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GitHub Issue 1188: Stop JDBC caching by default in QueryService #294

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GitHub Issue 1188: Stop JDBC caching by default in QueryService #294

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4eb5a8e
Migrate getSelectSQL callers to SelectBuilder API
labkey-jeckels May 24, 2026
be2b998
Eliminate redundant defaults
labkey-jeckels May 24, 2026
899e481
Merge remote-tracking branch 'origin/develop' into fb_selectCache
labkey-jeckels May 30, 2026
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4 changes: 2 additions & 2 deletions GenotypeAssays/src/org/labkey/genotypeassays/GeneticsTableCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -104,14 +104,14 @@ private void addAssayFieldsToAnalyses(AbstractTableInfo ti)
AssayProtocolSchema schema = ap.createProtocolSchema(ti.getUserSchema().getUser(), ti.getUserSchema().getContainer(), protocols.get(0), null);
TableInfo data = schema.getTable("data");

SQLFragment selectSql = QueryService.get().getSelectSQL(data, Collections.singleton(data.getColumn("analysisId")), new SimpleFilter(FieldKey.fromString("run/assayType"), GenotypeAssaysManager.SBT_LINEAGE_ASSAY_TYPE), null, 999999, 0, false);
SQLFragment selectSql = QueryService.get().getSelectBuilder(data).columns(Collections.singleton(data.getColumn("analysisId"))).filter(new SimpleFilter(FieldKey.fromString("run/assayType"), GenotypeAssaysManager.SBT_LINEAGE_ASSAY_TYPE)).maxRows(999999).buildSqlFragment();
SQLFragment sql = new SQLFragment("(select count(*) FROM (").append(selectSql).append(") a WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
ExprColumn newCol = new ExprColumn(ti, "numCachedResults", sql, JdbcType.INTEGER, ti.getColumn("rowid"));
newCol.setLabel("# Cached Lineages");
newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=assay." + ap.getName().replaceAll(" ", "") + "." + protocols.get(0).getName() + "&query.queryName=data&query.analysisId~eq=${rowid}&query.run/assayType~eq=" + GenotypeAssaysManager.SBT_LINEAGE_ASSAY_TYPE, (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer())));
ti.addColumn(newCol);

SQLFragment selectSql2 = QueryService.get().getSelectSQL(data, Collections.singleton(data.getColumn("analysisId")), new SimpleFilter(FieldKey.fromString("run/assayType"), GenotypeAssaysManager.HAPLOTYPE_ASSAY_TYPE), null, 999999, 0, false);
SQLFragment selectSql2 = QueryService.get().getSelectBuilder(data).columns(Collections.singleton(data.getColumn("analysisId"))).filter(new SimpleFilter(FieldKey.fromString("run/assayType"), GenotypeAssaysManager.HAPLOTYPE_ASSAY_TYPE)).maxRows(999999).buildSqlFragment();
SQLFragment sql2 = new SQLFragment("(select count(*) FROM (").append(selectSql2).append(") a WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
ExprColumn newCol2 = new ExprColumn(ti, "numCachedHaplotypes", sql2, JdbcType.INTEGER, ti.getColumn("rowid"));
newCol2.setLabel("# Cached Haplotypes");
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8 changes: 4 additions & 4 deletions tcrdb/src/org/labkey/tcrdb/TCRdbTableCustomizer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ private void addAssayFieldsToTable(AbstractTableInfo ti, String urlField, String
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("locus"), "None", CompareType.NEQ_OR_NULL);
filter.addCondition(FieldKey.fromString("disabled"), true, CompareType.NEQ_OR_NULL);

SQLFragment selectSql = QueryService.get().getSelectSQL(data, Arrays.asList(data.getColumn("analysisId"), data.getColumn("CDR3"), data.getColumn("locus"), data.getColumn("fraction"), data.getColumn("count"), data.getColumn("cDNA")), filter, null, Table.ALL_ROWS, Table.NO_OFFSET, false);
SQLFragment selectSql = QueryService.get().getSelectBuilder(data).columns(Arrays.asList(data.getColumn("analysisId"), data.getColumn("CDR3"), data.getColumn("locus"), data.getColumn("fraction"), data.getColumn("count"), data.getColumn("cDNA"))).filter(filter).buildSqlFragment();
DetailsURL details = DetailsURL.fromString("/query/executeQuery.view?schemaName=assay." + ap.getName().replaceAll(" ", "") + "." + protocols.get(0).getName() + "&query.queryName=data&query." + urlField + "~eq=${" + urlSourceCol + "}", (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer()));

SQLFragment sql = new SQLFragment("(select count(*) as expr FROM (").append(selectSql).append(") a ").append(whereClause).append(")");
Expand Down Expand Up @@ -173,7 +173,7 @@ private void addAssayFieldsToTable(AbstractTableInfo ti, String urlField, String
if (addRunColumns)
{
TableInfo runs = schema.getTable("runs");
SQLFragment runSelectSql = QueryService.get().getSelectSQL(runs, Collections.singletonList(runs.getColumn("analysisId")), null, null, Table.ALL_ROWS, Table.NO_OFFSET, false);
SQLFragment runSelectSql = QueryService.get().getSelectBuilder(runs).columns(Collections.singletonList(runs.getColumn("analysisId"))).buildSqlFragment();
DetailsURL runDetails = DetailsURL.fromString("/query/executeQuery.view?schemaName=assay." + ap.getName().replaceAll(" ", "") + "." + protocols.get(0).getName() + "&query.queryName=runs&query." + urlField + "~eq=${" + urlSourceCol + "}", (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer()));

SQLFragment sql5 = new SQLFragment("(select count(*) as expr FROM (").append(runSelectSql).append(") a ").append(whereClause).append(")");
Expand Down Expand Up @@ -206,7 +206,7 @@ private void addAssayClonotypeColumn(AbstractTableInfo ti)
SimpleFilter filter = new SimpleFilter(FieldKey.fromString("locus"), "None", CompareType.NEQ_OR_NULL);
filter.addCondition(FieldKey.fromString("disabled"), true, CompareType.NEQ_OR_NULL);

SQLFragment selectSql = QueryService.get().getSelectSQL(ti, Arrays.asList(ti.getColumn("analysisId"), ti.getColumn("cloneId"), ti.getColumn("Run"), ti.getColumn("cDNA"), ti.getColumn("cdr3"), ti.getColumn("locus")), filter, null, Table.ALL_ROWS, Table.NO_OFFSET, false);
SQLFragment selectSql = QueryService.get().getSelectBuilder(ti).columns(Arrays.asList(ti.getColumn("analysisId"), ti.getColumn("cloneId"), ti.getColumn("Run"), ti.getColumn("cDNA"), ti.getColumn("cdr3"), ti.getColumn("locus"))).filter(filter).buildSqlFragment();

String whereClause = " WHERE (a.cloneId = " + ExprColumn.STR_TABLE_ALIAS + ".cloneId AND a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysisId AND a.Run = " + ExprColumn.STR_TABLE_ALIAS + ".Run AND a.cDNA = " + ExprColumn.STR_TABLE_ALIAS + ".cDNA) ";
SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment(ti.getSqlDialect().concatenate("a.locus", "':'", "a.CDR3")), true, true, getNewlineSql(ti))).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
Expand Down Expand Up @@ -286,7 +286,7 @@ private void customizeClones(AbstractTableInfo ti)
if (ti.getColumn(colName) == null)
{
TableInfo data = schema.createDataTable(null,false);
SQLFragment dataSelectSql = QueryService.get().getSelectSQL(data, Arrays.asList(data.getColumn("subjectId"), data.getColumn("cdr3"), data.getColumn("fraction")), null, null, Table.ALL_ROWS, Table.NO_OFFSET, false);
SQLFragment dataSelectSql = QueryService.get().getSelectBuilder(data).columns(Arrays.asList(data.getColumn("subjectId"), data.getColumn("cdr3"), data.getColumn("fraction"))).buildSqlFragment();

SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("a.subjectId"), true, true, getNewlineSql(ti))).append(" as expr FROM (").append(dataSelectSql).append(") a WHERE a.cdr3 = " + ExprColumn.STR_TABLE_ALIAS + ".cdr3 AND a.fraction >= 0.005)");
ExprColumn col = new ExprColumn(ti, colName, sql, JdbcType.VARCHAR, ti.getColumn("cdr3"));
Expand Down