qiacubePosition"); |
| 3176 |
06 Mar 15 |
olle |
2827 |
String qiacubePositionStr = (String)jsonItem.get("qiacubePosition"); |
| 3176 |
06 Mar 15 |
olle |
2828 |
String qiacubeInstrumentPrefix = fetchQiacubeInstrumentPrefix(qiacubePositionStr); |
| 3176 |
06 Mar 15 |
olle |
2829 |
Number qiacubePosition = fetchQiacubePosition(qiacubePositionStr); |
| 3176 |
06 Mar 15 |
olle |
2830 |
|
| 3176 |
06 Mar 15 |
olle |
// DNA |
| 3433 |
29 Jun 15 |
olle |
2832 |
if (Meludi.itemIsSpecimen(itemName) || Meludi.itemIsDna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2833 |
{ |
| 3176 |
06 Mar 15 |
olle |
2834 |
JSONObject jsonDna = (JSONObject)jsonItem.get("dna"); |
| 3176 |
06 Mar 15 |
olle |
2835 |
Extract dna = null; |
| 3433 |
29 Jun 15 |
olle |
2836 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2837 |
{ |
| 3276 |
29 Apr 15 |
olle |
2838 |
Dna d = Dna.findByName(dc, itemName + ".d"); |
| 3276 |
29 Apr 15 |
olle |
2839 |
dna = d.getExtract(); |
| 3176 |
06 Mar 15 |
olle |
2840 |
} |
| 3433 |
29 Jun 15 |
olle |
2841 |
else if (Meludi.itemIsDna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2842 |
{ |
| 3176 |
06 Mar 15 |
olle |
2843 |
dna = Extract.getById(dc, itemId.intValue()); |
| 3432 |
29 Jun 15 |
olle |
2844 |
if (dna == null) |
| 3432 |
29 Jun 15 |
olle |
2845 |
{ |
| 3517 |
01 Oct 15 |
olle |
2846 |
Dna d = Dna.findByName(dc, itemName); |
| 3432 |
29 Jun 15 |
olle |
2847 |
dna = d.getExtract(); |
| 3432 |
29 Jun 15 |
olle |
2848 |
} |
| 3176 |
06 Mar 15 |
olle |
2849 |
} |
| 3176 |
06 Mar 15 |
olle |
2850 |
dna.setItemSubtype(Subtype.DNA.load(dc)); |
| 3176 |
06 Mar 15 |
olle |
2851 |
dna.setDescription((String)jsonDna.get("comment")); |
| 3176 |
06 Mar 15 |
olle |
2852 |
BioMaterialEvent dnaEvent = dna.getCreationEvent(); |
| 3433 |
29 Jun 15 |
olle |
2853 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2854 |
{ |
| 3176 |
06 Mar 15 |
olle |
2855 |
dnaEvent.setEventDate(qiacubeDate); |
| 3176 |
06 Mar 15 |
olle |
2856 |
dnaEvent.setProtocol(extractionProtocol); |
| 3176 |
06 Mar 15 |
olle |
2857 |
dnaEvent.setSource(specimen).setUsedQuantity(itemProcessedQuantity / 3); |
| 3176 |
06 Mar 15 |
olle |
2858 |
} |
| 3432 |
29 Jun 15 |
olle |
//float dnaVolume = ((Number)jsonDna.get("volume")).floatValue(); |
| 3432 |
29 Jun 15 |
olle |
//float dnaQubitConc = ((Number)jsonDna.get("qubitConc")).floatValue(); |
| 3432 |
29 Jun 15 |
olle |
2861 |
float dnaVolume = fetchFloatValue(jsonDna.get("volume")); |
| 3432 |
29 Jun 15 |
olle |
2862 |
float dnaQubitConc = fetchFloatValue(jsonDna.get("qubitConc")); |
| 3176 |
06 Mar 15 |
olle |
2863 |
dna.setOriginalQuantity(dnaVolume * dnaQubitConc / 1000); |
| 3432 |
29 Jun 15 |
olle |
//float dnaDeltaCt = ((Number)jsonDna.get("deltaCt")).floatValue(); |
| 3432 |
29 Jun 15 |
olle |
2865 |
float dnaDeltaCt = fetchFloatValue(jsonDna.get("deltaCt")); |
| 3433 |
29 Jun 15 |
olle |
2866 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2867 |
{ |
| 3276 |
29 Apr 15 |
olle |
2868 |
/* |
| 3176 |
06 Mar 15 |
olle |
//dna.setBioWell(StoragePlate.getChildBioWell(dc, specimenWell, "_sp", "_dna")); |
| 3253 |
17 Apr 15 |
olle |
dna.setBioWell((BioWell)freeDnaWells.get(numStoredDna)); |
| 3253 |
17 Apr 15 |
olle |
numStoredDna++; |
| 3276 |
29 Apr 15 |
olle |
2872 |
*/ |
| 3180 |
17 Mar 15 |
olle |
2873 |
Annotationtype.ISOLATION_DATE.setAnnotationValue(dc, dna, isolationDate); |
| 3501 |
21 Sep 15 |
olle |
2874 |
Annotationtype.EXTRACTION_OPERATOR.setAnnotationValue(dc, dna, extractionOperator); |
| 3176 |
06 Mar 15 |
olle |
2875 |
Annotationtype.QIACUBE_DATE.setAnnotationValue(dc, dna, qiacubeDate); |
| 3501 |
21 Sep 15 |
olle |
2876 |
Annotationtype.QIACUBE_OPERATOR.setAnnotationValue(dc, dna, qiacubeOperator); |
| 3176 |
06 Mar 15 |
olle |
2877 |
Annotationtype.QIACUBE_RUN_NO.setAnnotationValue(dc, dna, qiacubeRunNo); |
| 3176 |
06 Mar 15 |
olle |
2878 |
Annotationtype.QIACUBE_INSTRUMENT_PREFIX.setAnnotationValue(dc, dna, qiacubeInstrumentPrefix); |
| 3176 |
06 Mar 15 |
olle |
2879 |
Annotationtype.QIACUBE_POSITION.setAnnotationValue(dc, dna, qiacubePosition); |
| 3176 |
06 Mar 15 |
olle |
2880 |
} |
| 3176 |
06 Mar 15 |
olle |
2881 |
Annotationtype.QUBIT_CONC.setAnnotationValue(dc, dna, dnaQubitConc); |
| 3176 |
06 Mar 15 |
olle |
2882 |
Annotationtype.DELTA_CT.setAnnotationValue(dc, dna, dnaDeltaCt); |
| 3176 |
06 Mar 15 |
olle |
// Reagents |
| 3433 |
29 Jun 15 |
olle |
2884 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2885 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2887 |
Annotationtype.ALLPREP_FFPE_KIT.setAnnotationValue(dc, dna, allPrepFfpeKit); |
| 3176 |
06 Mar 15 |
olle |
2888 |
Annotationtype.XYLENE_SPECIMEN.setAnnotationValue(dc, dna, xyleneSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2889 |
Annotationtype.ETOH995_SPECIMEN.setAnnotationValue(dc, dna, etoh995Specimen); |
| 3176 |
06 Mar 15 |
olle |
2890 |
Annotationtype.BUFFER_PKD_SPECIMEN.setAnnotationValue(dc, dna, bufferPkdSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2891 |
Annotationtype.BUFFER_ATL_SPECIMEN.setAnnotationValue(dc, dna, bufferAtlSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2892 |
Annotationtype.PROTEINASE_K_SPECIMEN.setAnnotationValue(dc, dna, proteinaseKSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2893 |
Annotationtype.RNASE_A_SPECIMEN.setAnnotationValue(dc, dna, rnaseASpecimen); |
| 3176 |
06 Mar 15 |
olle |
2894 |
|
| 3176 |
06 Mar 15 |
olle |
// QIAcube reagents |
| 3176 |
06 Mar 15 |
olle |
2896 |
Annotationtype.ETOH995.setAnnotationValue(dc, dna, etoh995); |
| 3176 |
06 Mar 15 |
olle |
2897 |
Annotationtype.BUFFER_RLT.setAnnotationValue(dc, dna, bufferRlt); |
| 3176 |
06 Mar 15 |
olle |
2898 |
Annotationtype.BUFFER_FRN.setAnnotationValue(dc, dna, bufferFrn); |
| 3176 |
06 Mar 15 |
olle |
2899 |
Annotationtype.BUFFER_RPE.setAnnotationValue(dc, dna, bufferRpe); |
| 3176 |
06 Mar 15 |
olle |
2900 |
Annotationtype.BUFFER_AL.setAnnotationValue(dc, dna, bufferAl); |
| 3176 |
06 Mar 15 |
olle |
2901 |
Annotationtype.BUFFER_AW1.setAnnotationValue(dc, dna, bufferAw1); |
| 3176 |
06 Mar 15 |
olle |
2902 |
Annotationtype.BUFFER_AW2.setAnnotationValue(dc, dna, bufferAw2); |
| 3176 |
06 Mar 15 |
olle |
2903 |
Annotationtype.BUFFER_ATE.setAnnotationValue(dc, dna, bufferAte); |
| 3176 |
06 Mar 15 |
olle |
2904 |
Annotationtype.BUFFER_RDD.setAnnotationValue(dc, dna, bufferRdd); |
| 3176 |
06 Mar 15 |
olle |
2905 |
Annotationtype.RNASE_FREE_WATER.setAnnotationValue(dc, dna, rnaseFreeWater); |
| 3176 |
06 Mar 15 |
olle |
2906 |
Annotationtype.DNASE_MIX.setAnnotationValue(dc, dna, dnaseMix); |
| 3176 |
06 Mar 15 |
olle |
2907 |
Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, dna, rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
2908 |
Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, dna, qiaampMinEluteSpinColumn); |
| 3176 |
06 Mar 15 |
olle |
2909 |
} |
| 3517 |
01 Oct 15 |
olle |
// Quality control reagents |
| 3517 |
01 Oct 15 |
olle |
2911 |
Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, dna, kapaSybrFast); |
| 3517 |
01 Oct 15 |
olle |
2912 |
Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, dna, qualityControlPrimersQcpRgt); |
| 3517 |
01 Oct 15 |
olle |
2913 |
Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, dna, qualityControlTemplateQct); |
| 3517 |
01 Oct 15 |
olle |
2914 |
Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, dna, qubitDnaHighSens); |
| 3517 |
01 Oct 15 |
olle |
2915 |
Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, dna, qubitDnaBroadRange); |
| 3176 |
06 Mar 15 |
olle |
2916 |
} |
| 3176 |
06 Mar 15 |
olle |
2917 |
|
| 3176 |
06 Mar 15 |
olle |
// RNA |
| 3433 |
29 Jun 15 |
olle |
2919 |
if (Meludi.itemIsSpecimen(itemName) || Meludi.itemIsRna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2920 |
{ |
| 3176 |
06 Mar 15 |
olle |
2921 |
JSONObject jsonRna = (JSONObject)jsonItem.get("rna"); |
| 3176 |
06 Mar 15 |
olle |
2922 |
Extract rna = null; |
| 3433 |
29 Jun 15 |
olle |
2923 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2924 |
{ |
| 3276 |
29 Apr 15 |
olle |
2925 |
Rna r = Rna.findByName(dc, itemName + ".r"); |
| 3276 |
29 Apr 15 |
olle |
2926 |
rna = r.getExtract(); |
| 3176 |
06 Mar 15 |
olle |
2927 |
} |
| 3433 |
29 Jun 15 |
olle |
2928 |
else if (Meludi.itemIsRna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2929 |
{ |
| 3176 |
06 Mar 15 |
olle |
2930 |
rna = Extract.getById(dc, itemId.intValue()); |
| 3176 |
06 Mar 15 |
olle |
2931 |
} |
| 3176 |
06 Mar 15 |
olle |
2932 |
rna.setItemSubtype(Subtype.RNA.load(dc)); |
| 3176 |
06 Mar 15 |
olle |
2933 |
rna.setDescription((String)jsonRna.get("comment")); |
| 3176 |
06 Mar 15 |
olle |
2934 |
BioMaterialEvent rnaEvent = rna.getCreationEvent(); |
| 3433 |
29 Jun 15 |
olle |
2935 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2936 |
{ |
| 3176 |
06 Mar 15 |
olle |
2937 |
rnaEvent.setEventDate(qiacubeDate); |
| 3176 |
06 Mar 15 |
olle |
2938 |
rnaEvent.setProtocol(extractionProtocol); |
| 3176 |
06 Mar 15 |
olle |
2939 |
rnaEvent.setSource(specimen).setUsedQuantity(itemProcessedQuantity / 3); |
| 3176 |
06 Mar 15 |
olle |
2940 |
} |
| 3432 |
29 Jun 15 |
olle |
//float rnaVolume = ((Number)jsonRna.get("volume")).floatValue(); |
| 3432 |
29 Jun 15 |
olle |
//float rnaNdConc = ((Number)jsonRna.get("ndConc")).floatValue(); |
| 3432 |
29 Jun 15 |
olle |
2943 |
float rnaVolume = fetchFloatValue(jsonRna.get("volume")); |
| 3432 |
29 Jun 15 |
olle |
2944 |
float rnaNdConc = fetchFloatValue(jsonRna.get("ndConc")); |
| 3176 |
06 Mar 15 |
olle |
2945 |
rna.setOriginalQuantity(rnaVolume * rnaNdConc / 1000); |
| 3433 |
29 Jun 15 |
olle |
2946 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2947 |
{ |
| 3276 |
29 Apr 15 |
olle |
2948 |
/* |
| 3176 |
06 Mar 15 |
olle |
//rna.setBioWell(StoragePlate.getChildBioWell(dc, specimenWell, "_sp", "_rna")); |
| 3253 |
17 Apr 15 |
olle |
rna.setBioWell((BioWell)freeRnaWells.get(numStoredRna)); |
| 3176 |
06 Mar 15 |
olle |
numStoredRna++; |
| 3276 |
29 Apr 15 |
olle |
2952 |
*/ |
| 3180 |
17 Mar 15 |
olle |
2953 |
Annotationtype.ISOLATION_DATE.setAnnotationValue(dc, rna, isolationDate); |
| 3501 |
21 Sep 15 |
olle |
2954 |
Annotationtype.EXTRACTION_OPERATOR.setAnnotationValue(dc, rna, extractionOperator); |
| 3176 |
06 Mar 15 |
olle |
2955 |
Annotationtype.QIACUBE_DATE.setAnnotationValue(dc, rna, qiacubeDate); |
| 3501 |
21 Sep 15 |
olle |
2956 |
Annotationtype.QIACUBE_OPERATOR.setAnnotationValue(dc, rna, qiacubeOperator); |
| 3176 |
06 Mar 15 |
olle |
2957 |
Annotationtype.QIACUBE_RUN_NO.setAnnotationValue(dc, rna, qiacubeRunNo); |
| 3176 |
06 Mar 15 |
olle |
2958 |
Annotationtype.QIACUBE_INSTRUMENT_PREFIX.setAnnotationValue(dc, rna, qiacubeInstrumentPrefix); |
| 3176 |
06 Mar 15 |
olle |
2959 |
Annotationtype.QIACUBE_POSITION.setAnnotationValue(dc, rna, qiacubePosition); |
| 3176 |
06 Mar 15 |
olle |
2960 |
} |
| 3176 |
06 Mar 15 |
olle |
2961 |
preNormalize = Boolean.TRUE.equals(jsonRna.get("preNormalize")); |
| 3176 |
06 Mar 15 |
olle |
2962 |
flagged = jsonRna.get("flag") != null; |
| 3176 |
06 Mar 15 |
olle |
2963 |
/* |
| 3176 |
06 Mar 15 |
olle |
if (preNormalize) |
| 3176 |
06 Mar 15 |
olle |
2965 |
{ |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, rna, Rna.AUTO_PROCESSING_PRE_NORMALIZE); |
| 3176 |
06 Mar 15 |
olle |
2967 |
} |
| 3176 |
06 Mar 15 |
olle |
2968 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2969 |
/* |
| 3176 |
06 Mar 15 |
olle |
else if (flagged) |
| 3176 |
06 Mar 15 |
olle |
2971 |
{ |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.FLAG.setAnnotationValue(dc, rna, jsonRna.get("flag")); |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, rna, "Disable"); |
| 3176 |
06 Mar 15 |
olle |
flagged = true; |
| 3176 |
06 Mar 15 |
olle |
numFlagged++; |
| 3176 |
06 Mar 15 |
olle |
flaggedRna.add(rna); |
| 3176 |
06 Mar 15 |
olle |
2977 |
} |
| 3176 |
06 Mar 15 |
olle |
2978 |
*/ |
| 3176 |
06 Mar 15 |
olle |
2979 |
Annotationtype.ND_CONC.setAnnotationValue(dc, rna, rnaNdConc); |
| 3176 |
06 Mar 15 |
olle |
2980 |
Annotationtype.ND_260_BY_280.setAnnotationValue(dc, rna, jsonRna.get("nd260by280")); |
| 3176 |
06 Mar 15 |
olle |
2981 |
Annotationtype.ND_260_BY_230.setAnnotationValue(dc, rna, jsonRna.get("nd260by230")); |
| 3176 |
06 Mar 15 |
olle |
// Reagents |
| 3433 |
29 Jun 15 |
olle |
2983 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
2984 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
2986 |
Annotationtype.ALLPREP_FFPE_KIT.setAnnotationValue(dc, rna, allPrepFfpeKit); |
| 3176 |
06 Mar 15 |
olle |
2987 |
Annotationtype.XYLENE_SPECIMEN.setAnnotationValue(dc, rna, xyleneSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2988 |
Annotationtype.ETOH995_SPECIMEN.setAnnotationValue(dc, rna, etoh995Specimen); |
| 3176 |
06 Mar 15 |
olle |
2989 |
Annotationtype.BUFFER_PKD_SPECIMEN.setAnnotationValue(dc, rna, bufferPkdSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2990 |
Annotationtype.BUFFER_ATL_SPECIMEN.setAnnotationValue(dc, rna, bufferAtlSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2991 |
Annotationtype.PROTEINASE_K_SPECIMEN.setAnnotationValue(dc, rna, proteinaseKSpecimen); |
| 3176 |
06 Mar 15 |
olle |
2992 |
Annotationtype.RNASE_A_SPECIMEN.setAnnotationValue(dc, rna, rnaseASpecimen); |
| 3176 |
06 Mar 15 |
olle |
2993 |
|
| 3176 |
06 Mar 15 |
olle |
// QIAcube reagents |
| 3176 |
06 Mar 15 |
olle |
2995 |
Annotationtype.ETOH995.setAnnotationValue(dc, rna, etoh995); |
| 3176 |
06 Mar 15 |
olle |
2996 |
Annotationtype.BUFFER_RLT.setAnnotationValue(dc, rna, bufferRlt); |
| 3176 |
06 Mar 15 |
olle |
2997 |
Annotationtype.BUFFER_FRN.setAnnotationValue(dc, rna, bufferFrn); |
| 3176 |
06 Mar 15 |
olle |
2998 |
Annotationtype.BUFFER_RPE.setAnnotationValue(dc, rna, bufferRpe); |
| 3176 |
06 Mar 15 |
olle |
2999 |
Annotationtype.BUFFER_AL.setAnnotationValue(dc, rna, bufferAl); |
| 3176 |
06 Mar 15 |
olle |
3000 |
Annotationtype.BUFFER_AW1.setAnnotationValue(dc, rna, bufferAw1); |
| 3176 |
06 Mar 15 |
olle |
3001 |
Annotationtype.BUFFER_AW2.setAnnotationValue(dc, rna, bufferAw2); |
| 3176 |
06 Mar 15 |
olle |
3002 |
Annotationtype.BUFFER_ATE.setAnnotationValue(dc, rna, bufferAte); |
| 3176 |
06 Mar 15 |
olle |
3003 |
Annotationtype.BUFFER_RDD.setAnnotationValue(dc, rna, bufferRdd); |
| 3176 |
06 Mar 15 |
olle |
3004 |
Annotationtype.RNASE_FREE_WATER.setAnnotationValue(dc, rna, rnaseFreeWater); |
| 3176 |
06 Mar 15 |
olle |
3005 |
Annotationtype.DNASE_MIX.setAnnotationValue(dc, rna, dnaseMix); |
| 3176 |
06 Mar 15 |
olle |
3006 |
Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, rna, rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
3007 |
Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, rna, qiaampMinEluteSpinColumn); |
| 3176 |
06 Mar 15 |
olle |
3008 |
} |
| 3517 |
01 Oct 15 |
olle |
// Quality control reagents |
| 3517 |
01 Oct 15 |
olle |
3010 |
Annotationtype.KAPA_SYBR_FAST.setAnnotationValue(dc, rna, kapaSybrFast); |
| 3517 |
01 Oct 15 |
olle |
3011 |
Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, rna, qualityControlPrimersQcpRgt); |
| 3517 |
01 Oct 15 |
olle |
3012 |
Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, rna, qualityControlTemplateQct); |
| 3517 |
01 Oct 15 |
olle |
3013 |
Annotationtype.QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, rna, qubitDnaHighSens); |
| 3517 |
01 Oct 15 |
olle |
3014 |
Annotationtype.QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, rna, qubitDnaBroadRange); |
| 3176 |
06 Mar 15 |
olle |
3015 |
} |
| 3176 |
06 Mar 15 |
olle |
3016 |
|
| 3176 |
06 Mar 15 |
olle |
3017 |
String msg = ""; |
| 3433 |
29 Jun 15 |
olle |
3018 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3176 |
06 Mar 15 |
olle |
3019 |
{ |
| 3276 |
29 Apr 15 |
olle |
3020 |
msg += "RNA and DNA updated for " + itemName; |
| 3176 |
06 Mar 15 |
olle |
3021 |
} |
| 3433 |
29 Jun 15 |
olle |
3022 |
else if (Meludi.itemIsRna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
3023 |
{ |
| 3176 |
06 Mar 15 |
olle |
3024 |
msg += "RNA data updated for " + itemName; |
| 3176 |
06 Mar 15 |
olle |
3025 |
} |
| 3433 |
29 Jun 15 |
olle |
3026 |
else if (Meludi.itemIsDna(itemName)) |
| 3176 |
06 Mar 15 |
olle |
3027 |
{ |
| 3176 |
06 Mar 15 |
olle |
3028 |
msg += "DNA data updated for " + itemName; |
| 3176 |
06 Mar 15 |
olle |
3029 |
} |
| 3180 |
17 Mar 15 |
olle |
3030 |
/* |
| 3176 |
06 Mar 15 |
olle |
if (flagged) |
| 3176 |
06 Mar 15 |
olle |
3032 |
{ |
| 3176 |
06 Mar 15 |
olle |
msg += " (Flagged)"; |
| 3176 |
06 Mar 15 |
olle |
3034 |
} |
| 3180 |
17 Mar 15 |
olle |
3035 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3036 |
else if (!preNormalize) |
| 3176 |
06 Mar 15 |
olle |
3037 |
{ |
| 3176 |
06 Mar 15 |
olle |
3038 |
msg += " (No RNA normalization)"; |
| 3176 |
06 Mar 15 |
olle |
3039 |
} |
| 3176 |
06 Mar 15 |
olle |
3040 |
jsonMessages.add(msg); |
| 3176 |
06 Mar 15 |
olle |
3041 |
} |
| 3176 |
06 Mar 15 |
olle |
3042 |
|
| 3176 |
06 Mar 15 |
olle |
3043 |
/* |
| 3176 |
06 Mar 15 |
olle |
if (numFlagged > 0) |
| 3176 |
06 Mar 15 |
olle |
3045 |
{ |
| 3176 |
06 Mar 15 |
olle |
jsonMessages.add(numFlagged + " RNA added to " + flaggedRna.getName() + " list"); |
| 3176 |
06 Mar 15 |
olle |
3047 |
} |
| 3176 |
06 Mar 15 |
olle |
3048 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3049 |
|
| 3176 |
06 Mar 15 |
olle |
3050 |
dc.commit(); |
| 3276 |
29 Apr 15 |
olle |
3051 |
/* |
| 3176 |
06 Mar 15 |
olle |
for (Extract rna : newRna) |
| 3176 |
06 Mar 15 |
olle |
3053 |
{ |
| 3176 |
06 Mar 15 |
olle |
jsonCreatedRna.add(rna.getId()); |
| 3176 |
06 Mar 15 |
olle |
3055 |
} |
| 3176 |
06 Mar 15 |
olle |
json.put("createdRna", jsonCreatedRna); |
| 3176 |
06 Mar 15 |
olle |
for (Extract dna : newDna) |
| 3176 |
06 Mar 15 |
olle |
3058 |
{ |
| 3176 |
06 Mar 15 |
olle |
jsonCreatedDna.add(dna.getId()); |
| 3176 |
06 Mar 15 |
olle |
3060 |
} |
| 3176 |
06 Mar 15 |
olle |
json.put("createdDna", jsonCreatedDna); |
| 3276 |
29 Apr 15 |
olle |
3062 |
*/ |
| 3502 |
22 Sep 15 |
olle |
3063 |
CounterService.getInstance().setForceCount(); |
| 3176 |
06 Mar 15 |
olle |
3064 |
} |
| 3176 |
06 Mar 15 |
olle |
3065 |
else if ("RegisterNormalizedRNA".equals(cmd)) |
| 3176 |
06 Mar 15 |
olle |
3066 |
{ |
| 3176 |
06 Mar 15 |
olle |
3067 |
dc = sc.newDbControl(); |
| 3176 |
06 Mar 15 |
olle |
3068 |
|
| 3176 |
06 Mar 15 |
olle |
3069 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3176 |
06 Mar 15 |
olle |
3070 |
|
| 3176 |
06 Mar 15 |
olle |
3071 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3176 |
06 Mar 15 |
olle |
3072 |
JSONArray jsonRnaAliquots = (JSONArray)jsonReq.get("rnaAliquots"); |
| 3176 |
06 Mar 15 |
olle |
3073 |
|
| 3176 |
06 Mar 15 |
olle |
3074 |
/* |
| 3176 |
06 Mar 15 |
olle |
ItemSubtype subtypeNormalized = Subtype.RNA_NORMALIZED_ALIQUOT.load(dc); |
| 3176 |
06 Mar 15 |
olle |
3076 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3077 |
|
| 3176 |
06 Mar 15 |
olle |
3078 |
Date normalizationDate = Meludi.CONVERTER_STRING_TO_DATE.convert((String)jsonReq.get("normalizationDate")); |
| 3176 |
06 Mar 15 |
olle |
3079 |
String operator = (String)jsonReq.get("normalizationOperator"); |
| 3176 |
06 Mar 15 |
olle |
3080 |
|
| 3176 |
06 Mar 15 |
olle |
3081 |
for (int i = 0; i < jsonRnaAliquots.size(); ++i) |
| 3176 |
06 Mar 15 |
olle |
3082 |
{ |
| 3176 |
06 Mar 15 |
olle |
3083 |
JSONObject jsonRnaAliquot = (JSONObject)jsonRnaAliquots.get(i); |
| 3176 |
06 Mar 15 |
olle |
3084 |
|
| 3176 |
06 Mar 15 |
olle |
// Get the RNA extract which is the parent |
| 3176 |
06 Mar 15 |
olle |
3086 |
Number parentRnaId = (Number)jsonRnaAliquot.get("parentId"); |
| 3176 |
06 Mar 15 |
olle |
3087 |
Extract parentRna = Extract.getById(dc, parentRnaId.intValue()); |
| 3176 |
06 Mar 15 |
olle |
3088 |
|
| 3176 |
06 Mar 15 |
olle |
3089 |
/* |
| 3176 |
06 Mar 15 |
olle |
// Disable further processing of parent RNA |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.AUTO_PROCESSING.setAnnotationValue(dc, parentRna, "Disable"); |
| 3176 |
06 Mar 15 |
olle |
3092 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3093 |
|
| 3176 |
06 Mar 15 |
olle |
// Create a child RNAQC extract |
| 3176 |
06 Mar 15 |
olle |
3095 |
Extract normalizedRna = Extract.getNew(dc); |
| 3176 |
06 Mar 15 |
olle |
3096 |
/* |
| 3176 |
06 Mar 15 |
olle |
normalizedRna.setItemSubtype(subtypeNormalized); |
| 3176 |
06 Mar 15 |
olle |
3098 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3099 |
normalizedRna.setName((String)jsonRnaAliquot.get("name")); |
| 3176 |
06 Mar 15 |
olle |
3100 |
|
| 3176 |
06 Mar 15 |
olle |
3101 |
/* |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.DILUTION_DATE.setAnnotationValue(dc, normalizedRna, normalizationDate); |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.DILUTION_OPERATOR.setAnnotationValue(dc, normalizedRna, operator); |
| 3176 |
06 Mar 15 |
olle |
3104 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3105 |
|
| 3176 |
06 Mar 15 |
olle |
3106 |
BioMaterialEvent creationEvent = normalizedRna.getCreationEvent(); |
| 3176 |
06 Mar 15 |
olle |
3107 |
creationEvent.setEventDate(normalizationDate); |
| 3176 |
06 Mar 15 |
olle |
3108 |
|
| 3176 |
06 Mar 15 |
olle |
3109 |
Number usedQuantity = (Number)jsonRnaAliquot.get("usedQuantity"); |
| 3432 |
29 Jun 15 |
olle |
//normalizedRna.setOriginalQuantity(usedQuantity.floatValue()); |
| 3432 |
29 Jun 15 |
olle |
3111 |
normalizedRna.setOriginalQuantity(fetchFloatValue(usedQuantity)); |
| 3176 |
06 Mar 15 |
olle |
3112 |
BioMaterialEventSource evtSrc = creationEvent.setSource(parentRna); |
| 3432 |
29 Jun 15 |
olle |
//evtSrc.setUsedQuantity(usedQuantity.floatValue()); |
| 3432 |
29 Jun 15 |
olle |
3114 |
evtSrc.setUsedQuantity(fetchFloatValue(usedQuantity)); |
| 3176 |
06 Mar 15 |
olle |
3115 |
|
| 3176 |
06 Mar 15 |
olle |
3116 |
/* |
| 3176 |
06 Mar 15 |
olle |
Number ndConc = (Number)jsonRnaAliquot.get("NDConc"); |
| 3176 |
06 Mar 15 |
olle |
Annotationtype.ND_CONC.setAnnotationValue(dc, normalizedRna, ndConc.floatValue()); |
| 3176 |
06 Mar 15 |
olle |
3119 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3120 |
|
| 3176 |
06 Mar 15 |
olle |
3121 |
jsonMessages.add("Created '" + normalizedRna.getName() + "' normalized RNA"); |
| 3176 |
06 Mar 15 |
olle |
3122 |
dc.saveItem(normalizedRna); |
| 3176 |
06 Mar 15 |
olle |
3123 |
} |
| 3176 |
06 Mar 15 |
olle |
3124 |
|
| 3176 |
06 Mar 15 |
olle |
3125 |
dc.commit(); |
| 3176 |
06 Mar 15 |
olle |
3126 |
} |
| 3441 |
21 Jul 15 |
olle |
3127 |
else if ("CreateStartListsFromStartPlates".equals(cmd)) |
| 3441 |
21 Jul 15 |
olle |
3128 |
{ |
| 3441 |
21 Jul 15 |
olle |
3129 |
dc = sc.newDbControl(); |
| 3176 |
06 Mar 15 |
olle |
3130 |
|
| 3441 |
21 Jul 15 |
olle |
3131 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3441 |
21 Jul 15 |
olle |
3132 |
|
| 3441 |
21 Jul 15 |
olle |
3133 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3441 |
21 Jul 15 |
olle |
3134 |
JSONArray jsonStartPlateIds = (JSONArray)jsonReq.get("startplates"); |
| 3441 |
21 Jul 15 |
olle |
3135 |
|
| 3441 |
21 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doPost(): cmd = \"" + cmd + "\" jsonStartPlateIds = " + jsonStartPlateIds); |
| 3441 |
21 Jul 15 |
olle |
3137 |
|
| 3441 |
21 Jul 15 |
olle |
3138 |
List<Integer> startPlateIds = new ArrayList<Integer>(); |
| 3441 |
21 Jul 15 |
olle |
3139 |
int numSpecimen = 0; |
| 3441 |
21 Jul 15 |
olle |
3140 |
int numRna = 0; |
| 3441 |
21 Jul 15 |
olle |
3141 |
int numDna = 0; |
| 3441 |
21 Jul 15 |
olle |
3142 |
for (int i = 0; i < jsonStartPlateIds.size(); i++) |
| 3441 |
21 Jul 15 |
olle |
3143 |
{ |
| 3441 |
21 Jul 15 |
olle |
3144 |
JSONObject jsonStartPlateId = (JSONObject)jsonStartPlateIds.get(i); |
| 3441 |
21 Jul 15 |
olle |
3145 |
String startPlateIdStr = (String)jsonStartPlateId.get("id"); |
| 3441 |
21 Jul 15 |
olle |
3146 |
Integer startPlateId = Values.getInteger(startPlateIdStr, null); |
| 3441 |
21 Jul 15 |
olle |
3147 |
if (startPlateId != null) |
| 3441 |
21 Jul 15 |
olle |
3148 |
{ |
| 3441 |
21 Jul 15 |
olle |
3149 |
startPlateIds.add(startPlateId); |
| 3441 |
21 Jul 15 |
olle |
3150 |
} |
| 3441 |
21 Jul 15 |
olle |
3151 |
} |
| 3441 |
21 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doPost(): cmd = \"" + cmd + "\" startPlateIds = " + startPlateIds); |
| 3441 |
21 Jul 15 |
olle |
3153 |
|
| 3441 |
21 Jul 15 |
olle |
3154 |
JSONObject jsonStartItemList = new JSONObject(); |
| 3441 |
21 Jul 15 |
olle |
3155 |
JSONArray jsonSpecimen = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3156 |
JSONArray jsonRna = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3157 |
JSONArray jsonDna = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3158 |
JSONArray jsonItems = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3159 |
JSONArray jsonExtraItems = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3160 |
|
| 3441 |
21 Jul 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3441 |
21 Jul 15 |
olle |
3162 |
SnapshotManager manager = new SnapshotManager(); |
| 3441 |
21 Jul 15 |
olle |
3163 |
|
| 3441 |
21 Jul 15 |
olle |
3164 |
for (Integer startPlateId: startPlateIds) |
| 3441 |
21 Jul 15 |
olle |
3165 |
{ |
| 3441 |
21 Jul 15 |
olle |
3166 |
BioPlate startPlate = BioPlate.getById(dc, startPlateId); |
| 3441 |
21 Jul 15 |
olle |
3167 |
if (startPlate != null) |
| 3441 |
21 Jul 15 |
olle |
3168 |
{ |
| 3441 |
21 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doPost(): cmd = \"" + cmd + "\" startPlate.getName() = " + startPlate.getName()); |
| 3441 |
21 Jul 15 |
olle |
// Get start plate extraction date |
| 3441 |
21 Jul 15 |
olle |
3171 |
Date extractionDate = startPlate.getEventDate(); |
| 3441 |
21 Jul 15 |
olle |
3172 |
|
| 3441 |
21 Jul 15 |
olle |
// Get start plate extraction annotations |
| 3441 |
21 Jul 15 |
olle |
3174 |
Date isolationDate = (Date) Annotationtype.BATCH_ISOLATION_DATE.getAnnotationValue(dc, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3175 |
Number extractionProtocolId = (Number) Annotationtype.BATCH_EXTRACTION_PROTOCOL_ID.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3176 |
Protocol extractionProtocol = extractionProtocolId != null ? Protocol.getById(dc, extractionProtocolId.intValue()) : null; |
| 3441 |
21 Jul 15 |
olle |
3177 |
String extractionProtocolName = (String)Annotationtype.BATCH_EXTRACTION_PROTOCOL_NAME.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3178 |
Float rnaDefaultVolume = (Float)Annotationtype.BATCH_RNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3179 |
Float dnaDefaultVolume = (Float)Annotationtype.BATCH_DNA_DEFAULT_VOLUME_IN_MICROLITRE.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3180 |
|
| 3441 |
21 Jul 15 |
olle |
// Get start plate QIAcube annotations |
| 3441 |
21 Jul 15 |
olle |
3182 |
Date qiacubeDate = (Date) Annotationtype.BATCH_QIACUBE_DATE.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3183 |
String qiacubePrimaryPrefix = (String)Annotationtype.BATCH_QIACUBE_PRIMARY_PREFIX.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3184 |
String qiacubeSecondaryPrefix = (String)Annotationtype.BATCH_QIACUBE_SECONDARY_PREFIX.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3185 |
Integer qiacubeRunNo = (Integer)Annotationtype.BATCH_QIACUBE_RUN_NO.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3186 |
String qiacubeOperator = (String)Annotationtype.BATCH_QIACUBE_OPERATOR.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3187 |
String allPrepFfpeKit = (String)Annotationtype.BATCH_ALLPREP_FFPE_KIT.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3188 |
|
| 3441 |
21 Jul 15 |
olle |
// Get start plate item names annotations |
| 3441 |
21 Jul 15 |
olle |
3190 |
List<String> itemNameList = (List<String>) Annotationtype.SOURCE_ITEM_NAMES_LIST_STRING.getAnnotationValues(dc, startPlate, true, true); |
| 3441 |
21 Jul 15 |
olle |
3191 |
List<String> extraItemNameList = (List<String>) Annotationtype.EXTRA_QIACUBE_ITEM_NAMES_LIST_STRING.getAnnotationValues(dc, startPlate, true, true); |
| 3441 |
21 Jul 15 |
olle |
3192 |
Integer numExtraQiacubeItems = (Integer)Annotationtype.BATCH_NUMBER_EXTRA_QIACUBE_ITEMS.getAnnotationValue(dc, manager, startPlate); |
| 3441 |
21 Jul 15 |
olle |
3193 |
|
| 3441 |
21 Jul 15 |
olle |
// Convert item names to items |
| 3441 |
21 Jul 15 |
olle |
3195 |
List<Extract> meludiItemList = new ArrayList<Extract>(); |
| 3441 |
21 Jul 15 |
olle |
3196 |
List<Extract> extraItemList = new ArrayList<Extract>(); |
| 3441 |
21 Jul 15 |
olle |
3197 |
if (itemNameList != null) |
| 3441 |
21 Jul 15 |
olle |
3198 |
{ |
| 3441 |
21 Jul 15 |
olle |
3199 |
for (String itemName : itemNameList) |
| 3441 |
21 Jul 15 |
olle |
3200 |
{ |
| 3441 |
21 Jul 15 |
olle |
3201 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3202 |
{ |
| 3441 |
21 Jul 15 |
olle |
// A specimen is represented by its DNA child extract |
| 3441 |
21 Jul 15 |
olle |
3204 |
String dnaName = itemName + ".d"; |
| 3441 |
21 Jul 15 |
olle |
3205 |
Dna d = Dna.findByName(dc, dnaName); |
| 3441 |
21 Jul 15 |
olle |
3206 |
if (d != null) |
| 3441 |
21 Jul 15 |
olle |
3207 |
{ |
| 3441 |
21 Jul 15 |
olle |
3208 |
meludiItemList.add(d.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3209 |
} |
| 3441 |
21 Jul 15 |
olle |
3210 |
} |
| 3441 |
21 Jul 15 |
olle |
3211 |
else if (Meludi.itemIsRna(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3212 |
{ |
| 3441 |
21 Jul 15 |
olle |
3213 |
Rna r = Rna.findByName(dc, itemName); |
| 3441 |
21 Jul 15 |
olle |
3214 |
if (r != null) |
| 3441 |
21 Jul 15 |
olle |
3215 |
{ |
| 3441 |
21 Jul 15 |
olle |
3216 |
meludiItemList.add(r.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3217 |
} |
| 3441 |
21 Jul 15 |
olle |
3218 |
} |
| 3441 |
21 Jul 15 |
olle |
3219 |
else if (Meludi.itemIsDna(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3220 |
{ |
| 3441 |
21 Jul 15 |
olle |
3221 |
Dna d = Dna.findByName(dc, itemName); |
| 3441 |
21 Jul 15 |
olle |
3222 |
if (d != null) |
| 3441 |
21 Jul 15 |
olle |
3223 |
{ |
| 3441 |
21 Jul 15 |
olle |
3224 |
meludiItemList.add(d.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3225 |
} |
| 3441 |
21 Jul 15 |
olle |
3226 |
} |
| 3441 |
21 Jul 15 |
olle |
3227 |
} |
| 3441 |
21 Jul 15 |
olle |
3228 |
} |
| 3441 |
21 Jul 15 |
olle |
3229 |
|
| 3441 |
21 Jul 15 |
olle |
// Create default names for extra QIAcube items, if none are specified |
| 3441 |
21 Jul 15 |
olle |
3231 |
if (extraItemNameList == null || extraItemNameList.size() == 0) |
| 3441 |
21 Jul 15 |
olle |
3232 |
{ |
| 3441 |
21 Jul 15 |
olle |
3233 |
extraItemNameList = new ArrayList<String>(); |
| 3441 |
21 Jul 15 |
olle |
3234 |
if (numExtraQiacubeItems != null) |
| 3441 |
21 Jul 15 |
olle |
3235 |
{ |
| 3441 |
21 Jul 15 |
olle |
3236 |
for (int i = 1; i <= numExtraQiacubeItems; i++) |
| 3441 |
21 Jul 15 |
olle |
3237 |
{ |
| 3441 |
21 Jul 15 |
olle |
// Create extra item names as E01, E02, ... ,E09, E10, E11, ... |
| 3441 |
21 Jul 15 |
olle |
3239 |
// |
| 3441 |
21 Jul 15 |
olle |
// Note that these names will only be unique for a single start list |
| 3441 |
21 Jul 15 |
olle |
3241 |
// |
| 3441 |
21 Jul 15 |
olle |
3242 |
String itemName = "E"; |
| 3441 |
21 Jul 15 |
olle |
3243 |
if (i < 10) |
| 3441 |
21 Jul 15 |
olle |
3244 |
{ |
| 3441 |
21 Jul 15 |
olle |
3245 |
itemName += "0"; |
| 3441 |
21 Jul 15 |
olle |
3246 |
} |
| 3441 |
21 Jul 15 |
olle |
3247 |
extraItemNameList.add(itemName); |
| 3441 |
21 Jul 15 |
olle |
3248 |
} |
| 3441 |
21 Jul 15 |
olle |
3249 |
} |
| 3441 |
21 Jul 15 |
olle |
3250 |
} |
| 3441 |
21 Jul 15 |
olle |
3251 |
|
| 3441 |
21 Jul 15 |
olle |
// Convert extra QIAcube item names to items |
| 3441 |
21 Jul 15 |
olle |
3253 |
// |
| 3441 |
21 Jul 15 |
olle |
// Extra QIAcube items were not registered as items in MeLuDI |
| 3441 |
21 Jul 15 |
olle |
// prior to version 1.3, so these items may have to be created |
| 3441 |
21 Jul 15 |
olle |
// using the "Register new extra material" wizard, before running |
| 3441 |
21 Jul 15 |
olle |
// this command. |
| 3441 |
21 Jul 15 |
olle |
3258 |
// |
| 3441 |
21 Jul 15 |
olle |
3259 |
if (extraItemNameList != null && extraItemNameList.size() > 0) |
| 3441 |
21 Jul 15 |
olle |
3260 |
{ |
| 3441 |
21 Jul 15 |
olle |
3261 |
for (String itemName : extraItemNameList) |
| 3441 |
21 Jul 15 |
olle |
3262 |
{ |
| 3441 |
21 Jul 15 |
olle |
3263 |
if (Meludi.itemIsSpecimen(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3264 |
{ |
| 3441 |
21 Jul 15 |
olle |
// A specimen is represented by its DNA child extract |
| 3441 |
21 Jul 15 |
olle |
3266 |
String dnaName = itemName + ".d"; |
| 3441 |
21 Jul 15 |
olle |
3267 |
Dna d = Dna.findByName(dc, dnaName); |
| 3441 |
21 Jul 15 |
olle |
3268 |
if (d != null) |
| 3441 |
21 Jul 15 |
olle |
3269 |
{ |
| 3441 |
21 Jul 15 |
olle |
3270 |
extraItemList.add(d.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3271 |
} |
| 3441 |
21 Jul 15 |
olle |
3272 |
} |
| 3441 |
21 Jul 15 |
olle |
3273 |
else if (Meludi.itemIsRna(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3274 |
{ |
| 3441 |
21 Jul 15 |
olle |
3275 |
Rna r = Rna.findByName(dc, itemName); |
| 3441 |
21 Jul 15 |
olle |
3276 |
if (r != null) |
| 3441 |
21 Jul 15 |
olle |
3277 |
{ |
| 3441 |
21 Jul 15 |
olle |
3278 |
extraItemList.add(r.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3279 |
} |
| 3441 |
21 Jul 15 |
olle |
3280 |
} |
| 3441 |
21 Jul 15 |
olle |
3281 |
else if (Meludi.itemIsDna(itemName)) |
| 3441 |
21 Jul 15 |
olle |
3282 |
{ |
| 3441 |
21 Jul 15 |
olle |
3283 |
Dna d = Dna.findByName(dc, itemName); |
| 3441 |
21 Jul 15 |
olle |
3284 |
if (d != null) |
| 3441 |
21 Jul 15 |
olle |
3285 |
{ |
| 3441 |
21 Jul 15 |
olle |
3286 |
extraItemList.add(d.getExtract()); |
| 3441 |
21 Jul 15 |
olle |
3287 |
} |
| 3441 |
21 Jul 15 |
olle |
3288 |
} |
| 3441 |
21 Jul 15 |
olle |
3289 |
} |
| 3441 |
21 Jul 15 |
olle |
3290 |
} |
| 3441 |
21 Jul 15 |
olle |
3291 |
|
| 3441 |
21 Jul 15 |
olle |
// Create start item list |
| 3441 |
21 Jul 15 |
olle |
3293 |
ItemList startItemList = null; |
| 3441 |
21 Jul 15 |
olle |
3294 |
JSONArray jsonCreatedStartItemList = new JSONArray(); |
| 3441 |
21 Jul 15 |
olle |
3295 |
|
| 4200 |
01 Nov 16 |
olle |
// Set start item list name to start plate name with start plate prefix exchanged for start list prefix |
| 3441 |
21 Jul 15 |
olle |
3297 |
String startPlateName = startPlate.getName(); |
| 4150 |
03 Oct 16 |
olle |
3298 |
String startPlatePrefix = Meludi.fetchStartPlateItemPrefix(sc.getActiveProjectId()); |
| 4150 |
03 Oct 16 |
olle |
3299 |
String nameWithoutPrefix = startPlateName.substring(startPlatePrefix.length()); |
| 4150 |
03 Oct 16 |
olle |
3300 |
String itemListName = Meludi.fetchStartListItemPrefix(sc.getActiveProjectId()) + nameWithoutPrefix; |
| 3441 |
21 Jul 15 |
olle |
3301 |
if (itemListName != null && !itemListName.equals("")) |
| 3441 |
21 Jul 15 |
olle |
3302 |
{ |
| 3441 |
21 Jul 15 |
olle |
3303 |
startItemList = ItemList.getNew(dc, Item.EXTRACT); |
| 3441 |
21 Jul 15 |
olle |
3304 |
startItemList.setName(itemListName); |
| 3441 |
21 Jul 15 |
olle |
3305 |
jsonMessages.add("Created '" + startItemList.getName() + "' Start item list"); |
| 3441 |
21 Jul 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doPost(): cmd = \"" + cmd + "\" startItemList.getName() = " + startItemList.getName()); |
| 3441 |
21 Jul 15 |
olle |
3307 |
|
| 3441 |
21 Jul 15 |
olle |
// Set start list extraction annotations |
| 3441 |
21 Jul 15 |
olle |
3309 |
Annotationtype.LIST_EXTRACTION_DATE.setAnnotationValue(dc, startItemList, extractionDate); |
| 3441 |
21 Jul 15 |
olle |
3310 |
Annotationtype.LIST_ISOLATION_DATE.setAnnotationValue(dc, startItemList, isolationDate); |
| 3441 |
21 Jul 15 |
olle |
3311 |
Annotationtype.LIST_EXTRACTION_PROTOCOL_ID.setAnnotationValue(dc, startItemList, extractionProtocolId); |
| 3441 |
21 Jul 15 |
olle |
3312 |
Annotationtype.LIST_EXTRACTION_PROTOCOL_NAME.setAnnotationValue(dc, startItemList, extractionProtocolName); |
| 3441 |
21 Jul 15 |
olle |
3313 |
Annotationtype.LIST_RNA_DEFAULT_VOLUME_IN_MICROLITRE.setAnnotationValue(dc, startItemList, rnaDefaultVolume); |
| 3441 |
21 Jul 15 |
olle |
3314 |
Annotationtype.LIST_DNA_DEFAULT_VOLUME_IN_MICROLITRE.setAnnotationValue(dc, startItemList, dnaDefaultVolume); |
| 3441 |
21 Jul 15 |
olle |
3315 |
|
| 3441 |
21 Jul 15 |
olle |
// Set start list QIAcube annotations |
| 3441 |
21 Jul 15 |
olle |
3317 |
Annotationtype.LIST_QIACUBE_DATE.setAnnotationValue(dc, startItemList, qiacubeDate); |
| 3441 |
21 Jul 15 |
olle |
3318 |
Annotationtype.LIST_QIACUBE_PRIMARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubePrimaryPrefix); |
| 3441 |
21 Jul 15 |
olle |
3319 |
Annotationtype.LIST_QIACUBE_SECONDARY_PREFIX.setAnnotationValue(dc, startItemList, qiacubeSecondaryPrefix); |
| 3441 |
21 Jul 15 |
olle |
3320 |
Annotationtype.LIST_QIACUBE_RUN_NO.setAnnotationValue(dc, startItemList, qiacubeRunNo); |
| 3441 |
21 Jul 15 |
olle |
3321 |
Annotationtype.LIST_QIACUBE_OPERATOR.setAnnotationValue(dc, startItemList, qiacubeOperator); |
| 3441 |
21 Jul 15 |
olle |
3322 |
Annotationtype.LIST_ALLPREP_FFPE_KIT.setAnnotationValue(dc, startItemList, allPrepFfpeKit); |
| 3441 |
21 Jul 15 |
olle |
3323 |
|
| 3445 |
23 Jul 15 |
olle |
3324 |
if (extractionDate != null) |
| 3445 |
23 Jul 15 |
olle |
3325 |
{ |
| 3445 |
23 Jul 15 |
olle |
// A set extraction date = start plate creation date indicates |
| 3445 |
23 Jul 15 |
olle |
// that the plate is processed, i.e. that concentrations and delta-Ct |
| 3445 |
23 Jul 15 |
olle |
// values have been registered for extracts related to the plate. |
| 3445 |
23 Jul 15 |
olle |
// However, in MeLuDI v1.2.* the latter data was only registered for MeLuDI items, |
| 3445 |
23 Jul 15 |
olle |
// not for extra material. |
| 3445 |
23 Jul 15 |
olle |
3331 |
// |
| 3445 |
23 Jul 15 |
olle |
// A processed start item list is indicated by annotation |
| 3445 |
23 Jul 15 |
olle |
// "SamplePrepListIsProcessed" having value `true`. |
| 3445 |
23 Jul 15 |
olle |
// If the start plate was processed and not contained extra material, |
| 3445 |
23 Jul 15 |
olle |
// the created item list should also be indicated as processed. |
| 3445 |
23 Jul 15 |
olle |
// This should not be done for start lists with extra material, as it would |
| 3446 |
27 Jul 15 |
olle |
// prevent the start list from being opened in the "DNA/RNA registration/quantification" |
| 3445 |
23 Jul 15 |
olle |
// wizard, in order to register concentrations and delta-Ct values for the extra material. |
| 3445 |
23 Jul 15 |
olle |
3339 |
if (extraItemNameList == null || extraItemNameList.size() == 0) |
| 3445 |
23 Jul 15 |
olle |
3340 |
{ |
| 3445 |
23 Jul 15 |
olle |
// Mark created start item list as processed |
| 3445 |
23 Jul 15 |
olle |
3342 |
Annotationtype.SAMPLE_PREP_LIST_IS_PROCESSED.setAnnotationValue(dc, startItemList, true); |
| 3445 |
23 Jul 15 |
olle |
3343 |
} |
| 3445 |
23 Jul 15 |
olle |
3344 |
} |
| 3445 |
23 Jul 15 |
olle |
3345 |
|
| 3441 |
21 Jul 15 |
olle |
// Add extract member items to start item list |
| 3441 |
21 Jul 15 |
olle |
3347 |
for (Extract item: meludiItemList) |
| 3441 |
21 Jul 15 |
olle |
3348 |
{ |
| 3441 |
21 Jul 15 |
olle |
3349 |
startItemList.add(item); |
| 3441 |
21 Jul 15 |
olle |
3350 |
jsonMessages.add("Extract " + item.getName() + " added as member to start item list " + startItemList.getName()); |
| 3441 |
21 Jul 15 |
olle |
3351 |
} |
| 3441 |
21 Jul 15 |
olle |
3352 |
for (Extract item: extraItemList) |
| 3441 |
21 Jul 15 |
olle |
3353 |
{ |
| 3441 |
21 Jul 15 |
olle |
3354 |
startItemList.add(item); |
| 3441 |
21 Jul 15 |
olle |
3355 |
jsonMessages.add("Extract " + item.getName() + " added as member to start item list " + startItemList.getName()); |
| 3441 |
21 Jul 15 |
olle |
3356 |
} |
| 3441 |
21 Jul 15 |
olle |
3357 |
// |
| 3441 |
21 Jul 15 |
olle |
3358 |
dc.saveItem(startItemList); |
| 3441 |
21 Jul 15 |
olle |
3359 |
} |
| 3441 |
21 Jul 15 |
olle |
3360 |
} |
| 3441 |
21 Jul 15 |
olle |
3361 |
} |
| 3441 |
21 Jul 15 |
olle |
3362 |
|
| 3441 |
21 Jul 15 |
olle |
3363 |
dc.commit(); |
| 3502 |
22 Sep 15 |
olle |
3364 |
CounterService.getInstance().setForceCount(); |
| 3441 |
21 Jul 15 |
olle |
3365 |
} |
| 3501 |
21 Sep 15 |
olle |
3366 |
else if ("UpdateStartListsWithLotNumbersFromExtracts".equals(cmd)) |
| 3501 |
21 Sep 15 |
olle |
3367 |
{ |
| 3501 |
21 Sep 15 |
olle |
3368 |
dc = sc.newDbControl(); |
| 3501 |
21 Sep 15 |
olle |
3369 |
|
| 3501 |
21 Sep 15 |
olle |
3370 |
MeludiRole.checkPermission(dc, "'" + cmd + "' wizard", MeludiRole.SAMPLE_PREP, MeludiRole.ADMINISTRATOR); |
| 3501 |
21 Sep 15 |
olle |
3371 |
|
| 3501 |
21 Sep 15 |
olle |
3372 |
JSONObject jsonReq = (JSONObject)new JSONParser().parse(req.getReader()); |
| 3501 |
21 Sep 15 |
olle |
3373 |
JSONArray jsonStartItemListIds = (JSONArray)jsonReq.get("startitemlists"); |
| 3501 |
21 Sep 15 |
olle |
3374 |
|
| 3501 |
21 Sep 15 |
olle |
// Use stored annotation snapshots for performance reasons |
| 3501 |
21 Sep 15 |
olle |
3376 |
SnapshotManager manager = new SnapshotManager(); |
| 3501 |
21 Sep 15 |
olle |
3377 |
|
| 3501 |
21 Sep 15 |
olle |
3378 |
for (int i = 0; i < jsonStartItemListIds.size(); i++) |
| 3501 |
21 Sep 15 |
olle |
3379 |
{ |
| 3501 |
21 Sep 15 |
olle |
3380 |
JSONObject jsonStartItemListId = (JSONObject)jsonStartItemListIds.get(i); |
| 3501 |
21 Sep 15 |
olle |
3381 |
String startItemListIdStr = (String)jsonStartItemListId.get("id"); |
| 3501 |
21 Sep 15 |
olle |
3382 |
Integer startItemListId = Values.getInteger(startItemListIdStr, null); |
| 3501 |
21 Sep 15 |
olle |
3383 |
if (startItemListId != null) |
| 3501 |
21 Sep 15 |
olle |
3384 |
{ |
| 3501 |
21 Sep 15 |
olle |
3385 |
ItemList startItemList = ItemList.getById(dc, startItemListId); |
| 3501 |
21 Sep 15 |
olle |
3386 |
if (startItemList != null) |
| 3501 |
21 Sep 15 |
olle |
3387 |
{ |
| 3501 |
21 Sep 15 |
olle |
3388 |
StartList sl = new StartList(startItemList); |
| 3501 |
21 Sep 15 |
olle |
3389 |
boolean meludiItemsFirst = true; |
| 3501 |
21 Sep 15 |
olle |
3390 |
List<Extract> extractList = sl.fetchExtractListFromItemList(dc, StartList.ITEM_DNA, meludiItemsFirst); |
| 3501 |
21 Sep 15 |
olle |
3391 |
if (extractList == null) |
| 3501 |
21 Sep 15 |
olle |
3392 |
{ |
| 3501 |
21 Sep 15 |
olle |
// Try to find any RNA extract member items |
| 3501 |
21 Sep 15 |
olle |
3394 |
extractList = sl.fetchExtractListFromItemList(dc, StartList.ITEM_RNA, meludiItemsFirst); |
| 3501 |
21 Sep 15 |
olle |
3395 |
} |
| 3501 |
21 Sep 15 |
olle |
3396 |
if (extractList != null) |
| 3501 |
21 Sep 15 |
olle |
3397 |
{ |
| 3516 |
01 Oct 15 |
olle |
// Get first extract member item that was processed from specimen |
| 3516 |
01 Oct 15 |
olle |
3399 |
Extract e = null; |
| 3516 |
01 Oct 15 |
olle |
3400 |
for (Extract extract: extractList) |
| 3516 |
01 Oct 15 |
olle |
3401 |
{ |
| 3516 |
01 Oct 15 |
olle |
// Exclude input DNA and RNA, since these lack lot number annotations |
| 3516 |
01 Oct 15 |
olle |
3403 |
if (extract != null && !Meludi.itemIsExtractSourceItem(extract.getName())) |
| 3516 |
01 Oct 15 |
olle |
3404 |
{ |
| 3516 |
01 Oct 15 |
olle |
3405 |
e = extract; |
| 3516 |
01 Oct 15 |
olle |
3406 |
break; |
| 3516 |
01 Oct 15 |
olle |
3407 |
} |
| 3516 |
01 Oct 15 |
olle |
3408 |
} |
| 3501 |
21 Sep 15 |
olle |
3409 |
if (e != null) |
| 3501 |
21 Sep 15 |
olle |
3410 |
{ |
| 3501 |
21 Sep 15 |
olle |
//System.out.println(new Date() + " ExtractionServlet::doPost(): cmd = \"" + cmd + "\" startItemList.getName() = " + startItemList.getName() + " e.getName() = " + e.getName()); |
| 3501 |
21 Sep 15 |
olle |
// Get lot numbers etc from extract annotations |
| 3501 |
21 Sep 15 |
olle |
3413 |
|
| 3501 |
21 Sep 15 |
olle |
// Specimen reagents |
| 3501 |
21 Sep 15 |
olle |
3415 |
String xyleneSpecimen = (String) Annotationtype.XYLENE_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3416 |
String etoh995Specimen = (String) Annotationtype.ETOH995_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3417 |
String allPrepFfpeKit = (String) Annotationtype.ALLPREP_FFPE_KIT.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3418 |
String bufferPkdSpecimen = (String) Annotationtype.BUFFER_PKD_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3419 |
String bufferAtlSpecimen = (String) Annotationtype.BUFFER_ATL_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3420 |
String proteinaseKSpecimen = (String) Annotationtype.PROTEINASE_K_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3421 |
String rnaseASpecimen = (String) Annotationtype.RNASE_A_SPECIMEN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3422 |
|
| 3501 |
21 Sep 15 |
olle |
// QIAcube reagents |
| 3501 |
21 Sep 15 |
olle |
3424 |
String etoh995 = (String) Annotationtype.ETOH995.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3425 |
String bufferRlt = (String) Annotationtype.BUFFER_RLT.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3426 |
String bufferFrn = (String) Annotationtype.BUFFER_FRN.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3427 |
String bufferRpe = (String) Annotationtype.BUFFER_RPE.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3428 |
String bufferAl = (String) Annotationtype.BUFFER_AL.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3429 |
String bufferAw1 = (String) Annotationtype.BUFFER_AW1.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3430 |
String bufferAw2 = (String) Annotationtype.BUFFER_AW2.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3431 |
String bufferAte = (String) Annotationtype.BUFFER_ATE.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3432 |
String bufferRdd = (String) Annotationtype.BUFFER_RDD.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3433 |
String rnaseFreeWater = (String) Annotationtype.RNASE_FREE_WATER.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3434 |
String dnaseMix = (String) Annotationtype.DNASE_MIX.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3435 |
String rneasyMinEluteSpinColumn = (String) Annotationtype.RNEASY_MIN_ELUTE_SPIN_COL.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3436 |
String qiaampMinEluteSpinColumn = (String) Annotationtype.QIAAMP_MIN_ELUTE_SPIN_COL.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3437 |
|
| 3501 |
21 Sep 15 |
olle |
// Quality control reagents |
| 3501 |
21 Sep 15 |
olle |
3439 |
String kapaSybrFast = (String) Annotationtype.KAPA_SYBR_FAST.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3440 |
String qualityControlPrimersQcpRgt = (String) Annotationtype.QUALITY_CONTROL_PRIMERS_QCP_RGT.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3441 |
String qualityControlTemplateQct = (String) Annotationtype.QUALITY_CONTROL_TEMPLATE_QCT.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3442 |
String qubitDnaHighSens = (String) Annotationtype.QUBIT_DNA_HIGH_SENS.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3443 |
String qubitDnaBroadRange = (String) Annotationtype.QUBIT_DNA_BROAD_RANGE.getAnnotationValue(dc, manager, e); |
| 3501 |
21 Sep 15 |
olle |
3444 |
|
| 3501 |
21 Sep 15 |
olle |
// Set start list specimen reagents annotations |
| 3501 |
21 Sep 15 |
olle |
3446 |
Annotationtype.LIST_XYLENE_SPECIMEN.setAnnotationValue(dc, startItemList, xyleneSpecimen); |
| 3501 |
21 Sep 15 |
olle |
3447 |
Annotationtype.LIST_ETOH995_SPECIMEN.setAnnotationValue(dc, startItemList, etoh995Specimen); |
| 3501 |
21 Sep 15 |
olle |
3448 |
Annotationtype.LIST_ALLPREP_FFPE_KIT.setAnnotationValue(dc, startItemList, allPrepFfpeKit); |
| 3501 |
21 Sep 15 |
olle |
3449 |
Annotationtype.LIST_BUFFER_PKD_SPECIMEN.setAnnotationValue(dc, startItemList, bufferPkdSpecimen); |
| 3501 |
21 Sep 15 |
olle |
3450 |
Annotationtype.LIST_BUFFER_ATL_SPECIMEN.setAnnotationValue(dc, startItemList, bufferAtlSpecimen); |
| 3501 |
21 Sep 15 |
olle |
3451 |
Annotationtype.LIST_PROTEINASE_K_SPECIMEN.setAnnotationValue(dc, startItemList, proteinaseKSpecimen); |
| 3501 |
21 Sep 15 |
olle |
3452 |
Annotationtype.LIST_RNASE_A_SPECIMEN.setAnnotationValue(dc, startItemList, rnaseASpecimen); |
| 3501 |
21 Sep 15 |
olle |
3453 |
|
| 3501 |
21 Sep 15 |
olle |
// Set start list QIAcube reagents annotations |
| 3501 |
21 Sep 15 |
olle |
3455 |
Annotationtype.LIST_ETOH995.setAnnotationValue(dc, startItemList, etoh995); |
| 3501 |
21 Sep 15 |
olle |
3456 |
Annotationtype.LIST_BUFFER_RLT.setAnnotationValue(dc, startItemList, bufferRlt); |
| 3501 |
21 Sep 15 |
olle |
3457 |
Annotationtype.LIST_BUFFER_FRN.setAnnotationValue(dc, startItemList, bufferFrn); |
| 3501 |
21 Sep 15 |
olle |
3458 |
Annotationtype.LIST_BUFFER_RPE.setAnnotationValue(dc, startItemList, bufferRpe); |
| 3501 |
21 Sep 15 |
olle |
3459 |
Annotationtype.LIST_BUFFER_AL.setAnnotationValue(dc, startItemList, bufferAl); |
| 3501 |
21 Sep 15 |
olle |
3460 |
Annotationtype.LIST_BUFFER_AW1.setAnnotationValue(dc, startItemList, bufferAw1); |
| 3501 |
21 Sep 15 |
olle |
3461 |
Annotationtype.LIST_BUFFER_AW2.setAnnotationValue(dc, startItemList, bufferAw2); |
| 3501 |
21 Sep 15 |
olle |
3462 |
Annotationtype.LIST_BUFFER_ATE.setAnnotationValue(dc, startItemList, bufferAte); |
| 3501 |
21 Sep 15 |
olle |
3463 |
Annotationtype.LIST_BUFFER_RDD.setAnnotationValue(dc, startItemList, bufferRdd); |
| 3501 |
21 Sep 15 |
olle |
3464 |
Annotationtype.LIST_RNASE_FREE_WATER.setAnnotationValue(dc, startItemList, rnaseFreeWater); |
| 3501 |
21 Sep 15 |
olle |
3465 |
Annotationtype.LIST_DNASE_MIX.setAnnotationValue(dc, startItemList, dnaseMix); |
| 3501 |
21 Sep 15 |
olle |
3466 |
Annotationtype.LIST_RNEASY_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, rneasyMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
3467 |
Annotationtype.LIST_QIAAMP_MIN_ELUTE_SPIN_COL.setAnnotationValue(dc, startItemList, qiaampMinEluteSpinColumn); |
| 3501 |
21 Sep 15 |
olle |
3468 |
|
| 3501 |
21 Sep 15 |
olle |
// Set start list quality control reagents annotations |
| 3501 |
21 Sep 15 |
olle |
3470 |
Annotationtype.LIST_KAPA_SYBR_FAST.setAnnotationValue(dc, startItemList, kapaSybrFast); |
| 3501 |
21 Sep 15 |
olle |
3471 |
Annotationtype.LIST_QUALITY_CONTROL_PRIMERS_QCP_RGT.setAnnotationValue(dc, startItemList, qualityControlPrimersQcpRgt); |
| 3501 |
21 Sep 15 |
olle |
3472 |
Annotationtype.LIST_QUALITY_CONTROL_TEMPLATE_QCT.setAnnotationValue(dc, startItemList, qualityControlTemplateQct); |
| 3501 |
21 Sep 15 |
olle |
3473 |
Annotationtype.LIST_QUBIT_DNA_HIGH_SENS.setAnnotationValue(dc, startItemList, qubitDnaHighSens); |
| 3501 |
21 Sep 15 |
olle |
3474 |
Annotationtype.LIST_QUBIT_DNA_BROAD_RANGE.setAnnotationValue(dc, startItemList, qubitDnaBroadRange); |
| 3501 |
21 Sep 15 |
olle |
3475 |
|
| 3501 |
21 Sep 15 |
olle |
3476 |
jsonMessages.add("Updated '" + startItemList.getName() + "' Start item list with lot number annotations from first DNA extract"); |
| 3501 |
21 Sep 15 |
olle |
3477 |
} |
| 3501 |
21 Sep 15 |
olle |
3478 |
} |
| 3501 |
21 Sep 15 |
olle |
3479 |
} |
| 3501 |
21 Sep 15 |
olle |
3480 |
} |
| 3501 |
21 Sep 15 |
olle |
3481 |
} |
| 3501 |
21 Sep 15 |
olle |
3482 |
|
| 3501 |
21 Sep 15 |
olle |
3483 |
dc.commit(); |
| 3501 |
21 Sep 15 |
olle |
3484 |
} |
| 3441 |
21 Jul 15 |
olle |
3485 |
|
| 3176 |
06 Mar 15 |
olle |
3486 |
json.put("messages", jsonMessages); |
| 3176 |
06 Mar 15 |
olle |
3487 |
} |
| 3176 |
06 Mar 15 |
olle |
3488 |
catch (Throwable t) |
| 3176 |
06 Mar 15 |
olle |
3489 |
{ |
| 3176 |
06 Mar 15 |
olle |
3490 |
t.printStackTrace(); |
| 3176 |
06 Mar 15 |
olle |
3491 |
json.clear(); |
| 3176 |
06 Mar 15 |
olle |
3492 |
json.put("status", "error"); |
| 3176 |
06 Mar 15 |
olle |
3493 |
json.put("message", t.getMessage()); |
| 3176 |
06 Mar 15 |
olle |
3494 |
json.put("stacktrace", ThrowableUtil.stackTraceToString(t)); |
| 3176 |
06 Mar 15 |
olle |
3495 |
} |
| 3176 |
06 Mar 15 |
olle |
3496 |
finally |
| 3176 |
06 Mar 15 |
olle |
3497 |
{ |
| 3176 |
06 Mar 15 |
olle |
3498 |
if (dc != null) dc.close(); |
| 3176 |
06 Mar 15 |
olle |
3499 |
json.writeJSONString(resp.getWriter()); |
| 3176 |
06 Mar 15 |
olle |
3500 |
} |
| 3176 |
06 Mar 15 |
olle |
3501 |
|
| 3176 |
06 Mar 15 |
olle |
3502 |
} |
| 3176 |
06 Mar 15 |
olle |
3503 |
|
| 3176 |
06 Mar 15 |
olle |
3504 |
/** |
| 3318 |
08 May 15 |
olle |
* Returns specimen type for the sample, based on the latter's specimenType annotation. |
| 3318 |
08 May 15 |
olle |
* If a specimen type annotation is found, a more readable string of this |
| 3318 |
08 May 15 |
olle |
* content is returned. |
| 3318 |
08 May 15 |
olle |
3508 |
* |
| 3318 |
08 May 15 |
olle |
* @param dc DbControl The DbControl to use. |
| 3318 |
08 May 15 |
olle |
* @param manager SnapshotManager The SnapshotManager to use for speeding up annotation retrieval. |
| 3318 |
08 May 15 |
olle |
* @param s Sample The sample to find the specimen type for. |
| 3318 |
08 May 15 |
olle |
* @return String The specimen type for the sample. |
| 3318 |
08 May 15 |
olle |
3513 |
*/ |
| 3318 |
08 May 15 |
olle |
3514 |
private String fetchSpecimenType(DbControl dc, SnapshotManager manager, Sample s) |
| 3318 |
08 May 15 |
olle |
3515 |
{ |
| 3318 |
08 May 15 |
olle |
3516 |
String specimenType = (String) Annotationtype.SPECIMEN_TYPE.getAnnotationValue(dc, manager, s); |
| 3318 |
08 May 15 |
olle |
3517 |
specimenType = fetchSpecimenType(specimenType); |
| 3318 |
08 May 15 |
olle |
3518 |
return specimenType; |
| 3318 |
08 May 15 |
olle |
3519 |
} |
| 3318 |
08 May 15 |
olle |
3520 |
|
| 3318 |
08 May 15 |
olle |
3521 |
/** |
| 3318 |
08 May 15 |
olle |
* Returns specimen type for the extract, based on the latter's specimenTypeExtract annotation. |
| 3318 |
08 May 15 |
olle |
* If a specimen type annotation is found, a more readable string of this |
| 3318 |
08 May 15 |
olle |
* content is returned. |
| 3318 |
08 May 15 |
olle |
3525 |
* |
| 3318 |
08 May 15 |
olle |
* @param dc DbControl The DbControl to use. |
| 3318 |
08 May 15 |
olle |
* @param manager SnapshotManager The SnapshotManager to use for speeding up annotation retrieval. |
| 3318 |
08 May 15 |
olle |
* @param e Extract The extract to find the specimen type for. |
| 3318 |
08 May 15 |
olle |
* @return String The specimen type for the extract. |
| 3318 |
08 May 15 |
olle |
3530 |
*/ |
| 3318 |
08 May 15 |
olle |
3531 |
private String fetchSpecimenTypeExtract(DbControl dc, SnapshotManager manager, Extract e) |
| 3318 |
08 May 15 |
olle |
3532 |
{ |
| 3318 |
08 May 15 |
olle |
3533 |
String specimenType = (String) Annotationtype.SPECIMEN_TYPE_EXTRACT.getAnnotationValue(dc, manager, e); |
| 3318 |
08 May 15 |
olle |
3534 |
specimenType = fetchSpecimenType(specimenType); |
| 3318 |
08 May 15 |
olle |
3535 |
return specimenType; |
| 3318 |
08 May 15 |
olle |
3536 |
} |
| 3318 |
08 May 15 |
olle |
3537 |
|
| 3318 |
08 May 15 |
olle |
3538 |
/** |
| 3318 |
08 May 15 |
olle |
* Returns a more readable string of a specimen type. |
| 3318 |
08 May 15 |
olle |
3540 |
* |
| 3318 |
08 May 15 |
olle |
* @param dc DbControl The DbControl to use. |
| 3318 |
08 May 15 |
olle |
* @param manager SnapshotManager The SnapshotManager to use for speeding up annotation retrieval. |
| 3318 |
08 May 15 |
olle |
* @param rawSpecimenType String The original specimen type string. |
| 3318 |
08 May 15 |
olle |
* @return String A more readable string of the input specimen type string. |
| 3318 |
08 May 15 |
olle |
3545 |
*/ |
| 3318 |
08 May 15 |
olle |
3546 |
private String fetchSpecimenType(String rawSpecimenType) |
| 3318 |
08 May 15 |
olle |
3547 |
{ |
| 3318 |
08 May 15 |
olle |
3548 |
String specimenType = rawSpecimenType; |
| 3318 |
08 May 15 |
olle |
3549 |
if (specimenType != null) |
| 3318 |
08 May 15 |
olle |
3550 |
{ |
| 3318 |
08 May 15 |
olle |
3551 |
if (specimenType.equals("")) |
| 3318 |
08 May 15 |
olle |
3552 |
{ |
| 3318 |
08 May 15 |
olle |
3553 |
specimenType = "unknown"; |
| 3318 |
08 May 15 |
olle |
3554 |
} |
| 3318 |
08 May 15 |
olle |
3555 |
else if (specimenType.equals("Primary")) |
| 3318 |
08 May 15 |
olle |
3556 |
{ |
| 3318 |
08 May 15 |
olle |
3557 |
specimenType = "Primary tumour"; |
| 3318 |
08 May 15 |
olle |
3558 |
} |
| 3318 |
08 May 15 |
olle |
3559 |
else if (specimenType.equals("MetastasisDistant")) |
| 3318 |
08 May 15 |
olle |
3560 |
{ |
| 3318 |
08 May 15 |
olle |
3561 |
specimenType = "Metastasis"; |
| 3318 |
08 May 15 |
olle |
3562 |
} |
| 3318 |
08 May 15 |
olle |
3563 |
} |
| 3318 |
08 May 15 |
olle |
3564 |
return specimenType; |
| 3318 |
08 May 15 |
olle |
3565 |
} |
| 3318 |
08 May 15 |
olle |
3566 |
|
| 3318 |
08 May 15 |
olle |
3567 |
/** |
| 3176 |
06 Mar 15 |
olle |
* Returns the first character in input QIAcube position string, |
| 3176 |
06 Mar 15 |
olle |
* if uppercase letter followed by QIAcube position number, else `null`. |
| 3176 |
06 Mar 15 |
olle |
3570 |
* |
| 3176 |
06 Mar 15 |
olle |
* @param qiacubePositionStr String |
| 3176 |
06 Mar 15 |
olle |
* @return String The QIAcube instrument prefix, if capital letter followed by QIAcube position number, else `null`. |
| 3176 |
06 Mar 15 |
olle |
3573 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3574 |
private String fetchQiacubeInstrumentPrefix(String qiacubePositionStr) |
| 3176 |
06 Mar 15 |
olle |
3575 |
{ |
| 3176 |
06 Mar 15 |
olle |
3576 |
String qiacubeInstrumentPrefix = null; |
| 3176 |
06 Mar 15 |
olle |
3577 |
if (qiacubePositionStr != null && !qiacubePositionStr.equals("")) |
| 3176 |
06 Mar 15 |
olle |
3578 |
{ |
| 3176 |
06 Mar 15 |
olle |
// Check if string contains uppercase letter + QIAcube position number 1-12 |
| 3176 |
06 Mar 15 |
olle |
3580 |
if (qiacubePositionStr.matches("^[A-Z]([2-9]|1[0-2]?)$")) |
| 3176 |
06 Mar 15 |
olle |
3581 |
{ |
| 3176 |
06 Mar 15 |
olle |
3582 |
qiacubeInstrumentPrefix = qiacubePositionStr.substring(0,1); |
| 3176 |
06 Mar 15 |
olle |
3583 |
} |
| 3176 |
06 Mar 15 |
olle |
3584 |
} |
| 3176 |
06 Mar 15 |
olle |
3585 |
return qiacubeInstrumentPrefix; |
| 3176 |
06 Mar 15 |
olle |
3586 |
} |
| 3176 |
06 Mar 15 |
olle |
3587 |
|
| 3176 |
06 Mar 15 |
olle |
3588 |
/** |
| 3176 |
06 Mar 15 |
olle |
* Returns the QIAcube position, after removal of optional QIAcube instrument prefix. |
| 3176 |
06 Mar 15 |
olle |
3590 |
* |
| 3176 |
06 Mar 15 |
olle |
* @param qiacubePositionStr String |
| 3176 |
06 Mar 15 |
olle |
* @return Number The QIAcube position, after removal of optional QIAcube instrument prefix. |
| 3176 |
06 Mar 15 |
olle |
3593 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3594 |
private Number fetchQiacubePosition(String qiacubePositionStr) |
| 3176 |
06 Mar 15 |
olle |
3595 |
{ |
| 3176 |
06 Mar 15 |
olle |
3596 |
Number qiacubePosition = null; |
| 3176 |
06 Mar 15 |
olle |
3597 |
if (qiacubePositionStr != null && !qiacubePositionStr.equals("")) |
| 3176 |
06 Mar 15 |
olle |
3598 |
{ |
| 3176 |
06 Mar 15 |
olle |
3599 |
String qiacubePositionNumberStr = qiacubePositionStr; |
| 3176 |
06 Mar 15 |
olle |
// Check if string contains uppercase letter + QIAcube position number 1-12 |
| 3176 |
06 Mar 15 |
olle |
3601 |
if (qiacubePositionStr.matches("^[A-Z]([2-9]|1[0-2]?)$")) |
| 3176 |
06 Mar 15 |
olle |
3602 |
{ |
| 3176 |
06 Mar 15 |
olle |
3603 |
qiacubePositionNumberStr = qiacubePositionStr.substring(1, qiacubePositionStr.length()); |
| 3176 |
06 Mar 15 |
olle |
3604 |
} |
| 3176 |
06 Mar 15 |
olle |
3605 |
qiacubePosition = (Number)Integer.parseInt(qiacubePositionNumberStr); |
| 3176 |
06 Mar 15 |
olle |
3606 |
} |
| 3176 |
06 Mar 15 |
olle |
3607 |
return qiacubePosition; |
| 3176 |
06 Mar 15 |
olle |
3608 |
} |
| 3176 |
06 Mar 15 |
olle |
3609 |
|
| 3221 |
01 Apr 15 |
olle |
3610 |
/** |
| 3221 |
01 Apr 15 |
olle |
* Returns the float value for a number object, |
| 3221 |
01 Apr 15 |
olle |
* or 0.0, if the object is `null` or not a number. |
| 3221 |
01 Apr 15 |
olle |
3613 |
* |
| 3221 |
01 Apr 15 |
olle |
* @param object The number object. |
| 3221 |
01 Apr 15 |
olle |
* @return The object as float value, or 0.0, if the value is `null` or not a number. |
| 3221 |
01 Apr 15 |
olle |
3616 |
*/ |
| 3176 |
06 Mar 15 |
olle |
3617 |
private float fetchFloatValue(Object object) |
| 3176 |
06 Mar 15 |
olle |
3618 |
{ |
| 3176 |
06 Mar 15 |
olle |
3619 |
float value = 0.0f; |
| 3176 |
06 Mar 15 |
olle |
3620 |
if (object != null) |
| 3176 |
06 Mar 15 |
olle |
3621 |
{ |
| 3176 |
06 Mar 15 |
olle |
3622 |
try |
| 3176 |
06 Mar 15 |
olle |
3623 |
{ |
| 3221 |
01 Apr 15 |
olle |
3624 |
value = ((Number)object).floatValue(); |
| 3176 |
06 Mar 15 |
olle |
3625 |
} |
| 3176 |
06 Mar 15 |
olle |
3626 |
catch (NumberFormatException e) |
| 3176 |
06 Mar 15 |
olle |
3627 |
{} |
| 3176 |
06 Mar 15 |
olle |
3628 |
} |
| 3176 |
06 Mar 15 |
olle |
3629 |
return value; |
| 3176 |
06 Mar 15 |
olle |
3630 |
} |
| 3176 |
06 Mar 15 |
olle |
3631 |
|
| 3176 |
06 Mar 15 |
olle |
3632 |
@SuppressWarnings("unchecked") |
| 3180 |
17 Mar 15 |
olle |
3633 |
long findNumberOfPlates(DbControl dc, String platePrefix) |
| 3176 |
06 Mar 15 |
olle |
3634 |
{ |
| 3176 |
06 Mar 15 |
olle |
3635 |
String queryString = "%"; |
| 3180 |
17 Mar 15 |
olle |
3636 |
if (platePrefix != null) |
| 3176 |
06 Mar 15 |
olle |
3637 |
{ |
| 3180 |
17 Mar 15 |
olle |
3638 |
queryString = platePrefix + "%"; |
| 3176 |
06 Mar 15 |
olle |
3639 |
} |
| 3176 |
06 Mar 15 |
olle |
3640 |
|
| 3176 |
06 Mar 15 |
olle |
3641 |
ItemQuery<BioPlate> plateQuery = BioPlate.getQuery(); |
| 3176 |
06 Mar 15 |
olle |
3642 |
plateQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(queryString))); |
| 3176 |
06 Mar 15 |
olle |
3643 |
plateQuery.order(Orders.asc(Hql.property("name"))); |
| 3176 |
06 Mar 15 |
olle |
3644 |
long numPlates = plateQuery.count(dc); |
| 3176 |
06 Mar 15 |
olle |
3645 |
return numPlates; |
| 3176 |
06 Mar 15 |
olle |
3646 |
} |
| 3176 |
06 Mar 15 |
olle |
3647 |
|
| 3176 |
06 Mar 15 |
olle |
3648 |
@SuppressWarnings("unchecked") |
| 3180 |
17 Mar 15 |
olle |
3649 |
List<BioPlate> findPlates(DbControl dc, String platePrefix) |
| 3176 |
06 Mar 15 |
olle |
3650 |
{ |
| 3176 |
06 Mar 15 |
olle |
3651 |
String queryString = "%"; |
| 3180 |
17 Mar 15 |
olle |
3652 |
if (platePrefix != null) |
| 3176 |
06 Mar 15 |
olle |
3653 |
{ |
| 3180 |
17 Mar 15 |
olle |
3654 |
queryString = platePrefix + "%"; |
| 3176 |
06 Mar 15 |
olle |
3655 |
} |
| 3176 |
06 Mar 15 |
olle |
3656 |
|
| 3176 |
06 Mar 15 |
olle |
3657 |
ItemQuery<BioPlate> plateQuery = BioPlate.getQuery(); |
| 3176 |
06 Mar 15 |
olle |
3658 |
plateQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(queryString))); |
| 3176 |
06 Mar 15 |
olle |
3659 |
plateQuery.order(Orders.asc(Hql.property("name"))); |
| 3176 |
06 Mar 15 |
olle |
3660 |
List<BioPlate> plates = plateQuery.list(dc); |
| 3176 |
06 Mar 15 |
olle |
3661 |
return plates; |
| 3176 |
06 Mar 15 |
olle |
3662 |
} |
| 3180 |
17 Mar 15 |
olle |
3663 |
|
| 3180 |
17 Mar 15 |
olle |
3664 |
@SuppressWarnings("unchecked") |
| 3180 |
17 Mar 15 |
olle |
3665 |
BioPlate findPlateWithHighestNumber(DbControl dc, String platePrefix) |
| 3180 |
17 Mar 15 |
olle |
3666 |
{ |
| 3180 |
17 Mar 15 |
olle |
3667 |
String queryString = "%"; |
| 3180 |
17 Mar 15 |
olle |
3668 |
if (platePrefix != null) |
| 3180 |
17 Mar 15 |
olle |
3669 |
{ |
| 3180 |
17 Mar 15 |
olle |
3670 |
queryString = platePrefix + "%"; |
| 3180 |
17 Mar 15 |
olle |
3671 |
} |
| 3180 |
17 Mar 15 |
olle |
3672 |
|
| 3180 |
17 Mar 15 |
olle |
3673 |
ItemQuery<BioPlate> plateQuery = BioPlate.getQuery(); |
| 3180 |
17 Mar 15 |
olle |
3674 |
plateQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(queryString))); |
| 3180 |
17 Mar 15 |
olle |
3675 |
plateQuery.order(Orders.asc(Hql.property("name"))); |
| 3180 |
17 Mar 15 |
olle |
3676 |
List<BioPlate> plates = plateQuery.list(dc); |
| 3180 |
17 Mar 15 |
olle |
3677 |
BioPlate plateWithHighestNumber = null; |
| 3180 |
17 Mar 15 |
olle |
3678 |
int numPlates = plates.size(); |
| 3180 |
17 Mar 15 |
olle |
3679 |
if (numPlates > 0) |
| 3180 |
17 Mar 15 |
olle |
3680 |
{ |
| 3180 |
17 Mar 15 |
olle |
3681 |
plateWithHighestNumber = (BioPlate) plates.get(numPlates-1); |
| 3180 |
17 Mar 15 |
olle |
3682 |
} |
| 3180 |
17 Mar 15 |
olle |
3683 |
return plateWithHighestNumber; |
| 3180 |
17 Mar 15 |
olle |
3684 |
} |
| 3432 |
29 Jun 15 |
olle |
3685 |
|
| 3432 |
29 Jun 15 |
olle |
3686 |
@SuppressWarnings("unchecked") |
| 3432 |
29 Jun 15 |
olle |
3687 |
private ItemList findItemListWithHighestNumber(DbControl dc, String itemListPrefix) |
| 3432 |
29 Jun 15 |
olle |
3688 |
{ |
| 3432 |
29 Jun 15 |
olle |
3689 |
String queryString = "%"; |
| 3432 |
29 Jun 15 |
olle |
3690 |
if (itemListPrefix != null) |
| 3432 |
29 Jun 15 |
olle |
3691 |
{ |
| 3432 |
29 Jun 15 |
olle |
3692 |
queryString = itemListPrefix + "%"; |
| 3432 |
29 Jun 15 |
olle |
3693 |
} |
| 3432 |
29 Jun 15 |
olle |
3694 |
|
| 3432 |
29 Jun 15 |
olle |
3695 |
ItemQuery<ItemList> itemListQuery = ItemList.getQuery(); |
| 3432 |
29 Jun 15 |
olle |
3696 |
itemListQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(queryString))); |
| 3432 |
29 Jun 15 |
olle |
3697 |
itemListQuery.order(Orders.asc(Hql.property("name"))); |
| 3432 |
29 Jun 15 |
olle |
3698 |
List<ItemList> itemLists = itemListQuery.list(dc); |
| 3432 |
29 Jun 15 |
olle |
3699 |
ItemList itemListWithHighestNumber = null; |
| 3432 |
29 Jun 15 |
olle |
3700 |
int numItemLists = itemLists.size(); |
| 3432 |
29 Jun 15 |
olle |
3701 |
if (numItemLists > 0) |
| 3432 |
29 Jun 15 |
olle |
3702 |
{ |
| 3432 |
29 Jun 15 |
olle |
3703 |
itemListWithHighestNumber = (ItemList) itemLists.get(numItemLists-1); |
| 3432 |
29 Jun 15 |
olle |
3704 |
} |
| 3432 |
29 Jun 15 |
olle |
3705 |
return itemListWithHighestNumber; |
| 3432 |
29 Jun 15 |
olle |
3706 |
} |
| 5848 |
02 Mar 20 |
olle |
3707 |
|
| 5848 |
02 Mar 20 |
olle |
3708 |
@SuppressWarnings("unchecked") |
| 5848 |
02 Mar 20 |
olle |
3709 |
private void loadHistologyInfo(DbControl dc, Histology his) |
| 5848 |
02 Mar 20 |
olle |
3710 |
{ |
| 5848 |
02 Mar 20 |
olle |
3711 |
Sample s = his.getSample(); |
| 5848 |
02 Mar 20 |
olle |
3712 |
BioMaterialEvent created = s.getCreationEvent(); |
| 5848 |
02 Mar 20 |
olle |
3713 |
|
| 5848 |
02 Mar 20 |
olle |
3714 |
his.loadBioPlateLocation(); |
| 5848 |
02 Mar 20 |
olle |
3715 |
his.setAnnotation("registrationDate", Meludi.CONVERTER_DATE_TO_STRING.convert(s.getEntryDate())); |
| 5848 |
02 Mar 20 |
olle |
3716 |
his.setAnnotation("editable", s.hasPermission(Permission.WRITE)); |
| 5848 |
02 Mar 20 |
olle |
//his.loadDoNotUseAnnotations(dc, null); |
| 5848 |
02 Mar 20 |
olle |
3718 |
|
| 5848 |
02 Mar 20 |
olle |
//his.loadAnnotations(dc, "partitionDate", Annotationtype.PARTITION_DATE, Meludi.CONVERTER_DATE_TO_STRING); |
| 5848 |
02 Mar 20 |
olle |
3720 |
his.setAnnotation("originalQuantity", s.getOriginalQuantity()); |
| 5848 |
02 Mar 20 |
olle |
3721 |
his.setAnnotation("remainingQuantity", s.getRemainingQuantity()); |
| 5848 |
02 Mar 20 |
olle |
3722 |
|
| 5848 |
02 Mar 20 |
olle |
3723 |
if (created.getEventDate() != null) |
| 5848 |
02 Mar 20 |
olle |
3724 |
{ |
| 5848 |
02 Mar 20 |
olle |
3725 |
his.setAnnotation("embedDate", Meludi.CONVERTER_DATE_TO_STRING.convert(created.getEventDate())); |
| 5848 |
02 Mar 20 |
olle |
3726 |
/* |
| 5848 |
02 Mar 20 |
olle |
his.setAnnotation("embedProtocol", JsonUtil.getProtocolAsJSON(created.getProtocol())); |
| 5848 |
02 Mar 20 |
olle |
3728 |
*/ |
| 5848 |
02 Mar 20 |
olle |
3729 |
} |
| 5848 |
02 Mar 20 |
olle |
3730 |
|
| 5848 |
02 Mar 20 |
olle |
3731 |
ItemQuery<Sample> stainedQuery = s.getChildSamples(); |
| 5848 |
02 Mar 20 |
olle |
3732 |
Subtype.STAINED.addFilter(dc, stainedQuery); |
| 5848 |
02 Mar 20 |
olle |
3733 |
stainedQuery.include(Meludi.INCLUDE_IN_CURRENT_PROJECT); |
| 5848 |
02 Mar 20 |
olle |
3734 |
List<Sample> stained = stainedQuery.list(dc); |
| 5848 |
02 Mar 20 |
olle |
3735 |
System.out.println("CaseSummaryServlet::loadHistologyInfo(): stained.size() = " + stained.size()); |
| 5848 |
02 Mar 20 |
olle |
3736 |
if (stained.size() > 0) |
| 5848 |
02 Mar 20 |
olle |
3737 |
{ |
| 5848 |
02 Mar 20 |
olle |
3738 |
/* |
| 5848 |
02 Mar 20 |
olle |
Sample good = stained.get(0); |
| 5848 |
02 Mar 20 |
olle |
boolean goodIsGood = false; |
| 5848 |
02 Mar 20 |
olle |
for (Sample he : stained) |
| 5848 |
02 Mar 20 |
olle |
3742 |
{ |
| 5848 |
02 Mar 20 |
olle |
if (Boolean.TRUE.equals(Annotationtype.GOOD_STAIN.getAnnotationValue(dc, he))) |
| 5848 |
02 Mar 20 |
olle |
3744 |
{ |
| 5848 |
02 Mar 20 |
olle |
good = he; |
| 5848 |
02 Mar 20 |
olle |
goodIsGood = true; |
| 5848 |
02 Mar 20 |
olle |
break; |
| 5848 |
02 Mar 20 |
olle |
3748 |
} |
| 5848 |
02 Mar 20 |
olle |
3749 |
} |
| 5848 |
02 Mar 20 |
olle |
BioMaterialEvent heCreated = good.getCreationEvent(); |
| 5848 |
02 Mar 20 |
olle |
his.setAnnotation("stainDate", Meludi.CONVERTER_DATE_TO_STRING.convert(heCreated.getEventDate())); |
| 5848 |
02 Mar 20 |
olle |
his.setAnnotation("stainProtocol", JsonUtil.getProtocolAsJSON(good.getProtocol())); |
| 5848 |
02 Mar 20 |
olle |
his.setAnnotation("numStains", stained.size()); |
| 5848 |
02 Mar 20 |
olle |
if (goodIsGood) |
| 5848 |
02 Mar 20 |
olle |
3755 |
{ |
| 5848 |
02 Mar 20 |
olle |
// Image |
| 5848 |
02 Mar 20 |
olle |
File imageFile = null; |
| 5848 |
02 Mar 20 |
olle |
AnyToAny imageLink = null; |
| 5848 |
02 Mar 20 |
olle |
try |
| 5848 |
02 Mar 20 |
olle |
3760 |
{ |
| 5848 |
02 Mar 20 |
olle |
imageLink = AnyToAny.getByName(dc, good, "image"); |
| 5848 |
02 Mar 20 |
olle |
if (imageLink.getToType() == Item.FILE) |
| 5848 |
02 Mar 20 |
olle |
3763 |
{ |
| 5848 |
02 Mar 20 |
olle |
// This is linked to an existing file already, replace it |
| 5848 |
02 Mar 20 |
olle |
imageFile = (File)imageLink.getTo(); |
| 5848 |
02 Mar 20 |
olle |
3766 |
} |
| 5848 |
02 Mar 20 |
olle |
3767 |
} |
| 5848 |
02 Mar 20 |
olle |
catch (RuntimeException ex) |
| 5848 |
02 Mar 20 |
olle |
3769 |
{} |
| 5848 |
02 Mar 20 |
olle |
3770 |
|
| 5848 |
02 Mar 20 |
olle |
JSONObject jsonGood = new JSONObject(); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("id", good.getId()); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("name", good.getName()); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("bioWell", JsonUtil.getBioWellAsJSON(good.getBioWell(), true)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("comments", good.getDescription()); |
| 5848 |
02 Mar 20 |
olle |
3776 |
|
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreComplete", Annotationtype.SCORE_COMPLETE.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreInvasiveCancer", Annotationtype.SCORE_INVASIVE_CANCER.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreInsituCancer", Annotationtype.SCORE_INSITU_CANCER.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreLymphocytes", Annotationtype.SCORE_LYMPHOCYTES.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreNormal", Annotationtype.SCORE_NORMAL.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreStroma", Annotationtype.SCORE_STROMA.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("ScoreFat", Annotationtype.SCORE_FAT.getAnnotationValue(dc, good)); |
| 5848 |
02 Mar 20 |
olle |
if (imageFile != null) |
| 5848 |
02 Mar 20 |
olle |
3785 |
{ |
| 5848 |
02 Mar 20 |
olle |
JSONObject jsonImage = new JSONObject(); |
| 5848 |
02 Mar 20 |
olle |
jsonImage.put("id", imageFile.getId()); |
| 5848 |
02 Mar 20 |
olle |
jsonImage.put("path", imageFile.getPath().toString()); |
| 5848 |
02 Mar 20 |
olle |
jsonGood.put("image", jsonImage); |
| 5848 |
02 Mar 20 |
olle |
3790 |
} |
| 5848 |
02 Mar 20 |
olle |
3791 |
|
| 5848 |
02 Mar 20 |
olle |
his.setAnnotation("bestStain", jsonGood); |
| 5848 |
02 Mar 20 |
olle |
3793 |
} |
| 5848 |
02 Mar 20 |
olle |
3794 |
*/ |
| 5848 |
02 Mar 20 |
olle |
3795 |
|
| 5848 |
02 Mar 20 |
olle |
3796 |
his.setAnnotation("numStains", stained.size()); |
| 5848 |
02 Mar 20 |
olle |
3797 |
if (stained.size() > 1) |
| 5848 |
02 Mar 20 |
olle |
3798 |
{ |
| 5848 |
02 Mar 20 |
olle |
3799 |
for (int i = 0; i < 2; i++) |
| 5848 |
02 Mar 20 |
olle |
3800 |
{ |
| 5848 |
02 Mar 20 |
olle |
3801 |
Sample he = (Sample)stained.get(i); |
| 5848 |
02 Mar 20 |
olle |
3802 |
Integer tumourCellsPct = (Integer)Annotationtype.TUMOUR_CELLS_PERCENT.getAnnotationValue(dc, he); |
| 5848 |
02 Mar 20 |
olle |
3803 |
String heName = he.getName(); |
| 5848 |
02 Mar 20 |
olle |
3804 |
if (heName.contains(".F")) |
| 5848 |
02 Mar 20 |
olle |
3805 |
{ |
| 5848 |
02 Mar 20 |
olle |
3806 |
JSONObject jsonF = new JSONObject(); |
| 5848 |
02 Mar 20 |
olle |
3807 |
jsonF.put("id", he.getId()); |
| 5848 |
02 Mar 20 |
olle |
3808 |
jsonF.put("name", he.getName()); |
| 5848 |
02 Mar 20 |
olle |
3809 |
jsonF.put("bioWell", JsonUtil.getBioWellAsJSON(he.getBioWell(), true)); |
| 5848 |
02 Mar 20 |
olle |
3810 |
jsonF.put("tumourCellsPct", tumourCellsPct); |
| 5848 |
02 Mar 20 |
olle |
3811 |
his.setAnnotation("FStain", jsonF); |
| 5848 |
02 Mar 20 |
olle |
3812 |
} |
| 5848 |
02 Mar 20 |
olle |
3813 |
else if (heName.contains(".E")) |
| 5848 |
02 Mar 20 |
olle |
3814 |
{ |
| 5848 |
02 Mar 20 |
olle |
3815 |
JSONObject jsonE = new JSONObject(); |
| 5848 |
02 Mar 20 |
olle |
3816 |
jsonE.put("id", he.getId()); |
| 5848 |
02 Mar 20 |
olle |
3817 |
jsonE.put("name", he.getName()); |
| 5848 |
02 Mar 20 |
olle |
3818 |
jsonE.put("bioWell", JsonUtil.getBioWellAsJSON(he.getBioWell(), true)); |
| 5848 |
02 Mar 20 |
olle |
3819 |
jsonE.put("tumourCellsPct", tumourCellsPct); |
| 5848 |
02 Mar 20 |
olle |
3820 |
his.setAnnotation("EStain", jsonE); |
| 5848 |
02 Mar 20 |
olle |
3821 |
} |
| 5848 |
02 Mar 20 |
olle |
3822 |
} |
| 5848 |
02 Mar 20 |
olle |
3823 |
} |
| 5848 |
02 Mar 20 |
olle |
3824 |
} |
| 5848 |
02 Mar 20 |
olle |
3825 |
} |
| 3176 |
06 Mar 15 |
olle |
3826 |
} |