Merge pull request #3741 from solgenomics/topic/migrate_tools_brapiv2

Topic/migrate tools brapiv2 - pedigree tool
solgenomics · Sep 27, 2021 · fcd4678 · fcd4678
2 parents 7c55439 + acafcdb
commit fcd4678
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Showing 4 changed files with 57 additions and 34 deletions.
diff --git a/js/source/legacy/brapi/PedigreeViewer.js b/js/source/legacy/brapi/PedigreeViewer.js
@@ -84,27 +84,46 @@ function PedigreeViewer(server,auth,version,urlFunc){
             }).map(function(ped_pro_germId){
                 var mother = null, 
                     father = null;
-                if(ped_pro_germId[0].parent1Type=="FEMALE"){
-                    mother = ped_pro_germId[0].parent1DbId;
-                }
-                if(ped_pro_germId[0].parent1Type=="MALE"){
-                    father = ped_pro_germId[0].parent1DbId;
-                }
-                if(ped_pro_germId[0].parent2Type=="FEMALE"){
-                    mother = ped_pro_germId[0].parent2DbId;
-                }
-                if(ped_pro_germId[0].parent2Type=="MALE"){
-                    father = ped_pro_germId[0].parent2DbId;
+
+                if(version=='v1.3'){
+                    if(ped_pro_germId[0].parent1Type=="FEMALE"){
+                        mother = ped_pro_germId[0].parent1DbId;
+                    }
+                    if(ped_pro_germId[0].parent1Type=="MALE"){
+                        father = ped_pro_germId[0].parent1DbId;
+                    }
+                    if(ped_pro_germId[0].parent2Type=="FEMALE"){
+                        mother = ped_pro_germId[0].parent2DbId;
+                    }
+                    if(ped_pro_germId[0].parent2Type=="MALE"){
+                        father = ped_pro_germId[0].parent2DbId;
+                    }
+                    return {
+                        'id':ped_pro_germId[2],
+                        'mother_id':mother,
+                        'father_id':father,
+                        'name':ped_pro_germId[1].defaultDisplayName,
+                        'children':ped_pro_germId[1].progeny.filter(Boolean).map(function(d){
+                            return d.germplasmDbId;
+                        })
+                    };
+                } else {
+                    var i = ped_pro_germId[0].parents.map(function(e) { return e.parentType; }).indexOf('FEMALE');
+                    var j = ped_pro_germId[0].parents.map(function(e) { return e.parentType; }).indexOf('MALE');
+
+                    if(i>=0) mother = ped_pro_germId[0].parents[i].germplasmDbId;
+                    if(j>=0) father = ped_pro_germId[0].parents[j].germplasmDbId;
+
+                    return {
+                        'id':ped_pro_germId[2],
+                        'mother_id':mother,
+                        'father_id':father,
+                        'name':ped_pro_germId[1].germplasmName,
+                        'children':ped_pro_germId[1].progeny.filter(Boolean).map(function(d){
+                            return d.germplasmDbId;
+                        })
+                    };
                 }
-                return {
-                    'id':ped_pro_germId[2],
-                    'mother_id':mother,
-                    'father_id':father,
-                    'name':ped_pro_germId[1].defaultDisplayName,
-                    'children':ped_pro_germId[1].progeny.filter(Boolean).map(function(d){
-                        return d.germplasmDbId;
-                    })
-                };
             }).each(function(node){
                 loaded_nodes[node.id] = node;
             }).all(callback);

diff --git a/js/source/legacy/d3/d3-pedigree-tree.js b/js/source/legacy/d3/d3-pedigree-tree.js
@@ -30,11 +30,11 @@
 
     function pdgtree(){
       //create working nodes from input data (we dont want to modify the input) 
-      
+
       var node_list = _wrap_nodes(data);
       node_list.forEach(function(d){_setNodeLevels(d);});
       _setBestRootNodeLevels(node_list);
-      
+
       //create intermediate nodes for intergenerational links
       var intermediates = {};
       for (var n = node_list.length-1; n > -1; n--) {

diff --git a/lib/CXGN/BrAPI/v2/Germplasm.pm b/lib/CXGN/BrAPI/v2/Germplasm.pm
@@ -334,8 +334,6 @@ sub germplasm_pedigree {
                 };
             }
             $cross_plan = $cross_type;
-            $mother = $female_parent_name ? $female_parent_name : "NA";
-            $father = $male_parent_name ? $male_parent_name : "NA";
         }
 
         #Cross information
@@ -368,18 +366,24 @@ sub germplasm_pedigree {
             }
         }
 
-        my $parent = [
-            {
-                germplasmDbId=>qq|$female_parent_stock_id|,
+        #Add parents:
+        my $parent = [];
+        if ($female_parent_stock_id){
+            push @$parent, {
+                germplasmDbId=>$female_parent_stock_id ? qq|$female_parent_stock_id| : $female_parent_stock_id ,
                 germplasmName=>$mother,
                 parentType=>'FEMALE',
-            },
-            {
-                germplasmDbId=>qq|$male_parent_stock_id|,
+            };
+        }
+        if ($male_parent_stock_id){
+            push @$parent, {
+                germplasmDbId=>$male_parent_stock_id ? qq|$male_parent_stock_id| : $male_parent_stock_id,
                 germplasmName=>$father,
                 parentType=>'MALE',
-            },
-            ];
+            }
+
+        }
+
         %result = (
             crossingProjectDbId=>$membership_info[0][0],
             crossingYear=>$membership_info[0][5],

diff --git a/mason/pedigree/stock_pedigree.mas b/mason/pedigree/stock_pedigree.mas
@@ -215,7 +215,7 @@ $stock_id
 (function() {
     'use strict';
     var STOCK_ID = "<% $stock_id %>";
-    var base_url="/brapi/v1";
+    var base_url="/brapi/v2";
     var auth_token;
     var require_login = "<%  $c->get_conf('brapi_require_login') %>";
     if (require_login === '1'){
@@ -225,7 +225,7 @@ $stock_id
         }
     }
 
-    var pdg = PedigreeViewer(base_url,auth_token,'v1.3',function(dbId){
+    var pdg = PedigreeViewer(base_url,auth_token,'v2.0',function(dbId){
         return "/stock/"+dbId+"/view";
     });
     pdg.newTree(STOCK_ID,function(){