Merge pull request #454 from WildMeOrg/convert-kinalyzer

Convert Individual Search Kinalyzer export to more functional genetics export
WildMeOrg · Apr 10, 2024 · 0cc0faa · 0cc0faa
2 parents cf877f3 + d8afa1f
commit 0cc0faa
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Showing 2 changed files with 44 additions and 19 deletions.
diff --git a/src/main/java/org/ecocean/servlet/export/KinalyzerExport.java b/src/main/java/org/ecocean/servlet/export/KinalyzerExport.java
@@ -21,7 +21,12 @@
 
 
 
-//adds spots to a new encounter
+/*
+ * Originally created to support allele export for kinship analysis with the University of Chicago's
+ * Kinalyzer tool (now gone), this export format has been modified to be a generic inividual genetics tool,
+ * allowing for export of individual ID, haplotype, genetic sex, and named allele pairs for any species.
+ * 
+ */
 public class KinalyzerExport extends HttpServlet{
 
 
@@ -48,7 +53,7 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) thr
     String context="context0";
     context=ServletUtilities.getContext(request);
     Shepherd myShepherd = new Shepherd(context);
-    myShepherd.setAction("KinalyzerExport");
+    myShepherd.setAction("IndividualSearchGeneticsExport");
 
     //setup data dir
     String rootWebappPath = getServletContext().getRealPath("/");
@@ -58,7 +63,7 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) thr
     File encountersDir=new File(shepherdDataDir.getAbsolutePath()+"/encounters");
     if(!encountersDir.exists()){encountersDir.mkdirs();}
 
-    String kinFilename = "kinalyzer_export_" + request.getRemoteUser() + ".csv";
+    String kinFilename = "individualSearch_genetics_export_" + request.getRemoteUser() + ".csv";
     File kinFile = new File(encountersDir.getAbsolutePath()+"/" + kinFilename);
 
 
@@ -84,29 +89,47 @@ public void doPost(HttpServletRequest request, HttpServletResponse response) thr
         query2Individuals = queryResult2.getResult();
         int numSearch2Individuals = query2Individuals.size();
 
-        //now let's start writing output
-
+        //now let's start writing header row
+        String headerRow = "Individual ID, Individual Default Name, Haplotype, Genetic Sex";
 
         //Lines 2+: write the loci
         //let's calculate Fst for each of the loci
         //iterate through the loci
         List<String> loci=myShepherd.getAllLoci();
         int numLoci=loci.size();
-
-        //List<String> haplos=myShepherd.getAllHaplotypes();
-        //int numHaplos=haplos.size();
 
+        //let's add loci to the header row
+        for(int r=0;r<numLoci;r++){
+            String locus=loci.get(r);
+            headerRow+=", "+locus+" Allele1";
+            headerRow+=", "+locus+" Allele2";
+        }
+
+        //write out header row
+        outp.write(headerRow+"\r\n");
 
         //now write out POP2 for search2
         for(int i=0;i<numSearch2Individuals;i++){
           MarkedIndividual indie=(MarkedIndividual)query2Individuals.get(i);
           boolean hasValues=false;
-          //outp.write("Sample_ID,Individual_ID,Latitude,Longitude,Date_Time,Region,Sex,Haplotype"+locusString.toString()+",Occurrence_ID\n");
-
 
+          //add individual UUID
           String lociString=indie.getIndividualID()+",";
-          //NumberFormat myFormat = NumberFormat.getInstance();
-          //myFormat.setMinimumIntegerDigits(3);
+
+          //add individual default name
+          lociString+=indie.getDefaultName()+",";
+
+          //add individual haplotype
+          String haploString="";
+          if(indie.getHaplotype()!=null)haploString=indie.getHaplotype();
+          lociString+=haploString+",";
+
+          //add individualgenetic sex
+          String sexString="";
+          if(indie.getGeneticSex()!=null)sexString=indie.getGeneticSex();
+          lociString+=sexString+",";
+
+
           for(int r=0;r<numLoci;r++){
             String locus=loci.get(r);
             ArrayList<Integer> values=indie.getAlleleValuesForLocus(locus);
@@ -119,15 +142,16 @@ else if(indie.getAlleleValuesForLocus(locus).size()==1){
               lociString+=(values.get(0)+","+values.get(0)+",");
               hasValues=true;
             }
-            else{lociString+="-1,-1,";}
+            //else{lociString+="-1,-1,";}
+            else{lociString+=",,";}
 
           }
 
           int length=lociString.length();
 
           if(hasValues)outp.write(lociString.substring(0, (length-1))+"\r\n");
 
-          //test
+
 
         }
 
@@ -163,10 +187,12 @@ else if(indie.getAlleleValuesForLocus(locus).size()==1){
       //out.println("<p><strong>Error encountered</strong></p>");
       //out.println("<p>Please let the webmaster know you encountered an error at: KinalyzerExport servlet.</p>");
       e.printStackTrace();
-      myShepherd.rollbackDBTransaction();
-      myShepherd.closeDBTransaction();
+
+    }
+    finally{
+        myShepherd.rollbackDBTransaction();
+        myShepherd.closeDBTransaction();
     }
-    myShepherd=null;
     //out.close();
     //out=null;
   }

diff --git a/src/main/webapp/individualSearchResultsExport.jsp b/src/main/webapp/individualSearchResultsExport.jsp
@@ -178,8 +178,7 @@ Click here</a>
 </p>
 
 	<p>	<table border="1" bordercolor="black" cellspacing="0">
-			<tr><td bgcolor="#CCCCCC"><strong>Kinalyzer CSV File</strong></td></tr>
-			<tr><td bgcolor="#FFFFFF">Link: <a href="http://kinalyzer.cs.uic.edu">http://kinalyzer.cs.uic.edu</a></td></tr>
+			<tr><td bgcolor="#CCCCCC"><strong>Genetics Export CSV File</strong></td></tr>
 			<tr><td bgcolor="#FFFFFF">
 		<a href="//<%=CommonConfiguration.getURLLocation(request)%>/KinalyzerExport?<%=queryString%>">
 Click here</a>