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Auto-refactor lint cleanup
SequencedCollections: get(0) -> getFirst(), etc Add missing @NotNull/@nullable Simplify test assertions Map operation simplification Remove redundant throws clause Switch to parameterized log message C-style array -> Java-style array declaration Delete overridden methods identical to parent Switch statement -> enhanced switch statement Remove redundant imports
1 parent f650db7 commit d7b4d2e

57 files changed

Lines changed: 187 additions & 332 deletions

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‎EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java‎

Lines changed: 2 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323

2424
import static org.junit.Assert.assertEquals;
2525
import static org.junit.Assert.assertFalse;
26+
import static org.junit.Assert.assertNotEquals;
2627
import static org.junit.Assert.assertTrue;
2728
import static org.labkey.test.components.html.Input.Input;
2829

@@ -115,12 +116,6 @@ private void doSetup() throws Exception
115116
goToEHRFolder();
116117
}
117118

118-
@Override
119-
public BrowserType bestBrowser()
120-
{
121-
return BrowserType.CHROME;
122-
}
123-
124119
@Override
125120
protected String getModuleDirectory()
126121
{
@@ -591,8 +586,7 @@ private void assertDemographicsNoRowsHaveStatus(ReactAnimalHistoryPage page, Str
591586
List<String> statusValues = table.getColumnDataAsText("calculated_status");
592587
for (String status : statusValues)
593588
{
594-
assertFalse("Demographics should not contain status '" + excludedStatus + "' but found it",
595-
status.equals(excludedStatus));
589+
assertNotEquals("Demographics should not contain status '" + excludedStatus + "' but found it", status, excludedStatus);
596590
}
597591
}
598592
}

‎EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/model/EHRComplianceDBDomainKind.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
package org.labkey.ehr_compliancedb.model;
22

3+
import org.jetbrains.annotations.NotNull;
34
import org.labkey.api.data.Container;
45
import org.labkey.api.exp.property.Domain;
56
import org.labkey.api.gwt.client.model.GWTPropertyDescriptor;
@@ -42,7 +43,7 @@ public String getKindName()
4243
}
4344

4445
@Override
45-
public Set<String> getReservedPropertyNames(Domain domain, User user)
46+
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
4647
{
4748
return super.getReservedPropertyNames(domain, user);
4849
}

‎EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingContainerListener.java‎

Lines changed: 0 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,6 @@
1616

1717
package org.labkey.ehr_purchasing;
1818

19-
import org.jetbrains.annotations.NotNull;
2019
import org.labkey.api.data.Container;
2120
import org.labkey.api.data.ContainerManager.ContainerListener;
2221
import org.labkey.api.data.DbScope;
@@ -25,16 +24,8 @@
2524
import org.labkey.api.data.TableInfo;
2625
import org.labkey.api.security.User;
2726

28-
import java.beans.PropertyChangeEvent;
29-
import java.util.Collection;
30-
import java.util.Collections;
31-
3227
public class EHR_PurchasingContainerListener implements ContainerListener
3328
{
34-
@Override
35-
public void containerCreated(Container c, User user)
36-
{
37-
}
3829

3930
@Override
4031
public void containerDeleted(Container c, User user)
@@ -68,20 +59,4 @@ public void containerDeleted(Container c, User user)
6859
transaction.commit();
6960
}
7061
}
71-
72-
@Override
73-
public void propertyChange(PropertyChangeEvent evt)
74-
{
75-
}
76-
77-
@Override
78-
public void containerMoved(Container c, Container oldParent, User user)
79-
{
80-
}
81-
82-
@NotNull @Override
83-
public Collection<String> canMove(Container c, Container newParent, User user)
84-
{
85-
return Collections.emptyList();
86-
}
8762
}

‎EHR_SM/src/org/labkey/ehr_sm/EHR_SMContainerListener.java‎

Lines changed: 0 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -16,42 +16,18 @@
1616

1717
package org.labkey.ehr_sm;
1818

19-
import org.jetbrains.annotations.NotNull;
2019
import org.labkey.api.data.Container;
2120
import org.labkey.api.data.ContainerManager.ContainerListener;
2221
import org.labkey.api.data.PropertyManager;
2322
import org.labkey.api.security.User;
24-
import java.util.Collections;
25-
import java.util.Collection;
26-
27-
import java.beans.PropertyChangeEvent;
2823

2924
public class EHR_SMContainerListener implements ContainerListener
3025
{
31-
@Override
32-
public void containerCreated(Container c, User user)
33-
{
34-
}
3526

3627
@Override
3728
public void containerDeleted(Container c, User user)
3829
{
3930
PropertyManager.purgeObjectProperties(c);
4031
}
4132

42-
@Override
43-
public void propertyChange(PropertyChangeEvent evt)
44-
{
45-
}
46-
47-
@Override
48-
public void containerMoved(Container c, Container oldParent, User user)
49-
{
50-
}
51-
52-
@NotNull @Override
53-
public Collection<String> canMove(Container c, Container newParent, User user)
54-
{
55-
return Collections.emptyList();
56-
}
5733
}

‎EHR_SM/src/org/labkey/ehr_sm/EHR_SMCustomizer.java‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -50,7 +50,6 @@ public void customize(TableInfo tableInfo)
5050
if (tableInfo instanceof AbstractTableInfo && props.containsKey(tableInfo.getName()))
5151
{
5252
customizeSamples((AbstractTableInfo) tableInfo);
53-
return;
5453
}
5554
}
5655
}
@@ -111,7 +110,7 @@ private void customizeSamples(AbstractTableInfo ti)
111110

112111
ColumnInfo receivedCol = ti.getColumn(receivedDateCol);
113112
if (null == receivedCol)
114-
_log.warn("Sample type " + ti.getName() + " does not have column " + receivedDateCol + " for age at sample calculation.");
113+
_log.warn("Sample type {} does not have column {} for age at sample calculation.", ti.getName(), receivedDateCol);
115114

116115
TableInfo demographics = QueryService.get().getUserSchema(ti.getUserSchema().getUser(), ContainerService.get().getForPath(ehrContainerName), "study").getTable("demographics");
117116

‎EHR_SM/src/org/labkey/ehr_sm/EHR_SMModule.java‎

Lines changed: 0 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,6 @@
1717
package org.labkey.ehr_sm;
1818

1919
import org.jetbrains.annotations.NotNull;
20-
import org.labkey.api.data.Container;
2120
import org.labkey.api.data.ContainerManager;
2221
import org.labkey.api.module.CodeOnlyModule;
2322
import org.labkey.api.module.ModuleContext;
@@ -56,10 +55,4 @@ public void doStartup(ModuleContext moduleContext)
5655
ContainerManager.addContainerListener(new EHR_SMContainerListener());
5756
}
5857

59-
@Override
60-
@NotNull
61-
public Collection<String> getSummary(Container c)
62-
{
63-
return Collections.emptyList();
64-
}
6558
}

‎Viral_Load_Assay/src/org/labkey/viral_load_assay/ViralLoadCustomizer.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -60,7 +60,7 @@ private void appendVLCol(AbstractTableInfo ti, ColumnInfo subjectCol, ColumnInfo
6060
List<ExpProtocol> protocols = AssayService.get().getAssayProtocols(target, ap);
6161
if (protocols.size() == 1)
6262
{
63-
AssayProtocolSchema schema = ap.createProtocolSchema(ti.getUserSchema().getUser(), target, protocols.get(0), null);
63+
AssayProtocolSchema schema = ap.createProtocolSchema(ti.getUserSchema().getUser(), target, protocols.getFirst(), null);
6464
if (schema == null)
6565
{
6666
return;

‎Viral_Load_Assay/src/org/labkey/viral_load_assay/Viral_Load_AssayModule.java‎

Lines changed: 0 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -52,12 +52,6 @@ public String getName()
5252
return 12.28;
5353
}
5454

55-
@Override
56-
public boolean hasScripts()
57-
{
58-
return true;
59-
}
60-
6155
@Override
6256
@NotNull
6357
protected Collection<WebPartFactory> createWebPartFactories()

‎Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java‎

Lines changed: 2 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -385,8 +385,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
385385

386386
if (TYPE.Standard.equals(category))
387387
{
388-
if (map.get("sampleVol") == null)
389-
map.put("sampleVol", 1);
388+
map.putIfAbsent("sampleVol", 1);
390389

391390
if (!(map.get(QUANTITY_FIELD) instanceof Double))
392391
{
@@ -396,13 +395,8 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
396395
}
397396
else if (TYPE.NEG_CTL.equals(category))
398397
{
399-
if (map.get("sampleVol") == null)
400-
map.put("sampleVol", 1);
398+
map.putIfAbsent("sampleVol", 1);
401399

402-
if (map.get("cp") != null)
403-
{
404-
map.put("qcflag", "NTC had a value for CT");
405-
}
406400
}
407401

408402
for (String field : new String[]{"sampleVol", "volPerRxn", "eluateVol"})

‎Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java‎

Lines changed: 1 addition & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -492,9 +492,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
492492
if (map.get("well") != null) {
493493
map.put("well", ((String) map.get("well")).toUpperCase());
494494
}
495-
if (map.get("sampleType") == null) {
496-
map.put("sampleType", "vRNA");
497-
}
495+
map.putIfAbsent("sampleType", "vRNA");
498496

499497
if (!mergeTemplateRow(keyProperty, templateRows, map, context)) {
500498
continue;

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