eLabFTW integration via Galaxy file source

client/src/utils/upload-payload.js

@@ -12,6 +12,7 @@ export const URI_PREFIXES = [
     "drs://",
     "invenio://",
     "zenodo://",
+    "elabftw://",
 ];
 
 export function isUrl(content) {

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

@@ -238,3 +238,11 @@
   access_token: ${user.preferences['onedata|access_token']}
   onezone_domain: ${user.preferences['onedata|onezone_domain']}
   disable_tls_certificate_validation: ${user.preferences['onedata|disable_tls_certificate_validation']}
+
+- type: elabftw
+  id: elabftw
+  label: eLabFTW
+  doc: Import/export files from an eLabFTW instance.
+  api_key: ${user.user_vault.read_secret('preferences/elabftw/api_key')}
+  writable: true
+  endpoint: ${user.preferences['elabftw|endpoint']}

lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample

@@ -153,3 +153,17 @@ preferences:
               type: boolean
               required: False
               value: False
+
+    # Used in file_sources_conf.yml
+    elabftw:
+        description: Your eLabFTW Integration Settings
+        inputs:
+            - name: api_key
+              label: API key
+              type: secret
+              store: vault  # Requires setting up vault_config_file in your galaxy.yml
+              required: True
+            - name: endpoint
+              label: URL of the eLabFTW instance you want to access
+              type: text
+              required: True

lib/galaxy/files/sources/__init__.py

@@ -220,7 +220,7 @@ def write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> str:
         """Write file at native path to target_path (relative to uri root).
 
         :param target_path: url of the target file to write to within the filesource. e.g. `gxfiles://myftp1/myfile.txt`
@@ -231,6 +231,9 @@ def write_from(
         :type user_context: _type_, optional
         :param opts: A set of options to exercise additional control over the write_from method. Filesource specific, defaults to None
         :type opts: Optional[FilesSourceOptions], optional
+        :return: Actual url of the written file, fixed by the service backing the FileSource. May differ from the target
+            path.
+        :rtype: str
         """
 
     @abc.abstractmethod
@@ -296,7 +299,7 @@ def get_uri_root(self) -> str:
         """Return a prefix for the root (e.g. gxfiles://prefix/)."""
 
     @abc.abstractmethod
-    def list(
+    async def list(
         self,
         path="/",
         recursive=False,
@@ -443,7 +446,7 @@ def _serialization_props(self, user_context: "OptionalUserContext" = None) -> Fi
         Used in to_dict method if for_serialization is True.
         """
 
-    def list(
+    async def list(
         self,
         path="/",
         recursive=False,
@@ -467,9 +470,9 @@ def list(
             if offset is not None and offset < 0:
                 raise RequestParameterInvalidException("Offset must be greater than or equal to 0.")
 
-        return self._list(path, recursive, user_context, opts, limit, offset, query)
+        return await self._list(path, recursive, user_context, opts, limit, offset, query)
 
-    def _list(
+    async def _list(
         self,
         path="/",
         recursive=False,
@@ -511,10 +514,10 @@ def write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> str:
         self._ensure_writeable()
         self._check_user_access(user_context)
-        self._write_from(target_path, native_path, user_context=user_context, opts=opts)
+        return self._write_from(target_path, native_path, user_context=user_context, opts=opts) or target_path
 
     @abc.abstractmethod
     def _write_from(
@@ -523,7 +526,7 @@ def _write_from(
         native_path: str,
         user_context: "OptionalUserContext" = None,
         opts: Optional[FilesSourceOptions] = None,
-    ):
+    ) -> Optional[str]:
         pass
 
     def realize_to(

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -50,7 +50,7 @@ def __init__(self, **kwd: Unpack[FilesSourceProperties]):
     def _open_fs(self, user_context: OptionalUserContext = None, opts: Optional[FilesSourceOptions] = None) -> FS:
         """Subclasses must instantiate a PyFilesystem2 handle for this file system."""
 
-    def _list(
+    async def _list(
         self,
         path="/",
         recursive=False,