Fix readBytes for non-GitHub providers

modules/nextflow/src/main/groovy/nextflow/scm/BitbucketRepositoryProvider.groovy

@@ -159,8 +159,7 @@ final class BitbucketRepositoryProvider extends RepositoryProvider {
 
     @Override
     byte[] readBytes(String path) {
-
-        def url = getContentUrl(path)
-        invoke(url)?.getBytes()
+        final url = getContentUrl(path)
+        return invokeBytes(url)
     }
 }

modules/nextflow/src/main/groovy/nextflow/scm/BitbucketServerRepositoryProvider.groovy

@@ -107,8 +107,8 @@ final class BitbucketServerRepositoryProvider extends RepositoryProvider {
 
     @Override
     byte[] readBytes(String path) {
-        def url = getContentUrl(path)
-        invoke(url)?.getBytes()
+        final url = getContentUrl(path)
+        return invokeBytes(url)
     }
 
     @Override

modules/nextflow/src/main/groovy/nextflow/scm/GiteaRepositoryProvider.groovy

@@ -102,10 +102,8 @@ final class GiteaRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     byte[] readBytes(String path) {
-
         def url = getContentUrl(path)
-        def contents = invoke(url)
-        return contents?.getBytes()
+        return invokeBytes(url)
     }
 
 }

modules/nextflow/src/main/groovy/nextflow/scm/GithubRepositoryProvider.groovy

@@ -112,11 +112,9 @@ class GithubRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     byte[] readBytes(String path) {
-
         def url = getContentUrl(path)
         Map response  = invokeAndParseResponse(url)
         response.get('content')?.toString()?.decodeBase64()
-
     }
 
 }

modules/nextflow/src/main/groovy/nextflow/scm/GitlabRepositoryProvider.groovy

@@ -113,10 +113,8 @@ class GitlabRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     byte[] readBytes(String path) {
-
         def url = getContentUrl(path)
         Map response  = invokeAndParseResponse(url)
         response.get('content')?.toString()?.decodeBase64()
-
     }
 }

modules/nextflow/src/main/groovy/nextflow/scm/RepositoryProvider.groovy

@@ -224,14 +224,25 @@ abstract class RepositoryProvider {
      * @return The remote service response as a text
      */
     protected String invoke( String api ) {
+        final result = invokeBytes(api)
+        return result!=null ? new String(result) : null
+    }
+
+    /**
+     * Invoke the API request specified and return binary content
+     *
+     * @param api A API request url e.g. https://api.github.com/repos/nextflow-io/hello/raw/image.png
+     * @return The remote service response as byte array
+     */
+    protected byte[] invokeBytes( String api ) {
         assert api
         log.debug "Request [credentials ${getAuthObfuscated() ?: '-'}] -> $api"
         final request = newRequest(api)
         // submit the request
-        final HttpResponse<String> resp = httpSend(request)
+        final HttpResponse<byte[]> resp = httpSend0(request)
         // check the response code
         checkResponse(resp)
-        // return the body as string
+        // return the body as byte array
         return resp.body()
     }
 
@@ -263,7 +274,7 @@ abstract class RepositoryProvider {
      *
      * @param response A {@link HttpURLConnection} response instance
      */
-    protected checkResponse( HttpResponse<String> response ) {
+    protected checkResponse( HttpResponse<?> response ) {
         final code = response.statusCode()
         if( code==401 ) {
             log.debug "Response status: $code -- ${response.body()}"
@@ -447,6 +458,7 @@ abstract class RepositoryProvider {
             return isCausedByUnresolvedAddressException(t.cause)
     }
 
+    @Deprecated
     protected HttpResponse<String> httpSend(HttpRequest request) {
         if( httpClient==null )
             httpClient = newHttpClient()
@@ -460,10 +472,24 @@ abstract class RepositoryProvider {
         }
     }
 
+    private HttpResponse<byte[]> httpSend0(HttpRequest request) {
+        if( httpClient==null )
+            httpClient = newHttpClient()
+        if( retryConfig==null )
+            retryConfig = new RetryConfig()
+        try {
+            safeApply(()-> httpClient.send(request, HttpResponse.BodyHandlers.ofByteArray()))
+        }
+        catch (FailsafeException e) {
+            throw e.cause
+        }
+    }
+
     private HttpClient newHttpClient() {
         final builder = HttpClient.newBuilder()
             .version(HttpClient.Version.HTTP_1_1)
             .connectTimeout(Duration.ofSeconds(60))
+            .followRedirects(HttpClient.Redirect.NORMAL)
         // use virtual threads executor if enabled
         if( Threads.useVirtual() )
             builder.executor(Executors.newVirtualThreadPerTaskExecutor())

modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy

@@ -51,7 +51,6 @@ class AzureRepositoryProviderTest extends Specification {
         't-neumann/hello'                   | ['t-neumann', 'hello', 'hello']
         'ORGANIZATION/PROJECT/hello'        | ['ORGANIZATION','PROJECT','hello']
         'ORGANIZATION/PROJECT/_git/hello'   | ['ORGANIZATION','PROJECT','hello']
-
     }
 
     def 'should throw exception if wrong path' () {
@@ -69,7 +68,6 @@ class AzureRepositoryProviderTest extends Specification {
     }
 
     def 'should return repo url' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
@@ -85,7 +83,6 @@ class AzureRepositoryProviderTest extends Specification {
     }
 
     def 'should return project URL' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
@@ -97,29 +94,24 @@ class AzureRepositoryProviderTest extends Specification {
         't-neumann/hello'                   | 'https://dev.azure.com/t-neumann/hello'
         'ORGANIZATION/PROJECT/hello'        | 'https://dev.azure.com/ORGANIZATION/PROJECT/hello'
         'ORGANIZATION/PROJECT/_git/hello'   | 'https://dev.azure.com/ORGANIZATION/PROJECT/_git/hello'
-
     }
 
     def 'should return content URL' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
 
         expect:
         new AzureRepositoryProvider('t-neumann/hello', obj).getContentUrl('main.nf') == 'https://dev.azure.com/t-neumann/hello/_apis/git/repositories/hello/items?download=false&includeContent=true&includeContentMetadata=false&api-version=6.0&\$format=json&path=main.nf'
-
     }
 
     def 'should return content URL for revision' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject)
 
         expect:
         new AzureRepositoryProvider('t-neumann/hello', obj).setRevision("a-branch").getContentUrl('main.nf') == 'https://dev.azure.com/t-neumann/hello/_apis/git/repositories/hello/items?download=false&includeContent=true&includeContentMetadata=false&api-version=6.0&\$format=json&path=main.nf&versionDescriptor.version=a-branch'
-
     }
 
     /*
@@ -141,7 +133,6 @@ class AzureRepositoryProviderTest extends Specification {
         def result = repo.readText('main.nf')
         then:
         result == 'println "Hello from Azure repos!"'
-
     }
 
     @IgnoreIf({System.getenv('NXF_SMOKE')})

modules/nextflow/src/test/groovy/nextflow/scm/BitbucketRepositoryProviderTest.groovy

@@ -28,7 +28,6 @@ class BitbucketRepositoryProviderTest extends Specification {
 
     @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
     def testBitbucketCloneURL() {
-
         given:
         def token = System.getenv('NXF_BITBUCKET_ACCESS_TOKEN')
         def config = new ProviderConfig('bitbucket').setAuth(token)
@@ -39,16 +38,13 @@ class BitbucketRepositoryProviderTest extends Specification {
         url == "https://${config.user}@bitbucket.org/pditommaso/tutorial.git".toString()
     }
 
-
     def testGetHomePage() {
         expect:
         new BitbucketRepositoryProvider('pditommaso/tutorial').getRepositoryUrl() == "https://bitbucket.org/pditommaso/tutorial"
     }
 
-
     @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
     def testReadContent() {
-
         given:
         def token = System.getenv('NXF_BITBUCKET_ACCESS_TOKEN')
         def config = new ProviderConfig('bitbucket').setAuth(token)
@@ -59,7 +55,21 @@ class BitbucketRepositoryProviderTest extends Specification {
 
         then:
         result.trim().startsWith('#!/usr/bin/env nextflow')
+    }
 
+    @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
+    def 'should read binary data'() {
+        given:
+        def token = System.getenv('NXF_BITBUCKET_ACCESS_TOKEN')
+        def config = new ProviderConfig('bitbucket').setAuth(token)
+        def DATA = this.class.getResourceAsStream('/test-sandbucket.jpg').bytes
+
+        when:
+        def repo = new BitbucketRepositoryProvider('pditommaso/tutorial', config)
+        def result = repo.readBytes('sandbucket.jpg')
+
+        then:
+        result == DATA
     }
 
     @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
@@ -160,6 +170,5 @@ class BitbucketRepositoryProviderTest extends Specification {
         then:
         !data.contains('world')
         data.contains('mundo')
-
     }
 }

modules/nextflow/src/test/groovy/nextflow/scm/GiteaRepositoryProviderTest.groovy

@@ -19,7 +19,6 @@ package nextflow.scm
 import spock.lang.IgnoreIf
 import spock.lang.Requires
 import spock.lang.Specification
-
 /**
  *
  * @author Akira Sekiguchi <[email protected]>
@@ -28,76 +27,83 @@ class GiteaRepositoryProviderTest extends Specification {
 
     static final String CONFIG = '''
         providers {
-
             mygitea {
-                server = 'https://git.seqera.io'
-                endpoint = 'https://git.seqera.io/api/v1'
+                server = 'https://gitea.com'
+                endpoint = 'https://gitea.com/api/v1'
                 platform = 'gitea'
-                user = 'myname'
-                password = 'mypassword'
             }
-
         }
         '''
 
     def 'should return repo url' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('gitea', config.providers.mygitea as ConfigObject)
 
         expect:
-        new GiteaRepositoryProvider('pditommaso/hello', obj).getEndpointUrl() == 'https://git.seqera.io/api/v1/repos/pditommaso/hello'
+        new GiteaRepositoryProvider('pditommaso/hello', obj).getEndpointUrl() == 'https://gitea.com/api/v1/repos/pditommaso/hello'
     }
 
     def 'should return project URL' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('gitea', config.providers.mygitea as ConfigObject)
 
         expect:
-        new GiteaRepositoryProvider('pditommaso/hello', obj).getRepositoryUrl() == 'https://git.seqera.io/pditommaso/hello'
-
+        new GiteaRepositoryProvider('pditommaso/hello', obj).getRepositoryUrl() == 'https://gitea.com/pditommaso/hello'
     }
 
     def 'should return content URL' () {
-
         given:
         def config = new ConfigSlurper().parse(CONFIG)
         def obj = new ProviderConfig('gitea', config.providers.mygitea as ConfigObject)
 
         expect:
         new GiteaRepositoryProvider('pditommaso/hello', obj)
-                .getContentUrl('main.nf') == 'https://git.seqera.io/api/v1/repos/pditommaso/hello/raw/main.nf'
+                .getContentUrl('main.nf') == 'https://gitea.com/api/v1/repos/pditommaso/hello/raw/main.nf'
         and:
         new GiteaRepositoryProvider('pditommaso/hello', obj)
                 .setRevision('12345')
-                .getContentUrl('main.nf') == 'https://git.seqera.io/api/v1/repos/pditommaso/hello/raw/main.nf?ref=12345'
+                .getContentUrl('main.nf') == 'https://gitea.com/api/v1/repos/pditommaso/hello/raw/main.nf?ref=12345'
 
     }
 
     @IgnoreIf({System.getenv('NXF_SMOKE')})
     @Requires({System.getenv('NXF_GITEA_ACCESS_TOKEN')})
     def 'should read file content'() {
-
         given:
-        def token = System.getenv('NXF_GITEA_ACCESS_TOKEN')
-        def config = new ProviderConfig('gitea', new ConfigSlurper().parse(CONFIG).providers.mygitea as ConfigObject).setAuth(token)
+        def token =  System.getenv('NXF_GITEA_ACCESS_TOKEN')
+        def config = new ProviderConfig('gitea', new ConfigSlurper().parse(CONFIG).providers.mygitea as ConfigObject) .setAuth(token)
 
         when:
-        def repo = new GiteaRepositoryProvider('test-org/nextflow-ci-repo', config)
+        def repo = new GiteaRepositoryProvider('pditommaso/test-hello', config)
         def result = repo.readText('README.md')
         then:
-        result.contains('nextflow-ci-repo')
+        result.contains('Basic Nextflow script')
 
 //        when:
 //        repo = new GiteaRepositoryProvider('test-org/nextflow-ci-repo', config)
 //                        .setRevision('foo')
 //        result = repo.readText('README.md')
 //        then:
 //        result.contains("foo branch")
+    }
+
+    @IgnoreIf({System.getenv('NXF_SMOKE')})
+    @Requires({System.getenv('NXF_GITEA_ACCESS_TOKEN')})
+    def 'should read bytes gitea content'() {
+        given:
+        def token =  System.getenv('NXF_GITEA_ACCESS_TOKEN')
+        def config = new ProviderConfig('gitea', new ConfigSlurper().parse(CONFIG).providers.mygitea as ConfigObject) .setAuth(token)
+        def repo = new GiteaRepositoryProvider('pditommaso/test-hello', config)
+        and:
+        def DATA = this.class.getResourceAsStream('/test-asset.bin').bytes
+
+        when:
+        def result = repo.readBytes('test/test-asset.bin')
 
+        then:
+        result == DATA
     }
 
 }