Add URL encoding when revision name is used as HTTP query parameter

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

@@ -17,6 +17,7 @@
 package nextflow.scm
 
 import java.net.http.HttpResponse
+import java.nio.charset.StandardCharsets
 import java.util.regex.Pattern
 
 import groovy.transform.CompileDynamic
@@ -97,7 +98,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
                 'path':path
         ] as Map<String,Object>
         if( revision ) {
-            queryParams['versionDescriptor.version']=revision
+            queryParams['versionDescriptor.version']=URLEncoder.encode(revision, StandardCharsets.UTF_8)
 
             if( COMMIT_REGEX.matcher(revision).matches() )
                 queryParams['versionDescriptor.versionType'] = 'commit'
@@ -203,7 +204,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
         ] as Map<String,Object>
 
         if( revision ) {
-            queryParams['versionDescriptor.version'] = revision
+            queryParams['versionDescriptor.version'] = URLEncoder.encode(revision, StandardCharsets.UTF_8)
             if( COMMIT_REGEX.matcher(revision).matches() )
                 queryParams['versionDescriptor.versionType'] = 'commit'
         }
@@ -236,7 +237,7 @@ final class AzureRepositoryProvider extends RepositoryProvider {
         }
 
         if (revision) {
-            queryParams['versionDescriptor.version'] = revision
+            queryParams['versionDescriptor.version'] = URLEncoder.encode(revision, StandardCharsets.UTF_8)
             if (COMMIT_REGEX.matcher(revision).matches()) {
                 queryParams['versionDescriptor.versionType'] = 'commit'
             }

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

@@ -21,6 +21,9 @@ import groovy.json.JsonSlurper
 import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
+
+import java.nio.charset.StandardCharsets
+
 /**
  * Implements a repository provider for the private hosted BitBucket Server service
  *
@@ -73,7 +76,7 @@ final class BitbucketServerRepositoryProvider extends RepositoryProvider {
         //
         def result = "${config.endpoint}/rest/api/1.0/projects/${project}/repos/${repository}/raw/${path}"
         if( revision )
-            result += "?at=$revision"
+            result += "?at=${URLEncoder.encode(revision, StandardCharsets.UTF_8)}"
         return result
     }
 

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

@@ -20,6 +20,9 @@ package nextflow.scm
 import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+
+import java.nio.charset.StandardCharsets
+
 /**
  * Implements a repository provider for Gitea service
  *
@@ -86,7 +89,7 @@ final class GiteaRepositoryProvider extends RepositoryProvider {
         // note: `ref` is undocumented
         def result = "${config.endpoint}/repos/$project/raw/$path"
         if( revision )
-            result += "?ref=$revision"
+            result += "?ref=${URLEncoder.encode(revision, StandardCharsets.UTF_8)}"
         return result
     }
 
@@ -118,7 +121,7 @@ final class GiteaRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     List<RepositoryEntry> listDirectory(String path, int depth) {
-        final branch = revision ?: "master"
+        final branch = URLEncoder.encode(revision ?: "master", StandardCharsets.UTF_8)
         // Normalize path using base class helper
         final dirPath = normalizePath(path)
 

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

@@ -22,6 +22,8 @@ import groovy.transform.Memoized
 import groovy.util.logging.Slf4j
 import nextflow.SysEnv
 
+import java.nio.charset.StandardCharsets
+
 /**
  * Implements a repository provider for GitHub service
  *
@@ -69,7 +71,7 @@ class GithubRepositoryProvider extends RepositoryProvider {
         //
         def result = "${config.endpoint}/repos/$project/contents/$path"
         if( revision )
-            result += "?ref=$revision"
+            result += "?ref=${URLEncoder.encode(revision, StandardCharsets.UTF_8)}"
         return result
     }
 
@@ -205,7 +207,8 @@ class GithubRepositoryProvider extends RepositoryProvider {
         if (revision) {
             // Try to resolve the revision to a commit SHA
             try {
-                Map ref = invokeAndParseResponse("${config.endpoint}/repos/$project/git/refs/heads/$revision")
+
+                Map ref = invokeAndParseResponse("${config.endpoint}/repos/$project/git/refs/heads/${URLEncoder.encode(revision, StandardCharsets.UTF_8)}")
                 Map object = ref.get('object') as Map
                 return object.get('sha') as String
             } catch (Exception e) {

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

@@ -18,6 +18,9 @@ package nextflow.scm
 
 import groovy.json.JsonSlurper
 import groovy.util.logging.Slf4j
+
+import java.nio.charset.StandardCharsets
+
 /**
  * Implements a repository provider for GitHub service
  *
@@ -94,8 +97,8 @@ class GitlabRepositoryProvider extends RepositoryProvider {
         // see
         //  https://docs.gitlab.com/ee/api/repository_files.html#get-raw-file-from-repository
         //
-        final ref = revision ?: getDefaultBranch()
-        final encodedPath = URLEncoder.encode(path.stripStart('/'),'utf-8')
+        final ref = URLEncoder.encode(revision ?: getDefaultBranch(), StandardCharsets.UTF_8)
+        final encodedPath = URLEncoder.encode(path.stripStart('/'), StandardCharsets.UTF_8)
         return "${config.endpoint}/api/v4/projects/${getProjectName()}/repository/files/${encodedPath}?ref=${ref}"
     }
 
@@ -128,9 +131,9 @@ class GitlabRepositoryProvider extends RepositoryProvider {
     /** {@inheritDoc} */
     @Override
     List<RepositoryEntry> listDirectory(String path, int depth) {
-        final ref = revision ?: getDefaultBranch()
+        final ref = URLEncoder.encode(revision ?: getDefaultBranch(),StandardCharsets.UTF_8)
         final normalizedPath = normalizePath(path)
-        final encodedPath = normalizedPath ? URLEncoder.encode(normalizedPath, 'utf-8') : ""
+        final encodedPath = normalizedPath ? URLEncoder.encode(normalizedPath, StandardCharsets.UTF_8) : ""
 
         // Build the Tree API URL
         String url = "${config.endpoint}/api/v4/projects/${getProjectName()}/repository/tree"

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

@@ -112,6 +112,8 @@ class AzureRepositoryProviderTest extends Specification {
 
         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'
+        and:
+        new AzureRepositoryProvider('t-neumann/hello', obj).setRevision("test/branch+with&strangecharacters").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=test%2Fbranch%2Bwith%26strangecharacters'
     }
 
     /*
@@ -133,6 +135,8 @@ class AzureRepositoryProviderTest extends Specification {
         def result = repo.readText('main.nf')
         then:
         result == 'println "Hello from Azure repos!"'
+
+
     }
 
     @IgnoreIf({System.getenv('NXF_SMOKE')})
@@ -226,6 +230,15 @@ class AzureRepositoryProviderTest extends Specification {
         def result = repo.readText('file-on-dev.txt')
         then:
         result=='hello\n'
+
+        when:
+        // check revision with special branches
+        repo = new AzureRepositoryProvider('pditommaso/nf-azure-repo', config)
+        repo.revision = 'test/branch+with&special-chars'
+        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

@@ -123,6 +123,10 @@ class BitbucketRepositoryProviderTest extends Specification {
             .setRevision('test/tag/v2')
             .getContentUrl('main.nf') == 'https://api.bitbucket.org/2.0/repositories/pditommaso/tutorial/src/8f849beceb2ea479ef836809ca33d3daeeed25f9/main.nf'
 
+        and:
+        new BitbucketRepositoryProvider('pditommaso/tutorial', config)
+            .setRevision('test/branch+with&special-chars')
+            .getContentUrl('main.nf') == 'https://api.bitbucket.org/2.0/repositories/pditommaso/tutorial/src/755ba829cbc4f28dcb3c16b9dcc1c49c7ee47ff5/main.nf'
     }
 
     @Requires( { System.getenv('NXF_BITBUCKET_ACCESS_TOKEN') } )
@@ -171,6 +175,14 @@ class BitbucketRepositoryProviderTest extends Specification {
         then:
         !data.contains('world')
         data.contains('mundo')
+
+        when:
+        repo.setRevision('test/branch+with&special-chars')
+        and:
+        data = repo.readText('main.nf')
+        then:
+        data.contains('world')
+        !data.contains('WORLD')
     }
 
     @Unroll

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

@@ -94,6 +94,10 @@ class BitbucketServerRepositoryProviderTest extends Specification {
         new BitbucketServerRepositoryProvider('pditommaso/hello', obj)
                 .setRevision('foo')
                 .getContentUrl('main.nf') == 'https://bitbucket.server.com/rest/api/1.0/projects/pditommaso/repos/hello/raw/main.nf?at=foo'
+        and:
+        new BitbucketServerRepositoryProvider('pditommaso/hello', obj)
+                .setRevision('test/branch+with&strangecharacters')
+                .getContentUrl('main.nf') == 'https://bitbucket.server.com/rest/api/1.0/projects/pditommaso/repos/hello/raw/main.nf?at=test%2Fbranch%2Bwith%26strangecharacters'
 
     }
 

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

@@ -54,7 +54,10 @@ class GiteaRepositoryProviderTest extends Specification {
         new GiteaRepositoryProvider('pditommaso/hello', obj)
                 .setRevision('12345')
                 .getContentUrl('main.nf') == 'https://gitea.com/api/v1/repos/pditommaso/hello/raw/main.nf?ref=12345'
-
+        and:
+        new GiteaRepositoryProvider('pditommaso/hello', obj)
+                .setRevision('test/branch+with&strangecharacters')
+                .getContentUrl('main.nf') == 'https://gitea.com/api/v1/repos/pditommaso/hello/raw/main.nf?ref=test%2Fbranch%2Bwith%26strangecharacters'
     }
 
     @Unroll
@@ -92,6 +95,13 @@ class GiteaRepositoryProviderTest extends Specification {
 //        result = repo.readText('README.md')
 //        then:
 //        result.contains("foo branch")
+
+        when:
+        repo = new GiteaRepositoryProvider('pditommaso/test-hello', config)
+        repo.setRevision('test/branch+with&special-chars')
+        result = repo.readText('README.md')
+        then:
+        result.contains('Basic Nextflow script')
     }
 
     @IgnoreIf({System.getenv('NXF_SMOKE')})

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

@@ -52,6 +52,14 @@ class GithubRepositoryProviderTest extends Specification {
         def result = repo.readText('main.nf')
         then:
         result.trim().startsWith('#!/usr/bin/env nextflow')
+
+        //Read from branch
+        when:
+        repo.setRevision('test/branch+with&strangecharacters')
+        result = repo.readText('/test/branch_name')
+        then:
+        result.trim().startsWith('test/branch+with&strangecharacters')
+
     }
 
     @Requires({System.getenv('NXF_GITHUB_ACCESS_TOKEN')})
@@ -95,6 +103,11 @@ class GithubRepositoryProviderTest extends Specification {
                 .setRevision('the-commit-id')
                 .getContentUrl('main.nf') == 'https://github.com/repos/pditommaso/hello/contents/main.nf?ref=the-commit-id'
 
+        and:
+        new GithubRepositoryProvider('pditommaso/hello', obj)
+            .setRevision('test/branch+with&strangecharacters')
+            .getContentUrl('main.nf') == 'https://github.com/repos/pditommaso/hello/contents/main.nf?ref=test%2Fbranch%2Bwith%26strangecharacters'
+
     }
 
     def 'should user github token as creds' () {

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

@@ -77,6 +77,13 @@ class GitlabRepositoryProviderTest extends Specification {
         def result = repo.readText('main.nf')
         then:
         result.trim().startsWith('#!/usr/bin/env nextflow')
+
+        when:
+        repo = new GitlabRepositoryProvider('pditommaso/hello', config)
+        repo.setRevision('test/branch+with&special-chars')
+        result = repo.readText('main.nf')
+        then:
+        result.trim().startsWith('#!/usr/bin/env nextflow')
     }
 
     @Requires({System.getenv('NXF_GITLAB_ACCESS_TOKEN')})
@@ -134,6 +141,11 @@ class GitlabRepositoryProviderTest extends Specification {
                 .setRevision('the-commit-id')
                 .getContentUrl('main.nf') == 'https://gitlab.com/api/v4/projects/pditommaso%2Fhello/repository/files/main.nf?ref=the-commit-id'
 
+        and:
+        new GitlabRepositoryProvider('pditommaso/hello', obj)
+                .setRevision('test/branch+with&strangecharacters')
+                .getContentUrl('main.nf') == 'https://gitlab.com/api/v4/projects/pditommaso%2Fhello/repository/files/main.nf?ref=test%2Fbranch%2Bwith%26strangecharacters'
+
         and:
         new GitlabRepositoryProvider('pditommaso/hello', obj)
                 .getContentUrl('conf/extra.conf') == 'https://gitlab.com/api/v4/projects/pditommaso%2Fhello/repository/files/conf%2Fextra.conf?ref=master'