DatabaseIdentifier

elispotassay/src/org/labkey/elispot/query/ElispotRunDataTable.java

@@ -219,8 +219,7 @@ private PlateReader getReader(RenderContext ctx)
                 ColumnInfo plateReaderColumn = ctx.getFieldMap().get(FieldKey.fromParts("Run", "PlateReader"));
                 if (null != plateReaderColumn)
                 {
-                    String readerAlias = plateReaderColumn.getAlias();
-                    Object readerName = ctx.getRow().get(readerAlias);
+                    Object readerName = plateReaderColumn.getValue(ctx);
 
                     if (readerName != null)
                     {

flow/src/org/labkey/flow/controllers/executescript/ChooseRunsToAnalyzeForm.java

@@ -21,6 +21,7 @@
 import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.DataRegionSelection;
 import org.labkey.api.data.Filter;
+import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FieldKey;
@@ -226,25 +227,25 @@ public SimpleFilter getBaseFilter(TableInfo table, Filter filter)
 
             List<FlowRun> runs = FlowRun.getRunsForContainer(getContainer(), FlowProtocolStep.keywords);
             int runCount = 0;
-            StringBuilder sql = new StringBuilder("RowId IN (");
+            SQLFragment sql = new SQLFragment("RowId IN (");
             String comma = "";
             for (FlowRun run : runs)
             {
                 if (run.getPath() == null)
                     continue;
                 sql.append(comma);
                 comma = ",";
-                sql.append(run.getRunId());
+                sql.appendValue(run.getRunId());
                 runCount ++;
             }
             sql.append(")");
             if (runCount == 0)
             {
-                ret.addWhereClause("1 = 0", null);
+                ret.addWhereClause(new SQLFragment("1 = 0"));
             }
             else
             {
-                ret.addWhereClause(sql.toString(), new Object[0], FieldKey.fromParts("RowId"));
+                ret.addWhereClause(sql, FieldKey.fromParts("RowId"));
             }
             return ret;
         }

flow/src/org/labkey/flow/controllers/executescript/SamplesConfirmGridView.java

@@ -38,6 +38,7 @@
 import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.SimpleDisplayColumn;
 import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.exp.api.ExpData;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.security.User;
@@ -94,12 +95,11 @@ public SamplesConfirmGridView(User user, Container container, SelectedSamples da
     public SamplesConfirmGridView(User user, Container container, Collection<String> keywords, List<? extends ISampleInfo> samples, boolean resolving, Map<String, SelectedSamples.ResolvedSample> rows, Errors errors)
     {
         super(new SamplesConfirmDataRegion(), errors);
-
         boolean hasGroupInfo = samples.get(0) instanceof Workspace.SampleInfo;
 
         // Create the list of columns
         keywords = KeywordUtil.filterHidden(keywords);
-        Map<FieldKey, ColumnInfo> columns = new LinkedHashMap<>();
+        Map<FieldKey, BaseColumnInfo> columns = new LinkedHashMap<>();
         if (resolving)
         {
             columns.put(MATCHED_FLAG_FIELD_KEY, new BaseColumnInfo(MATCHED_FLAG_FIELD_KEY, JdbcType.BOOLEAN));
@@ -116,7 +116,6 @@ public SamplesConfirmGridView(User user, Container container, Collection<String>
         {
             FieldKey fieldKey = new FieldKey(null, keyword);
             var col = new BaseColumnInfo(fieldKey, JdbcType.VARCHAR);
-            col.setAlias(fieldKey.getName());
             if (!columns.containsKey(fieldKey))
             {
                 uniqueKeywords.add(keyword);
@@ -127,8 +126,9 @@ public SamplesConfirmGridView(User user, Container container, Collection<String>
                 LOG.warn("Ignoring duplicate columns for FieldKey '" + fieldKey + "', got: '" + col.getName() + "' and '" + columns.get(fieldKey).getName() + "'");
             }
         }
-
+        // these are "fake" columns (set fake aliases)
         int columnCount = columns.size();
+        columns.values().forEach(c -> c.setAlias(SqlDialect.makeDatabaseIdentifier(c.getName(), null)));
 
         List<String> columnNames = columns.keySet().stream().map(FieldKey::getName).collect(Collectors.toList());
         RowMapFactory<Object> factory = new RowMapFactory<>(columnNames);
@@ -189,7 +189,7 @@ public SamplesConfirmGridView(User user, Container container, Collection<String>
 
         // Initialize the ResultSet and DataRegion
         ResultSet rs = CachedResultSets.create(maps);
-        Results results = new ResultsImpl(rs, columns);
+        Results results = new ResultsImpl(rs, (Map<FieldKey,ColumnInfo>)(Map)columns);
         setResults(results);
 
         SamplesConfirmDataRegion dr = (SamplesConfirmDataRegion)getDataRegion();

flow/src/org/labkey/flow/query/FCSFileCoalescingColumn.java

@@ -134,7 +134,7 @@ public void declareJoins(String parentAlias, Map<String, SQLFragment> map)
         SQLFragment coalesceFrag = new SQLFragment();
         coalesceFrag.append("SELECT\n");
         for (FieldKey pkCol : pkCols)
-            coalesceFrag.append("  ").append(columnMap.get(pkCol).getAlias()).append("\n");
+            coalesceFrag.append("  ").appendIdentifier(columnMap.get(pkCol).getAlias()).append("\n");
 
         for (Map.Entry<String, Pair<FieldKey, FieldKey>> entry : pairs.entrySet())
         {
@@ -143,9 +143,9 @@ public void declareJoins(String parentAlias, Map<String, SQLFragment> map)
 
             coalesceFrag.append(",\n");
             coalesceFrag.append("  COALESCE(\n");
-            coalesceFrag.append(columnMap.get(pair.first).getAlias());
+            coalesceFrag.appendIdentifier(columnMap.get(pair.first).getAlias());
             coalesceFrag.append(", ");
-            coalesceFrag.append(columnMap.get(pair.second).getAlias());
+            coalesceFrag.appendIdentifier(columnMap.get(pair.second).getAlias());
             coalesceFrag.append(") AS ").append(name);
         }
         coalesceFrag.append("\n");
@@ -162,7 +162,7 @@ public void declareJoins(String parentAlias, Map<String, SQLFragment> map)
             frag.append(and);
             frag.append(parentAlias).append(".").append(pkCol);
             frag.append(" = ");
-            frag.append(name).append(".").append(columnMap.get(pkCol).getAlias());
+            frag.append(name).append(".").appendIdentifier(columnMap.get(pkCol).getAlias());
             and = " AND ";
         }
 

flow/src/org/labkey/flow/query/FlowSchema.java

@@ -554,7 +554,7 @@ public void addAllowablePermission(Class<? extends Permission> permission)
 
         BaseColumnInfo addExpColumn(@NotNull ColumnInfo underlyingColumn)
         {
-            ExprColumn ret = new ExprColumn(this, underlyingColumn.getAlias(), underlyingColumn.getValueSql(ExprColumn.STR_TABLE_ALIAS), underlyingColumn.getJdbcType());
+            ExprColumn ret = new ExprColumn(this, underlyingColumn.getAlias().getId(), underlyingColumn.getValueSql(ExprColumn.STR_TABLE_ALIAS), underlyingColumn.getJdbcType());
             ret.copyAttributesFrom(underlyingColumn);
             ret.setHidden(underlyingColumn.isHidden());
             if (underlyingColumn.getFk() instanceof RowIdForeignKey)
@@ -1180,7 +1180,7 @@ public void addVocabularyDomains()
         @Override
         public void addCondition(@NotNull SQLFragment condition, FieldKey... fieldKeys)
         {
-            _filter.addWhereClause(condition.getSQL(), condition.getParams().toArray(), fieldKeys);
+            _filter.addWhereClause(condition, fieldKeys);
         }
 
         @Override
@@ -2123,7 +2123,7 @@ SQLFragment generateBackgroundJuctionSql()
             selectInto.append(and);
             if (null == fgMap.get(m) || null == bgMap.get(m))
                 return null;
-            selectInto.append("F.").append(fgMap.get(m).getAlias()).append("=B.").append(bgMap.get(m).getAlias());
+            selectInto.append("F.").appendIdentifier(fgMap.get(m).getAlias()).append("=B.").appendIdentifier(bgMap.get(m).getAlias());
             and = " AND ";
         }
 

flow/src/org/labkey/flow/reports/FilterFlowReport.java

@@ -51,6 +51,7 @@
 import org.labkey.flow.controllers.well.WellController;
 import org.labkey.flow.data.FlowProtocol;
 import org.labkey.flow.data.ICSMetadata;
+import org.labkey.flow.persist.FlowManager;
 import org.labkey.flow.query.FlowSchema;
 import org.labkey.flow.query.FlowTableType;
 import org.springframework.beans.PropertyValue;
@@ -195,7 +196,7 @@ void addScriptProlog(ViewContext context, StringBuffer sb)
     // Copied from ScriptEngineReport.
     private String oldLegalName(FieldKey fkey)
     {
-        String r = AliasManager.makeLegalName(StringUtils.join(fkey.getParts(), "_"), null, false, false);
+        String r = AliasManager.makeLegalName(StringUtils.join(fkey.getParts(), "_"), FlowManager.get().getSchema().getSqlDialect(), false);
         return ColumnInfo.propNameFromName(r).toLowerCase();
     }
 

flow/src/org/labkey/flow/reports/PositivityFlowReport.java

@@ -23,11 +23,9 @@
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.exp.PropertyDescriptor;
 import org.labkey.api.exp.PropertyType;
-import org.labkey.api.query.AliasManager;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.reports.report.ReportDescriptor;
 import org.labkey.api.util.LinkBuilder;
-import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.util.Tuple3;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.HtmlView;
@@ -41,6 +39,7 @@
 import org.labkey.flow.controllers.protocol.ProtocolController;
 import org.labkey.flow.data.FlowProtocol;
 import org.labkey.flow.data.ICSMetadata;
+import org.labkey.flow.persist.FlowManager;
 import org.springframework.beans.PropertyValues;
 import org.springframework.validation.BindException;
 
@@ -50,10 +49,6 @@
 import java.util.Collections;
 import java.util.List;
 
-/**
- * User: kevink
- * Date: 5/26/11
- */
 public class PositivityFlowReport extends FilterFlowReport
 {
     public static final String TYPE = "Flow.PositivityReport";
@@ -137,15 +132,15 @@ protected void addSelectList(ViewContext context, String tableName, StringBuilde
 
         for (FieldKey fieldKey : getMetadataColumns(metadata))
         {
-            String alias = AliasManager.makeLegalName(fieldKey, null, false);
+            String alias = FlowManager.get().getSchema().getSqlDialect().makeLegalName(fieldKey, 0);
             query.append("  ").append(tableName).append(".").append(toSQL(fieldKey)).append(" AS ").append(alias).append(",\n");
         }
 
         SubsetSpec subset = getSubset();
         SubsetSpec subsetParent = getSubsetParent();
 
         String stat = subset + ":Count";
-        String parentStat = subsetParent == null ? "Count" : subsetParent.toString() + ":Count";
+        String parentStat = subsetParent == null ? "Count" : subsetParent + ":Count";
 
         query.append("  ").append(tableName).append(".Statistic(").append(toSQL(stat)).append(") AS stat,\n");
         query.append("  ").append(tableName).append(".Background(").append(toSQL(stat)).append(") AS stat_bg,\n");

luminex/src/org/labkey/luminex/LuminexManager.java

@@ -687,16 +687,16 @@ private Set<String> getWellKeysForRun(Integer runId, ExpProtocol protocol, Conta
 
         new TableSelector(table, cols.values(), filter, null).forEachMap(row ->
         {
-            String readerSerialNumber = (String)row.get(cols.get(readerSerialNumberFK).getAlias());
-            Date acquisitionDate = (Date)row.get(cols.get(acquisitionDateFK).getAlias());
+            String readerSerialNumber = (String)cols.get(readerSerialNumberFK).getValue(row);
+            Date acquisitionDate = (Date)cols.get(acquisitionDateFK).getValue(row);
             String dataFileHeaderKey = getDataFileHeaderKey(readerSerialNumber, acquisitionDate);
 
-            String analyteName = (String)row.get(cols.get(analyteFK).getAlias());
-            String description = (String)row.get(cols.get(descriptionFK).getAlias());
-            String type = (String)row.get(cols.get(typeFK).getAlias());
-            Object dilutionObj = row.get(cols.get(dilutionFK).getAlias());
+            String analyteName = (String)cols.get(analyteFK).getValue(row);
+            String description = (String)cols.get(descriptionFK).getValue(row);
+            String type = (String)cols.get(typeFK).getValue(row);
+            Object dilutionObj = cols.get(dilutionFK).getValue(row);
             Double dilution = dilutionObj != null ? Double.parseDouble(dilutionObj.toString()) : null;
-            String well = onlyExcludedWells ? (String)row.get(cols.get(wellFK).getAlias()) : null;
+            String well = onlyExcludedWells ? (String)cols.get(wellFK).getValue(row) : null;
 
             excludedWellKeys.add(createWellKey(dataFileHeaderKey, analyteName, description, type, dilution, well));
         });

luminex/src/org/labkey/luminex/query/GuideSetTable.java

@@ -620,10 +620,10 @@ private void removeGuideSetQCFlagsByFlagType(int guideSetRowId, String flagType)
             inClauseSql.append(ExperimentService.get().getTinfoAssayQCFlag(), "qc");
             inClauseSql.append(" ON a.AnalyteId = qc.IntKey1 AND a.").append(colName).append(" = qc.IntKey2 ");
             inClauseSql.append(" WHERE a.GuideSetId = ? AND qc.FlagType = ?)");
-            Object[] params = new Object[]{guideSetRowId, flagType};
+            inClauseSql.addAll(guideSetRowId, flagType);
 
             SimpleFilter filter = new SimpleFilter();
-            filter.addWhereClause(inClauseSql.getSQL(), params, FieldKey.fromParts("RowId"));
+            filter.addWhereClause(inClauseSql, FieldKey.fromParts("RowId"));
             Table.delete(ExperimentService.get().getTinfoAssayQCFlag(), filter);
         }
     }

ms2/src/org/labkey/ms2/AbstractPeptideDisplayColumn.java

@@ -31,7 +31,7 @@ protected Object getColumnValue(RenderContext ctx, ColumnInfo colInfo, String...
         Object result = null;
         if (colInfo != null)
         {
-            result = ctx.get(colInfo.getAlias());
+            result = colInfo.getValue(ctx);
         }
         if (result == null)
         {

ms2/src/org/labkey/ms2/GroupNumberDisplayColumn.java

@@ -94,17 +94,13 @@ public HtmlString getFormattedHtml(RenderContext ctx)
             }
             else
             {
-                if (row.get(_collectionIdColumn.getAlias()) == null)
-                {
-                    return HtmlString.EMPTY_STRING;
-                }
-                Number collectionIdObject = (Number) row.get(_collectionIdColumn.getAlias());
+                Number collectionIdObject = (Number) _collectionIdColumn.getValue(row);
                 if (collectionIdObject == null)
                 {
                     return HtmlString.EMPTY_STRING;
                 }
                 collectionId = collectionIdObject.longValue();
-                Number groupNumberObject = (Number) row.get(getColumnInfo().getAlias());
+                Number groupNumberObject = (Number) getColumnInfo().getValue(row);
                 if (groupNumberObject == null)
                 {
                     return HtmlString.EMPTY_STRING;

ms2/src/org/labkey/ms2/MS2Importer.java

@@ -296,7 +296,7 @@ protected int createRun()
         runMap.put("Status", IMPORT_STARTED);
         runMap.put("Type", getType());    // TODO: Change how we handle type: For pepXML, this is null at this point... okay for Comet
 
-        Map returnMap = Table.insert(_user, MS2Manager.getTableInfoRuns(), runMap);
+        Map<String,Object> returnMap = Table.insert(_user, MS2Manager.getTableInfoRuns(), runMap);
         return (Integer)returnMap.get("Run");
     }
 
@@ -445,7 +445,7 @@ WHERE Fraction IN (SELECT Fraction FROM ms2.Fractions WHERE Run = ?) AND
 
     static
     {
-        StringBuilder sql = new StringBuilder();
+        SQLFragment sql = new SQLFragment();
         /*
         UPDATE ms2.PeptidesData SET SeqId = (SELECT
             CASE (SELECT Count(*) FROM
@@ -483,10 +483,10 @@ WHERE Fraction IN (SELECT Fraction FROM ms2.Fractions WHERE Run = ?) AND
         sql.append(")");
         sql.append(" WHERE SeqId IS NULL AND Fraction = ?");
 
-        _updateSwissProtSeqIdSql = sql.toString();
+        _updateSwissProtSeqIdSql = sql.getSQL();
     }
 
-    private static final String _updateSeqIdEndOfLookupStringSql;
+    private static String _updateSeqIdEndOfLookupStringSql;
 
     static
     {
@@ -547,7 +547,7 @@ WHERE Fraction IN (SELECT Fraction FROM ms2.Fractions WHERE Run = ?) AND
 
     static
     {
-        StringBuilder sql = new StringBuilder();
+        SQLFragment sql = new SQLFragment();
 
         /*
             UPDATE ms2.peptidesdata p SET SeqId = (
@@ -577,10 +577,10 @@ WHERE Fraction IN (SELECT Fraction FROM ms2.Fractions WHERE Run = ?) AND
         sql.append("        END)");
         sql.append(" WHERE SeqId IS NULL AND Fraction = ?");
 
-        _updateSeqIdInexactMatchSql = sql.toString();
+        _updateSeqIdInexactMatchSql = sql.getSQL();
     }
 
-    private static SQLFragment _updateSequencePositionSql;
+    private static final SQLFragment _updateSequencePositionSql;
 
     static
     {
@@ -636,18 +636,21 @@ protected void updatePeptideColumns(MS2Progress progress)
 
             for (int fastaId : run.getFastaIds())
             {
+                assert 3 == StringUtils.countMatches(_updateSwissProtSeqIdSql,"?");
                 int rowCount = executor.execute(_updateSwissProtSeqIdSql, fastaId, fastaId, fraction.getFraction());
                 _log.info("Set SeqId values for " + rowCount + " peptides" + (fractionCount == 1 ? "" : (" for fraction " + ++i + " of " + fractionCount)) + " based on protein identifier match from SwissProt database for FASTA id " + fastaId);
             }
 
             for (int fastaId : run.getFastaIds())
             {
+                assert 3 == StringUtils.countMatches(_updateSeqIdEndOfLookupStringSql, "?");
                 int rowCount = executor.execute(_updateSeqIdEndOfLookupStringSql, fraction.getFraction(), fastaId, fraction.getFraction());
                 _log.info("Set SeqId values for " + rowCount + " peptides" + (fractionCount == 1 ? "" : (" for fraction " + ++i + " of " + fractionCount)) + " based on trailing FASTA header line for FASTA id " + fastaId);
             }
 
             for (int fastaId : run.getFastaIds())
             {
+                assert 2 == StringUtils.countMatches(_updateSpPrefixSeqIdSql, "?");
                 int rowCount = executor.execute(_updateSpPrefixSeqIdSql, fraction.getFraction(), fastaId);
                 _log.info("Set SeqId values for " + rowCount + " peptides" + (fractionCount == 1 ? "" : (" for fraction " + ++i + " of " + fractionCount)) + " based on 'sp|' prefix name match for FASTA id " + fastaId);
             }