Make default AWS region configurable, address PR comments

src/main/java/org/ga4gh/drs/AppConfig.java

@@ -10,8 +10,10 @@
 import org.ga4gh.drs.configuration.DataSourceRegistry;
 import org.ga4gh.drs.configuration.DrsConfig;
 import org.ga4gh.drs.configuration.DrsConfigContainer;
+import org.ga4gh.drs.configuration.S3;
 import org.ga4gh.drs.configuration.ServerProps;
 import org.ga4gh.drs.constant.DataSourceDefaults;
+import org.ga4gh.drs.constant.S3Defaults;
 import org.ga4gh.drs.constant.ServerPropsDefaults;
 import org.ga4gh.drs.constant.ServiceInfoDefaults;
 import org.ga4gh.drs.model.ServiceInfo;
@@ -31,6 +33,7 @@
 import org.springframework.context.annotation.Scope;
 import org.springframework.web.context.annotation.RequestScope;
 import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;
+import software.amazon.awssdk.regions.Region;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -85,6 +88,10 @@ public DrsConfigContainer defaultDrsConfigContainer(
 
         DataSourceRegistry dataSourceRegistry = drsConfigContainer.getDrsConfig().getDataSourceRegistry();
         dataSourceRegistry.setDataSources(DataSourceDefaults.REGISTRY);
+
+        S3 s3 = drsConfigContainer.getDrsConfig().getS3();
+        s3.setRegion(S3Defaults.S3_REGION);
+
         return drsConfigContainer;
     }
 
@@ -183,4 +190,11 @@ public DataSourceLookup dataSourceLookup() {
     public DrsObjectLoaderFactory drsObjectLoaderFactory() {
         return new DrsObjectLoaderFactory();
     }
+
+    @Bean
+    public Region defaultRegion(
+        @Qualifier(AppConfigConstants.MERGED_DRS_CONFIG_CONTAINER) DrsConfigContainer drsConfigContainer
+    ) {
+        return Region.of(drsConfigContainer.getDrsConfig().getS3().getRegion());
+    }
 }

src/main/java/org/ga4gh/drs/configuration/DrsConfig.java

@@ -1,5 +1,6 @@
 package org.ga4gh.drs.configuration;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
 import org.ga4gh.drs.model.ServiceInfo;
 
 public class DrsConfig {
@@ -8,10 +9,14 @@ public class DrsConfig {
     private ServiceInfo serviceInfo;
     private DataSourceRegistry dataSourceRegistry;
 
+    @JsonProperty("S3")
+    private S3 s3;
+
     public DrsConfig() {
         serverProps = new ServerProps();
         serviceInfo = new ServiceInfo();
         dataSourceRegistry = new DataSourceRegistry();
+        s3 = new S3();
     }
 
     public void setServerProps(ServerProps serverProps) {
@@ -37,4 +42,12 @@ public void setDataSourceRegistry(DataSourceRegistry dataSourceRegistry) {
     public DataSourceRegistry getDataSourceRegistry() {
         return dataSourceRegistry;
     }
+
+    public S3 getS3() {
+        return s3;
+    }
+
+    public void setS3(S3 S3) {
+        this.s3 = S3;
+    }
 }

src/main/java/org/ga4gh/drs/configuration/S3.java

@@ -0,0 +1,17 @@
+package org.ga4gh.drs.configuration;
+
+public class S3 {
+    private String region;
+
+    public S3() {
+
+    }
+
+    public String getRegion() {
+        return region;
+    }
+
+    public void setRegion(String region) {
+        this.region = region;
+    }
+}

src/main/java/org/ga4gh/drs/constant/S3Defaults.java

@@ -0,0 +1,6 @@
+package org.ga4gh.drs.constant;
+
+public class S3Defaults {
+
+    public static final String S3_REGION = "us-east-1";
+}

src/main/java/org/ga4gh/drs/utils/S3ClientRegionBasedProvider.java

@@ -1,5 +1,6 @@
 package org.ga4gh.drs.utils;
 
+import org.springframework.beans.factory.annotation.Autowired;
 import software.amazon.awssdk.regions.Region;
 import software.amazon.awssdk.services.s3.S3Client;
 import software.amazon.awssdk.services.s3.model.HeadBucketRequest;
@@ -10,12 +11,15 @@
 
 public class S3ClientRegionBasedProvider {
 
+    @Autowired
+    private static Region DEFAULT_REGION;
+
     public S3ClientRegionBasedProvider() {
 
     }
 
     private static S3Client mainClient = S3Client.builder()
-        .region(Region.US_EAST_1)
+        .region(DEFAULT_REGION)
         .build();
 
     private static Map<Region, S3Client> clients = new HashMap<>();
@@ -47,6 +51,6 @@ private static Region getRegion(String bucket) {
             }
         }
         // Default US_EAST_1
-        return Region.US_EAST_1;
+        return DEFAULT_REGION;
     }
 }

src/main/java/org/ga4gh/drs/utils/objectloader/S3DrsObjectLoader.java

@@ -52,7 +52,7 @@ public S3DrsObjectLoader(String objectId, String objectPath) {
         URI uri = URI.create(objectPath);
         bucket = uri.getHost();
         // Strip leading /
-        key = uri.getPath().substring(1);
+        key = uri.getPath().replaceAll("^/+$", "");
         // Get client based on region
         client = S3ClientRegionBasedProvider.getClient(bucket);
 

src/test/resources/config/test-config-00.yml

@@ -9,4 +9,6 @@ drsConfig:
     dataSources:
       - drsIdPattern: ^testdata\.(?<acc1>.+?)\.(?<acc2>.+?)\.(?<acc3>.+?)$
         objectPathTemplate: ./src/test/resources/data/{acc1}/{acc2}/{acc3}
-        protocol: FILE
+        protocol: FILE
+  S3:
+    region: us-east-1