sa version is now an env variable in annotation lambda (#597)

Illumina · Jun 2, 2021 · a62a4f8 · a62a4f8
1 parent 736043b
commit a62a4f8
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Showing 5 changed files with 12 additions and 14 deletions.
diff --git a/AnnotationLambda/AnnotationLambda.cs b/AnnotationLambda/AnnotationLambda.cs
@@ -156,7 +156,9 @@ private static AnnotationResources GetAnnotationResources(AnnotationConfig annot
             var genomeAssembly      = GenomeAssemblyHelper.Convert(annotationConfig.genomeAssembly);
             string cachePathPrefix  = LambdaUrlHelper.GetCacheFolder().UrlCombine(genomeAssembly.ToString()).UrlCombine(LambdaUrlHelper.DefaultCacheSource);
             string nirvanaS3Ref     = LambdaUrlHelper.GetRefUrl(genomeAssembly);
-            string saManifestUrl    = LambdaUtilities.GetManifestUrl(annotationConfig.supplementaryAnnotations ?? "latest", genomeAssembly);
+            // SaVersion will be provided as an environment variable. Defaults to "latest"
+            string saVersion = Environment.GetEnvironmentVariable("SaVersion");
+            string saManifestUrl    = LambdaUtilities.GetManifestUrl(string.IsNullOrEmpty(saVersion)? "latest": saVersion, genomeAssembly);
             var metrics = new PerformanceMetrics();
 
             var annotationResources = new AnnotationResources(nirvanaS3Ref, cachePathPrefix,

diff --git a/Cloud/Messages/Annotation/AnnotationConfig.cs b/Cloud/Messages/Annotation/AnnotationConfig.cs
@@ -6,15 +6,14 @@ public sealed class AnnotationConfig
     {
         // ReSharper disable InconsistentNaming
         // ReSharper disable NotAccessedField.Global
-        public string id;
-        public string genomeAssembly;
-        public string vcfUrl;
-        public string tabixUrl;
-        public S3Path outputDir;
-        public string outputPrefix;
-        public string supplementaryAnnotations;
-        public List<SaUrls> customAnnotations;
-        public string customStrUrl;
+        public string          id;
+        public string          genomeAssembly;
+        public string          vcfUrl;
+        public string          tabixUrl;
+        public S3Path          outputDir;
+        public string          outputPrefix;
+        public List<SaUrls>    customAnnotations;
+        public string          customStrUrl;
         public AnnotationRange annotationRange;
         // ReSharper restore NotAccessedField.Global
         // ReSharper restore InconsistentNaming

diff --git a/Cloud/Messages/Nirvana/NirvanaConfig.cs b/Cloud/Messages/Nirvana/NirvanaConfig.cs
@@ -12,7 +12,6 @@ public sealed class NirvanaConfig
         public string vcfUrl;
         public string tabixUrl;
         public S3Path outputDir;
-        public string supplementaryAnnotations;
         // ReSharper disable once UnassignedField.Global
         public List<SaUrls> customAnnotations;
         public string       customStrUrl;

diff --git a/NirvanaLambda/NirvanaLambda.cs b/NirvanaLambda/NirvanaLambda.cs
@@ -232,7 +232,6 @@ private static string DescribeAnnotationRegion(AnnotationRange ar)
             tabixUrl                 = config.tabixUrl,
             outputDir                = config.outputDir,
             outputPrefix             = GetIndexedPrefix(config.vcfUrl, jobIndex),
-            supplementaryAnnotations = config.supplementaryAnnotations,
             customAnnotations        = config.customAnnotations,
             customStrUrl             = config.customStrUrl,
             annotationRange          = annotationRange

diff --git a/UnitTests/NirvanaLambda/NirvanaConfigTests.cs b/UnitTests/NirvanaLambda/NirvanaConfigTests.cs
@@ -51,8 +51,7 @@ public void CheckFieldsNotNull_AsExpected()
                 accessKey = "1234567",
                 secretKey = "show me the money",
                 sessionToken = "a token"
-            },
-            supplementaryAnnotations = "latest"
+            }
         };
     }
 }