feat: remove storage account name if present from azure path

nextflow-io · Jan 26, 2024 · aee2c56 · aee2c56
1 parent 74c66ba
commit aee2c56
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Showing 2 changed files with 32 additions and 1 deletion.
diff --git a/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy b/plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzPathFactory.groovy
@@ -48,6 +48,11 @@ class AzPathFactory extends FileSystemPathFactory {
         if( uri.startsWith('az:///') )
             throw new IllegalArgumentException("Invalid Azure path URI - make sure the schema prefix does not container more than two slash characters - offending value: $uri")
 
+        final storageAccountName = AzConfig.getConfig().storage().accountName
+        if (uri.contains(storageAccountName)){
+            uri = uri.replace("${storageAccountName}.","")
+        }
+
         final storageConfigEnv = AzConfig.getConfig().storage().getEnv()
 
         final activeDirectoryConfigEnv = AzConfig.getConfig().activeDirectory().getEnv()

diff --git a/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy b/plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzPathFactoryTest.groovy
@@ -38,14 +38,40 @@ class AzPathFactoryTest extends Specification {
 
         cleanup:
         Global.session = null
-        
+
         where:
         AZ_URI                          | CONTAINER     | BLOB
         'az://my-data/foo/bar'          | 'my-data'     | 'foo/bar'
         'az://my-data/data/*{1,2}.fq.gz'| 'my-data'     | 'data/*{1,2}.fq.gz'
     }
 
 
+    def 'should create az azure path and remove storage account name if present' () {
+        given:
+        def CONFIG = [azure: [
+            storage: [
+                accountKey: System.getenv('AZURE_STORAGE_ACCOUNT_KEY'),
+                accountName: System.getenv('AZURE_STORAGE_ACCOUNT_NAME'),
+            ]
+        ]]
+        Global.session = Mock(Session) { getConfig() >> CONFIG }
+        and:
+
+        when:
+        def path = AzPathFactory.parse(AZ_URI)
+        then:
+        path instanceof AzPath
+        (path as AzPath).containerName == CONTAINER
+        (path as AzPath).blobName() == BLOB
+
+        cleanup:
+        Global.session = null
+
+        where:
+        storageAccount                              |  AZ_URI                                           | CONTAINER | BLOB
+        System.getenv('AZURE_STORAGE_ACCOUNT_NAME') | "az://${storageAccount}.my-data/foo/bar"          | 'my-data' | 'foo/bar'
+        System.getenv('AZURE_STORAGE_ACCOUNT_NAME') | "az://${storageAccount}.my-data/data/*{1,2}.fq.gz"| 'my-data' | 'data/*{1,2}.fq.gz'
+    }
 
     def 'should throw illegal path' () {
         given: