Merge pull request #592 from iVis-at-Bilkent/unstable

Merge unstable to master
iVis-at-Bilkent · May 20, 2020 · 2ae5159 · 2ae5159
2 parents ebb8d84 + 376e370
commit 2ae5159
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Showing 6 changed files with 123 additions and 69 deletions.
diff --git a/app/js/app-cy.js b/app/js/app-cy.js
@@ -585,7 +585,7 @@ module.exports = function (chiseInstance) {
             result = true;
         });
 
-        return !node.data()["expanding"] && result && !chiseInstance.elementUtilities.isResizedToContent(node) && (cy.zoom() > 0.5);
+        return !node.data("onLayout") && result && !chiseInstance.elementUtilities.isResizedToContent(node) && (cy.zoom() > 0.5);
       },
       resizeToContentFunction: appUtilities.resizeNodesToContent,
       resizeToContentCuePosition: 'bottom-right',
@@ -751,18 +751,28 @@ module.exports = function (chiseInstance) {
     });
 
     cy.on("expandcollapse.beforeexpand",function(event){
-     var node = event.target;
-      node.data("expanding", true);
-
+      var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties');
+      if(currentGeneralProperties.recalculateLayoutOnComplexityManagement){
+        var node = cy.nodes(":selected");
+        if(node.length == 1 && event.target.selected())
+         node[0].data("onLayout", true);
+      }
+    });
+
+    // To redraw expand/collapse cue after resize
+    cy.on("noderesize.resizeend", function (e, type, node) {
+      if(node.isParent() && node.selected())
+        node.trigger("select");
     });
+
    /*  cy.on("expandcollapse.afterexpand",function(event){
       var node = event.target;
      node.data("expanding", false);      
     }); */
     //Updates arrow-scale of edges after expand
     cy.on("expandcollapse.afterexpand", function(event) {
-        var currentArrowScale = Number($('#arrow-scale').val());
-        cy.edges().style('arrow-scale', currentArrowScale);
+      var currentArrowScale = Number($('#arrow-scale').val());
+      cy.edges().style('arrow-scale', currentArrowScale);
     });
 
     //Changes arrow-scale of pasted edges
@@ -1271,6 +1281,12 @@ module.exports = function (chiseInstance) {
         updateInfoBox(node);
       }
     }); */
+
+    cy.on("layoutstart",function(event){   
+     var node = cy.nodes(":selected").nodes(":parent");
+     if(node.length == 1)
+      node[0].data("onLayout", true);
+    });    
 
     cy.on('layoutstop', function (event) {
   		/*
@@ -1298,7 +1314,7 @@ module.exports = function (chiseInstance) {
         chiseInstance.elementUtilities.fitUnits(ele, locations); //Force fit
       }); */
 
-      cy.nodes().forEach(function(node){node.data("expanding", false); });
+      cy.nodes("[?onLayout]").forEach(function(node){node.removeData("onLayout"); });
     });
 
     // if the position of compound changes by repositioning its children

diff --git a/app/js/app-menu.js b/app/js/app-menu.js
@@ -97,7 +97,7 @@ module.exports = function() {
     topologyGrouping.clearAppliedFlag();
 
     // unlock graph topology in case it is locked
-    chiseInstance.elementUtilities.unlockGraphTopology();
+    chiseInstance.elementUtilities.unlockGraphTopology();    
 
     // if the event is triggered for the active instance do the followings
     if ( isActiveInstance ) {
@@ -109,13 +109,47 @@ module.exports = function() {
         $('#inspector-map-tab a').tab('show');
       }
 
-       if ( $('#inspector-console-tab')[0].style.display == "block") {
-            $('#inspector-console-tab')[0].style.display = "none";
-
+      if ($('#inspector-console-tab')[0].style.display == "block") {
+        $('#inspector-console-tab')[0].style.display = "none";
       }
+    }
+  });
+
+  // Event triggered before file loaded by URL/URI
+  $(document).on('sbgnvizLoadFromURL sbgnvizLoadFromURI', function(event, filename, cy) {
 
+    var chiseInstance = appUtilities.getChiseInstance(cy);    
+
+    var urlParams = appUtilities.getScratch(cy, 'urlParams');
+
+    // get current general properties for cy
+    var currentGeneralProperties = appUtilities.getScratch(cy, 'currentGeneralProperties');    
+
+    // inferNestingOnLoad and compoundPadding must be set before file loaded
+    if (urlParams) {
+      // filter map properties from the url parameters
+      var mapPropsFromUrl = appUtilities.filterMapProperties(urlParams);
+
+      if("inferNestingOnLoad" in mapPropsFromUrl) {
+        currentGeneralProperties.inferNestingOnLoad = (mapPropsFromUrl.inferNestingOnLoad == 'true');
+      }
+      else {
+        currentGeneralProperties.inferNestingOnLoad = false;
+      }     
+
+      if("compoundPadding" in mapPropsFromUrl){
+        currentGeneralProperties.compoundPadding = Number(mapPropsFromUrl.compoundPadding);
+        chiseInstance.setCompoundPadding(Number(mapPropsFromUrl.compoundPadding));
+      }
+      else {
+        currentGeneralProperties.compoundPadding = 0;
+        chiseInstance.setCompoundPadding(currentGeneralProperties.compoundPadding);
+      }
     }
 
+    // set 'currentGeneralProperties' on scratchpad of cy
+    appUtilities.setScratch(cy, 'currentGeneralProperties', currentGeneralProperties);    
+
   });
 
   $(document).on('updateGraphEnd', function(event, cy) {
@@ -565,6 +599,14 @@ module.exports = function() {
 
         // filter map properties from the url parameters
         var mapPropsFromUrl = appUtilities.filterMapProperties(urlParams);
+
+        if(!("inferNestingOnLoad" in mapPropsFromUrl)) {
+          mapPropsFromUrl.inferNestingOnLoad = false;
+        }   
+
+        if(!("compoundPadding" in mapPropsFromUrl)){
+          mapPropsFromUrl.compoundPadding = 0;
+        }              
 
         // merge the map properties coming from url into
         // the map properties read from file

diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js
@@ -751,11 +751,10 @@ appUtilities.defaultGeneralProperties = {
   allowCompoundNodeResize: true,
   mapColorScheme: 'black_white',
   mapColorSchemeStyle: 'solid',
-  mapType: function() {return appUtilities.getActiveChiseInstance().getMapType() || "Unknown"},
+  mapType: function() {return (appUtilities.getActiveChiseInstance().getMapType() || "Unknown");},
   mapName: "",
   mapDescription: "",
-  enableSIFTopologyGrouping: false,
-  experimentDescription: "",
+  experimentDescription: ""
 };
 
 appUtilities.setFileContent = function (fileName) {
@@ -839,11 +838,11 @@ appUtilities.getExpandCollapseOptions = function (_cy) {
       var cy = _cy || self.getActiveCy();
 
       if ( !self.getScratch(cy, 'currentGeneralProperties').recalculateLayoutOnComplexityManagement ) {
-        cy.trigger('fit-units-after-expandcollapse');
+//        cy.trigger('fit-units-after-expandcollapse');
         return;
       }
       self.triggerLayout(cy, false);
-      cy.trigger('fit-units-after-expandcollapse');
+//      cy.trigger('fit-units-after-expandcollapse');
     },
     expandCollapseCueSize: 12,
     expandCollapseCuePosition: function (node) {
@@ -2417,6 +2416,8 @@ appUtilities.setMapProperties = function(mapProperties, _chiseInstance) {
     chiseInstance.setShowComplexName(currentGeneralProperties.showComplexName);
     chiseInstance.refreshPaddings(); // Refresh/recalculate paddings
 
+    cy.edges().css('arrow-scale', currentGeneralProperties.arrowScale);
+
     if (currentGeneralProperties.enablePorts) {
       chiseInstance.enablePorts();
     }
@@ -2439,9 +2440,6 @@ appUtilities.setMapProperties = function(mapProperties, _chiseInstance) {
       chiseInstance.omitCompoundSizes();
     }
 
-    cy.edges().css('arrow-scale', currentGeneralProperties.arrowScale);
-    cy.style().update();
-
     // reset 'currentGeneralProperties' on scratchpad of cy
     appUtilities.setScratch(cy, 'currentGeneralProperties', currentGeneralProperties);
 
@@ -2476,7 +2474,12 @@ appUtilities.launchWithModelFile = function() {
 
   // attach url params to the object to be used on sbgnvizLoadFileEnd event
   // it will be cleared immediately after usage
-  appUtilities.setScratch(cyInstance, 'urlParams', paramObj);
+  if(url_path || uri_path) {
+    appUtilities.setScratch(cyInstance, 'urlParams', paramObj);
+  }
+  else {
+    appUtilities.setScratch(cyInstance, 'urlParams', undefined);
+  }
 
   var promptInvalidURIWarning = this.promptInvalidURIWarning;
   var promptInvalidURLWarning = this.promptInvalidURLWarning;
@@ -2489,9 +2492,6 @@ appUtilities.launchWithModelFile = function() {
     tutorial.introduction(true);
 
   function loadFromURL(filepath, chiseInstance, promptInvalidURLWarning){
-    // get current general properties
-    var currentGeneralProperties = appUtilities.getScratch(cyInstance, 'currentGeneralProperties');
-    var currentInferNestingOnLoad = currentGeneralProperties.inferNestingOnLoad;
 
     var loadCallbackSBGNMLValidity = function (text) {
       $.ajax({
@@ -2540,12 +2540,12 @@ appUtilities.launchWithModelFile = function() {
       success: function(data){
         // here we can get 404 as well, for example, so there are still error cases to handle
         if (!data.error && data.response.statusCode == 200 && data.response.body) {
+          $(document).trigger('sbgnvizLoadFromURL', [filename, cyInstance]);
           var fileToLoad = new File([data.response.body], filename, {
             type: 'text/' + fileExtension,
             lastModified: Date.now()
           });
 
-          currentGeneralProperties.inferNestingOnLoad = true;
           chiseInstance.loadNwtFile(fileToLoad, loadCallbackSBGNMLValidity, loadCallbackInvalidityWarning);
         }
         else {
@@ -2557,11 +2557,6 @@ appUtilities.launchWithModelFile = function() {
       }
     });
 
-    $(document).one("sbgnvizLoadFileEnd", function(){
-      currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad;
-      appUtilities.mapTabGeneralPanel.render();
-    });
-
   }
 
   function loadFromURI(uri, chiseInstance, promptInvalidURIWarning){
@@ -2574,8 +2569,6 @@ appUtilities.launchWithModelFile = function() {
 
     chiseInstance.startSpinner('paths-byURI-spinner');
 
-    var currentGeneralProperties = appUtilities.getScratch(cyInstance, 'currentGeneralProperties');
-    var currentInferNestingOnLoad = currentGeneralProperties.inferNestingOnLoad;
     var currentLayoutProperties = appUtilities.getScratch(cyInstance, 'currentLayoutProperties');
 
     $.ajax({
@@ -2587,9 +2580,8 @@ appUtilities.launchWithModelFile = function() {
         if (data.response.statusCode == 200 && data.response.body) {
           var xml = $.parseXML(data.response.body);
           $(document).trigger('sbgnvizLoadFile', [filename, cyInstance]);
-          currentGeneralProperties.inferNestingOnLoad = false;
+          $(document).trigger('sbgnvizLoadFromURI', [filename, cyInstance]);          
           chiseInstance.updateGraph(chiseInstance.convertSbgnmlToJson(xml), undefined, currentLayoutProperties);
-          currentGeneralProperties.inferNestingOnLoad = currentInferNestingOnLoad;
           chiseInstance.endSpinner('paths-byURI-spinner');
           $(document).trigger('sbgnvizLoadFileEnd', [filename,  cyInstance]);
         }
@@ -3010,19 +3002,23 @@ appUtilities.resizeNodesToContent = function(nodes){
   var chiseInstance = appUtilities.getActiveChiseInstance();
   var cy = appUtilities.getActiveCy();
   var collection;
-    if(nodes.length == 1){
-      collection = cy.collection();    
-      collection = collection.add(nodes[0]);   
-    }else{
-      collection = nodes;
-    }    
-
-    if(!chiseInstance.areCompoundSizesConsidered()){
-      collection = collection.difference(":parent,[class*='compartment'],[class*='submap']");
-    }
-    chiseInstance.resizeNodesToContent(collection, false);
-    cy.nodeResize('get').refreshGrapples();
-    cy.expandCollapse('get').clearVisualCue();
+  if(nodes.length == 1){
+    collection = cy.collection();    
+    collection = collection.add(nodes[0]);   
+  }else{
+    collection = nodes;
+  }    
+
+  if(!chiseInstance.areCompoundSizesConsidered()){
+    collection = collection.difference(":parent,[class*='compartment'],[class*='submap']");
+  }
+  chiseInstance.resizeNodesToContent(collection, false);
+  cy.nodeResize('get').refreshGrapples();
+  cy.expandCollapse('get').clearVisualCue();
+  // To redraw expand/collapse cue after resize to content
+  if(collection.length == 1 && (collection[0].isParent() || collection[0].data('collapsedChildren')) && collection[0].selected()) { 
+    cy.$(':selected').trigger('select'); 
+  };
 
 };
 

diff --git a/app/samples/drosophila_cell_cycle.nwt b/app/samples/drosophila_cell_cycle.nwt
@@ -562,7 +562,7 @@
       <start x="763.375" y="177.75"/>
       <end x="745.2678571428571" y="177.75"/>
     </arc>
-    <arc id="nwtE_1fcb9fb6-ba5a-4ccf-bd50-155ce657fedb" class="stimulation" source="89360553-bab4-532a-c6c7-624272c4e43b" target="nwtN_78d6cd14-2e5f-463f-9a30-27ce3baea7d9.2">
+    <arc id="nwtE_1fcb9fb6-ba5a-4ccf-bd50-155ce657fedb" class="stimulation" source="89360553-bab4-532a-c6c7-624272c4e43b" target="nwtN_78d6cd14-2e5f-463f-9a30-27ce3baea7d9">
       <start x="875.5645730534169" y="135.5"/>
       <next x="847.542424765152" y="213.7471460409822"/>
       <next x="738.497886764629" y="214.7270119241452"/>
@@ -617,13 +617,13 @@
       <start x="799" y="240.43456223215844"/>
       <end x="799" y="260.00000000000006"/>
     </arc>
-    <arc id="nwtE_b9e23793-a56e-4277-b278-6724f6a4d68a" class="stimulation" source="c3a94e68-cca7-3c6a-f546-33c23dc59923" target="9615ba87-e042-ef50-d78e-1ef00df34a6e.2">
+    <arc id="nwtE_b9e23793-a56e-4277-b278-6724f6a4d68a" class="stimulation" source="c3a94e68-cca7-3c6a-f546-33c23dc59923" target="9615ba87-e042-ef50-d78e-1ef00df34a6e">
       <start x="875.7289709255696" y="326.21254896064926"/>
       <next x="847.8464449746845" y="246.47997705747048"/>
       <next x="737.9834983175773" y="247.1334840883929"/>
       <end x="737.9947312772593" y="270.3571432226932"/>
     </arc>
-    <arc id="nwtE_a567dc9c-c17b-4e41-89ad-947bed2f4fd3" class="catalysis" source="7626c6b6-b0e0-b4b7-e5f3-f803fe319ef8" target="93e171d7-e846-2f4e-b4af-cafdabb596dd.1">
+    <arc id="nwtE_a567dc9c-c17b-4e41-89ad-947bed2f4fd3" class="catalysis" source="7626c6b6-b0e0-b4b7-e5f3-f803fe319ef8" target="93e171d7-e846-2f4e-b4af-cafdabb596dd">
       <start x="767.8264939279273" y="298.2980111331645"/>
       <next x="702.9999999999995" y="333.74999999999943"/>
       <next x="702.5266691532668" y="347.96471699095457"/>
@@ -653,12 +653,12 @@
       <start x="804.7678571428571" y="538.75"/>
       <end x="826.75" y="538.75"/>
     </arc>
-    <arc id="nwtE_bd3e280f-efff-4d5b-868c-d834b3d6cad4" class="catalysis" source="a2ee1683-eb5f-030d-3bbe-46c0a02cb659" target="nwtN_e742f544-55df-4fda-a7ee-65473425b2b5.2">
+    <arc id="nwtE_bd3e280f-efff-4d5b-868c-d834b3d6cad4" class="catalysis" source="a2ee1683-eb5f-030d-3bbe-46c0a02cb659" target="nwtN_e742f544-55df-4fda-a7ee-65473425b2b5">
       <start x="763.9884892268863" y="165.05526681360047"/>
       <next x="702.4738258670972" y="142.75082404149953"/>
       <end x="701.2673108079107" y="125.63512177066829"/>
     </arc>
-    <arc id="nwtE_a8832f81-1169-4768-87f4-390a771f7fff" class="catalysis" source="35a3e0be-6e00-7a99-fca5-18ed65c2fac1" target="f82eccc1-2bc9-bf87-08ab-1f26c4ad1e5d.2">
+    <arc id="nwtE_a8832f81-1169-4768-87f4-390a771f7fff" class="catalysis" source="35a3e0be-6e00-7a99-fca5-18ed65c2fac1" target="f82eccc1-2bc9-bf87-08ab-1f26c4ad1e5d">
       <start x="631.5622781050293" y="520.625"/>
       <next x="701.7355091200076" y="464.8703837231595"/>
       <end x="701.9129310851106" y="442.6740073154425"/>
@@ -679,7 +679,7 @@
       <start x="1045.767857142857" y="481.75000000000006"/>
       <end x="1070.75" y="481.75000000000006"/>
     </arc>
-    <arc id="nwtE_68ee44c6-86ba-499b-a798-db1c00254138" class="stimulation" source="c3a94e68-cca7-3c6a-f546-33c23dc59923" target="nwtN_7ffe3be6-9a33-4696-a593-d5c0a8a45a4c.1">
+    <arc id="nwtE_68ee44c6-86ba-499b-a798-db1c00254138" class="stimulation" source="c3a94e68-cca7-3c6a-f546-33c23dc59923" target="nwtN_7ffe3be6-9a33-4696-a593-d5c0a8a45a4c">
       <start x="898.4175879396985" y="445.53125000000006"/>
       <end x="898.8248449738131" y="470.8575468090057"/>
     </arc>
@@ -699,7 +699,7 @@
       <start x="1114.267857142857" y="547.75"/>
       <end x="1139.25" y="547.75"/>
     </arc>
-    <arc id="nwtE_80c9d1c6-bab7-478d-b509-e6fe7b24b152" class="stimulation" source="nwtN_5a3ef454-8d2b-46de-b3a1-f9a0c2409ee4" target="46137b33-99be-2b1f-5a29-f38f55849a0b.1">
+    <arc id="nwtE_80c9d1c6-bab7-478d-b509-e6fe7b24b152" class="stimulation" source="nwtN_5a3ef454-8d2b-46de-b3a1-f9a0c2409ee4" target="46137b33-99be-2b1f-5a29-f38f55849a0b">
       <start x="968" y="499.87500000000006"/>
       <end x="968" y="536.8571428571429"/>
     </arc>
@@ -743,15 +743,15 @@
       <start x="733.25" y="596.5178571428571"/>
       <end x="733.25" y="617.5"/>
     </arc>
-    <arc id="nwtE_9f593961-7d71-49ac-8c9b-eb8e899665e4" class="stimulation" source="89360553-bab4-532a-c6c7-624272c4e43b" target="a8404458-8ee5-6465-5d2e-4be53abad9f9.2">
+    <arc id="nwtE_9f593961-7d71-49ac-8c9b-eb8e899665e4" class="stimulation" source="89360553-bab4-532a-c6c7-624272c4e43b" target="a8404458-8ee5-6465-5d2e-4be53abad9f9">
       <start x="895.8985379750443" y="21.375"/>
       <next x="895.8646325311395" y="2.306492411467092"/>
       <next x="334.62761909656433" y="3.77560221892449"/>
       <next x="332.9955347233823" y="668.6351180438446"/>
       <next x="676.6188645851402" y="671.4050967869174"/>
       <end x="676.4563459796519" y="649.642770006905"/>
     </arc>
-    <arc id="nwtE_6ae825c1-a694-4326-9f5e-36e516db36f0" class="catalysis" source="2f567801-fc2c-e128-f352-1dfab2f0dbce" target="nwtN_713def92-298d-4eb9-bf64-35bfc38a4646.1">
+    <arc id="nwtE_6ae825c1-a694-4326-9f5e-36e516db36f0" class="catalysis" source="2f567801-fc2c-e128-f352-1dfab2f0dbce" target="nwtN_713def92-298d-4eb9-bf64-35bfc38a4646">
       <start x="609.0574244085002" y="656.875"/>
       <next x="609.1897360308067" y="664.67577341941"/>
       <next x="344.83677141584394" y="660.6017836771279"/>
@@ -767,7 +767,7 @@
       <start x="425.2791845941241" y="387.46875000000006"/>
       <end x="401.2204117739146" y="387.46875000000006"/>
     </arc>
-    <arc id="nwtE_85d06a5e-fd70-4ff6-99d8-ae053b4d75ea" class="catalysis" source="191857cc-7088-9f59-19c8-ad00bcf44b5e" target="nwtN_f14bd3e1-7c6d-49b6-ab82-2f69e2246853.1">
+    <arc id="nwtE_85d06a5e-fd70-4ff6-99d8-ae053b4d75ea" class="catalysis" source="191857cc-7088-9f59-19c8-ad00bcf44b5e" target="nwtN_f14bd3e1-7c6d-49b6-ab82-2f69e2246853">
       <start x="433.04704173698127" y="334.58583432907056"/>
       <end x="433.04704173698127" y="376.5758928571429"/>
     </arc>
@@ -788,7 +788,7 @@
       <start x="985.9921112946669" y="352.6317742742051"/>
       <end x="948.25" y="367.9163358754463"/>
     </arc>
-    <arc id="nwtE_a4ec4de6-fc5e-40a6-ba15-4a0a7de659ed" class="catalysis" source="f0a6c8f2-8384-fb32-c934-e51c7aa67e25" target="nwtN_11b88917-a429-4c8c-9ada-61c11265afb5.1">
+    <arc id="nwtE_a4ec4de6-fc5e-40a6-ba15-4a0a7de659ed" class="catalysis" source="f0a6c8f2-8384-fb32-c934-e51c7aa67e25" target="nwtN_11b88917-a429-4c8c-9ada-61c11265afb5">
       <start x="993.759968437524" y="315.7909429932749"/>
       <end x="993.759968437524" y="338.5931394592224"/>
     </arc>

diff --git a/index.html b/index.html
@@ -914,7 +914,7 @@ <h2 class="sbgn-text">About</h2>
                             <table width="100%" height="100%" align="center" valign="center">
                             <tbody>
                                 <tr><td>
-                                        <p id="about-newt-version" class="sbgn-text">Newt Editor version 3.0</p>
+                                        <p id="about-newt-version" class="sbgn-text">Newt Editor version 3.0.1</p>
                                     </td></tr>
 
                                 <tr><td>