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Add a warm validation server so the JVM is reused between validations #1

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Add a warm validation server so the JVM is reused between validations #1

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cb7a149
Add a warm validation server so the JVM is reused between validations
corneliusroemer-agent Aug 26, 2026
dd35580
Reject oversized requests as such, and make the server stoppable
corneliusroemer-agent Aug 26, 2026
982c7b6
Answer the caller when a validation runs out of heap
corneliusroemer-agent Aug 26, 2026
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55 changes: 11 additions & 44 deletions src/main/java/uk/ac/ebi/ena/readtools/v2/cli/ValidateCli.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,20 +16,15 @@
import java.util.List;
import java.util.stream.Collectors;
import uk.ac.ebi.ena.readtools.v2.FileFormat;
import uk.ac.ebi.ena.readtools.v2.validator.ReadsValidationException;
import uk.ac.ebi.ena.readtools.v2.validator.ValidatorWrapper;

/**
* Standalone CLI wrapper around {@link ValidatorWrapper}, running the same client-side read
* validation that webin-cli performs, without the manifest / upload machinery.
* Standalone CLI wrapper around the v2 validator, running the same client-side read validation that
* webin-cli performs, without the manifest / upload machinery.
*
* <p>Usage: java -cp readtools-all.jar uk.ac.ebi.ena.readtools.v2.cli.ValidateCli \ --format FASTQ
* [--full] file1 [file2]
*/
public class ValidateCli {
// webin-cli's own limits: quick = first 100k reads, extended = first 100M reads.
private static final long QUICK_READ_LIMIT = 100_000L;
private static final long EXTENDED_READ_LIMIT = 100_000_000L;

@Parameter(
names = {"--format", "-f"},
Expand All @@ -52,8 +47,15 @@ public class ValidateCli {
private boolean help = false;

public static void main(String[] args) {
// `java -jar readtools.jar server ...` starts the warm validation server instead.
if (args.length > 0 && "server".equals(args[0])) {
ValidateServer.main(java.util.Arrays.copyOfRange(args, 1, args.length));
return;
}

ValidateCli cli = new ValidateCli();
JCommander jc = JCommander.newBuilder().addObject(cli).programName("readtools-validate").build();
JCommander jc =
JCommander.newBuilder().addObject(cli).programName("readtools-validate").build();

try {
jc.parse(args);
Expand All @@ -73,41 +75,6 @@ public static void main(String[] args) {

private int run() {
List<File> fileList = files.stream().map(File::new).collect(Collectors.toList());
for (File f : fileList) {
if (!f.isFile()) {
System.err.println("ERROR: file not found: " + f.getPath());
return 2;
}
}

long limit = full ? EXTENDED_READ_LIMIT : QUICK_READ_LIMIT;
ValidatorWrapper wrapper = new ValidatorWrapper(fileList, format, limit);

try {
wrapper.run();
} catch (ReadsValidationException e) {
System.out.println("RESULT: INVALID");
System.out.println(" " + e.getMessage());
return 1;
} catch (RuntimeException e) {
System.out.println("RESULT: INVALID (file structure / parse error)");
System.out.println(" " + (e.getCause() != null ? e.getCause().getMessage() : e.getMessage()));
return 1;
}

System.out.println("RESULT: VALID");
System.out.println(" format: " + format);
System.out.println(" mode: " + (full ? "full (<=100M reads)" : "quick (<=100k reads)"));
if (format == FileFormat.FASTQ && fileList.size() > 1) {
System.out.println(" paired: " + wrapper.isPaired());
}
wrapper
.getFileQualityStats()
.forEach(
s ->
System.out.printf(
" %s: reads=%d, highQuality(avg>=30)=%d%n",
s.getFile().getName(), s.getReadCount(), s.getHighQualityReadCount()));
return 0;
return ValidationRunner.validate(fileList, format, full, System.out, System.err);
}
}
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