Add onedata objectstore

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

@@ -229,9 +229,12 @@
   public_name: ${user.preferences['zenodo_sandbox|public_name']}
   writable: true
 
+# Note for developers: you can easily set up a minimal, dockerized Onedata environment
+# using the so-called "demo-mode": https://onedata.org/#/home/documentation/topic/stable/demo-mode
 - 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']}
+  disableTlsCertificateValidation: ${user.preferences['onedata|disable_tls_certificate_validation']}

lib/galaxy/config/sample/object_store_conf.sample.yml

@@ -155,6 +155,38 @@ extra_dirs:
   - type: job_work
     path: database/job_working_directory_s3
 
+#
+# Sample Onedata Object Store
+#
+# Note for developers: you can easily set up a minimal, dockerized Onedata environment
+# using the so-called "demo-mode": https://onedata.org/#/home/documentation/topic/stable/demo-mode
+#
+
+type: onedata
+auth:
+  # an access token suitable for data access (allowing calls to the Oneprovider REST API).
+  access_token: ...
+connection:
+  # the domain of the Onezone service (e.g. "demo.onedata.org"), or its IP address for
+  # devel instances (see above).
+  onezone_domain: demo.onedata.org
+  # Allows connection to Onedata servers that do not present trusted SSL certificates. 
+  # SHOULD NOT be used unless you really know what you are doing.
+  disable_tls_certificate_validation: false
+space:
+  # the name of the Onedata space where the Galaxy data will be stored.
+  name: demo-space
+  # the relative directory path in the space under which the Galaxy data will be stored.
+  # Optional, if not provided, the data will be stored in the root of space.
+  path: galaxy-data
+cache:
+  path: database/object_store_cache_s3
+  size: 1000
+  cache_updated_data: true
+extra_dirs:
+  - type: job_work
+    path: database/job_working_directory_s3
+
 #
 # Sample iRODS Object Store configuration
 #

lib/galaxy/config/sample/object_store_conf.xml.sample

@@ -154,6 +154,42 @@
 </object_store>
 -->
 
+<!--
+    Sample Onedata Object Store
+
+    Note for developers: you can easily set up a minimal, dockerized Onedata environment
+    using the so-called "demo-mode": https://onedata.org/#/home/documentation/topic/stable/demo-mode
+
+    Onedata specific options:
+    //auth/@access_token -
+        an access token suitable for data access (allowing calls to the Oneprovider REST API).
+
+    //connection/@onezone_domain -
+        the domain of the Onezone service (e.g. "demo.onedata.org"), or its IP address for
+        devel instances (see above).
+
+    //connection/@disable_tls_certificate_validation - 
+        Allows connection to Onedata servers that do not present trusted SSL certificates. 
+        SHOULD NOT be used unless you really know what you are doing.
+
+    //space/@name -
+        the name of the Onedata space where the Galaxy data will be stored.
+
+    //space/@path -
+        the relative directory path in the space under which the Galaxy data will be stored.
+        Optional, if not provided, the data will be stored in the root of space.
+-->
+<!--
+<object_store type="onedata">
+    <auth access_token="..." />
+    <connection onezone_domain="demo.onedata.org" disable_tls_certificate_validation="False"/>
+    <space name="demo-space" path="galaxy-data" />
+    <cache path="database/object_store_cache" size="1000" cache_updated_data="True" />
+    <extra_dir type="job_work" path="database/job_working_directory_onedata"/>
+    <extra_dir type="temp" path="database/tmp_onedata"/>
+</object_store>
+-->
+
 <!--
     Sample iRODS Object Store
 -->

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

@@ -148,3 +148,8 @@ preferences:
               label: Your access token, suitable for REST API access in a Oneprovider service
               type: password
               required: False
+            - name: disable_tls_certificate_validation
+              label: Allow connection to Onedata servers that do not present trusted SSL certificates. SHOULD NOT be used unless you really know what you are doing.
+              type: boolean
+              required: False
+              value: False

lib/galaxy/dependencies/__init__.py

@@ -262,6 +262,9 @@ def check_fs_gcsfs(self):
     def check_google_cloud_storage(self):
         return "googlecloudstorage" in self.file_sources
 
+    def check_onedatafilerestclient(self):
+        return "onedata" in self.object_stores
+
     def check_fs_onedatarestfs(self):
         return "onedata" in self.file_sources
 

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.onedatarestfs # type: onedata
+fs.onedatarestfs # type: onedata, depends on onedatafilerestclient
 fs-basespace # type: basespace
 
 # Vault backend
@@ -40,6 +40,9 @@ pykube-ng==21.3.0
 # Synnefo / Pithos+ object store client
 kamaki
 
+# Onedata REST-based client for data access, required by the Onedata object store
+onedatafilerestclient
+
 watchdog
 
 # Error reporters optional modules

lib/galaxy/dependencies/dev-requirements.txt

@@ -76,6 +76,7 @@ myst-parser==3.0.0 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.17 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==1.26.4 ; python_version >= "3.9" and python_version < "3.13"
+onedatafilerestclient==21.2.5rc1 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.0 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/files/sources/onedata.py

@@ -25,7 +25,8 @@ def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None)
         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)
+        disable_tls_certificate_validation = props.pop("disableTlsCertificateValidation", False) or False
+        handle = OnedataRESTFS(onezone_domain, access_token, verify_ssl=not disable_tls_certificate_validation)
         return handle
 
 

lib/galaxy/objectstore/__init__.py

@@ -1434,6 +1434,10 @@ def type_to_object_store_class(store: str, fsmon: bool = False) -> Tuple[Type[Ba
         from .rucio import RucioObjectStore
 
         objectstore_class = RucioObjectStore
+    elif store == "onedata":
+        from .onedata import OnedataObjectStore
+
+        objectstore_class = OnedataObjectStore
     else:
         raise Exception(f"Unrecognized object store definition: {store}")
     # Disable the Pulsar object store for now until it receives some attention