From 37c85b2b9f24ef6031881d89e3770e999b96c746 Mon Sep 17 00:00:00 2001
From: John Wilkie <john@v7labs.com>
Date: Wed, 21 Aug 2024 12:24:02 +0100
Subject: [PATCH 1/4] Test commit

---
 darwin/dataset/remote_dataset_v2.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/darwin/dataset/remote_dataset_v2.py b/darwin/dataset/remote_dataset_v2.py
index 59f87b320..e21a554ae 100644
--- a/darwin/dataset/remote_dataset_v2.py
+++ b/darwin/dataset/remote_dataset_v2.py
@@ -842,3 +842,6 @@ def register_multi_slotted(
                 print(f"  - {item}")
         print(f"Reistration complete. Check your items in the dataset: {self.slug}")
         return results
+
+
+# Test comment

From bf2a03344003491cd1b55aa7567d19d5470bbb7a Mon Sep 17 00:00:00 2001
From: John Wilkie <john@v7labs.com>
Date: Wed, 21 Aug 2024 19:02:03 +0100
Subject: [PATCH 2/4] Don't download single-slotted items as multi-slotted
 items when force_slots=False

---
 darwin/dataset/download_manager.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/darwin/dataset/download_manager.py b/darwin/dataset/download_manager.py
index 4eede09eb..3ddd232f4 100644
--- a/darwin/dataset/download_manager.py
+++ b/darwin/dataset/download_manager.py
@@ -90,7 +90,7 @@ def download_all_images_from_annotations(
         if is_file_extension_allowed(image.name)
     }
 
-    annotations_to_download_path = []
+    annotations_to_download_path: List = []
     for annotation_path in annotations_path.glob(f"*.{annotation_format}"):
         annotation = parse_darwin_json(annotation_path, count=0)
         if annotation is None:
@@ -108,13 +108,18 @@ def download_all_images_from_annotations(
             ):
                 continue
 
-        annotations_to_download_path.append(annotation_path)
-        if len(annotation.slots) > 1:
-            force_slots = True
+        if not force_slots:
+            force_slots_for_item = False
+            if len(annotation.slots) > 1:
+                force_slots_for_item = True
 
-        for slot in annotation.slots:
-            if len(slot.source_files) > 1:
-                force_slots = True
+            for slot in annotation.slots:
+                if len(slot.source_files) > 1:
+                    force_slots_for_item = True
+        else:
+            force_slots_for_item = True
+
+        annotations_to_download_path.append((annotation_path, force_slots_for_item))
 
     if remove_extra:
         annotations = (
@@ -138,7 +143,7 @@ def download_all_images_from_annotations(
 
     # Create the generator with the partial functions
     download_functions: List = []
-    for annotation_path in annotations_to_download_path:
+    for annotation_path, force_slots in annotations_to_download_path:
         file_download_functions = lazy_download_image_from_annotation(
             api_key,
             annotation_path,

From 20cfc5215bec9f21e0201bb54cf52610b1008f57 Mon Sep 17 00:00:00 2001
From: John Wilkie <john@v7labs.com>
Date: Wed, 21 Aug 2024 23:08:29 +0100
Subject: [PATCH 3/4] Unit tests + simpler approach

---
 darwin/dataset/download_manager.py          |  17 ++---
 darwin/dataset/remote_dataset_v2.py         |   3 -
 tests/darwin/dataset/remote_dataset_test.py |  79 +++++++++++++++++++-
 tests/data.zip                              | Bin 296066 -> 300936 bytes
 4 files changed, 85 insertions(+), 14 deletions(-)

diff --git a/darwin/dataset/download_manager.py b/darwin/dataset/download_manager.py
index 3ddd232f4..752f37579 100644
--- a/darwin/dataset/download_manager.py
+++ b/darwin/dataset/download_manager.py
@@ -64,8 +64,9 @@ def download_all_images_from_annotations(
         Recreate folders
     video_frames : bool, default: False
         Pulls video frames images instead of video files
-    force_slots: bool
+    force_slots: bool, default: False
         Pulls all slots of items into deeper file structure ({prefix}/{item_name}/{slot_name}/{file_name})
+        If False, all multi-slotted items and items with slots containing multiple source files will be downloaded as the deeper file structure
 
     Returns
     -------
@@ -108,16 +109,12 @@ def download_all_images_from_annotations(
             ):
                 continue
 
-        if not force_slots:
-            force_slots_for_item = False
-            if len(annotation.slots) > 1:
-                force_slots_for_item = True
-
-            for slot in annotation.slots:
-                if len(slot.source_files) > 1:
-                    force_slots_for_item = True
-        else:
+        if force_slots:
             force_slots_for_item = True
+        else:
+            force_slots_for_item = len(annotation.slots) > 1 or any(
+                len(slot.source_files) > 1 for slot in annotation.slots
+            )
 
         annotations_to_download_path.append((annotation_path, force_slots_for_item))
 
diff --git a/darwin/dataset/remote_dataset_v2.py b/darwin/dataset/remote_dataset_v2.py
index e21a554ae..59f87b320 100644
--- a/darwin/dataset/remote_dataset_v2.py
+++ b/darwin/dataset/remote_dataset_v2.py
@@ -842,6 +842,3 @@ def register_multi_slotted(
                 print(f"  - {item}")
         print(f"Reistration complete. Check your items in the dataset: {self.slug}")
         return results
-
-
-# Test comment
diff --git a/tests/darwin/dataset/remote_dataset_test.py b/tests/darwin/dataset/remote_dataset_test.py
index fb2790bf9..c974ace0e 100644
--- a/tests/darwin/dataset/remote_dataset_test.py
+++ b/tests/darwin/dataset/remote_dataset_test.py
@@ -15,7 +15,10 @@
 from darwin.client import Client
 from darwin.config import Config
 from darwin.dataset import RemoteDataset
-from darwin.dataset.download_manager import _download_image_from_json_annotation
+from darwin.dataset.download_manager import (
+    _download_image_from_json_annotation,
+    download_all_images_from_annotations,
+)
 from darwin.dataset.release import Release, ReleaseStatus
 from darwin.dataset.remote_dataset_v2 import RemoteDatasetV2
 from darwin.dataset.upload_manager import LocalFile, UploadHandlerV2
@@ -25,6 +28,12 @@
 from tests.fixtures import *
 
 
+@pytest.fixture
+def mock_is_file_extension_allowed():
+    with patch("darwin.dataset.download_manager.is_file_extension_allowed") as mock:
+        yield mock
+
+
 @pytest.fixture
 def annotation_name() -> str:
     return "test_video.json"
@@ -1373,3 +1382,71 @@ def test_omits_unavailable_releases_when_retry_is_false(
         releases = remote_dataset.get_releases(include_unavailable=False)
         assert len(releases) == 1
         assert isinstance(releases[0], Release)
+
+
+def test_force_slots_true(mock_is_file_extension_allowed):
+    mock_is_file_extension_allowed.return_value = True
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        with zipfile.ZipFile("tests/data.zip") as zfile:
+            zfile.extractall(tmp_dir)
+            annotations_path = Path(tmp_dir) / "v7-darwin-json-v2/force_slots"
+            images_path = Path("images")
+            generator, count = download_all_images_from_annotations(
+                api_key="api_key",
+                annotations_path=annotations_path,
+                images_path=images_path,
+                force_slots=True,
+                force_replace=True,
+            )
+
+    download_funcs = list(generator())
+    planned_paths = [download_funcs[i].args[2] for i in range(count)]
+    expected_paths = [
+        Path("images/dir1/single_slotted_video_flat/0/mini_uct.mp4"),
+        Path("images/dir1/multiple_slots_multiple_source_files/0.1/slice_1.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/0.1/slice_2.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_1.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_2.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_3.dcm"),
+        Path("images/dir1/single_slotted_image_flat/0/001.png"),
+        Path("images/dir1/multi_slotted_item_flat/0/000000580654.jpg"),
+        Path("images/dir1/multi_slotted_item_flat/1/000000580676.jpg"),
+        Path("images/dir1/multi_slotted_item_flat/2/000000580703.jpg"),
+    ]
+    assert count == 10
+    for expected_path in expected_paths:
+        assert expected_path in planned_paths
+
+
+def test_force_slots_false(mock_is_file_extension_allowed):
+    mock_is_file_extension_allowed.return_value = True
+    with tempfile.TemporaryDirectory() as tmp_dir:
+        with zipfile.ZipFile("tests/data.zip") as zfile:
+            zfile.extractall(tmp_dir)
+            annotations_path = Path(tmp_dir) / "v7-darwin-json-v2/force_slots"
+            images_path = Path("images")
+            generator, count = download_all_images_from_annotations(
+                api_key="api_key",
+                annotations_path=annotations_path,
+                images_path=images_path,
+                force_slots=False,
+                force_replace=True,
+            )
+
+    download_funcs = list(generator())
+    planned_paths = [download_funcs[i].args[2] for i in range(count)]
+    expected_paths = [
+        Path("images/dir1/single_slotted_video_flat.mp4"),
+        Path("images/dir1/multiple_slots_multiple_source_files/0.1/slice_1.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/0.1/slice_2.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_1.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_2.dcm"),
+        Path("images/dir1/multiple_slots_multiple_source_files/1.1/slice_3.dcm"),
+        Path("images/dir1/single_slotted_image_flat.png"),
+        Path("images/dir1/multi_slotted_item_flat/0/000000580654.jpg"),
+        Path("images/dir1/multi_slotted_item_flat/1/000000580676.jpg"),
+        Path("images/dir1/multi_slotted_item_flat/2/000000580703.jpg"),
+    ]
+    assert count == 10
+    for expected_path in expected_paths:
+        assert expected_path in planned_paths
diff --git a/tests/data.zip b/tests/data.zip
index 0a675941aaac136184dac516c93b0082167bcbeb..fda8c0e0b496591404c7c8bfe3dc0afa266d8ad3 100644
GIT binary patch
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From e89f6bac3a660258e4c4d480ca69d5e004831b60 Mon Sep 17 00:00:00 2001
From: John Wilkie <john@v7labs.com>
Date: Thu, 22 Aug 2024 10:53:49 +0100
Subject: [PATCH 4/4] GHA permissions

---
 .github/workflows/EVENT_merge_to_master.yml | 4 ++++
 .github/workflows/EVENT_tag.yml             | 2 +-
 .github/workflows/JOB_typecheck.yml         | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/EVENT_merge_to_master.yml b/.github/workflows/EVENT_merge_to_master.yml
index d49415792..bb97e1134 100644
--- a/.github/workflows/EVENT_merge_to_master.yml
+++ b/.github/workflows/EVENT_merge_to_master.yml
@@ -9,6 +9,7 @@ on:
 
 permissions:
   contents: read
+  id-token: write # Necessary for the generate documentation job 
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -24,6 +25,9 @@ jobs:
     name: Documentation
     uses: ./.github/workflows/JOB_generate_documentation.yml
     secrets: inherit
+    permissions:
+      id-token: write
+      contents: read
 
   warn_on_fail:
     needs: [run_tests, documentation]
diff --git a/.github/workflows/EVENT_tag.yml b/.github/workflows/EVENT_tag.yml
index e0ac39292..bd4c16c0a 100644
--- a/.github/workflows/EVENT_tag.yml
+++ b/.github/workflows/EVENT_tag.yml
@@ -15,7 +15,7 @@ env:
   GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
 permissions:
-  contents: write
+  contents: read
 
 jobs:
   create_release:
diff --git a/.github/workflows/JOB_typecheck.yml b/.github/workflows/JOB_typecheck.yml
index 1ca9d2348..11a5c77b6 100644
--- a/.github/workflows/JOB_typecheck.yml
+++ b/.github/workflows/JOB_typecheck.yml
@@ -36,5 +36,5 @@ jobs:
     - name: MyPy typecheck
       shell: bash
       run: |
-        pip install pydantic==2.8.2
+        pip install pydantic
         bash ${{ github.workspace }}/deploy/format_lint.sh typecheck ${{ inputs.files }}