fix: improve code and fix test

lifebit-ai · Jan 4, 2024 · e1de8e3 · e1de8e3
1 parent 14ce722
commit e1de8e3
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Showing 2 changed files with 17 additions and 11 deletions.
diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -600,23 +600,29 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         if( this.environment?.containsKey('NXF_DEBUG') )
             vars << new KeyValuePair().withName('NXF_DEBUG').withValue(this.environment['NXF_DEBUG'])
 
-        vars.addAll(this.getLifebitEnv())
+        vars.addAll(this.getAwsCliOptimisationEnvs())
         return vars
     }
 
-    private List<KeyValuePair> getLifebitEnv() {
+    /**
+     * List of envs to fix AWS Client retries
+     * @return
+     */
+    List<KeyValuePair> getAwsCliOptimisationEnvs() {
         def vars = []
-        if( this.getAwsOptions().retryMode && this.getAwsOptions().retryMode in AwsOptions.VALID_RETRY_MODES) {
-            vars << new KeyValuePair().withName('AWS_RETRY_MODE').withValue(this.getAwsOptions().retryMode)
-            vars << new KeyValuePair().withName('AWS_METADATA_SERVICE_TIMEOUT').withValue(this.getAwsOptions().metadataServiceTimeout.toSeconds() as String)
-
+        def opts = this.getAwsOptions()
+        if ( opts.retryMode && opts.retryMode in AwsOptions.VALID_RETRY_MODES) {
+            vars << new KeyValuePair().withName('AWS_RETRY_MODE').withValue(opts.retryMode)
         }
-        if( this.getAwsOptions().maxTransferAttempts ) {
-            vars << new KeyValuePair().withName('AWS_MAX_ATTEMPTS').withValue(this.getAwsOptions().maxTransferAttempts as String)
-            vars << new KeyValuePair().withName('AWS_METADATA_SERVICE_NUM_ATTEMPTS').withValue(this.getAwsOptions().maxTransferAttempts as String)
+        if ( opts.maxTransferAttempts ) {
+            vars << new KeyValuePair().withName('AWS_MAX_ATTEMPTS').withValue(opts.maxTransferAttempts as String)
+            vars << new KeyValuePair().withName('AWS_METADATA_SERVICE_NUM_ATTEMPTS').withValue(opts.maxTransferAttempts as String)
         }
-        return vars
 
+        if ( opts.metadataServiceTimeout ) {
+            vars << new KeyValuePair().withName('AWS_METADATA_SERVICE_TIMEOUT').withValue(opts.metadataServiceTimeout.toSeconds() as String)
+        }
+        return vars
     }
 
     /**

diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsOptions.groovy
@@ -41,7 +41,7 @@ class AwsOptions implements CloudTransferOptions {
 
     public static final List<String> VALID_RETRY_MODES = ['legacy','standard','adaptive']
 
-    String retryMode
+    String retryMode = 'standard'
 
     String cliPath