diff --git a/EHR_App/test/src/org/labkey/test/tests/EHRAppTestSetupHelper.java b/EHR_App/test/src/org/labkey/test/tests/EHRAppTestSetupHelper.java index 29238d5cf..fcc7953b7 100644 --- a/EHR_App/test/src/org/labkey/test/tests/EHRAppTestSetupHelper.java +++ b/EHR_App/test/src/org/labkey/test/tests/EHRAppTestSetupHelper.java @@ -13,7 +13,6 @@ import java.io.File; import java.io.IOException; import java.util.Arrays; -import java.util.Collections; import java.util.List; import java.util.Map; import java.util.Objects; diff --git a/EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java b/EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java index 5376cb78d..585b7874c 100644 --- a/EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java +++ b/EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java @@ -74,7 +74,7 @@ protected File getStudyPolicyXML() @BeforeClass public static void setupProject() throws Exception { - EHR_AppTest init = (EHR_AppTest) getCurrentTest(); + EHR_AppTest init = getCurrentTest(); init.doSetup(); } diff --git a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/notification/EmployeeComplianceNotification.java b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/notification/EmployeeComplianceNotification.java index fc94cbdcd..0b04f4ebd 100644 --- a/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/notification/EmployeeComplianceNotification.java +++ b/EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/notification/EmployeeComplianceNotification.java @@ -15,15 +15,10 @@ */ package org.labkey.ehr_compliancedb.notification; -import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.apache.commons.lang3.time.DateUtils; -import org.labkey.api.module.ModuleLoader; -import org.labkey.api.module.Module; import org.labkey.api.data.CompareType; -import org.labkey.api.data.Results; import org.labkey.api.data.ColumnInfo; -import org.labkey.api.data.ResultsImpl; import org.labkey.api.data.Selector; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Sort; @@ -36,20 +31,15 @@ import org.labkey.api.query.UserSchema; import org.labkey.api.ldk.notification.AbstractNotification; import org.labkey.api.util.DateUtil; -import org.labkey.ehr_compliancedb.EHR_ComplianceDBModule; -import org.labkey.ehr_compliancedb.EHR_ComplianceDBUserSchema; -import java.util.Date; import java.sql.ResultSet; import java.sql.SQLException; import java.util.Calendar; import java.util.Date; -import java.util.HashMap; import java.util.HashSet; import java.util.Map; import java.util.Set; -import java.util.TreeMap; //Added 3-29-2016 Blasa @@ -153,12 +143,12 @@ private void EmployeeComplianceNotification(Container c, User u, final StringBui msg.append("Employee IDFirst NameLast NameCategoryUnitSupervisorLocation\n"); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException { - msg.append("" + (rs.getString("employeeid") == null ? "" : rs.getString("employeeid")) + "" + rs.getString("firstName") + "" + rs.getString("lastName") + "" + rs.getString("category") + "" + rs.getString("unit") + "" + rs.getString("supervisor") + "" + rs.getString("location")+ "\n"); + msg.append("" + (rs.getString("employeeid") == null ? "" : rs.getString("employeeid")) + "" + rs.getString("firstName") + "" + rs.getString("lastName") + "" + rs.getString("category") + "" + rs.getString("unit") + "" + rs.getString("supervisor") + "" + rs.getString("location") + "\n"); } }); diff --git a/EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingController.java b/EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingController.java index 181af159b..ff398e64e 100644 --- a/EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingController.java +++ b/EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingController.java @@ -36,13 +36,15 @@ public EHR_PurchasingController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { + @Override public ModelAndView getView(Object o, BindException errors) { - return new JspView("/org/labkey/ehr_purchasing/view/hello.jsp"); + return new JspView<>("/org/labkey/ehr_purchasing/view/hello.jsp"); } + @Override public void addNavTrail(NavTree root) { } } } diff --git a/EHR_SM/src/org/labkey/ehr_sm/EHR_SMController.java b/EHR_SM/src/org/labkey/ehr_sm/EHR_SMController.java index 97325b310..5c1706081 100644 --- a/EHR_SM/src/org/labkey/ehr_sm/EHR_SMController.java +++ b/EHR_SM/src/org/labkey/ehr_sm/EHR_SMController.java @@ -48,8 +48,9 @@ public EHR_SMController() } @RequiresPermission(ReadPermission.class) - public class BeginAction extends SimpleViewAction + public static class BeginAction extends SimpleViewAction { + @Override public ModelAndView getView(Object o, BindException errors) { JspView view = new JspView<>("/org/labkey/ehr_sm/view/hello.jsp"); @@ -57,6 +58,7 @@ public ModelAndView getView(Object o, BindException errors) return view; } + @Override public void addNavTrail(NavTree root) { } } @@ -100,6 +102,7 @@ public void setSelectedAnimalSampleTypes(String[] selectedAnimalSampleTypes) @RequiresPermission(AdminPermission.class) public class AdminAction extends FormViewAction { + @Override public void addNavTrail(NavTree root) { } @Override diff --git a/EHR_SM/test/src/org/labkey/test/tests/ehr_sm/EHR_SMTest.java b/EHR_SM/test/src/org/labkey/test/tests/ehr_sm/EHR_SMTest.java index d33cda1c0..1627de90a 100644 --- a/EHR_SM/test/src/org/labkey/test/tests/ehr_sm/EHR_SMTest.java +++ b/EHR_SM/test/src/org/labkey/test/tests/ehr_sm/EHR_SMTest.java @@ -42,7 +42,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException @BeforeClass public static void setupProject() { - EHR_SMTest init = (EHR_SMTest)getCurrentTest(); + EHR_SMTest init = getCurrentTest(); init.doSetup(); } diff --git a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java index a27c5c3a3..71600d53c 100644 --- a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java +++ b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java @@ -162,7 +162,7 @@ public JSONObject getMetadata(ViewContext ctx, ExpProtocol protocol) return meta; } - private class Parser extends DefaultAssayParser + private static class Parser extends DefaultAssayParser { private final Double CYCLE_LIMIT = 45.0; private static final String TASK_FIELD = "Task"; @@ -178,7 +178,7 @@ public Parser(AssayImportMethod method, Container c, User u, int assayId) @Override public Pair saveBatch(JSONObject json, File file, String fileName, ViewContext ctx) throws BatchValidationException { - Integer templateId = json.getInt("TemplateId"); + int templateId = json.getInt("TemplateId"); Pair result = super.saveBatch(json, file, fileName, ctx); @@ -217,7 +217,7 @@ protected String readRawFile(ImportContext context) throws BatchValidationExcept if (!inResults) { - if (row.size() == 0) + if (row.isEmpty()) continue; if (row.get(0).equals("Detector Name")) @@ -229,7 +229,7 @@ protected String readRawFile(ImportContext context) throws BatchValidationExcept if (inDetectors) { String detector = row.get(0); - Map map = new HashMap(); + Map map = new HashMap<>(); map.put("slope", Double.parseDouble(row.get(1))); map.put("intercept", Double.parseDouble(row.get(2))); map.put("rSquared", Double.parseDouble(row.get(3))); @@ -262,7 +262,7 @@ else if (row.get(0).startsWith("Document Name:")) } else { - out.writeNext(row.toArray(new String[row.size()])); + out.writeNext(row.toArray(new String[0])); } } @@ -284,7 +284,7 @@ else if (row.get(0).startsWith("Document Name:")) @Override protected List> processRowsFromFile(List> rows, ImportContext context) throws BatchValidationException { - List> newRows = new ArrayList>(); + List> newRows = new ArrayList<>(); ParserErrors errors = context.getErrors(); //add slope to run info @@ -308,7 +308,7 @@ protected List> processRowsFromFile(List { rowIdx++; Map row = rowsIter.next(); - Map map = new CaseInsensitiveHashMap(row); + Map map = new CaseInsensitiveHashMap<>(row); if (row.size() != 9) { @@ -444,7 +444,7 @@ private void calculateViralLoad(Map map, Double limitOfDetection { Map detectorInfo = _detectorMap.get(map.get(DETECTOR_FIELD)); Double ct = map.get("cp") == null ? null : Double.parseDouble(map.get("cp").toString()); - Double sampleVol = Double.parseDouble(String.valueOf(map.get("sampleVol"))); + double sampleVol = Double.parseDouble(String.valueOf(map.get("sampleVol"))); Double intercept = detectorInfo.get("intercept"); Double slope = detectorInfo.get("slope"); Double volPerRxn = Double.parseDouble(String.valueOf(map.get("volPerRxn"))); @@ -463,14 +463,14 @@ private void calculateViralLoad(Map map, Double limitOfDetection private void calculateViralLoads(List> rows) { - Map>> rowMap = new HashMap>>(); + Map>> rowMap = new HashMap<>(); Double lowestStd = 0.0; for (Map row : rows) { String key = (String)row.get(NAME_FIELD); List> list = rowMap.get(key); if (list == null) - list = new ArrayList>(); + list = new ArrayList<>(); if (TYPE.Standard.getTemplateText().equals(row.get(CATEGORY_FIELD))) { @@ -505,7 +505,7 @@ private void calculateViralLoads(List> rows) avgCopies = avgCopies / list.size(); Double stdDev = new StandardDeviation().evaluate(values); - Double cv = stdDev / avgCopies; + double cv = stdDev / avgCopies; //NOTE: at some point I should make this configurable //flag any record with %CV > 66, but only if at least 1 replicate has copies/rxn above limitOfDetection @@ -573,14 +573,14 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http response.setHeader("Pragma", "private"); response.setHeader("Cache-Control", "private"); - Map rowMap = new HashMap(); + Map rowMap = new HashMap<>(); int rowIdx = 0; for (JSONObject row : results) { rowIdx++; - List fields = new ArrayList(); + List fields = new ArrayList<>(); //build the row Integer wellNum = (Integer)wellMap.get(row.getString("well")); @@ -594,13 +594,13 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http fields.add(type.getTemplateText()); fields.add(TYPE.getQuantity(type, row.getString(SUBJECT_FIELD))); - rowMap.put(wellNum, fields.toArray(new String[fields.size()])); + rowMap.put(wellNum, fields.toArray(new String[0])); } if (errors.hasErrors()) throw errors; - List rows = new ArrayList(); + List rows = new ArrayList<>(); rows.add(new String[]{"*** SDS Setup File Version", "3"}); rows.add(new String[]{"*** Output Plate Size", "96"}); rows.add(new String[]{"*** Output Plate ID", json.getString("templateName") + ".sds"}); @@ -642,8 +642,8 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http private Map> getDetectorsForResults(List results) { - final Map> ret = new HashMap>(); - Set distinctAssays = new HashSet(); + final Map> ret = new HashMap<>(); + Set distinctAssays = new HashSet<>(); for (JSONObject row : results) { distinctAssays.add(row.getString(ASSAYNAME_FIELD)); @@ -651,12 +651,12 @@ private Map> getDetectorsForResults(List TableInfo table = Viral_Load_AssaySchema.getInstance().getSchema().getTable(Viral_Load_AssaySchema.TABLE_ABI7500_DETECTORS); TableSelector ts = new TableSelector(table, new SimpleFilter(FieldKey.fromString("assayName"), distinctAssays, CompareType.IN), null); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException { - Map row = new HashMap(); + Map row = new HashMap<>(); row.put("detector", object.getString("detector")); row.put("reporter", object.getString("reporter")); row.put("quencher", object.getString("quencher")); @@ -673,8 +673,8 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl //ensure each subject/date has at least 2 neg controls JSONObject resultDefaults = json.optJSONObject("Results"); JSONArray rawResults = json.getJSONArray("ResultRows"); - List results = new ArrayList(); - Set distinctWells = new HashSet(); + List results = new ArrayList<>(); + Set distinctWells = new HashSet<>(); Map wellMap = getWellMap96("well_96", "addressbyrow_96"); String[] requiredFields = new String[]{"well", SUBJECT_FIELD, CATEGORY_FIELD, ASSAYNAME_FIELD}; @@ -710,7 +710,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl if (missingRequired) continue; - TYPE type = null; + TYPE type; try { type = TYPE.getByDatabaseCategoryValue(row.getString(CATEGORY_FIELD)); @@ -782,7 +782,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl } Map> detectorRows = getDetectorsForResults(results); - if (detectorRows.size() == 0) + if (detectorRows.isEmpty()) { errors.addRowError(new ValidationException("No detectors were found for these samples.")); throw errors; diff --git a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java index 4d17758fd..9b21ac786 100644 --- a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java +++ b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java @@ -401,10 +401,10 @@ protected void calculateViralLoadForRoche(Map map) map.put("sampleVol", 1.0); //This is the size (ml or mg) of the source material (plasma/serum/urine/etc.) - Double sampleVol = Double.parseDouble(map.get("sampleVol").toString()); + double sampleVol = Double.parseDouble(map.get("sampleVol").toString()); - Double viralLoad = 0.0; - Double dilutionFactor = 0.0; + double viralLoad = 0.0; + double dilutionFactor = 0.0; if (copiesPerRxn != null && sampleVol > 0) { dilutionFactor = (1.0 / sampleVol) * (eluateVol / volPerRxn); @@ -417,8 +417,8 @@ protected void calculateViralLoadForRoche(Map map) } protected class Parser extends DefaultAssayParser { - private String HAS_RESULT = "__hasResult__"; - private int _assayId; + private final String HAS_RESULT = "__hasResult__"; + private final int _assayId; final String[] lookup = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ,.".split(""); //The expected number of columns in the import data private int _expectedColumnCount = Integer.MAX_VALUE; @@ -444,6 +444,7 @@ public Pair saveBatch(JSONObject json, File file, String } //Needs to be overridden within the Parser class of each ImportMethod that extends AbstractWNPRCImportMethod + @Override protected TabLoader getTabLoader(String contents) throws IOException { return null; } @@ -531,6 +532,7 @@ protected List> processRowsFromFile(List return newRows; } + @Override protected void ensureTemplateRowsHaveResults(Map> templateRows, ImportContext context) throws BatchValidationException { for (String key : templateRows.keySet()) { Map row = templateRows.get(key); @@ -563,7 +565,7 @@ private String uncompressUUID(String compressObjectId) { else if (hexString.length() == 2) { hexString = "0" + hexString; } - else if (hexString.length() == 0) { + else if (hexString.isEmpty()) { hexString = "000" + hexString; } @@ -577,19 +579,17 @@ else if (hexString.length() == 0) { } char[] objectId = base16Duples.toString().toCharArray(); - StringBuilder returnObjectId = new StringBuilder(); - - returnObjectId.append(objectId, 0, 8); - returnObjectId.append("-"); - returnObjectId.append(objectId, 8, 4); - returnObjectId.append("-"); - returnObjectId.append(objectId, 12, 4); - returnObjectId.append("-"); - returnObjectId.append(objectId, 16, 4); - returnObjectId.append("-"); - returnObjectId.append(objectId, 20, 12); - - return returnObjectId.toString(); + String returnObjectId = String.valueOf(objectId, 0, 8) + + "-" + + String.valueOf(objectId, 8, 4) + + "-" + + String.valueOf(objectId, 12, 4) + + "-" + + String.valueOf(objectId, 16, 4) + + "-" + + String.valueOf(objectId, 20, 12); + + return returnObjectId; } } diff --git a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java index 581f0d9aa..eda094736 100644 --- a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java +++ b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java @@ -157,7 +157,7 @@ protected void calculateViralLoadForRoche(Map map) if (!map.containsKey("sampleVol")) map.put("sampleVol", 1.0); - Double sampleVol = Double.parseDouble(map.get("sampleVol").toString()); + double sampleVol = Double.parseDouble(map.get("sampleVol").toString()); double viralLoad; if (copiesPerRxn != null) diff --git a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java index 5555add25..9af47f947 100644 --- a/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java +++ b/Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ViralLoadAssayDataProvider.java @@ -110,7 +110,7 @@ public JSONObject getTemplateMetadata(ViewContext ctx) @Override public List getSettingsItems(Container c, User u) { - List items = new ArrayList(); + List items = new ArrayList<>(); String categoryName = "Viral Load Assay"; if (ContainerManager.getSharedContainer().equals(c)) { diff --git a/Viral_Load_Assay/test/src/org/labkey/test/tests/external/labModules/ViralLoadAssayTest.java b/Viral_Load_Assay/test/src/org/labkey/test/tests/external/labModules/ViralLoadAssayTest.java index 1d082b917..67ea26493 100644 --- a/Viral_Load_Assay/test/src/org/labkey/test/tests/external/labModules/ViralLoadAssayTest.java +++ b/Viral_Load_Assay/test/src/org/labkey/test/tests/external/labModules/ViralLoadAssayTest.java @@ -1020,7 +1020,7 @@ private void verifyImportedVLs(int totalRows, Map expected, Da } expectedVals = expected.get(sb.toString()); } - assertNotNull("Unable to find expected values: " + sb.toString(), expectedVals); + assertNotNull("Unable to find expected values: " + sb, expectedVals); assertEquals("Incorrect subjectId on row: " + i, expectedVals[0], subjectId); assertEquals("Incorrect category on row: " + i, expectedVals[1], category); diff --git a/ehr/api-src/org/labkey/api/ehr/EHROwnable.java b/ehr/api-src/org/labkey/api/ehr/EHROwnable.java index 4f731a087..b654cfa0a 100644 --- a/ehr/api-src/org/labkey/api/ehr/EHROwnable.java +++ b/ehr/api-src/org/labkey/api/ehr/EHROwnable.java @@ -26,7 +26,7 @@ */ public abstract class EHROwnable { - protected Module _owner = null; + protected Module _owner; public EHROwnable(Module owner) { diff --git a/ehr/api-src/org/labkey/api/ehr/EHRService.java b/ehr/api-src/org/labkey/api/ehr/EHRService.java index 5203a37a8..03bf17929 100644 --- a/ehr/api-src/org/labkey/api/ehr/EHRService.java +++ b/ehr/api-src/org/labkey/api/ehr/EHRService.java @@ -239,7 +239,7 @@ public enum QCSTATES Scheduled("Scheduled"), Completed("Completed"); - private String _label; + private final String _label; QCSTATES(String label) { diff --git a/ehr/api-src/org/labkey/api/ehr/buttons/MarkCompletedButton.java b/ehr/api-src/org/labkey/api/ehr/buttons/MarkCompletedButton.java index e8c0268f5..5b7852dc1 100644 --- a/ehr/api-src/org/labkey/api/ehr/buttons/MarkCompletedButton.java +++ b/ehr/api-src/org/labkey/api/ehr/buttons/MarkCompletedButton.java @@ -34,7 +34,7 @@ public class MarkCompletedButton extends SimpleButtonConfigFactory protected String _schemaName; protected String _queryName; protected Boolean _forceDateOnlyField; - private Class _perm; + private final Class _perm; public MarkCompletedButton(Module owner, String schemaName, String queryName) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java b/ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java index eac335f6c..ea08bcc5f 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/AbstractFormSection.java @@ -66,7 +66,7 @@ abstract public class AbstractFormSection implements FormSection private List _configSources = new ArrayList<>(); - private List> _clientDependencies = new ArrayList<>(); + private final List> _clientDependencies = new ArrayList<>(); protected static final Logger _log = LogManager.getLogger(AbstractFormSection.class); @@ -195,8 +195,8 @@ public enum TEMPLATE_MODE ENCOUNTER("TEMPLATE_ENCOUNTER", "APPLYFORMTEMPLATE_ENCOUNTER"), NONE(null, null); - private String _formBtn; - private String _sectionBtn; + private final String _formBtn; + private final String _sectionBtn; TEMPLATE_MODE(String sectionBtn, String formBtn) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/BloodDrawFormSection.java b/ehr/api-src/org/labkey/api/ehr/dataentry/BloodDrawFormSection.java index 9866745d9..e0abeb37f 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/BloodDrawFormSection.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/BloodDrawFormSection.java @@ -22,7 +22,7 @@ public class BloodDrawFormSection extends SimpleGridPanel { - boolean _isRequest = false; + boolean _isRequest; public BloodDrawFormSection(boolean isRequest) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/BulkEditFormType.java b/ehr/api-src/org/labkey/api/ehr/dataentry/BulkEditFormType.java index 256932830..756fef798 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/BulkEditFormType.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/BulkEditFormType.java @@ -28,7 +28,7 @@ */ public class BulkEditFormType extends AbstractDataEntryForm { - private String _keyField; + private final String _keyField; protected BulkEditFormType(DataEntryFormContext ctx, Module owner, String name, String label, String category, String keyField, List sections) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java b/ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java index e4c06e657..971e9db6c 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/DefaultDataEntryFormFactory.java @@ -32,7 +32,7 @@ */ public class DefaultDataEntryFormFactory implements DataEntryFormFactory { - private Logger _log = LogManager.getLogger(DefaultDataEntryFormFactory.class); + private final Logger _log = LogManager.getLogger(DefaultDataEntryFormFactory.class); Class _clazz; Module _module; @@ -62,11 +62,11 @@ public DataEntryForm createForm(DataEntryFormContext ctx) /** Implementation for creating instances of {@link TaskForm} variations */ public static class TaskFactory implements DataEntryFormFactory { - private Module _owner; - private String _category; - private String _name; - private String _label; - private List _sections; + private final Module _owner; + private final String _category; + private final String _name; + private final String _label; + private final List _sections; public TaskFactory(Module owner, String category, String name, String label, List sections) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/EncounterForm.java b/ehr/api-src/org/labkey/api/ehr/dataentry/EncounterForm.java index 6d8673431..088db8639 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/EncounterForm.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/EncounterForm.java @@ -45,7 +45,7 @@ protected EncounterForm(DataEntryFormContext ctx, Module owner, String name, Str public static EncounterForm create(DataEntryFormContext ctx, Module owner, String category, String name, String label, List formSections) { - List sections = new ArrayList(); + List sections = new ArrayList<>(); sections.add(new TaskFormSection()); sections.add(new EncounterFormSection()); sections.add(new AnimalDetailsFormSection()); diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/RequestFormSection.java b/ehr/api-src/org/labkey/api/ehr/dataentry/RequestFormSection.java index c50b4bbc4..27925b477 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/RequestFormSection.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/RequestFormSection.java @@ -42,8 +42,8 @@ public JSONObject toJSON(DataEntryFormContext ctx, boolean includeFormElements) { JSONObject ret = super.toJSON(ctx, includeFormElements); - Map formConfig = new HashMap(); - Map bindConfig = new HashMap(); + Map formConfig = new HashMap<>(); + Map bindConfig = new HashMap<>(); bindConfig.put("createRecordOnLoad", true); formConfig.put("bindConfig", bindConfig); ret.put("formConfig", formConfig); diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/SingleQueryFormProvider.java b/ehr/api-src/org/labkey/api/ehr/dataentry/SingleQueryFormProvider.java index 277cb146e..c36fd096c 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/SingleQueryFormProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/SingleQueryFormProvider.java @@ -26,10 +26,10 @@ */ public class SingleQueryFormProvider { - private Module _owner; - private String _schemaName; - private String _queryName; - private SingleQueryFormSection _section; + private final Module _owner; + private final String _schemaName; + private final String _queryName; + private final SingleQueryFormSection _section; public SingleQueryFormProvider(Module owner, String schemaName, String queryName, SingleQueryFormSection section) { diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/forms/ArrivalFormType.java b/ehr/api-src/org/labkey/api/ehr/dataentry/forms/ArrivalFormType.java index a58ef110d..3c6b07458 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/forms/ArrivalFormType.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/forms/ArrivalFormType.java @@ -15,14 +15,11 @@ */ package org.labkey.api.ehr.dataentry.forms; -import org.labkey.api.ehr.dataentry.AnimalDetailsFormSection; import org.labkey.api.ehr.dataentry.DataEntryFormContext; import org.labkey.api.ehr.dataentry.FormSection; import org.labkey.api.ehr.dataentry.TaskForm; -import org.labkey.api.ehr.dataentry.TaskFormSection; import org.labkey.api.module.Module; -import java.util.Arrays; import java.util.List; public class ArrivalFormType extends TaskForm diff --git a/ehr/api-src/org/labkey/api/ehr/dataentry/forms/NewAnimalFormSection.java b/ehr/api-src/org/labkey/api/ehr/dataentry/forms/NewAnimalFormSection.java index f4968135c..8ef04522e 100644 --- a/ehr/api-src/org/labkey/api/ehr/dataentry/forms/NewAnimalFormSection.java +++ b/ehr/api-src/org/labkey/api/ehr/dataentry/forms/NewAnimalFormSection.java @@ -24,7 +24,7 @@ public class NewAnimalFormSection extends SimpleFormSection { - private boolean _allowSetSpecies; + private final boolean _allowSetSpecies; public NewAnimalFormSection(String schemaName, String queryName, String label, boolean allowSetSpecies) { diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/AbstractDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/AbstractDemographicsProvider.java index 8701854fb..796a7f71c 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/AbstractDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/AbstractDemographicsProvider.java @@ -110,7 +110,7 @@ public Map> getProperties(DefaultSchema defaultSchem if (debugEnabled) startRowProcessing = LocalDateTime.now(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -118,7 +118,7 @@ public void exec(ResultSet object) throws SQLException Results rs = new ResultsImpl(object, cols); String id = ti.getColumn("Id").getStringValue(rs); - Map map = ret.computeIfAbsent(id, (x)->new TreeMap<>()); + Map map = ret.computeIfAbsent(id, (x) -> new TreeMap<>()); processRow(rs, cols, map); } }); @@ -209,7 +209,7 @@ protected Sort getSort() protected Map getColumns(TableInfo ti) { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("Id")); keys.addAll(getFieldKeys()); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveAssignmentsDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveAssignmentsDemographicsProvider.java index 3bce93eda..09e259dac 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveAssignmentsDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveAssignmentsDemographicsProvider.java @@ -39,7 +39,7 @@ public ActiveAssignmentsDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveCasesDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveCasesDemographicsProvider.java index ea513de51..596f94b99 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveCasesDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveCasesDemographicsProvider.java @@ -39,7 +39,7 @@ public ActiveCasesDemographicsProvider(Module module) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("objectid")); keys.add(FieldKey.fromString("Id")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveFlagsDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveFlagsDemographicsProvider.java index e463285f2..2717d54f7 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveFlagsDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveFlagsDemographicsProvider.java @@ -39,7 +39,7 @@ public ActiveFlagsDemographicsProvider(Module module) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveProblemsDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveProblemsDemographicsProvider.java index e8345d484..7ad3e7b8e 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveProblemsDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveProblemsDemographicsProvider.java @@ -40,7 +40,7 @@ public ActiveProblemsDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveTreatmentsDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveTreatmentsDemographicsProvider.java index 587055609..8ea289ee9 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/ActiveTreatmentsDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/ActiveTreatmentsDemographicsProvider.java @@ -42,7 +42,7 @@ public ActiveTreatmentsDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("code")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/BirthDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/BirthDemographicsProvider.java index 024c7cb36..e3e5f3a78 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/BirthDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/BirthDemographicsProvider.java @@ -39,7 +39,7 @@ public BirthDemographicsProvider(Module owner) @Override protected Set getFieldKeys() { - Set keys = new HashSet(); + Set keys = new HashSet<>(); keys.add(FieldKey.fromString("lsid")); keys.add(FieldKey.fromString("Id")); keys.add(FieldKey.fromString("date")); diff --git a/ehr/api-src/org/labkey/api/ehr/demographics/WeightsDemographicsProvider.java b/ehr/api-src/org/labkey/api/ehr/demographics/WeightsDemographicsProvider.java index df9f2d58d..d30b59394 100644 --- a/ehr/api-src/org/labkey/api/ehr/demographics/WeightsDemographicsProvider.java +++ b/ehr/api-src/org/labkey/api/ehr/demographics/WeightsDemographicsProvider.java @@ -79,7 +79,7 @@ public Map> getProperties(DefaultSchema defaultSchem ts.setForDisplay(true); ts.setMaxRows(3); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -87,7 +87,7 @@ public void exec(ResultSet object) throws SQLException Results rs = new ResultsImpl(object, cols); String id = ti.getColumn("Id").getStringValue(rs); - Map map = ret.computeIfAbsent(id, (x)->new HashMap<>()); + Map map = ret.computeIfAbsent(id, (x) -> new HashMap<>()); processRow(rs, cols, map); } }); diff --git a/ehr/api-src/org/labkey/api/ehr/history/AbstractDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/AbstractDataSource.java index f1f1d442a..a5c251ac9 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/AbstractDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/AbstractDataSource.java @@ -59,11 +59,11 @@ */ abstract public class AbstractDataSource extends EHROwnable implements HistoryDataSource { - private String _schema; - private String _query; + private final String _schema; + private final String _query; private String _categoryText; private String _primaryGroup; - private String _name; + private final String _name; private boolean _showTime = false; protected String _subjectIdField = "Id"; protected static final Logger _log = LogManager.getLogger(HistoryDataSource.class); diff --git a/ehr/api-src/org/labkey/api/ehr/history/AntibioticSensitivityLabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/AntibioticSensitivityLabworkType.java index d6edf158b..1b45d73b0 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/AntibioticSensitivityLabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/AntibioticSensitivityLabworkType.java @@ -85,7 +85,7 @@ protected String getLine(Results rs, boolean redacted) throws SQLException protected Map> getRows(TableSelector ts, final Collection cols, final boolean redacted) { final Map>> rows = new CaseInsensitiveHashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultAlopeciaDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultAlopeciaDataSource.java index 266c69cff..8f01ab199 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultAlopeciaDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultAlopeciaDataSource.java @@ -36,11 +36,10 @@ public DefaultAlopeciaDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Alopecia Score", "score")); - sb.append(safeAppend(rs, "Cause", "cause")); + String sb = safeAppend(rs, "Alopecia Score", "score") + + safeAppend(rs, "Cause", "cause"); - return sb.toString(); + return sb; } } diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultAnimalRecordFlagDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultAnimalRecordFlagDataSource.java index 7e73e1ca8..fb91a3bbe 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultAnimalRecordFlagDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultAnimalRecordFlagDataSource.java @@ -38,11 +38,10 @@ public DefaultAnimalRecordFlagDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Remark", "remark")); - sb.append(safeAppend(rs, "Entered by", "performedby")); - return sb.toString(); + String sb = safeAppend(rs, "Remark", "remark") + + safeAppend(rs, "Entered by", "performedby"); + return sb; } @Override diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultArrivalDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultArrivalDataSource.java index 3ce362dc6..0f8ea3a3a 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultArrivalDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultArrivalDataSource.java @@ -38,12 +38,11 @@ public DefaultArrivalDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Source", "source/value")); - sb.append(safeAppend(rs, "Rearing Type", "rearingType/value")); - sb.append(safeAppend(rs, "Acquisition Type", "acquisitionType/value")); - sb.append(safeAppend(rs, "Remark", "remark")); - return sb.toString(); + String sb = safeAppend(rs, "Source", "source/value") + + safeAppend(rs, "Rearing Type", "rearingType/value") + + safeAppend(rs, "Acquisition Type", "acquisitionType/value") + + safeAppend(rs, "Remark", "remark"); + return sb; } @Override diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultCasesCloseDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultCasesCloseDataSource.java index 98493171a..ae36207bd 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultCasesCloseDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultCasesCloseDataSource.java @@ -53,13 +53,12 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx { return null; } - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Category", "category")); - sb.append(safeAppend(rs, "Case #", "caseno")); - sb.append("Opened On: ").append(DateUtil.formatDate(c, start)); + String sb = safeAppend(rs, "Category", "category") + + safeAppend(rs, "Case #", "caseno") + + "Opened On: " + DateUtil.formatDate(c, start); - return sb.toString(); + return sb; } @Override diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultDrugsDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultDrugsDataSource.java index ea83dc873..d71d90ead 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultDrugsDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultDrugsDataSource.java @@ -116,9 +116,8 @@ protected Set getColumnNames() Map> groupedRowMap = new HashMap<>(); for (HistoryRow r : rows) { - if (r instanceof HistoryRowImpl) + if (r instanceof HistoryRowImpl row) { - HistoryRowImpl row = (HistoryRowImpl)r; String key = row.getSubjectId() + "<>" + row.getSortDateString() + "<>" + row.getTimeString(); List existing = groupedRowMap.get(key); diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java index 45b87f8cb..59a1307a4 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultLabworkType.java @@ -63,9 +63,9 @@ public class DefaultLabworkType implements LabworkType protected String _performedByField = "performedby"; protected String _remarkField = "remark"; - private String _name; - private String _schemaName; - private String _queryName; + private final String _name; + private final String _schemaName; + private final String _queryName; protected String _testIdField = "testid"; protected String _resultField = "result"; @@ -190,7 +190,7 @@ protected Map> getResults(Container c, User u, SimpleFilter protected Map> getRows(TableSelector ts, final Collection cols, final boolean redacted) { final Map> rows = new CaseInsensitiveHashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -349,10 +349,9 @@ protected String getTestId(Results rs) throws SQLException protected String getResultTable(List results) { - StringBuilder sb = new StringBuilder(); - sb.append(""); - sb.append(""); - sb.append("
").append(StringUtils.join(results, "
")).append("
"); - return sb.toString(); + String sb = "" + + "" + + "
" + StringUtils.join(results, "
") + "
"; + return sb; } } diff --git a/ehr/api-src/org/labkey/api/ehr/history/DefaultProblemListCloseDataSource.java b/ehr/api-src/org/labkey/api/ehr/history/DefaultProblemListCloseDataSource.java index fd8df6d00..217a1d6cd 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/DefaultProblemListCloseDataSource.java +++ b/ehr/api-src/org/labkey/api/ehr/history/DefaultProblemListCloseDataSource.java @@ -54,12 +54,10 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx return null; } - StringBuilder sb = new StringBuilder(); + String sb = safeAppend(rs, "Category", "category") + + "Opened On: " + DateUtil.formatDate(c, start); - sb.append(safeAppend(rs, "Category", "category")); - sb.append("Opened On: ").append(DateUtil.formatDate(c, start)); - - return sb.toString(); + return sb; } @Override diff --git a/ehr/api-src/org/labkey/api/ehr/history/HistoryRowImpl.java b/ehr/api-src/org/labkey/api/ehr/history/HistoryRowImpl.java index d81ca760b..e50e06645 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/HistoryRowImpl.java +++ b/ehr/api-src/org/labkey/api/ehr/history/HistoryRowImpl.java @@ -29,14 +29,14 @@ */ public class HistoryRowImpl implements HistoryRow { - private HistoryDataSource _source; - private String _subjectId; - private Date _date; + private final HistoryDataSource _source; + private final String _subjectId; + private final Date _date; private Date _enddate; private Integer _projectId; - private String _primaryGroup; - private String _categoryText; - private String _categoryColor; + private final String _primaryGroup; + private final String _categoryText; + private final String _categoryColor; private String _performedBy; private String _caseId; private String _runId; @@ -44,11 +44,11 @@ public class HistoryRowImpl implements HistoryRow private String _qcStateLabel; private Boolean _isPublicData; private Boolean _showTime = false; - private String _taskId = null; - private Integer _taskRowId; - private String _formType; - private String _objectId; - private String _html; + private String _taskId; + private final Integer _taskRowId; + private final String _formType; + private final String _objectId; + private final String _html; protected static final Logger _log = LogManager.getLogger(HistoryRowImpl.class); diff --git a/ehr/api-src/org/labkey/api/ehr/history/SerologyLabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/SerologyLabworkType.java index 3972063c5..0cf2a1d74 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/SerologyLabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/SerologyLabworkType.java @@ -31,9 +31,9 @@ */ public class SerologyLabworkType extends DefaultLabworkType { - private String _sampleTypeField = "tissue/meaning"; - private String _methodField = "method"; - private String _numericResultsField = "numericresult"; + private final String _sampleTypeField = "tissue/meaning"; + private final String _methodField = "method"; + private final String _numericResultsField = "numericresult"; public SerologyLabworkType(Module module) { diff --git a/ehr/api-src/org/labkey/api/ehr/history/SortingLabworkType.java b/ehr/api-src/org/labkey/api/ehr/history/SortingLabworkType.java index 38c15fc0d..3bcbb8acd 100644 --- a/ehr/api-src/org/labkey/api/ehr/history/SortingLabworkType.java +++ b/ehr/api-src/org/labkey/api/ehr/history/SortingLabworkType.java @@ -44,9 +44,9 @@ */ public class SortingLabworkType extends DefaultLabworkType { - private String _testType; - private String _testCol = "testid"; - private String _sortCol = "sort_order"; + private final String _testType; + private final String _testCol = "testid"; + private final String _sortCol = "sort_order"; private Map _tests = null; @@ -66,7 +66,7 @@ private Map loadTests(boolean forceRefresh) _tests = new CaseInsensitiveHashMap<>(); TableSelector ts = new TableSelector(ti, PageFlowUtil.set(_sortCol, _testCol), new SimpleFilter(FieldKey.fromString("type"), _testType), null); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -84,7 +84,7 @@ public void exec(ResultSet rs) throws SQLException protected Map> getRows(TableSelector ts, final Collection cols, final boolean redacted) { final Map>> rows = new CaseInsensitiveHashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException diff --git a/ehr/api-src/org/labkey/api/ehr/security/EHRSecurityEscalator.java b/ehr/api-src/org/labkey/api/ehr/security/EHRSecurityEscalator.java index 512e77bec..8bb412098 100644 --- a/ehr/api-src/org/labkey/api/ehr/security/EHRSecurityEscalator.java +++ b/ehr/api-src/org/labkey/api/ehr/security/EHRSecurityEscalator.java @@ -79,7 +79,6 @@ protected SecurityEscalationAuditProvider.SecurityEscalationEvent getNewSecurity * specified here. * @param comment A useful comment explaining why the user needed to be escalated, or rather, what the code is doing * during the escalation. For example: "Updating - * @return */ public static SecurityEscalator beginEscalation(User user, Container container, String comment) { SecurityEscalator securityEscalator = new EHRSecurityEscalator(user, container, comment); diff --git a/ehr/api-src/org/labkey/api/ehr/table/AssignedAtTimeForeignKey.java b/ehr/api-src/org/labkey/api/ehr/table/AssignedAtTimeForeignKey.java index 702987f3e..163a1b6f4 100644 --- a/ehr/api-src/org/labkey/api/ehr/table/AssignedAtTimeForeignKey.java +++ b/ehr/api-src/org/labkey/api/ehr/table/AssignedAtTimeForeignKey.java @@ -34,9 +34,9 @@ public class AssignedAtTimeForeignKey extends LookupForeignKey { private static final Logger _log = LogManager.getLogger(AssignedAtTimeForeignKey.class); - private AbstractTableInfo _tableInfo; - private ColumnInfo _pkCol; - private UserSchema _ehrSchema; + private final AbstractTableInfo _tableInfo; + private final ColumnInfo _pkCol; + private final UserSchema _ehrSchema; public AssignedAtTimeForeignKey(AbstractTableInfo tableInfo, ColumnInfo pkCol, UserSchema ehrSchema) { @@ -66,7 +66,7 @@ public TableInfo getLookupTableInfo() List errors = new ArrayList<>(); TableInfo ti = qd.getTable(errors, true); - if (errors.size() > 0) + if (!errors.isEmpty()) { _log.error("Error creating lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); for (QueryException error : errors) diff --git a/ehr/api-src/org/labkey/api/ehr/table/AssignmentAtTimeForeignKey.java b/ehr/api-src/org/labkey/api/ehr/table/AssignmentAtTimeForeignKey.java index 6a0a7e273..cdf84af10 100644 --- a/ehr/api-src/org/labkey/api/ehr/table/AssignmentAtTimeForeignKey.java +++ b/ehr/api-src/org/labkey/api/ehr/table/AssignmentAtTimeForeignKey.java @@ -34,11 +34,11 @@ public class AssignmentAtTimeForeignKey extends LookupForeignKey { private static final Logger _log = LogManager.getLogger(AssignmentAtTimeForeignKey.class); - private AbstractTableInfo _tableInfo; - private ColumnInfo _pkCol; - private UserSchema _ehrSchema; - private String _dateColName; - private String _investLastNameCol; + private final AbstractTableInfo _tableInfo; + private final ColumnInfo _pkCol; + private final UserSchema _ehrSchema; + private final String _dateColName; + private final String _investLastNameCol; public AssignmentAtTimeForeignKey(AbstractTableInfo tableInfo, ColumnInfo pkCol, UserSchema ehrSchema, String dateColName, String investLastNameCol) { @@ -73,7 +73,7 @@ public TableInfo getLookupTableInfo() List errors = new ArrayList<>(); TableInfo ti = qd.getTable(errors, true); - if (errors.size() > 0) + if (!errors.isEmpty()) { _log.error("Error creating lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); for (QueryException error : errors) diff --git a/ehr/src/org/labkey/ehr/EHRActionResolver.java b/ehr/src/org/labkey/ehr/EHRActionResolver.java index 5b95ab307..ca0affeb8 100644 --- a/ehr/src/org/labkey/ehr/EHRActionResolver.java +++ b/ehr/src/org/labkey/ehr/EHRActionResolver.java @@ -42,7 +42,7 @@ protected SpringActionController.HTMLFileActionResolver getHTMLFileActionResolve return new EHRHTMLFileActionResolver(); } - private class EHRHTMLFileActionResolver extends SpringActionController.HTMLFileActionResolver + private static class EHRHTMLFileActionResolver extends SpringActionController.HTMLFileActionResolver { public EHRHTMLFileActionResolver() { diff --git a/ehr/src/org/labkey/ehr/EHRController.java b/ehr/src/org/labkey/ehr/EHRController.java index 12d3aef2a..b41bbfe6d 100644 --- a/ehr/src/org/labkey/ehr/EHRController.java +++ b/ehr/src/org/labkey/ehr/EHRController.java @@ -154,7 +154,7 @@ public void setIncludeFormElements(boolean includeFormElements) } @RequiresPermission(ReadPermission.class) - public class GetDataEntryItemsAction extends ReadOnlyApiAction + public static class GetDataEntryItemsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(GetDataEntryItemsForm form, BindException errors) @@ -191,7 +191,7 @@ public void setIncludeAll(boolean includeAll) } @RequiresPermission(AdminPermission.class) - public class CacheLivingAnimalsAction extends ConfirmAction + public static class CacheLivingAnimalsAction extends ConfirmAction { @Override public void validateCommand(CacheLivingAnimalsForm form, Errors errors) @@ -220,7 +220,7 @@ public boolean handlePost(CacheLivingAnimalsForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class PrimeDataEntryCacheAction extends ConfirmAction + public static class PrimeDataEntryCacheAction extends ConfirmAction { @Override public void validateCommand(Object form, Errors errors) @@ -275,7 +275,7 @@ public void setRequestIds(String[] requestIds) } @RequiresPermission(DeletePermission.class) - public class DiscardFormAction extends MutatingApiAction + public static class DiscardFormAction extends MutatingApiAction { @Override public ApiResponse execute(DiscardFormForm form, BindException errors) @@ -358,7 +358,7 @@ public void setQueryUpdateURL(boolean queryUpdateURL) } @RequiresPermission(UpdatePermission.class) - public class UpdateQueryAction extends SimpleViewAction + public static class UpdateQueryAction extends SimpleViewAction { private EHRQueryForm _form; @@ -590,7 +590,7 @@ public void setIds(String[] ids) } @RequiresPermission(ReadPermission.class) - public class GetDemographicsAction extends ReadOnlyApiAction + public static class GetDemographicsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(GetDemographicsForm form, BindException errors) @@ -624,7 +624,7 @@ public ApiResponse execute(GetDemographicsForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class SetGeneticCalculationTaskSettingsAction extends MutatingApiAction + public static class SetGeneticCalculationTaskSettingsAction extends MutatingApiAction { @Override public ApiResponse execute(ScheduleGeneticCalculationForm form, BindException errors) @@ -673,7 +673,7 @@ public void setHourOfDay(int hourOfDay) } @RequiresPermission(AdminPermission.class) - public class SetRecordDeleteSettingsAction extends MutatingApiAction + public static class SetRecordDeleteSettingsAction extends MutatingApiAction { @Override public ApiResponse execute(RecordDeleteForm form, BindException errors) @@ -733,13 +733,13 @@ public void setIncludeFlags(boolean includeFlags) } @RequiresPermission(ReadPermission.class) - public class GetAnimalDetailsAction extends ReadOnlyApiAction + public static class GetAnimalDetailsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(AnimalDetailsForm form, BindException errors) { - Map props = new HashMap(); - Set sources = new HashSet(); + Map props = new HashMap<>(); + Set sources = new HashSet<>(); if (form.isIncludeAssignment()) sources.add("assignment"); if (form.isIncludeFlags()) @@ -814,7 +814,7 @@ public void setAllowImportDuringBusinessHours(boolean allowImportDuringBusinessH } @RequiresPermission(AdminPermission.class) - public class GetGeneticCalculationTaskSettingsAction extends ReadOnlyApiAction + public static class GetGeneticCalculationTaskSettingsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(ScheduleGeneticCalculationForm form, BindException errors) @@ -836,7 +836,7 @@ public ApiResponse execute(ScheduleGeneticCalculationForm form, BindException er } @RequiresPermission(AdminPermission.class) - public class GetRecordDeleteSettingsAction extends ReadOnlyApiAction + public static class GetRecordDeleteSettingsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Object form, BindException errors) @@ -865,7 +865,7 @@ public void setRunId(String[] runId) } @RequiresPermission(ReadPermission.class) - public class GetLabResultSummary extends ReadOnlyApiAction + public static class GetLabResultSummary extends ReadOnlyApiAction { @Override public ApiResponse execute(LabResultSummaryForm form, BindException errors) @@ -981,7 +981,7 @@ public void setIncludeDistinctTypes(boolean includeDistinctTypes) @RequiresPermission(ReadPermission.class) //TODO: should enable @CSRF if we have SSRS updated to pass token. - public class GetClinicalHistoryAction extends ReadOnlyApiAction + public static class GetClinicalHistoryAction extends ReadOnlyApiAction { @Override public ApiResponse execute(HistoryForm form, BindException errors) @@ -1025,7 +1025,7 @@ public ApiResponse execute(HistoryForm form, BindException errors) } @RequiresPermission(ReadPermission.class) - public class GetCaseHistoryAction extends ReadOnlyApiAction + public static class GetCaseHistoryAction extends ReadOnlyApiAction { @Override public ApiResponse execute(HistoryForm form, BindException errors) @@ -1089,7 +1089,7 @@ public void setRebuildIndexes(boolean rebuildIndexes) } @RequiresPermission(AdminPermission.class) - public class EnsureDatasetPropertiesAction extends ConfirmAction + public static class EnsureDatasetPropertiesAction extends ConfirmAction { @Override public void validateCommand(EnsureDatasetPropertiesForm form, Errors errors) @@ -1115,7 +1115,7 @@ public ModelAndView getConfirmView(EnsureDatasetPropertiesForm form, BindExcepti msg.append("\t").append(message).append("
"); } - if (messages.size() > 0) + if (!messages.isEmpty()) msg.append("
Do you want to make these changes?"); else msg.append("There are no changes to be made"); @@ -1132,7 +1132,7 @@ public boolean handlePost(EnsureDatasetPropertiesForm form, BindException errors } @RequiresPermission(AdminPermission.class) - public class EnsureEHRSchemaIndexesAction extends ConfirmAction + public static class EnsureEHRSchemaIndexesAction extends ConfirmAction { @Override public void validateCommand(Object form, Errors errors) @@ -1166,7 +1166,7 @@ public boolean handlePost(Object form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class EnsureQcStatesAction extends ConfirmAction + public static class EnsureQcStatesAction extends ConfirmAction { @Override public void validateCommand(Object form, Errors errors) @@ -1192,7 +1192,7 @@ public ModelAndView getConfirmView(Object form, BindException errors) msg.append("\t").append(message).append("
"); } - if (messages.size() > 0) + if (!messages.isEmpty()) msg.append("
Do you want to make these changes?"); else msg.append("There are no changes to be made"); @@ -1209,7 +1209,7 @@ public boolean handlePost(Object form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class VerifyDatasetResourcesAction extends SimpleViewAction + public static class VerifyDatasetResourcesAction extends SimpleViewAction { public void validateCommand(Object form, Errors errors) { @@ -1233,7 +1233,7 @@ public ModelAndView getView(Object form, BindException errors) msg.append("\t").append(message).append("
"); } - if (messages.size() == 0) + if (messages.isEmpty()) msg.append("There are no missing files"); return new HtmlView(msg.toString()); @@ -1247,7 +1247,7 @@ public void addNavTrail(NavTree tree) } @RequiresPermission(AdminPermission.class) - public class DoGeneticCalculationsAction extends ConfirmAction + public static class DoGeneticCalculationsAction extends ConfirmAction { @Override public void validateCommand(Object form, Errors errors) @@ -1340,7 +1340,7 @@ public void setLookup(String lookup) } } - private abstract class BaseLookupsAction extends MutatingApiAction + private abstract static class BaseLookupsAction extends MutatingApiAction { protected final String _manifestDirectory = "data/"; protected final String _manifestDefault = "lookupsManifest"; @@ -1568,7 +1568,7 @@ public Object execute(PopulateLookupsForm form, BindException errors) throws Exc } @RequiresPermission(AdminPermission.class) - public class PopulateReportsAction extends MutatingApiAction + public static class PopulateReportsAction extends MutatingApiAction { private final String _reportsPath = "reports/reports.tsv"; private final String _additionalReportsPath = "reports/additionalReports.tsv"; @@ -1718,7 +1718,7 @@ public void setLinkTypes(String[] linkTypes) } @RequiresPermission(ReadPermission.class) - public class GetReportLinksAction extends ReadOnlyApiAction + public static class GetReportLinksAction extends ReadOnlyApiAction { @Override public ApiResponse execute(ReportLinkForm form, BindException errors) @@ -1820,12 +1820,12 @@ public void setQueryName(String queryName) } @RequiresPermission(ReadPermission.class) - public class GetDataEntryFormDetailsAction extends ReadOnlyApiAction + public static class GetDataEntryFormDetailsAction extends ReadOnlyApiAction { @Override public ApiResponse execute(EnterDataForm form, BindException errors) { - Map props = new HashMap(); + Map props = new HashMap<>(); if (form.getFormType() == null && form.getTaskId() == null && form.getRequestId() == null) { @@ -1874,7 +1874,7 @@ public ApiResponse execute(EnterDataForm form, BindException errors) } @RequiresPermission(EHRDataEntryPermission.class) - public class DataEntryFormAction extends SimpleViewAction + public static class DataEntryFormAction extends SimpleViewAction { private String _title = null; private DataEntryForm _def; @@ -1911,7 +1911,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(EHRDataEntryPermission.class) - public class DataEntryFormForQueryAction extends SimpleViewAction + public static class DataEntryFormForQueryAction extends SimpleViewAction { private String _title = null; @@ -1951,7 +1951,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(EHRDataEntryPermission.class) - public class DataEntryFormJsonForQueryAction extends ReadOnlyApiAction + public static class DataEntryFormJsonForQueryAction extends ReadOnlyApiAction { @Override public ApiResponse execute(EnterDataForm form, BindException errors) @@ -2073,7 +2073,7 @@ public void setLivingAnimalsOnly(Boolean livingAnimalsOnly) } @RequiresPermission(UpdatePermission.class) - public class ManageFlagsAction extends MutatingApiAction + public static class ManageFlagsAction extends MutatingApiAction { @Override public ApiResponse execute(ManageFlagsForm form, BindException errors) @@ -2185,7 +2185,7 @@ public List getIdList() } @RequiresPermission(ReadPermission.class) - public class BloodPlotDataAction extends ReadOnlyApiAction + public static class BloodPlotDataAction extends ReadOnlyApiAction { @Override @@ -2235,7 +2235,7 @@ public ApiResponse execute(IdForm idForm, BindException errors) } @RequiresPermission(AdminPermission.class) - public class ValidateDatasetColsAction extends ConfirmAction + public static class ValidateDatasetColsAction extends ConfirmAction { @Override public void validateCommand(Object form, Errors errors) @@ -2297,7 +2297,7 @@ public boolean handlePost(Object form, BindException errors) @RequiresPermission(ReadPermission.class) - public class GetAnimalLockAction extends ReadOnlyApiAction + public static class GetAnimalLockAction extends ReadOnlyApiAction { @Override public ApiResponse execute(Object form, BindException errors) @@ -2307,7 +2307,7 @@ public ApiResponse execute(Object form, BindException errors) } @RequiresPermission(EHRDataEntryPermission.class) - public class SetAnimalLockAction extends MutatingApiAction + public static class SetAnimalLockAction extends MutatingApiAction { @Override public ApiResponse execute(LockAnimalForm form, BindException errors) diff --git a/ehr/src/org/labkey/ehr/EHRManager.java b/ehr/src/org/labkey/ehr/EHRManager.java index 724110f07..1396e319c 100644 --- a/ehr/src/org/labkey/ehr/EHRManager.java +++ b/ehr/src/org/labkey/ehr/EHRManager.java @@ -364,7 +364,7 @@ public List ensureStudyQCStates(Container c, final User u, final boolean } } - if (commitChanges && toUpdate.size() > 0) + if (commitChanges && !toUpdate.isEmpty()) { Table.update(u, studyTable, toUpdate, s.getContainer().getId()); shouldClearCache = true; @@ -1131,7 +1131,7 @@ private void updatePropertyURI(Domain d, PropertyDescriptor pd) throws SQLExcept } } - if (oldIds.size() == 0) + if (oldIds.isEmpty()) { //this should not happen throw new SQLException("Unexpected: propertyId " + pd.getPropertyURI() + " does not exists for domain: " + d.getTypeURI()); @@ -1251,27 +1251,27 @@ public int discardTask(Container c, User u, String taskId) throws SQLException // forEachMap is much more efficient than iterating ResultSet and calling ResultSetUtil.mapRow(rs) TableSelector ts = new TableSelector(ti, colNames, filter, null); - ts.forEachMap(new Selector.ForEachBlock>() + ts.forEachMap(new Selector.ForEachBlock<>() { @Override public void exec(Map map) { - Map row = new CaseInsensitiveHashMap<>(); - row.putAll(map); + Map row = new CaseInsensitiveHashMap<>(); + row.putAll(map); - if (row.containsKey("requestid") && row.get("requestid") != null) - { - row.put("requestid", null); - row.put("qcstate", null); - row.put("taskid", null); - row.put("qcstateLabel", "Request: Approved"); + if (row.containsKey("requestid") && row.get("requestid") != null) + { + row.put("requestid", null); + row.put("qcstate", null); + row.put("taskid", null); + row.put("qcstateLabel", "Request: Approved"); - requestsToQueue.add(row); - } - else - { - keysToDelete.add(row); - } + requestsToQueue.add(row); + } + else + { + keysToDelete.add(row); + } } }); @@ -1402,7 +1402,7 @@ public Collection ensureFlagActive(User u, Container c, String flag, Dat filter.addCondition(FieldKey.fromString("date"), date, CompareType.DATE_LTE); TableSelector ts = new TableSelector(flagsTable, PageFlowUtil.set("lsid", "Id", "date", "enddate", "remark"), filter, null); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -1444,7 +1444,7 @@ public void exec(ResultSet rs) throws SQLException } BatchValidationException errors = new BatchValidationException(); - if (rows.size() > 0) + if (!rows.isEmpty()) flagsTable.getUpdateService().insertRows(u, flagsTable.getUserSchema().getContainer(), rows, errors, null, getExtraContext()); if (errors.hasErrors()) @@ -1498,7 +1498,7 @@ public Collection terminateFlagsIfExists(User u, Container c, String fla filter.addCondition(FieldKey.fromString("Id"), animalIds, CompareType.IN); filter.addCondition(FieldKey.fromString("isActive"), true); TableSelector ts = new TableSelector(flagsTable, PageFlowUtil.set("lsid", "Id", "date", "enddate", "remark"), filter, null); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -1517,7 +1517,7 @@ public void exec(ResultSet rs) throws SQLException try { - if (rows.size() > 0) + if (!rows.isEmpty()) { BatchValidationException batchValidationException = new BatchValidationException(); flagsTable.getUpdateService().updateRows(u, flagsTable.getUserSchema().getContainer(), rows, oldKeys, batchValidationException, null, getExtraContext()); @@ -1539,7 +1539,7 @@ public void exec(ResultSet rs) throws SQLException public Map getExtraContext() { - Map map = new HashMap(); + Map map = new HashMap<>(); map.put("quickValidation", true); map.put("generatedByServer", true); @@ -1604,7 +1604,7 @@ public List validateDatasetCols(Container c, User u, File xml) throws IO return ret; } - private String LOCK_PROP_KEY = getClass().getName() + "||animalLock"; + private final String LOCK_PROP_KEY = getClass().getName() + "||animalLock"; public void lockAnimalCreation(Container c, User u, Boolean lock, Integer startingId, Integer idCount) { diff --git a/ehr/src/org/labkey/ehr/EHRProperties.java b/ehr/src/org/labkey/ehr/EHRProperties.java index 084fe4f32..8a14d0f26 100644 --- a/ehr/src/org/labkey/ehr/EHRProperties.java +++ b/ehr/src/org/labkey/ehr/EHRProperties.java @@ -26,7 +26,7 @@ */ public class EHRProperties { - static private String URI = "urn:ehr.labkey.org/#"; + static private final String URI = "urn:ehr.labkey.org/#"; public static SystemProperty REMARK = new SystemProperty(URI + "Remark", PropertyType.MULTI_LINE) { diff --git a/ehr/src/org/labkey/ehr/EHRUpgradeCode.java b/ehr/src/org/labkey/ehr/EHRUpgradeCode.java index 648248889..52b3b172c 100644 --- a/ehr/src/org/labkey/ehr/EHRUpgradeCode.java +++ b/ehr/src/org/labkey/ehr/EHRUpgradeCode.java @@ -44,7 +44,7 @@ public void populateCalendar(final ModuleContext moduleContext) throws SQLExcept PreparedStatement stmt = transaction.getConnection().prepareStatement( "INSERT INTO ehr_lookups.calendar\n" + "\t(TargetDateTime, TargetDate, Year, Month, Day, DayAfter)\n" + - "\tVALUES (?, ?, ?, ?, ?, ?)");) + "\tVALUES (?, ?, ?, ?, ?, ?)")) { while (cal.get(Calendar.YEAR) < 2030) { diff --git a/ehr/src/org/labkey/ehr/buttons/LocationEditButton.java b/ehr/src/org/labkey/ehr/buttons/LocationEditButton.java index 811d8a611..e3747cec9 100644 --- a/ehr/src/org/labkey/ehr/buttons/LocationEditButton.java +++ b/ehr/src/org/labkey/ehr/buttons/LocationEditButton.java @@ -15,15 +15,10 @@ */ package org.labkey.ehr.buttons; -import org.labkey.api.ehr.buttons.EHRShowEditUIButton; import org.labkey.api.ehr.security.EHRLocationEditPermission; -import org.labkey.api.ehr.security.EHRProjectEditPermission; import org.labkey.api.ldk.buttons.ShowEditUIButton; import org.labkey.api.module.Module; -import java.util.HashMap; -import java.util.Map; - /** */ diff --git a/ehr/src/org/labkey/ehr/buttons/ProcedureEditButton.java b/ehr/src/org/labkey/ehr/buttons/ProcedureEditButton.java index 9a8cfb097..3e2e2bd4f 100644 --- a/ehr/src/org/labkey/ehr/buttons/ProcedureEditButton.java +++ b/ehr/src/org/labkey/ehr/buttons/ProcedureEditButton.java @@ -17,8 +17,6 @@ import org.labkey.api.ehr.buttons.EHRShowEditUIButton; import org.labkey.api.ehr.security.EHRProcedureManagementPermission; -import org.labkey.api.ehr.security.EHRProjectEditPermission; -import org.labkey.api.ldk.buttons.ShowEditUIButton; import org.labkey.api.module.Module; import java.util.HashMap; diff --git a/ehr/src/org/labkey/ehr/buttons/ProjectEditButton.java b/ehr/src/org/labkey/ehr/buttons/ProjectEditButton.java index c3509b7d8..282f382ad 100644 --- a/ehr/src/org/labkey/ehr/buttons/ProjectEditButton.java +++ b/ehr/src/org/labkey/ehr/buttons/ProjectEditButton.java @@ -17,8 +17,6 @@ import org.labkey.api.ehr.buttons.EHRShowEditUIButton; import org.labkey.api.ehr.security.EHRProjectEditPermission; -import org.labkey.api.ehr.security.EHRProtocolEditPermission; -import org.labkey.api.ldk.buttons.ShowEditUIButton; import org.labkey.api.module.Module; import java.util.HashMap; diff --git a/ehr/src/org/labkey/ehr/buttons/ProtocolEditButton.java b/ehr/src/org/labkey/ehr/buttons/ProtocolEditButton.java index d6fae9266..9886637fb 100644 --- a/ehr/src/org/labkey/ehr/buttons/ProtocolEditButton.java +++ b/ehr/src/org/labkey/ehr/buttons/ProtocolEditButton.java @@ -17,7 +17,6 @@ import org.labkey.api.ehr.buttons.EHRShowEditUIButton; import org.labkey.api.ehr.security.EHRProtocolEditPermission; -import org.labkey.api.ldk.buttons.ShowEditUIButton; import org.labkey.api.module.Module; import java.util.HashMap; diff --git a/ehr/src/org/labkey/ehr/dataentry/DataEntryManager.java b/ehr/src/org/labkey/ehr/dataentry/DataEntryManager.java index 781cefc90..0d364ef6e 100644 --- a/ehr/src/org/labkey/ehr/dataentry/DataEntryManager.java +++ b/ehr/src/org/labkey/ehr/dataentry/DataEntryManager.java @@ -56,9 +56,9 @@ public class DataEntryManager { private static final DataEntryManager _instance = new DataEntryManager(); private static final Logger _log = LogManager.getLogger(DataEntryManager.class); - private List _forms = new ArrayList<>(); - private Map> _defaultFieldKeys = new HashMap<>(); - private List _queryProviders = new ArrayList<>(); + private final List _forms = new ArrayList<>(); + private final Map> _defaultFieldKeys = new HashMap<>(); + private final List _queryProviders = new ArrayList<>(); private final Cache _cache; private DataEntryManager() @@ -205,10 +205,10 @@ public void primeCachesForContainer(Container c, User u) public static class DataEntryFormContextImpl implements DataEntryFormContext { - private User _user; - private Container _container; - private Map _tableMap = new HashMap<>(); - private Map _userSchemas = new HashMap<>(); + private final User _user; + private final Container _container; + private final Map _tableMap = new HashMap<>(); + private final Map _userSchemas = new HashMap<>(); private Map _datasetMap = null; public DataEntryFormContextImpl(Container c, User u) diff --git a/ehr/src/org/labkey/ehr/dataentry/RecordDeleteRunner.java b/ehr/src/org/labkey/ehr/dataentry/RecordDeleteRunner.java index ea72de8c2..b094197d7 100644 --- a/ehr/src/org/labkey/ehr/dataentry/RecordDeleteRunner.java +++ b/ehr/src/org/labkey/ehr/dataentry/RecordDeleteRunner.java @@ -150,7 +150,7 @@ private void deleteRecordsFromTable(TableInfo ti, String pkField) } _log.info("deleting " + keys.size() + " records from table: " + ti.getName() + " in container: " + ti.getUserSchema().getContainer().getPath()); - ti.getUpdateService().deleteRows(ti.getUserSchema().getUser(), ti.getUserSchema().getContainer(), keys, null, new HashMap()); + ti.getUpdateService().deleteRows(ti.getUserSchema().getUser(), ti.getUserSchema().getContainer(), keys, null, new HashMap<>()); } } catch (BatchValidationException | InvalidKeyException | QueryUpdateServiceException | SQLException e) diff --git a/ehr/src/org/labkey/ehr/dataentry/SingleQueryForm.java b/ehr/src/org/labkey/ehr/dataentry/SingleQueryForm.java index 741a9196f..5d001bfbc 100644 --- a/ehr/src/org/labkey/ehr/dataentry/SingleQueryForm.java +++ b/ehr/src/org/labkey/ehr/dataentry/SingleQueryForm.java @@ -35,7 +35,7 @@ */ public class SingleQueryForm extends AbstractDataEntryForm { - private TableInfo _table; + private final TableInfo _table; private SingleQueryForm(DataEntryFormContext ctx, Module owner, String name, String label, String category, TableInfo ti, List sections) { diff --git a/ehr/src/org/labkey/ehr/demographics/AnimalRecordImpl.java b/ehr/src/org/labkey/ehr/demographics/AnimalRecordImpl.java index 16464c8ea..3e0bc8e0f 100644 --- a/ehr/src/org/labkey/ehr/demographics/AnimalRecordImpl.java +++ b/ehr/src/org/labkey/ehr/demographics/AnimalRecordImpl.java @@ -230,7 +230,7 @@ private List> getListProperty(String prop) public String getCurrentRoom() { List> housing = getActiveHousing(); - if (housing != null && housing.size() > 0) + if (housing != null && !housing.isEmpty()) return (String)housing.get(0).get("room"); return null; @@ -240,7 +240,7 @@ public String getCurrentRoom() public String getCurrentCage() { List> housing = getActiveHousing(); - if (housing != null && housing.size() > 0) + if (housing != null && !housing.isEmpty()) return (String)housing.get(0).get("cage"); return null; @@ -300,7 +300,7 @@ public Date getMostRecentArrival() if (_props.containsKey("source")) { List> rows = (List)_props.get("source"); - if (rows.size() > 0) + if (!rows.isEmpty()) return (Date)rows.get(0).get("date"); } diff --git a/ehr/src/org/labkey/ehr/history/ClinicalHistoryManager.java b/ehr/src/org/labkey/ehr/history/ClinicalHistoryManager.java index b1ce77a96..9455ffd51 100644 --- a/ehr/src/org/labkey/ehr/history/ClinicalHistoryManager.java +++ b/ehr/src/org/labkey/ehr/history/ClinicalHistoryManager.java @@ -42,7 +42,7 @@ public class ClinicalHistoryManager private static final ClinicalHistoryManager _instance = new ClinicalHistoryManager(); private static final Logger _log = LogHelper.getLogger(ClinicalHistoryManager.class, "Management of clinical history data providers"); - private List _dataSources = new ArrayList<>(); + private final List _dataSources = new ArrayList<>(); private ClinicalHistoryManager() { @@ -104,7 +104,7 @@ public List getHistory(Container c, User u, String subjectId, String public void sortRowsByDate(List rows) { - Collections.sort(rows, new Comparator() + Collections.sort(rows, new Comparator<>() { @Override public int compare(HistoryRow o1, HistoryRow o2) diff --git a/ehr/src/org/labkey/ehr/history/DefaultDeliveryDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultDeliveryDataSource.java index 66ab9d741..6f04e5305 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultDeliveryDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultDeliveryDataSource.java @@ -39,14 +39,13 @@ public DefaultDeliveryDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Delivery Type", "deliveryType/value")); - sb.append(safeAppend(rs, "Sire", "sire")); - sb.append(safeAppend(rs, "Infant", "infant")); - sb.append(safeAppend(rs, "Remark", "remark")); + String sb = safeAppend(rs, "Delivery Type", "deliveryType/value") + + safeAppend(rs, "Sire", "sire") + + safeAppend(rs, "Infant", "infant") + + safeAppend(rs, "Remark", "remark"); - return sb.toString(); + return sb; } @Override diff --git a/ehr/src/org/labkey/ehr/history/DefaultEncountersDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultEncountersDataSource.java index 0cd6e2436..2f5940d44 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultEncountersDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultEncountersDataSource.java @@ -123,7 +123,7 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx } } - if (sb.length() > 0) + if (!sb.isEmpty()) { return sb.toString(); } @@ -164,9 +164,8 @@ protected Map>> getSnomedTags(Containe SimpleFilter newFilter = new SimpleFilter(); for (SimpleFilter.FilterClause fc : filter.getClauses()) { - if (fc instanceof CompareType.CompareClause) + if (fc instanceof CompareType.CompareClause cc) { - CompareType.CompareClause cc = (CompareType.CompareClause)fc; Object val = (cc.getParamVals() != null && cc.getParamVals().length > 0) ? cc.getParamVals()[0] : null; FieldKey fk = FieldKey.fromParts(FieldKey.fromString("recordid"), cc.getFieldKeys().get(0)); newFilter.addCondition(fk, val, cc.getCompareType()); @@ -188,7 +187,7 @@ protected Map>> getSnomedTags(Containe TableSelector ts = new TableSelector(snomed, columns.values(), newFilter, null); final Map>> snomedMap = new HashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException diff --git a/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java index 220d7e80c..6e8ae1f12 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultLabworkDataSource.java @@ -150,7 +150,7 @@ public Map> getFlags(Container c, User u, String id, Date m TableSelector ts = new TableSelector(ti, PageFlowUtil.set("parentid", "flag", "value"), filter, null); final Map> map = new HashMap<>(); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/ehr/src/org/labkey/ehr/history/DefaultObservationsDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultObservationsDataSource.java index 8ce214904..a2958b3f9 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultObservationsDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultObservationsDataSource.java @@ -89,7 +89,7 @@ protected List processRows(Container c, TableSelector ts, final bool //onprc issue 2324: because items within a task can have different times, the assumption of grouping on taskid can break. therefore group based on full date/time Date roundedDate = DateUtils.truncate((Date)rowMap.get("date"), Calendar.MINUTE); - String key = results.getString(FieldKey.fromString("taskid")) + "||" + rowMap.get("Id") + "||" + rowMap.get("categoryText") + "||" + rowMap.get("categoryGroup") + "||" + roundedDate.toString(); + String key = results.getString(FieldKey.fromString("taskid")) + "||" + rowMap.get("Id") + "||" + rowMap.get("categoryText") + "||" + rowMap.get("categoryGroup") + "||" + roundedDate; List> obsRows = idMap.get(key); if (obsRows == null) obsRows = new ArrayList<>(); @@ -192,7 +192,7 @@ else if (!EHRManager.OBS_CATEGORY_OBSERVATIONS.equals(category)) if (rs.getString(FieldKey.fromString("remark")) != null) { - if (sb.length() > 0) + if (!sb.isEmpty()) sb.append(". "); sb.append(rs.getString(FieldKey.fromString("remark"))); } @@ -205,7 +205,7 @@ else if (!EHRManager.OBS_CATEGORY_OBSERVATIONS.equals(category)) sb.append(""); } - if (sb.length() > 0) + if (!sb.isEmpty()) sb.append("\n"); return sb.toString(); diff --git a/ehr/src/org/labkey/ehr/history/DefaultPregnanciesDataSource.java b/ehr/src/org/labkey/ehr/history/DefaultPregnanciesDataSource.java index 826e92200..a7506a7ba 100644 --- a/ehr/src/org/labkey/ehr/history/DefaultPregnanciesDataSource.java +++ b/ehr/src/org/labkey/ehr/history/DefaultPregnanciesDataSource.java @@ -39,14 +39,13 @@ public DefaultPregnanciesDataSource(Module module) @Override protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException { - StringBuilder sb = new StringBuilder(); - sb.append(safeAppend(rs, "Sire", "sire")); - sb.append(safeAppend(rs, "Confirmation Type", "confirmationType/value")); - sb.append(safeAppend(rs, "Estimated Delivery Date", "estDeliveryDate")); - sb.append(safeAppend(rs, "Remark", "remark")); + String sb = safeAppend(rs, "Sire", "sire") + + safeAppend(rs, "Confirmation Type", "confirmationType/value") + + safeAppend(rs, "Estimated Delivery Date", "estDeliveryDate") + + safeAppend(rs, "Remark", "remark"); - return sb.toString(); + return sb; } @Override diff --git a/ehr/src/org/labkey/ehr/history/LabworkManager.java b/ehr/src/org/labkey/ehr/history/LabworkManager.java index 0fac8c87e..38202aa1d 100644 --- a/ehr/src/org/labkey/ehr/history/LabworkManager.java +++ b/ehr/src/org/labkey/ehr/history/LabworkManager.java @@ -18,10 +18,7 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.ehr.history.LabworkType; -import org.labkey.api.module.Module; import org.labkey.api.security.User; -import org.labkey.api.util.Pair; -import org.labkey.ehr.EHRServiceImpl; import java.util.ArrayList; import java.util.Collection; @@ -40,7 +37,7 @@ public class LabworkManager { private static final LabworkManager _instance = new LabworkManager(); - private List _types = new ArrayList<>(); + private final List _types = new ArrayList<>(); private LabworkManager() { diff --git a/ehr/src/org/labkey/ehr/notification/DataEntrySummary.java b/ehr/src/org/labkey/ehr/notification/DataEntrySummary.java index 36a9fcf48..a1ed5672c 100644 --- a/ehr/src/org/labkey/ehr/notification/DataEntrySummary.java +++ b/ehr/src/org/labkey/ehr/notification/DataEntrySummary.java @@ -108,7 +108,7 @@ protected void getRequestSummary(Container c, final User u, StringBuilder msg, S if (tsRequest.exists()) { hasRequests = true; - tsRequest.forEach(new Selector.ForEachBlock() + tsRequest.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -156,7 +156,7 @@ protected void getTaskSummary(Container c, final User u, StringBuilder msg, Set< if (tsTasks.exists()) { hasTasks = true; - tsTasks.forEach(new Selector.ForEachBlock() + tsTasks.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException diff --git a/ehr/src/org/labkey/ehr/notification/OverdueWeightsNotification.java b/ehr/src/org/labkey/ehr/notification/OverdueWeightsNotification.java index 50f650160..76f5fa4ee 100644 --- a/ehr/src/org/labkey/ehr/notification/OverdueWeightsNotification.java +++ b/ehr/src/org/labkey/ehr/notification/OverdueWeightsNotification.java @@ -91,7 +91,6 @@ public String getMessageBodyHTML(Container c, User u) /** * find animals not weighed in the past 60 days - * @param msg */ private void animalsNotWeightedInPast60Days(Container c, User u, StringBuilder msg) { @@ -187,7 +186,8 @@ private void getLivingWithoutWeight(final Container c, User u, final StringBuild if (ts.getRowCount() > 0) { msg.append("WARNING: The following animals do not have a weight:
\n"); - ts.forEach(new TableSelector.ForEachBlock(){ + ts.forEach(new TableSelector.ForEachBlock<>() + { @Override public void exec(ResultSet rs) throws SQLException { diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java index 40efb24d7..076698360 100644 --- a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java +++ b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java @@ -255,7 +255,7 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL()) "\tVALUES (?, ?, ?, ?, ?, ?, ?, ?)")) { log.info("Inserting rows"); - String line = null; + String line; int lineNum = 0; while ((line = reader.readLine()) != null) { diff --git a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsInitTask.java b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsInitTask.java index d028fa5c7..188125ddc 100644 --- a/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsInitTask.java +++ b/ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsInitTask.java @@ -142,13 +142,13 @@ public RecordedActionSet run() throws PipelineJobException long count = ts.getRowCount(); if (count > 0) { - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException { String[] row = new String[]{rs.getString("Id"), rs.getString("Dam"), rs.getString("Sire"), rs.getString("Gender"), rs.getString("Species")}; - for (int i=0;i errors = new ArrayList<>(); TableInfo ti = qd.getTable(errors, true); - if (errors.size() > 0 || ti == null) + if (!errors.isEmpty() || ti == null) { _log.warn("Error creating housing at time lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); for (QueryException e : errors) @@ -1712,7 +1711,7 @@ public TableInfo getLookupTableInfo() List errors = new ArrayList<>(); TableInfo ti = qd.getTable(errors, true); - if (errors.size() > 0) + if (!errors.isEmpty()) { _log.warn("Error creating survivorship lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); for (QueryException e : errors) @@ -1871,7 +1870,7 @@ public TableInfo getLookupTableInfo() List errors = new ArrayList<>(); TableInfo ti = qd.getTable(errors, true); - if (errors.size() > 0) + if (!errors.isEmpty()) { _log.warn("Error creating age at time lookup table for: " + schemaName + "." + queryName + " in container: " + targetSchema.getContainer().getPath()); for (QueryException e : errors) diff --git a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java index 73ca925ae..6231a2e08 100644 --- a/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java +++ b/ehr/src/org/labkey/ehr/utils/TriggerScriptHelper.java @@ -824,6 +824,7 @@ public void createDemographicsRecord(String id, Map props, public void updateDemographicsRecord(List> updatedRows) throws QueryUpdateServiceException, SQLException, BatchValidationException, InvalidKeyException { // updatedRows object may be a JS array where isEmpty() isn't reliable, so use size() == 0 instead + //noinspection SizeReplaceableByIsEmpty if (updatedRows == null || updatedRows.size() == 0) return; @@ -936,7 +937,7 @@ public String[] validateBloodAdditionalServices(String services, String tubeType return null; List testNames = Arrays.asList(StringUtils.split(services, ",;")); - if (testNames.size() == 0) + if (testNames.isEmpty()) return null; Map> serviceMap = getBloodDrawServicesMap(); @@ -981,13 +982,13 @@ public String[] validateBloodAdditionalServices(String services, String tubeType } } - if (msgs.size() == 0) + if (msgs.isEmpty()) { return null; } else { - return msgs.toArray(new String[msgs.size()]); + return msgs.toArray(new String[0]); } } @@ -1124,7 +1125,7 @@ private String checkOtherDrawsQuantity(String id, Date date, String rowObjectId, filter.addCondition(FieldKey.fromString("countsAgainstVolume"), true); // Don't pull database records that may be old versions of records that are changing in this transaction - if (ignoredObjectIds.size() > 0) + if (!ignoredObjectIds.isEmpty()) { filter.addCondition(FieldKey.fromString("objectid"), ignoredObjectIds, CompareType.NOT_IN); } @@ -1485,7 +1486,7 @@ public void sendRequestStateEmail(final String label, final List request { String subject = "EHR " + formtype + " " + label; Set recipients = getRecipients(notify1, notify2, notify3); - if (recipients.size() == 0) + if (recipients.isEmpty()) { _log.warn("No recipients, unable to send EHR trigger script email"); return; @@ -1639,7 +1640,7 @@ private Set getRecipients(Integer... userIds) { for (UserPrincipal u : SecurityManager.getAllGroupMembers((Group)up, MemberType.ACTIVE_USERS)) { - if (((User)u).isActive()) + if (u.isActive()) recipients.add(u); } } @@ -1655,7 +1656,7 @@ public String onAnimalArrival(String id, Map row, @Nullable Map< { List errorMsgs = new ArrayList<>(); - Map demographicsProps = new HashMap(); + Map demographicsProps = new HashMap<>(); for (String key : new String[]{"Id", "gender", "species", "dam", "sire", "origin", "source", "geographic_origin", "birth"}) { if (row.containsKey(key)) @@ -1730,7 +1731,7 @@ public Set hasDemographicsRecord(List ids) TableSelector ts = new TableSelector(ti, Collections.singleton("Id"), filter, null); - Set ret = new HashSet(); + Set ret = new HashSet<>(); ret.addAll(Arrays.asList(ts.getArray(String.class))); return ret; @@ -1738,7 +1739,7 @@ public Set hasDemographicsRecord(List ids) public void updateStatusField(List ids, Map> liveBirths, Map> arrivals, Map> deaths, Map> departures) throws QueryUpdateServiceException, SQLException, BatchValidationException, InvalidKeyException { - List> rows = new ArrayList>(); + List> rows = new ArrayList<>(); Set idsInDemographics = hasDemographicsRecord(ids); for (String id : ids) @@ -1885,7 +1886,7 @@ private Date getOpenEndedHousingOverlaps(String id, Date date, List ignoredObjectIds = new HashSet<>(); Date highestOpenEnded = null; - if (recordsInTransaction != null && recordsInTransaction.size() > 0) + if (recordsInTransaction != null) { for (Map origMap : recordsInTransaction) { @@ -2013,7 +2014,7 @@ private void sendMessage(String subject, String bodyHtml, Collection recipients = NotificationService.get().getRecipients(new DeathNotification(), getContainer()); - if (recipients.size() == 0) + if (recipients.isEmpty()) { _log.warn("No recipients, skipping death notification"); return; @@ -2070,7 +2071,7 @@ public void run() //find housing overlapping date of death TableInfo housing = getTableInfo("study", "demographicsLastHousing"); TableSelector housingTs = new TableSelector(housing, PageFlowUtil.set("room", "cage"), new SimpleFilter(FieldKey.fromString("Id"), id), null); - housingTs.forEach(new Selector.ForEachBlock() + housingTs.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -2100,7 +2101,7 @@ public void exec(ResultSet rs) throws SQLException if (assignmentTs.exists()) { - assignmentTs.forEach(new Selector.ForEachBlock() + assignmentTs.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -2137,7 +2138,7 @@ public void exec(ResultSet object) throws SQLException if (groupTs.exists()) { - groupTs.forEach(new Selector.ForEachBlock() + groupTs.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -2188,7 +2189,7 @@ public String verifyProtocolCounts(final String id, Integer project, final List< TableSelector ts = new TableSelector(ti, filter, null); final List errors = new ArrayList<>(); final String ALL_SPECIES = "All Species"; - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -2205,12 +2206,12 @@ public void exec(ResultSet rs) throws SQLException animals.add(id); - if (recordsInTransaction != null && recordsInTransaction.size() > 0) + if (recordsInTransaction != null) { for (Map r : recordsInTransaction) { - String id = (String)r.get("Id"); - Number project = (Number)r.get("project"); + String id = (String) r.get("Id"); + Number project = (Number) r.get("project"); if (id == null || project == null) { continue; @@ -2239,7 +2240,7 @@ public void exec(ResultSet rs) throws SQLException int remaining = totalAllowed - animals.size(); if (remaining < 0) { - errors.add("There are not enough spaces on protocol: " + protocol + ". Allowed: " + (totalAllowedNull ? "none": totalAllowed) + ", used: " + animals.size()); + errors.add("There are not enough spaces on protocol: " + protocol + ". Allowed: " + (totalAllowedNull ? "none" : totalAllowed) + ", used: " + animals.size()); } } }); @@ -2378,7 +2379,7 @@ private List> getAdditionalServicesToCreate(String services) return null; List testNames = Arrays.asList(StringUtils.split(services, ",;")); - if (testNames.size() == 0) + if (testNames.isEmpty()) return null; Map> serviceMap = getBloodDrawServicesMap(); @@ -2531,9 +2532,9 @@ public void closePreviousDatasetRecords(String dataset, List //sort on date records = new ArrayList<>(records); - records.sort(new Comparator>() + records.sort(new Comparator<>() { - private SimpleDateFormat dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd kk:mm"); + private final SimpleDateFormat dateTimeFormat = new SimpleDateFormat("yyyy-MM-dd kk:mm"); @Override public int compare(Map o1, Map o2) @@ -2621,9 +2622,9 @@ public int getOverlappingFlags(String id, String flag, String objectId, final Da } TableSelector ts = new TableSelector(flagTable, Collections.singleton("lsid"), filter, null); - Long count = ts.getRowCount(); + long count = ts.getRowCount(); - return count.intValue(); + return (int) count; } public void ensureSingleFlagCategoryActive(String id, String flag, String objectId, final Date enddate) @@ -2666,7 +2667,7 @@ public void ensureSingleFlagCategoryActive(String id, String flag, String object QueryUpdateService qus = flagsTable.getUpdateService(); TableSelector ts = new TableSelector(flagsTable, PageFlowUtil.set("lsid", "Id", "enddate"), filter, null); - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet rs) throws SQLException @@ -2683,7 +2684,7 @@ public void exec(ResultSet rs) throws SQLException try { - if (rows.size() > 0) + if (!rows.isEmpty()) { Map extraContext = getExtraContext(); extraContext.put("skipAnnounceChangedParticipants", true); @@ -2693,15 +2694,7 @@ public void exec(ResultSet rs) throws SQLException throw batchValidationException; } } - catch (InvalidKeyException e) - { - throw new RuntimeException(e); - } - catch (BatchValidationException e) - { - throw new RuntimeException(e); - } - catch (QueryUpdateServiceException e) + catch (InvalidKeyException | QueryUpdateServiceException | BatchValidationException e) { throw new RuntimeException(e); } @@ -2730,7 +2723,7 @@ public Integer getNextFlagCode() public void reportCageChange(List keys) { - if (keys == null || keys.size() == 0) + if (keys == null || keys.isEmpty()) return; SimpleFilter.OrClause clause = new SimpleFilter.OrClause(); diff --git a/ehr/test/src/org/labkey/test/pages/ehr/BaseColonyOverviewPage.java b/ehr/test/src/org/labkey/test/pages/ehr/BaseColonyOverviewPage.java index f7b27bd63..8d93160bc 100644 --- a/ehr/test/src/org/labkey/test/pages/ehr/BaseColonyOverviewPage.java +++ b/ehr/test/src/org/labkey/test/pages/ehr/BaseColonyOverviewPage.java @@ -39,7 +39,7 @@ protected WebElement getActiveTabPanel() return Locator.tag("div").withClasses("tab-pane", "active").notHidden().findElement(getDriver()); } - protected abstract class OverviewTab extends Component + protected abstract static class OverviewTab extends Component { private final WebElement el; diff --git a/ehr/test/src/org/labkey/test/pages/ehr/EHRLookupPage.java b/ehr/test/src/org/labkey/test/pages/ehr/EHRLookupPage.java index af4bd4967..b5ca42439 100644 --- a/ehr/test/src/org/labkey/test/pages/ehr/EHRLookupPage.java +++ b/ehr/test/src/org/labkey/test/pages/ehr/EHRLookupPage.java @@ -16,6 +16,7 @@ public EHRLookupPage(WebDriverWrapper driver) super(driver); waitForPage(); } + @Override public void waitForPage() { waitFor(() -> { diff --git a/ehr/test/src/org/labkey/test/pages/ehr/ParticipantViewPage.java b/ehr/test/src/org/labkey/test/pages/ehr/ParticipantViewPage.java index 9b73ebaf2..148665265 100644 --- a/ehr/test/src/org/labkey/test/pages/ehr/ParticipantViewPage.java +++ b/ehr/test/src/org/labkey/test/pages/ehr/ParticipantViewPage.java @@ -262,7 +262,7 @@ CategoryTab findSelectedCategory() } } - public abstract class Tab + public abstract static class Tab { final WebElement _el; private String _label; diff --git a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java index 7f940e60a..ed591a190 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java @@ -433,7 +433,7 @@ protected void populate(@LoggedParam String tableLabel) Locator completeDiv = Locator.tagContainingText("div", "Populate Complete"); List completeEl = completeDiv.findElements(getDriver()); clickButton("Populate " + tableLabel, 0); - if (completeEl.size() > 0) + if (!completeEl.isEmpty()) longWait().until(ExpectedConditions.stalenessOf(completeEl.get(0))); waitForElement(completeDiv, POPULATE_TIMEOUT_MS); Assert.assertFalse("Error populating " + tableLabel, elementContains(Locator.id("msgbox"), "ERROR")); @@ -447,7 +447,7 @@ protected void deleteDataFrom(@LoggedParam String tableLabel) Locator completeDiv = Locator.tagContainingText("div", "Delete Complete"); List completeEl = completeDiv.findElements(getDriver()); clickButton(("All".equals(tableLabel) ? "Delete " : "Delete Data From ") + tableLabel, 0); - if (completeEl.size() > 0) + if (!completeEl.isEmpty()) longWait().until(ExpectedConditions.stalenessOf(completeEl.get(0))); waitForElement(completeDiv, POPULATE_TIMEOUT_MS); Assert.assertFalse("Error deleting " + tableLabel, elementContains(Locator.id("msgbox"), "ERROR")); diff --git a/ehr/test/src/org/labkey/test/tests/ehr/AbstractGenericEHRTest.java b/ehr/test/src/org/labkey/test/tests/ehr/AbstractGenericEHRTest.java index e8c71fc68..420181f31 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/AbstractGenericEHRTest.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/AbstractGenericEHRTest.java @@ -320,7 +320,7 @@ public void testCalculatedAgeColumns() private void calculateAverage() { - if (_saveRowsTimes.size() == 0) + if (_saveRowsTimes.isEmpty()) return; long sum = 0; diff --git a/ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java b/ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java index c392bdfaa..d071b9376 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/ComplianceTrainingTest.java @@ -50,7 +50,7 @@ @BaseWebDriverTest.ClassTimeout(minutes = 5) public abstract class ComplianceTrainingTest extends BaseWebDriverTest implements AdvancedSqlTest { - private String listZIP = TestFileUtils.getLabKeyRoot() + "/server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip"; + private final String listZIP = TestFileUtils.getLabKeyRoot() + "/server/modules/ehrModules/EHR_ComplianceDB/tools/SOP_Lists.zip"; @Override protected String getProjectName() @@ -61,7 +61,7 @@ protected String getProjectName() @BeforeClass public static void doSetup() { - ComplianceTrainingTest initTest = (ComplianceTrainingTest)getCurrentTest(); + ComplianceTrainingTest initTest = getCurrentTest(); initTest.setUpTest(); initTest.cleanupRecords(false); } @@ -74,7 +74,7 @@ public static void doSetup() private final String requirementName1 = prefix + "req1"; private final String requirementName2 = prefix + "req2"; private final String requirementName3 = prefix + "req3"; - private EHRClientAPIHelper _apiHelper = new EHRClientAPIHelper(this, getProjectName()); + private final EHRClientAPIHelper _apiHelper = new EHRClientAPIHelper(this, getProjectName()); @@ -358,7 +358,7 @@ protected void setUpTest() select.addFilter(new Filter("requirementname", reqName, Filter.Operator.EQUAL)); SelectRowsResponse resp = select.execute(cn, getProjectName()); - if (resp.getRows().size() == 0) + if (resp.getRows().isEmpty()) { insertCmd = new InsertRowsCommand("ehr_compliancedb", "requirements"); rowMap = new HashMap<>(); @@ -374,7 +374,7 @@ protected void setUpTest() select.addFilter(new Filter("categoryname", category, Filter.Operator.EQUAL)); resp = select.execute(cn, getProjectName()); - if (resp.getRows().size() == 0) + if (resp.getRows().isEmpty()) { insertCmd = new InsertRowsCommand("ehr_compliancedb", "employeecategory"); rowMap = new HashMap<>(); diff --git a/ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java b/ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java index 1d77ab029..b646ac472 100644 --- a/ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java +++ b/ehr/test/src/org/labkey/test/tests/ehr/EHRBillingHelper.java @@ -43,8 +43,8 @@ public class EHRBillingHelper { - private BaseWebDriverTest _test; - private String _projectName; + private final BaseWebDriverTest _test; + private final String _projectName; private String _folderName; private String _modulePath; private String _containerPath; @@ -168,7 +168,7 @@ public void verifyBillingInvoicedItemsUsingAPI(String InvoicedId, List> entry : item.getColumnTextCheckMap().entrySet()) { - List input = new ArrayList(); + List input = new ArrayList<>(); for (Map row : resp.getRows()) { if (row.get(entry.getKey()) != null) @@ -225,7 +225,6 @@ public void verifyBillingInvoicedItems(String invoiceId, List item { results.setFilter("chargeId/chargeCategoryid", "Equals", item.getChargeCategoryID()); filterDescription += separator + "ChargeCategoryId: " + item.getChargeCategoryID(); - separator = ", "; } assertEquals("Wrong row count for " + filterDescription, item.getRowCount(), results.getDataRowCount()); @@ -266,13 +265,13 @@ private DataRegionTable goToInvoiceItemsForId(String invoiceId) public static class InvoicedItem { private String _animalId; - private String _category; - private int _rowCount; - private String _totalCost; - private String _totalQuantity; + private final String _category; + private final int _rowCount; + private final String _totalCost; + private final String _totalQuantity; private String _chargeCategoryId; private String _chargeID; - private Map> _columnTextChecks = new HashMap<>(); + private final Map> _columnTextChecks = new HashMap<>(); public InvoicedItem(String category, int rowCount, String totalQuantity, String totalCost) { diff --git a/ehr/test/src/org/labkey/test/util/ehr/EHRTestHelper.java b/ehr/test/src/org/labkey/test/util/ehr/EHRTestHelper.java index 6d8e036a8..3f10bd6af 100644 --- a/ehr/test/src/org/labkey/test/util/ehr/EHRTestHelper.java +++ b/ehr/test/src/org/labkey/test/util/ehr/EHRTestHelper.java @@ -55,7 +55,7 @@ public class EHRTestHelper { - private BaseWebDriverTest _test; + private final BaseWebDriverTest _test; public EHRTestHelper(BaseWebDriverTest test) { @@ -104,7 +104,7 @@ public Boolean waitForElementWithValue(final BaseWebDriverTest test, final Strin WebDriverWait wait = new WebDriverWait(test.getDriver(), Duration.ofSeconds(secTimeout)); try { - return wait.until(new ExpectedCondition() + return wait.until(new ExpectedCondition<>() { @Override public Boolean apply(WebDriver d) diff --git a/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/BillingNotificationProvider.java b/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/BillingNotificationProvider.java index f023d2b1b..9d88084e2 100644 --- a/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/BillingNotificationProvider.java +++ b/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/BillingNotificationProvider.java @@ -29,52 +29,52 @@ public interface BillingNotificationProvider /** * @return Center specific Billing module. */ - public Module getModule(); + Module getModule(); /** * @return Notification Name - ex. 'Billing Notification' or 'Finance Notification'. */ - public String getName(); + String getName(); /** * @return Scheduled cron job string - ex. "0 0 8 * * ?" will send notification every day at 8:00 am */ - public String getCronString(); + String getCronString(); /** * @return Description of your scheduled cron job. ex "Every Day at 8:00AM" */ - public String getScheduleDescription(); + String getScheduleDescription(); /** * @return Description of what your billing notification entails. */ - public String getDescription(); + String getDescription(); /** * @return Map of Category and queryName to run. Queries are expected to be ehr_billing queries. */ - public Map getCategoriesToQuery(); + Map getCategoriesToQuery(); /** * @return Map of Category and Containers in which the corresponding queries listed in getCategoriesToQuery() live. */ - public Map getQueryCategoryContainerMapping(Container c); + Map getQueryCategoryContainerMapping(Container c); /** * @return List of field descriptors, essentially a calculated column in your queries that you'd want to show as part of the notification. */ - public List getFieldDescriptor(); + List getFieldDescriptor(); /** * @return Additional notifications that are not covered in BillingNotification.java */ - public List getAdditionalNotifications(User user); + List getAdditionalNotifications(User user); /** * @return name or abbreviation of your Primate Center */ - public String getCenterName(); + String getCenterName(); /** * @param u User @@ -83,12 +83,12 @@ public interface BillingNotificationProvider * @param msg a StringBuilder instance to append message to if preferred esp. in the case when billing schema is not enabled in a given container * @return false if billing public linked schema is not enabled in a given container c, true otherwise. */ - public boolean isBillingSchemaEnabled(User u, Container c, String alertType, StringBuilder msg); + boolean isBillingSchemaEnabled(User u, Container c, String alertType, StringBuilder msg); /** * @return Name of center specific billing schema */ - public String getCenterSpecificBillingSchema(); + String getCenterSpecificBillingSchema(); /** * @param u User @@ -98,7 +98,7 @@ public interface BillingNotificationProvider * @return A List of {@link ChargeCategoryInfo} - ChargeCategoryInfo class holds data to display under the 'Charge Summary' section of the notification per custom category. * See WNPRC Billing's implementation of this method for an example. */ - public default List getAdditionalChargeCategoryInfo(User u, Container c, Date startDate, Date endDate) + default List getAdditionalChargeCategoryInfo(User u, Container c, Date startDate, Date endDate) { return Collections.emptyList(); } diff --git a/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/FieldDescriptor.java b/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/FieldDescriptor.java index e039ddf4b..7b0936840 100644 --- a/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/FieldDescriptor.java +++ b/ehr_billing/api-src/org/labkey/api/ehr_billing/notification/FieldDescriptor.java @@ -21,10 +21,10 @@ import java.sql.SQLException; public class FieldDescriptor { - private String _fieldName; - private boolean _flagIfNonNull; - private String _label; - private boolean _shouldHighlight; + private final String _fieldName; + private final boolean _flagIfNonNull; + private final String _label; + private final boolean _shouldHighlight; public FieldDescriptor(String fieldName, boolean flagIfNonNull, String label, boolean shouldHighlight) { diff --git a/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/BillingPipelineJobSupport.java b/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/BillingPipelineJobSupport.java index 77134d230..7b638aa30 100644 --- a/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/BillingPipelineJobSupport.java +++ b/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/BillingPipelineJobSupport.java @@ -23,15 +23,15 @@ public interface BillingPipelineJobSupport { - public Date getStartDate(); + Date getStartDate(); - public Date getEndDate(); + Date getEndDate(); - public String getComment(); + String getComment(); - public String getName(); + String getName(); - public File getAnalysisDir(); + File getAnalysisDir(); /* * Returns Pair of previous matching billing run's objectId and rowId diff --git a/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/InvoicedItemsProcessingService.java b/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/InvoicedItemsProcessingService.java index e92a1e98f..29d3d1648 100644 --- a/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/InvoicedItemsProcessingService.java +++ b/ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/InvoicedItemsProcessingService.java @@ -16,7 +16,6 @@ package org.labkey.api.ehr_billing.pipeline; import org.apache.logging.log4j.Logger; -import org.apache.logging.log4j.LogManager; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; diff --git a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingContainerListener.java b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingContainerListener.java index bb6f03640..4ddc08c4a 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingContainerListener.java +++ b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingContainerListener.java @@ -19,7 +19,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager.ContainerListener; -import org.labkey.api.data.DatabaseTableType; import org.labkey.api.data.DbScope; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Table; diff --git a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingController.java b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingController.java index a16262e5c..ceeac238e 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingController.java +++ b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingController.java @@ -79,7 +79,7 @@ public EHR_BillingController() } @RequiresPermission(UpdatePermission.class) - public class RunBillingPipelineAction extends MutatingApiAction + public static class RunBillingPipelineAction extends MutatingApiAction { @Override public ApiResponse execute(BillingPipelineForm form, BindException errors) @@ -129,13 +129,13 @@ public ApiResponse execute(BillingPipelineForm form, BindException errors) } @RequiresPermission(EHR_BillingAdminPermission.class) - public class DeleteBillingPeriodAction extends ConfirmAction + public static class DeleteBillingPeriodAction extends ConfirmAction { @Override public void validateCommand(QueryForm form, Errors errors) { Set ids = DataRegionSelection.getSelected(form.getViewContext(), true); - if (ids.size() == 0) + if (ids.isEmpty()) { errors.reject(ERROR_MSG, "Must select at least one item to delete"); } @@ -175,7 +175,7 @@ public boolean handlePost(QueryForm form, BindException errors) throws BatchVali } @RequiresPermission(ReadPermission.class) - public class UpdateQueryAction extends SimpleViewAction + public static class UpdateQueryAction extends SimpleViewAction { private QueryForm _form; diff --git a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingManager.java b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingManager.java index 25f54ba25..88bdeaab8 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingManager.java +++ b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingManager.java @@ -25,7 +25,6 @@ import org.labkey.api.data.Table; import org.labkey.api.data.TableInfo; import org.labkey.api.data.TableSelector; -import org.labkey.api.ehr.EHRService; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.module.Module; import org.labkey.api.module.ModuleLoader; @@ -48,7 +47,7 @@ public class EHR_BillingManager { - private static EHR_BillingManager _instance = new EHR_BillingManager(); + private static final EHR_BillingManager _instance = new EHR_BillingManager(); public static final String EHR_BillingContainerPropName = "BillingContainer"; private EHR_BillingManager() @@ -101,7 +100,7 @@ public List deleteBillingRuns(User user, Container container, Collection { Map map = new CaseInsensitiveHashMap<>(); map.put("invoiceId", null); - map = Table.update(user, miscCharges, map, objectid); + Table.update(user, miscCharges, map, objectid); } TableSelector tsInvoiceRuns = new TableSelector(invoiceRuns, objectIdFilter, null); diff --git a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingUserSchema.java b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingUserSchema.java index a00b8a3f0..f78fdf4ba 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingUserSchema.java +++ b/ehr_billing/src/org/labkey/ehr_billing/EHR_BillingUserSchema.java @@ -18,7 +18,6 @@ import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.DbSchema; import org.labkey.api.data.TableInfo; import org.labkey.api.query.SimpleUserSchema; import org.labkey.api.security.User; diff --git a/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotification.java b/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotification.java index d5f56a949..fdde62318 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotification.java +++ b/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotification.java @@ -295,10 +295,10 @@ private void getProjectSummary(Container c, User u, final Calendar start, Calend TableInfo ti = qd.getTable(us, errors, true); Map params = new HashMap<>(); - Long numDays = ((DateUtils.truncate(new Date(), Calendar.DATE).getTime() - start.getTimeInMillis()) / DateUtils.MILLIS_PER_DAY) + 1; + long numDays = ((DateUtils.truncate(new Date(), Calendar.DATE).getTime() - start.getTimeInMillis()) / DateUtils.MILLIS_PER_DAY) + 1; params.put("StartDate", start.getTime()); params.put("EndDate", endDate.getTime()); - params.put("NumDays", numDays.intValue()); + params.put("NumDays", (int) numDays); Set fieldKeys = new HashSet<>(); for (ColumnInfo col : ti.getColumns()) @@ -319,7 +319,7 @@ private void getProjectSummary(Container c, User u, final Calendar start, Calend final double[] totalQuantity = {0.0}; // 1 element final array since 'final' is required in the below exec method final double[] totalCost = {0.0};// 1 element final array since 'final' is required in the below exec method - ts.forEach(new Selector.ForEachBlock() + ts.forEach(new Selector.ForEachBlock<>() { @Override public void exec(ResultSet object) throws SQLException @@ -327,7 +327,7 @@ public void exec(ResultSet object) throws SQLException Results rs = new ResultsImpl(object, cols); Double unitCost = rs.getDouble(FieldKey.fromString("unitCost")); - Double quantity = rs.getDouble(FieldKey.fromString("quantity")); + double quantity = rs.getDouble(FieldKey.fromString("quantity")); totalQuantity[0] += quantity; totalCost[0] += (unitCost * quantity); diff --git a/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotificationServiceImpl.java b/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotificationServiceImpl.java index 2caea8e7f..8c93af56c 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotificationServiceImpl.java +++ b/ehr_billing/src/org/labkey/ehr_billing/notification/BillingNotificationServiceImpl.java @@ -24,7 +24,7 @@ public class BillingNotificationServiceImpl extends BillingNotificationService { - private Map _billingNotificationProviders = new HashMap<>(); + private final Map _billingNotificationProviders = new HashMap<>(); @Override diff --git a/ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java b/ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java index bc51ea8fe..c7ef4b20d 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java +++ b/ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingTask.java @@ -494,7 +494,7 @@ private void runProcessing(BillingPipelineJobProcess process, Container billingR procedureRow.put("chargeId", chargeId); // add additional charge info - ChargeInfo ci = getChargeInfo(chargeId, chargeInfoArrayList, (Date) procedureRow.get("date")); + ChargeInfo ci = getChargeInfo(chargeId, chargeInfoArrayList, procedureRow.get("date")); procedureRow.put("item", ci.getItem()); procedureRow.put("category", ci.getCategory()); @@ -509,7 +509,7 @@ private void runProcessing(BillingPipelineJobProcess process, Container billingR // calculate total cost with additional/other rate (ex. tier rate for WNPRC) Double otherRate = (Double) procedureRow.get("otherRate"); Double unitCostWithOtherRate; - Double totalCostWithOtherRate; + double totalCostWithOtherRate; if (null != otherRate && null != processingService.getAdditionalUnitCostColName() && null != processingService.getAdditionalTotalCostColName()) diff --git a/ehr_billing/src/org/labkey/ehr_billing/query/EHRBillingTriggerHelper.java b/ehr_billing/src/org/labkey/ehr_billing/query/EHRBillingTriggerHelper.java index 64f71cca7..c1ee5fd06 100644 --- a/ehr_billing/src/org/labkey/ehr_billing/query/EHRBillingTriggerHelper.java +++ b/ehr_billing/src/org/labkey/ehr_billing/query/EHRBillingTriggerHelper.java @@ -41,9 +41,9 @@ */ public class EHRBillingTriggerHelper { - private Container _container; - private User _user; - private Map> _cachedCharges = new HashMap<>(); + private final Container _container; + private final User _user; + private final Map> _cachedCharges = new HashMap<>(); public EHRBillingTriggerHelper(int userId, String containerId) { diff --git a/snd/api-src/org/labkey/api/snd/Event.java b/snd/api-src/org/labkey/api/snd/Event.java index a1ac4df9e..f1b307c2e 100644 --- a/snd/api-src/org/labkey/api/snd/Event.java +++ b/snd/api-src/org/labkey/api/snd/Event.java @@ -59,7 +59,7 @@ public class Event private String _objectId; // This will store a count of the different severity of exceptions - private Map _exceptionCount = new HashMap<>(); + private final Map _exceptionCount = new HashMap<>(); private ValidationException _eventException = null; public static final String EVENT_ID = "eventId"; @@ -428,7 +428,7 @@ public JSONObject toJSON(Container c, User u) if (severity == null) severity = ValidationException.SEVERITY.WARN; - if (msg.length() > 0) + if (!msg.isEmpty()) msg.append(", "); msg.append(count + " warning"); @@ -442,7 +442,7 @@ public JSONObject toJSON(Container c, User u) if (severity == null) severity = ValidationException.SEVERITY.INFO; - if (msg.length() > 0) + if (!msg.isEmpty()) msg.append(", "); msg.append(count + " info"); @@ -450,7 +450,7 @@ public JSONObject toJSON(Container c, User u) msg.append("s"); } - if (msg.length() > 0) + if (!msg.isEmpty()) { msg.append(" found"); diff --git a/snd/api-src/org/labkey/api/snd/EventNarrativeOption.java b/snd/api-src/org/labkey/api/snd/EventNarrativeOption.java index 5726d7e6f..a1595408b 100644 --- a/snd/api-src/org/labkey/api/snd/EventNarrativeOption.java +++ b/snd/api-src/org/labkey/api/snd/EventNarrativeOption.java @@ -22,7 +22,7 @@ public enum EventNarrativeOption HTML_NARRATIVE("htmlNarrative"), REDACTED_HTML_NARRATIVE("redactedHtmlNarrative"); - private String _key; + private final String _key; EventNarrativeOption(String key) { diff --git a/snd/api-src/org/labkey/api/snd/EventTrigger.java b/snd/api-src/org/labkey/api/snd/EventTrigger.java index ed3f9d2e8..2b16abea6 100644 --- a/snd/api-src/org/labkey/api/snd/EventTrigger.java +++ b/snd/api-src/org/labkey/api/snd/EventTrigger.java @@ -16,10 +16,8 @@ package org.labkey.api.snd; import org.labkey.api.data.Container; -import org.labkey.api.query.BatchValidationException; import org.labkey.api.security.User; -import java.util.List; import java.util.Map; public interface EventTrigger diff --git a/snd/api-src/org/labkey/api/snd/SNDDomainKind.java b/snd/api-src/org/labkey/api/snd/SNDDomainKind.java index d7c57a078..6df4027f9 100644 --- a/snd/api-src/org/labkey/api/snd/SNDDomainKind.java +++ b/snd/api-src/org/labkey/api/snd/SNDDomainKind.java @@ -17,9 +17,7 @@ import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; -import org.labkey.api.data.CoreSchema; import org.labkey.api.data.SQLFragment; -import org.labkey.api.data.dialect.SqlDialect; import org.labkey.api.exp.property.Domain; import org.labkey.api.gwt.client.model.GWTPropertyDescriptor; import org.labkey.api.query.ExtendedTableDomainKind; diff --git a/snd/api-src/org/labkey/api/snd/SNDSequencer.java b/snd/api-src/org/labkey/api/snd/SNDSequencer.java index 94d1a1e94..699c57af5 100644 --- a/snd/api-src/org/labkey/api/snd/SNDSequencer.java +++ b/snd/api-src/org/labkey/api/snd/SNDSequencer.java @@ -29,8 +29,8 @@ public enum SNDSequencer EVENTID ("org.labkey.snd.api.Event", 2000000), EVENTDATAID ("org.labkey.snd.api.EventData", 5000000); - private String sequenceName; - private int minId; + private final String sequenceName; + private final int minId; SNDSequencer(String name, int id) { diff --git a/snd/api-src/org/labkey/api/snd/SuperPackage.java b/snd/api-src/org/labkey/api/snd/SuperPackage.java index 2bf9cd95b..0d24c1daf 100644 --- a/snd/api-src/org/labkey/api/snd/SuperPackage.java +++ b/snd/api-src/org/labkey/api/snd/SuperPackage.java @@ -26,7 +26,6 @@ import java.util.ArrayList; import java.util.List; import java.util.Map; -import java.util.function.Function; import static org.labkey.api.snd.Package.PKG_ATTRIBUTES; diff --git a/snd/src/org/labkey/snd/SNDController.java b/snd/src/org/labkey/snd/SNDController.java index a38af14f3..834041044 100644 --- a/snd/src/org/labkey/snd/SNDController.java +++ b/snd/src/org/labkey/snd/SNDController.java @@ -102,7 +102,7 @@ private Map getExtraFields(JSONArray jsonExtras) } @RequiresLogin - public class BeginAction extends SimpleRedirectAction + public static class BeginAction extends SimpleRedirectAction { @Override public URLHelper getRedirectURL(Object o) @@ -258,7 +258,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) superPackage.setRequired(false); // Top level super packages required is always false - if (null != jsonSubPackages && jsonSubPackages.length() > 0) + if (null != jsonSubPackages && !jsonSubPackages.isEmpty()) { for (JSONObject jsonSubPackage : JsonUtil.toJSONObjectList(jsonSubPackages)) { @@ -415,7 +415,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) return new ApiSimpleResponse(); } - private class SuperPackageInfo + private static class SuperPackageInfo { int _sortOrder; boolean _required; @@ -460,7 +460,7 @@ private void setAdditionalSuperPackageInfo(LinkedList superPac } @RequiresPermission(SNDPackageViewerPermission.class) - public class GetPackagesAction extends ReadOnlyApiAction + public static class GetPackagesAction extends ReadOnlyApiAction { @Override public void validateForm(SimpleApiJsonForm form, Errors errors) @@ -525,7 +525,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) } SNDService sndService = SNDService.get(); - if (ids.size() > 0 && sndService != null) + if (!ids.isEmpty() && sndService != null) { pkgs.addAll(sndService.getPackages(getViewContext().getContainer(), getUser(), ids, includeExtraFields, includeLookups, includeFullSubpackages)); @@ -576,7 +576,7 @@ public void validateForm(SimpleApiJsonForm form, Errors errors) errors.reject(ERROR_MSG, "Missing referenceId."); } - if (!json.has("startDate") || json.getString("startDate") == null || json.getString("startDate").equals("")) + if (!json.has("startDate") || json.getString("startDate") == null || json.getString("startDate").isEmpty()) { errors.reject(ERROR_MSG, "Missing startDate."); } @@ -627,7 +627,7 @@ public void validateForm(SimpleApiJsonForm form, Errors errors) } } - if (json.has("endDate") && (json.isNull("endDate") || json.getString("endDate").equals(""))) + if (json.has("endDate") && (json.isNull("endDate") || json.getString("endDate").isEmpty())) { json.remove("endDate"); } @@ -733,7 +733,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) throws } @RequiresPermission(SNDProjectViewerPermission.class) - public class GetProjectAction extends ReadOnlyApiAction + public static class GetProjectAction extends ReadOnlyApiAction { @Override public void validateForm(SimpleApiJsonForm form, Errors errors) @@ -789,7 +789,7 @@ public ApiResponse execute(SimpleApiJsonForm form, BindException errors) } @RequiresPermission(ReadPermission.class) - public class GetEventAction extends ReadOnlyApiAction + public static class GetEventAction extends ReadOnlyApiAction { @Override public void validateForm(SimpleApiJsonForm form, Errors errors) @@ -1063,7 +1063,7 @@ private List parseEventData(JSONArray eventDataJson) throws IOExcepti { List eventDataList = new ArrayList<>(); - if ((eventDataJson != null) && (eventDataJson.length() > 0)) + if ((eventDataJson != null) && (!eventDataJson.isEmpty())) { for (int i = 0; i < eventDataJson.length(); i++) { @@ -1113,7 +1113,7 @@ private List parseAttributeData(JSONArray attributesDataJson) { List attributesDataList = new ArrayList<>(); - if ((attributesDataJson != null) && (attributesDataJson.length() > 0)) + if ((attributesDataJson != null) && (!attributesDataJson.isEmpty())) { String propertyName = null; int propertyId = -1; @@ -1152,7 +1152,7 @@ else if (propertyId != -1) } @RequiresPermission(AdminPermission.class) - public class RegisterTestTriggerFactoryAction extends ReadOnlyApiAction + public static class RegisterTestTriggerFactoryAction extends ReadOnlyApiAction { @Override public Object execute(SimpleApiJsonForm form, BindException errors) @@ -1191,7 +1191,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class ClearNarrativeCacheAction extends MutatingApiAction + public static class ClearNarrativeCacheAction extends MutatingApiAction { @Override public Object execute(SimpleApiJsonForm form, BindException errors) @@ -1202,7 +1202,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class FillInNarrativeCacheAction extends MutatingApiAction + public static class FillInNarrativeCacheAction extends MutatingApiAction { @Override public Object execute(SimpleApiJsonForm form, BindException errors) @@ -1213,7 +1213,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class PopulateQCStatesAction extends MutatingApiAction + public static class PopulateQCStatesAction extends MutatingApiAction { @Override public Object execute(SimpleApiJsonForm form, BindException errors) @@ -1225,7 +1225,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors) } @RequiresPermission(AdminPermission.class) - public class SecurityAction extends SimpleViewAction + public static class SecurityAction extends SimpleViewAction { @Override @@ -1271,7 +1271,7 @@ public URLHelper getSuccessURL(Object o) } @RequiresPermission(AdminPermission.class) - public class AdminAction extends SimpleViewAction + public static class AdminAction extends SimpleViewAction { @Override @@ -1292,7 +1292,7 @@ public void addNavTrail(NavTree root) } @RequiresPermission(AdminPermission.class) - public class UpdateRoleAction extends MutatingApiAction + public static class UpdateRoleAction extends MutatingApiAction { @Override public Object execute(SimpleApiJsonForm form, BindException errors) diff --git a/snd/src/org/labkey/snd/SNDManager.java b/snd/src/org/labkey/snd/SNDManager.java index d04bd0cc8..83c2015b6 100644 --- a/snd/src/org/labkey/snd/SNDManager.java +++ b/snd/src/org/labkey/snd/SNDManager.java @@ -68,7 +68,6 @@ import org.labkey.api.security.User; import org.labkey.api.security.roles.FolderAdminRole; import org.labkey.api.security.roles.RoleManager; -import org.labkey.api.settings.AppProps; import org.labkey.api.settings.LookAndFeelProperties; import org.labkey.api.snd.AttributeData; import org.labkey.api.snd.Category; @@ -122,7 +121,7 @@ public class SNDManager private final Cache>> _cache; - private List _attributeLookups = new ArrayList<>(); + private final List _attributeLookups = new ArrayList<>(); public static final String RANGE_PARTICIPANTID = "ParticipantId"; @@ -262,7 +261,7 @@ public Object getLookupDisplayValue(User u, Container c, String schema, String t throw new RuntimeException(e); } - if (rows == null || rows.size() < 1) + if (rows == null || rows.isEmpty()) return null; return rows.get(0).get(tableInfo.getTitleColumn()); @@ -297,7 +296,7 @@ public Object normalizeLookupValue(User u, Container c, String schema, String ta SqlSelector selector = new SqlSelector(userSchema.getDbSchema(), sql); List lookupRows = selector.getArrayList(Object.class); - if (lookupRows.size() < 1) + if (lookupRows.isEmpty()) return null; return lookupRows.get(0); @@ -573,11 +572,6 @@ private Map getPackageCategories(Container c, User u, int pkgId * Return a cached map of Package Categories by PkgId * If pkgIds is not null, get for list of pkgIds, else get for entire database. * - * @param c - * @param u - * @param pkgIds - * @param errors - * @return */ private Map> getBulkPackageCategories(Container c, User u, @Nullable List pkgIds, BatchValidationException errors) { @@ -657,10 +651,6 @@ public Package addExtraFieldsToPackage(Container c, User u, Package pkg, @Nullab /** * Retrieve extensible fields as an argument and add them as extraFields to pkg object - * @param pkg - * @param extraFields - * @param row - * @return */ public Package addExtraFieldsToPackage(Package pkg, List extraFields, @Nullable Map row) { @@ -714,7 +704,7 @@ public static List getSuperPkgIdsForPkg(Container c, User u, Integer pa sql.append(" WHERE sp.PkgId = ?").add(packageId); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(SuperPackage.class).size() > 0) + if (!selector.getArrayList(SuperPackage.class).isEmpty()) return selector.getArrayList(Integer.class); else return null; @@ -755,7 +745,7 @@ public static List getSuperPkgs(Container c, User u, List sql.append(")"); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(SuperPackage.class).size() > 0) + if (!selector.getArrayList(SuperPackage.class).isEmpty()) return selector.getArrayList(SuperPackage.class); else return null; @@ -780,7 +770,7 @@ public static List convertToTopLevelSuperPkgs(Container c, User u, sql.append(") AND sp2.ParentSuperPkgId IS NULL"); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(SuperPackage.class).size() > 0) + if (!selector.getArrayList(SuperPackage.class).isEmpty()) return selector.getArrayList(SuperPackage.class); else return null; @@ -792,7 +782,7 @@ public static List convertToTopLevelSuperPkgs(Container c, User u, @Nullable public static List filterTopLevelSuperPkgs(Container c, User u, List superPackageIds) { - if ((superPackageIds == null) || (superPackageIds.size() == 0)) + if ((superPackageIds == null) || (superPackageIds.isEmpty())) return null; UserSchema schema = getSndUserSchema(c, u); @@ -804,7 +794,7 @@ public static List filterTopLevelSuperPkgs(Container c, User u, Li sql.append(") AND sp.ParentSuperPkgId IS NULL"); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(SuperPackage.class).size() > 0) + if (!selector.getArrayList(SuperPackage.class).isEmpty()) return selector.getArrayList(SuperPackage.class); else return null; @@ -823,7 +813,7 @@ public static List getChildSuperPkgs(Container c, User u, Integer sql.append(" WHERE sp.ParentSuperPkgId = ?").add(parentSuperPackageId); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(Integer.class).size() > 0) + if (!selector.getArrayList(Integer.class).isEmpty()) return selector.getArrayList(SuperPackage.class); else return null; @@ -835,7 +825,7 @@ public static List getChildSuperPkgs(Container c, User u, Integer @Nullable public static List filterChildSuperPkgs(Container c, User u, List superPackageIds, Integer parentSuperPackageId) { - if ((superPackageIds == null) || (superPackageIds.size() == 0)) + if ((superPackageIds == null) || (superPackageIds.isEmpty())) return null; UserSchema schema = getSndUserSchema(c, u); @@ -847,7 +837,7 @@ public static List filterChildSuperPkgs(Container c, User u, List< sql.append(") AND sp.ParentSuperPkgId = ?").add(parentSuperPackageId); SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); - if (selector.getArrayList(SuperPackage.class).size() > 0) + if (!selector.getArrayList(SuperPackage.class).isEmpty()) return selector.getArrayList(SuperPackage.class); else return null; @@ -864,7 +854,7 @@ public static List getDeletedChildSuperPkgs(Container c, User u, List 0)) + if ((superPackages != null) && (!superPackages.isEmpty())) { sql.append(" sp.SuperPkgId NOT IN ("); Iterator superPackageIterator = superPackages.iterator(); @@ -881,7 +871,7 @@ public static List getDeletedChildSuperPkgs(Container c, User u, List 0) + if (!selector.getArrayList(Integer.class).isEmpty()) return selector.getArrayList(Integer.class); else return null; @@ -952,7 +942,7 @@ private SuperPackage getFullSuperPackage(Container c, User u, int superPkgId, bo List pkgIds = new ArrayList<>(); pkgIds.add(superPackage.getPkgId()); List pkgs = getPackages(c, u, pkgIds, true, true, true, errors); - if (pkgs.size() > 0) + if (!pkgs.isEmpty()) { superPackage.setPkg(pkgs.get(0)); } @@ -1115,19 +1105,6 @@ private Package createPackage(Container c, User u, Map row, bool /** * Does same as createPackage but retrieves superPackage and package info from cached map objects from arguments instead of database queries - * @param c - * @param u - * @param row - * @param packageExtraFields - * @param superPackages - * @param childrenByParentId - * @param pkgCategoriesByPkgId - * @param lookups - * @param includeExtraFields - * @param includeLookups - * @param includeFullSubpackages - * @param errors - * @return */ private Package getBulkPackage(Container c, User u, Map row, List packageExtraFields, List superPackages, Map> childrenByParentId, @@ -1216,20 +1193,6 @@ public List getPackages(Container c, User u, List pkgIds, bool /** * Does same as getPackages but retrieves the superPackage and package info from cached object maps instead of database queries - * @param c - * @param u - * @param pkgIds - * @param pkgQus - * @param packageExtraFields - * @param superPackages - * @param childrenByParentId - * @param pkgCategoriesByPkgId - * @param lookups - * @param includeExtraFields - * @param includeLookups - * @param includeFullSubpackages - * @param errors - * @return */ public List getBulkPackages(Container c, User u, List pkgIds, QueryUpdateService pkgQus, List packageExtraFields, List superPackages, @@ -1396,7 +1359,7 @@ private boolean isValidReferenceId(Container c, User u, Project project, boolean rows.add(r); } - if (rows.size() > 0) + if (!rows.isEmpty()) { Map row = rows.get(0); if ((Integer) row.get("ReferenceId") != project.getReferenceId() && Boolean.parseBoolean((String) row.get("HasEvent"))) @@ -1426,7 +1389,7 @@ private boolean isValidReferenceId(Container c, User u, Project project, boolean rows.add(r); } - if (rows.size() > 0) + if (!rows.isEmpty()) { for (Map row : rows) { @@ -1954,7 +1917,7 @@ private EventData getEventData(Container c, User u, @Nullable Integer eventDataI TableInfo eventDataTable = getTableInfo(schema, SNDSchema.EVENTDATA_TABLE_NAME); Map properties = null; - EventData eventData = null; + EventData eventData; TableSelector ts = null; // Get from EventData table @@ -2287,12 +2250,12 @@ private String getProjectObjectId(Container c, User u, Event event) SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql); List results = selector.getArrayList(String.class); - if (results.size() < 1) + if (results.isEmpty()) { event.setException(new ValidationException("Project|revision not found: " + event.getProjectIdRev())); } - return results.size() > 0 ? results.get(0) : null; + return !results.isEmpty() ? results.get(0) : null; } } } @@ -2546,7 +2509,7 @@ private String insertExpObjectProperties(Container c, User u, Event event, Event // Validate first to catch validation errors. Relying on exception thrown in insertProperties creates issues // with nested transactions containing a lock. List validationExceptions = validateProperty(c, u, propertyDescriptor, objectProperty); - if (validationExceptions.size() > 0) + if (!validationExceptions.isEmpty()) { attributeData.setException(event, validationExceptions.get(0)); // just handling on exception } @@ -2629,7 +2592,7 @@ private void ensureSuperPkgsBelongToProject(Container c, User u, Event event) event.setException(new ValidationException("Project is not found.")); } - if (!event.hasErrors() && event.getEventData() != null && event.getEventData().size() > 0) + if (!event.hasErrors() && event.getEventData() != null && !event.getEventData().isEmpty()) { UserSchema schema = getSndUserSchema(c, u); @@ -2697,7 +2660,7 @@ private void ensureValidPackage(Event event, EventData eventData, Package pkg) Map incomingProps = Maps.newHashMap(); boolean found; - if (attributes.size() > 0) + if (!attributes.isEmpty()) { for (AttributeData attribute : attributes) { @@ -2825,7 +2788,7 @@ public Event createEvent(Container c, User u, Event event, boolean validateOnly) QueryUpdateService eventNotesQus = null; // make sure there is an event note to insert - event notes are optional - trim spaces - if (event.getEventNotesRow(c).containsKey("note") && event.getEventNotesRow(c).get("note") != null && event.getEventNotesRow(c).get("note").toString().trim().length() > 0) + if (event.getEventNotesRow(c).containsKey("note") && event.getEventNotesRow(c).get("note") != null && !event.getEventNotesRow(c).get("note").toString().trim().isEmpty()) eventNotesQus = getNewQueryUpdateService(schema, SNDSchema.EVENTNOTES_TABLE_NAME); try (DbScope.Transaction tx = eventTable.getSchema().getScope().ensureTransaction()) @@ -3029,7 +2992,7 @@ public Event updateEvent(Container c, User u, Event event, boolean validateOnly) QueryUpdateService eventNotesQus = null; // make sure there is an event note to insert - event notes are optional - trim spaces - if (event.getEventNotesRow(c).containsKey("note") && event.getEventNotesRow(c).get("note") != null && event.getEventNotesRow(c).get("note").toString().trim().length() > 0) + if (event.getEventNotesRow(c).containsKey("note") && event.getEventNotesRow(c).get("note") != null && !event.getEventNotesRow(c).get("note").toString().trim().isEmpty()) eventNotesQus = getNewQueryUpdateService(schema, SNDSchema.EVENTNOTES_TABLE_NAME); QueryUpdateService eventsCacheQus = getNewQueryUpdateService(schema, SNDSchema.EVENTSCACHE_TABLE_NAME); @@ -3089,7 +3052,7 @@ public int updateNarrativeCache(Container container, User user, Setcach /* deletes and updates cached narratives */ public int updateNarrativeCache(Container container, User user, SetcacheData, @NotNull Logger log, boolean isUpdate) { - if (cacheData.size() > 0) + if (!cacheData.isEmpty()) { log.info("Deleting affected narrative cache rows."); List> rows = new ArrayList<>(); @@ -3651,7 +3614,7 @@ public List> getActiveProjects(Container c, User u, ArrayLis Map extraFields = project.getExtraFields(); - if (extraFields.size() > 0) + if (!extraFields.isEmpty()) { for (Map.Entry pd : extraFields.entrySet()) { @@ -3693,7 +3656,7 @@ public List> getActiveProjects(Container c, User u, ArrayLis // add projectItems List> pItems = getProjectItemsList(c, u, project.getProjectId(), project.getRevisionNum(), eventDate == null ? activeProjectItemsOnly : false); - if (pItems.size() > 0) + if (!pItems.isEmpty()) { projectMap.put("ProjectItems", pItems); } @@ -3952,7 +3915,7 @@ private Map getBulkSuperPkgs(Container c, User u, List fullTreeSuperPkgs; if (!isFullReload) { - fullTreeSuperPkgs = new ArrayList(); + fullTreeSuperPkgs = new ArrayList<>(); pkgIds.forEach(pkgId -> { SQLFragment packageSql = new SQLFragment("SELECT * FROM "); packageSql.append(SNDSchema.NAME + "." + SNDSchema.SUPERPKGS_FUNCTION_NAME + "(?)").add(pkgId); @@ -4315,10 +4278,6 @@ private Map>> getNextLevelEven /** * Query EventNotes table for set of eventIds * - * @param c - * @param u - * @param eventIds - * @return */ private Map getBulkEventNotes(Container c, User u, List eventIds) { @@ -4340,10 +4299,6 @@ private Map getBulkEventNotes(Container c, User u, List getBulkProjectIdRevs(Container c, User u, List objectIds) { @@ -4366,14 +4321,6 @@ private Map getBulkProjectIdRevs(Container c, User u, List TableSelector getTableSelector(Container c, User u, List filterValues, String tableName, String filterColumn, String sortColumn, String isNullColumn) { diff --git a/snd/src/org/labkey/snd/SNDServiceImpl.java b/snd/src/org/labkey/snd/SNDServiceImpl.java index 375d86e04..9cfeb2b5d 100644 --- a/snd/src/org/labkey/snd/SNDServiceImpl.java +++ b/snd/src/org/labkey/snd/SNDServiceImpl.java @@ -354,7 +354,7 @@ public Event saveEvent(Container c, User u, Event event, boolean validateOnly) if ((event.getEventData() == null || event.getEventData().isEmpty()) && (!event.getEventNotesRow(c).containsKey("note") || event.getEventNotesRow(c).get("note") == null || - event.getEventNotesRow(c).get("note").toString().trim().length() == 0)) + event.getEventNotesRow(c).get("note").toString().trim().isEmpty())) { event = SNDManager.get().deleteEvent(c, u, event); } diff --git a/snd/src/org/labkey/snd/query/AttributeDataTable.java b/snd/src/org/labkey/snd/query/AttributeDataTable.java index 3d0ffaa6d..3c907ed08 100644 --- a/snd/src/org/labkey/snd/query/AttributeDataTable.java +++ b/snd/src/org/labkey/snd/query/AttributeDataTable.java @@ -221,7 +221,7 @@ private int insertObject(Container c, User u, String uri, List p catch (ValidationException e) { logger.error(e.getMessage() + " PkgId " + pkgId, e); - throw new UnexpectedException(e, e.getMessage() + "For PkgId: " + pkgId + ".\n"); + throw UnexpectedException.wrap(e, e.getMessage() + "For PkgId: " + pkgId + ".\n"); } return inserted; @@ -341,7 +341,7 @@ else if (stringValue != null) } } - if (prevObjProps.size() > 0 && pkgId != null) + if (!prevObjProps.isEmpty() && pkgId != null) { inserted = insertObject(container, user, prevUri, prevObjProps, pkgId, inserted, logger); } diff --git a/snd/src/org/labkey/snd/query/CategoriesTable.java b/snd/src/org/labkey/snd/query/CategoriesTable.java index 1a8eaa8e9..840c830e4 100644 --- a/snd/src/org/labkey/snd/query/CategoriesTable.java +++ b/snd/src/org/labkey/snd/query/CategoriesTable.java @@ -53,8 +53,6 @@ public class CategoriesTable extends SimpleTable * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public CategoriesTable(SNDUserSchema schema, TableInfo table, ContainerFilter cf) { diff --git a/snd/src/org/labkey/snd/query/EventDataTable.java b/snd/src/org/labkey/snd/query/EventDataTable.java index 5345dabc6..f7ddb2d1f 100644 --- a/snd/src/org/labkey/snd/query/EventDataTable.java +++ b/snd/src/org/labkey/snd/query/EventDataTable.java @@ -59,14 +59,13 @@ public class EventDataTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public EventDataTable(SNDUserSchema schema, TableInfo table) { super(schema, table); } + @Override public void addColumns() { BaseColumnInfo objectid = new BaseColumnInfo("ObjectId", this, JdbcType.INTEGER) @@ -104,10 +103,10 @@ public boolean hasPermission(@NotNull UserPrincipal user, @NotNull Class 0 && null != data.get(0)) + if(!data.isEmpty() && null != data.get(0)) { DataIteratorBuilder rowsWithObjectURI = new ListofMapsDataIterator.Builder(data.get(0).keySet(), data); rowCount = _importRowsUsingDIB(user, container, rowsWithObjectURI, null, dataIteratorContext, extraScriptContext); diff --git a/snd/src/org/labkey/snd/query/EventNotesDataIterator.java b/snd/src/org/labkey/snd/query/EventNotesDataIterator.java index e1c3803ff..6c569bed0 100644 --- a/snd/src/org/labkey/snd/query/EventNotesDataIterator.java +++ b/snd/src/org/labkey/snd/query/EventNotesDataIterator.java @@ -22,12 +22,12 @@ public class EventNotesDataIterator extends AbstractDataIterator { private static final SNDManager _sndManager = SNDManager.get(); private static final String EVENT_ID_COL = "eventId"; - private User _user; - private Container _container; - private int _eventIdColIndex; - private Set _eventIds = new HashSet<>(); - private DataIterator _in; - private Logger log = LogHelper.getLogger(EventNotesDataIterator.class, "Fill out event notes"); + private final User _user; + private final Container _container; + private final int _eventIdColIndex; + private final Set _eventIds = new HashSet<>(); + private final DataIterator _in; + private final Logger log = LogHelper.getLogger(EventNotesDataIterator.class, "Fill out event notes"); public static DataIterator wrap(DataIterator in, DataIteratorContext context, Container c, User u) { diff --git a/snd/src/org/labkey/snd/query/EventNotesTable.java b/snd/src/org/labkey/snd/query/EventNotesTable.java index 2995536a4..9f7146f91 100644 --- a/snd/src/org/labkey/snd/query/EventNotesTable.java +++ b/snd/src/org/labkey/snd/query/EventNotesTable.java @@ -19,7 +19,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; import org.labkey.api.dataiterator.DataIteratorBuilder; import org.labkey.api.dataiterator.DataIteratorContext; @@ -46,8 +45,6 @@ public class EventNotesTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public EventNotesTable(SNDUserSchema schema, TableInfo table) { @@ -57,10 +54,10 @@ public EventNotesTable(SNDUserSchema schema, TableInfo table) @Override public QueryUpdateService getUpdateService() { - return new EventNotesTable.UpdateService(this); + return new UpdateService(this); } - protected class UpdateService extends SNDQueryUpdateService + protected static class UpdateService extends SNDQueryUpdateService { public UpdateService(SimpleUserSchema.SimpleTable ti) { diff --git a/snd/src/org/labkey/snd/query/EventsCacheTable.java b/snd/src/org/labkey/snd/query/EventsCacheTable.java index 2be1d3cd5..14228c5e1 100644 --- a/snd/src/org/labkey/snd/query/EventsCacheTable.java +++ b/snd/src/org/labkey/snd/query/EventsCacheTable.java @@ -16,11 +16,9 @@ package org.labkey.snd.query; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.TableInfo; import org.labkey.api.query.FieldKey; import org.labkey.api.query.QueryUpdateService; -import org.labkey.api.query.SimpleUserSchema; import org.labkey.api.security.UserPrincipal; import org.labkey.api.security.permissions.Permission; import org.labkey.snd.SNDUserSchema; @@ -36,8 +34,6 @@ public class EventsCacheTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public EventsCacheTable(SNDUserSchema schema, TableInfo table) { diff --git a/snd/src/org/labkey/snd/query/EventsTable.java b/snd/src/org/labkey/snd/query/EventsTable.java index 43d7867d6..99775d834 100644 --- a/snd/src/org/labkey/snd/query/EventsTable.java +++ b/snd/src/org/labkey/snd/query/EventsTable.java @@ -19,7 +19,6 @@ import org.jetbrains.annotations.NotNull; import org.jetbrains.annotations.Nullable; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.DbScope; import org.labkey.api.data.TableInfo; import org.labkey.api.dataiterator.DataIteratorBuilder; @@ -59,8 +58,6 @@ public class EventsTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ private final SNDManager _sndManager = SNDManager.get(); @@ -145,7 +142,7 @@ public int mergeRows(User user, Container container, DataIteratorBuilder rows, B Set eventIds = handleNarrativeCache(rows, configParameters, errors); - int result = 0; + int result; int maxMergeRows = SNDManager.MAX_MERGE_ROWS * 10; // Large merge triggers importRows path diff --git a/snd/src/org/labkey/snd/query/LookupSetsTable.java b/snd/src/org/labkey/snd/query/LookupSetsTable.java index f4f3666e7..5c1325e2c 100644 --- a/snd/src/org/labkey/snd/query/LookupSetsTable.java +++ b/snd/src/org/labkey/snd/query/LookupSetsTable.java @@ -15,8 +15,6 @@ public class LookupSetsTable extends SimpleTable { * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public LookupSetsTable(SNDUserSchema schema, TableInfo table, ContainerFilter cf) { super(schema, table, cf); } diff --git a/snd/src/org/labkey/snd/query/LookupSetsVirtualTable.java b/snd/src/org/labkey/snd/query/LookupSetsVirtualTable.java index 862163708..ff3c58da3 100644 --- a/snd/src/org/labkey/snd/query/LookupSetsVirtualTable.java +++ b/snd/src/org/labkey/snd/query/LookupSetsVirtualTable.java @@ -18,12 +18,8 @@ import org.labkey.api.data.ColumnInfo; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerFilter; -import org.labkey.api.data.JdbcType; -import org.labkey.api.data.SQLFragment; import org.labkey.api.data.TableInfo; -import org.labkey.api.query.ExprColumn; import org.labkey.api.query.SimpleUserSchema.SimpleTable; -import org.labkey.snd.SNDSchema; import org.labkey.snd.SNDUserSchema; import java.util.Map; @@ -38,7 +34,7 @@ public class LookupSetsVirtualTable extends SimpleTable private static final String LABEL_COL = "Label"; private static final String DESCRIPTION_COL = "Description"; private static final String LOOKUPSETID_COL = "LookupSetId"; - private Integer _lookupSetId; + private final Integer _lookupSetId; public LookupSetsVirtualTable(SNDUserSchema schema, TableInfo table, String setName, Map map, ContainerFilter cf) diff --git a/snd/src/org/labkey/snd/query/LookupsTable.java b/snd/src/org/labkey/snd/query/LookupsTable.java index e29ed493b..743aec595 100644 --- a/snd/src/org/labkey/snd/query/LookupsTable.java +++ b/snd/src/org/labkey/snd/query/LookupsTable.java @@ -45,8 +45,6 @@ public class LookupsTable extends SimpleTable * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public LookupsTable(SNDUserSchema schema, TableInfo table, ContainerFilter cf) { @@ -81,10 +79,10 @@ public LookupsTable init() { @Override public QueryUpdateService getUpdateService() { - return new LookupsTable.UpdateService(this); + return new UpdateService(this); } - protected class UpdateService extends SNDQueryUpdateService + protected static class UpdateService extends SNDQueryUpdateService { public UpdateService(SimpleTable ti) { diff --git a/snd/src/org/labkey/snd/query/PackagesTable.java b/snd/src/org/labkey/snd/query/PackagesTable.java index 4330748a9..e87d34e89 100644 --- a/snd/src/org/labkey/snd/query/PackagesTable.java +++ b/snd/src/org/labkey/snd/query/PackagesTable.java @@ -69,8 +69,6 @@ public class PackagesTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public PackagesTable(SNDUserSchema schema, TableInfo table) { diff --git a/snd/src/org/labkey/snd/query/ProjectsTable.java b/snd/src/org/labkey/snd/query/ProjectsTable.java index 1d0f3a1f5..ac65e0c59 100644 --- a/snd/src/org/labkey/snd/query/ProjectsTable.java +++ b/snd/src/org/labkey/snd/query/ProjectsTable.java @@ -53,8 +53,6 @@ public class ProjectsTable extends SimpleTable * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public ProjectsTable(SNDUserSchema schema, TableInfo table, ContainerFilter cf) { diff --git a/snd/src/org/labkey/snd/query/SuperPackagesTable.java b/snd/src/org/labkey/snd/query/SuperPackagesTable.java index be4fdebc6..30467691f 100644 --- a/snd/src/org/labkey/snd/query/SuperPackagesTable.java +++ b/snd/src/org/labkey/snd/query/SuperPackagesTable.java @@ -17,7 +17,6 @@ import org.jetbrains.annotations.NotNull; import org.labkey.api.data.Container; -import org.labkey.api.data.ContainerFilter; import org.labkey.api.data.JdbcType; import org.labkey.api.data.SQLFragment; import org.labkey.api.data.SimpleFilter; @@ -57,8 +56,6 @@ public class SuperPackagesTable extends AbstractSNDTableInfo * Create the simple table. * SimpleTable doesn't add columns until .init() has been called to allow derived classes to fully initialize themselves before adding columns. * - * @param schema - * @param table */ public SuperPackagesTable(SNDUserSchema schema, TableInfo table) { diff --git a/snd/src/org/labkey/snd/security/QCStateActionEnum.java b/snd/src/org/labkey/snd/security/QCStateActionEnum.java index eb05b9ab2..8c43089cd 100644 --- a/snd/src/org/labkey/snd/security/QCStateActionEnum.java +++ b/snd/src/org/labkey/snd/security/QCStateActionEnum.java @@ -46,8 +46,8 @@ public enum QCStateActionEnum DELETE("Delete", new SNDCompletedDeletePermission(), new SNDInProgressDeletePermission(), new SNDRejectedDeletePermission(), new SNDReviewRequiredDeletePermission()), READ("Read", new SNDCompletedReadPermission(), new SNDInProgressReadPermission(), new SNDRejectedReadPermission(), new SNDReviewRequiredReadPermission()); - private List _permissions = new ArrayList<>(); - private String _name; + private final List _permissions = new ArrayList<>(); + private final String _name; QCStateActionEnum(String name, SNDQCStatePermission... perms) { diff --git a/snd/src/org/labkey/snd/security/permissions/SNDQCStatePermission.java b/snd/src/org/labkey/snd/security/permissions/SNDQCStatePermission.java index ca858c1a0..4534541ff 100644 --- a/snd/src/org/labkey/snd/security/permissions/SNDQCStatePermission.java +++ b/snd/src/org/labkey/snd/security/permissions/SNDQCStatePermission.java @@ -21,7 +21,7 @@ public class SNDQCStatePermission extends AbstractPermission { - private QCStateEnum _qcState; + private final QCStateEnum _qcState; SNDQCStatePermission(String name, String description, QCStateEnum qcState) { diff --git a/snd/src/org/labkey/snd/trigger/SNDTriggerManager.java b/snd/src/org/labkey/snd/trigger/SNDTriggerManager.java index ea8ee7a82..8fded32c7 100644 --- a/snd/src/org/labkey/snd/trigger/SNDTriggerManager.java +++ b/snd/src/org/labkey/snd/trigger/SNDTriggerManager.java @@ -46,7 +46,7 @@ public static SNDTriggerManager get() return _instance; } - private Map _eventTriggerFactories = new HashMap<>(); + private final Map _eventTriggerFactories = new HashMap<>(); /** * Called from SNDService to allow event trigger factories to be registered. These will be queried for category @@ -169,7 +169,7 @@ public void fireInsertTriggers(Container c, User u, Event event, Map factories = getTriggerFactories(c); // Nothing to do - if (factories.size() < 1) + if (factories.isEmpty()) return; List triggerActions = getTriggerActions(event, topLevelEventDataPkgs, factories); @@ -189,7 +189,7 @@ public void fireUpdateTriggers(Container c, User u, Event event, Map factories = getTriggerFactories(c); // Nothing to do - if (factories.size() < 1) + if (factories.isEmpty()) return; List triggers = getTriggerActions(event, topLevelEventDataSuperPkgs, factories); diff --git a/snd/src/org/labkey/snd/trigger/test/triggers/CalciumTestTrigger.java b/snd/src/org/labkey/snd/trigger/test/triggers/CalciumTestTrigger.java index 53bbff728..73da24009 100644 --- a/snd/src/org/labkey/snd/trigger/test/triggers/CalciumTestTrigger.java +++ b/snd/src/org/labkey/snd/trigger/test/triggers/CalciumTestTrigger.java @@ -38,7 +38,7 @@ private void ensureAmountForUnits(Event event, EventData eventData, Package pkg) AttributeData unitsAttribute = TriggerHelper.getAttribute("units", eventData, pkg); String amountValue = amountAttribute.getValue(); String unitsValue = unitsAttribute.getValue(); - Double newAmountValue = Double.parseDouble(amountValue); + double newAmountValue = Double.parseDouble(amountValue); if (unitsValue != null && amountValue != null) { diff --git a/snd/src/org/labkey/snd/trigger/test/triggers/ChlorideTestTrigger.java b/snd/src/org/labkey/snd/trigger/test/triggers/ChlorideTestTrigger.java index aa302b058..08704b6cf 100644 --- a/snd/src/org/labkey/snd/trigger/test/triggers/ChlorideTestTrigger.java +++ b/snd/src/org/labkey/snd/trigger/test/triggers/ChlorideTestTrigger.java @@ -39,7 +39,7 @@ private void ensureAmountForUnits(Event event, EventData eventData, Package pkg) AttributeData unitsAttribute = TriggerHelper.getAttribute("units", eventData, pkg); String amountValue = amountAttribute.getValue(); String unitsValue = unitsAttribute.getValue(); - Double newAmountValue; + double newAmountValue; if (unitsValue != null && amountValue != null) { diff --git a/snd/src/org/labkey/snd/trigger/test/triggers/TriggerHelper.java b/snd/src/org/labkey/snd/trigger/test/triggers/TriggerHelper.java index cc390e9e8..f13a47d13 100644 --- a/snd/src/org/labkey/snd/trigger/test/triggers/TriggerHelper.java +++ b/snd/src/org/labkey/snd/trigger/test/triggers/TriggerHelper.java @@ -30,7 +30,7 @@ public class TriggerHelper { public static final String orderPropName = "triggerOrder"; - private static Map ELECTROLYTES_TRIGGER_ORDER = new HashMap<>(); + private static final Map ELECTROLYTES_TRIGGER_ORDER = new HashMap<>(); static { ELECTROLYTES_TRIGGER_ORDER.put("Chloride Test Trigger", 0); diff --git a/snd/test/src/org/labkey/test/components/snd/AttributeGridRow.java b/snd/test/src/org/labkey/test/components/snd/AttributeGridRow.java index 5f47cb0f8..9d849f823 100644 --- a/snd/test/src/org/labkey/test/components/snd/AttributeGridRow.java +++ b/snd/test/src/org/labkey/test/components/snd/AttributeGridRow.java @@ -69,7 +69,7 @@ public String getDataType() public AttributeGridRow selectLookupKey(String key) { elementCache().lookupKeySelect.selectByVisibleText(key); - if (!key.equals("")) + if (!key.isEmpty()) { getWrapper().waitForElement(elementCache().DEFAULT_VALUE_SELECT); } @@ -205,7 +205,7 @@ protected class ElementCache extends Component.ElementCache public static class AttributeGridRowFinder extends WebDriverComponent.WebDriverComponentFinder { private Locator _locator; - private AttributesGrid _grid; + private final AttributesGrid _grid; private AttributeGridRowFinder(AttributesGrid grid) { diff --git a/snd/test/src/org/labkey/test/pages/snd/EditCategoriesPage.java b/snd/test/src/org/labkey/test/pages/snd/EditCategoriesPage.java index 12540e7eb..528d1744a 100644 --- a/snd/test/src/org/labkey/test/pages/snd/EditCategoriesPage.java +++ b/snd/test/src/org/labkey/test/pages/snd/EditCategoriesPage.java @@ -15,14 +15,11 @@ */ package org.labkey.test.pages.snd; -import org.apache.commons.lang3.NotImplementedException; import org.labkey.test.Locator; import org.labkey.test.WebDriverWrapper; import org.labkey.test.WebTestHelper; import org.labkey.test.components.snd.CategoryEditRow; import org.labkey.test.pages.LabKeyPage; -import org.labkey.test.selenium.LazyWebElement; -import org.openqa.selenium.SearchContext; import org.openqa.selenium.WebDriver; import org.openqa.selenium.WebElement; diff --git a/snd/test/src/org/labkey/test/pages/snd/EditPackagePage.java b/snd/test/src/org/labkey/test/pages/snd/EditPackagePage.java index 7b9e3ee11..c49482d4d 100644 --- a/snd/test/src/org/labkey/test/pages/snd/EditPackagePage.java +++ b/snd/test/src/org/labkey/test/pages/snd/EditPackagePage.java @@ -19,7 +19,6 @@ import org.labkey.test.WebDriverWrapper; import org.labkey.test.WebTestHelper; import org.labkey.test.components.html.Checkbox; -import org.labkey.test.components.html.Input; import org.labkey.test.components.snd.AttributesGrid; import org.labkey.test.components.snd.FilterSelect; import org.labkey.test.components.snd.SuperPackageRow; @@ -31,8 +30,6 @@ import java.util.List; -import static org.junit.Assert.assertTrue; - public class EditPackagePage extends LabKeyPage { public EditPackagePage(WebDriver driver) diff --git a/snd/test/src/org/labkey/test/pages/snd/PackageListPage.java b/snd/test/src/org/labkey/test/pages/snd/PackageListPage.java index b25d41aa1..e5f5c9339 100644 --- a/snd/test/src/org/labkey/test/pages/snd/PackageListPage.java +++ b/snd/test/src/org/labkey/test/pages/snd/PackageListPage.java @@ -18,7 +18,6 @@ import org.labkey.test.Locator; import org.labkey.test.WebDriverWrapper; import org.labkey.test.WebTestHelper; -import org.labkey.test.components.html.BootstrapMenu; import org.labkey.test.components.html.Checkbox; import org.labkey.test.components.html.Input; import org.labkey.test.components.snd.PackageViewerResult; diff --git a/snd/test/src/org/labkey/test/tests/snd/SNDTest.java b/snd/test/src/org/labkey/test/tests/snd/SNDTest.java index 824db2a20..06e6a1236 100644 --- a/snd/test/src/org/labkey/test/tests/snd/SNDTest.java +++ b/snd/test/src/org/labkey/test/tests/snd/SNDTest.java @@ -219,7 +219,7 @@ public class SNDTest extends BaseWebDriverTest implements SqlserverOnlyTest " } \n" + "})"; - private static String SAVEPACKAGEAPI_CHILDREN = "LABKEY.Ajax.request({ \n" + + private static final String SAVEPACKAGEAPI_CHILDREN = "LABKEY.Ajax.request({ \n" + " method: 'POST', \n" + " url: LABKEY.ActionURL.buildURL('snd', 'savePackage.api'), \n" + " success: function(){ callback('Success!'); }, \n" + @@ -289,7 +289,7 @@ public class SNDTest extends BaseWebDriverTest implements SqlserverOnlyTest " } \n" + " });"; - private static String UPDATESUPERPACKAGEAPI_CHILDREN = "LABKEY.Ajax.request({\n" + + private static final String UPDATESUPERPACKAGEAPI_CHILDREN = "LABKEY.Ajax.request({\n" + " method: 'POST', \n" + " url: LABKEY.ActionURL.buildURL('snd', 'savePackage.api'), \n" + " success: function(){ callback('Success!'); },\n" + @@ -368,7 +368,7 @@ public class SNDTest extends BaseWebDriverTest implements SqlserverOnlyTest " } \n" + " });"; - private static String UPDATESUPERPACKAGEAPI_CLONE = "LABKEY.Ajax.request({ \n" + + private static final String UPDATESUPERPACKAGEAPI_CLONE = "LABKEY.Ajax.request({ \n" + " method: 'POST', \n" + " url: LABKEY.ActionURL.buildURL('snd', 'savePackage.api'), \n" + " success: function(){ callback('Success!'); }, \n" + @@ -448,7 +448,7 @@ public class SNDTest extends BaseWebDriverTest implements SqlserverOnlyTest " } \n" + " });"; - private static String UPDATESUPERPACKAGEAPI_NOCHILDREN = "LABKEY.Ajax.request({ \n" + + private static final String UPDATESUPERPACKAGEAPI_NOCHILDREN = "LABKEY.Ajax.request({ \n" + " method: 'POST', \n" + " url: LABKEY.ActionURL.buildURL('snd', 'savePackage.api'), \n" + " success: function(){ callback('Success!'); }, \n" + @@ -966,16 +966,16 @@ private void populateLookups() InsertRowsCommand command = new InsertRowsCommand("snd", "LookupSets"); List> lookupSetRows = Arrays.asList( - new HashMap(Maps.of("SetName", "SurgeryType", + new HashMap<>(Maps.of("SetName", "SurgeryType", "Label", "Surgery Type", "Description", "These are surgery types", "ObjectId", UUID.randomUUID().toString())), - new HashMap(Maps.of("SetName", "BloodDrawType", + new HashMap<>(Maps.of("SetName", "BloodDrawType", "ObjectId", UUID.randomUUID().toString())), - new HashMap(Maps.of("SetName", "GenderType", + new HashMap<>(Maps.of("SetName", "GenderType", "Label", "Gender", "ObjectId", UUID.randomUUID().toString())), - new HashMap(Maps.of("SetName", "VolumeUnitTypes", + new HashMap<>(Maps.of("SetName", "VolumeUnitTypes", "Label", "Volume", "Description", "Units of volume", "ObjectId", UUID.randomUUID().toString()))); @@ -1475,7 +1475,7 @@ public void addCategoryViaUI() throws Exception // create a new one via the UI catPage.addCategory(ourNewCategory, true); - catPage = catPage.clickSave(); + catPage.clickSave(); waitFor(()-> false, 2000); SelectRowsCommand catsCmd = new SelectRowsCommand("snd", "PkgCategories"); @@ -1572,7 +1572,7 @@ public void testExtensibleColumns() throws Exception insertRowsCommand.addRow(TEST1ROW2MAP); insertRowsCommand.addRow(TEST1ROW3MAP); SaveRowsResponse resp = insertRowsCommand.execute(cn, getProjectName() + "/" + TEST1SUBFOLDER); - assertEquals(resp.getRowsAffected().intValue(), 3); + assertEquals(3, resp.getRowsAffected().intValue()); goToSchemaBrowser(); selectQuery("snd", "Pkgs"); @@ -1592,7 +1592,7 @@ public void testExtensibleColumns() throws Exception UpdateRowsCommand updateRowsCommand = new UpdateRowsCommand("snd", "Pkgs"); updateRowsCommand.addRow(TEST1ROW3AMAP); resp = updateRowsCommand.execute(cn, getProjectName() + "/" + TEST1SUBFOLDER); - assertEquals(resp.getRowsAffected().intValue(), 1); + assertEquals(1, resp.getRowsAffected().intValue()); goToSchemaBrowser(); selectQuery("snd", "Pkgs"); @@ -1604,7 +1604,7 @@ public void testExtensibleColumns() throws Exception DeleteRowsCommand deleteRowsCommand = new DeleteRowsCommand("snd", "Pkgs"); deleteRowsCommand.addRow(TEST1ROW2MAP); resp = deleteRowsCommand.execute(cn, getProjectName() + "/" + TEST1SUBFOLDER); - assertEquals(resp.getRowsAffected().intValue(), 1); + assertEquals(1, resp.getRowsAffected().intValue()); goToSchemaBrowser(); selectQuery("snd", "Pkgs"); @@ -2119,7 +2119,7 @@ private void runTestsInAPIFrameWork() private String getPermissionTableValue(int row, int col) { List els = ((Locator.XPathLocator)getSimpleTableCell(Locator.id("category-security"), row, col)).child("div").child("a").child("input").findElements(getDriver()); - if (els.size() > 0) + if (!els.isEmpty()) { return els.get(0).getAttribute("value"); } @@ -2130,7 +2130,7 @@ private String getPermissionTableValue(int row, int col) private void clickRoleInOpenDropDown(String name) { List els = Locator.tagWithClassContaining("div", "btn-group open").child("ul").child("li").child("a").withText(name).findElements(getDriver()); - if (els.size() > 0) + if (!els.isEmpty()) { els.get(0).click(); }