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refactors buildObjectIdentity into super class #949

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refactors buildObjectIdentity into super class #949

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22 changes: 22 additions & 0 deletions kbase-extension/static/kbase/js/kbwidget.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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;
},

}
);

Expand Down
22 changes: 0 additions & 22 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseDomainAnnotation.js
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
56 changes: 17 additions & 39 deletions ...xtension/static/kbase/js/widgets/function_output/kbaseExpressionConditionsetBaseWidget.js
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Original file line number Diff line number Diff line change
@@ -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 <[email protected]>
Expand Down Expand Up @@ -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;
},
Expand All @@ -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;
},

Expand Down Expand Up @@ -198,7 +198,7 @@ define([

var $vizContainer = $("<div/>");
this.$elem.append( $vizContainer );
this.buildWidget( $vizContainer );
this.buildWidget( $vizContainer );
},

buildOverviewDiv: function($containerDiv){
Expand Down Expand Up @@ -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 = [];
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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;
}

});
});
});
22 changes: 0 additions & 22 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionEstimateK.js
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
22 changes: 0 additions & 22 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionFeatureClusters.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
27 changes: 3 additions & 24 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionGenesetBaseWidget.js
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 <[email protected]>
Expand Down Expand Up @@ -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;
}

});
});
});
21 changes: 0 additions & 21 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseExpressionMatrix.js
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down
22 changes: 0 additions & 22 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseFeatureSet.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down
22 changes: 0 additions & 22 deletions kbase-extension/static/kbase/js/widgets/function_output/kbaseMSA.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand Down
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