From b6903f0b1615a5d907370362cf4b1d9e38ab00b7 Mon Sep 17 00:00:00 2001
From: Jim Thomason <jim@japanesewartuba.com>
Date: Fri, 27 Jan 2017 13:25:42 -0600
Subject: [PATCH] refactors buildObjectIdentity in various widgets into a
 single method way up in kbwidget. Needs further testing.

---
 kbase-extension/static/kbase/js/kbwidget.js   | 22 ++++++++
 .../function_output/kbaseDomainAnnotation.js  | 22 --------
 .../kbaseExpressionConditionsetBaseWidget.js  | 56 ++++++-------------
 .../kbaseExpressionEstimateK.js               | 22 --------
 .../kbaseExpressionFeatureClusters.js         | 22 --------
 .../kbaseExpressionGenesetBaseWidget.js       | 27 +--------
 .../function_output/kbaseExpressionMatrix.js  | 21 -------
 .../function_output/kbaseFeatureSet.js        | 22 --------
 .../js/widgets/function_output/kbaseMSA.js    | 22 --------
 .../function_output/kbaseMatrix2DAbstract.js  | 22 --------
 .../function_output/kbaseReportView.js        | 40 ++++---------
 .../js/widgets/function_output/kbaseTree.js   | 44 ++++-----------
 12 files changed, 63 insertions(+), 279 deletions(-)

diff --git a/kbase-extension/static/kbase/js/kbwidget.js b/kbase-extension/static/kbase/js/kbwidget.js
index 4b9f3e3ff6..76ff250ad3 100644
--- a/kbase-extension/static/kbase/js/kbwidget.js
+++ b/kbase-extension/static/kbase/js/kbwidget.js
@@ -923,6 +923,28 @@ define (
                 return 'uuid-' + result;
             },
 
+            buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
+                var obj = {};
+                if (wsRef) {
+                  obj['ref'] = wsRef;
+                } else {
+                  if (/^\d+$/.exec(workspaceID))
+                    obj['wsid'] = workspaceID;
+                  else
+                    obj['workspace'] = workspaceID;
+
+                  // same for the id
+                  if (/^\d+$/.exec(objectID))
+                    obj['objid'] = objectID;
+                  else
+                    obj['name'] = objectID;
+
+                  if (objectVer)
+                    obj['ver'] = objectVer;
+                }
+                return obj;
+            },
+
         }
     );
 
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseDomainAnnotation.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseDomainAnnotation.js
index 2625ad6dde..f7c27a7eeb 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseDomainAnnotation.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseDomainAnnotation.js
@@ -461,28 +461,6 @@ define (
                 });
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        },
-
         clientError: function(error){
             this.loading(false);
             this.showMessage(error.error.error);
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionConditionsetBaseWidget.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionConditionsetBaseWidget.js
index 7287c801a2..7e4a3e98eb 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionConditionsetBaseWidget.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionConditionsetBaseWidget.js
@@ -1,11 +1,11 @@
 /**
  * Base class for viewers visualizaing expression of a set of conditions from various aspects
- * 
+ *
  * The descendant classes should override:
  * 1. getSubmtrixParams - to set params for get_submatrix_stat method from the KBaseFeatureValues service
  * 2. buildWidget - to create a custom visuzualization
  *
- * 
+ *
  *
  *
  * Pavel Novichkov <psnovichkov@lbl.gov>
@@ -73,7 +73,7 @@ define([
 
             // Create a message pane
             this.$messagePane = $("<div/>").addClass("kbwidget-message-pane kbwidget-hide-message");
-            this.$elem.append(this.$messagePane);       
+            this.$elem.append(this.$messagePane);
 
             return this;
         },
@@ -86,12 +86,12 @@ define([
                     "service_wizard");
                 this.genericClient = new GenericClient(serviceWizardURL, auth);
             } else {
-                this.featureValueClient = new KBaseFeatureValues(this.options.featureValueURL, auth);   
+                this.featureValueClient = new KBaseFeatureValues(this.options.featureValueURL, auth);
             }
-            this.ws = new Workspace(this.options.wsURL, auth);         
+            this.ws = new Workspace(this.options.wsURL, auth);
 
             // Let's go...
-            this.loadAndRender();           
+            this.loadAndRender();
             return this;
         },
 
@@ -198,7 +198,7 @@ define([
 
             var $vizContainer = $("<div/>");
             this.$elem.append( $vizContainer );
-            this.buildWidget( $vizContainer );            
+            this.buildWidget( $vizContainer );
         },
 
         buildOverviewDiv: function($containerDiv){
@@ -229,22 +229,22 @@ define([
                         { sTitle: "Name", mData: "id"},
                         // { sTitle: "Function", mData: "function"},
                         { sTitle: "Min", mData:"min" },
-                        { sTitle: "Max", mData:"max" },  
-                        { sTitle: "Avg", mData:"avg" },                                                      
+                        { sTitle: "Max", mData:"max" },
+                        { sTitle: "Avg", mData:"avg" },
                         { sTitle: "Std", mData:"std"},
                         { sTitle: "Missing", mData:"missing_values" }
                     ],
                     "oLanguage": {
                                 "sEmptyTable": "No conditions found!",
                                 "sSearch": "Search: "
-                    }                    
+                    }
                 } );
 
             $overviewSwitch.click(function(){
                 $overvewContainer.toggle();
             });
         },
-      
+
         buildConditionsTableData: function(){
             var submatrixStat = this.submatrixStat;
             var tableData = [];
@@ -278,12 +278,12 @@ define([
                        .append($("<td />").append(value));
             return $row;
         },
-        
+
         loading: function(isLoading) {
             if (isLoading)
                 this.showMessage("<img src='" + this.options.loadingImage + "'/>");
             else
-                this.hideMessage();                
+                this.hideMessage();
         },
 
         showMessage: function(message) {
@@ -318,44 +318,22 @@ define([
                                  "and will be fixed shortly."
                 }
             }
-            
+
             var $errorDiv = $("<div>")
                             .addClass("alert alert-danger")
                             .append("<b>Error:</b>")
                             .append("<br>" + errString);
             this.$elem.empty();
             this.$elem.append($errorDiv);
-        },            
+        },
 
         uuid: function() {
-            return 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g, 
+            return 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'.replace(/[xy]/g,
                 function(c) {
                     var r = Math.random()*16|0, v = c == 'x' ? r : (r&0x3|0x8);
                     return v.toString(16);
                 });
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-                
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        }
-
     });
-});
\ No newline at end of file
+});
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionEstimateK.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionEstimateK.js
index 2326e7b57b..60fbe6d7df 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionEstimateK.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionEstimateK.js
@@ -240,28 +240,6 @@ define (
 				});
 		},
 
-		buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-			var obj = {};
-			if (wsRef) {
-				obj['ref'] = wsRef;
-			} else {
-				if (/^\d+$/.exec(workspaceID))
-					obj['wsid'] = workspaceID;
-				else
-					obj['workspace'] = workspaceID;
-
-				// same for the id
-				if (/^\d+$/.exec(objectID))
-					obj['objid'] = objectID;
-				else
-					obj['name'] = objectID;
-
-				if (objectVer)
-					obj['ver'] = objectVer;
-			}
-			return obj;
-		},
-
 		clientError: function(error){
 			this.loading(false);
 			this.showMessage(error.error.error);
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionFeatureClusters.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionFeatureClusters.js
index 2e37a4f622..6d1ff49681 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionFeatureClusters.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionFeatureClusters.js
@@ -504,28 +504,6 @@ define (
 			this.$messagePane.empty();
 		},
 
-		buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-			var obj = {};
-			if (wsRef) {
-				obj['ref'] = wsRef;
-			} else {
-				if (/^\d+$/.exec(workspaceID))
-					obj['wsid'] = workspaceID;
-				else
-					obj['workspace'] = workspaceID;
-
-				// same for the id
-				if (/^\d+$/.exec(objectID))
-					obj['objid'] = objectID;
-				else
-					obj['name'] = objectID;
-
-				if (objectVer)
-					obj['ver'] = objectVer;
-			}
-			return obj;
-		},
-
 		clientError: function(error){
 			this.loading(false);
 			this.showMessage(error.error.error);
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionGenesetBaseWidget.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionGenesetBaseWidget.js
index 3fe240c20b..786efaa8d9 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionGenesetBaseWidget.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionGenesetBaseWidget.js
@@ -1,11 +1,11 @@
 /**
  * Base class for viewers visualizaing expression of a set of genes from various aspects
- * 
+ *
  * The descendant classes should override:
  * 1. getSubmtrixParams - to set params for get_submatrix_stat method from the KBaseFeatureValues service
  * 2. buildWidget - to create a custom visuzualization
  *
- * 
+ *
  *
  *
  * Pavel Novichkov <psnovichkov@lbl.gov>
@@ -315,27 +315,6 @@ define([
                     return v.toString(16);
                 });
         },
-        buildObjectIdentity: function (workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        }
 
     });
-});
\ No newline at end of file
+});
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionMatrix.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionMatrix.js
index c5c19ebc0b..1b1174e491 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionMatrix.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionMatrix.js
@@ -323,27 +323,6 @@ define (
                 });
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        },
 
         clientError: function(error){
             this.loading(false);
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseFeatureSet.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseFeatureSet.js
index c0e89d3fad..79f587ea5a 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseFeatureSet.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseFeatureSet.js
@@ -248,28 +248,6 @@ define (
             this.$elem.append($errorDiv);
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        },
-
         loading: function(doneLoading) {
             if (doneLoading)
                 this.hideMessage();
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseMSA.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseMSA.js
index 1c8401fad1..b29f551451 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseMSA.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseMSA.js
@@ -207,28 +207,6 @@ define (
             };
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-            	obj['ref'] = wsRef;
-            } else {
-            	if (/^\d+$/.exec(workspaceID))
-            		obj['wsid'] = workspaceID;
-            	else
-            		obj['workspace'] = workspaceID;
-
-            	// same for the id
-            	if (/^\d+$/.exec(objectID))
-            		obj['objid'] = objectID;
-            	else
-            		obj['name'] = objectID;
-
-            	if (objectVer)
-            		obj['ver'] = objectVer;
-            }
-            return obj;
-        },
-
         loading: function(doneLoading) {
             if (doneLoading)
                 this.hideMessage();
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseMatrix2DAbstract.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseMatrix2DAbstract.js
index 52bb6c18fe..f1e9a02227 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseMatrix2DAbstract.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseMatrix2DAbstract.js
@@ -489,28 +489,6 @@ define (
                 });
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        }
-
     });
 });
 
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseReportView.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseReportView.js
index 4f4df4f5c6..29c5721b69 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseReportView.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseReportView.js
@@ -242,8 +242,8 @@ define([
             };
         },
 
-        // preserved for a minute. The approach below blocks off the report and presents a 
-        // translucent layer and link on top of the report area. The premise is that the 
+        // preserved for a minute. The approach below blocks off the report and presents a
+        // translucent layer and link on top of the report area. The premise is that the
         // content is nearly useless, so don't encourage users to try to use it.
 
         // openReportWindow: function (arg) {
@@ -473,7 +473,7 @@ define([
                         // We may receive this if a 'ready' was received
                         // from another cell. Perhaps there is a better
                         // way of filtering messages before getting here!
-                        // TODO: implement an address feature to allow a 
+                        // TODO: implement an address feature to allow a
                         //   message bus to ignore messages not sent to it.
                         //   we use the frame id for this, but it should actually
                         //   be a feature of the message bus itself.
@@ -712,7 +712,7 @@ define([
                 // REPORT SECTION
 
                 /*
-                The "inline" report can come from either the direct_html property or the direct_html_link_index. 
+                The "inline" report can come from either the direct_html property or the direct_html_link_index.
                 The direct_html_link_index will take precedence since it offers a better method for referencing
                 content within an iframe. Generally the app developer should use either method, not both
                  */
@@ -722,7 +722,7 @@ define([
                 if (report.direct_html && report.direct_html.length > 0) {
                     hasDirectHtml = true;
                 }
-                if (typeof report.direct_html_link_index === 'number' && 
+                if (typeof report.direct_html_link_index === 'number' &&
                     report.direct_html_link_index >= 0) {
                     hasDirectHtmlIndex = true;
                 }
@@ -761,7 +761,7 @@ define([
                                 };
                             }
                         } else {
-                            // If the direct_html is a full document we cannot (yet?) insert 
+                            // If the direct_html is a full document we cannot (yet?) insert
                             // the necessary code to gracefully handle resizing and click-passthrough.
                             if (/<html/.test(report.direct_html)) {
                                 console.warn('Html document inserted into iframe', report);
@@ -771,8 +771,8 @@ define([
                                     events: events
                                 });
                             } else {
-                                // note that for direct_html, we set the max height. this content is expected 
-                                // to be smaller than linked content, and we will want the container 
+                                // note that for direct_html, we set the max height. this content is expected
+                                // to be smaller than linked content, and we will want the container
                                 // to shrink, but if it is larger, we simply don't want it to be too tall.
                                 iframe = _this.makeIframe({
                                     content: report.direct_html,
@@ -991,26 +991,6 @@ define([
             this.$elem.empty();
             this.$elem.append($errorDiv);
         },
-        buildObjectIdentity: function (workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-                obj['ref'] = wsRef;
-            } else {
-                if (/^\d+$/.exec(workspaceID))
-                    obj['wsid'] = workspaceID;
-                else
-                    obj['workspace'] = workspaceID;
-
-                // same for the id
-                if (/^\d+$/.exec(objectID))
-                    obj['objid'] = objectID;
-                else
-                    obj['name'] = objectID;
-
-                if (objectVer)
-                    obj['ver'] = objectVer;
-            }
-            return obj;
-        }
+
     });
-});
\ No newline at end of file
+});
diff --git a/kbase-extension/static/kbase/js/widgets/function_output/kbaseTree.js b/kbase-extension/static/kbase/js/widgets/function_output/kbaseTree.js
index 2cde0bd8ac..f962b89984 100644
--- a/kbase-extension/static/kbase/js/widgets/function_output/kbaseTree.js
+++ b/kbase-extension/static/kbase/js/widgets/function_output/kbaseTree.js
@@ -122,11 +122,11 @@ define (
                 		console.log(err);
                 	});
                 }
-                
+
                 function EasyTreeForNarrative(canvasId, treeString, nodeIdToNameMap, leafClickListener, nodeColorFunc) {
-                    
+
                     var kn_g_tree = kn_parse(treeString);
-                    
+
                     if (nodeIdToNameMap) {
                         for (var nodePos in kn_g_tree.node) {
                             var nodeId = kn_g_tree.node[nodePos].name;
@@ -137,7 +137,7 @@ define (
                             }
                         }
                     }
-                    
+
                     if (nodeColorFunc) {
                         for (var nodePos in kn_g_tree.node) {
                             var node = kn_g_tree.node[nodePos];
@@ -147,10 +147,10 @@ define (
                             }
                         }
                     }
-                    
+
                     var kn_g_conf = new Object();
                     var canvas = document.getElementById(canvasId);
-                    
+
                     var conf = kn_g_conf;
                     conf.c_box = new Array();
                     conf.width = 1000; conf.height = 600;
@@ -179,7 +179,7 @@ define (
                     var changeLayoutY = 0;
                     var changeLayoutW = 0;
                     var changeLayoutH = 0;
-                    
+
                     function plot(canvas, kn_g_tree, kn_g_conf) {
                         kn_plot_core(canvas, kn_g_tree, kn_g_conf);
                         var text = "Change layout";
@@ -198,7 +198,7 @@ define (
                         changeLayoutW = w;
                         changeLayoutH = h;
                     }
-                    
+
                     function changeLayout(isCircular) {
                         kn_g_conf.is_circular = isCircular;
                         kn_g_conf.height = kn_g_conf.is_circular? kn_g_conf.width : kn_g_conf.ymargin * 2 + kn_g_tree.n_tips * kn_g_conf.yskip;
@@ -285,12 +285,12 @@ define (
                         canvas_parent.removeChild(canvas);
                         canvas_parent.appendChild(o);
                         o.appendChild(canvas);
-                        
+
                         if (canvas.addEventListener) canvas.addEventListener('click', ev_canvas, false);
                         else canvas.attachEvent('onclick', ev_canvas);
                     }
                 };
-                
+
                 new EasyTreeForNarrative(self.canvasId, tree.tree, tree.default_node_labels, function(node) {
                 	if ((!tree.ws_refs) || (!tree.ws_refs[node.id])) {
                 		var node_name = tree.default_node_labels[node.id];
@@ -341,28 +341,6 @@ define (
             };
         },
 
-        buildObjectIdentity: function(workspaceID, objectID, objectVer, wsRef) {
-            var obj = {};
-            if (wsRef) {
-            	obj['ref'] = wsRef;
-            } else {
-            	if (/^\d+$/.exec(workspaceID))
-            		obj['wsid'] = workspaceID;
-            	else
-            		obj['workspace'] = workspaceID;
-
-            	// same for the id
-            	if (/^\d+$/.exec(objectID))
-            		obj['objid'] = objectID;
-            	else
-            		obj['name'] = objectID;
-
-            	if (objectVer)
-            		obj['ver'] = objectVer;
-            }
-            return obj;
-        },
-
         loading: function(doneLoading) {
             if (doneLoading)
                 this.hideMessage();
@@ -396,4 +374,4 @@ define (
         }
 
     });
-});
\ No newline at end of file
+});