Merge pull request galaxyproject#21372 from mvdbeek/debug_ascp

Various fixes around ascp file source

Author: mvdbeek

client/src/utils/url.ts

@@ -30,6 +30,7 @@ export const URI_PREFIXES = [
     "dataverse://",
     "elabftw://",
     "zip://",
+    "ascp://",
 ];
 
 export function isUrl(content: string): boolean {

doc/source/admin/data.md

@@ -455,6 +455,8 @@ Example configuration for EBI SRA downloads:
     -----BEGIN RSA PRIVATE KEY-----
     <YOUR ACTUAL SSH PRIVATE KEY CONTENT>
     -----END RSA PRIVATE KEY-----
+  # SSH key passphrase. https://embl.service-now.com/kb?id=kb_article_view&sys_kb_id=4cc60cf8c398a610bf313dfc0501314c#mcetoc_1idpn4k0to
+  ssh_key_passphrase: sample_passphrase
 ```
 
 The plugin is **download-only** and supports automatic retry with exponential backoff for transient 

lib/galaxy/config/sample/file_sources_conf.yml.sample

@@ -91,6 +91,8 @@
     -----BEGIN RSA PRIVATE KEY-----
     <YOUR ACTUAL SSH PRIVATE KEY CONTENT>
     -----END RSA PRIVATE KEY-----
+  # SSH key passphrase. https://embl.service-now.com/kb?id=kb_article_view&sys_kb_id=4cc60cf8c398a610bf313dfc0501314c#mcetoc_1idpn4k0to
+  ssh_key_passphrase: sample_passphrase
   # Note: This plugin is download-only (writable: false, browsable: false)
 
 # Example: Custom Aspera endpoint with encryption enabled

lib/galaxy/files/sources/ascp.py

@@ -23,7 +23,10 @@
 """
 
 import logging
-from typing import Union
+from typing import (
+    Optional,
+    Union,
+)
 
 from galaxy.files.models import (
     FilesSourceRuntimeContext,
@@ -40,7 +43,6 @@
 log = logging.getLogger(__name__)
 
 PLUGIN_TYPE = "ascp"
-REQUIRED_PACKAGE = "ascp"  # Note: This is the binary, not a Python package
 
 
 class AscpFilesSourceTemplateConfiguration(FsspecBaseFileSourceTemplateConfiguration):
@@ -57,6 +59,7 @@ class AscpFilesSourceTemplateConfiguration(FsspecBaseFileSourceTemplateConfigura
 
     ascp_path: Union[str, TemplateExpansion] = "ascp"
     ssh_key_content: Union[str, TemplateExpansion]  # SSH key content as string (required)
+    ssh_key_passphrase: Union[str, TemplateExpansion, None] = None  # Passphrase for the SSH key (required)
     user: Union[str, TemplateExpansion]  # Required field
     host: Union[str, TemplateExpansion]  # Required field
     rate_limit: Union[str, TemplateExpansion] = "300m"
@@ -81,6 +84,7 @@ class AscpFilesSourceConfiguration(FsspecBaseFileSourceConfiguration):
 
     ascp_path: str = "ascp"
     ssh_key_content: str  # SSH key content as string (required)
+    ssh_key_passphrase: Optional[str] = None  # Passphrase for the SSH key (optional)
     user: str  # Required field
     host: str  # Required field
     rate_limit: str = "300m"
@@ -129,7 +133,7 @@ class AscpFilesSource(FsspecFilesSource[AscpFilesSourceTemplateConfiguration, As
 
     plugin_type = PLUGIN_TYPE
     required_module = AscpFileSystem
-    required_package = REQUIRED_PACKAGE
+    required_package = "fsspec"  # Dummy requirement, need no external package
 
     template_config_class = AscpFilesSourceTemplateConfiguration
     resolved_config_class = AscpFilesSourceConfiguration
@@ -158,6 +162,7 @@ def _open_fs(
         return AscpFileSystem(
             ascp_path=config.ascp_path,
             ssh_key=config.ssh_key_content,
+            ssh_key_passphrase=config.ssh_key_passphrase,
             user=config.user,
             host=config.host,
             rate_limit=config.rate_limit,

lib/galaxy/files/sources/ascp_fsspec.py

@@ -56,6 +56,7 @@ class AscpFileSystem(AbstractFileSystem):
     Args:
         ascp_path: Path to the ascp binary (default: "ascp")
         ssh_key: SSH private key content as a string (required)
+        ssh_key_passphrase: SSH private key passphrase as a string
         user: Username for ascp connection (e.g., "era-fasp")
         host: Hostname (e.g., "fasp.sra.ebi.ac.uk")
         rate_limit: Transfer rate limit (default: "300m")
@@ -72,8 +73,9 @@ class AscpFileSystem(AbstractFileSystem):
 
     def __init__(
         self,
+        ssh_key: str,
+        ssh_key_passphrase: Optional[str] = None,
         ascp_path: str = "ascp",
-        ssh_key: Optional[str] = None,
         user: Optional[str] = None,
         host: Optional[str] = None,
         rate_limit: str = "300m",
@@ -99,6 +101,7 @@ def __init__(
         super().__init__(**kwargs)
         self.ascp_path = ascp_path
         self.ssh_key = ssh_key
+        self.ssh_key_passphrase = ssh_key_passphrase
         self.user = user
         self.host = host
         self.rate_limit = rate_limit
@@ -118,7 +121,15 @@ def __init__(
                 "Please ensure ascp is installed and accessible in your PATH."
             )
 
-    def _get_file(self, rpath: str, lpath: str, **kwargs: Any) -> None:
+    def isdir(self, path):
+        """Is this entry directory-like?"""
+        return False
+
+    def isfile(self, path):
+        """Is this entry file-like?"""
+        return True
+
+    def get_file(self, rpath: str, lpath: str, **kwargs: Any) -> None:
         """Download a file from remote path to local path using ascp with retry logic.
 
         This method handles:
@@ -237,12 +248,18 @@ def _execute_ascp_transfer(self, rpath: str, lpath: str, attempt: int) -> None:
 
             log.debug(f"Executing ascp command (key path hidden): {self._sanitize_cmd_for_log(cmd)}")
 
+            if self.ssh_key_passphrase:
+                env = os.environ.copy()
+                env["ASPERA_SCP_PASS"] = self.ssh_key_passphrase
+            else:
+                env = None
             # Execute ascp
             result = subprocess.run(
                 cmd,
                 capture_output=True,
                 text=True,
                 check=False,  # We'll handle errors manually
+                env=env,
             )
 
             if result.returncode != 0: