Replace direct user of char() as string with SqlFragment in GroupConcats

Author: bbimber

GenotypeAssays/src/org/labkey/genotypeassays/GeneticsTableCustomizer.java

@@ -143,8 +143,7 @@ private void customizeSummaryByLineage(AbstractTableInfo ti)
             newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=assay." + ap.getName().replaceAll(" ", "") + "." + protocols.get(0).getName() + "&query.queryName=data&query.analysisId~eq=${analysis_id}", (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer())));
             ti.addColumn(newCol);
 
-            String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult.").append(d.getStorageTableName()).append(" a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = ").append(ti.getSqlDialect().getBooleanTRUE()).append(") WHERE a.analysisId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".analysis_id AND a.result IS NULL AND hs.name = ").append(ExprColumn.STR_TABLE_ALIAS).append(".lineages)");
+            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, getNewlineSql(ti))).append(" as expr FROM assayresult.").append(d.getStorageTableName()).append(" a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = ").append(ti.getSqlDialect().getBooleanTRUE()).append(") WHERE a.analysisId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".analysis_id AND a.result IS NULL AND hs.name = ").append(ExprColumn.STR_TABLE_ALIAS).append(".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");
             ti.addColumn(newCol3);
@@ -169,7 +168,7 @@ private void customizeSummaryGrouped(AbstractTableInfo ti)
 
             Domain d = ap.getResultsDomain(protocols.get(0));
             String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
+            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, getNewlineSql(ti))).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");
             ti.addColumn(newCol3);

tcrdb/src/org/labkey/tcrdb/TCRdbTableCustomizer.java

@@ -136,7 +136,7 @@ private void addAssayFieldsToTable(AbstractTableInfo ti, String urlField, String
             newCol3.setURL(details);
             ti.addColumn(newCol3);
 
-            SQLFragment sql4 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("CDR3"), true, true, getChr(ti) + "(10)")).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
+            SQLFragment sql4 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("CDR3"), true, true, getNewlineSql(ti))).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
             ExprColumn newCol4 = new ExprColumn(ti, "distinctCDR3s" + colNameSuffix, sql4, JdbcType.VARCHAR, ti.getColumn("rowid"));
             newCol4.setLabel("Distinct CDR3s" + colLabelSuffix);
             newCol4.setURL(details);
@@ -199,7 +199,7 @@ private void addAssayClonotypeColumn(AbstractTableInfo ti)
         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);
 
         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, getChr(ti) + "(10)")).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
+        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(" )");
         ExprColumn newCol = new ExprColumn(ti, "clonotypes", sql, JdbcType.VARCHAR, ti.getColumn("analysisId"), ti.getColumn("cloneId"));
         newCol.setLabel("Clonotype for Clone");
         newCol.setDescription("CDR3 clonotypes for this cloneId");
@@ -215,7 +215,7 @@ private void addClonotypeForLocusCol(AbstractTableInfo ti, SQLFragment selectSql
         DetailsURL detailsURL = details.clone();
         detailsURL.addParameter("data.locus~eq", locus);
 
-        SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("CDR3"), true, true, getChr(ti) + "(10)")).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
+        SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("CDR3"), true, true, getNewlineSql(ti))).append(" FROM (").append(selectSql).append(") a ").append(whereClause).append(" )");
         ExprColumn newCol = new ExprColumn(ti, "clonotype" + locus + colNameSuffix, sql, JdbcType.VARCHAR, ti.getColumn("rowid"));
         newCol.setLabel("Clonotype: " + locus + colLabelSuffix);
         newCol.setDescription("Showing CDR3 clonotypes for " + locus + " with fraction >=0.05");
@@ -250,7 +250,7 @@ private void customizeClones(AbstractTableInfo ti)
             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 sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("a.subjectId"), true, true, getChr(ti) + "(10)")).append(" as expr FROM (").append(dataSelectSql).append(") a WHERE a.cdr3 = " + ExprColumn.STR_TABLE_ALIAS + ".cdr3 AND a.fraction >= 0.005)");
+            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"));
             col.setLabel("Animals with CDR3");
             col.setURL(details);
@@ -265,7 +265,7 @@ private void customizeAssayData(AbstractTableInfo ti)
         String colName = "cloneNames";
         if (ti.getColumn(colName) == null)
         {
-            SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("c.cloneName"), true, true, getChr(ti) + "(10)")).append(" as expr FROM " + TCRdbSchema.NAME + "." + TCRdbSchema.TABLE_CLONES + " c WHERE c.cdr3 = " + ExprColumn.STR_TABLE_ALIAS + ".cdr3)");
+            SQLFragment sql = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("c.cloneName"), true, true, getNewlineSql(ti))).append(" as expr FROM " + TCRdbSchema.NAME + "." + TCRdbSchema.TABLE_CLONES + " c WHERE c.cdr3 = " + ExprColumn.STR_TABLE_ALIAS + ".cdr3)");
             ExprColumn col = new ExprColumn(ti, colName, sql, JdbcType.VARCHAR, ti.getColumn("cdr3"));
             col.setLabel("Clone Name(s)");
             ti.addColumn(col);