Merge unstable into master

PathwayCommons · Sep 11, 2017 · 6cf86f0 · 6cf86f0
2 parents a760377 + 4841471
commit 6cf86f0
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Showing 4 changed files with 56 additions and 11 deletions.
diff --git a/package.json b/package.json
@@ -20,7 +20,7 @@
     "body-parser": "^1.15.1",
     "clipboard": "^1.7.1",
     "cookie-parser": "^1.4.3",
-    "cytoscape": "^3.2.1",
+    "cytoscape": "^3.2.3",
     "cytoscape-automove": "^1.3.1",
     "cytoscape-cose-bilkent": "^1.6.10",
     "cytoscape-cxtmenu": "^2.10.3",

diff --git a/src/client/components/document-filler.js b/src/client/components/document-filler.js
@@ -36,9 +36,11 @@ class DocumentFiller extends React.Component {
 
     let toJson = res => res.json();
 
-    let animateResult = () => { return;
+    let animateResult = () => {
       let linkout = ReactDom.findDOMNode(this).querySelector('.document-filler-linkout');
 
+      linkout.style.opacity = 0;
+
       if( linkout ){
         anime({ targets: linkout, opacity: [0, 1], duration: 2000, easing: 'linear' });
       }

diff --git a/src/server/routes/api/document/index.js b/src/server/routes/api/document/index.js
@@ -48,7 +48,7 @@ let runLayout = doc => {
   let cy = new Cytoscape({
     elements: makeCyEles( doc.elements() ),
     layout: { name: 'grid' },
-    // styleEnabled: true // TODO cy 3.2 bug if style enabled
+    styleEnabled: true
   });
 
   let runLayout = () => {

diff --git a/src/server/routes/api/document/reach.js b/src/server/routes/api/document/reach.js
@@ -7,6 +7,9 @@ const FormData = require('form-data');
 const Organism = require('../../../../model/organism');
 
 const REACH_URL = 'http://agathon.sista.arizona.edu:8080/odinweb/api/text';
+const MERGE_ENTS_WITH_SAME_GROUND = true;
+const ALLOW_IMPLICIT_ORG_SPEC = false;
+const REMOVE_DISCONNECTED_ENTS = true;
 
 module.exports = {
   get: function( text ){
@@ -25,6 +28,7 @@ module.exports = {
       let elements = [];
       let elementsMap = new Map();
       let elementsReachMap = new Map();
+      let groundReachMap = new Map();
       let organisms = [];
 
       let enableOrg = org => {
@@ -35,8 +39,6 @@ module.exports = {
         }
       };
 
-      let allowImplicitOrgSpec = false;
-
       let entFrames = _.get( res, ['entities', 'frames'] ) || [];
       let evtFrames = _.get( res, ['events', 'frames'] ) || [];
       let senFrames = _.get( res, ['sentences', 'frames'] ) || [];
@@ -49,6 +51,8 @@ module.exports = {
       let frameIsEntity = frame => frame['frame-type'] === 'entity-mention';
       let frameIsEvent = frame => frame['frame-type'] === 'event-mention';
       let getArgId = arg => arg.arg;
+      let groundIsSame = (g1, g2) => g1.namespace === g2.namespace && g1.id === g2.id;
+      let elIsIntn = el => el.entries != null;
 
       let getSentenceText = id => {
         let f = getFrame(id);
@@ -60,10 +64,35 @@ module.exports = {
         }
       };
 
-      let addElement = (el, frame) => {
-        elements.push( el );
-        elementsMap.set( el.id, el );
-        elementsReachMap.set( getReachId( frame ), el );
+      let addElement = (el, frame, ground) => {
+        let foundMerge = false;
+
+        if( MERGE_ENTS_WITH_SAME_GROUND && ground != null ){
+          let prevGround, prevReachId;
+
+          groundReachMap.forEach( ( gnd, rid ) => {
+            if( groundIsSame( gnd, ground ) ){
+              foundMerge = true;
+              prevGround = gnd;
+              prevReachId = rid;
+            }
+          } );
+
+          if( foundMerge ){
+            el = elementsReachMap.get( prevReachId );
+            ground = prevGround;
+          }
+        }
+
+        let reachId = getReachId( frame );
+
+        if( !foundMerge ){
+          elements.push( el );
+          elementsMap.set( el.id, el );
+        }
+
+        elementsReachMap.set( reachId, el );
+        groundReachMap.set( reachId, ground );
       };
 
       entFrames.forEach( addFrame );
@@ -88,13 +117,13 @@ module.exports = {
         let orgIsSupported = org != null && org !== Organism.OTHER;
 
         // implicit mention of org
-        if( orgIsSupported && allowImplicitOrgSpec ){
+        if( orgIsSupported && ALLOW_IMPLICIT_ORG_SPEC ){
           enableOrg( org );
         }
 
         ent.name = frame.text;
 
-        addElement( ent, frame );
+        addElement( ent, frame, ground );
       } );
 
       // add explicit organisms
@@ -154,6 +183,20 @@ module.exports = {
         }
       } );
 
+      if( REMOVE_DISCONNECTED_ENTS ){
+        let interactions = elements.filter( elIsIntn );
+        let pptIds = ( () => {
+          let set = new Set();
+
+          interactions.forEach( intn => intn.entries.forEach( en => set.add( en.id ) ) );
+
+          return set;
+        } )();
+        let elIsInSomeIntn = el => pptIds.has( el.id );
+
+        elements = elements.filter( el => elIsIntn(el) || elIsInSomeIntn(el) );
+      }
+
       return {
         elements,
         organisms