Merge pull request galaxyproject#16690 from lopiola/onedata-files-sou…

…rce-plugin

 Use fs.onedatarestfs for Onedata files source plugin implementation

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

@@ -197,3 +197,10 @@
   doc: Invenio RDM turn-key research data management repository
   label: Invenio RDM Demo Repository
   url: https://inveniordm.web.cern.ch/
+
+- type: onedata
+  id: onedata1
+  label: Onedata
+  doc: Your Onedata files - configure an access token via user preferences
+  accessToken: ${user.preferences['onedata|access_token']}
+  onezoneDomain: ${user.preferences['onedata|onezone_domain']}

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

@@ -111,3 +111,16 @@ preferences:
               label: Whether to make draft records publicly available or restricted.
               type: boolean
               required: False
+
+    # Used in file_sources_conf.yml
+    onedata:
+        description: Your Onedata account
+        inputs:
+            - name: onezone_domain
+              label: Domain of the Onezone service (e.g. "demo.onedata.org")
+              type: text
+              required: False
+            - name: access_token
+              label: Your access token, suitable for REST API access in a Oneprovider service
+              type: password
+              required: False

lib/galaxy/dependencies/__init__.py

@@ -265,7 +265,7 @@ def check_fs_gcsfs(self):
     def check_google_cloud_storage(self):
         return "googlecloudstorage" in self.file_sources
 
-    def check_fs_onedatafs(self):
+    def check_fs_onedatarestfs(self):
         return "onedata" in self.file_sources
 
     def check_fs_basespace(self):

lib/galaxy/dependencies/conditional-requirements.txt

@@ -24,7 +24,7 @@ fs.googledrivefs # type: googledrive
 fs-gcsfs # type: googlecloudstorage
 # fs-gcsfs doesn't pin google-cloud-storage, and old versions log noisy exceptions and break test discovery
 google-cloud-storage>=2.8.0  # type: googlecloudstorage
-fs-onedatafs # type: onedata
+fs.onedatarestfs # type: onedata
 fs-basespace # type: basespace
 
 # Vault backend

lib/galaxy/files/sources/onedata.py

@@ -1,30 +1,32 @@
 try:
-    from fs.onedatafs import OnedataFS
+    from fs.onedatarestfs import OnedataRESTFS
 except ImportError:
-    OnedataFS = None
+    OnedataRESTFS = None
 
-from typing import (
-    Optional,
-    Union,
-)
+from typing import Optional
 
-from . import (
-    FilesSourceOptions,
-    FilesSourceProperties,
-)
+from . import FilesSourceOptions
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
 
-class OneDataFilesSource(PyFilesystem2FilesSource):
+def remove_prefix(prefix, string):
+    if string.startswith(prefix):
+        string = string[len(prefix) :]
+    return string
+
+
+class OnedataFilesSource(PyFilesystem2FilesSource):
     plugin_type = "onedata"
-    required_module = OnedataFS
-    required_package = "fs-onedatafs"
+    required_module = OnedataRESTFS
+    required_package = "fs.onedatarestfs"
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
-        extra_props: Union[FilesSourceProperties, dict] = opts.extra_props or {} if opts else {}
-        handle = OnedataFS(**{**props, **extra_props})
+        onezone_domain = props.pop("onezoneDomain", "") or ""
+        onezone_domain = remove_prefix("http://", remove_prefix("https://", onezone_domain))
+        access_token = props.pop("accessToken", "") or ""
+        handle = OnedataRESTFS(onezone_domain, access_token)
         return handle
 
 
-__all__ = ("OneDataFilesSource",)
+__all__ = ("OnedataFilesSource",)