Rename source and sink to empty set #658

iVis-at-Bilkent · Jun 1, 2021 · 290adf6 · 290adf6
1 parent 0fdf1fd
commit 290adf6
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Showing 14 changed files with 65 additions and 65 deletions.
diff --git a/app/img/nodes/source-and-sink.svg → app/img/nodes/empty-set.svg b/app/img/nodes/source-and-sink.svg → app/img/nodes/empty-set.svg
diff --git a/app/img/pd-legend.svg b/app/img/pd-legend.svg
diff --git a/app/js/app-menu.js b/app/js/app-menu.js
@@ -908,7 +908,7 @@ module.exports = function() {
         var cy = chiseInstance.getCy();
 
         //Remove processes and other nodes which cannot be resized according to content
-        var toBeResized = cy.nodes().difference('node[class*="process"],[class*="association"],[class*="dissociation"],[class="source and sink"],[class="and"],[class="or"],[class="not"],[class="delay"],:parent');
+        var toBeResized = cy.nodes().difference('node[class*="process"],[class*="association"],[class*="dissociation"],[class="empty set"],[class="and"],[class="or"],[class="not"],[class="delay"],:parent');
 
         appUtilities.resizeNodesToContent(toBeResized);
 

diff --git a/app/js/app-utilities.js b/app/js/app-utilities.js
@@ -1180,7 +1180,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#ffffff',
       'nucleic acid feature': '#ffffff',
       'perturbing agent': '#ffffff',
-      'source and sink': '#ffffff',
+      'empty set': '#ffffff',
       'complex': '#ffffff',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1227,7 +1227,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#bdbdbd',
       'nucleic acid feature': '#bdbdbd',
       'perturbing agent': '#bdbdbd',
-      'source and sink': '#ffffff',
+      'empty set': '#ffffff',
       'complex': '#d9d9d9',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1274,7 +1274,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#f0f0f0',
       'nucleic acid feature': '#f0f0f0',
       'perturbing agent': '#f0f0f0',
-      'source and sink': '#f0f0f0',
+      'empty set': '#f0f0f0',
       'complex': '#d9d9d9',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1321,7 +1321,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#9ecae1',
       'nucleic acid feature': '#9ecae1',
       'perturbing agent': '#9ecae1',
-      'source and sink': '#9ecae1',
+      'empty set': '#9ecae1',
       'complex': '#c6dbef',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1368,7 +1368,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#eff3ff',
       'nucleic acid feature': '#eff3ff',
       'perturbing agent': '#eff3ff',
-      'source and sink': '#eff3ff',
+      'empty set': '#eff3ff',
       'complex': '#c6dbef',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1415,7 +1415,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#92c5de',
       'nucleic acid feature': '#f4a582',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#d1e5f0',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1462,7 +1462,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#f4a582',
       'nucleic acid feature': '#92c5de',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#fddbc7',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1509,7 +1509,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#80cdc1',
       'nucleic acid feature': '#dfc27d',
       'perturbing agent': '#f5f5f5',
-      'source and sink': '#f5f5f5',
+      'empty set': '#f5f5f5',
       'complex': '#c7eae5',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1556,7 +1556,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#dfc27d',
       'nucleic acid feature': '#80cdc1',
       'perturbing agent': '#f5f5f5',
-      'source and sink': '#f5f5f5',
+      'empty set': '#f5f5f5',
       'complex': '#f6e8c3',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1603,7 +1603,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#b2abd2',
       'nucleic acid feature': '#fdb863',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#d8daeb',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1650,7 +1650,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#fdb863',
       'nucleic acid feature': '#b2abd2',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#fee0b6',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1697,7 +1697,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#c2a5cf',
       'nucleic acid feature': '#a6dba0',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#e7d4e8',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1744,7 +1744,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#a6dba0',
       'nucleic acid feature': '#c2a5cf',
       'perturbing agent': '#f7f7f7',
-      'source and sink': '#f7f7f7',
+      'empty set': '#f7f7f7',
       'complex': '#d9f0d3',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1791,7 +1791,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#f4a582',
       'nucleic acid feature': '#bababa',
       'perturbing agent': '#ffffff',
-      'source and sink': '#ffffff',
+      'empty set': '#ffffff',
       'complex': '#fddbc7',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1838,7 +1838,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#bababa',
       'nucleic acid feature': '#f4a582',
       'perturbing agent': '#ffffff',
-      'source and sink': '#ffffff',
+      'empty set': '#ffffff',
       'complex': '#e0e0e0',
       'process': '#ffffff',
       'omitted process': '#ffffff',
@@ -1884,7 +1884,7 @@ appUtilities.mapColorSchemes = mapColorSchemes = {
       'macromolecule': '#ffffff',
       'nucleic acid feature': '#ffffff',
       'perturbing agent': '#ffffff',
-      'source and sink': '#ffffff',
+      'empty set': '#ffffff',
       'complex': '#ffffff',
       'process': '#ffffff',
       'omitted process': '#ffffff',

diff --git a/app/js/inspector-utilities.js b/app/js/inspector-utilities.js
@@ -1423,7 +1423,7 @@ inspectorUtilities.fixRadioButtons = function (errorCode,eles,cy) {
                      html +="<p style=\"text-align:center\" > To fix, reverse the consumption arc:</p>";
             }  */
             else if(errors[currentPage].pattern == "pd10103") {
-                     html += "<p style=\"text-align:center\" > To fix, split the <i>source and sink</i> glyph for each consumption arc:</p> ";       
+                     html += "<p style=\"text-align:center\" > To fix, split the <i>empty set</i> glyph for each consumption arc:</p> ";       
             }else if(radioButtonRules.includes(errors[currentPage].pattern)) {
                     var params = { handled: handled };
                     html= inspectorUtilities.handleRadioButtons(errors[currentPage].pattern,html,eles,cy,params);
@@ -1437,7 +1437,7 @@ inspectorUtilities.fixRadioButtons = function (errorCode,eles,cy) {
 
             }
             else if(errors[currentPage].pattern == "pd10107") {
-                     html += "<p style=\"text-align:center\" > To fix, split the <i>source and sink</i> glyph for each production arc:</p>";
+                     html += "<p style=\"text-align:center\" > To fix, split the <i>empty set</i> glyph for each production arc:</p>";
                        var connectedEdges = eles.connectedEdges().filter('[class="production"]');
                        for (var i = 0; i < connectedEdges.length; i++) {
                            viewUtilitilesInstance.highlight(connectedEdges[i], 1);

diff --git a/app/resources/libsbgn-0.3.xsd b/app/resources/libsbgn-0.3.xsd
@@ -663,7 +663,7 @@
                                 <xsd:enumeration value="nucleic acid feature multimer"/>
                                 <xsd:enumeration value="complex"/>
                                 <xsd:enumeration value="complex multimer"/>
-                                <xsd:enumeration value="source and sink"/>
+                                <xsd:enumeration value="empty set"/>
                                 <!-- Activities (AF) -->
                                 <!-- perturbation is deprecated in AF as Activity Node in milestone 3. -->
                                 <xsd:enumeration value="perturbation"/>

diff --git a/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt b/app/samples/activated_stat1alpha_induction_of_the_irf1_gene.nwt
@@ -73,7 +73,7 @@ using logical operators</mapDescription>
         <rearrangeAfterExpandCollapse>true</rearrangeAfterExpandCollapse>
       </mapProperties>
     </extension>
-    <glyph id="glyph8" class="source and sink">
+    <glyph id="glyph8" class="empty set">
       <bbox x="219.34507961077375" y="426.0211623750535" w="22" h="22"/>
     </glyph>
     <glyph id="glyph6" class="process">
@@ -89,7 +89,7 @@ using logical operators</mapDescription>
         <bbox x="384.1620543768622" y="416.0211623750535" w="40" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="glyph7" class="source and sink">
+    <glyph id="glyph7" class="empty set">
       <bbox x="322.0837185192559" y="499.0054808397" w="22" h="22"/>
     </glyph>
     <glyph id="glyph5" class="process">

diff --git a/app/samples/drosophila_cell_cycle.nwt b/app/samples/drosophila_cell_cycle.nwt
@@ -193,7 +193,7 @@
         <bbox x="642" y="257.75000000000006" w="16" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="8c6d3816-85c1-358b-5893-20995009088c" class="source and sink" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
+    <glyph id="8c6d3816-85c1-358b-5893-20995009088c" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
       <bbox x="542" y="268.75000000000006" w="25" h="25"/>
     </glyph>
     <glyph id="f5f91ced-d47f-07e1-03f4-9307020437ef" class="process" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
@@ -222,7 +222,7 @@
         <bbox x="578.75" y="515.25" w="16" h="12"/>
       </glyph>
     </glyph>
-    <glyph id="0088e5e3-506d-b360-cc23-6ca191128211" class="source and sink" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
+    <glyph id="0088e5e3-506d-b360-cc23-6ca191128211" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
       <bbox x="480.25" y="526.25" w="25" h="25"/>
     </glyph>
     <glyph id="d6a6f52d-8036-ba76-8a3e-dfa5dcd6d57e" class="process" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
@@ -248,7 +248,7 @@
       <port id="nwtN_5d0ff9d3-a331-4b27-a9bf-5f3e6471f4a7.1" x="789.8571428571429" y="538.75"/>
       <port id="nwtN_5d0ff9d3-a331-4b27-a9bf-5f3e6471f4a7.2" x="804.1428571428571" y="538.75"/>
     </glyph>
-    <glyph id="nwtN_18ca18bf-e112-4b17-acba-35e845505d26" class="source and sink" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
+    <glyph id="nwtN_18ca18bf-e112-4b17-acba-35e845505d26" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
       <bbox x="830.5" y="526.25" w="25" h="25"/>
     </glyph>
     <glyph id="nwtN_5a3ef454-8d2b-46de-b3a1-f9a0c2409ee4" class="macromolecule" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
@@ -260,15 +260,15 @@
       <port id="nwtN_7ffe3be6-9a33-4696-a593-d5c0a8a45a4c.1" x="891.8571428571429" y="481.75000000000006"/>
       <port id="nwtN_7ffe3be6-9a33-4696-a593-d5c0a8a45a4c.2" x="906.1428571428571" y="481.75000000000006"/>
     </glyph>
-    <glyph id="nwtN_617312c5-bae0-423e-a711-c6adfee4193b" class="source and sink" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
+    <glyph id="nwtN_617312c5-bae0-423e-a711-c6adfee4193b" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
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+    <glyph id="nwtN_0949a2cf-db5f-461a-b93f-51a21cdf1543" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
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@@ -281,23 +281,23 @@
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+    <glyph id="682cd847-d9d2-5765-6915-b974cb1d689e" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
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+    <glyph id="nwtN_e973c31b-714f-47be-a2c2-e8e46b4d8ebf" class="empty set" compartmentRef="nwtN_31dec67c-8c37-40ec-bfad-d038cf1dc815">
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@@ -315,10 +315,10 @@
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