Fix for issues #410, #412 application fails to start due to NoUniqueB…

…eanDefinitionException when only hg38 data sources are defined
exomiser · Nov 23, 2021 · 1192984 · 1192984
1 parent ea9942a
commit 1192984
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Showing 9 changed files with 63 additions and 30 deletions.
diff --git a/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/Main.java b/exomiser-cli/src/main/java/org/monarchinitiative/exomiser/cli/Main.java
@@ -1,7 +1,7 @@
 /*
  * The Exomiser - A tool to annotate and prioritize genomic variants
  *
- * Copyright (c) 2016-2020 Queen Mary University of London.
+ * Copyright (c) 2016-2021 Queen Mary University of London.
  * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -24,6 +24,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration;
 
 import java.util.Locale;
 
@@ -33,7 +34,7 @@
  *
  * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk>
  */
-@SpringBootApplication
+@SpringBootApplication(exclude = {DataSourceAutoConfiguration.class})
 public class Main {
 
     private static final Logger logger = LoggerFactory.getLogger(Main.class);

diff --git a/...in/java/org/monarchinitiative/exomiser/autoconfigure/genome/AbstractGenomeProperties.java b/...in/java/org/monarchinitiative/exomiser/autoconfigure/genome/AbstractGenomeProperties.java
@@ -51,6 +51,10 @@ public abstract class AbstractGenomeProperties implements GenomeProperties {
     // datastore
     private String testPathogenicityScorePath = "";
 
+    protected AbstractGenomeProperties(GenomeAssembly assembly) {
+        this.assembly = assembly;
+    }
+
     @Override
     public Path getDataDirectory() {
         return dataDirectory;
@@ -61,10 +65,6 @@ public void setDataDirectory(String dataDirectory) {
         this.dataDirectory = Paths.get(dataDirectory);
     }
 
-    public AbstractGenomeProperties(GenomeAssembly assembly) {
-        this.assembly = assembly;
-    }
-
     public GenomeAssembly getAssembly() {
         return assembly;
     }

diff --git a/...c/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/Hg19GenomeProperties.java b/...c/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/Hg19GenomeProperties.java
@@ -26,7 +26,6 @@
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Primary;
 
 /**
  * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk>
@@ -44,17 +43,20 @@ public Hg19GenomeProperties() {
     // the default configuration is contained in the application.properties shipped in the jar's classpath
     // this can be overridden by the user in their own application.properties.
 
-    @Primary
     @Bean
     @ConfigurationProperties("exomiser.hg19.genome.datasource")
     public DataSourceProperties hg19genomeDataSourceProperties() {
         return new DataSourceProperties();
     }
 
-    @Primary
-    @Bean(name = "hg19genomeDataSource")
+    @Bean
     @ConfigurationProperties("exomiser.hg19.genome.datasource.hikari")
+    public HikariDataSource hg19genomeDataSource(DataSourceProperties hg19genomeDataSourceProperties) {
+        return hg19genomeDataSourceProperties.initializeDataSourceBuilder().type(HikariDataSource.class).build();
+    }
+
+    @Override
     public HikariDataSource genomeDataSource() {
-        return hg19genomeDataSourceProperties().initializeDataSourceBuilder().type(HikariDataSource.class).build();
+        return hg19genomeDataSource(hg19genomeDataSourceProperties());
     }
 }
diff --git a/...c/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/Hg38GenomeProperties.java b/...c/main/java/org/monarchinitiative/exomiser/autoconfigure/genome/Hg38GenomeProperties.java
@@ -44,10 +44,14 @@ public DataSourceProperties hg38genomeDataSourceProperties() {
         return new DataSourceProperties();
     }
 
-    @Bean(name = "hg38genomeDataSource")
+    @Bean
     @ConfigurationProperties("exomiser.hg38.genome.datasource.hikari")
-    public HikariDataSource genomeDataSource() {
-        return hg38genomeDataSourceProperties().initializeDataSourceBuilder().type(HikariDataSource.class).build();
+    public HikariDataSource hg38genomeDataSource(DataSourceProperties hg38genomeDataSourceProperties) {
+        return hg38genomeDataSourceProperties.initializeDataSourceBuilder().type(HikariDataSource.class).build();
     }
 
+    @Override
+    public HikariDataSource genomeDataSource() {
+        return hg38genomeDataSource(hg38genomeDataSourceProperties());
+    }
 }
diff --git a/...main/java/org/monarchinitiative/exomiser/autoconfigure/phenotype/PhenotypeProperties.java b/...main/java/org/monarchinitiative/exomiser/autoconfigure/phenotype/PhenotypeProperties.java
@@ -1,7 +1,7 @@
 /*
  * The Exomiser - A tool to annotate and prioritize genomic variants
  *
- * Copyright (c) 2016-2019 Queen Mary University of London.
+ * Copyright (c) 2016-2021 Queen Mary University of London.
  * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -48,10 +48,10 @@ public DataSourceProperties phenotypeDataSourceProperties() {
         return new DataSourceProperties();
     }
 
-    @Bean(name = "phenotypeDataSource")
+    @Bean
     @ConfigurationProperties("exomiser.phenotype.datasource.hikari")
-    public HikariDataSource phenotypeDataSource() {
-        return phenotypeDataSourceProperties().initializeDataSourceBuilder().type(HikariDataSource.class).build();
+    public HikariDataSource phenotypeDataSource(DataSourceProperties phenotypeDataSourceProperties) {
+        return phenotypeDataSourceProperties.initializeDataSourceBuilder().type(HikariDataSource.class).build();
     }
 
     //Random walk matrix for hiPhive and exomeWalker

diff --git a/...test/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfigurationTest.java b/...test/java/org/monarchinitiative/exomiser/autoconfigure/ExomiserAutoConfigurationTest.java
@@ -20,7 +20,6 @@
 
 package org.monarchinitiative.exomiser.autoconfigure;
 
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.exomiser.core.Exomiser;
 import org.monarchinitiative.exomiser.core.genome.GenomeAnalysisServiceProvider;
@@ -43,7 +42,6 @@ public class ExomiserAutoConfigurationTest extends AbstractAutoConfigurationTest
 
     // n.b there are issues with the @PreDestroy shutdown hooks for classes in the GenomeAnalysisServiceConfigurer using the MVStore
     // so all the relevant beans are being tested in one go
-    @Disabled("File lock exception when run as part of full test suite")
     @Test
     public void testAutoConfiguration() {
         load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710", "exomiser.hg38.data-version=1710", "exomiser.phenotype.data-version=1710");
@@ -59,6 +57,36 @@ public void testAutoConfiguration() {
         assertThat(phenotypeMatchService, instanceOf(PhenotypeMatchService.class));
     }
 
+    @Test
+    public void testHg19OnlyAutoConfiguration() {
+        load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710", "exomiser.phenotype.data-version=1710");
+        Exomiser exomiser = (Exomiser) context.getBean("exomiser");
+        assertThat(exomiser, instanceOf(Exomiser.class));
+
+        GenomeAnalysisServiceProvider genomeAnalysisServiceProvider = (GenomeAnalysisServiceProvider) context.getBean("genomeAnalysisServiceProvider");
+        assertThat(genomeAnalysisServiceProvider, instanceOf(GenomeAnalysisServiceProvider.class));
+        assertThat(genomeAnalysisServiceProvider.hasServiceFor(GenomeAssembly.HG19), is(true));
+        assertThat(genomeAnalysisServiceProvider.hasServiceFor(GenomeAssembly.HG38), is(false));
+
+        PhenotypeMatchService phenotypeMatchService = (PhenotypeMatchService) context.getBean("phenotypeMatchService");
+        assertThat(phenotypeMatchService, instanceOf(PhenotypeMatchService.class));
+    }
+
+    @Test
+    public void testHg38OnlyAutoConfiguration() {
+        load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg38.data-version=1710", "exomiser.phenotype.data-version=1710");
+        Exomiser exomiser = (Exomiser) context.getBean("exomiser");
+        assertThat(exomiser, instanceOf(Exomiser.class));
+
+        GenomeAnalysisServiceProvider genomeAnalysisServiceProvider = (GenomeAnalysisServiceProvider) context.getBean("genomeAnalysisServiceProvider");
+        assertThat(genomeAnalysisServiceProvider, instanceOf(GenomeAnalysisServiceProvider.class));
+        assertThat(genomeAnalysisServiceProvider.hasServiceFor(GenomeAssembly.HG19), is(false));
+        assertThat(genomeAnalysisServiceProvider.hasServiceFor(GenomeAssembly.HG38), is(true));
+
+        PhenotypeMatchService phenotypeMatchService = (PhenotypeMatchService) context.getBean("phenotypeMatchService");
+        assertThat(phenotypeMatchService, instanceOf(PhenotypeMatchService.class));
+    }
+
     @Configuration
     @ImportAutoConfiguration(value = ExomiserAutoConfiguration.class)
     protected static class EmptyConfiguration {

diff --git a/...tiative/exomiser/autoconfigure/genome/Hg19GenomeAnalysisServiceAutoConfigurationTest.java b/...tiative/exomiser/autoconfigure/genome/Hg19GenomeAnalysisServiceAutoConfigurationTest.java
@@ -39,11 +39,11 @@
 public class Hg19GenomeAnalysisServiceAutoConfigurationTest extends AbstractAutoConfigurationTest {
 
     @Test
-    public synchronized void genomeAnalysisService() throws Exception {
+    public void genomeAnalysisService() throws Exception {
 
-        load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710", "exomiser.hg19.local-frequency-path=../local/local_freq.tsv.gz");
+        load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710");
 
-        GenomeAnalysisService genomeAnalysisService = (GenomeAnalysisService) this.context.getBean("hg19genomeAnalysisService");
+        GenomeAnalysisService genomeAnalysisService = (GenomeAnalysisService) context.getBean("hg19genomeAnalysisService");
         assertThat(genomeAnalysisService.getGenomeAssembly(), equalTo(GenomeAssembly.HG19));
 
         assertThat(context.getBean("hg19jannovarData"), instanceOf(JannovarData.class));
@@ -60,7 +60,7 @@ public synchronized void genomeAnalysisService() throws Exception {
     }
 
     @Test
-    public synchronized void genomeAnalysisServiceWithOptionalTestPathDao() throws Exception {
+    public void genomeAnalysisServiceWithOptionalTestPathDao() throws Exception {
 
         String testPathogenicitySourcePath = TEST_DATA.resolve("remm/remmData.tsv.gz").toAbsolutePath().toString();
         load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg19.data-version=1710", "exomiser.hg19.test-pathogenicity-score-path=" + testPathogenicitySourcePath);

diff --git a/...tiative/exomiser/autoconfigure/genome/Hg38GenomeAnalysisServiceAutoConfigurationTest.java b/...tiative/exomiser/autoconfigure/genome/Hg38GenomeAnalysisServiceAutoConfigurationTest.java
@@ -43,7 +43,7 @@ public void genomeAnalysisService() throws Exception {
 
         load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg38.data-version=1710");
 
-        GenomeAnalysisService genomeAnalysisService = (GenomeAnalysisService) this.context.getBean("hg38genomeAnalysisService");
+        GenomeAnalysisService genomeAnalysisService = (GenomeAnalysisService) context.getBean("hg38genomeAnalysisService");
         assertThat(genomeAnalysisService.getGenomeAssembly(), equalTo(GenomeAssembly.HG38));
 
         assertThat(context.getBean("hg38jannovarData"), instanceOf(JannovarData.class));
@@ -61,6 +61,7 @@ public void genomeAnalysisService() throws Exception {
 
     @Test
     public void genomeAnalysisServiceWithOptionalTestPathDao() throws Exception {
+
         String testPathogenicitySourcePath = TEST_DATA.resolve("remm/remmData.tsv.gz").toAbsolutePath().toString();
         load(EmptyConfiguration.class, TEST_DATA_ENV, "exomiser.hg38.data-version=1710", "exomiser.hg38.test-pathogenicity-score-path=" + testPathogenicitySourcePath);
 

diff --git a/.../monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfigurationTest.java b/.../monarchinitiative/exomiser/autoconfigure/phenotype/PrioritiserAutoConfigurationTest.java
@@ -1,7 +1,7 @@
 /*
  * The Exomiser - A tool to annotate and prioritize genomic variants
  *
- * Copyright (c) 2016-2020 Queen Mary University of London.
+ * Copyright (c) 2016-2021 Queen Mary University of London.
  * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
  *
  * This program is free software: you can redistribute it and/or modify
@@ -20,7 +20,6 @@
 
 package org.monarchinitiative.exomiser.autoconfigure.phenotype;
 
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.monarchinitiative.exomiser.autoconfigure.AbstractAutoConfigurationTest;
 import org.monarchinitiative.exomiser.autoconfigure.DataDirectoryAutoConfiguration;
@@ -59,11 +58,9 @@ public void onlyLoadsWhenPhenotypeDataVersionIsPresent() {
         assertThat(context.getBean("phenotypeDataDirectory"), not(nullValue()));
     }
 
-    //this works in prod, but fails to autowire the phenotypeDataSource in test, despite being able to load the dataSource.
-    @Disabled
     @Test
     public void canDefinePhenotypeDataDirectory() {
-        Path definedDir = TEST_DATA.resolve("user-defined");
+        Path definedDir = TEST_DATA.resolve("1710_phenotype");
         load(EmptyConfiguration.class, TEST_DATA_ENV, DATA_VERSION, "exomiser.phenotype.data-directory=" + definedDir);
         Path phenotypeDataDirectory = (Path) this.context.getBean("phenotypeDataDirectory");
         assertThat(phenotypeDataDirectory, equalTo(definedDir));