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Use PreparedStatement instead of looping Table.insert #739

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Merged
bbimber merged 5 commits into from
Mar 20, 2024
Merged

Use PreparedStatement instead of looping Table.insert #739

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774a617
Use PreparedStatement to try to improve insert perf for kinship task
bbimber Mar 15, 2024
554815f
Restore row count logging
bbimber Mar 15, 2024
41414e9
Process PreparedStatement in batches
bbimber Mar 16, 2024
5fa0841
Give the option to cancel kinship import mid-job if job is cancelled
bbimber Mar 18, 2024
0967e0f
Fix bad commit
bbimber Mar 18, 2024
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2 changes: 2 additions & 0 deletions ehr/resources/pipeline/kinship/populateKinship.r
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Original file line number Diff line number Diff line change
Expand Up @@ -67,4 +67,6 @@ for (species in unique(allPed$Species)){
}

# write TSV to disk
print(paste0('Total kinship records: ', nrow(newRecords)))
newRecords <- dplyr::arrange(newRecords, Id, Id2)
write.table(newRecords, file = "kinship.txt", append = FALSE, row.names = FALSE, quote = FALSE, sep = '\t')
51 changes: 36 additions & 15 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@
import org.labkey.api.exp.property.Domain;
import org.labkey.api.pipeline.AbstractTaskFactory;
import org.labkey.api.pipeline.AbstractTaskFactorySettings;
import org.labkey.api.pipeline.CancelledException;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineJobException;
import org.labkey.api.pipeline.RecordedAction;
Expand All @@ -59,9 +60,9 @@

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.LineNumberReader;
import java.sql.PreparedStatement;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -151,7 +152,7 @@ public RecordedActionSet run() throws PipelineJobException
FileAnalysisJobSupport support = (FileAnalysisJobSupport) job;

processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger());
processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryPath().toFile(), job.getLogger(), job);

if (GeneticCalculationsJob.isKinshipValidation())
{
Expand All @@ -165,10 +166,10 @@ public RecordedActionSet run() throws PipelineJobException
public static void standaloneProcessKinshipAndInbreeding(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
{
processInbreeding(c, u, pipelineDir, log);
processKinship(c, u, pipelineDir, log);
processKinship(c, u, pipelineDir, log, null);
}

private static void processKinship(Container c, User u, File pipelineDir, Logger log) throws PipelineJobException
private static void processKinship(Container c, User u, File pipelineDir, Logger log, @Nullable PipelineJob job) throws PipelineJobException
{
File output = new File(pipelineDir, KINSHIP_FILE);
if (!output.exists())
Expand Down Expand Up @@ -240,13 +241,22 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())
}

try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction();
BufferedReader reader = Readers.getReader(output))
BufferedReader reader = Readers.getReader(output);
PreparedStatement stmt = transaction.getConnection().prepareStatement(
"INSERT INTO " + EHRSchema.EHR_SCHEMANAME + ".kinship\n" +
"\t(Id, Id2, coefficient, container, created, createdby, modified, modifiedby)\n" +
"\tVALUES (?, ?, ?, ?, ?, ?, ?, ?)"))
{
log.info("Inserting rows");
String line = null;
int lineNum = 0;
while ((line = reader.readLine()) != null)
{
if (job != null && job.isCancelled())
{
throw new CancelledException();
}

String[] fields = line.split("\t");
if (fields.length < 3)
continue;
Expand All @@ -260,34 +270,45 @@ else if (kinshipTable.getSqlDialect().isPostgreSQL())
assert fields[0].length() < 80 : "Field Id value too long: [" + fields[0] + ']';
assert fields[1].length() < 80 : "Field Id2 value too long: [" + fields[1] + "]";

row.put("Id", fields[0]);
row.put("Id2", fields[1]);
stmt.setString(1, fields[0]); // Id
stmt.setString(2, fields[1]); // Id2
try
{
row.put("coefficient", Double.parseDouble(fields[2]));
stmt.setDouble(3, Double.parseDouble(fields[2])); // coefficient
}
catch (NumberFormatException e)
{
throw new PipelineJobException("Invalid kinship coefficient on line " + (lineNum + 1) + " for IDs " + fields[0] + " and " + fields[1] + ": " + fields[2], e);
}

row.put("container", c.getId());
row.put("created", new Date());
row.put("createdby", u.getUserId());
Table.insert(u, kinshipTable, row);
stmt.setString(4, c.getId()); // container
java.sql.Date now = new java.sql.Date(new Date().getTime());
stmt.setDate(5, now); // created
stmt.setInt(6, u.getUserId()); // createdby
stmt.setDate(7, now); // modified
stmt.setInt(8, u.getUserId()); // modifiedby

stmt.addBatch();

lineNum++;

if (lineNum % 100000 == 0)
{
log.info("processed " + lineNum + " rows");
stmt.executeBatch();
}

if (lineNum % 250000 == 0)
{
log.info("imported " + lineNum + " rows");
}
}

log.info("Inserted " + lineNum + " rows into ehr.kinship");
stmt.executeBatch();
transaction.commit();
log.info("Inserted " + lineNum + " rows into ehr.kinship");
}
}
catch (RuntimeSQLException | IOException e)
catch (RuntimeSQLException | SQLException | IOException e)
{
throw new PipelineJobException(e);
}
Expand Down