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Add metadata json as a required parameter
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bartcharbon committed Nov 27, 2024
1 parent 613bfb5 commit 0b4a2ac
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Showing 9 changed files with 851 additions and 37 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,8 @@ class AppCommandLineOptions {
static final String OPT_INPUT_LONG = "input";
static final String OPT_OUTPUT = "o";
static final String OPT_OUTPUT_LONG = "output";
static final String OPT_METADATA = "m";
static final String OPT_METADATA_LONG = "metadata";
static final String OPT_PED = "pd";
static final String OPT_PED_LONG = "pedigree";
static final String OPT_PROBANDS = "pb";
Expand Down Expand Up @@ -44,6 +46,13 @@ class AppCommandLineOptions {
.longOpt(OPT_OUTPUT_LONG)
.desc("Output VCF file (.vcf or .vcf.gz).")
.build());
appOptions.addOption(
Option.builder(OPT_METADATA)
.hasArg(true)
.required()
.longOpt(OPT_METADATA_LONG)
.desc("VCF metadata file (.json).")
.build());
appOptions.addOption(
Option.builder(OPT_PED)
.hasArg(true)
Expand Down Expand Up @@ -97,6 +106,7 @@ static Options getAppVersionOptions() {
static void validateCommandLine(CommandLine commandLine) {
validateInput(commandLine);
validateOutput(commandLine);
validateMetadata(commandLine);
}

private static void validateInput(CommandLine commandLine) {
Expand Down Expand Up @@ -132,4 +142,25 @@ private static void validateOutput(CommandLine commandLine) {
format("Output file '%s' already exists", outputPath));
}
}

private static void validateMetadata(CommandLine commandLine) {
Path metadataPath = Path.of(commandLine.getOptionValue(OPT_METADATA));
if (!Files.exists(metadataPath)) {
throw new IllegalArgumentException(
format("Metadata file '%s' does not exist.", metadataPath));
}
if (Files.isDirectory(metadataPath)) {
throw new IllegalArgumentException(
format("Metadata file '%s' is a directory.", metadataPath));
}
if (!Files.isReadable(metadataPath)) {
throw new IllegalArgumentException(
format("Metadata file '%s' is not readable.", metadataPath));
}
String inputPathStr = metadataPath.toString();
if (!inputPathStr.endsWith(".json")) {
throw new IllegalArgumentException(
format("Metadata file '%s' is not a .json file.", inputPathStr));
}
}
}
Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,7 @@ public void run(String... args) {
private Settings mapSettings(CommandLine commandLine) {
String inputPathValue = commandLine.getOptionValue(OPT_INPUT);
Path inputPath = Path.of(inputPathValue);
Path metadataPath = Path.of(commandLine.getOptionValue(OPT_METADATA));

Path outputPath;
if (commandLine.hasOption(OPT_OUTPUT)) {
Expand Down Expand Up @@ -111,7 +112,7 @@ private Settings mapSettings(CommandLine commandLine) {

return Settings.builder().inputVcfPath(inputPath).inputPedPaths(pedPaths)
.outputPath(outputPath).probands(probandNames).overwrite(overwriteOutput).
pathogenicClasses(pathogenicClasses).debug(debugMode)
pathogenicClasses(pathogenicClasses).metadataPath(metadataPath).debug(debugMode)
.build();
}

Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ public class Settings {
Path inputVcfPath;
List<Path> inputPedPaths;
Path outputPath;
Path metadataPath;
List<String> probands;
Set<String> pathogenicClasses;
boolean overwrite;
Expand Down
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
package org.molgenis.vcf.inheritance.matcher.util;

import org.molgenis.vcf.inheritance.matcher.model.Settings;
import org.molgenis.vcf.utils.metadata.FieldMetadataService;

public interface VepMetadataServiceFactory {
FieldMetadataService create();
FieldMetadataService create(Settings settings);
}
Original file line number Diff line number Diff line change
@@ -1,45 +1,19 @@
package org.molgenis.vcf.inheritance.matcher.util;

import org.molgenis.vcf.inheritance.matcher.model.Settings;
import org.molgenis.vcf.utils.metadata.FieldMetadataService;
import org.molgenis.vcf.utils.metadata.FieldMetadataServiceImpl;
import org.springframework.stereotype.Component;

import java.io.*;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;

/**
* Quirky class to enable reuse of {@link FieldMetadataService} from vip-utils
*/
@Component
public class VepMetadataServiceFactoryImpl implements VepMetadataServiceFactory {
private static final String EMPTY_METADATA_JSON = """
{
"format": {
},
"info": {
"CSQ": {
"nestedFields": {
}
}
}
}
""";

@Override
@SuppressWarnings("java:S5443")
public FieldMetadataService create() {
File json;
try {
Path path = Files.createTempFile("metadata", ".json");
byte[] buf = EMPTY_METADATA_JSON.getBytes(StandardCharsets.UTF_8);
Files.write(path, buf);
json = path.toFile();
json.deleteOnExit();
} catch (IOException e) {
throw new UncheckedIOException(e);
}
return new FieldMetadataServiceImpl(json);
public FieldMetadataService create(Settings settings) {
return new FieldMetadataServiceImpl(settings.getMetadataPath().toFile());
}
}
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ public VcfReaderFactoryImpl(VepMetadataServiceFactoryImpl vepMetadataServiceFact
public VcfReader create(Settings settings) {
Path inputVcfPath = settings.getInputVcfPath();
VCFFileReader vcfFileReader = new VCFFileReader(inputVcfPath.toFile(), false);
VepMetadata vepMetadata = new VepMetadata(vcfFileReader.getFileHeader(), vepMetadataServiceFactoryImpl.create());
VepMetadata vepMetadata = new VepMetadata(vcfFileReader.getFileHeader(), vepMetadataServiceFactoryImpl.create(settings));
return new VcfReader(vcfFileReader, new VcfRecordFactoryImpl(vepMetadata), settings.getPathogenicClasses());
}
}
12 changes: 8 additions & 4 deletions src/test/java/org/molgenis/vcf/inheritance/matcher/AppIT.java
Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,11 @@ class AppIT {
@Test
void testNoVep() throws IOException {
String inputFile = ResourceUtils.getFile("classpath:integration_noVEPinheritance.vcf").toString();
String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
String pedigree = ResourceUtils.getFile("classpath:pedigree_complex.ped").toString();
String outputFile = sharedTempDir.resolve("actual.vcf").toString();

String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree};
String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-m", metadataFile};
SpringApplication.run(App.class, args);

String outputVcf = Files.readString(Path.of(outputFile));
Expand All @@ -35,9 +36,10 @@ void testNoVep() throws IOException {
@Test
void testNoPed() throws IOException {
String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
String outputFile = sharedTempDir.resolve("actual.vcf").toString();

String[] args = {"-i", inputFile, "-o", outputFile, "-c", "P"};
String[] args = {"-i", inputFile, "-o", outputFile, "-c", "P", "-m", metadataFile};
SpringApplication.run(App.class, args);

String outputVcf = Files.readString(Path.of(outputFile));
Expand All @@ -51,10 +53,11 @@ void testNoPed() throws IOException {
@Test
void testProband() throws IOException {
String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
String pedigree = ResourceUtils.getFile("classpath:pedigree_complex.ped").toString();
String outputFile = sharedTempDir.resolve("actual.vcf").toString();

String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force" ,"-c","P,B"};
String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force" ,"-c","P,B", "-m", metadataFile};
SpringApplication.run(App.class, args);

String outputVcf = Files.readString(Path.of(outputFile));
Expand All @@ -68,10 +71,11 @@ void testProband() throws IOException {
@Test
void testNoParents() throws IOException {
String inputFile = ResourceUtils.getFile("classpath:integration.vcf").toString();
String metadataFile = ResourceUtils.getFile("classpath:metadata.json").toString();
String pedigree = ResourceUtils.getFile("classpath:pedigree_fam_no_parents.ped").toString();
String outputFile = sharedTempDir.resolve("actual.vcf").toString();

String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force"};
String[] args = {"-i", inputFile, "-o", outputFile, "-pd", pedigree, "-pb", "Patient,Patient2", "--force", "-m", metadataFile};
SpringApplication.run(App.class, args);

String outputVcf = Files.readString(Path.of(outputFile));
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,12 @@

import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.molgenis.vcf.inheritance.matcher.model.Settings;

import java.nio.file.Path;

import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;

class VepMetadataServiceFactoryImplTest {
private VepMetadataServiceFactoryImpl vepMetadataServiceFactoryImpl;
Expand All @@ -13,7 +19,9 @@ void setUp() {

@Test
void create() {
Settings settings = mock(Settings.class);
when(settings.getMetadataPath()).thenReturn(Path.of("TEST"));
// test that no exception is thrown
vepMetadataServiceFactoryImpl.create();
vepMetadataServiceFactoryImpl.create(settings);
}
}
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