Changeset 1957

Timestamp:

Apr 30, 2013, 10:04:56 AM (9 years ago)

Author:

olle

Message:

Refs #487. First version of the INCA export.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/index.jsp (modified) (1 diff)
• resources/personal/export_inca.jsp (added)
• src/net/sf/basedb/reggie/servlet/ExportServlet.java (modified) (8 diffs)

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

@@ -341 +341 @@
             <ul>
             <li><a href="personal/export_monthly_oplist.jsp?ID=<%=ID%>">Export monthly operation list</a>
+            <li><a href="personal/export_inca.jsp?ID=<%=ID%>">INCA export</a>
             </ul>
           </dd>

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

@@ -5 +5 @@
 import java.util.Calendar;
 import java.util.Date;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Set;
@@ -20 +21 @@
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.ItemQuery;
+import net.sf.basedb.core.ItemSubtype;
+import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.core.SessionControl;
@@ -57 +60 @@
     try
     {
-      if ("ExportMonthlyOpList".equals(cmd))
+      if ("ExportMonthlyOpList".equals(cmd) || "ExportINCA".equals(cmd))
       {
         boolean exportSubtype = Values.getBoolean(req.getParameter("exportSubtype"));
@@ -64 +67 @@
         // This can be any time point in the desired month/year
         long timeInMillis = Values.getLong(req.getParameter("time"));
-        // Negative value indicate that we should load the whole year
+        // A value of 1 (1970.01.01 00:00:00 001) indicates no time restriction
+        boolean allSamples = (timeInMillis == 1);
+        // Negative value indicates that we should load the whole year
         boolean fullYear = timeInMillis < 0;
         timeInMillis = Math.abs(timeInMillis);
@@ -93 +98 @@
         // ...that has a creation date (=operation date) between the start and end time points
         specimenQuery.join(Hql.innerJoin(null, "creationEvent", "ce", true));
-        specimenQuery.restrict(Restrictions.gteq(Hql.property("ce", "eventDate"), Expressions.parameter("start", start)));
-        specimenQuery.restrict(Restrictions.lt(Hql.property("ce", "eventDate"), Expressions.parameter("end", end)));
-        
-        // FETCH JOIN of CASE and PATIENT + the CASE creation event
-        // for performance reasons
-        specimenQuery.join(Hql.innerJoin(null, "parent", "cse", true));
-        specimenQuery.join(Hql.innerJoin("cse", "creationEvent", "ce2", true));
-        specimenQuery.join(Hql.innerJoin("cse", "parent", "pat", true));
-        
-        // ...only include 'Specimen' or 'NoSpecimen' items
-        specimenQuery.restrict(
-          Restrictions.or(
-            Subtype.SPECIMEN.restriction(dc, null),
-            Subtype.NO_SPECIMEN.restriction(dc, null)
-          ));
+        if (!allSamples)
+        {
+          specimenQuery.restrict(Restrictions.gteq(Hql.property("ce", "eventDate"), Expressions.parameter("start", start)));
+          specimenQuery.restrict(Restrictions.lt(Hql.property("ce", "eventDate"), Expressions.parameter("end", end)));
+        }
+
+        if ("ExportMonthlyOpList".equals(cmd))
+        {
+          // FETCH JOIN of CASE and PATIENT + the CASE creation event
+          // for performance reasons
+          specimenQuery.join(Hql.innerJoin(null, "parent", "cse", true));
+          specimenQuery.join(Hql.innerJoin("cse", "creationEvent", "ce2", true));
+          specimenQuery.join(Hql.innerJoin("cse", "parent", "pat", true));
+          
+          // ...only include 'Specimen' or 'NoSpecimen' items
+          specimenQuery.restrict(
+            Restrictions.or(
+              Subtype.SPECIMEN.restriction(dc, null),
+              Subtype.NO_SPECIMEN.restriction(dc, null)
+            ));
+        }
+        else if ("ExportINCA".equals(cmd))
+        {
+          // ...include 'Specimen', 'NoSpecimen', and 'Blood' items
+          specimenQuery.restrict(
+            Restrictions.or(
+              Subtype.SPECIMEN.restriction(dc, null),
+              Subtype.NO_SPECIMEN.restriction(dc, null),
+              Subtype.BLOOD.restriction(dc, null)
+            ));
+        }
         
         List<Sample> samples = specimenQuery.list(dc);
@@ -116 +137 @@
         Set<PersonalOpDate> opDates = new TreeSet<PersonalOpDate>();
         Pattern caseNamePattern = Pattern.compile("\\..*"); // Pattern to strip suffix from case name (eg. everything after first '.')
-        for (Sample s : samples)
-        {
-          // Check the BiopsyType annotation
-          // We should only export those with 'SpecimenSurgery' or a missing value
-          String biopsyType = (String)Annotationtype.BIOPSY_TYPE.getAnnotationValue(dc, manager, s);
-          
-          if (biopsyType == null || biopsyType.equals("SpecimenSurgery"))
+        if ("ExportMonthlyOpList".equals(cmd))
+        {
+          for (Sample s : samples)
           {
-            // The parent is the 'Case' and the grandparent is the 'Patient'
-            // Ignore samples that don't have parent items
-            BioMaterial theCase = s.getParent();
-            if (theCase instanceof Sample)
-            {
-              BioMaterial patient = ((Sample)theCase).getParent();
-              if (patient instanceof BioSource)
-              {
-                // Get the personal number of the patient
-                String pnr = (String)Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, manager, patient);
-
-                if (pnr != null)
-                {
-                  // Finally, we now have the information that should be exported
-                  Site site = Site.findByCaseName(s.getName());
-                  String laterality = (String)Annotationtype.LATERALITY.getAnnotationValue(dc, manager, theCase);
-                  String consent = (String)Annotationtype.CONSENT.getAnnotationValue(dc, manager, theCase);
-                  String opDate = dateFormat.format(s.getCreationEvent().getEventDate());
-                  String subtype = exportSubtype ? s.getItemSubtype().getName() : null;
-                  String patientId = exportPatientId ? patient.getName() : null;
-                  String caseName = caseNamePattern.matcher(s.getName()).replaceFirst("");
-                  opDates.add(new PersonalOpDate(pnr, opDate, site, laterality, subtype, caseName, consent, patientId));
+            // Check the BiopsyType annotation
+            // We should only export those with 'SpecimenSurgery' or a missing value
+            String biopsyType = (String)Annotationtype.BIOPSY_TYPE.getAnnotationValue(dc, manager, s);
+            
+            if (biopsyType == null || biopsyType.equals("SpecimenSurgery"))
+            {
+              // The parent is the 'Case' and the grandparent is the 'Patient'
+              // Ignore samples that don't have parent items
+              BioMaterial theCase = s.getParent();
+              if (theCase instanceof Sample)
+              {
+                BioMaterial patient = ((Sample)theCase).getParent();
+                if (patient instanceof BioSource)
+                {
+                  // Get the personal number of the patient
+                  String pnr = (String)Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, manager, patient);
+
+                  if (pnr != null)
+                  {
+                    // Finally, we now have the information that should be exported
+                    Site site = Site.findByCaseName(s.getName());
+                    String laterality = (String)Annotationtype.LATERALITY.getAnnotationValue(dc, manager, theCase);
+                    String consent = (String)Annotationtype.CONSENT.getAnnotationValue(dc, manager, theCase);
+                    String opDate = dateFormat.format(s.getCreationEvent().getEventDate());
+                    String subtype = exportSubtype ? s.getItemSubtype().getName() : null;
+                    String patientId = exportPatientId ? patient.getName() : null;
+                    String caseName = caseNamePattern.matcher(s.getName()).replaceFirst("");
+                    opDates.add(new PersonalOpDate(pnr, opDate, site, laterality, subtype, caseName, consent, patientId));
+                  }
                 }
               }
@@ -151 +175 @@
           }
         }
-        
+        else if ("ExportINCA".equals(cmd))
+        {
+          // Get item subtype constants for later use
+          ItemSubtype subtypeSpecimen = Subtype.SPECIMEN.load(dc);
+          ItemSubtype subtypeNoSpecimen = Subtype.NO_SPECIMEN.load(dc);
+          ItemSubtype subtypeBlood = Subtype.BLOOD.load(dc);
+
+          // Step 1: Store up to two entries for each patient, one for each laterality
+          //         represented by a Specimen/NoSpecimen, or if no Specimen or
+          //         NoSpecimen exists, a blood sample. Priority Specimen > NoSpecimen > Blood.
+          HashMap<String,Sample> patientNumberSampleLeftHashMap = new HashMap<String,Sample>();
+          HashMap<String,Sample> patientNumberSampleRightHashMap = new HashMap<String,Sample>();
+          for (Sample s : samples)
+          {
+            // Find patient id
+            BioMaterial theCase = null;
+            BioMaterial patient = null;
+            String laterality = null;
+            if (s.getItemSubtype().equals(subtypeBlood))
+            {
+              // The parent is the 'Patient' for blood samples and cases
+              patient = s.getParent();
+            }
+            else if (s.getItemSubtype().equals(subtypeSpecimen) || s.getItemSubtype().equals(subtypeNoSpecimen))
+            {
+              // The parent is the 'Case' and the grandparent is the 'Patient' for specimens and no specimens
+              theCase = (MeasuredBioMaterial) s.getParent();
+              if (theCase != null && theCase instanceof Sample)
+              {
+                patient = ((Sample)theCase).getParent();
+                laterality = (String)Annotationtype.LATERALITY.getAnnotationValue(dc, manager, theCase);
+              }
+            }
+
+            if (patient instanceof BioSource)
+            {
+              // Check if patient number exists in hash map
+              String patientNumber = patient.getName();
+              if (patientNumber != null)
+              {
+                if (laterality != null && laterality.equals("LEFT"))
+                {
+                  // Optional update of hash map for left laterality
+                  patientNumberSampleLeftHashMap = updatePatientNumberSampleHashMap(dc, manager,
+                      patientNumberSampleLeftHashMap, patientNumber, s, laterality);
+                }
+                else if (laterality != null && laterality.equals("RIGHT"))
+                {
+                  // Optional update of hash map for right laterality
+                  patientNumberSampleRightHashMap = updatePatientNumberSampleHashMap(dc, manager,
+                      patientNumberSampleRightHashMap, patientNumber, s, laterality);
+                }
+                else if (laterality == null || laterality.equals(""))
+                {
+                  // We do not know what the laterality is (if any),
+                  // so both hash maps are updated.
+                  patientNumberSampleLeftHashMap = updatePatientNumberSampleHashMap(dc, manager,
+                      patientNumberSampleLeftHashMap, patientNumber, s, laterality);
+                  patientNumberSampleRightHashMap = updatePatientNumberSampleHashMap(dc, manager,
+                      patientNumberSampleRightHashMap, patientNumber, s, laterality);
+                }
+              }
+            }
+          }
+
+          // Step 2: Export up to two entries for each patient, with priority Specimen > NoSpecimen > Blood
+          for (Sample s : samples)
+          {
+            // Check if sample stored for patient number
+            if (!patientNumberSampleLeftHashMap.containsValue(s) && !patientNumberSampleRightHashMap.containsValue(s))
+            {
+              continue;
+            }
+            // Find patient id
+            BioMaterial theCase = null;
+            BioMaterial patient = null;
+            if (s.getItemSubtype().equals(subtypeBlood))
+            {
+              // The parent is the 'Patient' for blood samples and cases
+              patient = s.getParent();
+              // Only include blood sample if both samples for
+              // left and right laterality are blood samples
+              Sample sampleLeft = patientNumberSampleLeftHashMap.get(patient.getName());
+              Sample sampleRight = patientNumberSampleRightHashMap.get(patient.getName());
+              if (sampleLeft == null || !sampleLeft.getItemSubtype().equals(subtypeBlood))
+              {
+                continue;
+              }
+              else if (sampleRight == null || !sampleRight.getItemSubtype().equals(subtypeBlood))
+              {
+                continue;
+              }
+            }
+            else if (s.getItemSubtype().equals(subtypeSpecimen) || s.getItemSubtype().equals(subtypeNoSpecimen))
+            {
+              // The parent is the 'Case' and the grandparent is the 'Patient' for specimens and no specimens
+              theCase = (MeasuredBioMaterial) s.getParent();
+              if (theCase != null && theCase instanceof Sample)
+              {
+                patient = ((Sample)theCase).getParent();
+              }
+            }
+
+            if (patient instanceof BioSource)
+            {
+              // Get the personal number of the patient
+              String pnr = (String)Annotationtype.PERSONAL_NUMBER.getAnnotationValue(dc, manager, patient);
+
+              if (pnr != null)
+              {
+                // Finally, we now have the information that should be exported
+                Site site = Site.findByCaseName(s.getName());
+                String laterality = null;
+                String consent = null;
+                if (theCase != null)
+                {
+                  laterality = (String)Annotationtype.LATERALITY.getAnnotationValue(dc, manager, theCase);
+                  // For specimen and no specimen samples, consent is coupled to the case
+                  consent = (String)Annotationtype.CONSENT.getAnnotationValue(dc, manager, theCase);
+                }
+                else
+                {
+                  // For blood samples, consent is coupled to the sample
+                  consent = (String)Annotationtype.CONSENT.getAnnotationValue(dc, manager, s);
+                }
+                String opDate = dateFormat.format(s.getCreationEvent().getEventDate());
+                String subtype = exportSubtype ? s.getItemSubtype().getName() : null;
+                String patientId = exportPatientId ? patient.getName() : null;
+                String caseName = caseNamePattern.matcher(s.getName()).replaceFirst("");
+                if (subtype.equals("Blood"))
+                {
+                  subtype = "BloodOnly";
+                }
+                opDates.add(new PersonalOpDate(pnr, opDate, site, laterality, subtype, caseName, consent, patientId));
+              }
+            }
+          }
+        }
+
+        // Default settings for monthly operation list export
+        String filenamePrefix = "opdates-";
+        String tableHeaderStart = "PersonalNr\tScanBId\tOpDate\tLaterality\tSite";
         DateFormatter monthFormat = new DateFormatter(fullYear ? "yyyy-'all'" : "yyyy-MM");
-        resp.setHeader("Content-Disposition", "attachment; filename=opdates-" + monthFormat.format(start) + ".tsv");
+        String dateString = monthFormat.format(start);
+        if (allSamples)
+        {
+          // Set date string to period from 2010 to current month
+          Date today = new Date();
+          dateString = "2010-" + monthFormat.format(today);
+        }
+        if ("ExportINCA".equals(cmd))
+        {
+          filenamePrefix = "incaexport-";
+          tableHeaderStart = "PersonalNo\tScanBId\tDate\tLaterality\tSite";
+        }
+        // Write export file
+        resp.setHeader("Content-Disposition", "attachment; filename=" + filenamePrefix + dateString + ".tsv");
         resp.setContentType("text/plain");
         resp.setCharacterEncoding("UTF-8");
         PrintWriter os = resp.getWriter();
-        os.write("PersonalNr\tScanBId\tOpDate\tLaterality\tSite");
-        if (exportSubtype) os.write("\tSpecimen");
+        os.write(tableHeaderStart);
+        if (exportSubtype) os.write("\tSample");
         if (exportPatientId) os.write("\tPatientId");
         os.write("\tConsent\n");
@@ -183 +361 @@
     
   }
+
+  private HashMap<String, Sample> updatePatientNumberSampleHashMap(
+      DbControl dc, SnapshotManager manager,
+      HashMap<String, Sample> patientNumberSampleHashMap, String patientNumber,
+      Sample s, String laterality)
+  {
+    // Get item subtype constants
+    ItemSubtype subtypeSpecimen = Subtype.SPECIMEN.load(dc);
+    ItemSubtype subtypeNoSpecimen = Subtype.NO_SPECIMEN.load(dc);
+    ItemSubtype subtypeBlood = Subtype.BLOOD.load(dc);
+    // Sample data retrieval
+    Sample storedSample = null;
+    ItemSubtype storedSampleSubtype = null;
+    String storedSampleLaterality = null;
+    if (patientNumberSampleHashMap.containsKey(patientNumber))
+    {
+      storedSample = (Sample) patientNumberSampleHashMap.get(patientNumber);
+      storedSampleSubtype = storedSample.getItemSubtype();
+      if (storedSampleSubtype.equals(subtypeSpecimen) || storedSampleSubtype.equals(subtypeNoSpecimen))
+      {
+        // The parent is the 'Case' for specimens and no specimens
+        BioMaterial curCase = (MeasuredBioMaterial) storedSample.getParent();
+        if (curCase != null && curCase instanceof Sample)
+        {
+          storedSampleLaterality = (String)Annotationtype.LATERALITY.getAnnotationValue(dc, manager, curCase);
+        }
+      }
+    }
+    // Update section
+    if (storedSampleSubtype == null)
+    {
+      // Patient number not in hash map, store sample
+      patientNumberSampleHashMap.put(patientNumber, s);
+    }
+    else if (storedSampleSubtype.equals(subtypeSpecimen))
+    {
+      if (s.getItemSubtype().equals(subtypeSpecimen))
+      {
+        // Replace stored entry if sample has laterality and stored sample does not
+        // If laterality equal, store sample if specimen with earlier date
+        if ((storedSampleLaterality == null || storedSampleLaterality.equals(""))
+            && (laterality != null && !laterality.equals("")))
+        {
+          patientNumberSampleHashMap.put(patientNumber, s);
+        }
+        else if (s.getCreationEvent().getEventDate().before(storedSample.getCreationEvent().getEventDate()))
+        {
+          patientNumberSampleHashMap.put(patientNumber, s);
+        }
+      }
+    }
+    else if (storedSampleSubtype.equals(subtypeNoSpecimen))
+    {
+      // Replace stored entry if sample equals specimen
+      if (s.getItemSubtype().equals(subtypeSpecimen))
+      {
+        patientNumberSampleHashMap.put(patientNumber, s);
+      }
+      else if (s.getItemSubtype().equals(subtypeNoSpecimen))
+      {
+        // Replace stored entry if sample has laterality and stored sample does not
+        // If laterality equal, store sample if specimen with earlier date
+        if ((storedSampleLaterality == null || storedSampleLaterality.equals(""))
+            && (laterality != null && !laterality.equals("")))
+        {
+          patientNumberSampleHashMap.put(patientNumber, s);
+        }
+        else if (s.getCreationEvent().getEventDate().before(storedSample.getCreationEvent().getEventDate()))
+        {
+          patientNumberSampleHashMap.put(patientNumber, s);
+        }
+      }
+    }
+    else if (storedSampleSubtype.equals(subtypeBlood))
+    {
+      // Replace stored entry if sample equals specimen or no specimen
+      if (s.getItemSubtype().equals(subtypeSpecimen)
+          || s.getItemSubtype().equals(subtypeNoSpecimen))
+      {
+        patientNumberSampleHashMap.put(patientNumber, s);
+      }
+      else if (s.getItemSubtype().equals(subtypeBlood))
+      {
+        // Store sample if blood sample with earlier date
+        if (s.getCreationEvent().getEventDate().before(storedSample.getCreationEvent().getEventDate()))
+        {
+          patientNumberSampleHashMap.put(patientNumber, s);
+        }
+      }
+    }
+    return patientNumberSampleHashMap;
+  }
+
 
   class PersonalOpDate