From b21ab574fad2e26ebe5fd3bab764ec2e12de9673 Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Mon, 30 Jun 2025 12:58:04 -0700 Subject: [PATCH 1/4] Fix data region column name references Remove unnecessary logging parameters from CustomizeViewHelper Update CustomizeViewHelper to use FieldKey --- .../test/src/org/labkey/test/tests/OConnorExperimentTest.java | 2 +- .../test/src/org/labkey/test/tests/HaplotypeAssayTest.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java index 559a5877..9ef8d875 100644 --- a/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java +++ b/OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java @@ -146,7 +146,7 @@ protected void verifyExperimentWebpart(int row, String description, @Nullable St assertEquals(description, table.getDataAsText(row, "Description")); if (type != null) { - assertEquals(type, table.getDataAsText(row, "ExperimentType")); + assertEquals(type, table.getDataAsText(row, "ExperimentTypeId")); } // Make sure each component of the ParentExperiments column is rendered with a link to the begin page for that experiment diff --git a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java index 4fe84922..4defc645 100644 --- a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java +++ b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java @@ -286,7 +286,7 @@ private void verifyFirstRun() verifyColumnDataValues(drt, "Animal", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5"); verifyColumnDataValues(drt, "TotalReads", "1000", "2000", "3000", "4000", "5000"); verifyColumnDataValues(drt, "IdentifiedReads", "300", "1000", "600", "2500", "3250"); - verifyColumnDataValues(drt, "%Unknown", "70.0", "50.0", "80.0", "37.5", "35.0"); + verifyColumnDataValues(drt, "PercentUnknown", "70.0", "50.0", "80.0", "37.5", "35.0"); verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001", "A023", "A001", "A004", "A002a"); verifyColumnDataValues(drt, "MHC-AHaplotype2", "A023", "A021", "A001", "A023", "A002a"); verifyColumnDataValues(drt, "MHC-BHaplotype1", "B015c", "B012b", "B001c", "B012b", "B002"); @@ -344,7 +344,7 @@ private void verifySecondRun(String prefix) verifyColumnDataValues(drt, "Animal", "ID-4", "ID-5", "ID-6", "ID-7", "ID-8", "ID-9"); verifyColumnDataValues(drt, "TotalReads", "4000", "5000", "6000", "7000", " ", "0"); verifyColumnDataValues(drt, "IdentifiedReads", "2500", "3250", "3000", "3500", " ", "1"); - verifyColumnDataValues(drt, "%Unknown", "37.5", "35.0", "50.0", "50.0", " ", " "); + verifyColumnDataValues(drt, "PercentUnknown", "37.5", "35.0", "50.0", "50.0", " ", " "); verifyColumnDataValues(drt, prefix+"-AHaplotype1", "A001", " ", "A033", "A004", "A004", "A004"); verifyColumnDataValues(drt, prefix+"-AHaplotype2", "A023", " ", "A033", " ", "A004", "A004"); verifyColumnDataValues(drt, prefix+"-BHaplotype1", "B015c", " ", "B012b", "B033", "B033", "B033"); From 5134f643d94cb2a9c8412a6204d3fb06b245ca3a Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 1 Jul 2025 11:00:32 -0700 Subject: [PATCH 2/4] Fix more column references --- .../org/labkey/test/tests/HaplotypeAssayTest.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java index 4defc645..56193975 100644 --- a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java +++ b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java @@ -287,12 +287,12 @@ private void verifyFirstRun() verifyColumnDataValues(drt, "TotalReads", "1000", "2000", "3000", "4000", "5000"); verifyColumnDataValues(drt, "IdentifiedReads", "300", "1000", "600", "2500", "3250"); verifyColumnDataValues(drt, "PercentUnknown", "70.0", "50.0", "80.0", "37.5", "35.0"); - verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001", "A023", "A001", "A004", "A002a"); - verifyColumnDataValues(drt, "MHC-AHaplotype2", "A023", "A021", "A001", "A023", "A002a"); - verifyColumnDataValues(drt, "MHC-BHaplotype1", "B015c", "B012b", "B001c", "B012b", "B002"); - verifyColumnDataValues(drt, "MHC-BHaplotype2", "B025a", "B017a", "B017a", "B012b", "B002"); + verifyColumnDataValues(drt, "mhcAHaplotype1", "A001", "A023", "A001", "A004", "A002a"); + verifyColumnDataValues(drt, "mhcAHaplotype2", "A023", "A021", "A001", "A023", "A002a"); + verifyColumnDataValues(drt, "mhcBHaplotype1", "B015c", "B012b", "B001c", "B012b", "B002"); + verifyColumnDataValues(drt, "mhcBHaplotype2", "B025a", "B017a", "B017a", "B012b", "B002"); verifyColumnDataValues(drt, "Enabled", "true", "true", "true", "true", "true"); - verifyColumnDataValues(drt, "ClientAnimalId", "x123", "x234", "x345", "x456", "x567"); + verifyColumnDataValues(drt, "AnimalId/ClientAnimalId", "x123", "x234", "x345", "x456", "x567"); // verify concatenated haplotype strings List concatenated = drt.getColumnDataAsText("ConcatenatedHaplotypes"); @@ -307,8 +307,8 @@ private void verifyFirstRun() goToQuery("Animal"); drt = new DataRegionTable("query", this); assertEquals("Unexpected number of Animal records", 5, drt.getDataRowCount()); - verifyColumnDataValues(drt, "Lab Animal Id", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5"); - verifyColumnDataValues(drt, "Client Animal Id", "x123", "x234", "x345", "x456", "x567"); + verifyColumnDataValues(drt, "LabAnimalId", "ID-1", "ID-2", "ID-3", "ID-4", "ID-5"); + verifyColumnDataValues(drt, "ClientAnimalId", "x123", "x234", "x345", "x456", "x567"); verifyHaplotypeRecordsByType(11, 5, 6); } From 04d25ad37131f468a3e4bb728336507ac7be489a Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 1 Jul 2025 14:50:11 -0700 Subject: [PATCH 3/4] missed some --- .../labkey/test/tests/HaplotypeAssayTest.java | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java index 56193975..52a18354 100644 --- a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java +++ b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java @@ -160,10 +160,10 @@ private void verifyAribitraryHaplotypeAssay() clickAndWait(Locator.linkWithText(DRB_RUN)); DataRegionTable drt = new DataRegionTable("Data", this); - verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001", "A023", "A001", "A004", "A002a"); - verifyColumnDataValues(drt, "MHC-AHaplotype2", "A023", "A021", "A001", "A023", "A002a"); - verifyColumnDataValues(drt, "MHC-DRB Haplotype 1", "D025a", "D012b", "D001c", "D012b", "D002"); - verifyColumnDataValues(drt, "MHC-DRB Haplotype 2", "D015c", "D017a", "D017a", "D012b", "D002"); + verifyColumnDataValues(drt, "mhcAHaplotype1", "A001", "A023", "A001", "A004", "A002a"); + verifyColumnDataValues(drt, "mhcAHaplotype2", "A023", "A021", "A001", "A023", "A002a"); + verifyColumnDataValues(drt, "mhcDRBHaplotype1", "D025a", "D012b", "D001c", "D012b", "D002"); + verifyColumnDataValues(drt, "mhcDRBHaplotype2", "D015c", "D017a", "D017a", "D012b", "D002"); importRun(STR_RUN, DRB_ASSAY, STR_RUN_FILE, true); @@ -398,14 +398,14 @@ private void verifyExtraHaplotypeAssignment() waitForElement(Locator.paginationText(1, 39, 39)); // ADD: animal ID-5, haplotype A001 - DataRegionTable.findDataRegion(this).clickInsertNewRow(); + DataRegionTable.DataRegion(getDriver()).find().clickInsertNewRow(); selectOptionByText(Locator.name("quf_HaplotypeId"), "A001"); selectOptionByText(Locator.name("quf_AnimalAnalysisId"), animalAnalysisId); setFormElement(Locator.name("quf_DiploidNumber"), "1"); clickButton("Submit"); // ADD: animal ID-5, haplotype B002 - DataRegionTable.findDataRegion(this).clickInsertNewRow(); + DataRegionTable.DataRegion(getDriver()).find().clickInsertNewRow(); selectOptionByText(Locator.name("quf_HaplotypeId"), "B002"); selectOptionByText(Locator.name("quf_AnimalAnalysisId"), animalAnalysisId); setFormElement(Locator.name("quf_DiploidNumber"), "1"); @@ -416,10 +416,10 @@ private void verifyExtraHaplotypeAssignment() goToAssayRun("first run"); drt = new DataRegionTable("Data", this); drt.setFilter("AnimalId", "Equals", "ID-5"); - verifyColumnDataValues(drt, "MHC-AHaplotype1", "A001"); - verifyColumnDataValues(drt, "MHC-AHaplotype2", "A002a"); - verifyColumnDataValues(drt, "MHC-BHaplotype1", "B002"); - verifyColumnDataValues(drt, "MHC-BHaplotype2", "B002"); + verifyColumnDataValues(drt, "mhcAHaplotype1", "A001"); + verifyColumnDataValues(drt, "mhcAHaplotype2", "A002a"); + verifyColumnDataValues(drt, "mhcBHaplotype1", "B002"); + verifyColumnDataValues(drt, "mhcBHaplotype2", "B002"); drt.clearFilter("AnimalId"); // NOTE: this should clean up what it has done in order to make the test more modular... From ade63d1f3afe42f18a1e9ab257a6a81ef700599e Mon Sep 17 00:00:00 2001 From: labkey-tchad Date: Tue, 1 Jul 2025 15:49:00 -0700 Subject: [PATCH 4/4] More fixes --- .../src/org/labkey/test/tests/HaplotypeAssayTest.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java index 52a18354..21fceee4 100644 --- a/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java +++ b/genotyping/test/src/org/labkey/test/tests/HaplotypeAssayTest.java @@ -325,7 +325,7 @@ private void verifySecondRun() // validate extra column in view DataRegionTable drt = new DataRegionTable("Data", this); - verifyColumnDataValues(drt, "ClientAnimalId", "x456", "x567", "x678", "x789", "x888", "x999"); + verifyColumnDataValues(drt, "AnimalId/ClientAnimalId", "x456", "x567", "x678", "x789", "x888", "x999"); // verify that the animal and haplotype rows were properly inserted goToQuery("Animal"); @@ -345,10 +345,10 @@ private void verifySecondRun(String prefix) verifyColumnDataValues(drt, "TotalReads", "4000", "5000", "6000", "7000", " ", "0"); verifyColumnDataValues(drt, "IdentifiedReads", "2500", "3250", "3000", "3500", " ", "1"); verifyColumnDataValues(drt, "PercentUnknown", "37.5", "35.0", "50.0", "50.0", " ", " "); - verifyColumnDataValues(drt, prefix+"-AHaplotype1", "A001", " ", "A033", "A004", "A004", "A004"); - verifyColumnDataValues(drt, prefix+"-AHaplotype2", "A023", " ", "A033", " ", "A004", "A004"); - verifyColumnDataValues(drt, prefix+"-BHaplotype1", "B015c", " ", "B012b", "B033", "B033", "B033"); - verifyColumnDataValues(drt, prefix+"-BHaplotype2", "B025a", " ", "B012b", "B033", "B033", "B033"); + verifyColumnDataValues(drt, prefix+"AHaplotype1", "A001", " ", "A033", "A004", "A004", "A004"); + verifyColumnDataValues(drt, prefix+"AHaplotype2", "A023", " ", "A033", " ", "A004", "A004"); + verifyColumnDataValues(drt, prefix+"BHaplotype1", "B015c", " ", "B012b", "B033", "B033", "B033"); + verifyColumnDataValues(drt, prefix+"BHaplotype2", "B025a", " ", "B012b", "B033", "B033", "B033"); verifyColumnDataValues(drt, "Enabled", "true", "true", "true", "true", "true", "true"); // verify concatenated haplotype strings