added CLI params for orthanc push

base_client.py

@@ -10,7 +10,7 @@ def pacs_pull(self):
         pass
 
     @abstractmethod
-    def anonymize(self, dicom_dir: str, params: str, pv_id: int):
+    def anonymize(self, dicom_dir: str, params: str, send_params: dict, pv_id: int):
         pass
 
     @abstractmethod

chrisClient.py

@@ -38,7 +38,7 @@ def pacs_pull(self):
     def pacs_push(self):
         pass
 
-    def anonymize(self, dicom_dir: str, tag_struct: str, pv_id: int):
+    def anonymize(self, dicom_dir: str, tag_struct: str, send_params: dict, pv_id: int):
 
         pl_id = self.__get_plugin_id({"name": "pl-dsdircopy", "version": "1.0.2"})
         pl_sub_id = self.__get_plugin_id({"name": "pl-pfdicom_tagsub", "version": "3.3.4"})
@@ -59,10 +59,10 @@ def anonymize(self, dicom_dir: str, tag_struct: str, pv_id: int):
         dir_send_data = {
             "previous_id": tag_sub_id,
             'inputFileFilter': "**/*dcm",
-            "orthancUrl": params["push"]["url"],
-            "username":params["push"]["username"],
-            "password": params["push"]["password"],
-            "pushToRemote": params["push"]["aec"]
+            "orthancUrl": send_params["url"],
+            "username": send_params["username"],
+            "password": send_params["password"],
+            "pushToRemote": send_params["aec"]
         }
         pl_inst_id = self.__create_feed(pl_dcm_id, dir_send_data)
 

reg_chxr.py

@@ -24,7 +24,7 @@
 logger.remove()
 logger.add(sys.stderr, format=logger_format)
 
-__version__ = '1.0.5'
+__version__ = '1.0.6'
 
 DISPLAY_TITLE = r"""
        _                               _               
@@ -72,6 +72,37 @@
     type=str,
     help='directive to use to anonymize DICOMs'
 )
+parser.add_argument(
+    '--orthancUrl', '-o',
+    dest='orthancUrl',
+    type=str,
+    help='Orthanc server url',
+    default='http://0.0.0.0:8042'
+)
+
+parser.add_argument(
+    '--orthancUsername', '-u',
+    dest='username',
+    type=str,
+    help='Orthanc server username',
+    default='orthanc'
+)
+
+parser.add_argument(
+    '--orthancPassword', '-p',
+    dest='password',
+    type=str,
+    help='Orthanc server password',
+    default='orthanc'
+)
+
+parser.add_argument(
+    '--pushToRemote', '-r',
+    dest='pushToRemote',
+    type=str,
+    help='Remote modality',
+    default=''
+)
 parser.add_argument('-V', '--version', action='version',
                     version=f'%(prog)s {__version__}')
 
@@ -125,6 +156,7 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
             # for each individual series, check if total file count matches total file registered
             for series in data:
                 pacs_search_params = sanitize_for_cube(series)
+                file_count = int(series["NumberOfSeriesRelatedInstances"])
                 registered_file_count = cube_cl.get_pacs_registered(pacs_search_params)
 
                 # poll CUBE at regular interval for the status of file registration
@@ -135,17 +167,23 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
                     poll_count += 1
                     time.sleep(wait_poll)
                     registered_file_count = cube_cl.get_pacs_registered(pacs_search_params)
-                    LOG(f"Registered file count is {registered_file_count}")
+                    LOG(f"{registered_file_count} series found in CUBE.")
 
                 # check if polling timed out before registration is finished
                 if registered_file_count == 0:
                     raise Exception(f"PACS file registration unsuccessful. Please try again.")
-                LOG(f"{registered_file_count} files were successfully registered to CUBE.")
+                LOG(f"{file_count} files successfully registered to CUBE.")
+                send_params = {
+                    "url": options.orthancUrl,
+                    "username": options.username,
+                    "password": options.password,
+                    "aec": options.pushToRemote
+                }
                 dicom_dir = cube_cl.get_pacs_files(pacs_search_params)
 
                 # create connection object
                 cube_con = ChrisClient(options.CUBEurl, options.CUBEuser, options.CUBEpassword)
-                cube_con.anonymize(dicom_dir, options.tagStruct, options.pluginInstanceID)
+                cube_con.anonymize(dicom_dir, options.tagStruct,send_params, options.pluginInstanceID)
 
 
 def sanitize_for_cube(series: dict) -> dict: