added hl7 folder monitor

orthanc_tools/hl7Lib/__init__.py

@@ -12,3 +12,4 @@
 from .hl7_report_parser import Hl7ReportParser
 from .hl7_worklist_parser_assistovet import Hl7WorklistParserAssistovet
 from .hl7_worklist_parser_vetera import Hl7WorklistParserVetera
+from .hl7_folder_monitor import Hl7FolderMonitor

orthanc_tools/hl7Lib/hl7_folder_monitor.py

@@ -0,0 +1,116 @@
+import sys, os
+import time
+from threading import Thread
+import hl7
+import logging
+from .hl7_message_parser import Hl7MessageParser
+logger = logging.getLogger(__name__)
+
+def run_in_separate_thread(monitor):
+    monitor.monitor_folder()
+
+class Hl7FolderMonitor:
+
+    def __init__(self, folder_path, handlers: dict, interval: int = 30):
+        '''
+        folder_path: the absolute path of the folder which will be monitored (for HL7 files to be found)
+        handlers: dict: message type and callback. ex: {'ORM^O01': 'process_message'}
+        interval: time (s) between to check of the folder
+        '''
+        self._folder_path = folder_path
+        # An error message will probably never arrive from a file...
+        # self._handlers = {
+        #     'ERR': (handle_error_message,)
+        #     }
+        self._handlers = {}
+        self.add_handlers(handlers)
+        self._interval = interval
+        self.thread = None
+        self._is_running = False
+        self._parser = Hl7MessageParser()
+        self._parser.set_field_definition('message_type', 'MSH.F9')
+
+    def add_handlers(self, handlers: dict):
+        self._handlers.update(handlers)
+
+    def monitor_folder(self):
+        self._is_running = True
+
+        while self._is_running is True:
+            # get files from folder
+            for path in os.listdir(self._folder_path):
+                full_path = os.path.join(self._folder_path, path)
+
+                # quick parse and call handler if present
+                with open(full_path, newline="\r") as f:
+                    file_content = f.read()
+                    message = self._parser.parse(file_content)
+                    message_type = message['message_type']
+                    if message_type in self._handlers:
+                        self._handlers[message_type](file_content)
+                    else:
+                        logger.error(f"No handler found for {message_type} message. Keeping file for debug...")
+                        continue
+
+                # delete file
+                os.remove(full_path)
+
+            # wait interval before next check
+            time.sleep(self._interval)
+
+        self._is_running = False
+
+    def start(self):
+        """ run the server in a separate thread
+        call server.stop() from another thread to stop the server
+        """
+        self.thread = Thread(target = run_in_separate_thread, args = (self,))
+        self.thread.start()
+
+    def stop(self):
+        """stops a server that has been started with start()"""
+        self._is_running = False
+        if self.thread is not None:
+            self.thread.join()
+            self.thread = None
+
+    def __enter__(self):
+        self.start()
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        self.stop()
+
+    def is_running(self):
+        return self._is_running
+
+
+def default_message_handler(message):
+    return NotImplementedError("Please implement a message handler.")
+
+# An error message will probably never arrive from a file...
+# def handle_error_message(self, message: str, error_description: str = None) -> hl7.Message:
+#
+#     hl7_request = hl7.parse(message)  # we need to re-parse it here only the build the response
+#
+#     hl7_response = hl7.parse('MSH|^~\&|{sending_application}||{receiving_application}|{receiving_facility}|{date_time}||ACK^O01|{ack_message_id}|P|2.3||||||8859/1\rMSA|AR|{message_id}|{error}'.format(  # TODO: handle encoding
+#         sending_application = hl7_request['MSH.F5.R1.C1'],
+#         receiving_application = hl7_request['MSH.F3.R1.C1'],
+#         receiving_facility = hl7_request['MSH.F4.R1.C1'],
+#         date_time = datetime.now().strftime("%Y%m%d%H%M%S"),
+#         message_id = hl7_request['MSH.F10.R1.C1'],
+#         ack_message_id = str(random.randrange(0, 10 ** 15)),
+#         error = error_description
+#     ))
+#     return hl7_response
+
+# this is just a very quick usage example that does nothing usefull since it uses abstract handler
+if __name__ == "__main__":
+    server = Hl7FolderMonitor('/home/messages', {
+        'ORM^O01': (default_message_handler,)
+    })
+    # terminate with Ctrl-C
+    try:
+        server.monitor_folder()
+    except KeyboardInterrupt:
+        sys.exit(0)

orthanc_tools/hl7Lib/hl7_worklist_parser_vetera.py

@@ -11,7 +11,7 @@ def __init__(self, specific_fields: dict = None, patient_name_components_count:
             'PatientSpeciesDescription': 'PID.F35',
             'PatientBreedDescription': 'PID.F36',
             'PatientSexNeutered': 'PID.F37',
-            'BreedRegistrationNumber': 'PID.F38', # TO BE CONFIRMED (waiting for Vetera's feeback)
+            'BreedRegistrationNumber': 'PID.F38',
             '_scheduledProcedureStepStartDateTime': 'OBR.F6',
             'Modality': 'OBR.F21',
             'RequestingPhysician': 'OBR.F32'
@@ -20,28 +20,3 @@ def __init__(self, specific_fields: dict = None, patient_name_components_count:
             vetera_dict.update(specific_fields)
 
         super(Hl7WorklistParserVetera, self).__init__(vetera_dict, patient_name_components_count)
-
-
-
-    def parse(self, hl7_message: str) -> typing.Dict:
-        # let's parse the default fields
-        values = Hl7WorklistParser.parse(self, hl7_message=hl7_message)
-
-        # let's parse according to rules specific to Vetera
-        owner = self._get('PID.F5.R1.C1', default_value="")
-        name = self._get('PID.F5.R1.C2', default_value="")
-
-        # TODO confirm with the customer that this is what they want (because the owner name won't appear in Orthanc UI)
-        values['ResponsiblePerson'] = owner
-        values['PatientName'] = name
-
-        if values.get('_scheduledProcedureStepStartDateTime') is not None:
-            datetimeString = values.get('_scheduledProcedureStepStartDateTime')
-            values['ScheduledProcedureStepStartDate'] = datetimeString[:8]  # date is made of the 8 first chars of the string
-            if len(datetimeString) == 12:
-                values['ScheduledProcedureStepStartTime'] = datetimeString[8:12] + "00"
-            elif len(datetimeString) == 14:
-                values['ScheduledProcedureStepStartTime'] = datetimeString[8:14]
-
-        return values
-

orthanc_tools/hl7Lib/tests/test_hl7_folder_monitor.py

@@ -0,0 +1,87 @@
+import os
+import time
+import unittest
+import hl7  # https://python-hl7.readthedocs.org/en/latest/
+from orthanc_tools import hl7Lib
+import re
+from orthanc_tools import Hl7FolderMonitor
+import tempfile
+from orthanc_api_client import helpers
+from orthanc_tools import Hl7WorklistParserVetera, DicomWorklistBuilder, Hl7OrmWorklistMsgHandler
+
+def hl7_echo_message_handler(incoming_hl7_message: str) -> hl7.Message:
+    """
+    This is a 'stupid' handler that just repeats the message it receives (useful for testing)
+    """
+    pass
+    return hl7.parse(incoming_hl7_message)
+
+
+class TestHl7FolderMonitor(unittest.TestCase):
+
+    def test_start_and_stop(self):
+        with tempfile.TemporaryDirectory() as temp_dir:
+            monitor = Hl7FolderMonitor(temp_dir, {
+            }, 5)
+
+            # just make sure we can start/stop the server
+            self.assertFalse(monitor.is_running())
+
+            monitor.start()
+            self.assertTrue(monitor.is_running())
+
+            monitor.stop()
+            self.assertFalse(monitor.is_running())
+
+    def test_callback_and_deletion(self):
+        # start a monitor that will check the folder and delete the file after the callback
+        with tempfile.TemporaryDirectory() as temp_dir:
+            monitor = Hl7FolderMonitor(temp_dir, {'ORM^O01': hl7_echo_message_handler}, 3)
+
+            # validate that ORM^O01 messages has been received
+            hl7_str = "MSH|^~\&|TOTO|TUTU|SOFTNAME|CHABC|201602011049||ORM^O01|exp_ANE_5|P|2.3.1\rPID|1||8123456DK01||DUPONT^ALBERT ANTHONY|||||||||||||123456"
+
+            file_path = temp_dir + "/test.hl7"
+            f = open(file_path, "w")
+            f.write(hl7_str)
+            f.close()
+            self.assertEqual(1, len(os.listdir(temp_dir)))
+
+            monitor.start()
+
+            # wait until the file has been deleted
+            helpers.wait_until(lambda: len(os.listdir(temp_dir)) == 0, 4)
+            self.assertEqual(0, len(os.listdir(temp_dir)))
+            monitor.stop()
+
+    def test_worklist_creation(self):
+        # start a monitor that will check the folder and create the wl file
+        with tempfile.TemporaryDirectory() as temp_dir_hl7:
+            with tempfile.TemporaryDirectory() as temp_dir_wl:
+                orm_parser = Hl7WorklistParserVetera()
+                worklist_builder = DicomWorklistBuilder(folder=temp_dir_wl)
+                orm_handler = Hl7OrmWorklistMsgHandler(parser=orm_parser, builder=worklist_builder)
+
+                monitor = Hl7FolderMonitor(temp_dir_hl7, {'ORM^O01': orm_handler.handle_orm_message}, 3)
+
+                hl7_str = "MSH|^~\&|VETERA|VETERA|conquest|conquest|20170731081517||ORM^O01|1000000001|P|2.5.0|||||\r"\
+                    "PID|1|999888777||123456789012345|GP.Software^Vetera||20070501|F|||||||||||||||||||||||||||Katze|Balinese|ALTERED|ZH-123|\r"\
+                    "ORC|NW||||||||20170731081517||||||||||\r"\
+                    "OBR|||1000000001|HD||20170731081517|||||||||||||||DX|||ZUG||||||||Dr. P. Muster||||\r"
+
+                file_path = temp_dir_hl7 + "/test.hl7"
+                f = open(file_path, "w")
+                f.write(hl7_str)
+                f.close()
+
+                self.assertEqual(1, len(os.listdir(temp_dir_hl7)))
+
+                monitor.start()
+
+                # wait until the hl7 file has been deleted, so that, the wl file should have been created
+                helpers.wait_until(lambda: len(os.listdir(temp_dir_hl7)) == 0, 4)
+
+                self.assertEqual(1, len(os.listdir(temp_dir_wl)))
+                monitor.stop()
+
+

orthanc_tools/hl7Lib/tests/test_hl7_orm_worklist_msg_handler.py

@@ -370,8 +370,7 @@ def test_vetera_worklists(self):
                 #TODO:
                 # check the content of the file
                 with dcmread(worklist_file_path) as wl:
-                    self.assertEqual("Vetera", wl.PatientName)
-                    self.assertEqual("GP.Software", wl.ResponsiblePerson)
+                    self.assertEqual("GP.Software^Vetera", wl.PatientName)
                     self.assertEqual("20070501", wl.PatientBirthDate)
                     self.assertEqual("999888777", wl.PatientID)
                     self.assertEqual("ISO_IR 100", wl.SpecificCharacterSet)  # default char set if not specified in HL7 message

release-notes.md

@@ -2,7 +2,7 @@ v 0.14.5
 ========
 - `Hl7WorklistParser` update: some different parsers implemented, to handle different the message providers.
 
-- v 0.14.4
+v 0.14.4
 ========
 - `OrthancFolderImporter` update: allows to modify/filter instance before upload.