Add SMB file source implementation and template

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

@@ -127,6 +127,20 @@
   config_path: ""
   port: 2222
 
+- type: smb
+  id: smb-example
+  label: "SMB Share Example"
+  doc: "Connect to a Windows/Samba SMB share"
+  host: "smb.example.com"
+  domain: "DOMAIN"
+  user: "username"
+  passwd: "password"
+  port: 445
+  encrypt: false
+  share_access: ""
+  path: "share/folder"
+  writable: false
+
 - type: s3fs
   label: My MinIO storage
   endpoint_url: "https://minio.usegalaxy.eu"

lib/galaxy/dependencies/__init__.py

@@ -348,6 +348,9 @@ def check_huggingface_hub(self):
     def check_omero_py(self):
         return "omero" in self.file_sources
 
+    def check_smbprotocol(self):
+        return "smb" in self.file_sources
+
 
 def strip_comment(line):
     # lifted from https://github.com/tox-dev/tox/commit/3c6b4f204e89852c4b7536b246a66d20be6d39ec

lib/galaxy/dependencies/conditional-requirements.txt

@@ -35,6 +35,7 @@ rspace-client>=2.6.1,<3  # type: rspace
 adlfs
 huggingface_hub
 omero-py #type: omero
+smbprotocol #type: smb
 
 # Vault backend
 hvac

lib/galaxy/files/sources/smb.py

@@ -0,0 +1,88 @@
+from typing import (
+    Optional,
+    Union,
+)
+
+# file source requires conditional dependency smbclient
+try:
+    from fsspec.implementations.smb import SMBFileSystem
+except ModuleNotFoundError:
+    SMBFileSystem = None
+
+from galaxy.files.models import FilesSourceRuntimeContext
+from galaxy.files.sources._fsspec import (
+    CacheOptionsDictType,
+    FsspecBaseFileSourceConfiguration,
+    FsspecBaseFileSourceTemplateConfiguration,
+    FsspecFilesSource,
+)
+from galaxy.util.config_templates import TemplateExpansion
+
+
+class SmbFileSourceTemplateConfiguration(FsspecBaseFileSourceTemplateConfiguration):
+    domain: Optional[Union[str, TemplateExpansion]] = None
+    host: Union[str, TemplateExpansion]
+    user: Optional[Union[str, TemplateExpansion]] = None
+    passwd: Optional[Union[str, TemplateExpansion]] = None
+    port: Union[int, TemplateExpansion] = 445
+    encrypt: Union[bool, TemplateExpansion] = False
+    share_access: Optional[Union[str, TemplateExpansion]] = None
+
+    path: Union[str, TemplateExpansion]
+
+
+class SmbFileSourceConfiguration(FsspecBaseFileSourceConfiguration):
+    domain: Optional[str] = None
+    host: str
+    user: Optional[str] = None
+    passwd: Optional[str] = None
+    port: int = 445
+    encrypt: bool = False
+    share_access: Optional[str] = None
+    path: str
+
+
+class SmbFilesSource(FsspecFilesSource[SmbFileSourceTemplateConfiguration, SmbFileSourceConfiguration]):
+    plugin_type = "smb"
+    required_module = SMBFileSystem
+    required_package = "fsspec"
+
+    template_config_class = SmbFileSourceTemplateConfiguration
+    resolved_config_class = SmbFileSourceConfiguration
+
+    def _open_fs(
+        self,
+        context: FilesSourceRuntimeContext[SmbFileSourceConfiguration],
+        cache_options: CacheOptionsDictType,
+    ):
+        cfg = context.config
+        # Build username with optional domain
+        username = f"{cfg.domain}\\{cfg.user}" if cfg.domain and cfg.user else cfg.user
+        # Determine share access: explicit config overrides, otherwise infer from writable flag
+        share_access = cfg.share_access
+        if share_access is None:
+            # Allow read access for other handles if we only read, otherwise exclusive
+            share_access = "r" if getattr(cfg, "writable", False) else ""
+        return SMBFileSystem(
+            host=cfg.host,
+            port=cfg.port,
+            username=username,
+            password=cfg.passwd,
+            encrypt=cfg.encrypt,
+            share_access=share_access,
+        )
+
+    def _to_filesystem_path(self, path: str) -> str:
+        base = self.template_config.path.rstrip("/")
+        rel = path.lstrip("/")
+        return f"{base}/{rel}" if rel else base or "/"
+
+    def _adapt_entry_path(self, filesystem_path: str) -> str:
+        base = self.template_config.path.rstrip("/")
+        if base and filesystem_path.startswith(base):
+            vp = filesystem_path[len(base) :]
+            return vp if vp.startswith("/") else f"/{vp}"
+        return filesystem_path
+
+
+__all__ = ("SmbFilesSource",)

lib/galaxy/files/templates/examples/smb.yml

@@ -0,0 +1,58 @@
+- id: smb
+  version: 0
+  name: SMB Share
+  description: |
+    Connect to Windows/Samba SMB shares using the fsspec SMBFileSystem.
+  configuration:
+    type: smb
+    host: "{{ variables.host }}"
+    domain: "{{ variables.domain }}"
+    user: "{{ variables.user }}"
+    passwd: "{{ secrets.password }}"
+    port: "{{ variables.port }}"
+    encrypt: "{{ variables.encrypt }}"
+
+    path: "{{ variables.path }}"
+    writable: "{{ variables.writable }}"
+  variables:
+    host:
+      label: SMB Host
+      type: string
+      help: Hostname or IP address of the SMB server.
+    user:
+      label: Username
+      type: string
+      optional: true
+      help: Username for authentication.
+    domain:
+      label: Domain
+      type: string
+      optional: true
+      help: Domain for the SMB server (e.g., INTRANET).
+    path:
+      label: Share Path
+      type: string
+      help: The share and directory path on the server, e.g., "share/folder".
+    port:
+      label: Port
+      type: integer
+      optional: true
+      default: 445
+      help: SMB port (usually 445).
+    encrypt:
+      label: Encrypt
+      type: boolean
+      optional: true
+      default: false
+      help: Whether to force encryption.
+    writable:
+      label: Writable?
+      type: boolean
+      optional: true
+      default: false
+      help: Allow Galaxy to write to this SMB share.
+  secrets:
+    password:
+      label: Password
+      optional: true
+      help: Password for authentication.

lib/galaxy/files/templates/models.py

@@ -48,6 +48,7 @@
     "dataverse",
     "huggingface",
     "omero",
+    "smb",
 ]
 
 
@@ -155,6 +156,33 @@ class FtpFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class SMBFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["smb"]
+    host: Union[str, TemplateExpansion]
+    domain: Optional[Union[str, TemplateExpansion]] = None
+    user: Optional[Union[str, TemplateExpansion]] = None
+    passwd: Optional[Union[str, TemplateExpansion]] = None
+    port: Union[int, TemplateExpansion] = 445
+    encrypt: Union[bool, TemplateExpansion] = False
+    path: Union[str, TemplateExpansion]
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class SMBFileSourceConfiguration(StrictModel):
+    type: Literal["smb"]
+    host: str
+    domain: Optional[str] = None
+    user: Optional[str] = None
+    passwd: Optional[str] = None
+    port: int = 445
+    encrypt: bool = False
+    share_access: Optional[str] = None
+    path: str
+    writable: bool = False
+
+
 class AzureFileSourceTemplateConfiguration(StrictModel):
     type: Literal["azure"]
     account_name: Union[str, TemplateExpansion]
@@ -369,6 +397,7 @@ class OmeroFileSourceConfiguration(StrictModel):
         DataverseFileSourceTemplateConfiguration,
         HuggingFaceFileSourceTemplateConfiguration,
         OmeroFileSourceTemplateConfiguration,
+        SMBFileSourceTemplateConfiguration,
     ],
     Field(discriminator="type"),
 ]
@@ -391,6 +420,7 @@ class OmeroFileSourceConfiguration(StrictModel):
         DataverseFileSourceConfiguration,
         HuggingFaceFileSourceConfiguration,
         OmeroFileSourceConfiguration,
+        SMBFileSourceConfiguration,
     ],
     Field(discriminator="type"),
 ]
@@ -471,6 +501,7 @@ def template_to_configuration(
     "dataverse": DataverseFileSourceConfiguration,
     "huggingface": HuggingFaceFileSourceConfiguration,
     "omero": OmeroFileSourceConfiguration,
+    "smb": SMBFileSourceConfiguration,
 }