From ba428104b3231d28e00ac3007f9fb23a241861d0 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Wed, 19 Jun 2024 10:11:39 +0200
Subject: [PATCH 01/10] Add onedata file source template

---
 .../sample/file_sources_conf.yml.sample       |  6 ++--
 lib/galaxy/files/sources/onedata.py           |  6 ++--
 .../templates/examples/production_onedata.yml | 30 +++++++++++++++++++
 lib/galaxy/files/templates/models.py          | 23 +++++++++++++-
 4 files changed, 58 insertions(+), 7 deletions(-)
 create mode 100644 lib/galaxy/files/templates/examples/production_onedata.yml

diff --git a/lib/galaxy/config/sample/file_sources_conf.yml.sample b/lib/galaxy/config/sample/file_sources_conf.yml.sample
index 534e77736541..0bc5e9e10aed 100644
--- a/lib/galaxy/config/sample/file_sources_conf.yml.sample
+++ b/lib/galaxy/config/sample/file_sources_conf.yml.sample
@@ -235,6 +235,6 @@
   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']}
+  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']}
diff --git a/lib/galaxy/files/sources/onedata.py b/lib/galaxy/files/sources/onedata.py
index af7c104c9eaf..a46bf761b1a1 100644
--- a/lib/galaxy/files/sources/onedata.py
+++ b/lib/galaxy/files/sources/onedata.py
@@ -22,10 +22,10 @@ class OnedataFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
-        onezone_domain = props.pop("onezoneDomain", "") or ""
+        onezone_domain = props.pop("onezone_domain", "") or ""
         onezone_domain = remove_prefix("http://", remove_prefix("https://", onezone_domain))
-        access_token = props.pop("accessToken", "") or ""
-        disable_tls_certificate_validation = props.pop("disableTlsCertificateValidation", False) or False
+        access_token = props.pop("access_token", "") or ""
+        disable_tls_certificate_validation = props.pop("disable_tls_certificate_validation", False) or False
         handle = OnedataRESTFS(onezone_domain, access_token, verify_ssl=not disable_tls_certificate_validation)
         return handle
 
diff --git a/lib/galaxy/files/templates/examples/production_onedata.yml b/lib/galaxy/files/templates/examples/production_onedata.yml
new file mode 100644
index 000000000000..d8d458398b49
--- /dev/null
+++ b/lib/galaxy/files/templates/examples/production_onedata.yml
@@ -0,0 +1,30 @@
+- id: onedata
+  version: 0
+  name: Onedata Storage
+  description: |
+    This template allows connecting to Onedata servers.
+
+    Onedata is a global data management system providing a unified data access
+    interface across different storage providers. More information on Onedata
+    can be found in [Onedata's website](https://onedata.org/#/home).
+  variables:
+    onezone_domain:
+      label: Onezone domain
+      type: string
+      help: Domain of the Onezone service (e.g. datahub.egi.eu) to connect to.
+    disable_tls_certificate_validation:
+      label: Disable tls certificate validation?
+      type: boolean
+      help: |
+        Allows connection to Onedata servers that do not present trusted SSL certificates.
+        SHOULD NOT be used unless you really know what you are doing.
+      default: False
+  secrets:
+    access_token:
+      label: REST Access Token
+      help: Your access token, suitable for REST API access in a Oneprovider service.
+  configuration:
+    type: onedata
+    access_token: "{{ secrets.access_token }}"
+    onezone_domain: "{{ variables.onezone_domain }}"
+    disable_tls_certificate_validation: "{{ variables.disable_tls_certificate_validation }}"
diff --git a/lib/galaxy/files/templates/models.py b/lib/galaxy/files/templates/models.py
index 2e22cc904c30..e4b7fcea49e8 100644
--- a/lib/galaxy/files/templates/models.py
+++ b/lib/galaxy/files/templates/models.py
@@ -25,7 +25,7 @@
     UserDetailsDict,
 )
 
-FileSourceTemplateType = Literal["ftp", "posix", "s3fs", "azure"]
+FileSourceTemplateType = Literal["ftp", "posix", "s3fs", "azure", "onedata"]
 
 
 class PosixFileSourceTemplateConfiguration(StrictModel):
@@ -104,17 +104,37 @@ class AzureFileSourceConfiguration(StrictModel):
     writable: bool = False
 
 
+class OnedataFileSourceTemplateConfiguration(StrictModel):
+    type: Literal["onedata"]
+    access_token: Union[str, TemplateExpansion]
+    onezone_domain: Union[str, TemplateExpansion]
+    disable_tls_certificate_validation: Union[bool, TemplateExpansion] = False
+    writable: Union[bool, TemplateExpansion] = False
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class OnedataFileSourceConfiguration(StrictModel):
+    type: Literal["onedata"]
+    access_token: str
+    onezone_domain: str
+    disable_tls_certificate_validation: bool = False
+    writable: bool = False
+
+
 FileSourceTemplateConfiguration = Union[
     PosixFileSourceTemplateConfiguration,
     S3FSFileSourceTemplateConfiguration,
     FtpFileSourceTemplateConfiguration,
     AzureFileSourceTemplateConfiguration,
+    OnedataFileSourceTemplateConfiguration,
 ]
 FileSourceConfiguration = Union[
     PosixFileSourceConfiguration,
     S3FSFileSourceConfiguration,
     FtpFileSourceConfiguration,
     AzureFileSourceConfiguration,
+    OnedataFileSourceConfiguration,
 ]
 
 
@@ -175,6 +195,7 @@ def template_to_configuration(
     "posix": PosixFileSourceConfiguration,
     "s3fs": S3FSFileSourceConfiguration,
     "azure": AzureFileSourceConfiguration,
+    "onedata": OnedataFileSourceConfiguration,
 }
 
 

From ddf2a4891ab33b56dc4791840bdddfe6b41bf429 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Wed, 19 Jun 2024 10:14:13 +0200
Subject: [PATCH 02/10] Add onedata object store template

---
 .../sample/object_store_conf.sample.yml       |  2 +-
 lib/galaxy/objectstore/onedata.py             |  4 +-
 .../templates/examples/production_onedata.yml | 46 +++++++++++++++++
 lib/galaxy/objectstore/templates/models.py    | 51 ++++++++++++++++++-
 4 files changed, 99 insertions(+), 4 deletions(-)
 create mode 100644 lib/galaxy/objectstore/templates/examples/production_onedata.yml

diff --git a/lib/galaxy/config/sample/object_store_conf.sample.yml b/lib/galaxy/config/sample/object_store_conf.sample.yml
index afbcfc22323b..97d6413824bb 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -234,7 +234,7 @@ space:
   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
+  galaxy_root_dir: galaxy-data
 cache:
   path: database/object_store_cache_s3
   size: 1000
diff --git a/lib/galaxy/objectstore/onedata.py b/lib/galaxy/objectstore/onedata.py
index 7fc8d5b72c27..8a6aef16bf00 100644
--- a/lib/galaxy/objectstore/onedata.py
+++ b/lib/galaxy/objectstore/onedata.py
@@ -107,8 +107,8 @@ def __init__(self, config, config_dict):
 
         cache_dict = config_dict.get("cache") or {}
         self.enable_cache_monitor, self.cache_monitor_interval = enable_cache_monitor(config, config_dict)
-        self.cache_size = cache_dict["size"] or self.config.object_store_cache_size
-        self.staging_path = cache_dict["path"] or self.config.object_store_cache_path
+        self.cache_size = cache_dict.get("size") or self.config.object_store_cache_size
+        self.staging_path = cache_dict.get("path") or self.config.object_store_cache_path
         self.cache_updated_data = cache_dict.get("cache_updated_data", True)
 
         extra_dirs = {e["type"]: e["path"] for e in config_dict.get("extra_dirs", [])}
diff --git a/lib/galaxy/objectstore/templates/examples/production_onedata.yml b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
new file mode 100644
index 000000000000..55f6ee2e8a73
--- /dev/null
+++ b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
@@ -0,0 +1,46 @@
+- id: onedata
+  name: Onedata Storage
+  version: 0
+  description: |
+    This template allows using Onedata storage.
+
+    Onedata is a global data management system providing a unified data access
+    interface across different storage providers. More information on Onedata
+    can be found in [Onedata's website](https://onedata.org/#/home).
+  variables:
+    onezone_domain:
+      label: Onezone Domain
+      type: string
+      help: Domain of the Onezone service (e.g. datahub.egi.eu) to connect to.
+    disable_tls_certificate_validation:
+      label: Disable tls certificate validation?
+      type: boolean
+      help: |
+        Allows connection to Onedata servers that do not present trusted SSL certificates.
+        SHOULD NOT be used unless you really know what you are doing.
+      default: False
+    space_name:
+      label: Space Name
+      type: string
+      help: The name of the Onedata space where the Galaxy data will be stored.
+    galaxy_root_dir:
+      label: Galaxy root directory
+      type: string
+      help: |
+        The relative directory path in the space under which the Galaxy data
+        will be stored.
+      default: ""
+  secrets:
+    access_token:
+      label: REST Access Token
+      help: Your access token, suitable for REST API access in a Oneprovider service.
+  configuration:
+    type: onedata
+    auth:
+      access_token: '{{ secrets.access_token }}'
+    connection:
+      onezone_domain: "{{ variables.onezone_domain }}"
+      disable_tls_certificate_validation: "{{ variables.disable_tls_certificate_validation }}"
+    space:
+      name: "{{ variables.space_name }}"
+      galaxy_root_dir: "{{ variables.galaxy_root_dir }}"
diff --git a/lib/galaxy/objectstore/templates/models.py b/lib/galaxy/objectstore/templates/models.py
index dcbabb760434..a066163d5b37 100644
--- a/lib/galaxy/objectstore/templates/models.py
+++ b/lib/galaxy/objectstore/templates/models.py
@@ -32,7 +32,7 @@
 
 ObjectStoreTemplateVariableType = TemplateVariableType
 ObjectStoreTemplateVariableValueType = TemplateVariableValueType
-ObjectStoreTemplateType = Literal["aws_s3", "azure_blob", "boto3", "disk", "generic_s3"]
+ObjectStoreTemplateType = Literal["aws_s3", "azure_blob", "boto3", "disk", "generic_s3", "onedata"]
 
 
 class S3AuthTemplate(StrictModel):
@@ -266,12 +266,59 @@ class GenericS3ObjectStoreConfiguration(StrictModel):
     badges: BadgeList = None
 
 
+class OnedataAuthTemplate(StrictModel):
+    access_token: Union[str, TemplateExpansion]
+
+
+class OnedataAuth(StrictModel):
+    access_token: str
+
+
+class OnedataConnectionTemplate(StrictModel):
+    onezone_domain: Union[str, TemplateExpansion]
+    disable_tls_certificate_validation: Union[bool, TemplateExpansion] = False
+
+
+class OnedataConnection(StrictModel):
+    onezone_domain: str
+    disable_tls_certificate_validation: bool = False
+
+
+class OnedataSpaceTemplate(StrictModel):
+    name: Union[str, TemplateExpansion]
+    galaxy_root_dir: Optional[Union[str, TemplateExpansion]] = ""
+
+
+class OnedataSpace(StrictModel):
+    name: str
+    galaxy_root_dir: str
+
+
+class OnedataObjectStoreTemplateConfiguration(StrictModel):
+    type: Literal["onedata"]
+    auth: OnedataAuthTemplate
+    connection: OnedataConnectionTemplate
+    space: OnedataSpaceTemplate
+    badges: BadgeList = None
+    template_start: Optional[str] = None
+    template_end: Optional[str] = None
+
+
+class OnedataObjectStoreConfiguration(StrictModel):
+    type: Literal["onedata"]
+    auth: OnedataAuth
+    connection: OnedataConnection
+    space: OnedataSpace
+    badges: BadgeList = None
+
+
 ObjectStoreTemplateConfiguration = Union[
     AwsS3ObjectStoreTemplateConfiguration,
     Boto3ObjectStoreTemplateConfiguration,
     GenericS3ObjectStoreTemplateConfiguration,
     DiskObjectStoreTemplateConfiguration,
     AzureObjectStoreTemplateConfiguration,
+    OnedataObjectStoreTemplateConfiguration,
 ]
 ObjectStoreConfiguration = Union[
     AwsS3ObjectStoreConfiguration,
@@ -279,6 +326,7 @@ class GenericS3ObjectStoreConfiguration(StrictModel):
     DiskObjectStoreConfiguration,
     AzureObjectStoreConfiguration,
     GenericS3ObjectStoreConfiguration,
+    OnedataObjectStoreConfiguration,
 ]
 
 
@@ -345,6 +393,7 @@ def template_to_configuration(
     "generic_s3": GenericS3ObjectStoreConfiguration,
     "azure_blob": AzureObjectStoreConfiguration,
     "disk": DiskObjectStoreConfiguration,
+    "onedata": OnedataObjectStoreConfiguration,
 }
 
 

From d2ccc07f1d58765b57196039e1b38b642db5f554 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 24 Jun 2024 20:05:52 +0200
Subject: [PATCH 03/10] Unify onedata object store yml and xml configs

---
 lib/galaxy/config/sample/object_store_conf.sample.yml | 5 ++++-
 lib/galaxy/config/sample/object_store_conf.xml.sample | 9 ++++++---
 lib/galaxy/objectstore/onedata.py                     | 2 +-
 3 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/config/sample/object_store_conf.sample.yml b/lib/galaxy/config/sample/object_store_conf.sample.yml
index 97d6413824bb..f597abd9a667 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -231,8 +231,11 @@ connection:
   disable_tls_certificate_validation: false
 space:
   # the name of the Onedata space where the Galaxy data will be stored.
+  # If there is more than one space with the same name, you can explicitly
+  # specify which one to select by using the format <space_name>@<space_id>
+  # (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
   name: demo-space
-  # the relative directory path in the space under which the Galaxy data will be stored.
+  # the relative directory path in the space at which the Galaxy data will be stored.
   # Optional, if not provided, the data will be stored in the root of space.
   galaxy_root_dir: galaxy-data
 cache:
diff --git a/lib/galaxy/config/sample/object_store_conf.xml.sample b/lib/galaxy/config/sample/object_store_conf.xml.sample
index 1b9d997271e9..301b12463f9e 100644
--- a/lib/galaxy/config/sample/object_store_conf.xml.sample
+++ b/lib/galaxy/config/sample/object_store_conf.xml.sample
@@ -174,16 +174,19 @@
 
     //space/@name -
         the name of the Onedata space where the Galaxy data will be stored.
+        If there is more than one space with the same name, you can explicitly
+        specify which one to select by using the format <space_name>@<space_id>
+        (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
 
-    //space/@path -
-        the relative directory path in the space under which the Galaxy data will be stored.
+    //space/@galaxy_root_dir -
+        the relative directory path in the space at 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="datahub.egi.eu" disable_tls_certificate_validation="False"/>
-    <space name="demo-space" path="galaxy-data" />
+    <space name="demo-space" galaxy_root_dir="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"/>
diff --git a/lib/galaxy/objectstore/onedata.py b/lib/galaxy/objectstore/onedata.py
index 8a6aef16bf00..1c95c9cc2a93 100644
--- a/lib/galaxy/objectstore/onedata.py
+++ b/lib/galaxy/objectstore/onedata.py
@@ -44,7 +44,7 @@ def _parse_config_xml(config_xml):
 
         space_xml = _get_config_xml_elements(config_xml, "space")[0]
         space_name = space_xml.get("name")
-        galaxy_root_dir = space_xml.get("path", "")
+        galaxy_root_dir = space_xml.get("galaxy_root_dir", "")
 
         cache_dict = parse_caching_config_dict_from_xml(config_xml)
 

From 784c5bfd41ec21617cf145d3d6eeb80ee45f3f4f Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 24 Jun 2024 20:06:59 +0200
Subject: [PATCH 04/10] Improve onedata templates docs

---
 .../templates/examples/production_onedata.yml |  9 ++++++---
 .../templates/examples/production_onedata.yml | 20 +++++++++++++------
 2 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/files/templates/examples/production_onedata.yml b/lib/galaxy/files/templates/examples/production_onedata.yml
index d8d458398b49..7722687a4af6 100644
--- a/lib/galaxy/files/templates/examples/production_onedata.yml
+++ b/lib/galaxy/files/templates/examples/production_onedata.yml
@@ -6,7 +6,7 @@
 
     Onedata is a global data management system providing a unified data access
     interface across different storage providers. More information on Onedata
-    can be found in [Onedata's website](https://onedata.org/#/home).
+    can be found on [Onedata's website](https://onedata.org/#/home).
   variables:
     onezone_domain:
       label: Onezone domain
@@ -21,8 +21,11 @@
       default: False
   secrets:
     access_token:
-      label: REST Access Token
-      help: Your access token, suitable for REST API access in a Oneprovider service.
+      label: Access Token
+      help: |
+        Your [access token](https://onedata.org/#/home/documentation/topic/stable/tokens),
+        suitable for REST API access in a Oneprovider service. May be confined
+        to read-only data access.
   configuration:
     type: onedata
     access_token: "{{ secrets.access_token }}"
diff --git a/lib/galaxy/objectstore/templates/examples/production_onedata.yml b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
index 55f6ee2e8a73..6d9f15241876 100644
--- a/lib/galaxy/objectstore/templates/examples/production_onedata.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
@@ -6,7 +6,7 @@
 
     Onedata is a global data management system providing a unified data access
     interface across different storage providers. More information on Onedata
-    can be found in [Onedata's website](https://onedata.org/#/home).
+    can be found on [Onedata's website](https://onedata.org/#/home).
   variables:
     onezone_domain:
       label: Onezone Domain
@@ -22,18 +22,26 @@
     space_name:
       label: Space Name
       type: string
-      help: The name of the Onedata space where the Galaxy data will be stored.
+      help: |
+        The name of the Onedata space where the Galaxy data will be stored.
+        If there is more than one space with the same name, you can explicitly
+        specify which one to select by using the format <space_name>@<space_id>
+        (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
     galaxy_root_dir:
       label: Galaxy root directory
       type: string
       help: |
-        The relative directory path in the space under which the Galaxy data
-        will be stored.
+        The relative directory path in the space at which the Galaxy data
+        will be stored. If empty, the data will be stored in the space's
+        root directory.
       default: ""
   secrets:
     access_token:
-      label: REST Access Token
-      help: Your access token, suitable for REST API access in a Oneprovider service.
+      label: Access Token
+      help: |
+        Your [access token](https://onedata.org/#/home/documentation/topic/stable/tokens),
+        suitable for REST API access in a Oneprovider service. Must allow both
+        read and write data access.
   configuration:
     type: onedata
     auth:

From 39c181990c1dfb7a1d17a4623151307d64a36347 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 24 Jun 2024 20:07:18 +0200
Subject: [PATCH 05/10] Add writable to onedata file source template

---
 .../files/templates/examples/production_onedata.yml       | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/lib/galaxy/files/templates/examples/production_onedata.yml b/lib/galaxy/files/templates/examples/production_onedata.yml
index 7722687a4af6..10514d39cbfe 100644
--- a/lib/galaxy/files/templates/examples/production_onedata.yml
+++ b/lib/galaxy/files/templates/examples/production_onedata.yml
@@ -19,6 +19,13 @@
         Allows connection to Onedata servers that do not present trusted SSL certificates.
         SHOULD NOT be used unless you really know what you are doing.
       default: False
+    writable:
+      label: Writable?
+      type: boolean
+      help: |
+        Allow Galaxy to write data to this Onedata storage.
+        Requires access token with write data access.
+      default: False
   secrets:
     access_token:
       label: Access Token
@@ -31,3 +38,4 @@
     access_token: "{{ secrets.access_token }}"
     onezone_domain: "{{ variables.onezone_domain }}"
     disable_tls_certificate_validation: "{{ variables.disable_tls_certificate_validation }}"
+    writable: "{{ variables.writable }}"

From 735e977ea529e47db983635999149babb149c0da Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Tue, 25 Jun 2024 17:02:56 +0200
Subject: [PATCH 06/10] Update onedata libraries to 21.2.5.2

---
 .../config/sample/object_store_conf.sample.yml     |  8 ++++----
 .../dependencies/conditional-requirements.txt      |  2 +-
 lib/galaxy/dependencies/dev-requirements.txt       |  2 +-
 lib/galaxy/files/sources/onedata.py                | 14 ++++++++++++--
 lib/galaxy/objectstore/onedata.py                  | 13 +++++++++++--
 pyproject.toml                                     |  2 +-
 6 files changed, 30 insertions(+), 11 deletions(-)

diff --git a/lib/galaxy/config/sample/object_store_conf.sample.yml b/lib/galaxy/config/sample/object_store_conf.sample.yml
index f597abd9a667..f87b82452313 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -220,22 +220,22 @@ extra_dirs:
 
 type: onedata
 auth:
-  # an access token suitable for data access (allowing calls to the Oneprovider REST API).
+  # 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. datahub.egi.eu), or its IP address for
+  # The domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
   # devel instances (see above).
   onezone_domain: datahub.egi.eu
   # 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.
+  # The name of the Onedata space where the Galaxy data will be stored.
   # If there is more than one space with the same name, you can explicitly
   # specify which one to select by using the format <space_name>@<space_id>
   # (e.g. demo@7285220ecc636075ae5759aec7ad65d3cha8f9).
   name: demo-space
-  # the relative directory path in the space at which the Galaxy data will be stored.
+  # The relative directory path in the space at which the Galaxy data will be stored.
   # Optional, if not provided, the data will be stored in the root of space.
   galaxy_root_dir: galaxy-data
 cache:
diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index e672eaca7d20..abebd8fd0a13 100644
--- a/lib/galaxy/dependencies/conditional-requirements.txt
+++ b/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==21.2.5.1 # type: onedata, depends on onedatafilerestclient
+fs.onedatarestfs==21.2.5.2 # type: onedata, depends on onedatafilerestclient
 fs-basespace # type: basespace
 fs-azureblob # type: azure
 
diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 9315593bc0b2..8e9d0db4f533 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -82,7 +82,7 @@ myst-parser==3.0.1 ; python_version >= "3.8" and python_version < "3.13"
 nh3==0.2.18 ; python_version >= "3.8" and python_version < "3.13"
 numpy==1.24.4 ; python_version >= "3.8" and python_version < "3.9"
 numpy==2.0.0 ; python_version >= "3.9" and python_version < "3.13"
-onedatafilerestclient==21.2.5.1 ; python_version >= "3.8" and python_version < "3.13"
+onedatafilerestclient==21.2.5.2 ; python_version >= "3.8" and python_version < "3.13"
 outcome==1.3.0.post0 ; python_version >= "3.8" and python_version < "3.13"
 packaging==24.1 ; python_version >= "3.8" and python_version < "3.13"
 pathspec==0.12.1 ; python_version >= "3.8" and python_version < "3.13"
diff --git a/lib/galaxy/files/sources/onedata.py b/lib/galaxy/files/sources/onedata.py
index a46bf761b1a1..87f455c68dd9 100644
--- a/lib/galaxy/files/sources/onedata.py
+++ b/lib/galaxy/files/sources/onedata.py
@@ -5,6 +5,7 @@
 
 from typing import Optional
 
+from galaxy.util import mapped_chars
 from . import FilesSourceOptions
 from ._pyfilesystem2 import PyFilesystem2FilesSource
 
@@ -22,11 +23,20 @@ class OnedataFilesSource(PyFilesystem2FilesSource):
 
     def _open_fs(self, user_context=None, opts: Optional[FilesSourceOptions] = None):
         props = self._serialization_props(user_context)
+
+        access_token = props.pop("access_token", "") or ""
         onezone_domain = props.pop("onezone_domain", "") or ""
         onezone_domain = remove_prefix("http://", remove_prefix("https://", onezone_domain))
-        access_token = props.pop("access_token", "") or ""
         disable_tls_certificate_validation = props.pop("disable_tls_certificate_validation", False) or False
-        handle = OnedataRESTFS(onezone_domain, access_token, verify_ssl=not disable_tls_certificate_validation)
+
+        alt_space_fqn_separators = [mapped_chars["@"]] if "@" in mapped_chars else None
+
+        handle = OnedataRESTFS(
+            onezone_domain,
+            access_token,
+            alt_space_fqn_separators=alt_space_fqn_separators,
+            verify_ssl=not disable_tls_certificate_validation,
+        )
         return handle
 
 
diff --git a/lib/galaxy/objectstore/onedata.py b/lib/galaxy/objectstore/onedata.py
index 1c95c9cc2a93..80f45a365d78 100644
--- a/lib/galaxy/objectstore/onedata.py
+++ b/lib/galaxy/objectstore/onedata.py
@@ -15,7 +15,10 @@
 except ImportError:
     OnedataFileRESTClient = None
 
-from galaxy.util import string_as_bool
+from galaxy.util import (
+    mapped_chars,
+    string_as_bool,
+)
 from ._caching_base import CachingConcreteObjectStore
 from .caching import (
     enable_cache_monitor,
@@ -125,8 +128,14 @@ def _initialize(self):
             f"(disable_tls_certificate_validation={self.disable_tls_certificate_validation})"
         )
 
+        alt_space_fqn_separators = [mapped_chars["@"]] if "@" in mapped_chars else None
         verify_ssl = not self.disable_tls_certificate_validation
-        self._client = OnedataFileRESTClient(self.onezone_domain, self.access_token, verify_ssl=verify_ssl)
+        self._client = OnedataFileRESTClient(
+            self.onezone_domain,
+            self.access_token,
+            alt_space_fqn_separators=alt_space_fqn_separators,
+            verify_ssl=verify_ssl,
+        )
 
         self._ensure_staging_path_writable()
         self._start_cache_monitor_if_needed()
diff --git a/pyproject.toml b/pyproject.toml
index 27804756a180..e0c7dff067e6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -143,7 +143,7 @@ isort = "*"
 lxml = "!=4.2.2"
 markdown-it-reporter = "*"
 myst-parser = "*"
-onedatafilerestclient = "==21.2.5.1"
+onedatafilerestclient = "==21.2.5.2"
 pkce = "*"
 playwright = "*"
 pytest = "*"

From 6b162bb7e623ddccc2fb70d02ab157fbdf06d553 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Thu, 27 Jun 2024 13:43:57 +0200
Subject: [PATCH 07/10] Add info about minimal supported Onezone version

---
 .../config/sample/object_store_conf.sample.yml    |  2 +-
 .../config/sample/object_store_conf.xml.sample    |  2 +-
 .../sample/user_preferences_extra_conf.yml.sample |  2 +-
 .../templates/examples/production_onedata.yml     | 15 +++++++++------
 .../templates/examples/production_onedata.yml     |  9 +++++----
 5 files changed, 17 insertions(+), 13 deletions(-)

diff --git a/lib/galaxy/config/sample/object_store_conf.sample.yml b/lib/galaxy/config/sample/object_store_conf.sample.yml
index f87b82452313..90fcf2fcccd1 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -224,7 +224,7 @@ auth:
   access_token: ...
 connection:
   # The domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
-  # devel instances (see above).
+  # devel instances (see above). The minimal supported Onezone version is 21.02.4.
   onezone_domain: datahub.egi.eu
   # Allows connection to Onedata servers that do not present trusted SSL certificates. 
   # SHOULD NOT be used unless you really know what you are doing.
diff --git a/lib/galaxy/config/sample/object_store_conf.xml.sample b/lib/galaxy/config/sample/object_store_conf.xml.sample
index 301b12463f9e..db4271765203 100644
--- a/lib/galaxy/config/sample/object_store_conf.xml.sample
+++ b/lib/galaxy/config/sample/object_store_conf.xml.sample
@@ -166,7 +166,7 @@
 
     //connection/@onezone_domain -
         the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
-        devel instances (see above).
+        devel instances (see above). The minimal supported Onezone version is 21.02.4.
 
     //connection/@disable_tls_certificate_validation - 
         Allows connection to Onedata servers that do not present trusted SSL certificates. 
diff --git a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
index 72689e31bf44..9f38f40bba1d 100644
--- a/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
+++ b/lib/galaxy/config/sample/user_preferences_extra_conf.yml.sample
@@ -141,7 +141,7 @@ preferences:
         description: Your Onedata account
         inputs:
             - name: onezone_domain
-              label: Domain of the Onezone service (e.g. datahub.egi.eu)
+              label: Domain of the Onezone service (e.g. datahub.egi.eu). The minimal supported Onezone version is 21.02.4.
               type: text
               required: False
             - name: access_token
diff --git a/lib/galaxy/files/templates/examples/production_onedata.yml b/lib/galaxy/files/templates/examples/production_onedata.yml
index 10514d39cbfe..97e950377580 100644
--- a/lib/galaxy/files/templates/examples/production_onedata.yml
+++ b/lib/galaxy/files/templates/examples/production_onedata.yml
@@ -2,11 +2,13 @@
   version: 0
   name: Onedata Storage
   description: |
-    This template allows connecting to Onedata servers.
+    If you have an account in Onedata, you can use such a file source to upload
+    your data directly from Onedata to Galaxy. You can also perform
+    an "Export datasets to remote files source" of a dataset from Galaxy to
+    Onedata.
 
-    Onedata is a global data management system providing a unified data access
-    interface across different storage providers. More information on Onedata
-    can be found on [Onedata's website](https://onedata.org/#/home).
+    The minimal supported Onezone version is 21.02.4.
+    More information on Onedata can be found on [Onedata's website](https://onedata.org/#/home).
   variables:
     onezone_domain:
       label: Onezone domain
@@ -24,7 +26,7 @@
       type: boolean
       help: |
         Allow Galaxy to write data to this Onedata storage.
-        Requires access token with write data access.
+        Requires an access token with write data access.
       default: False
   secrets:
     access_token:
@@ -32,7 +34,8 @@
       help: |
         Your [access token](https://onedata.org/#/home/documentation/topic/stable/tokens),
         suitable for REST API access in a Oneprovider service. May be confined
-        to read-only data access.
+        to read-only data access, unless you wish to use the
+        "Export datasets to remote files source" tool (write permissions are needed then).
   configuration:
     type: onedata
     access_token: "{{ secrets.access_token }}"
diff --git a/lib/galaxy/objectstore/templates/examples/production_onedata.yml b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
index 6d9f15241876..f50a137da447 100644
--- a/lib/galaxy/objectstore/templates/examples/production_onedata.yml
+++ b/lib/galaxy/objectstore/templates/examples/production_onedata.yml
@@ -2,11 +2,12 @@
   name: Onedata Storage
   version: 0
   description: |
-    This template allows using Onedata storage.
+    If you have an account in Onedata, you can use such an object store as
+    a storage location for your Galaxy datasets; they will be stored in
+    the Onedata space of your choice.
 
-    Onedata is a global data management system providing a unified data access
-    interface across different storage providers. More information on Onedata
-    can be found on [Onedata's website](https://onedata.org/#/home).
+    The minimal supported Onezone version is 21.02.4.
+    More information on Onedata can be found on [Onedata's website](https://onedata.org/#/home).
   variables:
     onezone_domain:
       label: Onezone Domain

From a263d883830d035f890a19505888ee878d69cb8c Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 15 Jul 2024 14:34:42 +0200
Subject: [PATCH 08/10] Remove production_ prefix from onedata templates

---
 .../templates/examples/{production_onedata.yml => onedata.yml}    | 0
 .../templates/examples/{production_onedata.yml => onedata.yml}    | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename lib/galaxy/files/templates/examples/{production_onedata.yml => onedata.yml} (100%)
 rename lib/galaxy/objectstore/templates/examples/{production_onedata.yml => onedata.yml} (100%)

diff --git a/lib/galaxy/files/templates/examples/production_onedata.yml b/lib/galaxy/files/templates/examples/onedata.yml
similarity index 100%
rename from lib/galaxy/files/templates/examples/production_onedata.yml
rename to lib/galaxy/files/templates/examples/onedata.yml
diff --git a/lib/galaxy/objectstore/templates/examples/production_onedata.yml b/lib/galaxy/objectstore/templates/examples/onedata.yml
similarity index 100%
rename from lib/galaxy/objectstore/templates/examples/production_onedata.yml
rename to lib/galaxy/objectstore/templates/examples/onedata.yml

From ea9c79ae8c447e54bb4ec424fadef4a605d901ee Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 3 Sep 2024 11:46:56 +0200
Subject: [PATCH 09/10] Rebuild API client

---
 client/src/api/schema/schema.ts | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/client/src/api/schema/schema.ts b/client/src/api/schema/schema.ts
index 05a06bc61dc7..b8a076a8e0ac 100644
--- a/client/src/api/schema/schema.ts
+++ b/client/src/api/schema/schema.ts
@@ -8785,7 +8785,7 @@ export interface components {
              * Type
              * @enum {string}
              */
-            type: "ftp" | "posix" | "s3fs" | "azure";
+            type: "ftp" | "posix" | "s3fs" | "azure" | "onedata";
             /** Variables */
             variables?:
                 | (
@@ -13748,7 +13748,7 @@ export interface components {
              * Type
              * @enum {string}
              */
-            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
+            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3" | "onedata";
             /** Variables */
             variables?:
                 | (
@@ -16503,7 +16503,7 @@ export interface components {
              * Type
              * @enum {string}
              */
-            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3";
+            type: "aws_s3" | "azure_blob" | "boto3" | "disk" | "generic_s3" | "onedata";
             /**
              * Uuid
              * Format: uuid4
@@ -16578,7 +16578,7 @@ export interface components {
              * Type
              * @enum {string}
              */
-            type: "ftp" | "posix" | "s3fs" | "azure";
+            type: "ftp" | "posix" | "s3fs" | "azure" | "onedata";
             /** Uri Root */
             uri_root: string;
             /**

From 6ab1f7c35758e1a3c6527442be143eec279b2af9 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 4 Sep 2024 12:10:29 +0200
Subject: [PATCH 10/10] Add onedata client things

---
 client/src/api/fileSources.ts                             | 1 +
 client/src/components/FileSources/FileSourceTypeSpan.vue  | 7 ++++++-
 client/src/components/ObjectStore/ObjectStoreTypeSpan.vue | 1 +
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/client/src/api/fileSources.ts b/client/src/api/fileSources.ts
index 68935db4573f..eb984b938e8f 100644
--- a/client/src/api/fileSources.ts
+++ b/client/src/api/fileSources.ts
@@ -4,3 +4,4 @@ export type FileSourceTemplateSummary = components["schemas"]["FileSourceTemplat
 export type FileSourceTemplateSummaries = FileSourceTemplateSummary[];
 
 export type UserFileSourceModel = components["schemas"]["UserFileSourceModel"];
+export type FileSourceTypes = UserFileSourceModel["type"];
diff --git a/client/src/components/FileSources/FileSourceTypeSpan.vue b/client/src/components/FileSources/FileSourceTypeSpan.vue
index 95129c85a085..e41b3b32858d 100644
--- a/client/src/components/FileSources/FileSourceTypeSpan.vue
+++ b/client/src/components/FileSources/FileSourceTypeSpan.vue
@@ -1,13 +1,18 @@
 <script setup lang="ts">
 import { computed } from "vue";
 
+import type { FileSourceTypes } from "@/api/fileSources";
+
 const MESSAGES = {
     posix: "This is a simple path based storage location that assumes the all the relevant paths are already mounted on the Galaxy server and target worker nodes.",
     s3fs: "This is an remote file source plugin based on the Amazon Simple Storage Service (S3) interface. The AWS interface has become an industry standard and many storage vendors support it and use it to expose 'object' based storage.",
+    azure: "This is an remote file source plugin based on the Azure service.",
+    onedata: "This is an remote file source plugin based on the Onedata service.",
+    ftp: "This is an remote file source plugin based on the FTP protocol.",
 };
 
 interface Props {
-    type: "posix" | "s3fs";
+    type: FileSourceTypes;
 }
 
 const props = defineProps<Props>();
diff --git a/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue b/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
index 20ff0f7ffcc9..84b946515ac4 100644
--- a/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
+++ b/client/src/components/ObjectStore/ObjectStoreTypeSpan.vue
@@ -11,6 +11,7 @@ const MESSAGES = {
     boto3: "This is a storage location based on the Amazon Simple Storage Service (S3) interface, but likely not stored by Amazon. The AWS interface has become an industry standard and many storage vendors support it and use it to expose object based storage.",
     generic_s3:
         "This is a storage location based on the Amazon Simple Storage Service (S3) interface, but likely not stored by Amazon. The AWS interface has become an industry standard and many storage vendors support it and use it to expose object based storage.",
+    onedata: "This is a storage location based on the Onedata system.",
 };
 
 interface Props {