Remove panels.yaml and use json

genepi · Jul 24, 2024 · a084bac · a084bac
1 parent 1de0444
commit a084bac
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Showing 29 changed files with 455 additions and 412 deletions.
diff --git a/pom.xml b/pom.xml
@@ -107,12 +107,6 @@
 			<scope>test</scope>
 		</dependency>
 
-		<dependency>
-			<groupId>com.esotericsoftware.yamlbeans</groupId>
-			<artifactId>yamlbeans</artifactId>
-			<version>1.14</version>
-		</dependency>
-
 		<dependency>
 			<groupId>genepi</groupId>
 			<artifactId>genepi-io</artifactId>

diff --git a/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java b/src/main/java/genepi/imputationserver/steps/InputValidationCommand.java
@@ -74,6 +74,10 @@ public void setReport(String report) {
 		this.report = report;
 	}
 
+	public void setReference(String reference) {
+		this.reference = reference;
+	}
+
 	public void setPhasing(String phasing) {
 		this.phasing = phasing;
 	}
@@ -82,10 +86,6 @@ public void setPopulation(String population) {
 		this.population = population;
 	}
 
-	public void setRefPanel(RefPanel panel) {
-		this.panel = panel;
-	}
-
 	public void setBuild(String build) {
 		this.build = build;
 	}
@@ -131,13 +131,11 @@ public Integer call() throws Exception {
 			output = new OutputWriter();
 		}
 
-		if (panel == null) {
-			try {
-				panel = RefPanel.loadFromJson(reference);
-			} catch (Exception e) {
-				output.error("Unable to parse reference panel:" ,e);
-				return -1;
-			}
+		try {
+			panel = RefPanel.loadFromJson(reference);
+		} catch (Exception e) {
+			output.error("Unable to parse reference panel:" ,e);
+			return -1;
 		}
 
 		if (!checkParameters()) {

diff --git a/src/main/java/genepi/imputationserver/steps/QualityControlCommand.java b/src/main/java/genepi/imputationserver/steps/QualityControlCommand.java
@@ -76,14 +76,14 @@ public void setFiles(List<String> files) {
 		this.files = files;
 	}
 
-	public void setRefPanel(RefPanel panel) {
-		this.panel = panel;
-	}
-
 	public void setChainFile(String chainFile) {
 		this.chainFile = chainFile;
 	}
 
+	public void setReference(String reference) {
+		this.reference = reference;
+	}
+
 	public void setPopulation(String population) {
 		this.population = population;
 	}
@@ -125,13 +125,11 @@ public Integer call() throws Exception {
 			output = new OutputWriter();
 		}
 
-		if (panel == null) {
-			try {
-				panel = RefPanel.loadFromJson(reference);
-			} catch (Exception e) {
-				output.error("Unable to parse reference panel:", e);
-				return -1;
-			}
+		try {
+			panel = RefPanel.loadFromJson(reference);
+		} catch (Exception e) {
+			output.error("Unable to parse reference panel:", e);
+			return -1;
 		}
 
 		if (!analyzeFiles()) {

diff --git a/src/main/java/genepi/imputationserver/util/RefPanel.java b/src/main/java/genepi/imputationserver/util/RefPanel.java
@@ -1,13 +1,11 @@
 package genepi.imputationserver.util;
 
-import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import com.esotericsoftware.yamlbeans.YamlReader;
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import com.google.gson.JsonIOException;
@@ -289,35 +287,10 @@ public static RefPanel fromProperties(Object properties) throws IOException {
 
 	}
 
-	public static void resolveEnvVariable(Map<String, Object> properties, String folder) {
-		for (String key : properties.keySet()) {
-			Object value = properties.get(key);
-			if (value instanceof String) {
-				String valueString = value.toString().replaceAll("\\$\\{app_local_folder\\}", folder);
-				properties.put(key, valueString);
-			}
-		}
-	}
-
 	public static RefPanel loadFromJson(String filename) throws JsonSyntaxException, JsonIOException, IOException {
 		Gson gson = (new GsonBuilder()).create();
 		Map<String, Object> panel = gson.fromJson(new FileReader(filename), Map.class);
 		return fromProperties(panel);
 	}
 
-	public static RefPanel loadFromYamlFile(String filename, String id) throws IOException {
-
-		YamlReader reader = new YamlReader(new FileReader(filename));
-		List<Map<String, Object>> panels = reader.read(List.class);
-		for (Map<String, Object> panel : panels) {
-			if (panel.get("id").equals(id)) {
-				resolveEnvVariable(panel, (new File(filename).getParent()));
-				return fromProperties(panel);
-			}
-		}
-
-		throw new IOException("Reference panel '" + id + "' not found in file '" + filename + "'.");
-
-	}
-
 }
diff --git a/src/test/java/genepi/imputationserver/steps/InputValidationCommandTest.java b/src/test/java/genepi/imputationserver/steps/InputValidationCommandTest.java
@@ -27,13 +27,10 @@ public class InputValidationCommandTest extends AbstractTestcase {
 	@Test
 	public void testHg19DataWithBuild38() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/three";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setBuild("hg38");
 
 		assertEquals(-1, (int) command.call());
@@ -44,24 +41,13 @@ public void testHg19DataWithBuild38() throws Exception {
 
 	}
 
-	@Test(expected = IOException.class)
-	public void testWithWrongReferencePanel() throws IOException {
-
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
-		RefPanel.loadFromYamlFile(panels, "missing-reference-panel");
-
-	}
-
 	@Test
 	public void testHg38DataWithBuild19() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr20/panels.txt";
 		String inputFolder = "test-data/data/chr20-unphased-hg38";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr20/hapmap2.json");
 		command.setBuild("hg19");
 		command.setPopulation("eur");
 
@@ -76,13 +62,10 @@ public void testHg38DataWithBuild19() throws Exception {
 	@Test
 	public void testWrongVcfFile() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/wrong_vcf";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(-1, (int) command.call());
@@ -96,13 +79,10 @@ public void testWrongVcfFile() throws Exception {
 	@Test
 	public void testMixedPopulation() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("mixed");
 
 		assertEquals(0, (int) command.call());
@@ -112,13 +92,10 @@ public void testMixedPopulation() throws Exception {
 	@Test
 	public void testCorrectHrcPopulation() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hrc-fake");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hrc-fake.json");
 		command.setPopulation("mixed");
 
 		assertEquals(0, (int) command.call());
@@ -128,13 +105,10 @@ public void testCorrectHrcPopulation() throws Exception {
 	@Test
 	public void testWrongHrcPopulation() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hrc-fake");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hrc-fake.json");
 		command.setPopulation("aas");
 
 		assertEquals(-1, (int) command.call());
@@ -149,13 +123,10 @@ public void testWrongHrcPopulation() throws Exception {
 	@Test
 	public void testWrong1KP3Population() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "phase3-fake");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/phase3-fake.json");
 		command.setPopulation("asn");
 
 		assertEquals(-1, (int) command.call());
@@ -170,34 +141,27 @@ public void testWrong1KP3Population() throws Exception {
 	@Test
 	public void testWrongTopmedPopulation() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "TOPMedfreeze6-fake");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/TOPMedfreeze6-fake.json");
 		command.setPopulation("asn");
 
 		assertEquals(-1, (int) command.call());
 
 		OutputReader log = new OutputReader(CLOUDGENE_LOG);
-		log.view();
 		assertTrue(log.hasInMemory("::group type=error::"));
 		assertTrue(log.hasInMemory("Population 'asn' is not supported by reference panel 'TOPMedfreeze6-fake'"));
 	}
 
 	@Test
 	public void testUnorderedVcfFile() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		// input folder contains no vcf or vcf.gz files
 		String inputFolder = "test-data/data/unorderd";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(-1, (int) command.call());
@@ -211,13 +175,10 @@ public void testUnorderedVcfFile() throws Exception {
 	@Test
 	public void testWrongChromosomes() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/wrong_chrs";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(-1, (int) command.call());
@@ -230,19 +191,15 @@ public void testWrongChromosomes() throws Exception {
 	@Test
 	public void testSingleUnphasedVcfWithEagle() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/single";
 
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(0, (int) command.call());
 
 		OutputReader log = new OutputReader(CLOUDGENE_LOG);
-		log.view();
 		assertTrue(log.hasInMemory("1 valid VCF file(s) found."));
 		assertTrue(log.hasInMemory("Samples: 41"));
 		assertTrue(log.hasInMemory("Chromosomes: 1"));
@@ -257,13 +214,10 @@ public void testSingleUnphasedVcfWithEagle() throws Exception {
 	@Test
 	public void testThreeUnphasedVcfWithEagle() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
 		String inputFolder = "test-data/data/three";
-		// create workflow context
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
 
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(0, (int) command.call());
@@ -283,15 +237,10 @@ public void testThreeUnphasedVcfWithEagle() throws Exception {
 	@Test
 	public void testTabixIndexCreationChr20() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
-		// input folder contains no vcf or vcf.gz files
 		String inputFolder = "test-data/data/chr20-phased";
 
-		// create workflow context
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(0, (int) command.call());
@@ -321,15 +270,10 @@ public void testTabixIndexCreationChr20() throws Exception {
 	@Test
 	public void testTabixIndexCreationChr1() throws Exception {
 
-		String panels = "test-data/configs/hapmap-chr1/panels.txt";
-		// input folder contains no vcf or vcf.gz files
 		String inputFolder = "test-data/data/single";
 
-		// create workflow context
-		RefPanel panel = RefPanel.loadFromYamlFile(panels, "hapmap2");
-
 		InputValidationCommand command = buildCommand(inputFolder);
-		command.setRefPanel(panel);
+		command.setReference("test-data/configs/hapmap-chr1/hapmap2.json");
 		command.setPopulation("eur");
 
 		assertEquals(0, (int) command.call());