Skip to content

Luminex Levey-Jennings report data query performance improvements #588

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
cnathe merged 1 commit into from
Mar 6, 2023
Merged

Luminex Levey-Jennings report data query performance improvements #588

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
75 changes: 44 additions & 31 deletions luminex/webapp/luminex/LeveyJenningsPlotHelpers.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,32 @@ LABKEY.LeveyJenningsPlotHelper.getTrackingDataStore = function(config)
whereClause += config.whereClause;
}

// this version of the guide set range values SQL will prevent the need for multiple LEFT OUTER JOINs to the GuideSetCurveFit table
var guideSetRangeValuesSQL = "SELECT gs.RowId, gs.Created, gs.ValueBased,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.EC504PLAverage ELSE cf.EC504PLAverage END AS GuideSetEC504PLAverage,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.EC504PLStdDev ELSE cf.EC504PLStdDev END AS GuideSetEC504PLStdDev,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.EC505PLAverage ELSE cf.EC505PLAverage END AS GuideSetEC505PLAverage,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.EC505PLStdDev ELSE cf.EC505PLStdDev END AS GuideSetEC505PLStdDev,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.AUCAverage ELSE cf.AUCAverage END AS GuideSetAUCAverage,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.AUCStdDev ELSE cf.AUCStdDev END AS GuideSetAUCStdDev,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.MaxFIAverage ELSE gs.TitrationMaxFIAverage END AS GuideSetHighMFIAverage,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.MaxFIStdDev ELSE gs.TitrationMaxFIStdDev END AS GuideSetHighMFIStdDev,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.MaxFIAverage ELSE gs.SinglePointControlFIAverage END AS GuideSetMFIAverage,\n" +
" CASE WHEN gs.ValueBased=true THEN gs.MaxFIStdDev ELSE gs.SinglePointControlFIStdDev END AS GuideSetMFIStdDev\n" +
"FROM GuideSet gs\n" +
"LEFT JOIN (\n" +
" SELECT\n" +
" GuideSetId,\n" +
" MIN(CASE WHEN CurveType = 'Trapezoidal' THEN AUCAverage ELSE NULL END) AS AUCAverage,\n" +
" MIN(CASE WHEN CurveType = 'Trapezoidal' THEN AUCStdDev ELSE NULL END) AS AUCStdDev,\n" +
" MIN(CASE WHEN CurveType = 'Four Parameter' THEN EC50Average ELSE NULL END) AS EC504PLAverage,\n" +
" MIN(CASE WHEN CurveType = 'Four Parameter' THEN EC50StdDev ELSE NULL END) AS EC504PLStdDev,\n" +
" MIN(CASE WHEN CurveType = 'Five Parameter' THEN EC50Average ELSE NULL END) AS EC505PLAverage,\n" +
" MIN(CASE WHEN CurveType = 'Five Parameter' THEN EC50StdDev ELSE NULL END) AS EC505PLStdDev\n" +
" FROM GuideSetCurveFit\n" +
" GROUP BY GuideSetId\n" +
") cf ON gs.RowId = cf.GuideSetId";

// generate sql for the data store (columns depend on the control type)
// issue 22267 : add IFDEFINED to "optional" assay design fields
var sql = "SELECT Analyte"
Expand All @@ -45,58 +71,46 @@ LABKEY.LeveyJenningsPlotHelper.getTrackingDataStore = function(config)
+ ", IFDEFINED(" + controlTypeColName + ".Run.NotebookNo)"
+ ", IFDEFINED(" + controlTypeColName + ".Run.AssayType)"
+ ", IFDEFINED(" + controlTypeColName + ".Run.ExpPerformer)"
+ ", GuideSet.Created AS GuideSetCreated"
+ ", GuideSet AS GuideSetId"
+ ", gs.Created AS GuideSetCreated"
+ ", IncludeInGuideSetCalculation"
+ ", GuideSet.ValueBased AS GuideSetValueBased";
+ ", gs.ValueBased AS GuideSetValueBased";
if (config.controlType == "Titration")
{
sql += ", \"Four ParameterCurveFit\".EC50 AS EC504PL, \"Four ParameterCurveFit\".EC50QCFlagsEnabled AS EC504PLQCFlagsEnabled"
+ ", \"Five ParameterCurveFit\".EC50 AS EC505PL, \"Five ParameterCurveFit\".EC50QCFlagsEnabled AS EC505PLQCFlagsEnabled"
+ ", TrapezoidalCurveFit.AUC, TrapezoidalCurveFit.AUCQCFlagsEnabled"
+ ", MaxFI AS HighMFI, MaxFIQCFlagsEnabled AS HighMFIQCFlagsEnabled"
//columns needed for guide set ranges (value based or run based)
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.EC504PLAverage ELSE GuideSet.\"Four ParameterCurveFit\".EC50Average END AS GuideSetEC504PLAverage"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.EC504PLStdDev ELSE GuideSet.\"Four ParameterCurveFit\".EC50StdDev END AS GuideSetEC504PLStdDev"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.EC505PLAverage ELSE GuideSet.\"Five ParameterCurveFit\".EC50Average END AS GuideSetEC505PLAverage"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.EC505PLStdDev ELSE GuideSet.\"Five ParameterCurveFit\".EC50StdDev END AS GuideSetEC505PLStdDev"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.AUCAverage ELSE GuideSet.TrapezoidalCurveFit.AUCAverage END AS GuideSetAUCAverage"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.AUCStdDev ELSE GuideSet.TrapezoidalCurveFit.AUCStdDev END AS GuideSetAUCStdDev"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.MaxFIAverage ELSE GuideSet.TitrationMaxFIAverage END AS GuideSetHighMFIAverage"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.MaxFIStdDev ELSE GuideSet.TitrationMaxFIStdDev END AS GuideSetHighMFIStdDev"
+ ", gs.GuideSetEC504PLAverage"
+ ", gs.GuideSetEC504PLStdDev"
+ ", gs.GuideSetEC505PLAverage"
+ ", gs.GuideSetEC505PLStdDev"
+ ", gs.GuideSetAUCAverage"
+ ", gs.GuideSetAUCStdDev"
+ ", gs.GuideSetHighMFIAverage"
+ ", gs.GuideSetHighMFIStdDev"
+ " FROM AnalyteTitration "
+ " LEFT JOIN (" + guideSetRangeValuesSQL + ") AS gs ON GuideSet = gs.RowId"
+ whereClause;
}
else if (config.controlType == "SinglePoint")
{
sql += ", AverageFiBkgd AS MFI, AverageFiBkgdQCFlagsEnabled AS MFIQCFlagsEnabled"
//columns needed for guide set ranges (value based or run based)
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.MaxFIAverage ELSE GuideSet.SinglePointControlFIAverage END AS GuideSetMFIAverage"
+ ", CASE WHEN GuideSet.ValueBased=true THEN GuideSet.MaxFIStdDev ELSE GuideSet.SinglePointControlFIStdDev END AS GuideSetMFIStdDev"
+ ", gs.GuideSetMFIAverage"
+ ", gs.GuideSetMFIStdDev"
+ " FROM AnalyteSinglePointControl "
+ " LEFT JOIN (" + guideSetRangeValuesSQL + ") AS gs ON GuideSet = gs.RowId"
+ whereClause;
}

if (config.orderBy)
sql += config.orderBy;

// NOTE: watch out for this case. mixing with other params might end badly (consider override)
// used in LABKEY.LeveyJenningsPlotHelper.getLeveyJenningsPlotWindow
if (config.centerDate)
{
var finalSql = "( " + sql;
finalSql += " AND Analyte.Data.AcquisitionDate >= CAST('" + config.centerDate + "' AS DATE)";
finalSql += " ORDER BY Analyte.Data.AcquisitionDate ASC, "+controlTypeColName+".Run.Created ASC LIMIT 30 )";
finalSql += " UNION ( " + sql;
finalSql += " AND Analyte.Data.AcquisitionDate < CAST('" + config.centerDate + "' AS DATE)";
finalSql += " ORDER BY Analyte.Data.AcquisitionDate DESC, "+controlTypeColName+".Run.Created DESC LIMIT 30 )";

sql = finalSql; // swap back
}

var store = new LABKEY.ext.Store({
autoLoad: false,
schemaName: 'assay.Luminex.' + LABKEY.QueryKey.encodePart(config.assayName),
sql: sql,
sort: config.sort ? config.sort : '-Analyte/Data/AcquisitionDate, -' + controlTypeColName + '/Run/Created',
maxRows: config.maxRows ? config.maxRows : -1,
containerFilter: LABKEY.Query.containerFilter.allFolders,
scope: config.scope
});
Expand Down Expand Up @@ -269,7 +283,6 @@ LABKEY.LeveyJenningsPlotHelper.getLeveyJenningsPlotWindow = function(protocolId,
var _getConfig = function(assayName)
{
// note make sure to mix assayName into config...

LABKEY.Query.selectRows({
schemaName: 'assay.Luminex.' + LABKEY.QueryKey.encodePart(assayName),
queryName: 'Analyte'+controlType,
Expand All @@ -291,7 +304,7 @@ LABKEY.LeveyJenningsPlotHelper.getLeveyJenningsPlotWindow = function(protocolId,
scope: this, // shouldn't matter but might blow up without it.
plotType: plotType,
runId: row[controlType+'/Run'],
centerDate: row['Analyte/Data/AcquisitionDate']
sort: 'Analyte/Data/AcquisitionDate, ' + controlType + '/Run/Created',
};

_createWindow(config);
Expand Down
8 changes: 2 additions & 6 deletions luminex/webapp/luminex/LeveyJenningsTrackingDataPanel.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -243,20 +243,16 @@ LABKEY.LeveyJenningsTrackingDataPanel = Ext.extend(Ext.grid.GridPanel, {
}

// create a new store now that the graph params are selected and bind it to the grid
var controlTypeColName = this.controlType == "SinglePoint" ? "SinglePointControl" : this.controlType;
var orderByClause = " ORDER BY Analyte.Data.AcquisitionDate DESC, " + controlTypeColName + ".Run.Created DESC"
+ " LIMIT " + (hasReportFilter ? "10000" : this.defaultRowSize);

var storeConfig = {
assayName: this.assayName,
controlName: this.controlName,
controlType: this.controlType,
analyte: this.analyte,
isotype: this.isotype,
conjugate: this.conjugate,
maxRows: !hasReportFilter ? this.defaultRowSize : undefined,
scope: this,
loadListener: this.storeLoaded,
orderBy: orderByClause
};

if (whereClause != "")
Expand All @@ -269,7 +265,7 @@ LABKEY.LeveyJenningsTrackingDataPanel = Ext.extend(Ext.grid.GridPanel, {
this.store.on('exception', function(store, type, action, options, response){
var errorJson = Ext.util.JSON.decode(response.responseText);
if (errorJson.exception) {
Ext.get('EC504PLTrendPlotDiv').update("<span class='labkey-error'>" + errorJson.exception + "</span>");
Ext.get(document.querySelector('.ljTrendPlot').id).update("<span class='labkey-error'>" + errorJson.exception + "</span>");
}
});

Expand Down