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getGroupConcat(SQLFragment)
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+10
-10
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2 files changed

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-10
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‎SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisCustomizer.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ private void addFileSetCol(AbstractTableInfo ti)
7878
String name = "fileSets";
7979
if (ti.getColumn(name) == null)
8080
{
81-
SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, "','")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
81+
SQLFragment sql = new SQLFragment("(SELECT ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("s.name"), true, true, ",")).append(" FROM sequenceanalysis.analysisSetMembers m JOIN sequenceanalysis.analysisSets s ON (s.rowid = m.analysisSet) WHERE m.outputFileId = " + ExprColumn.STR_TABLE_ALIAS + ".rowId)");
8282
ExprColumn newCol = new ExprColumn(ti, name, sql, JdbcType.VARCHAR, ti.getColumn("rowId"));
8383
newCol.setLabel("File Sets");
8484
newCol.setDisplayColumnFactory(new FileSetDisplayColumnFactory());

‎SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -134,7 +134,7 @@ private TableInfo createAnalysesTable(TableInfo sourceTable, ContainerFilter cf)
134134
{
135135
String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
136136
SQLFragment sql = new SQLFragment("(SELECT ").
137-
append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, chr + "(10)")).
137+
append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, new SQLFragment(chr + "(10)"))).
138138
append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " rd WHERE rd.analysis_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
139139
ExprColumn newCol = new ExprColumn(ret, "outputFileTypes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
140140
newCol.setLabel("Output File Types");
@@ -189,7 +189,7 @@ private TableInfo createOutputFiles(TableInfo sourceTable, ContainerFilter cf)
189189
if (ret.getColumn("analysisSets") == null)
190190
{
191191
String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
192-
SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("a.name"), true, true, chr + "(10)")).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SET_MEMBERS + " asm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SETS + " a ON (asm.analysisSet = a.rowid) WHERE asm.dataid = " + ExprColumn.STR_TABLE_ALIAS + ".dataid)");
192+
SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("a.name"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SET_MEMBERS + " asm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSIS_SETS + " a ON (asm.analysisSet = a.rowid) WHERE asm.dataid = " + ExprColumn.STR_TABLE_ALIAS + ".dataid)");
193193
ExprColumn newCol = new ExprColumn(ret, "analysisSets", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
194194
newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=analysisSetMembers&query.dataid~eq=${dataid}", ret.getContainer().isWorkbook() ? ret.getContainer().getParent() : ret.getContainer()));
195195
newCol.setLabel("Analyses Using This File");
@@ -283,14 +283,14 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
283283
newCol.setLabel("Total Files");
284284
ret.addColumn(newCol);
285285

286-
SQLFragment sql2 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("d.Name"), true, true, "','")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.data d ON (d.RowId = rd.fileId1 OR d.RowId = rd.fileId2) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
286+
SQLFragment sql2 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("d.Name"), true, true, ",")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.data d ON (d.RowId = rd.fileId1 OR d.RowId = rd.fileId2) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
287287
ExprColumn newCol2 = new ExprColumn(ret, "fileNames", sql2, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
288288
newCol2.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=readData&query.readset~eq=${rowid}"));
289289
newCol2.setLabel("File Names");
290290
newCol2.setDescription("This will display a comma-separated list of all file names with reads. This can be useful for SRA submissions.");
291291
ret.addColumn(newCol2);
292292

293-
SQLFragment sql3 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.sra_accession"), true, true, "','")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
293+
SQLFragment sql3 = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.sra_accession"), true, true, ",")).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
294294
ExprColumn newCol3 = new ExprColumn(ret, "sraRuns", sql3, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
295295
newCol3.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=readData&query.readset~eq=${rowid}"));
296296
newCol3.setLabel("SRA Runs");
@@ -327,7 +327,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
327327
if (ret.getColumn("distinctGenomes") == null)
328328
{
329329
String chr = ret.getSqlDialect().isPostgreSQL() ? "chr" : "char";
330-
SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("l.name"), true, true, (chr + "(10)"))).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " l ON (a.library_id = l.rowid) WHERE a.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
330+
SQLFragment sql = new SQLFragment("(SELECT ").append(ret.getSqlDialect().getGroupConcat(new SQLFragment("l.name"), true, true, new SQLFragment(chr + "(10)"))).append(new SQLFragment(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " a JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " l ON (a.library_id = l.rowid) WHERE a.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)"));
331331
ExprColumn newCol = new ExprColumn(ret, "distinctGenomes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
332332
newCol.setLabel("Genomes With Alignments For Readset");
333333
newCol.setWidth("200");
@@ -351,7 +351,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
351351
{
352352
String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
353353
SQLFragment sql = new SQLFragment("(SELECT ").
354-
append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, chr + "(10)")).
354+
append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.category"), true, true, new SQLFragment(chr + "(10)"))).
355355
append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_OUTPUTFILES + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
356356
ExprColumn newCol = new ExprColumn(ret, "outputFileTypes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
357357
newCol.setLabel("Output File Types");
@@ -390,7 +390,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
390390

391391
if (ret.getColumn("runIds") == null)
392392
{
393-
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.runId"), true, true, "','")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
393+
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("rd.runId"), true, true, ",")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
394394
ExprColumn newCol = new ExprColumn(ret, "runIds", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
395395
newCol.setLabel("Run(s)");
396396

@@ -400,7 +400,7 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
400400

401401
if (ret.getColumn("jobIds") == null)
402402
{
403-
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("runs.jobId"), true, true, "','")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.experimentrun runs ON (rd.runId = runs.rowId) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
403+
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("runs.jobId"), true, true, ",")).append(" FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd JOIN exp.experimentrun runs ON (rd.runId = runs.rowId) WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
404404
ExprColumn newCol = new ExprColumn(ret, "jobIds", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
405405
newCol.setLabel("Job(s)");
406406

@@ -453,7 +453,7 @@ private TableInfo createRefSequencesTable(TableInfo sourceTable)
453453
{
454454
SharedDataTable<?> ret = new SharedDataTable<>(this, sourceTable);
455455
String chr = sourceTable.getSqlDialect().isPostgreSQL() ? "chr" : "char";
456-
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("r.name"), true, true, chr + "(10)")).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS + " rm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " r ON (rm.library_id = r.rowid) WHERE rm.ref_nt_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
456+
SQLFragment sql = new SQLFragment("(SELECT ").append(sourceTable.getSqlDialect().getGroupConcat(new SQLFragment("r.name"), true, true, new SQLFragment(chr + "(10)"))).append(" as expr FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARY_MEMBERS + " rm JOIN " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_REF_LIBRARIES + " r ON (rm.library_id = r.rowid) WHERE rm.ref_nt_id = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
457457
ExprColumn newCol = new ExprColumn(ret, "genomes", sql, JdbcType.VARCHAR, sourceTable.getColumn("rowid"));
458458
newCol.setLabel("Genome(s) Using Sequence");
459459
newCol.setWidth("200");

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