From 9bd2c84ad20b10aa0fff542485826a390db5cec5 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Tue, 1 Oct 2024 21:27:53 +1000
Subject: [PATCH] fixed up datatype option for stage

---
 .pre-commit-config.yaml  | 50 ++++++++++++++++++++--------------------
 scripts/get_pet_tst.py   | 23 ++++++++++++++++++
 xnat_ingest/cli/stage.py |  2 +-
 xnat_ingest/session.py   |  5 ++--
 4 files changed, 52 insertions(+), 28 deletions(-)
 create mode 100644 scripts/get_pet_tst.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7a881d3..3904cd4 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,28 +1,28 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 22.3.0
-    hooks:
-    -   id: black
-        exclude: ^(arcana/_version\.py|versioneer\.py)$
-        args:
-          - -l 88
--   repo: https://github.com/codespell-project/codespell
-    rev: v2.1.0
-    hooks:
-    -   id: codespell
-        exclude: ^(xnat_checks/_version\.py|versioneer\.py)$
-        args:
-        -   --ignore-words=.codespell-ignorewords
--   repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-    -   id: flake8
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.3.0
+      hooks:
+          - id: trailing-whitespace
+          - id: end-of-file-fixer
+          - id: check-yaml
+          - id: check-added-large-files
+    - repo: https://github.com/psf/black
+      rev: 22.3.0
+      hooks:
+          - id: black
+            exclude: ^(arcana/_version\.py|versioneer\.py)$
+            args:
+                - -l 88
+    - repo: https://github.com/codespell-project/codespell
+      rev: v2.1.0
+      hooks:
+          - id: codespell
+            exclude: ^(xnat_checks/_version\.py|versioneer\.py)$
+            args:
+                - --ignore-words=.codespell-ignorewords
+    - repo: https://github.com/PyCQA/flake8
+      rev: 7.0.0
+      hooks:
+          - id: flake8
diff --git a/scripts/get_pet_tst.py b/scripts/get_pet_tst.py
new file mode 100644
index 0000000..b905798
--- /dev/null
+++ b/scripts/get_pet_tst.py
@@ -0,0 +1,23 @@
+import tempfile
+from pathlib import Path
+from fileformats.medimage import DicomSeries
+from medimages4tests.dummy.dicom.pet.wholebody.siemens.biograph_vision.vr20b import (  # type: ignore[import-untyped]
+    get_image as get_pet_image,
+)
+
+
+tmp_path = Path(tempfile.mkdtemp())
+
+series = DicomSeries(
+    get_pet_image(
+        tmp_path,
+        first_name="first",
+        last_name="last",
+        StudyInstanceUID="StudyInstanceUID",
+        PatientID="PatientID",
+        AccessionNumber="AccessionNumber",
+        StudyID="xnat_project",
+    ).iterdir()
+)
+
+print(series.metadata["StudyID"])
diff --git a/xnat_ingest/cli/stage.py b/xnat_ingest/cli/stage.py
index cddcc1f..ce11f53 100644
--- a/xnat_ingest/cli/stage.py
+++ b/xnat_ingest/cli/stage.py
@@ -287,7 +287,7 @@ def stage(
         additional_loggers=additional_loggers,
     )
     datatypes: list[ty.Type[FileSet]]
-    if datatype is None:
+    if not datatype:
         datatypes = [DicomSeries]
     else:
         datatypes = [FileSet.from_mime(dt) for dt in datatype]  # type: ignore[misc]
diff --git a/xnat_ingest/session.py b/xnat_ingest/session.py
index 4a516e6..2953237 100644
--- a/xnat_ingest/session.py
+++ b/xnat_ingest/session.py
@@ -357,8 +357,9 @@ def get_id(field_type: str, field_name: str) -> str:
                             )
                     else:
                         raise ImagingSessionParseError(
-                            f"Did not find '{field_name}' field in {resource}, "
-                            "cannot uniquely identify the resource"
+                            f"Did not find '{field_name}' field in {resource!r}, "
+                            "cannot uniquely identify the resource, found:\n"
+                            + "\n".join(resource.metadata)
                         )
                 if index is not None:
                     value = value[index]