Improve generics around QueryPropertyChange, other misc cleanup (#7009)

Author: labkey-jeckels

api/src/org/labkey/api/query/AbstractQueryChangeListener.java

@@ -40,13 +40,13 @@ public void queryCreated(User user, Container container, ContainerFilter scope,
     protected abstract void queryCreated(User user, Container container, ContainerFilter scope, SchemaKey schema, String query);
 
     @Override
-    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange> changes)
+    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange<?>> changes)
     {
-        for (QueryPropertyChange change : changes)
+        for (QueryPropertyChange<?> change : changes)
             queryChanged(user, container, scope, schema, change);
     }
 
-    protected abstract void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, QueryPropertyChange change);
+    protected abstract void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, QueryPropertyChange<?> change);
 
     @Override
     public void queryDeleted(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull Collection<String> queries)

api/src/org/labkey/api/query/QueryChangeListener.java

@@ -61,7 +61,7 @@ public interface QueryChangeListener
      * @param property The QueryProperty that has changed.
      * @param changes The set of change events.  Each QueryPropertyChange is associated with a single table or query.
      */
-    void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange> changes);
+    void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange<?>> changes);
 
     /**
      * This method is called when a set of tables or queries are deleted from the given container and schema.

api/src/org/labkey/api/query/QueryDefinition.java

@@ -155,8 +155,8 @@ public interface QueryDefinition
      * TableQueryDefinition and file-based queries cannot be deleted.
      * Fires the {@link QueryChangeListener#queryChanged(User, Container, ContainerFilter, SchemaKey, QueryProperty, Collection)} event.
      */
-    Collection<QueryPropertyChange> save(User user, Container container) throws SQLException;
-    Collection<QueryPropertyChange> save(User user, Container container, boolean fireChangeEvent) throws SQLException;
+    Collection<QueryPropertyChange<?>> save(User user, Container container) throws SQLException;
+    Collection<QueryPropertyChange<?>> save(User user, Container container, boolean fireChangeEvent) throws SQLException;
 
     /**
      * Delete the QueryDefinition.

api/src/org/labkey/api/query/QueryService.java

@@ -409,11 +409,11 @@ enum AuditAction
                 "%s was inserted or updated.",
                 "inserted or updated");
 
-        String _commentDetailed;
-        String _commentDetailedFormat;
-        String _commentSummary;
-        String _verbPastTense;
-        static String vowels = "aeiou";
+        final String _commentDetailed;
+        final String _commentDetailedFormat;
+        final String _commentSummary;
+        final String _verbPastTense;
+        final static String vowels = "aeiou";
 
         AuditAction(String commentSummary, String commentDetailedFormat, String verbPastTense)
         {
@@ -476,7 +476,7 @@ public String getDefaultCommentSummary()
 
     Collection<String> getQueryDependents(User user, Container container, ContainerFilter scope, SchemaKey schema, Collection<String> queries);
     void fireQueryCreated(User user, Container container, ContainerFilter scope, SchemaKey schema, Collection<String> queries);
-    void fireQueryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, QueryChangeListener.QueryProperty property, Collection<QueryChangeListener.QueryPropertyChange> changes);
+    void fireQueryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, QueryChangeListener.QueryProperty property, Collection<QueryChangeListener.QueryPropertyChange<?>> changes);
     void fireQueryDeleted(User user, Container container, ContainerFilter scope, SchemaKey schema, Collection<String> queries);
 
 

api/src/org/labkey/api/reader/BufferedReader.java

@@ -35,6 +35,7 @@ We use this implementation as it grows its buffer incrementally instead of alloc
  */
 
 import org.jetbrains.annotations.NotNull;
+import org.labkey.api.util.IntegerUtils;
 
 import java.io.IOException;
 import java.io.Reader;
@@ -476,7 +477,7 @@ public long skip(long amount) throws IOException {
                 return 0;
             }
             if (count - pos >= amount) {
-                pos += amount;
+                pos = IntegerUtils.asInteger(pos + amount);
                 return amount;
             }
 
@@ -487,7 +488,7 @@ public long skip(long amount) throws IOException {
                     return read;
                 }
                 if (count - pos >= amount - read) {
-                    pos += amount - read;
+                    pos = IntegerUtils.asInteger(pos + amount - read);
                     return amount;
                 }
                 // Couldn't get all the characters, skip what we read

api/src/org/labkey/api/reports/report/ReportDescriptor.java

@@ -588,7 +588,7 @@ protected String adjustPropertyValue(@Nullable FolderExportContext context, Stri
 
     // Let subclasses decide how they need to handle query/schema name changes, return true if changes have been made to the
     // descriptor. It is up to the caller to save the report changes
-    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange> changes, User user, Container container, boolean isSchemaUpdate)
+    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange<?>> changes, User user, Container container, boolean isSchemaUpdate)
     {
         return false;
     }

api/src/org/labkey/api/visualization/GenericChartReportDescriptor.java

@@ -17,26 +17,13 @@
 
 import org.json.JSONObject;
 import org.labkey.api.data.Container;
-import org.labkey.api.data.DisplayColumn;
-import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.property.DomainProperty;
-import org.labkey.api.query.CustomView;
 import org.labkey.api.query.QueryChangeListener;
-import org.labkey.api.query.QueryDefinition;
-import org.labkey.api.query.QueryException;
-import org.labkey.api.query.QueryService;
-import org.labkey.api.query.QuerySettings;
-import org.labkey.api.query.QueryView;
-import org.labkey.api.query.UserSchema;
-import org.labkey.api.query.ValidationException;
 import org.labkey.api.reports.model.ReportPropsManager;
 import org.labkey.api.reports.report.view.ReportUtil;
 import org.labkey.api.security.User;
 import org.labkey.api.util.Pair;
-import org.labkey.api.view.ViewContext;
-import org.labkey.api.writer.ContainerUser;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.List;
@@ -83,7 +70,7 @@ public Map<String, Object> getReportProps()
     }
 
     @Override
-    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange> changes, User user, Container container, boolean isSchemaUpdate)
+    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange<?>> changes, User user, Container container, boolean isSchemaUpdate)
     {
         if (getJSON() != null)
         {
@@ -95,7 +82,7 @@ public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.Qu
             String schemaName = queryJson.optString("schemaName", null);
             if ((queryName != null && !isSchemaUpdate) || (schemaName != null && isSchemaUpdate))
             {
-                for (QueryChangeListener.QueryPropertyChange qpc : changes)
+                for (QueryChangeListener.QueryPropertyChange<?> qpc : changes)
                 {
                     if (isSchemaUpdate)
                     {
@@ -204,64 +191,4 @@ private String updateJSON(String json)
 
         return newJson.toString();
     }
-
-    public QueryView getSourceQueryView(ViewContext viewContext, String schemaName, String queryName, String viewName, String dataRegionName) throws ValidationException
-    {
-        UserSchema schema = QueryService.get().getUserSchema(viewContext.getUser(), viewContext.getContainer(), schemaName);
-        if (schema == null)
-        {
-            throw new ValidationException("Invalid schema name: " + schemaName + ". ");
-        }
-        QuerySettings settings = schema.getSettings(viewContext, dataRegionName == null ? "query" : dataRegionName, queryName, viewName);
-        QueryView queryView = schema.createView(viewContext, settings, null);
-        if (queryView == null)
-        {
-            throw new ValidationException("Invalid query/view.");
-        }
-
-        return queryView;
-    }
-
-    // TODO: Delete?
-    private List<DisplayColumn> getDisplayColumns(ContainerUser context, String schemaName, String queryName, String viewName) throws ValidationException
-    {
-        UserSchema schema = QueryService.get().getUserSchema(context.getUser(), context.getContainer(), schemaName);
-        if (schema == null)
-        {
-            throw new ValidationException("Invalid schema name: " + schemaName + ". ");
-        }
-        QueryDefinition queryDefinition = schema.getQueryDef(queryName);
-        if (queryDefinition == null)
-            queryDefinition = QueryService.get().createQueryDefForTable(schema, queryName);
-
-        if (queryDefinition != null)
-        {
-            List<QueryException> errors = new ArrayList<>();
-            TableInfo tableInfo = queryDefinition.getTable(schema, errors, true);
-            if (tableInfo != null)
-            {
-                if (errors.isEmpty())
-                {
-                    CustomView customView = QueryService.get().getCustomView(context.getUser(), context.getContainer(), null, schemaName, queryName, viewName);
-                    return queryDefinition.getDisplayColumns(customView, tableInfo);
-                }
-                else
-                {
-                    StringBuilder sb = new StringBuilder();
-                    String delim = "";
-
-                    for (QueryException error : errors)
-                    {
-                        sb.append(delim).append(error.getMessage());
-                        delim = "\n";
-                    }
-                    throw new ValidationException("Unable to get table or query: " + sb);
-                }
-            }
-            else
-                throw new ValidationException("Unable to create the source table: " + queryName + " it may no longer exist, or you don't have access to it.");
-        }
-        else
-            throw new ValidationException("Unable to get a query definition for table : " + queryName);
-    }
 }

api/src/org/labkey/api/visualization/TimeChartReportDescriptor.java

@@ -173,7 +173,7 @@ private void convertPTIDSinGroups(JSONObject json, Map<String, String> alternate
     }
 
     @Override
-    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange> changes, User user, Container container, boolean isSchemaUpdate)
+    public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.QueryPropertyChange<?>> changes, User user, Container container, boolean isSchemaUpdate)
     {
         if (getJSON() != null)
         {
@@ -188,7 +188,7 @@ public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.Qu
 
             // most property updates only care about the query name old value string and new value string
             Map<String, String> nameChangeMap = new HashMap<>();
-            for (QueryChangeListener.QueryPropertyChange qpc : changes)
+            for (QueryChangeListener.QueryPropertyChange<?> qpc : changes)
             {
                 nameChangeMap.put((String)qpc.getOldValue(), (String)qpc.getNewValue());
             }
@@ -331,13 +331,13 @@ public boolean updateSchemaQueryNameReferences(Collection<QueryChangeListener.Qu
         return false;
     }
 
-    private boolean updateJSONObjectQueryNameReference(JSONObject json, boolean isSchemaChange, Collection<QueryChangeListener.QueryPropertyChange> changes)
+    private boolean updateJSONObjectQueryNameReference(JSONObject json, boolean isSchemaChange, Collection<QueryChangeListener.QueryPropertyChange<?>> changes)
     {
         String propName = isSchemaChange ? "schemaName" : "queryName";
         String oldValue = json.optString(propName, null);
         if (oldValue != null)
         {
-            for (QueryChangeListener.QueryPropertyChange qpc : changes)
+            for (QueryChangeListener.QueryPropertyChange<?> qpc : changes)
             {
                 if (oldValue.equals(qpc.getOldValue()))
                 {

experiment/src/org/labkey/experiment/ExperimentQueryChangeListener.java

@@ -63,7 +63,7 @@ private List<ExpDataClassImpl> getRenamedDataClasses(Container container, String
     }
 
     @Override
-    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange> changes)
+    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange<?>> changes)
     {
         boolean isSamples = schema.toString().equalsIgnoreCase("samples");
         boolean isData = schema.toString().equalsIgnoreCase("exp.data");
@@ -74,7 +74,7 @@ public void queryChanged(User user, Container container, ContainerFilter scope,
             return;
 
         Map<String, String> queryNameChangeMap = new CaseInsensitiveHashMap<>();
-        for (QueryPropertyChange qpc : changes)
+        for (QueryPropertyChange<?> qpc : changes)
         {
             String oldVal = (String)qpc.getOldValue();
             String newVal = (String)qpc.getNewValue();

experiment/src/org/labkey/experiment/PropertyQueryChangeListener.java

@@ -61,13 +61,13 @@ private void updateLookupSchema(String newValue, String oldSchema, Container con
     }
 
     @Override
-    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange> changes)
+    public void queryChanged(User user, Container container, ContainerFilter scope, SchemaKey schema, @NotNull QueryProperty property, @NotNull Collection<QueryPropertyChange<?>> changes)
     {
         // is there any other schema change other than assay renaming?
         boolean isSchemaChange = schema.toString().toLowerCase().startsWith("assay.general.");
 
         Map<String, String> queryNameChangeMap = new CaseInsensitiveHashMap<>();
-        for (QueryPropertyChange qpc : changes)
+        for (QueryPropertyChange<?> qpc : changes)
         {
             String oldVal = qpc.getOldValue() != null ? qpc.getOldValue().toString() : null;
             String newVal = qpc.getNewValue() != null ? qpc.getNewValue().toString() : null;