From 2d65374c1341b21322fe630077335fd236dcb180 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 27 May 2024 15:11:44 +0200
Subject: [PATCH 1/5] Replace demo.onedata.org with datahub.egi.eu

---
 lib/galaxy/config/sample/object_store_conf.sample.yml         | 4 ++--
 lib/galaxy/config/sample/object_store_conf.xml.sample         | 4 ++--
 .../config/sample/user_preferences_extra_conf.yml.sample      | 2 +-
 3 files changed, 5 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 27e18e2796cb..afbcfc22323b 100644
--- a/lib/galaxy/config/sample/object_store_conf.sample.yml
+++ b/lib/galaxy/config/sample/object_store_conf.sample.yml
@@ -223,9 +223,9 @@ 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
+  # the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
   # devel instances (see above).
-  onezone_domain: demo.onedata.org
+  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
diff --git a/lib/galaxy/config/sample/object_store_conf.xml.sample b/lib/galaxy/config/sample/object_store_conf.xml.sample
index b27b7125d42b..1b9d997271e9 100644
--- a/lib/galaxy/config/sample/object_store_conf.xml.sample
+++ b/lib/galaxy/config/sample/object_store_conf.xml.sample
@@ -165,7 +165,7 @@
         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
+        the domain of the Onezone service (e.g. datahub.egi.eu), or its IP address for
         devel instances (see above).
 
     //connection/@disable_tls_certificate_validation - 
@@ -182,7 +182,7 @@
 <!--
 <object_store type="onedata">
     <auth access_token="..." />
-    <connection onezone_domain="demo.onedata.org" disable_tls_certificate_validation="False"/>
+    <connection onezone_domain="datahub.egi.eu" 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"/>
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 a69370f2c741..72689e31bf44 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. "demo.onedata.org")
+              label: Domain of the Onezone service (e.g. datahub.egi.eu)
               type: text
               required: False
             - name: access_token

From d718a93866fb1a4aadbf95010660328da9944941 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 27 May 2024 15:15:06 +0200
Subject: [PATCH 2/5] Update OnedataObjectStore to new onedatafilerestclient
 API

---
 lib/galaxy/objectstore/onedata.py | 88 +++++++++++++++++++------------
 1 file changed, 53 insertions(+), 35 deletions(-)

diff --git a/lib/galaxy/objectstore/onedata.py b/lib/galaxy/objectstore/onedata.py
index 23f8d9f77448..7fc8d5b72c27 100644
--- a/lib/galaxy/objectstore/onedata.py
+++ b/lib/galaxy/objectstore/onedata.py
@@ -7,8 +7,9 @@
 from datetime import datetime
 
 try:
-    from onedatafilerestclient import (
-        OnedataFileRESTClient,
+    from onedatafilerestclient import OnedataFileRESTClient
+    from onedatafilerestclient.errors import (
+        OnedataError,
         OnedataRESTError,
     )
 except ImportError:
@@ -131,7 +132,7 @@ def _initialize(self):
         self._start_cache_monitor_if_needed()
 
     @classmethod
-    def parse_xml(clazz, config_xml):
+    def parse_xml(cls, config_xml):
         return _parse_config_xml(config_xml)
 
     def to_dict(self):
@@ -155,54 +156,54 @@ def to_dict(self):
         )
         return as_dict
 
-    def _construct_onedata_path(self, rel_path):
+    def _build_remote_path(self, rel_path):
         return os.path.join(self.galaxy_root_dir, rel_path)
 
     def _get_remote_size(self, rel_path):
         try:
-            onedata_path = self._construct_onedata_path(rel_path)
-            return self._client.get_attributes(self.space_name, file_path=onedata_path)["size"]
-        except OnedataRESTError:
+            remote_path = self._build_remote_path(rel_path)
+            return self._client.get_attributes(self.space_name, attributes=["size"], file_path=remote_path)["size"]
+        except OnedataError:
             log.exception("Could not get '%s' size from Onedata", rel_path)
             return -1
 
     def _exists_remotely(self, rel_path):
         try:
-            onedata_path = self._construct_onedata_path(rel_path)
-            self._client.get_attributes(self.space_name, file_path=onedata_path)
+            remote_path = self._build_remote_path(rel_path)
+            self._client.get_attributes(self.space_name, attributes=["type", "size"], file_path=remote_path)
             return True
-        except OnedataRESTError as ex:
-            if ex.http_code == 404:
-                return False
-            elif ex.http_code == 400 and ex.error_details.get("errno", None) == "enoent":
-                return False
-            else:
-                log.exception("Trouble checking '%s' existence in Onedata", rel_path)
+        except OnedataError as ex:
+            if _is_not_found_onedata_rest_error(ex):
                 return False
 
+            log.exception("Trouble checking '%s' existence in Onedata", rel_path)
+            return False
+
     def _download(self, rel_path):
         try:
             dst_path = self._get_cache_path(rel_path)
 
             log.debug("Pulling file '%s' into cache to %s", rel_path, dst_path)
 
-            onedata_path = self._construct_onedata_path(rel_path)
-            file_size = self._client.get_attributes(self.space_name, file_path=onedata_path)["size"]
+            remote_path = self._build_remote_path(rel_path)
+            file_size = self._client.get_attributes(self.space_name, attributes=["size"], file_path=remote_path)["size"]
 
             # Test if cache is large enough to hold the new file
             if not self._caching_allowed(rel_path, file_size):
                 return False
 
             with open(dst_path, "wb") as dst:
-                for chunk in self._client.iter_file_content(self.space_name, STREAM_CHUNK_SIZE, file_path=onedata_path):
+                for chunk in self._client.iter_file_content(
+                    self.space_name, chunk_size=STREAM_CHUNK_SIZE, file_path=remote_path
+                ):
                     dst.write(chunk)
 
             log.debug("Pulled '%s' into cache to %s", rel_path, dst_path)
 
             return True
-        except OnedataRESTError:
+        except OnedataError:
             log.exception("Problem downloading file '%s'", rel_path)
-        return False
+            return False
 
     def _push_to_storage(self, rel_path, source_file=None, from_string=None):
         """
@@ -211,7 +212,7 @@ def _push_to_storage(self, rel_path, source_file=None, from_string=None):
         ``rel_path`` as the path.
         """
         try:
-            source_file = source_file if source_file else self._get_cache_path(rel_path)
+            source_file = source_file or self._get_cache_path(rel_path)
             if os.path.exists(source_file):
                 if os.path.getsize(source_file) == 0 and self._exists_remotely(rel_path):
                     log.debug(
@@ -226,12 +227,14 @@ def _push_to_storage(self, rel_path, source_file=None, from_string=None):
                         os.path.getsize(source_file),
                         rel_path,
                     )
-                    onedata_path = self._construct_onedata_path(rel_path)
+                    remote_path = self._build_remote_path(rel_path)
 
                     if not self._exists_remotely(rel_path):
-                        self._client.create_file(self.space_name, onedata_path, "REG", create_parents=True)
-
-                    file_id = self._client.get_file_id(self.space_name, onedata_path)
+                        file_id = self._client.create_file(
+                            self.space_name, file_path=remote_path, file_type="REG", create_parents=True
+                        )
+                    else:
+                        file_id = self._client.get_file_id(self.space_name, file_path=remote_path)
 
                     if source_file:
                         with open(source_file, "rb") as src:
@@ -241,14 +244,18 @@ def _push_to_storage(self, rel_path, source_file=None, from_string=None):
                                 if not chunk:
                                     break
 
-                                self._client.put_file_content(self.space_name, file_id, offset, chunk)
+                                self._client.put_file_content(
+                                    self.space_name, data=chunk, offset=offset, file_id=file_id
+                                )
                                 offset += len(chunk)
                     else:
-                        self._client.put_file_content(self.space_name, file_id, 0, from_string.encode("utf-8"))
+                        self._client.put_file_content(
+                            self.space_name, data=from_string.encode("utf-8"), file_id=file_id
+                        )
 
                     end_time = datetime.now()
                     log.debug(
-                        "Pushed cache file '%s' under '%s' (%s bytes transfered in %s sec)",
+                        "Pushed cache file '%s' under '%s' (%s bytes transferred in %s sec)",
                         source_file,
                         rel_path,
                         os.path.getsize(source_file),
@@ -257,25 +264,36 @@ def _push_to_storage(self, rel_path, source_file=None, from_string=None):
                 return True
             else:
                 log.error("Source file does not exist.", rel_path, source_file)
-        except OnedataRESTError:
+        except OnedataError:
             log.exception("Trouble pushing Onedata key '%s' from file '%s'", rel_path, source_file)
             raise
         return False
 
     def _delete_existing_remote(self, rel_path) -> bool:
         try:
-            onedata_path = self._construct_onedata_path(rel_path)
-            self._client.remove(self.space_name, onedata_path)
+            onedata_path = self._build_remote_path(rel_path)
+            self._client.remove(self.space_name, file_path=onedata_path)
             return True
-        except OnedataRESTError:
+        except OnedataError:
             log.exception("Could not delete '%s' from Onedata", rel_path)
             return False
 
-    def _get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, _obj, **_kwargs):
         return None
 
-    def _get_store_usage_percent(self, obj):
+    def _get_store_usage_percent(self, _obj):
         return 0.0
 
     def shutdown(self):
         self._shutdown_cache_monitor()
+
+
+def _is_not_found_onedata_rest_error(ex):
+    if isinstance(ex, OnedataRESTError):
+        if ex.http_code == 404:
+            return True
+
+        if ex.http_code == 400 and ex.category == "posix":
+            return ex.details["errno"] == "enoent"
+
+    return False

From dcc509673dece194142ff2a878ecdd5ee98132d0 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Mon, 27 May 2024 15:20:46 +0200
Subject: [PATCH 3/5] Update onedatafilerestclient requirement

---
 lib/galaxy/dependencies/conditional-requirements.txt | 2 +-
 lib/galaxy/dependencies/dev-requirements.txt         | 2 +-
 pyproject.toml                                       | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/dependencies/conditional-requirements.txt b/lib/galaxy/dependencies/conditional-requirements.txt
index 113e62083a74..f35fa4fc6cc1 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 # type: onedata, depends on onedatafilerestclient
+fs.onedatarestfs==21.2.5.1 # 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 231a88f234f8..c7c95fe3832b 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -79,7 +79,7 @@ myst-parser==3.0.1 ; 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"
+onedatafilerestclient==21.2.5.1 ; 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"
diff --git a/pyproject.toml b/pyproject.toml
index 2f7355735122..f7b93e63990c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -143,7 +143,7 @@ isort = "*"
 lxml = "!=4.2.2"
 markdown-it-reporter = "*"
 myst-parser = "*"
-onedatafilerestclient = "==21.2.5rc1"
+onedatafilerestclient = "==21.2.5.1"
 pkce = "*"
 playwright = "*"
 pytest = "*"

From 2ec50fb0ac427ea47c1fcc4a22043486e8b2a406 Mon Sep 17 00:00:00 2001
From: Bartosz Walkowicz <wallko1@hotmail.com>
Date: Tue, 11 Jun 2024 13:31:42 +0200
Subject: [PATCH 4/5] Use only single filterdir in _get_total_matches_count

---
 lib/galaxy/files/sources/_pyfilesystem2.py | 17 +----------------
 1 file changed, 1 insertion(+), 16 deletions(-)

diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py
index 5fa7917f3ac2..a64b7f9b82ac 100644
--- a/lib/galaxy/files/sources/_pyfilesystem2.py
+++ b/lib/galaxy/files/sources/_pyfilesystem2.py
@@ -85,22 +85,7 @@ def _list(
             raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
 
     def _get_total_matches_count(self, fs: FS, path: str, filter: Optional[List[str]] = None) -> int:
-        # For some reason, using "*" as glob does not return all files and directories, only files.
-        # So we need to count files and directories "*/" separately.
-        # Also, some filesystems do not properly support directories count (like Google Cloud Storage),
-        # so we need to catch TypeError exceptions and fallback to 0.
-        files_glob_pattern = f"{path}/{filter[0] if filter else '*'}"
-        try:
-            files_count = fs.glob(files_glob_pattern).count().files
-        except TypeError:
-            files_count = 0
-
-        directory_glob_pattern = f"{files_glob_pattern}/"
-        try:
-            directories_count = fs.glob(directory_glob_pattern).count().directories
-        except TypeError:
-            directories_count = 0
-        return files_count + directories_count
+        return sum(1 for _ in fs.filterdir(path, namespaces=["details"], files=filter, dirs=filter))
 
     def _to_page(self, limit: Optional[int] = None, offset: Optional[int] = None) -> Optional[Tuple[int, int]]:
         if limit is None and offset is None:

From 396c3e44dfd00cc849999831a18f756fb1c31d2f Mon Sep 17 00:00:00 2001
From: bwalkowi <wallko1@hotmail.com>
Date: Wed, 12 Jun 2024 11:20:45 +0000
Subject: [PATCH 5/5] Use basic namespace when counting files with scandir
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: David López <46503462+davelopez@users.noreply.github.com>
---
 lib/galaxy/files/sources/_pyfilesystem2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/files/sources/_pyfilesystem2.py b/lib/galaxy/files/sources/_pyfilesystem2.py
index a64b7f9b82ac..afcff2884961 100644
--- a/lib/galaxy/files/sources/_pyfilesystem2.py
+++ b/lib/galaxy/files/sources/_pyfilesystem2.py
@@ -85,7 +85,7 @@ def _list(
             raise MessageException(f"Problem listing file source path {path}. Reason: {e}") from e
 
     def _get_total_matches_count(self, fs: FS, path: str, filter: Optional[List[str]] = None) -> int:
-        return sum(1 for _ in fs.filterdir(path, namespaces=["details"], files=filter, dirs=filter))
+        return sum(1 for _ in fs.filterdir(path, namespaces=["basic"], files=filter, dirs=filter))
 
     def _to_page(self, limit: Optional[int] = None, offset: Optional[int] = None) -> Optional[Tuple[int, int]]:
         if limit is None and offset is None: