Merge branch 'main' into milanmlft/606-add-api-uploader

Author: stefpiatek

cli/src/pixl_cli/_io.py

@@ -94,9 +94,14 @@ def _load_csv(filepath: Path) -> pd.DataFrame:
     messages_df = pd.read_csv(filepath, header=0, dtype=str)
     messages_df = _map_columns(messages_df, MAP_CSV_TO_MESSAGE_KEYS)
     _raise_if_column_names_not_found(messages_df, [col.name for col in DF_COLUMNS])
-    messages_df["series_uid"] = (
-        messages_df.get("series_uid", pd.Series("")).replace(np.nan, "").str.strip()
+
+    if "series_uid" not in messages_df.columns:
+        messages_df["series_uid"] = ""
+    messages_df["series_uid"] = messages_df["series_uid"].replace(np.nan, "").str.strip()
+    messages_df["accession_number"] = (
+        messages_df["accession_number"].replace(np.nan, "").str.strip()
     )
+    messages_df["study_uid"] = messages_df["study_uid"].replace(np.nan, "").str.strip()
     messages_df["pseudo_patient_id"] = messages_df["pseudo_patient_id"].replace(np.nan, None)
 
     # Parse non string columns

pixl_imaging/src/pixl_imaging/_processing.py

@@ -373,7 +373,7 @@ async def _get_missing_instances(
         logger.trace(
             "Instance {} is missing from study {}",
             sop_instance_uid,
-            study.message.study_uid,
+            str(study.message.study_uid),
         )
         missing_instances.append(uids_for_query)
 

projects/configs/uclh-hic-hearing-health.yaml

@@ -0,0 +1,80 @@
+#  Copyright (c) 2024 University College London Hospitals NHS Foundation Trust
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+project:
+    name: "uclh-hic-hearing-health"
+    modalities:
+      - "CT"
+      - "MR"
+
+tag_operation_files:
+    base:
+        - "base.yaml"
+        - "ct.yaml"
+        - "mri.yaml"
+        - "diffusion-weighted-mri.yaml"
+    manufacturer_overrides: ["mri.yaml", "mri-diffusion.yaml"]
+
+allowed_manufacturers:
+  - regex: "^ge medical systems"
+    exclude_series_numbers:
+        - 1200
+        - 1201
+        - 1202
+        - 1203
+        - 1301
+        - 1501
+        - 1000
+        - 9000
+        - 1151418
+  - regex: "afga"
+  - regex: "siemens"
+  - regex: "newtom"
+  - regex: "toshiba"
+  - regex: "morita"
+  - regex: "fonar"
+  - regex: "philips"
+  - regex: "canon"
+    exclude_series_numbers:
+        - 9000
+
+min_instances_per_series: 6
+
+series_filters:
+    - "localizer"
+    - "localiser"
+    - "scout"
+    - "positioning"
+    - "mip"
+    - "fused"
+    - "save"
+    - "lungscreening result"
+    - "key_images"
+    - "color"
+    - "casc"
+    - "cascoring_docu_1"
+    - "dose"
+    - "patient protocol"
+    - "enhancement curve"
+    - "summary"
+    - "report"
+    - "medrad injection images"
+    - "sectra reconstruction"
+    - "impax volume viewing"
+    - "evidence documents"
+    - "export"
+
+destination:
+    dicom: "ftps"
+    parquet: "ftps"

pyproject.toml

@@ -55,7 +55,7 @@ dev = [
     "mypy==1.13.0",
     "pre-commit==4.0.1",
     "pytest==8.3.4",
-    "ruff==0.8.3",
+    "ruff>=0.11",
     "pytest-mock==3.14.0",
     "httpx==0.28.*",
     "pytest-asyncio==0.24.0",