Merge 25.9 to develop

labkey-teamcity · labkey-teamcity · commit ae258a6acb9b · 2025-09-03T12:56:05.000Z
diff --git a/api/src/org/labkey/api/assay/AbstractTsvAssayProvider.java b/api/src/org/labkey/api/assay/AbstractTsvAssayProvider.java
@@ -41,6 +41,7 @@ public abstract class AbstractTsvAssayProvider extends AbstractAssayProvider
     public static final String ASSAY_SCHEMA_NAME = "assayresult";
     public static final String ROW_ID_COLUMN_NAME = "RowId";
     public static final String DATA_ID_COLUMN_NAME = "DataId";
+    public static final String GPAT_PROTOCOL_LSID_PREFIX = "GeneralAssayProtocol";
 
     public AbstractTsvAssayProvider(String protocolLSIDPrefix, String runLSIDPrefix, AssayDataType dataType, Module declaringModule)
     {
diff --git a/api/src/org/labkey/api/data/DataRegion.java b/api/src/org/labkey/api/data/DataRegion.java
@@ -1911,7 +1911,7 @@ protected String getRecordSelectorValue(RenderContext ctx)
                 // of values (even if they're empty) between commas for deterministic parsing (bug 6755)
                 checkboxValue.append(and);
                 if (null != v)
-                    checkboxValue.append(PageFlowUtil.filter(v.toString()));
+                    checkboxValue.append(v);
                 and = ",";
             }
         }
@@ -1924,7 +1924,7 @@ protected String getRecordSelectorValue(RenderContext ctx)
                 // of values (even if they're empty) between commas for deterministic parsing (bug 6755)
                 checkboxValue.append(and);
                 if (null != v)
-                    checkboxValue.append(PageFlowUtil.filter(v.toString()));
+                    checkboxValue.append(v);
                 and = ",";
             }
         }
diff --git a/api/src/org/labkey/api/query/QueryKey.java b/api/src/org/labkey/api/query/QueryKey.java
@@ -200,8 +200,8 @@ else if (contains(ILLEGAL, String.valueOf(c)))
 
     static protected boolean contains(String[] strs, String s)
     {
-        for (int i = 0; i < strs.length; i++)
-            if (strs[i].equals(s))
+        for (String str : strs)
+            if (str.equals(s))
                 return true;
 
         return false;
@@ -221,7 +221,7 @@ protected QueryKey(QueryKey<T> parent, @NotNull String name)
         _hash = _name.toLowerCase().hashCode() ^ Objects.hashCode(_parent);
     }
 
-    protected QueryKey(QueryKey<T> parent, Enum name)
+    protected QueryKey(QueryKey<T> parent, Enum<?> name)
     {
         this(parent, name.toString());
     }
@@ -251,7 +251,7 @@ public boolean equals(Object other)
     {
         if (other == null || !(getClass().equals(other.getClass())))
             return false;
-        QueryKey that = (QueryKey) other;
+        QueryKey<?> that = (QueryKey<?>) other;
         return strEqualsIgnoreCase(_name, that._name) &&
                 Objects.equals(_parent, that._parent);
     }
@@ -349,7 +349,7 @@ protected boolean needsQuotes(String part)
         return true;
     }
 
-    public boolean startsWith(@NotNull QueryKey<? extends QueryKey> prefix)
+    public boolean startsWith(@NotNull QueryKey<? extends QueryKey<?>> prefix)
     {
         if (size() < prefix.size())
             return false;
diff --git a/assay/src/org/labkey/assay/TsvAssayProvider.java b/assay/src/org/labkey/assay/TsvAssayProvider.java
@@ -153,7 +153,7 @@ public class TsvAssayProvider extends AbstractTsvAssayProvider
 
     public TsvAssayProvider()
     {
-        this("GeneralAssayProtocol", "GeneralAssayRun", "General" + RESULT_LSID_PREFIX_PART, ModuleLoader.getInstance().getModule(assayModuleClass));
+        this(GPAT_PROTOCOL_LSID_PREFIX, "GeneralAssayRun", "General" + RESULT_LSID_PREFIX_PART, ModuleLoader.getInstance().getModule(assayModuleClass));
     }
 
     protected TsvAssayProvider(String protocolLSIDPrefix, String runLSIDPrefix, String resultRowLSIDPrefix, Module declaringModule)
diff --git a/core/src/org/labkey/core/webdav/DavController.java b/core/src/org/labkey/core/webdav/DavController.java
@@ -3607,8 +3607,7 @@ private static FileTime getLastModified(InputStream in) throws IOException
     {
         try
         {
-            SAXParserFactory factory = SAXParserFactory.newInstance();
-            SAXParser saxParser = factory.newSAXParser();
+            SAXParser saxParser = XmlBeansUtil.SAX_PARSER_FACTORY.newSAXParser();
             final List<StringBuilder> lastModifieds = new ArrayList<>();
 
             saxParser.parse(new InputSource(in), new DefaultHandler()
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -296,6 +296,7 @@
 import static java.util.Collections.singleton;
 import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toSet;
+import static org.labkey.api.assay.AbstractTsvAssayProvider.GPAT_PROTOCOL_LSID_PREFIX;
 import static org.labkey.api.data.CompareType.IN;
 import static org.labkey.api.data.DbScope.CommitTaskOption.POSTCOMMIT;
 import static org.labkey.api.data.DbScope.CommitTaskOption.POSTROLLBACK;
@@ -4229,6 +4230,7 @@ public void deleteExperimentRuns(Container container, final User user, @Nullable
 
         try (DbScope.Transaction transaction = ensureTransaction())
         {
+            AssayService assayService = AssayService.get();
             // This can be slightly expensive to fetch, so don't do it multiple times if runs share protocols
             Map<ExpProtocol, ProtocolImplementation> protocolImpls = new HashMap<>();
 
@@ -4264,18 +4266,21 @@ public void deleteExperimentRuns(Container container, final User user, @Nullable
                                 throw new UnauthorizedException("Cannot delete rows from dataset " + dataset);
                             }
 
-                            AssayProvider provider = AssayService.get().getProvider(protocol);
-                            if (provider != null)
+                            if (assayService != null)
                             {
-                                AssayTableMetadata tableMetadata = provider.getTableMetadata(protocol);
-                                SimpleFilter filter = new SimpleFilter(tableMetadata.getRunRowIdFieldKeyFromResults(), run.getRowId());
-                                Collection<String> lsids = new TableSelector(tableInfo, singleton("LSID"), filter, null).getCollection(String.class);
+                                AssayProvider provider = assayService.getProvider(protocol);
+                                if (provider != null)
+                                {
+                                    AssayTableMetadata tableMetadata = provider.getTableMetadata(protocol);
+                                    SimpleFilter filter = new SimpleFilter(tableMetadata.getRunRowIdFieldKeyFromResults(), run.getRowId());
+                                    Collection<String> lsids = new TableSelector(tableInfo, singleton("LSID"), filter, null).getCollection(String.class);
 
-                                // Add an audit event to the link to study history
-                                publishService.addRecallAuditEvent(run.getContainer(), user, dataset, lsids.size(), null);
+                                    // Add an audit event to the link to study history
+                                    publishService.addRecallAuditEvent(run.getContainer(), user, dataset, lsids.size(), null);
 
-                                // Do the actual delete on the dataset for the rows in question
-                                dataset.deleteDatasetRows(user, lsids);
+                                    // Do the actual delete on the dataset for the rows in question
+                                    dataset.deleteDatasetRows(user, lsids);
+                                }
                             }
                         }
                     }
@@ -4339,12 +4344,12 @@ public void deleteExperimentRuns(Container container, final User user, @Nullable
                 //  ideally this would be transacted as a commit task but we decided against it due to complications
                 run.archiveDataFiles(user);
                 // Re-index replaced run if replacing run is deleted
-                if (run.getReplacesRuns() != null)
+                if (assayService != null && run.getReplacesRuns() != null)
                 {
                     List<ExpRunImpl> replacedRuns = run.getReplacesRuns();
                     transaction.addCommitTask(() ->
                         replacedRuns.forEach(replacedRun ->
-                                AssayService.get().indexAssayRun(SearchService.get().defaultTask().getQueue(container, SearchService.PRIORITY.modified), replacedRun.getRowId())
+                                assayService.indexAssayRun(SearchService.get().defaultTask().getQueue(container, SearchService.PRIORITY.modified), replacedRun.getRowId())
                         ),
                         DbScope.CommitTaskOption.POSTCOMMIT
                     );
@@ -6469,8 +6474,12 @@ public Protocol saveProtocol(
             if (newProtocol)
             {
                 // if protocol exists, throw error
-                if (AssayService.get().getAssayProtocolByName(protocol.getContainer(), protocol.getName()) != null)
-                    throw new RuntimeSQLException(new SQLException("Assay design with name '" + protocol.getName() + "' already exists."));
+                if (GPAT_PROTOCOL_LSID_PREFIX.equals(protocol.getLSIDNamespacePrefix()) && AssayService.get() != null)
+                {
+                    ExpProtocol existingProtocol = AssayService.get().getAssayProtocolByName(protocol.getContainer(), protocol.getName());
+                    if (existingProtocol != null && GPAT_PROTOCOL_LSID_PREFIX.equals(existingProtocol.getLSIDNamespacePrefix()))
+                        throw new RuntimeSQLException(new SQLException("Assay design with name '" + protocol.getName() + "' already exists."));
+                }
 
                 result = Table.insert(user, getTinfoProtocol(), protocol);
             }
@@ -9793,26 +9802,30 @@ public Map<String, Integer> moveAssayRuns(@NotNull List<? extends ExpRun> assayR
                 AbstractQueryUpdateService.addTransactionAuditEvent(transaction, user, auditEvent);
             }
 
-            for (Map.Entry<ExpProtocol, List<ExpRun>> entry: protocolMap.entrySet())
+            AssayService assayService = AssayService.get();
+            if (assayService != null)
             {
-                ExpProtocol protocol = entry.getKey();
-                AssayProvider provider = AssayService.get().getProvider(protocol);
-                List<ExpRun> runs = entry.getValue();
-                if (provider != null)
+                for (Map.Entry<ExpProtocol, List<ExpRun>> entry: protocolMap.entrySet())
                 {
-                    provider.moveRuns(runs, targetContainer, user, assayMoveData);
-                    Map<String, Integer> counts = assayMoveData.counts();
-                    int auditEventCount = expService.moveAuditEvents(targetContainer, runLsids);
-                    counts.put("auditEvents", counts.getOrDefault("auditEvents", 0) + auditEventCount);
-                    if (auditBehavior != null && AuditBehaviorType.NONE != auditBehavior)
+                    ExpProtocol protocol = entry.getKey();
+                    AssayProvider provider = assayService.getProvider(protocol);
+                    List<ExpRun> runs = entry.getValue();
+                    if (provider != null)
                     {
-                        for (ExpRun run : runs)
+                        provider.moveRuns(runs, targetContainer, user, assayMoveData);
+                        Map<String, Integer> counts = assayMoveData.counts();
+                        int auditEventCount = expService.moveAuditEvents(targetContainer, runLsids);
+                        counts.put("auditEvents", counts.getOrDefault("auditEvents", 0) + auditEventCount);
+                        if (auditBehavior != null && AuditBehaviorType.NONE != auditBehavior)
                         {
-                            run.setContainer(targetContainer);
+                            for (ExpRun run : runs)
+                            {
+                                run.setContainer(targetContainer);
 
-                            // Issue 52570: include source and target containers in the audit event message
-                            String message = String.format("Moved from %s to %s", container.getPath(), targetContainer.getPath());
-                            auditRunEvent(user, protocol, run, null, "Assay run was moved.", userComment, message);
+                                // Issue 52570: include source and target containers in the audit event message
+                                String message = String.format("Moved from %s to %s", container.getPath(), targetContainer.getPath());
+                                auditRunEvent(user, protocol, run, null, "Assay run was moved.", userComment, message);
+                            }
                         }
                     }
                 }
diff --git a/query/src/org/labkey/query/LinkedSchema.java b/query/src/org/labkey/query/LinkedSchema.java
@@ -16,6 +16,7 @@
 package org.labkey.query;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.Strings;
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -106,7 +107,7 @@ public static LinkedSchema get(User user, Container container, LinkedSchemaDef d
         Container sourceContainer = def.lookupSourceContainer();
         if (sourceContainer == null)
         {
-            LOG.warn("Source container '" + def.getSourceContainerId() + "' not found for linked schema " + def.getUserSchemaName());
+            LOG.warn("Source container '{}' not found for linked schema {}", def.getSourceContainerId(), def.getUserSchemaName());
             return null;
         }
 
@@ -117,7 +118,7 @@ public static LinkedSchema get(User user, Container container, LinkedSchemaDef d
         UserSchema sourceSchema = getSourceSchema(def, sourceSchemaName, sourceContainer, user);
         if (sourceSchema == null)
         {
-            LOG.warn("Source schema '" + sourceSchemaName + "' not found in container '" + sourceContainer.getPath() + "' for linked schema " + def.getUserSchemaName());
+            LOG.warn("Source schema '{}' not found in container '{}' for linked schema {}", sourceSchemaName, sourceContainer.getPath(), def.getUserSchemaName());
             return null;
         }
 
@@ -166,7 +167,7 @@ private static UserSchema getSourceSchema(LinkedSchemaDef def, String sourceSche
         // Disallow recursive linked schema
         if (def.lookupContainer() == sourceContainer && def.getUserSchemaName().equals(sourceSchemaName))
         {
-            LOG.warn("Disallowed recursive linked schema definition '" + sourceSchemaName + "' in container '" + sourceContainer.getPath() + "'");
+            LOG.warn("Disallowed recursive linked schema definition '{}' in container '{}'", sourceSchemaName, sourceContainer.getPath());
             return null;
         }
 
@@ -343,7 +344,7 @@ protected LinkedTableInfo createWrappedTable(String name, @NotNull TableInfo sou
         if (null != metaData && null != metaData.getIncludeColumnsList())
         {
             String cols = StringUtils.trim(metaData.getIncludeColumnsList());
-            if (!StringUtils.equals("*",cols))
+            if (!Strings.CS.equals("*",cols))
             {
                 includedFields = Arrays.stream(StringUtils.split(cols,";"))
                     .map((col)->new FieldKey(null,col))
@@ -483,7 +484,7 @@ public static String generateLabKeySQL(TableInfo sourceTable, SQLWhereClauseSour
             for (QueryService.ParameterDecl decl : parameterDecls)
             {
                 sql.append(paramSep);
-                sql.append("  \"").append(decl.getName()).append("\" ").append(decl.getJdbcType().name());
+                sql.append(" ").append(FieldKey.fromParts(decl.getName()).toSQLString()).append(" ").append(decl.getJdbcType().name());
                 if (decl.getDefault() != null)
                     sql.append(" DEFAULT ").append(decl.getDefault());
                 paramSep = ",\n";
@@ -499,7 +500,7 @@ public static String generateLabKeySQL(TableInfo sourceTable, SQLWhereClauseSour
             if (col.isAdditionalQueryColumn())
                 continue;
             sql.append(columnSep);
-            sql.append("\"").append(col.getName()).append("\"");
+            sql.append(col.getFieldKey().toSQLString());
             if (col.isHidden())
                 sql.append(" @hidden");
 

Original file line number	Diff line number	Diff line change
`@@ -41,6 +41,7 @@ public abstract class AbstractTsvAssayProvider extends AbstractAssayProvider`
`41`	`41`	`public static final String ASSAY_SCHEMA_NAME = "assayresult";`
`42`	`42`	`public static final String ROW_ID_COLUMN_NAME = "RowId";`
`43`	`43`	`public static final String DATA_ID_COLUMN_NAME = "DataId";`
	`44`	`+ public static final String GPAT_PROTOCOL_LSID_PREFIX = "GeneralAssayProtocol";`
`44`	`45`
`45`	`46`	`public AbstractTsvAssayProvider(String protocolLSIDPrefix, String runLSIDPrefix, AssayDataType dataType, Module declaringModule)`
`46`	`47`	`{`
Original file line number	Diff line number	Diff line change
`@@ -1911,7 +1911,7 @@ protected String getRecordSelectorValue(RenderContext ctx)`
`1911`	`1911`	`// of values (even if they're empty) between commas for deterministic parsing (bug 6755)`
`1912`	`1912`	`checkboxValue.append(and);`
`1913`	`1913`	`if (null != v)`
`1914`		`- checkboxValue.append(PageFlowUtil.filter(v.toString()));`
	`1914`	`+ checkboxValue.append(v);`
`1915`	`1915`	`and = ",";`
`1916`	`1916`	`}`
`1917`	`1917`	`}`
`@@ -1924,7 +1924,7 @@ protected String getRecordSelectorValue(RenderContext ctx)`
`1924`	`1924`	`// of values (even if they're empty) between commas for deterministic parsing (bug 6755)`
`1925`	`1925`	`checkboxValue.append(and);`
`1926`	`1926`	`if (null != v)`
`1927`		`- checkboxValue.append(PageFlowUtil.filter(v.toString()));`
	`1927`	`+ checkboxValue.append(v);`
`1928`	`1928`	`and = ",";`
`1929`	`1929`	`}`
`1930`	`1930`	`}`
Original file line number	Diff line number	Diff line change
`@@ -200,8 +200,8 @@ else if (contains(ILLEGAL, String.valueOf(c)))`
`200`	`200`
`201`	`201`	`static protected boolean contains(String[] strs, String s)`
`202`	`202`	`{`
`203`		`- for (int i = 0; i < strs.length; i++)`
`204`		`- if (strs[i].equals(s))`
	`203`	`+ for (String str : strs)`
	`204`	`+ if (str.equals(s))`
`205`	`205`	`return true;`
`206`	`206`
`207`	`207`	`return false;`
`@@ -221,7 +221,7 @@ protected QueryKey(QueryKey<T> parent, @NotNull String name)`
`221`	`221`	`_hash = _name.toLowerCase().hashCode() ^ Objects.hashCode(_parent);`
`222`	`222`	`}`
`223`	`223`
`224`		`- protected QueryKey(QueryKey<T> parent, Enum name)`
	`224`	`+ protected QueryKey(QueryKey<T> parent, Enum<?> name)`
`225`	`225`	`{`
`226`	`226`	`this(parent, name.toString());`
`227`	`227`	`}`
`@@ -251,7 +251,7 @@ public boolean equals(Object other)`
`251`	`251`	`{`
`252`	`252`	`if (other == null \|\| !(getClass().equals(other.getClass())))`
`253`	`253`	`return false;`
`254`		`- QueryKey that = (QueryKey) other;`
	`254`	`+ QueryKey<?> that = (QueryKey<?>) other;`
`255`	`255`	`return strEqualsIgnoreCase(_name, that._name) &&`
`256`	`256`	`Objects.equals(_parent, that._parent);`
`257`	`257`	`}`
`@@ -349,7 +349,7 @@ protected boolean needsQuotes(String part)`
`349`	`349`	`return true;`
`350`	`350`	`}`
`351`	`351`
`352`		`- public boolean startsWith(@NotNull QueryKey<? extends QueryKey> prefix)`
	`352`	`+ public boolean startsWith(@NotNull QueryKey<? extends QueryKey<?>> prefix)`
`353`	`353`	`{`
`354`	`354`	`if (size() < prefix.size())`
`355`	`355`	`return false;`
Original file line number	Diff line number	Diff line change
`@@ -153,7 +153,7 @@ public class TsvAssayProvider extends AbstractTsvAssayProvider`
`153`	`153`
`154`	`154`	`public TsvAssayProvider()`
`155`	`155`	`{`
`156`		`- this("GeneralAssayProtocol", "GeneralAssayRun", "General" + RESULT_LSID_PREFIX_PART, ModuleLoader.getInstance().getModule(assayModuleClass));`
	`156`	`+ this(GPAT_PROTOCOL_LSID_PREFIX, "GeneralAssayRun", "General" + RESULT_LSID_PREFIX_PART, ModuleLoader.getInstance().getModule(assayModuleClass));`
`157`	`157`	`}`
`158`	`158`
`159`	`159`	`protected TsvAssayProvider(String protocolLSIDPrefix, String runLSIDPrefix, String resultRowLSIDPrefix, Module declaringModule)`
Original file line number	Diff line number	Diff line change
`@@ -3607,8 +3607,7 @@ private static FileTime getLastModified(InputStream in) throws IOException`
`3607`	`3607`	`{`
`3608`	`3608`	`try`
`3609`	`3609`	`{`
`3610`		`- SAXParserFactory factory = SAXParserFactory.newInstance();`
`3611`		`- SAXParser saxParser = factory.newSAXParser();`
	`3610`	`+ SAXParser saxParser = XmlBeansUtil.SAX_PARSER_FACTORY.newSAXParser();`
`3612`	`3611`	`final List<StringBuilder> lastModifieds = new ArrayList<>();`
`3613`	`3612`
`3614`	`3613`	`saxParser.parse(new InputSource(in), new DefaultHandler()`