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Merged
cnathe merged 16 commits into from
Feb 9, 2023
Merged

Issue 46774: Remove Ruminex package references from Luminex transform script #578

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e995b9e
Remove Ruminex package usage and calculations from labkey_luminex_tra…
cnathe Feb 6, 2023
86efa5d
Remove Ruminex related props from Luminex test assay configurations a…
cnathe Feb 6, 2023
0a3627e
missed from previous commit
cnathe Feb 6, 2023
22a6ef9
Remove Rumi reference and import of Rumi5PL curve fit calculations
cnathe Feb 6, 2023
0952f40
Revert changes in LuminexDataHandler as we need to keep those for bac…
cnathe Feb 7, 2023
5674d8d
Misc Luminex test fixes/changes to remove checks for EC50 5PL related…
cnathe Feb 7, 2023
7146a9e
Update TestLuminexAssay.xar to remove Ruminex related assay design props
cnathe Feb 7, 2023
ae1b2aa
Misc Luminex test fixes/changes to remove checks for EC50 5PL related…
cnathe Feb 7, 2023
6da17bc
Misc Luminex test fixes/changes to remove checks for EC50 5PL related…
cnathe Feb 8, 2023
8529f6c
Misc Luminex test fixes/changes to remove checks for EC50 5PL related…
cnathe Feb 8, 2023
c24816e
Hide EC50 4PL/5PL related columns and guide set inputs for Levey-Jenn…
cnathe Feb 8, 2023
633c412
Hide EC50 4PL/5PL related columns and guide set inputs for Levey-Jenn…
cnathe Feb 8, 2023
db708ee
Update L-J test to verify EC50 5PL tab is not present
cnathe Feb 8, 2023
982cdd7
remove EC50 5PL checks for guide set details dialog
cnathe Feb 8, 2023
36f2b2f
GuideSetWindow.js fix for query to get info on which curve fit types …
cnathe Feb 8, 2023
4284da1
Merge branch 'develop' into fb_removeRuminex
cnathe Feb 9, 2023
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350 changes: 8 additions & 342 deletions luminex/resources/transformscripts/labkey_luminex_transform.R
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2 changes: 1 addition & 1 deletion luminex/src/org/labkey/luminex/LuminexDataHandler.java
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Expand Up @@ -1055,7 +1055,7 @@ else if (well.getDose() == 0.0)
return null;
}

/** @return null if we can't find matching Rumi curve fit data */
/** @return null if we can't find matching Rumi/drc curve fit data */
@Nullable
private CurveFit importRumiCurveFit(StatsService.CurveFitType fitType, LuminexDataRow dataRow, LuminexWellGroup wellGroup, User user, Titration titration, Analyte analyte, CurveFit[] existingCurveFits)
{
Expand Down
13 changes: 9 additions & 4 deletions luminex/src/org/labkey/luminex/query/AnalyteTitrationTable.java
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Expand Up @@ -116,6 +116,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)

addColumn(wrapColumn(getRealTable().getColumn("IncludeInGuideSetCalculation")));

List<String> curveTypes = _userSchema.getCurveTypes();
addCurveTypeColumns();

var ljPlots = addWrapColumn("L-J Plots", getRealTable().getColumn(FieldKey.fromParts("TitrationId")));
Expand Down Expand Up @@ -144,8 +145,10 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep

NavTree ljPlotsNav = new NavTree("Levey-Jennings Plot Menu");
ljPlotsNav.setImage(AppProps.getInstance().getContextPath() + "/luminex/ljPlotIcon.png", 27, 20);
ljPlotsNav.addChild("EC50 - 4PL", String.format(jsFuncCall, protocolId, analyte, titration, "EC504PL"));
ljPlotsNav.addChild("EC50 - 5PL Rumi", String.format(jsFuncCall, protocolId, analyte, titration, "EC505PL"));
if (curveTypes.contains(StatsService.CurveFitType.FOUR_PARAMETER.getLabel()))
ljPlotsNav.addChild("EC50 - 4PL", String.format(jsFuncCall, protocolId, analyte, titration, "EC504PL"));
if (curveTypes.contains(StatsService.CurveFitType.FIVE_PARAMETER.getLabel()))
ljPlotsNav.addChild("EC50 - 5PL Rumi", String.format(jsFuncCall, protocolId, analyte, titration, "EC505PL"));
ljPlotsNav.addChild("AUC", String.format(jsFuncCall, protocolId, analyte, titration, "AUC"));
ljPlotsNav.addChild("High MFI", String.format(jsFuncCall, protocolId, analyte, titration, "HighMFI"));

Expand Down Expand Up @@ -187,8 +190,10 @@ public boolean isFilterable()
defaultCols.add(FieldKey.fromParts("Titration", "Run", "Conjugate"));
defaultCols.add(FieldKey.fromParts("Analyte", "Properties", "LotNumber"));
defaultCols.add(FieldKey.fromParts("GuideSet", "Created"));
defaultCols.add(FieldKey.fromParts(StatsService.CurveFitType.FOUR_PARAMETER.getLabel() + "CurveFit", "EC50"));
defaultCols.add(FieldKey.fromParts(StatsService.CurveFitType.FIVE_PARAMETER.getLabel() + "CurveFit", "EC50"));
if (curveTypes.contains(StatsService.CurveFitType.FOUR_PARAMETER.getLabel()))
defaultCols.add(FieldKey.fromParts(StatsService.CurveFitType.FOUR_PARAMETER.getLabel() + "CurveFit", "EC50"));
if (curveTypes.contains(StatsService.CurveFitType.FIVE_PARAMETER.getLabel()))
defaultCols.add(FieldKey.fromParts(StatsService.CurveFitType.FIVE_PARAMETER.getLabel() + "CurveFit", "EC50"));
defaultCols.add(FieldKey.fromParts("MaxFI"));
defaultCols.add(FieldKey.fromParts("TrapezoidalCurveFit", "AUC"));
setDefaultVisibleColumns(defaultCols);
Expand Down
29 changes: 26 additions & 3 deletions luminex/src/org/labkey/luminex/view/leveyJenningsReport.jsp
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Expand Up @@ -62,7 +62,9 @@
var defaultRowSize = 30;

// local variables for storing the selected graph parameters
var _protocolId, _protocolName, _controlName, _controlType, _analyte, _isotype, _conjugate, _protocolExists = false, _networkExists = false;
var _protocolId, _protocolName, _controlName, _controlType, _analyte, _isotype, _conjugate,
_protocolExists = false, _networkExists = false,
_has4PLCurveFit = false, _has5PLCurveFit = false;

function init()
{
Expand All @@ -87,13 +89,28 @@
return;
}

var getByNameQueryComplete = false, executeSqlQueryComplete = false;
var getByNameQueryComplete = false, executeSqlQueryComplete = false, getCurveFitTypes = false;
var loader = function() {
if (getByNameQueryComplete && executeSqlQueryComplete) {
if (getByNameQueryComplete && executeSqlQueryComplete && getCurveFitTypes) {
initializeReportPanels();
}
};

// Query to see if 4PL and/or 5PL curve fit data exists for this assay
LABKEY.Query.selectDistinctRows({
schemaName: 'assay.Luminex.' + _protocolName,
queryName: 'CurveFit',
column: 'CurveType',
scope: this,
success: function(results){
var curveTypes = results.values;
_has4PLCurveFit = curveTypes.indexOf('Four Parameter') > -1;
_has5PLCurveFit = curveTypes.indexOf('Five Parameter') > -1;
getCurveFitTypes = true;
loader();
}
});

// Query the assay design to check for the required columns for the L-J report and the existance of Network and Protocol columns
LABKEY.Assay.getByName({
name: _protocolName,
Expand Down Expand Up @@ -208,6 +225,8 @@
assayName: _protocolName,
networkExists: _networkExists,
protocolExists: _protocolExists,
has4PLCurveFit: _has4PLCurveFit,
has5PLCurveFit: _has5PLCurveFit,
listeners: {
'currentGuideSetUpdated': function() {
guideSetPanel.toggleExportBtn(false);
Expand All @@ -233,6 +252,8 @@
defaultRowSize: defaultRowSize,
networkExists: _networkExists,
protocolExists: _protocolExists,
has4PLCurveFit: _has4PLCurveFit,
has5PLCurveFit: _has5PLCurveFit,
listeners: {
'reportFilterApplied': function(startDate, endDate, network, networkAny, protocol, protocolAny) {
trendPlotPanel.setTrendPlotLoading();
Expand All @@ -254,6 +275,8 @@
defaultRowSize: defaultRowSize,
networkExists: _networkExists,
protocolExists: _protocolExists,
has4PLCurveFit: _has4PLCurveFit,
has5PLCurveFit: _has5PLCurveFit,
listeners: {
'appliedGuideSetUpdated': function() {
guideSetPanel.toggleExportBtn(false);
Expand Down
Binary file modified luminex/test/sampledata/luminex/TestLuminexAssay.xar
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5 changes: 2 additions & 3 deletions luminex/test/src/org/labkey/test/tests/luminex/LuminexAsyncImportTest.java
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Expand Up @@ -141,7 +141,6 @@ private void reimportLuminexRunPageTwo(String runId, String isotype, String conj
assertFormElementEquals(Locator.name("conjugate"), conjugate);
assertFormElementEquals(Locator.name("stndCurveFitInput"), stndCurveFitInput);
assertFormElementEquals(Locator.name("unkCurveFitInput"), unkCurveFitInput);
uncheckCheckbox(Locator.name("curveFitLogTransform"));
assertFormElementEquals(Locator.name("notebookNo"), notebookNo);
assertFormElementEquals(Locator.name("assayType"), assayType);
assertFormElementEquals(Locator.name("expPerformer"), expPerformer);
Expand Down Expand Up @@ -169,12 +168,12 @@ private void assertLuminexLogInfoPresent()
assertTextPresentInThisOrder("----- Start Run Properties -----", "----- End Run Properties -----");
assertTextPresent("Uploaded Files", "Assay ID", "Isotype", "Conjugate", "Test Date", "Replaces Previous File", "Date file was modified",
"Specimen Type", "Additive", "Derivative", "Subtract Negative Bead", "Calc of Standards", "Calc of Unknown",
"Curve Fit Log", "Notebook Number", "Assay Type", "Experiment Performer", "Calculate Positivity",
"Notebook Number", "Assay Type", "Experiment Performer", "Calculate Positivity",
"Baseline Visit", "Positivity Fold Change");

//Check for Batch Properties
assertTextPresentInThisOrder("----- Start Batch Properties -----", "----- End Batch Properties -----");
assertTextPresent("Participant Visit", "Species", "Lab ID", "Analysis", "Network", "Transform Script Version", "Ruminex Version");
assertTextPresent("Participant Visit", "Species", "Lab ID", "Analysis", "Network", "Transform Script Version");
}

@LogMethod
Expand Down
58 changes: 5 additions & 53 deletions luminex/test/src/org/labkey/test/tests/luminex/LuminexEC50Test.java
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Expand Up @@ -20,14 +20,11 @@
import org.junit.experimental.categories.Category;
import org.labkey.test.BaseWebDriverTest;
import org.labkey.test.Locator;
import org.labkey.test.SortDirection;
import org.labkey.test.categories.Assays;
import org.labkey.test.categories.Daily;
import org.labkey.test.pages.ReactAssayDesignerPage;
import org.labkey.test.util.DataRegionTable;
import org.labkey.test.util.RReportHelper;

import java.io.IOException;
import java.util.List;

import static org.junit.Assert.assertEquals;
Expand All @@ -38,8 +35,7 @@
public class LuminexEC50Test extends LuminexTest
{
private final String EC50_RUN_NAME = "EC50";
private final String rum4 = "Four Parameter";
private final String rum5 = "Five Parameter";
private final String drc4 = "Four Parameter";
private final String trapezoidal = "Trapezoidal";

@BeforeClass
Expand All @@ -58,11 +54,9 @@ public static void updateAssayDefinition()
public void testEC50()
{
LuminexRTransformTest rTransformTest = new LuminexRTransformTest();
rTransformTest.uploadRunWithoutRumiCalc();
rTransformTest.reImportRunWithRumiCalc();
rTransformTest.uploadRun();

createNewAssayRun(TEST_ASSAY_LUM, EC50_RUN_NAME);
checkCheckbox(Locator.name("curveFitLogTransform"));
uploadMultipleCurveData();
clickButton("Save and Finish", longWaitForPage);

Expand All @@ -73,14 +67,6 @@ public void testEC50()
checkEC50dataAndFailureFlag();
}

private boolean checkRversion() throws IOException
{
// quick check to see if we are using 32-bit or 64-bit R
log("Checking R 32-bit vs 64-bit");
RReportHelper _rReportHelper = new RReportHelper(this);
return _rReportHelper.getRScriptOutput(".Machine$sizeof.pointer").contains("[1] 8");
}

private void checkEC50dataAndFailureFlag()
{
// expect to already be viewing CurveFit query
Expand All @@ -98,27 +84,17 @@ private void checkEC50dataAndFailureFlag()
List<String> ec50 = table.getColumnDataAsText("EC50");
List<String> auc= table.getColumnDataAsText("AUC");
List<String> inflectionPoint = table.getColumnDataAsText("Inflection");
int rum5ec50count = 0;

log("Write this");
for(int i=0; i<formula.size(); i++)
{
if(formula.get(i).equals(rum4))
if(formula.get(i).equals(drc4))
{
//ec50=populated=inflectionPoint
assertEquals(ec50.get(i), inflectionPoint.get(i));
//auc=unpopulated
assertEquals(" ", auc.get(i));
}
else if(formula.get(i).equals(rum5))
{
// ec50 will be populated for well formed curves (i.e. not expected for every row, so we'll keep a count and check at the end of the loop)
if (!ec50.get(i).equals(" ") && ec50.get(i).length() > 0)
rum5ec50count++;

// auc should not be populated
assertEquals(" ", auc.get(i));
}
else if(formula.get(i).equals(trapezoidal))
{
//ec50 should not be populated
Expand All @@ -128,30 +104,6 @@ else if(formula.get(i).equals(trapezoidal))
assertTrue( "AUC was unpopulated for row " + i, auc.get(i).length()>0);
}
}
assertEquals("Unexpected number of Five Parameter EC50 values (expected 10 of 14).", 10, rum5ec50count);

// check that the 5PL parameters are within the expected ranges (note: exact values can change based on R 32-bit vs R 64-bit)
// NOTE: the first two EC50s will be significantly different on Mac due to machine episolon. The test is adjusted for this, as these are "blanks" and thus provide the noisiest answers.
Double[] FiveParameterEC50mins = {107.64, 460.75, 36465.56, 21075.08, 7826.89, 32211.66, 44972.77, 107.64, 0.4199, 0.03962};
Double[] FiveParameterEC50maxs = {112.85, 486.5, 36469.5, 21075.29, 7826.90, 32211.67, 45012.09, 112.85, 0.43771, 0.03967};
table.setFilter("CurveType", "Equals", "Five Parameter");
table.setFilter("EC50", "Is Not Blank", "");
table.setSort("EC50", SortDirection.ASC);
table.setSort("AnalyteId", SortDirection.ASC);
table.setSort("TitrationId", SortDirection.ASC);
ec50 = table.getColumnDataAsText("EC50");
assertEquals("Unexpected number of Five Parameter EC50 values (expected " + FiveParameterEC50maxs.length + ")", FiveParameterEC50maxs.length, ec50.size());
for (int i = 0; i < ec50.size(); i++)
{
Double val = Double.parseDouble(ec50.get(i));
Double min = FiveParameterEC50mins[i];
Double max = FiveParameterEC50maxs[i];
Double expected = (max + min) / 2;
Double delta = (max - min) / 2;
assertEquals(String.format("Unexpected 5PL EC50 value for %s - %s", table.getDataAsText(i, "Titration"), table.getDataAsText(i, "Analyte")), expected, val, delta);
}
table.clearFilter("EC50");
table.clearFilter("CurveType");

// expect to already be viewing CurveFit query
assertTextPresent("CurveFit");
Expand All @@ -166,9 +118,9 @@ else if(formula.get(i).equals(trapezoidal))
assertTrue("Unexpected analyte for Four Parameter curve fit failure", values.size() == 1 && values.get(0).equals("ENV6"));
table.clearFilter("CurveType");

// expect four 5PL curve fit failures
// expect no 5PL curve fits
table.setFilter("CurveType", "Equals", "Five Parameter");
assertEquals("Unexpected number of Five Parameter curve fit failure flags", 4, table.getDataRowCount());
assertEquals("Unexpected number of Five Parameter curve fit rows", 0, table.getDataRowCount());
table.clearFilter("CurveType");

table.clearFilter("FailureFlag");
Expand Down
27 changes: 8 additions & 19 deletions luminex/test/src/org/labkey/test/tests/luminex/LuminexGuideSetDisablingTest.java
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Expand Up @@ -133,8 +133,6 @@ private void createValueBasedGuideSet()

metricInputs.put("EC504PLAverage", 42158.22);
metricInputs.put("EC504PLStdDev", 4833.76);
metricInputs.put("EC505PLAverage", 40987.31);
metricInputs.put("EC505PLStdDev", 4280.84);
metricInputs.put("AUCAverage", 85268.04);
metricInputs.put("AUCStdDev", 738.55);
metricInputs.put("MaxFIAverage", 32507.27);
Expand Down Expand Up @@ -187,7 +185,6 @@ public void verifyQCFlagsDisabledOnImport()
clickButtonContainingText("Details", 0);
waitForElement(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC505PLCheckBox"));
click(Locator.checkboxByName("MFICheckBox"));
click(Locator.checkboxByName("AUCCheckBox"));
click(SAVE_BTN);
Expand Down Expand Up @@ -216,24 +213,19 @@ public void verifyQCFlagToggling()
_guideSetHelper.setUpLeveyJenningsGraphParams(RUN_BASED_ANALYTE);
final String plate1_AUC = "64608.73";
final String plate2_AUC = "61889.88";
final String plate1_EC50_5PL = "2.66";
final String plate2_EC50_5PL = "5.67";

validateFlaggedForQC(plate1_EC50_5PL, plate1_AUC, plate2_AUC);
validateFlaggedForQC(plate1_AUC, plate2_AUC);

clickButtonContainingText("Details", 0);
// toggle off the AUC QC flag and then validate errors
waitForElement(Locator.checkboxByName("AUCCheckBox"));
click(Locator.checkboxByName("AUCCheckBox"));
saveGuideSetParameters();

validateFlaggedForQC(plate1_EC50_5PL);

// toggle off the rest of the QC flags and then validate errors
clickButtonContainingText("Details", 0);
waitForElement(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC505PLCheckBox"));
click(Locator.checkboxByName("MFICheckBox"));
saveGuideSetParameters();

Expand All @@ -243,12 +235,11 @@ public void verifyQCFlagToggling()
clickButtonContainingText("Details", 0);
waitForElement(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC504PLCheckBox"));
click(Locator.checkboxByName("EC505PLCheckBox"));
click(Locator.checkboxByName("MFICheckBox"));
click(Locator.checkboxByName("AUCCheckBox"));
saveGuideSetParameters();

validateFlaggedForQC(plate2_AUC, plate1_EC50_5PL, plate1_AUC);
validateFlaggedForQC(plate2_AUC, plate1_AUC);
}

private void saveGuideSetParameters()
Expand Down Expand Up @@ -287,10 +278,9 @@ public void verifyGuideSetParameterDetailsWindow()
clickGuideSetDetailsByComment(RUN_BASED_COMMENT);
validateGuideSetRunDetails("Run-based", "Titration");
validateGuideSetMetricsDetails(new String[][]{
{"5.284", "0.323", "2" },
{"5.339", "0.540", "2" },
{"32086.500", "331.633", "2" },
{"63299.346", "149.318", "2" },
{"5.284", "0.323", "2" }, // EC50 4PL
{"32086.500", "331.633", "2" }, // MFI
{"63299.346", "149.318", "2" }, // AUC
});
// validate checkboxes are not displayed
assertTextPresent("# Runs");
Expand All @@ -301,10 +291,9 @@ public void verifyGuideSetParameterDetailsWindow()
clickGuideSetDetailsByComment(VALUE_BASED_COMMENT);
validateGuideSetRunDetails("Value-based", "Titration");
validateGuideSetMetricsDetails(new String[][]{
{"42158.220", "4833.760"},
{"40987.310", "4280.840"},
{"32507.270", "189.830"},
{"85268.040", "738.550"}
{"42158.220", "4833.760"}, // EC50 4PL
{"32507.270", "189.830"}, // MFI
{"85268.040", "738.550"} // AUC
});
// validate checkboxes are not displayed
assertTextNotPresent("# Runs");
Expand Down
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