Merge pull request #89 from dwikler/fix-comments-PR88

Fix comments pr88

.gitignore

@@ -158,3 +158,15 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Flake8 linting toom configuration file
+.flake8
+
+# Personal files and test code snippets
+scratchpad/
+
+# Ignore SQLite database files
+*.sqlite
+
+# Visual Studio Code settings
+.vscode/settings.json

.vscode/settings.json

@@ -77,5 +77,14 @@
         "watchscu",
         "whatsthis"
     ],
-    "python.REPL.enableREPLSmartSend": false
+    "python.REPL.enableREPLSmartSend": false,
+    "python.testing.unittestArgs": [
+        "-v",
+        "-s",
+        "./tdwii_plus_examples/tests",
+        "-p",
+        "test_*.py",
+    ],
+    "python.testing.pytestEnabled": false,
+    "python.testing.unittestEnabled": true
 }

pyproject.toml

@@ -8,7 +8,7 @@ readme = "README.md"
 packages = [{include = "tdwii_plus_examples"}]
 
 [tool.poetry.dependencies]
-python = ">=3.10, <3.11"
+python = ">=3.10, <3.13"
 pydicom = "^2.4.0"
 pynetdicom = "^2.1.0"
 pyside6 = "^6.6.0"

tdwii_plus_examples/cstorehandler.py

@@ -38,7 +38,7 @@
         "BR", "RTBYREC", "RTBRACHYRECORD",
         "RT Brachy Treatment Record Storage"),
     "1.2.840.10008.5.1.4.1.1.481.7": (
-        "SR", "SUMREC", "RTSUMRECORD",
+        "SUM", "SUMREC", "RTSUMRECORD",
         "RT Treatment Summary Record Storage"),
     "1.2.840.10008.5.1.4.1.1.481.8": (
         "RN", "RTIONPLN", "RTIONPLAN",

tdwii_plus_examples/cstorescp.py

@@ -2,7 +2,9 @@
 from argparse import Namespace
 import logging
 
-from pydicom.uid import UID, ImplicitVRLittleEndian, AllTransferSyntaxes
+from pydicom.uid import (
+    UID, ImplicitVRLittleEndian, ExplicitVRLittleEndian, AllTransferSyntaxes
+)
 from pynetdicom import DEFAULT_TRANSFER_SYNTAXES, evt
 from pynetdicom.presentation import (
     StoragePresentationContexts,
@@ -87,9 +89,11 @@ def __init__(self,
         transfer_syntaxes: list of str/pydicom.uid.UID
             A list of transfer syntaxes UIDs or names to support
             (names must be valid Transfer Syntax Keywords from PS3.6 Annex A,
-            invalid UIDs and names will be ignored)
+            invalid UIDs and names will be ignored).
+            The order of the transfer syntaxes in the list can be used to set
+            the preferred syntax to accept when multiple ones are proposed.
             Optional, default: None, pynetdicom default transfer syntaxes are
-            supported
+            supported with Explicit VR Little Endian as the preferred syntax.
 
         custom_handler: function
             A function to handle C-STORE requests
@@ -217,12 +221,17 @@ def _add_contexts(self):
             sop_classes = self._valid_sop_classes
         self.logger.debug(f"Supported Storage SOP Classes: {sop_classes}")
 
-        if self.transfer_syntaxes is None:
-            transfer_syntaxes = DEFAULT_TRANSFER_SYNTAXES
+        if self.transfer_syntaxes is None or not self.transfer_syntaxes:
+            self.logger.debug("No transfer syntaxes specified, using defaults")
+            transfer_syntaxes = DEFAULT_TRANSFER_SYNTAXES.copy()
+            # Make ExplicitVRLittleEndian the preferred transfer syntax
+            transfer_syntaxes.remove(UID(ExplicitVRLittleEndian))
+            transfer_syntaxes = [UID(ExplicitVRLittleEndian)] + \
+                transfer_syntaxes
         else:
             if ImplicitVRLittleEndian not in self._valid_transfer_syntaxes:
-                transfer_syntaxes = [ImplicitVRLittleEndian] + \
-                    self._valid_transfer_syntaxes
+                transfer_syntaxes = self._valid_transfer_syntaxes + [
+                    ImplicitVRLittleEndian]
             else:
                 transfer_syntaxes = self._valid_transfer_syntaxes
         self.logger.debug(f"Supported Transfer Syntaxes: {transfer_syntaxes}")

tdwii_plus_examples/tests/cli/test_storescp.py

@@ -18,7 +18,7 @@ def test_main(self, mock_parse_args, MockCStoreSCP):
             bind_address='127.0.0.1',
             port=12345,
             sop_classes=['SecondaryCaptureImageStorage'],
-            transfer_syntaxes=['ImplicitVRLittleEndian'],
+            transfer_syntaxes=['ExplicitVRLittleEndian'],
             custom_handler='my_handler',
             output_directory='/var/tmp/output',
             verbose=False,
@@ -46,7 +46,7 @@ def test_main(self, mock_parse_args, MockCStoreSCP):
                 port=12345,
                 logger=logging.getLogger('storescp'),
                 sop_classes=['SecondaryCaptureImageStorage'],
-                transfer_syntaxes=['ImplicitVRLittleEndian'],
+                transfer_syntaxes=['ExplicitVRLittleEndian'],
                 custom_handler=mock_handler,  # Ensure this is the mock function
                 store_directory='/var/tmp/output'
             )

tdwii_plus_examples/tests/test_basescp_integration.py

@@ -4,6 +4,7 @@
 import subprocess
 import time
 import re
+import sys
 from tdwii_plus_examples.basescp import BaseSCP
 from pynetdicom.sop_class import Verification
 
@@ -20,10 +21,10 @@ def _add_contexts(self):
 class TestBaseSCP(unittest.TestCase):
 
     def setUp(self):
-        # Set up the logger for the BaseSCP to INFO level
+        # Set up the logger for the BaseSCP to DEBUG level
         # with a memory handler to store up to 100 log messages
         self.scp_logger = logging.getLogger('basescp')
-        self.scp_logger.setLevel(logging.INFO)
+        self.scp_logger.setLevel(logging.DEBUG)
         self.memory_handler = MemoryHandler(100)
         self.scp_logger.addHandler(self.memory_handler)
 
@@ -43,8 +44,11 @@ def test_run_and_check_log(self):
         # Run the SCP
         self.scp.run()
 
+        # Ensure the correct Python interpreter is used for the subprocess call
+        python_executable = sys.executable
+
         # Send an echo request using pynetdicom's echoscu.py
-        subprocess.check_call(['python', '-m', 'pynetdicom', 'echoscu',
+        subprocess.check_call([python_executable, '-m', 'pynetdicom', 'echoscu',
                                'localhost', '11112',
                                '-aet', 'ECHOSCU', '-aec', 'BASE_SCP'])
 

tdwii_plus_examples/tests/test_cechoscp_integration.py

@@ -1,3 +1,4 @@
+import sys
 import unittest
 import logging
 from logging.handlers import MemoryHandler
@@ -31,8 +32,11 @@ def test_run_and_check_log(self):
         # Run the SCP
         self.scp.run()
 
+        # Ensure the correct Python interpreter is used for the subprocess call
+        python_executable = sys.executable
+
         # Send an echo request using pynetdicom's echoscu.py
-        subprocess.check_call(['python', '-m', 'pynetdicom', 'echoscu',
+        subprocess.check_call([python_executable, '-m', 'pynetdicom', 'echoscu',
                                'localhost', '11112',
                                '-aet', 'ECHOSCU', '-aec', 'ECHO_SCP'])
 

tdwii_plus_examples/tests/test_cstorehandler.py

@@ -1,7 +1,9 @@
+import sys
 import unittest
 import tempfile
 import shutil
 import os
+import logging
 from unittest.mock import MagicMock, patch
 from parameterized import parameterized
 from pydicom.dataset import Dataset, FileMetaDataset
@@ -34,6 +36,11 @@ class TestHandleCStoreEvent(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         cls.temp_dir = tempfile.mkdtemp()
+        cls.logger = logging.getLogger("TestHandleCStoreEvent")
+        handler = logging.StreamHandler()
+        handler.setLevel(logging.DEBUG)
+        cls.logger.addHandler(handler)
+        cls.logger.setLevel(logging.DEBUG)
 
     def setUp(self):
         # Create a mock event
@@ -78,16 +85,16 @@ def test_handle_cstore(self, ignore, output_directory, expected_status,
         status_ds = handle_cstore(self.mock_event, mock_args, mock_logger)
 
         # Debugging output
-        # print(
-        #     "\nTest case parameters:\n ignore = %s"
-        #     "\n output_directory = %s"
-        #     "\n expected_status = 0x%04X" % (
-        #         ignore, mock_args.output_directory, expected_status))
-        # print(
-        #     "\nTest case results:"
-        #     "\n actual status = 0x%04X"
-        #     "\n logger calls : %s," % (
-        #         status_ds.Status, mock_logger.mock_calls))
+        self.logger.debug(
+            "\nTest case parameters:\n ignore = %s"
+            "\n output_directory = %s"
+            "\n expected_status = 0x%04X" % (
+                ignore, mock_args.output_directory, expected_status))
+        self.logger.debug(
+            "\nTest case results:"
+            "\n actual status = 0x%04X"
+            "\n logger calls : %s," % (
+                status_ds.Status, mock_logger.mock_calls))
 
         # Check the status
         self.assertEqual(status_ds.Status, expected_status)
@@ -100,8 +107,10 @@ def test_handle_cstore(self, ignore, output_directory, expected_status,
             mock_logger.error.assert_called_once_with(
                 "args.output_directory attribute not present or None")
         elif '/invalid/path' in output_directory:
-            mock_logger.exception.assert_called_once_with(
-                "Unable to create the output directory: /invalid/path\0")
+            expected_message = "Unable to create the output directory: /invalid/path\0"
+            if sys.platform.startswith('win'):
+                expected_message = expected_message.replace("/invalid/path", "C:/invalid/path")
+            mock_logger.exception.assert_called_once_with(expected_message)
         elif expected_status == 0xC210:
             mock_logger.exception.assert_called_once_with(
                 "Unable to decode the data set and/or the command set")