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Auto-refactor lint cleanup #931

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3 changes: 2 additions & 1 deletion snd/api-src/org/labkey/api/snd/SNDDomainKind.java
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Expand Up @@ -15,6 +15,7 @@
*/
package org.labkey.api.snd;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.CompareType;
import org.labkey.api.data.Container;
import org.labkey.api.data.SQLFragment;
Expand Down Expand Up @@ -72,7 +73,7 @@ public boolean ensurePropertyLookup()
}

@Override
public Set<String> getReservedPropertyNames(Domain domain, User user)
public @NotNull Set<String> getReservedPropertyNames(Domain domain, User user)
{
Set<String> result = new HashSet<>();
result.add("Description");
Expand Down
5 changes: 2 additions & 3 deletions snd/src/org/labkey/snd/PackageUserSchema.java
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Expand Up @@ -36,7 +36,6 @@
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.List;
Expand Down Expand Up @@ -223,7 +222,7 @@ protected void initializeColumns()
@Override
protected SQLFragment getFromSQLExpanded(String alias, Set<FieldKey> cols)
{
boolean hasEventDataColumn = cols.stream().anyMatch(fk -> eventDataCols.contains(fk.getParts().get(0)));
boolean hasEventDataColumn = cols.stream().anyMatch(fk -> eventDataCols.contains(fk.getParts().getFirst()));
return getFromSQLJoin(alias, hasEventDataColumn);
}

Expand Down Expand Up @@ -419,7 +418,7 @@ protected void initializeColumns()
List<QueryException> errors = new ArrayList<>();
queryTableInfo = qdef.getTable(_snd, errors, false);
if (!errors.isEmpty())
throw errors.get(0);
throw errors.getFirst();
if (null == queryTableInfo)
throw new QueryException("Unexpected error compiling query");

Expand Down
25 changes: 0 additions & 25 deletions snd/src/org/labkey/snd/SNDContainerListener.java
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Expand Up @@ -16,24 +16,15 @@

package org.labkey.snd;

import org.jetbrains.annotations.NotNull;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager.ContainerListener;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.Table;
import org.labkey.api.security.User;

import java.beans.PropertyChangeEvent;
import java.util.Collection;
import java.util.Collections;

public class SNDContainerListener implements ContainerListener
{
@Override
public void containerCreated(Container c, User user)
{
}

@Override
public void containerDeleted(Container c, User user)
Expand All @@ -59,20 +50,4 @@ public void containerDeleted(Container c, User user)
transaction.commit();
}
}

@Override
public void propertyChange(PropertyChangeEvent evt)
{
}

@Override
public void containerMoved(Container c, Container oldParent, User user)
{
}

@NotNull @Override
public Collection<String> canMove(Container c, Container newParent, User user)
{
return Collections.emptyList();
}
}
36 changes: 18 additions & 18 deletions snd/src/org/labkey/snd/SNDManager.java
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Expand Up @@ -246,7 +246,7 @@ public Object getLookupDisplayValue(User u, Container c, String schema, String t
QueryUpdateService lookupQus = getQueryUpdateService(tableInfo);

Map<String, Object> keyRow = new HashMap<>();
String pk = tableInfo.getPkColumnNames().get(0); // Only handling single value pks
String pk = tableInfo.getPkColumnNames().getFirst(); // Only handling single value pks
keyRow.put(pk, key);

List<Map<String, Object>> pkRows = new ArrayList<>();
Expand All @@ -265,7 +265,7 @@ public Object getLookupDisplayValue(User u, Container c, String schema, String t
if (rows == null || rows.isEmpty())
return null;

return rows.get(0).get(tableInfo.getTitleColumn());
return rows.getFirst().get(tableInfo.getTitleColumn());
}

/**
Expand All @@ -284,7 +284,7 @@ public Object normalizeLookupValue(User u, Container c, String schema, String ta
String pk;
if (tableInfo.getPkColumnNames() != null)
{
pk = tableInfo.getPkColumnNames().get(0); // Only handling single value pks
pk = tableInfo.getPkColumnNames().getFirst(); // Only handling single value pks
}
else
{
Expand All @@ -300,7 +300,7 @@ public Object normalizeLookupValue(User u, Container c, String schema, String ta
if (lookupRows.isEmpty())
return null;

return lookupRows.get(0);
return lookupRows.getFirst();
}

/**
Expand Down Expand Up @@ -726,7 +726,7 @@ public static SuperPackage getTopLevelSuperPkgForPkg(Container c, User u, Intege
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);

if (selector.getArrayList(SuperPackage.class).size() == 1)
return selector.getArrayList(SuperPackage.class).get(0);
return selector.getArrayList(SuperPackage.class).getFirst();
else
return null;
}
Expand Down Expand Up @@ -905,7 +905,7 @@ public boolean isDescendent(Container c, User u, int topLevelSuperPkgId, int pkg
sql.append(" WHERE SuperPkgId = ?");
sql.add(topLevelSuperPkgId);
SqlSelector selector = new SqlSelector(schema.getDbSchema(), sql);
Integer topLevelPkgId = selector.getArrayList(Integer.class).get(0);
Integer topLevelPkgId = selector.getArrayList(Integer.class).getFirst();

sql = new SQLFragment("SELECT * FROM ");
sql.append(SNDSchema.NAME + "." + SNDSchema.SUPERPKGS_FUNCTION_NAME + "(?)");
Expand Down Expand Up @@ -945,7 +945,7 @@ private SuperPackage getFullSuperPackage(Container c, User u, int superPkgId, bo
List<Package> pkgs = getPackages(c, u, pkgIds, true, true, true, errors);
if (!pkgs.isEmpty())
{
superPackage.setPkg(pkgs.get(0));
superPackage.setPkg(pkgs.getFirst());
}
}

Expand Down Expand Up @@ -982,7 +982,7 @@ else if (includeFullSubpackages)
{
pkgIds = new ArrayList<>();
pkgIds.add(sPkg.getPkgId());
childPkg = getPackages(c, u, pkgIds, true, true, true, errors).get(0);
childPkg = getPackages(c, u, pkgIds, true, true, true, errors).getFirst();
sPkg.setPkg(childPkg);
}
}
Expand Down Expand Up @@ -1362,7 +1362,7 @@ private boolean isValidReferenceId(Container c, User u, Project project, boolean

if (!rows.isEmpty())
{
Map<String, Object> row = rows.get(0);
Map<String, Object> row = rows.getFirst();
if ((Integer) row.get("ReferenceId") != project.getReferenceId() && Boolean.parseBoolean((String) row.get("HasEvent")))
{
errors.addRowError(new ValidationException("This is an in use project. Reference Id cannot be changed."));
Expand Down Expand Up @@ -1752,7 +1752,7 @@ public String getProjectObjectId(Container c, User u, Project project, BatchVali
if (!selector.exists())
return null;

return selector.getArrayList(String.class).get(0);
return selector.getArrayList(String.class).getFirst();
}

/**
Expand Down Expand Up @@ -2257,7 +2257,7 @@ private String getProjectObjectId(Container c, User u, Event event)
event.setException(new ValidationException("Project|revision not found: " + event.getProjectIdRev()));
}

return !results.isEmpty() ? results.get(0) : null;
return !results.isEmpty() ? results.getFirst() : null;
}
}
}
Expand Down Expand Up @@ -2513,7 +2513,7 @@ private String insertExpObjectProperties(Container c, User u, Event event, Event
List<ValidationException> validationExceptions = validateProperty(c, u, propertyDescriptor, objectProperty);
if (!validationExceptions.isEmpty())
{
attributeData.setException(event, validationExceptions.get(0)); // just handling on exception
attributeData.setException(event, validationExceptions.getFirst()); // just handling on exception
}
else
{
Expand Down Expand Up @@ -2649,7 +2649,7 @@ private Package getPackageForSuperPackage(Container c, User u, int superPkgId, B
List<Integer> pkgIds = Lists.newArrayList(selector.getObject(Integer.class));


return getPackages(c, u, pkgIds, false, false, true, errors).get(0);
return getPackages(c, u, pkgIds, false, false, true, errors).getFirst();
}

/**
Expand Down Expand Up @@ -3063,7 +3063,7 @@ public int updateNarrativeCache(Container container, User user, Set<Integer>cach

if (cacheData.size() > MAX_MERGE_ROWS)
{
log.info("More than " + MAX_MERGE_ROWS + " rows. Truncating narrative cache");
log.info("More than {} rows. Truncating narrative cache", MAX_MERGE_ROWS);
clearNarrativeCache(container, user, errors);
if (isUpdate)
log.info("Not automatically populating narrative cache. Must refresh manually.");
Expand Down Expand Up @@ -3202,7 +3202,7 @@ public void populateNarrativeCache(Container c, User u, List<Integer> eventIds,
rows.add(row);
int currentCount = count.incrementAndGet();
if (logger != null && currentCount % 1000 == 0) {
logger.info(currentCount + " narratives generated.");
logger.info("{} narratives generated.", currentCount);
}
});
try (DbScope.Transaction tx = sndSchema.getDbSchema().getScope().ensureTransaction()) {
Expand Down Expand Up @@ -3637,7 +3637,7 @@ public List<Map<String, Object>> getActiveProjects(Container c, User u, ArrayLis
try
{
String pk, title;
pk = luTi.getPkColumnNames().get(0); // Only handling single value pks
pk = luTi.getPkColumnNames().getFirst(); // Only handling single value pks
title = luTi.getTitleColumn();

if (pk != null)
Expand Down Expand Up @@ -3961,7 +3961,7 @@ private Map<Integer, SuperPackage> getBulkSuperPkgs(Container c, User u, List<GW
List<Integer> packageIds = Collections.singletonList(pkgId);
List<Package> packages = getBulkPackages(c, u, packageIds, pkgQus, packageExtraFields, fullTreeSuperPkgs, childrenByParentId, pkgCategoriesByPkgId, lookups, true, true, true, errors);
if (!packages.isEmpty()) {
superPackage.setPkg(packages.get(0));
superPackage.setPkg(packages.getFirst());
}
superPackage.setChildPackages(childrenByTopLevelPkgId.get(pkgId));
}
Expand Down Expand Up @@ -4008,7 +4008,7 @@ private Map<Integer, List<SuperPackage>> getBulkChildSuperPkgs (Container c, Use
.forEach((SuperPackage superPackage) -> {
if (includeFullSubpackages) {
List<Integer> packageIds = Collections.singletonList(superPackage.getPkgId());
superPackage.setPkg(getBulkPackages(c, u, packageIds, pkgQus, packageExtraFields, allSuperPackages, childrenByParentId, pkgCategoriesByPkgId, lookups, true, true, true, errors).get(0));
superPackage.setPkg(getBulkPackages(c, u, packageIds, pkgQus, packageExtraFields, allSuperPackages, childrenByParentId, pkgCategoriesByPkgId, lookups, true, true, true, errors).getFirst());
}
if (superPackage.getParentSuperPkgId().intValue() == root.getSuperPkgId().intValue()) {
children.add(addChildren(superPackage, superPackages));
Expand Down
8 changes: 0 additions & 8 deletions snd/src/org/labkey/snd/SNDModule.java
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Expand Up @@ -19,7 +19,6 @@
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.audit.AuditLogService;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.exp.api.ExperimentService;
import org.labkey.api.exp.property.PropertyService;
Expand Down Expand Up @@ -130,13 +129,6 @@ public QuerySchema createSchema(final DefaultSchema schema, Module module)
});
}

@Override
@NotNull
public Collection<String> getSummary(Container c)
{
return Collections.emptyList();
}

@Override
@NotNull
public Set<String> getSchemaNames()
Expand Down
4 changes: 2 additions & 2 deletions snd/src/org/labkey/snd/SNDServiceImpl.java
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Expand Up @@ -443,11 +443,11 @@ private JSONArray lookupValuesToJson(Container c, User u, String schema, String

if (!table.getPkColumnNames().isEmpty())
{
pk = table.getPkColumnNames().get(0);
pk = table.getPkColumnNames().getFirst();

if (title == null)
{
title = table.getPkColumnNames().get(0);
title = table.getPkColumnNames().getFirst();
}
}

Expand Down
5 changes: 1 addition & 4 deletions snd/src/org/labkey/snd/pipeline/SNDDataHandler.java
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Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.snd.pipeline;

import org.apache.commons.io.FileUtils;
import org.apache.logging.log4j.Logger;
import org.apache.xmlbeans.XmlException;
import org.apache.xmlbeans.XmlOptions;
Expand Down Expand Up @@ -55,8 +54,6 @@
import org.txbiomed.snd.SuperPackagesType;
import org.txbiomed.snd.USDACategoryType;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
Expand Down Expand Up @@ -145,7 +142,7 @@ private void parseAndSavePackages(@NotNull ExportDocument.Export export, @NotNul
{
Package pkg = parsePackage(packageType, info); //convert auto-generated objects/tokens to SND's Package objects
sndService.savePackage(info.getContainer(), info.getUser(), pkg, null,false, true); //save to db
log.info("Saving package: " + packageType.getId() + "-" + packageType.getDescription());
log.info("Saving package: {}-{}", packageType.getId(), packageType.getDescription());
}
}

Expand Down
14 changes: 7 additions & 7 deletions snd/src/org/labkey/snd/query/AttributeDataTable.java
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Expand Up @@ -216,11 +216,11 @@ private int insertObject(Container c, User u, String uri, List<ObjectProperty> p
OntologyManager.insertProperties(c, u, uri, true, properties);
inserted += props.size();
if (inserted % 10000 < props.size())
logger.info("Inserted/updated " + inserted + " rows.");
logger.info("Inserted/updated {} rows.", inserted);
}
catch (ValidationException e)
{
logger.error(e.getMessage() + " PkgId " + pkgId, e);
logger.error("{} PkgId {}", e.getMessage(), pkgId, e);
throw UnexpectedException.wrap(e, e.getMessage() + "For PkgId: " + pkgId + ".\n");
}

Expand Down Expand Up @@ -292,11 +292,11 @@ else if (stringValue != null)
{
if (pd.getLookupSchema() != null && pd.getLookupQuery() != null)
{
logger.info("Value null for property " + pd.getName() + ". Value skipped. Verify lookup " + pd.getLookupSchema() + "." + pd.getLookupQuery() + " contains " + stringValue);
logger.info("Value null for property {}. Value skipped. Verify lookup {}.{} contains {}", pd.getName(), pd.getLookupSchema(), pd.getLookupQuery(), stringValue);
}
else
{
logger.info("Value null for property " + pd.getName() + ". Value skipped.");
logger.info("Value null for property {}. Value skipped.", pd.getName());
}
}

Expand Down Expand Up @@ -347,7 +347,7 @@ else if (stringValue != null)
}

OntologyManager.clearPropertyCache();
logger.info("End updating exp.ObjectProperty. Inserted/Updated " + inserted + " rows.");
logger.info("End updating exp.ObjectProperty. Inserted/Updated {} rows.", inserted);

_sndManager.updateNarrativeCache(container, user, cacheEventIds, logger);

Expand All @@ -373,7 +373,7 @@ public int mergeRows(User user, Container container, DataIteratorBuilder rows, B
if (distinctEventIds.size() >= max_merge_rows)
{
data.clear();
log.info("More than " + max_merge_rows + " rows. using importRows method.");
log.info("More than {} rows. using importRows method.", max_merge_rows);
return importRows(user, container, rows, errors, configParameters, extraScriptContext);
}
log.info("Merging rows.");
Expand Down Expand Up @@ -444,7 +444,7 @@ public List<Map<String, Object>> deleteRows(User user, Container container, List
deleteObjProp.append("and propertyId = ?");
deleteObjProp.add(propertyId);
executor.execute(deleteObjProp);
log.info("Deleting a row in exp.ObjectProperty with objectId = " + objectId + ", and propertyId = " + propertyId);
log.info("Deleting a row in exp.ObjectProperty with objectId = {}, and propertyId = {}", objectId, propertyId);

//narrative cache to update
cacheData.add((Integer) row.get("EventId"));
Expand Down
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