generate label based on patient id and study count in xnat project

pixl_core/src/core/uploader/_xnat.py

@@ -17,9 +17,14 @@
 from __future__ import annotations
 
 import os
+from io import BytesIO
 from typing import TYPE_CHECKING, BinaryIO, Optional
+from zipfile import ZIP_DEFLATED, ZipFile
 
 import xnat
+import xnat.datatypes
+import xnat.type_hints
+from pydicom import dcmread
 
 from core.uploader.base import Uploader
 
@@ -77,6 +82,28 @@ def _upload_dicom_image(
         zip_content = get_study_zip_archive(study_id)
         self.upload_to_xnat(zip_content, study_tags)
 
+    def _split_zip_by_modality(self, zip_content: BinaryIO) -> dict[str, BinaryIO]:
+        """Split a zip file by modality."""
+        zip_content_by_modality = {}
+        with ZipFile(zip_content) as zipped_study:
+            for file_info in zipped_study.infolist():
+                with zipped_study.open(file_info) as file:
+                    dataset = dcmread(file)
+                    modality = dataset.Modality
+                    patient_id = dataset.PatientID
+                    label = f"{patient_id}_{modality}"
+                    if label not in zip_content_by_modality:
+                        zip_content_by_modality[label] = BytesIO()
+                    with ZipFile(
+                        zip_content_by_modality[label], "a", compression=ZIP_DEFLATED
+                    ) as zipped_modality:
+                        zipped_modality.writestr(file_info.filename, file.read())
+
+        for zipped_modality in zip_content_by_modality.values():
+            zipped_modality.seek(0)
+
+        return zip_content_by_modality
+
     def upload_to_xnat(
         self,
         zip_content: BinaryIO,
@@ -87,17 +114,48 @@ def upload_to_xnat(
             user=self.user,
             password=self.password,
         ) as session:
+            experiment = self._get_experiment_label(
+                session=session,
+                patient_id=study_tags.patient_id,
+            )
+
             session.services.import_(
                 data=zip_content,
                 overwrite=self.overwrite,
-                destination=self.destination,
+                destination=self.project_slug,
                 project=self.project_slug,
                 subject=study_tags.patient_id,
-                experiment=study_tags.pseudo_anon_image_id,
+                experiment=experiment,
                 content_type="application/zip",
                 import_handler="DICOM-zip",
             )
 
+    def _get_experiment_label(
+        self,
+        session: xnat.XNATSession,
+        patient_id: str,
+    ) -> str:
+        """
+        Create a unique experiment label based on the PatientID and number of existing DICOM studies
+        for the patient.
+        """
+        project: xnat.mixin.ProjectData = session.projects[self.project_slug]
+        try:
+            subject: xnat.mixin.SubjectData = project.subjects[patient_id]
+        except KeyError:
+            n_archive_experiments = 0
+        else:
+            n_archive_experiments = len(subject.experiments)
+
+        n_prearchive_experiments = len(
+            session.prearchive.find(
+                project=self.project_slug,
+                subject=patient_id,
+            )
+        )
+        n_experiments = n_archive_experiments + n_prearchive_experiments
+        return f"{patient_id}_{n_experiments + 1}"
+
     def upload_parquet_files(self, parquet_export: ParquetExport) -> None:  # noqa: ARG002
         msg = "XNATUploader does not support parquet files"
         raise NotImplementedError(msg)

pixl_dcmd/tests/test_main.py

@@ -45,7 +45,6 @@
 )
 from pytest_pixl.dicom import generate_dicom_dataset
 from pytest_pixl.helpers import run_subprocess
-from conftest import ids_for_parameterised_test
 
 if typing.TYPE_CHECKING:
     from core.project_config.pixl_config_model import PixlConfig
@@ -191,7 +190,9 @@ def test_anonymise_and_validate_as_external_user(
 
 
 @pytest.mark.parametrize(
-    ("yaml_file"), PROJECT_CONFIGS_DIR.glob("*.yaml"), ids=ids_for_parameterised_test
+    ("yaml_file"),
+    PROJECT_CONFIGS_DIR.glob("*.yaml"),
+    ids=lambda yaml_file: str(yaml_file.stem),
 )
 def test_anonymise_and_validate_dicom(caplog, request, yaml_file) -> None:
     """