Add directory traversal API to RepositoryProvider abstraction

adr/20250929-repository-directory-traversal.md

@@ -0,0 +1,84 @@
+ # ADR: Repository Directory Traversal API
+
+**Date**: 2025-09-29  
+**Status**: Accepted  
+**Context**: Need for standardized directory listing across Git hosting providers
+
+## Decision
+
+Introduce a `listDirectory(String path, int depth)` method to the `RepositoryProvider` abstraction to enable unified directory traversal across different Git hosting platforms.
+
+## Context
+
+Nextflow requires the ability to explore repository directory structures across multiple Git hosting providers (GitHub, GitLab, Bitbucket, Azure DevOps, Gitea) without full repository clones. Each provider has different API capabilities and constraints for directory listing operations.
+
+## Technical Implementation
+
+### Core Algorithm
+
+All providers follow a consistent pattern:
+1. **Path Resolution**: Normalize path to provider API format
+2. **Strategy Selection**: Choose recursive vs iterative approach based on API capabilities
+3. **HTTP Request**: Execute provider-specific API calls
+4. **Response Processing**: Parse to standardized `RepositoryEntry` objects
+5. **Depth Filtering**: Apply client-side limits when APIs lack precise depth control
+
+### API Strategy Classification
+
+**Strategy A: Native Recursive (GitHub, GitLab, Azure)**
+- Single HTTP request with recursive parameters
+- Server-side tree traversal
+- Performance: O(1) API calls
+
+**Strategy B: Iterative Traversal (Bitbucket Server, Gitea)**
+- Multiple HTTP requests per directory level  
+- Client-side recursion management
+- Performance: O(n) API calls where n = number of directories
+
+**Strategy C: Limited Support (Bitbucket Cloud)**
+- Single-level listing only
+- Throws exceptions for depth > 1
+
+### Provider Implementation Details
+
+| Provider | Endpoint | Recursive Support | Performance |
+|----------|----------|-------------------|-------------|
+| GitHub | `/git/trees/{sha}?recursive=1` | Native | Optimal |
+| GitLab | `/repository/tree?recursive=true` | Native | Optimal |
+| Azure | `/items?recursionLevel=Full` | Native | Optimal |
+| Bitbucket Server | `/browse/{path}` | Manual iteration | Multiple calls |
+| Gitea | `/contents/{path}` | Manual iteration | Multiple calls |
+| Bitbucket Cloud | `/src/{commit}/{path}` | None | Unsupported |
+
+### HTTP API Constraints
+
+- **Rate Limiting**: 60-5000 requests/hour depending on provider and authentication
+- **Response Size**: Controlled by `NXF_GIT_RESPONSE_MAX_LENGTH` environment variable
+- **Timeouts**: 60-second connect timeout across all providers
+- **Authentication**: Required for private repositories and higher rate limits
+
+## Consequences
+
+### Positive
+- **Unified Interface**: Consistent API across all Git hosting providers
+- **Performance Optimization**: Uses native recursive APIs where available
+- **Graceful Degradation**: Falls back to iterative traversal when needed
+- **Error Resilience**: Handles partial failures and API limitations
+
+### Negative
+- **Provider Inconsistency**: Performance varies significantly between providers
+- **API Rate Limits**: Multiple calls required for some providers may hit limits faster
+- **Memory Usage**: Large directory structures loaded entirely into memory
+
+### Neutral
+- **Complexity**: Abstraction layer adds code complexity but improves maintainability
+- **Testing**: Comprehensive test coverage required for each provider implementation
+
+## Implementation Notes
+
+- Local Git repositories use JGit TreeWalk for optimal performance
+- Client-side depth filtering ensures consistent behavior across providers
+- Error handling varies by provider: some return empty lists, others throw exceptions
+- Future enhancements could include caching based on commit SHA and pagination support
+
+This decision enables Nextflow to efficiently explore repository structures regardless of the underlying Git hosting platform, with automatic optimization based on each provider's API capabilities.

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

@@ -214,4 +214,87 @@ final class AzureRepositoryProvider extends RepositoryProvider {
         return invokeBytes(url)
     }
 
+    /** {@inheritDoc} */
+    @Override
+    List<RepositoryEntry> listDirectory(String path, int depth) {
+        // Build the Items API URL
+        def normalizedPath = normalizePath(path)
+        // For Azure API, root directory should be represented as "/" not empty string
+        if (!normalizedPath) {
+            normalizedPath = "/"
+        }
+
+        def queryParams = [
+            'recursionLevel': depth > 1 ? 'Full' : 'OneLevel',  // Use Full for depth > 1 to get nested content
+            "api-version": 6.0,
+            '$format': 'json'
+        ] as Map<String,Object>
+
+        // Only add scopePath if it's not the root directory
+        if (normalizedPath != "/") {
+            queryParams['scopePath'] = normalizedPath
+        }
+
+        if (revision) {
+            queryParams['versionDescriptor.version'] = revision
+            if (COMMIT_REGEX.matcher(revision).matches()) {
+                queryParams['versionDescriptor.versionType'] = 'commit'
+            }
+        }
+
+        def queryString = queryParams.collect({ "$it.key=$it.value"}).join('&')
+        def url = "$endpointUrl/items?$queryString"
+
+        try {
+            Map response = invokeAndParseResponse(url)
+            List<Map> items = response?.value as List<Map>
+
+            if (!items) {
+                return []
+            }
+
+            List<RepositoryEntry> entries = []
+
+            for (Map item : items) {
+                // Skip the root directory itself
+                String itemPath = item.get('path') as String
+                if (itemPath == path || (!path && itemPath == "/")) {
+                    continue
+                }
+
+                // Filter entries based on depth using base class helper
+                if (shouldIncludeAtDepth(itemPath, path, depth)) {
+                    entries.add(createRepositoryEntry(item, path))
+                }
+            }
+
+            return entries.sort { it.name }
+
+        } catch (Exception e) {
+            // Azure Items API may have different permissions or availability than other APIs
+            // Return empty list to allow graceful degradation
+            return []
+        }
+    }
+
+    private RepositoryEntry createRepositoryEntry(Map item, String basePath) {
+        String itemPath = item.get('path') as String
+        String name = itemPath?.split('/')?.last() ?: "unknown"
+
+        // Determine type based on Azure's gitObjectType
+        String gitObjectType = item.get('gitObjectType') as String
+        EntryType type = (gitObjectType == 'tree') ? EntryType.DIRECTORY : EntryType.FILE
+
+        String sha = item.get('objectId') as String
+        Long size = item.get('size') as Long
+
+        return new RepositoryEntry(
+            name: name,
+            path: itemPath,
+            type: type,
+            sha: sha,
+            size: size
+        )
+    }
+
 }

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

@@ -193,4 +193,65 @@ final class BitbucketRepositoryProvider extends RepositoryProvider {
         final url = getContentUrl(path)
         return invokeBytes(url)
     }
+
+    /** {@inheritDoc} */
+    @Override
+    List<RepositoryEntry> listDirectory(String path, int depth) {
+        final ref = revision ? getRefForRevision(revision) : getMainBranch()
+        // Normalize path using base class helper
+        final dirPath = normalizePath(path)
+
+        // Build the src API URL - BitBucket's src endpoint returns directory listings when path is a directory
+        String url = "${config.endpoint}/2.0/repositories/$project/src/$ref/$dirPath"
+
+        try {
+            // Make the API call
+            Map response = invokeAndParseResponse(url)
+            List<Map> values = response?.values as List<Map>
+
+            if (!values) {
+                return []
+            }
+
+            List<RepositoryEntry> entries = []
+
+            for (Map entry : values) {
+                String entryPath = entry.get('path') as String
+                // Filter entries based on depth using base class helper
+                if (shouldIncludeAtDepth(entryPath, path, depth)) {
+                    entries.add(createRepositoryEntry(entry, path))
+                }
+            }
+
+            return entries.sort { it.name }
+
+        } catch (Exception e) {
+            // If API call fails, it might be because the path is not a directory
+            // or the API doesn't support directory listing
+            throw new UnsupportedOperationException("Directory listing not supported by BitBucket API for path: $path", e)
+        }
+    }
+
+    private RepositoryEntry createRepositoryEntry(Map entry, String basePath) {
+        String entryPath = entry.get('path') as String
+        String name = entryPath?.split('/')?.last() ?: entry.get('name') as String
+
+        // Determine type based on BitBucket's response
+        String type = entry.get('type') as String
+        EntryType entryType = (type == 'commit_directory') ? EntryType.DIRECTORY : EntryType.FILE
+
+        String sha = entry.get('commit')?.get('hash') as String
+        Long size = entry.get('size') as Long
+
+        // Ensure absolute path using base class helper
+        String fullPath = ensureAbsolutePath(entryPath)
+
+        return new RepositoryEntry(
+            name: name,
+            path: fullPath,
+            type: entryType,
+            sha: sha,
+            size: size
+        )
+    }
 }

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

@@ -111,6 +111,12 @@ final class BitbucketServerRepositoryProvider extends RepositoryProvider {
         return invokeBytes(url)
     }
 
+    /** {@inheritDoc} */
+    @Override
+    List<RepositoryEntry> listDirectory(String path, int depth) {
+        throw new UnsupportedOperationException("BitbucketServerRepositoryProvider does not support 'listDirectory' operation")
+    }
+
     @Override
     List<TagInfo> getTags() {
         final result = new ArrayList<TagInfo>()

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

@@ -19,11 +19,13 @@ package nextflow.scm
 
 import groovy.transform.CompileDynamic
 import groovy.transform.CompileStatic
+import groovy.util.logging.Slf4j
 /**
  * Implements a repository provider for Gitea service
  *
  * @author Akira Sekiguchi <[email protected]>
  */
+@Slf4j
 @CompileStatic
 final class GiteaRepositoryProvider extends RepositoryProvider {
 
@@ -113,4 +115,118 @@ final class GiteaRepositoryProvider extends RepositoryProvider {
         return invokeBytes(url)
     }
 
+    /** {@inheritDoc} */
+    @Override
+    List<RepositoryEntry> listDirectory(String path, int depth) {
+        final branch = revision ?: "master"
+        // Normalize path using base class helper
+        final dirPath = normalizePath(path)
+
+        // Build the contents API URL - Gitea follows GitHub-like API pattern
+        String url = "${config.endpoint}/repos/$project/contents"
+        if (dirPath) {
+            url += "/$dirPath"
+        }
+        url += "?ref=$branch"
+
+        try {
+            // Make the API call
+            def response = invoke(url)
+            List<Map> contents = new groovy.json.JsonSlurper().parseText(response) as List<Map>
+
+            if (!contents) {
+                return []
+            }
+
+            List<RepositoryEntry> entries = []
+
+            for (Map entry : contents) {
+                String entryPath = entry.get('path') as String
+                // Filter entries based on depth using base class helper
+                if (shouldIncludeAtDepth(entryPath, path, depth)) {
+                    entries.add(createRepositoryEntry(entry))
+                }
+            }
+
+            // If depth > 1, we need to recursively get subdirectory contents
+            if (depth > 1) {
+                for (Map entry : contents) {
+                    if (entry.get('type') == 'dir') {
+                        String entryName = entry.get('name') as String
+                        String subPath = dirPath ? "$dirPath/$entryName" : entryName
+                        entries.addAll(getRecursiveEntries(subPath, depth, branch, 2))
+                    }
+                }
+            }
+
+            return entries.sort { it.name }
+
+        } catch (Exception e) {
+            throw new UnsupportedOperationException("Directory listing failed for Gitea path: $path", e)
+        }
+    }
+
+    private List<RepositoryEntry> getRecursiveEntries(String basePath, int maxDepth, String branch, int currentDepth) {
+        if (currentDepth > maxDepth) {
+            return []
+        }
+
+        List<RepositoryEntry> allEntries = []
+
+        // Get current level entries first
+        final normalizedBasePath = normalizePath(basePath)
+        String url = "${config.endpoint}/repos/$project/contents"
+        if (normalizedBasePath) {
+            url += "/$normalizedBasePath"
+        }
+        url += "?ref=$branch"
+
+        try {
+            def response = invoke(url)
+            List<Map> contents = new groovy.json.JsonSlurper().parseText(response) as List<Map>
+
+            for (Map entry : contents) {
+                String entryPath = entry.get('path') as String
+
+                // Add entries from the current level that match the depth criteria
+                if (shouldIncludeAtDepth(entryPath, basePath, maxDepth)) {
+                    allEntries.add(createRepositoryEntry(entry))
+                }
+
+                // Recurse into subdirectories if we haven't reached max depth
+                if (entry.get('type') == 'dir' && currentDepth < maxDepth) {
+                    String entryName = entry.get('name') as String
+                    String subPath = normalizedBasePath ? "$normalizedBasePath/$entryName" : entryName
+                    allEntries.addAll(getRecursiveEntries(subPath, maxDepth, branch, currentDepth + 1))
+                }
+            }
+        } catch (Exception e) {
+            log.debug("Failed to process directory during recursive listing: ${e.message}")
+            // Continue processing other directories if one fails
+        }
+
+        return allEntries
+    }
+
+    private RepositoryEntry createRepositoryEntry(Map entry) {
+        String name = entry.get('name') as String
+        String path = entry.get('path') as String
+        String type = entry.get('type') as String
+
+        EntryType entryType = (type == 'dir') ? EntryType.DIRECTORY : EntryType.FILE
+        String sha = entry.get('sha') as String
+        Long size = entry.get('size') as Long
+
+        // Ensure absolute path using base class helper
+        String fullPath = ensureAbsolutePath(path)
+
+        return new RepositoryEntry(
+            name: name,
+            path: fullPath,
+            type: entryType,
+            sha: sha,
+            size: size
+        )
+    }
+
 }