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bbimberbbimber
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Updates from code inspection (#163)
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‎GenotypeAssays/build.gradle‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
import org.labkey.gradle.util.BuildUtils;
1+
import org.labkey.gradle.util.BuildUtils
22

33
dependencies {
44
BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:LabDevKitModules:LDK", depProjectConfig: "apiJarFile")

‎GenotypeAssays/src/org/labkey/genotypeassays/AlignmentDisplayColumn.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -71,7 +71,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
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Integer analysisId = ctx.get(new FieldKey(getBoundColumn().getFieldKey().getParent(), "analysis_id"), Integer.class);
7272
if (lineages != null)
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{
74-
out.write("<br><a class=\"labkey-text-link\" style=\"max-width: 500px;\" onclick=\"GenotypeAssays.window.EditAlignmentsWindow.editLineage(" + PageFlowUtil.jsString(analysisId.toString()) + "," + PageFlowUtil.jsString(lineages.toString()) + ", " + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + ", " + PageFlowUtil.jsString(filterOperator) + ", " + PageFlowUtil.jsString(String.valueOf(filterVal)) + ");\">");
74+
out.write("<br><a class=\"labkey-text-link\" style=\"max-width: 500px;\" onclick=\"GenotypeAssays.window.EditAlignmentsWindow.editLineage(" + PageFlowUtil.jsString(analysisId.toString()) + "," + PageFlowUtil.jsString(lineages) + ", " + PageFlowUtil.jsString(ctx.getCurrentRegion().getName()) + ", " + PageFlowUtil.jsString(filterOperator) + ", " + PageFlowUtil.jsString(String.valueOf(filterVal)) + ");\">");
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out.write("Edit Lineage</a>");
7676
}
7777
}

‎GenotypeAssays/src/org/labkey/genotypeassays/GeneticsTableCustomizer.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,9 +28,8 @@ public class GeneticsTableCustomizer extends AbstractTableCustomizer implements
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@Override
2929
public void customize(TableInfo table)
3030
{
31-
if (table instanceof AbstractTableInfo)
31+
if (table instanceof AbstractTableInfo ti)
3232
{
33-
AbstractTableInfo ti = (AbstractTableInfo) table;
3433
if (matches(ti, "sequenceanalysis", "sequence_analyses"))
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{
3635
customizeAnalyses(ti);

‎GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -53,6 +53,7 @@ public GenotypeAssaysController()
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@RequiresPermission(ReadPermission.class)
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public class MigrateLegacySSPAction extends ConfirmAction<Object>
5555
{
56+
@Override
5657
public void validateCommand(Object form, Errors errors)
5758
{
5859

@@ -68,6 +69,7 @@ public ModelAndView getConfirmView(Object form, BindException errors) throws Exc
6869
return new HtmlView("This allows an admin to copy any primers stored in the original SSP Assay module into the new genotyping module. Any data has already been copied. Do you want to continue?");
6970
}
7071

72+
@Override
7173
public boolean handlePost(Object form, BindException errors) throws Exception
7274
{
7375
try
@@ -101,6 +103,7 @@ public boolean handlePost(Object form, BindException errors) throws Exception
101103
}
102104
}
103105

106+
@Override
104107
public URLHelper getSuccessURL(Object form)
105108
{
106109
return getContainer().getStartURL(getUser());
@@ -110,6 +113,7 @@ public URLHelper getSuccessURL(Object form)
110113
@RequiresPermission(UpdatePermission.class)
111114
public class CacheAnalysesAction extends MutatingApiAction<CacheAnalysesForm>
112115
{
116+
@Override
113117
public ApiResponse execute(CacheAnalysesForm form, BindException errors)
114118
{
115119
Map<String, Object> resultProperties = new HashMap<>();
@@ -188,6 +192,7 @@ public void setJson(String json)
188192
@RequiresPermission(UpdatePermission.class)
189193
public class CacheHaplotypesAction extends MutatingApiAction<CacheAnalysesForm>
190194
{
195+
@Override
191196
public ApiResponse execute(CacheAnalysesForm form, BindException errors)
192197
{
193198
Map<String, Object> resultProperties = new HashMap<>();

‎GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -23,10 +23,10 @@
2323
public class SSPImportHelper
2424
{
2525
private Map<String, String> _allowableResults = null;
26-
private ExpProtocol _protocol;
27-
private AssayProvider _provider;
28-
private User _u;
29-
private Container _c;
26+
private final ExpProtocol _protocol;
27+
private final AssayProvider _provider;
28+
private final User _u;
29+
private final Container _c;
3030

3131
public SSPImportHelper(ExpProtocol protocol, AssayProvider provider, User u, Container c)
3232
{

‎GenotypeAssays/src/org/labkey/genotypeassays/buttons/HaplotypeReviewButton.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
import org.labkey.api.view.template.ClientDependency;
88
import org.labkey.genotypeassays.GenotypeAssaysModule;
99

10-
import java.util.Arrays;
10+
import java.util.List;
1111

1212
/**
1313
* User: bimber
@@ -18,7 +18,7 @@ public class HaplotypeReviewButton extends SimpleButtonConfigFactory
1818
{
1919
public HaplotypeReviewButton()
2020
{
21-
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Haplotype Review", "GenotypeAssays.buttons.haplotypeHandler(dataRegionName);", Arrays.asList(ClientDependency.supplierFromPath("genotypeassays/buttons.js")));
21+
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Haplotype Review", "GenotypeAssays.buttons.haplotypeHandler(dataRegionName);", List.of(ClientDependency.supplierFromPath("genotypeassays/buttons.js")));
2222
}
2323

2424
@Override

‎GenotypeAssays/src/org/labkey/genotypeassays/buttons/PublishSBTHaplotypesButton.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
import org.labkey.genotypeassays.GenotypeAssaysModule;
77

88
import java.util.Arrays;
9+
import java.util.List;
910

1011
/**
1112
* User: bimber
@@ -16,6 +17,6 @@ public class PublishSBTHaplotypesButton extends SimpleButtonConfigFactory
1617
{
1718
public PublishSBTHaplotypesButton()
1819
{
19-
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Publish/Cache Selected", "GenotypeAssays.window.PublishResultsWindow.haplotypeButtonHandler(dataRegionName);", Arrays.asList(ClientDependency.supplierFromPath("genotypeassays/window/PublishResultsWindow.js")));
20+
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Publish/Cache Selected", "GenotypeAssays.window.PublishResultsWindow.haplotypeButtonHandler(dataRegionName);", List.of(ClientDependency.supplierFromPath("genotypeassays/window/PublishResultsWindow.js")));
2021
}
2122
}

‎GenotypeAssays/src/org/labkey/genotypeassays/buttons/PublishSBTResultsButton.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,6 +6,7 @@
66
import org.labkey.genotypeassays.GenotypeAssaysModule;
77

88
import java.util.Arrays;
9+
import java.util.List;
910

1011
/**
1112
* User: bimber
@@ -16,6 +17,6 @@ public class PublishSBTResultsButton extends SimpleButtonConfigFactory
1617
{
1718
public PublishSBTResultsButton()
1819
{
19-
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Publish/Cache Selected", "GenotypeAssays.window.PublishResultsWindow.buttonHandler(dataRegionName);", Arrays.asList(ClientDependency.supplierFromPath("genotypeassays/window/PublishResultsWindow.js")));
20+
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "Publish/Cache Selected", "GenotypeAssays.window.PublishResultsWindow.buttonHandler(dataRegionName);", List.of(ClientDependency.supplierFromPath("genotypeassays/window/PublishResultsWindow.js")));
2021
}
2122
}

‎GenotypeAssays/src/org/labkey/genotypeassays/buttons/SBTReviewButton.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88
import org.labkey.genotypeassays.GenotypeAssaysModule;
99

1010
import java.util.Arrays;
11+
import java.util.List;
1112

1213
/**
1314
* User: bimber
@@ -18,7 +19,7 @@ public class SBTReviewButton extends SimpleButtonConfigFactory
1819
{
1920
public SBTReviewButton()
2021
{
21-
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "SBT Review", "GenotypeAssays.buttons.sbtReviewHandler(dataRegionName);", Arrays.asList(ClientDependency.supplierFromPath("genotypeassays/buttons.js")));
22+
super(ModuleLoader.getInstance().getModule(GenotypeAssaysModule.class), "SBT Review", "GenotypeAssays.buttons.sbtReviewHandler(dataRegionName);", List.of(ClientDependency.supplierFromPath("genotypeassays/buttons.js")));
2223
}
2324

2425
@Override

‎GenotypeAssays/test/src/org/labkey/test/tests/external/labModules/GenotypeAssaysTest.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ public class GenotypeAssaysTest extends AbstractLabModuleAssayTest
6969
{"Subj1", "gDNA", "1", "3", "method", "3/3/2012", "TestPrimer3", "neg"}
7070
};
7171

72-
private String[][] SSP_PIVOT_DATA = new String[][]{
72+
private final String[][] SSP_PIVOT_DATA = new String[][]{
7373
{"Subject Id","Freezer Id","Lane Number","Method","Sample Date","TestPrimer4","Sequence","TestPrimer1","TestPrimer2","TestPrimer5","Comment"},
7474
{"Subj1","1","1","method","1/2/2011","","atg","POS","","","comment"},
7575
{"Subj1","1","2","method","2/5/2012","+","","pos","Y","IND","comment"},
@@ -108,6 +108,7 @@ private void createSSPPrimers() throws Exception
108108
}
109109
}
110110

111+
@Override
111112
@Test
112113
public void testSteps() throws Exception
113114
{

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