From bc3a9ebcd6599cca4d30ca5ee0c1876f3952fb5f Mon Sep 17 00:00:00 2001
From: tmushayahama <tmushayahama@gmail.com>
Date: Mon, 7 May 2018 12:54:59 -0700
Subject: [PATCH] bp only mapping correctly to the first 4 options
 https://github.com/geneontology/simple-annoton-editor/issues/61

---
 app/annoton/annoton-node.js | 23 +++++++++++++++++++++++
 app/annoton/sae-graph.js    |  7 +++++++
 app/graph.service.js        | 26 +++++++++++++++++---------
 3 files changed, 47 insertions(+), 9 deletions(-)

diff --git a/app/annoton/annoton-node.js b/app/annoton/annoton-node.js
index 001d2d7..897cf4e 100644
--- a/app/annoton/annoton-node.js
+++ b/app/annoton/annoton-node.js
@@ -147,11 +147,34 @@ export default class AnnotonNode {
     self.addEvidence();
   }
 
+  deepCopyValues(node) {
+    const self = this;
+
+    self.term.control.value = node.term.control.value;
+    self.evidence = node.evidence;
+
+    self.modelId = node.modelId;
+    self.annoton = node.annoton;
+    self.ontologyClass = node.ontologyClass;
+    self.assignedBy = node.assignedBy;
+    self.termRequiredList = node.termRequiredList;
+    self.evidenceRequiredLis = node.evidenceRequiredList
+    self.evidenceNotRequiredList = node.evidenceNotRequiredList;
+    self.errors = node.errors;
+    self.warnings = node.warnings;
+    self.status = node.status;
+
+    self.edgeOption = node.edgeOption;
+    self.isComplement = node.isComplement;
+  }
+
   copyValues(node) {
     const self = this;
 
     self.term.control.value = node.term.control.value;
     self.evidence = node.evidence;
+    self.assignedBy = node.assignedBy;
+    self.isComplement = node.isComplement;
   }
 
   addEvidences(evidences, except) {
diff --git a/app/annoton/sae-graph.js b/app/annoton/sae-graph.js
index 119043d..275da36 100644
--- a/app/annoton/sae-graph.js
+++ b/app/annoton/sae-graph.js
@@ -46,6 +46,13 @@ export default class SaeGraph {
     this.addEdge(source, object, edge)
   };
 
+  editEdge(subjectId, objectId, srcEdge) {
+    const self = this;
+    let destEdge = self.getEdge(subjectId, objectId);
+
+    destEdge.edge = srcEdge;
+  }
+
   getEdge(subjectId, objectId) {
     const self = this;
     let edge = self.edges[subjectId];
diff --git a/app/graph.service.js b/app/graph.service.js
index 9caa070..76f8a38 100644
--- a/app/graph.service.js
+++ b/app/graph.service.js
@@ -547,7 +547,6 @@ export default class GraphService {
           }
         } else {
           annoton.parser.setCardinalityError(annotonNode, gpObjectNode.term, self.saeConstants.edge.enabledBy.id);
-          //  self.graphToAnnatonDFS(graph, annoton, mfEdgesIn, annotonNode, true);
         }
 
         if (isDoomed) {
@@ -638,9 +637,6 @@ export default class GraphService {
 
     if (annoton.parser.parseCardinality(graph, annotonNode, mfEdgesIn, edge.nodes)) {
       each(mfEdgesIn, function (toMFEdge) {
-        if (!toMFEdge) {
-          return;
-        }
         let predicateId = toMFEdge.predicate_id();
         let evidence = self.edgeToEvidence(graph, toMFEdge);
         let toMFObject = toMFEdge.object_id();
@@ -649,6 +645,16 @@ export default class GraphService {
           self.config.addGPAnnotonData(annoton, toMFObject);
         }
 
+        if (annoton.annotonModelType === self.saeConstants.annotonModelType.options.bpOnly.name) {
+          let causalEdge = _.find(self.saeConstants.causalEdges, {
+            id: predicateId
+          })
+
+          if (causalEdge) {
+            self.adjustBPOnly(annoton, causalEdge);
+          }
+        }
+
         each(edge.nodes, function (node) {
           if (predicateId === node.edge.id) {
             if (predicateId === self.saeConstants.edge.hasPart.id && toMFObject !== node.object.id) {
@@ -861,8 +867,6 @@ export default class GraphService {
 
     let gpNode = annoton.getGPNode();
 
-    self.adjustBPOnly(annoton);
-
     let row = {
       gp: gpNode.term.control.value.label,
       original: JSON.parse(JSON.stringify(annoton)),
@@ -1028,14 +1032,17 @@ export default class GraphService {
 
   }
 
-  adjustBPOnly(annoton) {
+  adjustBPOnly(annoton, srcEdge) {
     const self = this;
     let mfNode = annoton.getNode('mf');
     let bpNode = annoton.getNode('bp');
 
+
+
     if (mfNode && bpNode && annoton.annotonModelType === self.saeConstants.annotonModelType.options.bpOnly.name) {
       mfNode.displaySection = self.saeConstants.displaySection.fd;
       mfNode.displayGroup = self.saeConstants.displayGroup.mf;
+      annoton.editEdge('mf', 'bp', srcEdge);
       bpNode.relationship = annoton.getEdge('mf', 'bp').edge;
     }
   }
@@ -1169,9 +1176,10 @@ export default class GraphService {
 
     each(srcAnnoton.nodes, function (srcNode) {
       if (srcNode.hasValue()) {
-        let destNode = self.config.generateNode(srcNode.id);
+        // let destNode = self.config.generateNode(srcNode.id);
 
-        destNode.copyValues(srcNode);
+        // destNode.copyValues(srcNode);
+        let destNode = srcNode;
         destAnnoton.addNode(destNode);
       }
     });