From 5b889cffc78b0159f76bc767967d2b539c3b34b4 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 29 Jan 2025 10:56:17 +0100
Subject: [PATCH 01/23] add limit and offset to show_folder

---
 bioblend/_tests/TestGalaxyFolders.py   | 21 ++++++++++++++++++++-
 bioblend/_tests/TestGalaxyHistories.py |  3 +--
 bioblend/_tests/TestGalaxyTools.py     |  3 +--
 bioblend/_tests/test_util.py           |  3 +--
 bioblend/galaxy/folders/__init__.py    | 18 +++++++++++++++---
 5 files changed, 38 insertions(+), 10 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index d519fb8dc..a589eb018 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -3,7 +3,10 @@
     List,
 )
 
-from . import GalaxyTestBase
+from . import (
+    GalaxyTestBase,
+    test_util,
+)
 
 FOO_DATA = "foo\nbar\n"
 
@@ -36,6 +39,22 @@ def test_show_folder_contents(self):
         assert "metadata" in f2
         assert self.name == f2["metadata"]["folder_name"]
 
+    @test_util.skip_unless_galaxy("release_21.05")
+    def test_show_folder_contents_limit(self):
+        subfolders = []
+        for i in range(12):
+            subfolders.append(self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}"))
+
+        # check defaults for limit and offset
+        f2 = self.gi.folders.show_folder(self.folder["id"], contents=True)
+        assert len(f2["folder_contents"]) == 10
+        assert f2["folder_contents"][0]["name"] == f"{self.name} 0"
+
+        # check non defaults
+        f2 = self.gi.folders.show_folder(self.folder["id"], contents=True, limit=1, offset=1)
+        assert len(f2["folder_contents"]) == 1
+        assert f2["folder_contents"][0]["name"] == f"{self.name} 1"
+
     def test_delete_folder(self):
         self.sub_folder = self.gi.folders.create_folder(self.folder["id"], self.name)
         self.gi.folders.delete_folder(self.sub_folder["id"])
diff --git a/bioblend/_tests/TestGalaxyHistories.py b/bioblend/_tests/TestGalaxyHistories.py
index b1ae681b9..7d8ec1ee8 100644
--- a/bioblend/_tests/TestGalaxyHistories.py
+++ b/bioblend/_tests/TestGalaxyHistories.py
@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import os
 import shutil
diff --git a/bioblend/_tests/TestGalaxyTools.py b/bioblend/_tests/TestGalaxyTools.py
index 2b3892a3c..b545f01f5 100644
--- a/bioblend/_tests/TestGalaxyTools.py
+++ b/bioblend/_tests/TestGalaxyTools.py
@@ -1,5 +1,4 @@
-"""
-"""
+""" """
 
 import os
 from typing import (
diff --git a/bioblend/_tests/test_util.py b/bioblend/_tests/test_util.py
index cdf1e8eeb..1cc47cd15 100644
--- a/bioblend/_tests/test_util.py
+++ b/bioblend/_tests/test_util.py
@@ -1,5 +1,4 @@
-""" General support infrastructure not tied to any particular test.
-"""
+"""General support infrastructure not tied to any particular test."""
 
 import os
 import random
diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 99f1c5bde..e7ed43326 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -45,7 +45,9 @@ def create_folder(self, parent_folder_id: str, name: str, description: Optional[
             payload["description"] = description
         return self._post(payload=payload, id=parent_folder_id)
 
-    def show_folder(self, folder_id: str, contents: bool = False) -> Dict[str, Any]:
+    def show_folder(
+        self, folder_id: str, contents: bool = False, limit: Optional[int] = 10, offset: Optional[int] = 0
+    ) -> Dict[str, Any]:
         """
         Display information about a folder.
 
@@ -56,11 +58,21 @@ def show_folder(self, folder_id: str, contents: bool = False) -> Dict[str, Any]:
         :param contents: True to get the contents of the folder, rather
           than just the folder details.
 
+        :type limit: int
+        :param limit: Maximum number of contents to return (default: 10).
+
+        :type offset: int
+        :param contents: Return contents from this specified position (default: 0).
+
         :rtype: dict
         :return: dictionary including details of the folder
         """
-
-        return self._get(id=folder_id, contents=contents)
+        params = {}
+        if limit:
+            params["limit"] = limit
+        if offset:
+            params["offset"] = offset
+        return self._get(id=folder_id, contents=contents, params=params)
 
     def delete_folder(self, folder_id: str, undelete: bool = False) -> Dict[str, Any]:
         """

From c49b94aa4ce38189b0cdfe296b1fd4a17b235db1 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 15:33:09 +0100
Subject: [PATCH 02/23] add include_deleted

---
 bioblend/galaxy/folders/__init__.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index e7ed43326..b2c3c992f 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -46,7 +46,12 @@ def create_folder(self, parent_folder_id: str, name: str, description: Optional[
         return self._post(payload=payload, id=parent_folder_id)
 
     def show_folder(
-        self, folder_id: str, contents: bool = False, limit: Optional[int] = 10, offset: Optional[int] = 0
+        self,
+        folder_id: str,
+        contents: bool = False,
+        limit: Optional[int] = 10,
+        offset: Optional[int] = 0,
+        include_deleted: bool = False,
     ) -> Dict[str, Any]:
         """
         Display information about a folder.
@@ -64,10 +69,13 @@ def show_folder(
         :type offset: int
         :param contents: Return contents from this specified position (default: 0).
 
+        :type include_deleted: bool
+        :param include_deleted: Returns also deleted contents.
+
         :rtype: dict
         :return: dictionary including details of the folder
         """
-        params = {}
+        params: Dict[str, Any] = {"include_deleted": include_deleted}
         if limit:
             params["limit"] = limit
         if offset:

From f5a26d67812cb0ea74599358e063eaa9a3bd93ed Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 18:32:38 +0100
Subject: [PATCH 03/23] Simply test subfolder creation

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index a589eb018..078f27584 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -41,9 +41,7 @@ def test_show_folder_contents(self):
 
     @test_util.skip_unless_galaxy("release_21.05")
     def test_show_folder_contents_limit(self):
-        subfolders = []
-        for i in range(12):
-            subfolders.append(self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}"))
+        subfolders = [self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}") for i in range(12)]
 
         # check defaults for limit and offset
         f2 = self.gi.folders.show_folder(self.folder["id"], contents=True)

From 107d985bdb55aec7da69a4593f0c96d3fc3ba3cb Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 18:33:43 +0100
Subject: [PATCH 04/23] Just use the upstream default values

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/galaxy/folders/__init__.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index b2c3c992f..0d7f53287 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -49,8 +49,8 @@ def show_folder(
         self,
         folder_id: str,
         contents: bool = False,
-        limit: Optional[int] = 10,
-        offset: Optional[int] = 0,
+        limit: int = 10,
+        offset: int = 0,
         include_deleted: bool = False,
     ) -> Dict[str, Any]:
         """
@@ -75,11 +75,11 @@ def show_folder(
         :rtype: dict
         :return: dictionary including details of the folder
         """
-        params: Dict[str, Any] = {"include_deleted": include_deleted}
-        if limit:
-            params["limit"] = limit
-        if offset:
-            params["offset"] = offset
+        params = {
+            "limit": limit,
+            "offset": offset,
+            "include_deleted": include_deleted,
+        }
         return self._get(id=folder_id, contents=contents, params=params)
 
     def delete_folder(self, folder_id: str, undelete: bool = False) -> Dict[str, Any]:

From 82dc9cbc498ecfad7f3893e6b954f49c38cfa54c Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 18:38:10 +0100
Subject: [PATCH 05/23] Revert to loop and drop subfolders variable

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 078f27584..53ad5aeb6 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -41,7 +41,8 @@ def test_show_folder_contents(self):
 
     @test_util.skip_unless_galaxy("release_21.05")
     def test_show_folder_contents_limit(self):
-        subfolders = [self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}") for i in range(12)]
+        for i in range(12):
+            self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}")
 
         # check defaults for limit and offset
         f2 = self.gi.folders.show_folder(self.folder["id"], contents=True)

From 5f22c37490a23569a60583813d8d9ee3da323a09 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 18:38:38 +0100
Subject: [PATCH 06/23] add test for include_deleted

---
 bioblend/_tests/TestGalaxyFolders.py | 31 ++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 078f27584..29541a862 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -53,6 +53,37 @@ def test_show_folder_contents_limit(self):
         assert len(f2["folder_contents"]) == 1
         assert f2["folder_contents"][0]["name"] == f"{self.name} 1"
 
+    def test_show_folder_contents_include_deleted(self):
+        history = self.gi.histories.create_history(name="Test History")
+        self._test_dataset(history["id"])
+        contents = self.gi.histories.show_history(history["id"], contents=True, types=["dataset"])
+        hda = contents[0]
+
+        # create 2 library data sets within a new folder in the library
+        subfolder = self.gi.folders.create_folder(self.folder["id"], f"{self.name}")
+        ldda1 = self.gi.libraries.copy_from_dataset(
+            library_id=self.library["id"], dataset_id=hda["id"], folder_id=subfolder["id"], message="Added HDA"
+        )
+        ldda2 = self.gi.libraries.copy_from_dataset(
+            library_id=self.library["id"], dataset_id=hda["id"], folder_id=subfolder["id"], message="Added HDA"
+        )
+        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True)
+        assert len(subfolder_info["folder_contents"]) == 2
+        assert subfolder_info["folder_contents"][0]["type"] == "file"
+
+        # delete the library datasets and check if include_deleted works
+        self.gi.libraries.delete_library_dataset(self.library["id"], ldda1["id"])
+        self.gi.libraries.delete_library_dataset(self.library["id"], ldda2["id"], purged=True)
+        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True, include_deleted=True)
+        assert len(subfolder_info["folder_contents"]) == 2
+        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True)
+        assert len(subfolder_info["folder_contents"]) == 0
+
+        # delete the library folder
+        self.gi.folders.delete_folder(subfolder["id"])
+        self.gi.histories.delete_dataset(history["id"], hda["id"])
+        self.gi.histories.delete_history(history["id"])
+
     def test_delete_folder(self):
         self.sub_folder = self.gi.folders.create_folder(self.folder["id"], self.name)
         self.gi.folders.delete_folder(self.sub_folder["id"])

From 7a36f0aa8522007d2fb2986944bdb5c2dcb864fc Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 19:42:13 +0100
Subject: [PATCH 07/23] Simplify test

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index a802cf9e6..808518294 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -56,29 +56,26 @@ def test_show_folder_contents_limit(self):
 
     def test_show_folder_contents_include_deleted(self):
         history = self.gi.histories.create_history(name="Test History")
-        self._test_dataset(history["id"])
-        contents = self.gi.histories.show_history(history["id"], contents=True, types=["dataset"])
-        hda = contents[0]
+        hda_id = self._test_dataset(history["id"])
 
-        # create 2 library data sets within a new folder in the library
-        subfolder = self.gi.folders.create_folder(self.folder["id"], f"{self.name}")
+        # Create 2 library datasets into the library folder
         ldda1 = self.gi.libraries.copy_from_dataset(
-            library_id=self.library["id"], dataset_id=hda["id"], folder_id=subfolder["id"], message="Added HDA"
+            library_id=self.library["id"], dataset_id=hda_id, folder_id=self.folder["id"], message="Added HDA"
         )
         ldda2 = self.gi.libraries.copy_from_dataset(
-            library_id=self.library["id"], dataset_id=hda["id"], folder_id=subfolder["id"], message="Added HDA"
+            library_id=self.library["id"], dataset_id=hda_id, folder_id=self.folder["id"], message="Added HDA"
         )
-        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True)
-        assert len(subfolder_info["folder_contents"]) == 2
-        assert subfolder_info["folder_contents"][0]["type"] == "file"
+        folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
+        assert len(folder_info["folder_contents"]) == 2
+        assert folder_info["folder_contents"][0]["type"] == "file"
 
-        # delete the library datasets and check if include_deleted works
+        # Delete the library datasets and check if include_deleted works
         self.gi.libraries.delete_library_dataset(self.library["id"], ldda1["id"])
         self.gi.libraries.delete_library_dataset(self.library["id"], ldda2["id"], purged=True)
-        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True, include_deleted=True)
-        assert len(subfolder_info["folder_contents"]) == 2
-        subfolder_info = self.gi.folders.show_folder(subfolder["id"], contents=True)
-        assert len(subfolder_info["folder_contents"]) == 0
+        folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True, include_deleted=True)
+        assert len(folder_info["folder_contents"]) == 2
+        folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
+        assert len(folder_info["folder_contents"]) == 0
 
         # delete the library folder
         self.gi.folders.delete_folder(subfolder["id"])

From 40a7810d5df1f5b409a5e1db1ba4604444ed81b8 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 19:42:28 +0100
Subject: [PATCH 08/23] Simplify test

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 808518294..e810a5a40 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -77,9 +77,6 @@ def test_show_folder_contents_include_deleted(self):
         folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
         assert len(folder_info["folder_contents"]) == 0
 
-        # delete the library folder
-        self.gi.folders.delete_folder(subfolder["id"])
-        self.gi.histories.delete_dataset(history["id"], hda["id"])
         self.gi.histories.delete_history(history["id"])
 
     def test_delete_folder(self):

From e64a4caf248d38844bccf7a1e57e2c8606921cb2 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 20:26:19 +0100
Subject: [PATCH 09/23] test content counts

---
 bioblend/_tests/TestGalaxyFolders.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index e810a5a40..1659d4103 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -73,9 +73,18 @@ def test_show_folder_contents_include_deleted(self):
         self.gi.libraries.delete_library_dataset(self.library["id"], ldda1["id"])
         self.gi.libraries.delete_library_dataset(self.library["id"], ldda2["id"], purged=True)
         folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True, include_deleted=True)
+        # check if there are 2 contents and the number is correct
         assert len(folder_info["folder_contents"]) == 2
+        assert folder_info["metadata"]["total_rows"] == 2
+        # if called without contents=True an item_count is reported .. lets also check this
+        folder_info = self.gi.folders.show_folder(self.folder["id"], include_deleted=True)
+        assert folder_info["item_count"] == 2
+
         folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
         assert len(folder_info["folder_contents"]) == 0
+        assert folder_info["metadata"]["total_rows"] == 0
+        folder_info = self.gi.folders.show_folder(self.folder["id"])
+        assert folder_info["item_count"] == 0
 
         self.gi.histories.delete_history(history["id"])
 

From a7c2ff6c9504fdbeff1b9ae40e7479ae7ff43e5c Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Thu, 30 Jan 2025 22:05:01 +0100
Subject: [PATCH 10/23] fix test and add docs

---
 bioblend/_tests/TestGalaxyFolders.py | 3 ++-
 bioblend/galaxy/folders/__init__.py  | 3 +++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 1659d4103..0317254e8 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -83,8 +83,9 @@ def test_show_folder_contents_include_deleted(self):
         folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
         assert len(folder_info["folder_contents"]) == 0
         assert folder_info["metadata"]["total_rows"] == 0
+        # show folders with contents=False does not respect include_deleted
         folder_info = self.gi.folders.show_folder(self.folder["id"])
-        assert folder_info["item_count"] == 0
+        assert folder_info["item_count"] == 2
 
         self.gi.histories.delete_history(history["id"])
 
diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 0d7f53287..db730ba71 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -65,12 +65,15 @@ def show_folder(
 
         :type limit: int
         :param limit: Maximum number of contents to return (default: 10).
+          Only considered for contents=True.
 
         :type offset: int
         :param contents: Return contents from this specified position (default: 0).
+          Only considered for contents=True.
 
         :type include_deleted: bool
         :param include_deleted: Returns also deleted contents.
+          Only considered for contents=True.
 
         :rtype: dict
         :return: dictionary including details of the folder

From 11e879307346ca7588775e6ddab5a55557307f2a Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 31 Jan 2025 09:53:35 +0100
Subject: [PATCH 11/23] total_rows became available only after

https://github.com/galaxyproject/galaxy/pull/10204
---
 bioblend/_tests/TestGalaxyFolders.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 0317254e8..332c38e73 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -54,6 +54,7 @@ def test_show_folder_contents_limit(self):
         assert len(f2["folder_contents"]) == 1
         assert f2["folder_contents"][0]["name"] == f"{self.name} 1"
 
+    @test_util.skip_unless_galaxy("release_21.01")
     def test_show_folder_contents_include_deleted(self):
         history = self.gi.histories.create_history(name="Test History")
         hda_id = self._test_dataset(history["id"])

From 30c4c91e5b931effeaf15b5af9d1df5275e6049b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 31 Jan 2025 12:11:26 +0100
Subject: [PATCH 12/23] add contents generator

---
 bioblend/_tests/TestGalaxyFolders.py | 15 ++++++++++++
 bioblend/galaxy/datasets/__init__.py |  7 ++++++
 bioblend/galaxy/folders/__init__.py  | 35 ++++++++++++++++++++++++++++
 3 files changed, 57 insertions(+)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 332c38e73..dc393e9f7 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -54,6 +54,21 @@ def test_show_folder_contents_limit(self):
         assert len(f2["folder_contents"]) == 1
         assert f2["folder_contents"][0]["name"] == f"{self.name} 1"
 
+    @test_util.skip_unless_galaxy("release_21.05")
+    def test_folder_contents(self):
+        for i in range(12):
+            self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}")
+
+        # check defaults for limit and offset
+        f2 = list(self.gi.folders.contents(self.folder["id"]))
+        assert len(f2) == 12
+        assert f2[0]["name"] == f"{self.name} 0"
+
+        # check non defaults
+        f2 = list(self.gi.folders.contents(self.folder["id"], limit=1))
+        assert len(f2) == 12
+        assert f2[0]["name"] == f"{self.name} 0"
+
     @test_util.skip_unless_galaxy("release_21.01")
     def test_show_folder_contents_include_deleted(self):
         history = self.gi.histories.create_history(name="Test History")
diff --git a/bioblend/galaxy/datasets/__init__.py b/bioblend/galaxy/datasets/__init__.py
index f164fddeb..c4cdad1ac 100644
--- a/bioblend/galaxy/datasets/__init__.py
+++ b/bioblend/galaxy/datasets/__init__.py
@@ -64,6 +64,13 @@ def show_dataset(self, dataset_id: str, hda_ldda: HdaLdda = "hda") -> Dict[str,
         }
         return self._get(id=dataset_id, params=params)
 
+    # def delete(self, dataset_ids, hda_ldda: HdaLdda = "hda", purge: bool = False) -> Dict[str, Any]:
+    #     datasets = []
+    #     for dataset_id in dataset_ids:
+    #         datasets.append({"src": hda_ldda, "id": dataset_id})
+    #     payload = {"datasets": datasets, "purge": purge}
+    #     return self._delete(payload=payload)
+
     def _initiate_download(
         self, dataset_id: str, stream_content: bool, require_ok_state: bool = True, maxwait: float = 12000
     ) -> Tuple[Dict[str, Any], str, Response]:
diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index db730ba71..45495a404 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -5,6 +5,7 @@
 from typing import (
     Any,
     Dict,
+    Iterable,
     List,
     Literal,
     Optional,
@@ -85,6 +86,40 @@ def show_folder(
         }
         return self._get(id=folder_id, contents=contents, params=params)
 
+    def contents(
+        self,
+        folder_id: str,
+        limit: int = 10,
+        include_deleted: bool = False,
+    ) -> Iterable[Dict[str, Any]]:
+        """
+        Iterate over folder contents.
+
+        :type folder_id: str
+        :param folder_id: the folder's encoded id, prefixed by 'F'
+
+        :type limit: int
+        :param limit: Batch size to be used internally (default: 10).
+
+        :type include_deleted: bool
+        :param include_deleted: Include also deleted contents.
+
+        :rtype: dict
+        :return: A generator for the folder contents
+        """
+        total_rows: Optional[int] = None
+        params = {
+            "limit": limit,
+            "offset": 0,
+            "include_deleted": include_deleted,
+        }
+
+        while total_rows is None or params["offset"] <= total_rows:
+            chunk = self._get(id=folder_id, contents=True, params=params)
+            total_rows = chunk["metadata"]["total_rows"]
+            yield from chunk["folder_contents"]
+            params["offset"] += limit
+
     def delete_folder(self, folder_id: str, undelete: bool = False) -> Dict[str, Any]:
         """
         Marks the folder with the given ``id`` as `deleted` (or removes the

From 4a46da3b1e79a647b8d1cba9effdb9f10f906f03 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Sat, 1 Feb 2025 14:33:09 +0100
Subject: [PATCH 13/23] Rename content to content_iter

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 6 +++---
 bioblend/galaxy/folders/__init__.py  | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index dc393e9f7..8110734e7 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -55,17 +55,17 @@ def test_show_folder_contents_limit(self):
         assert f2["folder_contents"][0]["name"] == f"{self.name} 1"
 
     @test_util.skip_unless_galaxy("release_21.05")
-    def test_folder_contents(self):
+    def test_folder_contents_iter(self):
         for i in range(12):
             self.gi.folders.create_folder(self.folder["id"], f"{self.name} {i}")
 
         # check defaults for limit and offset
-        f2 = list(self.gi.folders.contents(self.folder["id"]))
+        f2 = list(self.gi.folders.contents_iter(self.folder["id"]))
         assert len(f2) == 12
         assert f2[0]["name"] == f"{self.name} 0"
 
         # check non defaults
-        f2 = list(self.gi.folders.contents(self.folder["id"], limit=1))
+        f2 = list(self.gi.folders.contents_iter(self.folder["id"], limit=1))
         assert len(f2) == 12
         assert f2[0]["name"] == f"{self.name} 0"
 
diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 45495a404..3eb9d449b 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -86,7 +86,7 @@ def show_folder(
         }
         return self._get(id=folder_id, contents=contents, params=params)
 
-    def contents(
+    def contents_iter(
         self,
         folder_id: str,
         limit: int = 10,

From 687d281c008244447288aebb48a7535889d815cc Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 09:11:30 +0100
Subject: [PATCH 14/23] Use sys.maxsize for iteration

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/galaxy/folders/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 3eb9d449b..c210f6f64 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -2,6 +2,7 @@
 Contains possible interactions with the Galaxy library folders
 """
 
+import sys
 from typing import (
     Any,
     Dict,
@@ -107,14 +108,14 @@ def contents_iter(
         :rtype: dict
         :return: A generator for the folder contents
         """
-        total_rows: Optional[int] = None
+        total_rows = sys.maxsize
         params = {
             "limit": limit,
             "offset": 0,
             "include_deleted": include_deleted,
         }
 
-        while total_rows is None or params["offset"] <= total_rows:
+        while params["offset"] <= total_rows:
             chunk = self._get(id=folder_id, contents=True, params=params)
             total_rows = chunk["metadata"]["total_rows"]
             yield from chunk["folder_contents"]

From 2f93514ed6242125035ccabe35daeafa0334f8c7 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 09:21:04 +0100
Subject: [PATCH 15/23] overload show_folder

---
 bioblend/galaxy/folders/__init__.py | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index c210f6f64..3ec97c08c 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -10,6 +10,7 @@
     List,
     Literal,
     Optional,
+    overload,
     TYPE_CHECKING,
     Union,
 )
@@ -47,6 +48,22 @@ def create_folder(self, parent_folder_id: str, name: str, description: Optional[
             payload["description"] = description
         return self._post(payload=payload, id=parent_folder_id)
 
+    @overload
+    def show_folder(
+        self,
+        folder_id: str,
+    ) -> Dict[str, Any]: ...
+
+    @overload
+    def show_folder(
+        self,
+        folder_id: str,
+        contents: bool = False,
+        limit: int = 10,
+        offset: int = 0,
+        include_deleted: bool = False,
+    ) -> Dict[str, Any]: ...
+
     def show_folder(
         self,
         folder_id: str,
@@ -78,7 +95,13 @@ def show_folder(
           Only considered for contents=True.
 
         :rtype: dict
-        :return: dictionary including details of the folder
+        :return: dictionary including details of the folder.
+          For contents=False the dict contains infos on the folder.
+          For contents=True the dict contains the keys "metadata" (a dict with
+          infos on the folder) and "folder_contents" (a list of dicts with info
+          on the childs).
+
+        Notes: For iterating over folder contents there is also contents_iter.
         """
         params = {
             "limit": limit,

From a90a19da1093c66974e1f8786a30ae4f9831ea1d Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 13:11:11 +0100
Subject: [PATCH 16/23] Apply suggestions from code review

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/galaxy/folders/__init__.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 3ec97c08c..40de1f4de 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -52,13 +52,14 @@ def create_folder(self, parent_folder_id: str, name: str, description: Optional[
     def show_folder(
         self,
         folder_id: str,
+        contents: Literal[False] = False,
     ) -> Dict[str, Any]: ...
 
     @overload
     def show_folder(
         self,
         folder_id: str,
-        contents: bool = False,
+        contents: Literal[True],
         limit: int = 10,
         offset: int = 0,
         include_deleted: bool = False,
@@ -83,16 +84,15 @@ def show_folder(
           than just the folder details.
 
         :type limit: int
-        :param limit: Maximum number of contents to return (default: 10).
-          Only considered for contents=True.
+        :param limit: When ``contents=True``, maximum number of items to return.
 
         :type offset: int
-        :param contents: Return contents from this specified position (default: 0).
-          Only considered for contents=True.
+        :param contents: When ``contents=True``, number of items to skip. Return
+          contents starting with item offset+1.
 
         :type include_deleted: bool
-        :param include_deleted: Returns also deleted contents.
-          Only considered for contents=True.
+        :param include_deleted: When ``contents=True``, whether to include
+          deleted items.
 
         :rtype: dict
         :return: dictionary including details of the folder.
@@ -123,10 +123,10 @@ def contents_iter(
         :param folder_id: the folder's encoded id, prefixed by 'F'
 
         :type limit: int
-        :param limit: Batch size to be used internally (default: 10).
+        :param limit: Batch size to be used internally.
 
         :type include_deleted: bool
-        :param include_deleted: Include also deleted contents.
+        :param include_deleted: Whether to include deleted items.
 
         :rtype: dict
         :return: A generator for the folder contents

From 9317cb127735935072838cda27d0a724b99c2969 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 13:31:29 +0100
Subject: [PATCH 17/23] Update bioblend/_tests/TestGalaxyFolders.py

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/_tests/TestGalaxyFolders.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 8110734e7..89ad515be 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -92,9 +92,6 @@ def test_show_folder_contents_include_deleted(self):
         # check if there are 2 contents and the number is correct
         assert len(folder_info["folder_contents"]) == 2
         assert folder_info["metadata"]["total_rows"] == 2
-        # if called without contents=True an item_count is reported .. lets also check this
-        folder_info = self.gi.folders.show_folder(self.folder["id"], include_deleted=True)
-        assert folder_info["item_count"] == 2
 
         folder_info = self.gi.folders.show_folder(self.folder["id"], contents=True)
         assert len(folder_info["folder_contents"]) == 0

From b442c174864ea260b52b976e2e314befbde5fb9c Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 15:55:12 +0100
Subject: [PATCH 18/23] revert accidental change

---
 bioblend/galaxy/datasets/__init__.py | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/bioblend/galaxy/datasets/__init__.py b/bioblend/galaxy/datasets/__init__.py
index c4cdad1ac..f164fddeb 100644
--- a/bioblend/galaxy/datasets/__init__.py
+++ b/bioblend/galaxy/datasets/__init__.py
@@ -64,13 +64,6 @@ def show_dataset(self, dataset_id: str, hda_ldda: HdaLdda = "hda") -> Dict[str,
         }
         return self._get(id=dataset_id, params=params)
 
-    # def delete(self, dataset_ids, hda_ldda: HdaLdda = "hda", purge: bool = False) -> Dict[str, Any]:
-    #     datasets = []
-    #     for dataset_id in dataset_ids:
-    #         datasets.append({"src": hda_ldda, "id": dataset_id})
-    #     payload = {"datasets": datasets, "purge": purge}
-    #     return self._delete(payload=payload)
-
     def _initiate_download(
         self, dataset_id: str, stream_content: bool, require_ok_state: bool = True, maxwait: float = 12000
     ) -> Tuple[Dict[str, Any], str, Response]:

From 080f24a3a489833b0179ee91379436cf65c10c46 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 15:58:09 +0100
Subject: [PATCH 19/23] rewording

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 bioblend/galaxy/folders/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 40de1f4de..5dc46abb0 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -88,7 +88,7 @@ def show_folder(
 
         :type offset: int
         :param contents: When ``contents=True``, number of items to skip. Return
-          contents starting with item offset+1.
+          contents starting from item offset+1.
 
         :type include_deleted: bool
         :param include_deleted: When ``contents=True``, whether to include

From 136fc5ec7dfd2f36ebe37594fcc67da9a84c2d97 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 17:00:28 +0100
Subject: [PATCH 20/23] return is Iterator

---
 bioblend/galaxy/folders/__init__.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 40de1f4de..c1a2a2796 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -6,7 +6,7 @@
 from typing import (
     Any,
     Dict,
-    Iterable,
+    Iterator,
     List,
     Literal,
     Optional,
@@ -115,7 +115,7 @@ def contents_iter(
         folder_id: str,
         limit: int = 10,
         include_deleted: bool = False,
-    ) -> Iterable[Dict[str, Any]]:
+    ) -> Iterator[Dict[str, Any]]:
         """
         Iterate over folder contents.
 
@@ -127,9 +127,6 @@ def contents_iter(
 
         :type include_deleted: bool
         :param include_deleted: Whether to include deleted items.
-
-        :rtype: dict
-        :return: A generator for the folder contents
         """
         total_rows = sys.maxsize
         params = {

From 7a6ee4a5c89c634c31d31b059eeb2a65387bb8d3 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 17:02:44 +0100
Subject: [PATCH 21/23] rename limit

---
 bioblend/galaxy/folders/__init__.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index c1a2a2796..26d4f18a0 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -113,7 +113,7 @@ def show_folder(
     def contents_iter(
         self,
         folder_id: str,
-        limit: int = 10,
+        batch_size: int = 10,
         include_deleted: bool = False,
     ) -> Iterator[Dict[str, Any]]:
         """
@@ -122,7 +122,7 @@ def contents_iter(
         :type folder_id: str
         :param folder_id: the folder's encoded id, prefixed by 'F'
 
-        :type limit: int
+        :type batch_size: int
         :param limit: Batch size to be used internally.
 
         :type include_deleted: bool
@@ -130,7 +130,7 @@ def contents_iter(
         """
         total_rows = sys.maxsize
         params = {
-            "limit": limit,
+            "limit": batch_size,
             "offset": 0,
             "include_deleted": include_deleted,
         }

From 9ce501387f4f585273fcdd5043309c5cc20f7e2d Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 17:08:48 +0100
Subject: [PATCH 22/23] finish parameter renaming

---
 bioblend/galaxy/folders/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bioblend/galaxy/folders/__init__.py b/bioblend/galaxy/folders/__init__.py
index 35710007d..9c1fc79ad 100644
--- a/bioblend/galaxy/folders/__init__.py
+++ b/bioblend/galaxy/folders/__init__.py
@@ -123,7 +123,7 @@ def contents_iter(
         :param folder_id: the folder's encoded id, prefixed by 'F'
 
         :type batch_size: int
-        :param limit: Batch size to be used internally.
+        :param batch_size: Batch size to be used internally.
 
         :type include_deleted: bool
         :param include_deleted: Whether to include deleted items.
@@ -139,7 +139,7 @@ def contents_iter(
             chunk = self._get(id=folder_id, contents=True, params=params)
             total_rows = chunk["metadata"]["total_rows"]
             yield from chunk["folder_contents"]
-            params["offset"] += limit
+            params["offset"] += batch_size
 
     def delete_folder(self, folder_id: str, undelete: bool = False) -> Dict[str, Any]:
         """

From a0b9337ae87365ff1e907d3143534a21a1c3525b Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 Feb 2025 17:12:49 +0100
Subject: [PATCH 23/23] more missing renaming

---
 bioblend/_tests/TestGalaxyFolders.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bioblend/_tests/TestGalaxyFolders.py b/bioblend/_tests/TestGalaxyFolders.py
index 89ad515be..4c1a8e98e 100644
--- a/bioblend/_tests/TestGalaxyFolders.py
+++ b/bioblend/_tests/TestGalaxyFolders.py
@@ -65,7 +65,7 @@ def test_folder_contents_iter(self):
         assert f2[0]["name"] == f"{self.name} 0"
 
         # check non defaults
-        f2 = list(self.gi.folders.contents_iter(self.folder["id"], limit=1))
+        f2 = list(self.gi.folders.contents_iter(self.folder["id"], batch_size=1))
         assert len(f2) == 12
         assert f2[0]["name"] == f"{self.name} 0"