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FlowJo 10.8 validation #355

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Mar 4, 2022
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FlowJo 10.8 validation #355

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48 changes: 38 additions & 10 deletions flow/enginesrc/org/labkey/flow/analysis/model/FlowJoWorkspace.java
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Original file line number Diff line number Diff line change
Expand Up @@ -573,7 +573,7 @@ protected void readStat(Element elStat, SubsetSpec subset, @Nullable AttributeSe
{
// FlowJo v9.7 changed attribute 'value' to 'statValue'
String strValue = StringUtils.trimToNull(getAttribute(elStat, "value", "statValue"));
if (strValue != null && !strValue.equals("\ufffd") && !strValue.equals("¥"))
if (strValue != null && !strValue.equals("\ufffd") && !strValue.equals("¥") && !strValue.equals("NaN"))
{
double value;
try
Expand Down Expand Up @@ -789,15 +789,36 @@ public void loadPC_10_0_5() throws Exception
assertPC(workspace, "10.0.5");
}

@Test
public void loadPC_10_8() throws Exception
{
Workspace workspace = loadWorkspace("flow/versions/v10.8.wsp");
assertPC(workspace, "10.8");
}

private void assertPC(Workspace workspace, String version)
{
assertEquals(72, workspace.getSampleCount());
assertEquals(72, workspace._sampleAnalyses.size());
assertEquals(72, workspace._sampleAnalysisResults.size());
assertEquals(2, workspace.getGroups().size());
assertEquals("panel 1", workspace.getGroups().get(1).getGroupName().toString());
assertEquals(72, workspace.getGroups().get(1).getSampleIds().size());
assertEquals(2, workspace.getGroupAnalyses().size());

GroupInfo panel1Group;
if (version.equals("10.8"))
{
assertEquals(3, workspace.getGroups().size());
assertEquals("All Samples", workspace.getGroups().get(0).getGroupName().toString());
assertEquals("Compensation", workspace.getGroups().get(1).getGroupName().toString());
panel1Group = workspace.getGroups().get(2);
}
else
{
assertEquals(2, workspace.getGroups().size());
assertEquals("All Samples", workspace.getGroups().get(0).getGroupName().toString());
panel1Group = workspace.getGroups().get(1);
}
assertEquals("panel 1", panel1Group.getGroupName().toString());
assertEquals(72, panel1Group.getSampleIds().size());
assertEquals(version.equals("10.8") ? 3 : 2, workspace.getGroupAnalyses().size());
assertEquals(11, workspace.getParameterNames().size());
assertEquals(0, workspace.getWarnings().size());

Expand All @@ -819,7 +840,7 @@ private void assertPC(Workspace workspace, String version)
assertEquals(3821, stats.get(new StatisticSpec("Viable/Lymphocytes/CD3+CD4+:Count")).intValue());
assertEquals(33.465, stats.get(new StatisticSpec("Viable/Lymphocytes/CD3+CD4+:Freq_Of_Parent")), 0.001d);
}
else if (version.equals("10.0.5"))
else if (version.equals("10.0.5") || version.equals("10.8"))
{
assertEquals(3811, stats.get(new StatisticSpec("Viable/Lymphocytes/CD3+CD4+:Count")).intValue());
assertEquals(33.194, stats.get(new StatisticSpec("Viable/Lymphocytes/CD3+CD4+:Freq_Of_Parent")), 0.001d);
Expand Down Expand Up @@ -923,6 +944,13 @@ public void loadPCAdvanced_10_4() throws Exception
assertAdvanced(workspace, "10.4.2", false);
}

@Test
public void loadPCAdvanced_10_8() throws Exception
{
Workspace workspace = loadWorkspace("flow/advanced/advanced-v10.8.wsp");
assertAdvanced(workspace, "10.8", false);
}

private boolean isVersionGreaterThan10_0_7(String version)
{
int[] version10_0_7 = new int[]{10, 0, 7};
Expand Down Expand Up @@ -990,7 +1018,7 @@ else if ("10.2".equals(version))
assertTrue(workspace.getWarnings().get(0).contains("Lymphocytes/CD45+: Median statistic value missing"));
assertTrue(workspace.getWarnings().get(1).contains("Lymphocytes/T cells/CD4 T: Coefficient of Variation statistic value missing"));
}
else if ("10.4.2".equals(version))
else if ("10.4.2".equals(version) || "10.8".equals(version))
{
assertEquals(4, workspace.getWarnings().size());
assertTrue(workspace.getWarnings().get(0).contains("Lymphocytes/T cells/CD4 T: Coefficient of Variation statistic value missing"));
Expand All @@ -1004,7 +1032,7 @@ else if ("10.4.2".equals(version))

String windowsSampleId = "2";
String sampleFileName = "931115-B02- Sample 01.fcs";
if ("10.2".equals(version) || "10.4.2".equals(version))
if ("10.2".equals(version) || "10.4.2".equals(version) || "10.8".equals(version))
{
windowsSampleId = "6";
sampleFileName = "931115-C02- Sample 02.fcs";
Expand Down Expand Up @@ -1153,7 +1181,7 @@ else if ("10.0.5".equals(version))
assertEquals(0.0500d, stats.get(new StatisticSpec("Lymphocytes/T cells/CD4 T:Frequency")), 0.001d);
assertEquals(2867.0d, stats.get(new StatisticSpec("A and not B:Count")).intValue(), 0.001d);
}
else if ("10.2".equals(version) || "10.4.2".equals(version))
else if ("10.2".equals(version) || "10.4.2".equals(version) || "10.8".equals(version))
{
assertEquals(105, stats.get(new StatisticSpec("Lymphocytes:Count")).intValue());
assertEquals(1.05d, stats.get(new StatisticSpec("Lymphocytes:Freq_Of_Parent")), 0.001d);
Expand All @@ -1170,7 +1198,7 @@ else if ("10.2".equals(version) || "10.4.2".equals(version))
assertEquals(0.0400d, stats.get(new StatisticSpec("Lymphocytes/T cells/CD4 T:Frequency")), 0.001d);
assertEquals(2616.0d, stats.get(new StatisticSpec("A and not B:Count")).intValue(), 0.001d);
}
else if ("10.0.6".equals(version) || "10.0.7".equals(version) || "10.0.8".equals(version) || "10.2".equals(version))
else if ("10.0.6".equals(version) || "10.0.7".equals(version) || "10.0.8".equals(version))
{
// It's tiresome caring about stat values
assertNotEquals(0, stats.get(new StatisticSpec("Lymphocytes:Count")).intValue());
Expand Down