Changeset 5740

Timestamp:

Nov 20, 2019, 8:30:18 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

Merged Reggie 4.23.3 to the trunk.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• . (modified) (1 prop)
• resources/index.js (modified) (1 diff)
• resources/libprep/mrna_protocol.js (modified) (1 diff)
• resources/libprep/select_rna.js (modified) (4 diffs)
• resources/personal/map-external-data.js (modified) (3 diffs)
• resources/personal/map-external-data.jsp (modified) (2 diffs)
• src/net/sf/basedb/reggie/activity/ActivityDef.java (modified) (1 diff)
• src/net/sf/basedb/reggie/activity/ActivityEntry.java (modified) (1 diff)
• src/net/sf/basedb/reggie/activity/ActivityLog.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/ExportServlet.java (modified) (18 diffs)
• src/net/sf/basedb/reggie/servlet/SessionServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/index.js

@@ -359 +359 @@
     msg += '<div class="snake-quote-source">Indiana Jones - Raiders of the Lost Ark</div>';
     Forms.showNotification('caseName', msg, 'snake-quote', 'pointer-above');
-  }
-
+    var url = 'Session.servlet?ID='+App.getSessionId();
+    url += '&cmd=ReggieTheSnakeWasSummoned';
+    Wizard.asyncJsonRequest(url);
+  }
   
   return index;

extensions/net.sf.basedb.reggie/trunk/resources/libprep/mrna_protocol.js

@@ -184 +184 @@
         totalVolume = mrna.DilutionVolume;
       }
-      else if (totalVolume > mrna.DilutionVolume)
+      else if (totalVolume - 0.05 > mrna.DilutionVolume) // Use 0.05 to avoid issues with 50.0000000001 > 50.0
       {
         remarks[remarks.length] = 'Large mix; Use '+Reggie.formatNumber(mrna.DilutionVolume, 'µl', 1);

extensions/net.sf.basedb.reggie/trunk/resources/libprep/select_rna.js

@@ -1696 +1696 @@
       }
 
-      if (info && info.id && info.bioWell && !rna.stratagene)
+      if (info && info.id && !rna.stratagene)
       {
         rna.usedQuantity = Math.max(Math.min(info.remainingQuantity, rna.qc ? QUANTITY_QC : QUANTITY_REGULAR), QUANTITY_MINIMAL); // µg
@@ -1738 +1738 @@
         else
         {
-          warningMsg[warningMsg.length] = 'No quantity';
+          if (!rna.external) warningMsg[warningMsg.length] = 'No quantity';
         }
         if (info.rqs)
@@ -1750 +1750 @@
           if (info.rin < QUALITY_SCORE_WARNING_LIMIT) warningMsg[warningMsg.length] = 'Low RIN value';
         }
-        else if (!info.preNormalized)
+        else if (!info.preNormalized && !rna.external)
         {
           warningMsg[warningMsg.length] = 'No RQS/RIN value';
@@ -1759 +1759 @@
           text += '<div class="volumes"><span class="volume">'+Numbers.formatNumber(volRNA, 1)+'</span> + <span class="water">'+Numbers.formatNumber(water, 1)+'µl</span></div>';
         }
+        else 
+        {
+          if (!rna.external) warningMsg[warningMsg.length] = 'No NDConc value';
+        }
+        if (info.QiacubeDate)
+        {
+          text += '<div class="qiacube-date">'+info.QiacubeDate+'</div>';
+        }
+        else if (info.DilutionDate)
+        {
+          text += '<div class="dilution-date">'+info.DilutionDate+'</div>';
+        }
         else
         {
-          warningMsg[warningMsg.length] = 'No NDConc value';
-        }
-        if (info.QiacubeDate)
-        {
-          text += '<div class="qiacube-date">'+info.QiacubeDate+'</div>';
-        }
-        else if (info.DilutionDate)
-        {
-          text += '<div class="dilution-date">'+info.DilutionDate+'</div>';
-        }
-        else
-        {
-          warningMsg[warningMsg.length] = info.preNormalized ? 'No DilutionDate value' : 'No QiacubeDate value';
+          if (!rna.external) warningMsg[warningMsg.length] = info.preNormalized ? 'No DilutionDate value' : 'No QiacubeDate value';
         }
         if (info.AutoProcessing)

extensions/net.sf.basedb.reggie/trunk/resources/personal/map-external-data.js

@@ -30 +30 @@
   {
     var frm = document.forms['reggie'];
-    var fromPnr = frm.mapFrom.value == 'PersonalNo';
+    var fromPnr = frm.mapFrom.value == 'PersonalNo' || frm.mapFrom.value == 'PAD';
     
     Doc.showHide('exportPersonalNo', !fromPnr);
+    Doc.showHide('alsoExportPad', !fromPnr);
     Doc.showHide('exportPatientId', fromPnr);
     Doc.showHide('alsoExportCaseId', fromPnr);
@@ -63 +64 @@
         preview += Strings.encodeTags(line) + '\n';
       }
-      if (mapFrom == null && line.match(/^[QCS]\d+\t.*$/)) // We look for lines starting with 'Q', 'C' or 'S' followed by {digits} and a {tab}
+      if (mapFrom == null) 
       {
-        var firstChar = line.charAt(0);
-        if (firstChar == 'Q')
+        if (line.match(/^[QCS]\d+\t.*$/))// We look for lines starting with 'Q', 'C' or 'S' followed by {digits} and a {tab}
         {
-          mapFrom = 'PatientId';
+          var firstChar = line.charAt(0);
+          if (firstChar == 'Q')
+          {
+            mapFrom = 'PatientId';
+          }
+          else if (firstChar == 'C')
+          {
+            mapFrom = 'CaseId';
+          }
+          else if (firstChar == 'S')
+          {
+            mapFrom = 'SpecimenId';
+          }
         }
-        else if (firstChar == 'C')
+        else if (lineNo == 0 && line.match(/^[^\t]*pad/i)) // If the first header column contains 'pad' (ignoring case) we assume it contains PAD values
         {
-          mapFrom = 'CaseId';
-        }
-        else if (firstChar == 'S')
-        {
-          mapFrom = 'SpecimenId';
+          mapFrom = 'PAD';
         }
       }
@@ -108 +116 @@
     url += '&exportCaseId='+(frm.exportCaseId.checked ? 1 : 0);
     url += '&exportSpecimenId='+(frm.exportSpecimenId.checked ? 1 : 0);
+    url += '&exportPad='+(frm.exportPad.checked ? 1 : 0);
     url += '&sortOutput='+(frm.sortOutputOrder.checked ? 1 : 0);
     Wizard.showLoadingAnimation('Working...', 'map-data-progress');

extensions/net.sf.basedb.reggie/trunk/resources/personal/map-external-data.jsp

@@ -101 +101 @@
           <select name="mapFrom" id="mapFrom">
             <option value="PersonalNo">Personal number
+            <option value="PAD">PAD
             <option value="PatientId">Patient release ID
             <option value="CaseId">Case release ID
@@ -115 +116 @@
         <td class="input" style="padding-top: 4px; padding-bottom: 4px;">
           <div id="exportPersonalNo" style="display: none;"><input type="checkbox" checked disabled>Personal number</div>
+          <div id="alsoExportPad" style="display: none;"><label><input type="checkbox" name="exportPad" id="exportPad">PAD</label></div>
           <div id="exportPatientId" style="display: none;"><input type="checkbox" checked disabled>Patient release ID</div>
           <div id="alsoExportCaseId" style="display: none;"><label><input type="checkbox" name="exportCaseId" id="exportCaseId">Case release ID</label></div>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/activity/ActivityDef.java

@@ -242 +242 @@
   */
   public static final ActivityDef IMPORTED_RNA_ALIQUOTS = new ActivityDef("imported-rna-aliquots", "Imported 1 aliquot for RNAseq analysis", "Imported {COUNT} aliquots for RNAseq analysis");
-
+  
+  /**
+    Reggie the Snake was summoned.
+  */
+  public static final ActivityDef REGGIE_THE_SNAKE_WAS_SUMMONED = new ActivityDef("reggie-the-snake-was-summoned", "🐍 Reggie the Snake was summoned", "🐍🐍 Reggie the Snake was summoned {COUNT} times");
   
   private final String id;

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/activity/ActivityEntry.java

@@ -50 +50 @@
   {
     return LocalDateTime.ofInstant(getEventDate().toInstant(), ZoneId.systemDefault()).truncatedTo(ChronoUnit.DAYS);
+  }
+  
+  /**
+    Get the age of the event in seconds.
+    @since 4.23.3
+  */
+  public default int getAgeInSeconds()
+  {
+    return (int)((System.currentTimeMillis() - getEventDate().getTime()) / 1000);
   }
   

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/activity/ActivityLog.java

@@ -394 +394 @@
       int ageInDays = (int)ChronoUnit.DAYS.between(a.getEventDay(), today);
       boolean remove = ageInDays > maxAgeInDays || (ageInDays > 1 && numPassed >= maxEntries);
+      if (a.getMessage().contains("Reggie the Snake") && a.getAgeInSeconds() > 180)
+      {
+        // Reggie the Snake never stays more than 3 minutes
+        remove = true;
+      }
       if (!remove) numPassed++;
       return remove;
@@ -403 +408 @@
     to the disc at regular intervals.
   */
-  static class SaveActivityLog
+  public static class SaveActivityLog
     extends TimerTask
   {
-    SaveActivityLog() 
+    public SaveActivityLog() 
     {}
     

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/ExportServlet.java

@@ -51 +51 @@
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Annotations;
-import net.sf.basedb.core.query.Expression;
 import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
@@ -513 +512 @@
   }
 
-  @SuppressWarnings({"unchecked", "rawtypes"})
   @Override
   protected void doPost(HttpServletRequest req, HttpServletResponse resp)
@@ -538 +536 @@
         
         String mapFrom = Values.getString(req.getParameter("mapFrom"), "PersonalNo");
-        String mapFromFriendlyName = "personal number";
         boolean exportCaseId = Values.getBoolean(req.getParameter("exportCaseId"));
         boolean exportSpecimenId = Values.getBoolean(req.getParameter("exportSpecimenId"));
+        boolean exportPad = Values.getBoolean(req.getParameter("exportPad"));
         boolean sortOutput = Values.getBoolean(req.getParameter("sortOutput"));
 
         SnapshotManager manager = new SnapshotManager();
-        Object[] headerOut = new Object[2];
-        ValueConverter<BioSource, String>[] dataConvert = new ValueConverter[1];
-        List<Object[]> dataOut = new ArrayList<>();
-
-        ItemQuery<BioSource> findPat = BioSource.getQuery();
-        Subtype.PATIENT.addFilter(dc, findPat);
-        findPat.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        List<OutputColumn> outColumns = new ArrayList<>();
+        PatientLoader loader = null;
+        if ("PatientId".equals(mapFrom))
+        {
+          loader = PatientLoader.fromPatientId(dc);
+          outColumns.add(new PatientToPersonalNumberConverter(dc, manager));
+          if (exportPad) outColumns.add(ReleaseIdToPadConverter.fromPatientId(dc, manager));
+        }
+        else if ("CaseId".equals(mapFrom))
+        {
+          loader = PatientLoader.fromCaseId(dc);
+          outColumns.add(new PatientToPersonalNumberConverter(dc, manager));
+          if (exportPad) outColumns.add(ReleaseIdToPadConverter.fromCaseId(dc, manager));
+        }
+        else if ("SpecimenId".equals(mapFrom))
+        {
+          loader = PatientLoader.fromSpecimenId(dc);
+          outColumns.add(new PatientToPersonalNumberConverter(dc, manager));
+          if (exportPad) outColumns.add(ReleaseIdToPadConverter.fromSpecimenId(dc, manager));
+        }
+        else if ("PAD".equals(mapFrom))
+        {
+          PatientLoaderFromPad padLoader = new PatientLoaderFromPad(dc);
+          loader = padLoader;
+          outColumns.add(new PatientToReleaseIdConverter());
+          if (exportCaseId) outColumns.add(padLoader.toCaseId());
+          if (exportSpecimenId) outColumns.add(padLoader.toSpecimenId());
+        }
+        else // "PersonalNo"
+        {
+          loader = PatientLoader.fromPersonalNumber(dc);
+          outColumns.add(new PatientToReleaseIdConverter());
+          if (exportCaseId) outColumns.add(new PatientToCaseReleaseIdConverter(dc));
+          if (exportSpecimenId) outColumns.add(new PatientToSpecimenReleaseIdConverter(dc));
+        }
         
-        // Modify the query and output headers depending on the "mapFrom" parameter
-        // we should be able to execute it with a value from the file and find a patient item
-        Expression mapFromParameter = Expressions.parameter("mapFrom");
-        if ("PatientId".equals(mapFrom))
-        {
-          mapFromFriendlyName = "patient release ID";
-          findPat.restrict(Restrictions.eq(Hql.property("externalId"), mapFromParameter));
-          dataConvert[0] = new PatientToPersonalNumberConverter(dc, manager);
-          headerOut[0] = "PersonalNumber";
-        }
-        else if ("CaseId".equals(mapFrom))
-        {
-          mapFromFriendlyName = "case release ID";
-          findPat.join(Hql.innerJoin("childCreationEvents", "cce"));
-          findPat.join(Hql.innerJoin("cce", "event", "evt"));
-          findPat.join(Hql.innerJoin("evt", "bioMaterial", "cse")); // 'cse' should now reference a case
-          findPat.restrict(Restrictions.eq(Hql.property("cse", "externalId"), mapFromParameter));
-          dataConvert[0] = new PatientToPersonalNumberConverter(dc, manager);
-          headerOut[0] = "PersonalNumber";
-        }
-        else if ("SpecimenId".equals(mapFrom))
-        {
-          mapFromFriendlyName = "specimen release ID";
-          findPat.join(Hql.innerJoin("childCreationEvents", "cce"));
-          findPat.join(Hql.innerJoin("cce", "event", "evt"));
-          findPat.join(Hql.innerJoin("evt", "bioMaterial", "cse")); // 'cse' should now reference a case
-          findPat.join(Hql.innerJoin("cse", "childCreationEvents", "cce2"));
-          findPat.join(Hql.innerJoin("cce2", "event", "evt2"));
-          findPat.join(Hql.innerJoin("evt2", "bioMaterial", "spm")); // 'spm' should now reference a specimen/nospecimen
-          findPat.restrict(Restrictions.eq(Hql.property("spm", "externalId"), mapFromParameter));
-          dataConvert[0] = new PatientToPersonalNumberConverter(dc, manager);
-          headerOut[0] = "PersonalNumber";
-        }
-        else // "PersonalNo"
-        {
-          findPat.join(Annotations.innerJoin(null, Annotationtype.PERSONAL_NUMBER.load(dc), "pnr"));
-          findPat.restrict(Restrictions.eq(Hql.alias("pnr"), mapFromParameter));
-          
-          int numCols = 2 + (exportCaseId ? 1 : 0) + (exportSpecimenId ? 1 : 0);
-          if (numCols > headerOut.length) // We need more output columns
-          {
-            headerOut = new Object[numCols];
-            dataConvert = new ValueConverter[numCols-1]; // The last column need to converter
-          }
-          int col = 0;
-          dataConvert[col] = new PatientToReleaseIdConverter();
-          headerOut[col++] = "PatientId";
-          if (exportCaseId)
-          {
-            headerOut[col] = "CaseId";
-            dataConvert[col++] = new PatientToCaseReleaseIdConverter(dc);
-          }
-          if (exportSpecimenId)
-          {
-            headerOut[col] = "SpecimenId";
-            dataConvert[col++] = new PatientToSpecimenReleaseIdConverter(dc);
-          }
-        }
 
         InputStream uploadIn = null;
@@ -640 +608 @@
           }
         
-          int lastCol = headerOut.length - 1;
+          int lastCol = outColumns.size();
+          Object[] headerOut = new Object[lastCol+1];
+          for (int colNo = 0; colNo < lastCol; colNo++)
+          {
+            headerOut[colNo] = outColumns.get(colNo).getHeader();
+          }
           headerOut[lastCol] = dataIn[1];
         
-          int lineIn = 0;
           int lineOut = 0;
           int linesSkipped = 0;
+          InputLine inputLine = new InputLine();
+          List<Object[]> dataOut = new ArrayList<>();
           
           String data = uploadReader.readLine();
@@ -651 +625 @@
           {
             parsedCharacters += data.length() + 1;
-            lineIn++;
-            progress.display((int)(100*parsedCharacters / totalBytes), "Working... " + lineIn + " lines parsed so far...");
+            inputLine.lineNo++;
+            progress.display((int)(100*parsedCharacters / totalBytes), "Working... " + inputLine.lineNo + " lines parsed so far...");
             
             dataIn = data.split("\t", 2);
             if (dataIn.length != 2) 
             {
-              throw new IOException("On line " + lineIn + ": The file need at least 2 data columns");
+              throw new IOException("On line " + inputLine.lineNo + ": The file need at least 2 data columns");
             }
 
-            String fromId = Values.getStringOrNull(dataIn[0]);
-            if (fromId == null)
+            inputLine.fromId = Values.getStringOrNull(dataIn[0]);
+            if (inputLine.fromId == null)
             {
-              throw new IOException("On line " + lineIn + ": " + mapFromFriendlyName + " is missing");
+              throw new IOException("On line " + inputLine.lineNo + ": " + loader.getMapFromFriendlyName() + " is missing");
             }
-  
-            findPat.setParameter("mapFrom", fromId, Type.STRING);
-            List<BioSource> patients = findPat.list(dc);
-            if (patients.size() == 0)
+            
+            inputLine.patient = loader.convert(inputLine);
+  
+            if (inputLine.patient == null)
             {
               linesSkipped++;
               if (linesSkipped > 100 && lineOut == 0)
               {
-                throw new IOException("On line " + lineIn + ": No patients found after " + lineIn + " lines. Is this the correct file?");
+                throw new IOException("On line " + inputLine.lineNo + ": No patients found after " + inputLine.lineNo + " lines. Is this the correct file?");
               }
-            }
-            else if (patients.size() > 1)
-            {
-              throw new IOException("On line " + lineIn + ": Found " + patients.size() + " patients with same " + mapFromFriendlyName + ": " + fromId);
             }
             else
             {
-              BioSource pat = patients.get(0);
               Object[] output = new Object[headerOut.length];
-              for (int c = 0; c < lastCol; c++)
+              for (int colNo = 0; colNo < lastCol; colNo++)
               {
-                output[c] = dataConvert[c].convert(pat);
+                output[colNo] = outColumns.get(colNo).convert(inputLine);
               }
               output[lastCol] = dataIn[1];
@@ -697 +666 @@
           if (lineOut == 0)
           {
-            throw new IOException("On line " + lineIn + ": No patients found. Is this the correct file?");
+            throw new IOException("On line " + inputLine.lineNo + ": No patients found. Is this the correct file?");
           }
 
@@ -714 +683 @@
           tmpWriter.flush();
           tmpOut.flush();
-          jsonMessages.add("Parsed " + lineIn + " lines from input file");
+          jsonMessages.add("Parsed " + inputLine.lineNo + " lines from input file");
           jsonMessages.add("Wrote " + lineOut + " lines to output file");
           if (linesSkipped > 0)
@@ -724 +693 @@
             jsonMessages.add("A patient was found for all lines");
           }
-          json.put("numLinesIn", lineIn);
+          json.put("numLinesIn", inputLine.lineNo);
           json.put("numLinesOut", lineOut);
           json.put("numNotFound", linesSkipped);
@@ -1506 +1475 @@
   
   /**
+    Represents a line from the input file.
+    TODO -- add more data here ?
+  */
+  static class InputLine
+  {
+    int lineNo;
+    String fromId;
+    BioSource patient;
+  }
+  
+  /**
+    Implementations need to take an input line and
+    find a single patient for that line.
+  */
+  static abstract class PatientLoader
+    implements ValueConverter<InputLine, BioSource>
+  {
+    static PatientLoader fromPersonalNumber(DbControl dc)
+    {
+      ItemQuery<BioSource> query = BioSource.getQuery();
+      query.join(Annotations.innerJoin(null, Annotationtype.PERSONAL_NUMBER.load(dc), "pnr"));
+      query.restrict(Restrictions.eq(Hql.alias("pnr"), Expressions.parameter("fromId")));
+      return new PatientLoaderByQuery(dc, query, "personal number");
+    }
+    
+    static PatientLoader fromPatientId(DbControl dc)
+    {
+      ItemQuery<BioSource> query = BioSource.getQuery();
+      query.restrict(Restrictions.eq(Hql.property("externalId"), Expressions.parameter("fromId")));
+      return new PatientLoaderByQuery(dc, query, "patient release ID");
+    }
+    
+    static PatientLoader fromCaseId(DbControl dc)
+    {
+      ItemQuery<BioSource> query = BioSource.getQuery();
+      query.join(Hql.innerJoin("childCreationEvents", "cce"));
+      query.join(Hql.innerJoin("cce", "event", "evt"));
+      query.join(Hql.innerJoin("evt", "bioMaterial", "cse")); // 'cse' should now reference a case
+      query.restrict(Restrictions.eq(Hql.property("cse", "externalId"), Expressions.parameter("fromId")));
+      return new PatientLoaderByQuery(dc, query, "case release ID");
+    }
+    
+    static PatientLoader fromSpecimenId(DbControl dc)
+    {
+      ItemQuery<BioSource> query = BioSource.getQuery();
+      query.join(Hql.innerJoin("childCreationEvents", "cce"));
+      query.join(Hql.innerJoin("cce", "event", "evt"));
+      query.join(Hql.innerJoin("evt", "bioMaterial", "cse")); // 'cse' should now reference a case
+      query.join(Hql.innerJoin("cse", "childCreationEvents", "cce2"));
+      query.join(Hql.innerJoin("cce2", "event", "evt2"));
+      query.join(Hql.innerJoin("evt2", "bioMaterial", "spm")); // 'spm' should now reference a specimen/nospecimen
+      query.restrict(Restrictions.eq(Hql.property("spm", "externalId"), Expressions.parameter("fromId")));
+      return new PatientLoaderByQuery(dc, query, "specimen release ID");
+    }
+    
+    final String mapFromFriendlyName;
+    final DbControl dc;
+
+    PatientLoader(DbControl dc, String mapFromFriendlyName)
+    {
+      this.dc = dc;
+      this.mapFromFriendlyName = mapFromFriendlyName;
+    }
+    
+    public String getMapFromFriendlyName()
+    {
+      return mapFromFriendlyName;
+    }
+  }
+  
+  /**
+    Patient loader implementation that can find the patient by executing a
+    query using the source id as a parameter.
+  */
+  static class PatientLoaderByQuery
+    extends PatientLoader
+  {
+    
+    private final ItemQuery<BioSource> patientQuery;
+    
+    PatientLoaderByQuery(DbControl dc, ItemQuery<BioSource> patientQuery, String mapFromFriendlyName)
+    {
+      super(dc, mapFromFriendlyName);
+      this.patientQuery = patientQuery;
+      Subtype.PATIENT.addFilter(dc, patientQuery);
+      patientQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    }
+    
+    @Override
+    public BioSource convert(InputLine ctx) 
+    {
+      patientQuery.setParameter("fromId", ctx.fromId, Type.STRING);
+      List<BioSource> patients = patientQuery.list(dc);
+      if (patients.size() > 1)
+      {
+        throw new RuntimeException("On line " + ctx.lineNo + ": Found " + patients.size() + " patients with same " + mapFromFriendlyName + ": " + ctx.fromId);
+      }
+      return patients.size() == 0 ? null : patients.get(0);
+    }
+  }
+  
+  /**
+    Patient loader implementation when the source value is a PAD value. This implementation
+    is used instead of the PatientLoaderByQuery for improved performance when 
+    output columns for case and/or specimen release ID are required. The implementation
+    executes an initial query to find the specimen item(s) with the given PAD and then
+    uses the specimen to find other items. This avoids executing the slow query against 
+    the PAD annotation more than once.
+  */
+  static class PatientLoaderFromPad
+    extends PatientLoader
+  {
+    
+    private final ItemQuery<Sample> specimenQuery;
+    private final ItemQuery<BioSource> patientQuery;
+    private List<Integer> currentSpecimen;
+
+    public PatientLoaderFromPad(DbControl dc)
+    {
+      super(dc, "PAD");
+      
+      specimenQuery = Sample.getQuery();
+      specimenQuery.restrict(
+        Restrictions.or(
+          Subtype.SPECIMEN.restriction(dc, null),
+          Subtype.NO_SPECIMEN.restriction(dc, null)
+        ));
+      specimenQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+      specimenQuery.join(Annotations.innerJoin(null, Annotationtype.PAD.load(dc), "pad"));
+      specimenQuery.restrict(Restrictions.eq(Hql.alias("pad"), Expressions.parameter("fromId")));
+      
+      patientQuery = BioSource.getQuery();
+      Subtype.PATIENT.addFilter(dc, patientQuery);
+      patientQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+      patientQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
+      patientQuery.join(Hql.innerJoin("cce", "event", "evt"));
+      patientQuery.join(Hql.innerJoin("evt", "bioMaterial", "cse")); // 'cse' should now reference a case
+      patientQuery.join(Hql.innerJoin("cse", "childCreationEvents", "cce2"));
+      patientQuery.join(Hql.innerJoin("cce2", "event", "evt2"));
+      patientQuery.join(Hql.innerJoin("evt2", "bioMaterial", "spm")); // 'spm' should now reference a specimen/nospecimen
+      patientQuery.restrict(Restrictions.in(Hql.alias("spm"), Expressions.parameter("specimen")));
+      patientQuery.setDistinct(true);
+    }
+    
+    @Override
+    public String getMapFromFriendlyName()
+    {
+      return "PAD";
+    }
+
+    @Override
+    public BioSource convert(InputLine ctx) 
+    {
+      specimenQuery.setParameter("fromId", ctx.fromId, Type.STRING);
+      currentSpecimen = specimenQuery.idList(dc);
+      
+      if (currentSpecimen.size() == 0) return null;
+      
+      patientQuery.setParameter("specimen", currentSpecimen, Type.INT);
+      List<BioSource> patients = patientQuery.list(dc);
+      if (patients.size() > 1)
+      {
+        throw new RuntimeException("On line " + ctx.lineNo + ": Found " + patients.size() + " patients with same PAD: " + ctx.fromId);
+      }
+      return patients.size() == 0 ? null : patients.get(0);
+    }
+    
+    /**
+      Create an output implementation for the specimen release id.
+    */
+    public OutputColumn toSpecimenId()
+    {
+      ItemQuery<Sample> query = Sample.getQuery();
+      query.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("specimen")));
+      return new PadToReleaseIdConverter("SpecimenId", dc, query, this);
+    }
+    
+    /**
+      Create an output implementation for the case release id.
+    */
+    public OutputColumn toCaseId()
+    {
+      ItemQuery<Sample> query = Sample.getQuery();
+      Subtype.CASE.addFilter(dc, query);
+      query.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+      query.join(Hql.innerJoin("childCreationEvents", "cce"));
+      query.join(Hql.innerJoin("cce", "event", "evt"));
+      query.join(Hql.innerJoin("evt", "bioMaterial", "spm")); // 'spm' should now reference a specimen/nospecimen
+      query.restrict(Restrictions.in(Hql.alias("spm"), Expressions.parameter("specimen")));
+      return new PadToReleaseIdConverter("CaseId", dc, query, this);
+    }
+  }
+  
+  
+  /**
+    Implementation need to generate an output column
+    for a given line.
+  */
+  static abstract class OutputColumn
+    implements ValueConverter<InputLine, String>
+  {
+    
+    private final String header;
+    OutputColumn(String header)
+    {
+      this.header = header;
+    }
+    
+    public String getHeader()
+    {
+      return header;
+    }
+  }
+  
+  /**
     Get the external (release) ID from the patient.
   */
   static class PatientToReleaseIdConverter
-    implements ValueConverter<BioSource, String>
+    extends OutputColumn
   {
     PatientToReleaseIdConverter()
-    {}
-
-    @Override
-    public String convert(BioSource patient) 
-    {
-      return patient.getExternalId();
+    {
+      super("PatientId");
+    }
+
+    @Override
+    public String convert(InputLine ctx) 
+    {
+      return ctx.patient.getExternalId();
     }
   }
@@ -1526 +1712 @@
   */
   static class PatientToCaseReleaseIdConverter
-    implements ValueConverter<BioSource, String>
+    extends OutputColumn
   {
     private final DbControl dc;
@@ -1534 +1720 @@
     PatientToCaseReleaseIdConverter(DbControl dc)
     {
+      super("CaseId");
       this.dc = dc;
       this.toRelaseId = new ToReleaseIdFormatter();
@@ -1545 +1732 @@
   
     @Override
-    public String convert(BioSource patient) 
-    {
-      caseQuery.setEntityParameter("pat", patient);
+    public String convert(InputLine ctx) 
+    {
+      caseQuery.setEntityParameter("pat", ctx.patient);
       List<Sample> cases = caseQuery.list(dc);
       return Values.getString(cases, ",", true, toRelaseId);
@@ -1558 +1745 @@
   */
   static class PatientToSpecimenReleaseIdConverter
-    implements ValueConverter<BioSource, String>
+    extends OutputColumn
   {
     private final DbControl dc;
@@ -1566 +1753 @@
     PatientToSpecimenReleaseIdConverter(DbControl dc)
     {
+      super("SpecimenId");
       this.dc = dc;
       this.toRelaseId = new ToReleaseIdFormatter();
@@ -1582 +1770 @@
   
     @Override
-    public String convert(BioSource patient) 
-    {
-      specimenQuery.setEntityParameter("pat", patient);
+    public String convert(InputLine ctx) 
+    {
+      specimenQuery.setEntityParameter("pat", ctx.patient);
       List<Sample> specimen = specimenQuery.list(dc);
       return Values.getString(specimen, ",", true, toRelaseId);
@@ -1594 +1782 @@
   */
   static class PatientToPersonalNumberConverter
-    implements ValueConverter<BioSource, String>
+    extends OutputColumn
   {
     
@@ -1602 +1790 @@
     PatientToPersonalNumberConverter(DbControl dc, SnapshotManager manager)
     {
+      super("PersonalNumber");
       this.dc = dc;
       this.manager = manager;
@@ -1607 +1796 @@
   
     @Override
-    public String convert(BioSource patient) 
-    {
-      return (String)Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, manager, patient);
-    }
+    public String convert(InputLine ctx) 
+    {
+      return (String)Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, manager, ctx.patient);
+    }
+  }
+  
+  /**
+    Maps a release id from patient, case or specimen to PAD
+    (one or more) on specimen items. Use one of the factor methods
+    to get an instance for the proper release id type.
+  */
+  static class ReleaseIdToPadConverter
+    extends OutputColumn
+  {
+    private final DbControl dc;
+    private final SnapshotManager manager;
+    private final ItemQuery<Sample> specimenQuery;
+    
+    /**
+      Get the PAD when the source id is a specimen release id.
+    */
+    static ReleaseIdToPadConverter fromSpecimenId(DbControl dc, SnapshotManager manager)
+    {
+      ItemQuery<Sample> query = Sample.getQuery();
+      query.restrict(Restrictions.eq(Hql.property("externalId"), Expressions.parameter("fromId")));
+      return new ReleaseIdToPadConverter(dc, manager, query);
+    }
+    
+    /**
+      Get the PAD(s) when the source id is a case release id.
+    */
+    static ReleaseIdToPadConverter fromCaseId(DbControl dc, SnapshotManager manager)
+    {
+      ItemQuery<Sample> query = Sample.getQuery();
+      query.join(Hql.innerJoin("parent", "cse"));
+      query.restrict(Restrictions.eq(Hql.property("cse", "externalId"), Expressions.parameter("fromId")));
+      return new ReleaseIdToPadConverter(dc, manager, query);
+    }
+    
+    /**
+      Get the PAD(s) when the source id is a patient release id.
+    */
+    static ReleaseIdToPadConverter fromPatientId(DbControl dc, SnapshotManager manager)
+    {
+      ItemQuery<Sample> query = Sample.getQuery();
+      query.join(Hql.innerJoin("parent", "cse"));
+      query.join(Hql.innerJoin("cse", "parent", "pat"));
+      query.restrict(Restrictions.eq(Hql.property("pat", "externalId"), Expressions.parameter("fromId")));
+      return new ReleaseIdToPadConverter(dc, manager, query);
+    }
+    
+    private ReleaseIdToPadConverter(DbControl dc, SnapshotManager manager, ItemQuery<Sample> specimenQuery)
+    {
+      super("PAD");
+      this.dc = dc;
+      this.manager = manager;
+      this.specimenQuery = specimenQuery;
+      specimenQuery.restrict(
+        Restrictions.or(
+          Subtype.SPECIMEN.restriction(dc, null),
+          Subtype.NO_SPECIMEN.restriction(dc, null)
+        ));
+      specimenQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+    }
+  
+    @Override
+    public String convert(InputLine ctx) 
+    {
+      specimenQuery.setParameter("fromId", ctx.fromId, Type.STRING);
+      List<Sample> specimen = specimenQuery.list(dc);
+      String pad = null;
+      if (specimen.size() > 1)
+      {
+        Set<String> allPad = new TreeSet<>();
+        for (Sample s : specimen)
+        {
+          allPad.add((String)Annotationtype.PAD.getAnnotationValue(dc, manager, s));
+        }
+        pad = Values.getString(allPad, ",", true);
+      }
+      else if (specimen.size() == 1)
+      {
+        pad = (String)Annotationtype.PAD.getAnnotationValue(dc, manager, specimen.get(0));
+      }
+      return pad;
+    }
+    
+  }
+  
+  /**
+    Output release id for case or specimen items that has been previously found by the
+    PatientLoaderFromPad implementation.
+  */
+  static class PadToReleaseIdConverter
+    extends OutputColumn
+  {
+    
+    
+    private final DbControl dc;
+    private final ItemQuery<Sample> query;
+    private final PatientLoaderFromPad padLoader;
+    
+    private PadToReleaseIdConverter(String header, DbControl dc, ItemQuery<Sample> query, PatientLoaderFromPad padLoader)
+    {
+      super(header);
+      this.dc = dc;
+      this.query = query;
+      this.padLoader = padLoader;
+    }
+    
+    @Override
+    public String convert(InputLine ctx) 
+    {
+      if (padLoader.currentSpecimen.size() == 0) return null;
+      
+      query.setParameter("specimen", padLoader.currentSpecimen, Type.INT);
+      List<Sample> items = query.list(dc);
+      String idValues = null;
+      if (items.size() > 1)
+      {
+        Set<String> allId = new TreeSet<>();
+        for (Sample s : items)
+        {
+          allId.add(s.getExternalId());
+        }
+        idValues = Values.getString(allId, ",", true);
+      }
+      else if (items.size() == 1)
+      {
+        idValues = items.get(0).getExternalId();
+      }
+      return idValues;
+    }
+
   }
   

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SessionServlet.java

@@ -17 +17 @@
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.Application;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Directory;
@@ -25 +26 @@
 import net.sf.basedb.reggie.JsonUtil;
 import net.sf.basedb.reggie.Reggie;
+import net.sf.basedb.reggie.activity.ActivityDef;
 import net.sf.basedb.reggie.activity.ActivityEntry;
 import net.sf.basedb.reggie.activity.ActivityLog;
@@ -206 +208 @@
         }
       }
+      else if ("ReggieTheSnakeWasSummoned".equals(cmd))
+      {
+        sc = Reggie.getSessionControl(req);
+        dc = sc.newDbControl();
+        ActivityDef.REGGIE_THE_SNAKE_WAS_SUMMONED.merge(dc, 1).setUser("Indiana Jones");
+        dc.commit();
+        // Makes Reggie the Snake go away after at least 200 seconds
+        Application.getScheduler().schedule(new ActivityLog.SaveActivityLog(), 200000, true);
+      }
       
     }