run anon pipeline in the plugin

base_client.py

@@ -0,0 +1,22 @@
+from abc import ABC, abstractmethod
+
+class BaseClient(ABC):
+    @abstractmethod
+    def create_con(self, params: dict):
+        pass
+
+    @abstractmethod
+    def pacs_pull(self):
+        pass
+
+    @abstractmethod
+    def anonymize(self, dicom_dir: str, params: str, pv_id: int):
+        pass
+
+    @abstractmethod
+    def pacs_push(self):
+        pass
+
+    @abstractmethod
+    def health_check(self):
+        pass

chrisClient.py

@@ -0,0 +1,80 @@
+### Python Chris Client Implementation ###
+
+from base_client import BaseClient
+from chrisclient import client
+from chris_pacs_service import PACSClient
+import json
+import time
+from loguru import logger
+import sys
+
+LOG = logger.debug
+
+logger_format = (
+    "<green>{time:YYYY-MM-DD HH:mm:ss}</green> │ "
+    "<level>{level: <5}</level> │ "
+    "<yellow>{name: >28}</yellow>::"
+    "<cyan>{function: <30}</cyan> @"
+    "<cyan>{line: <4}</cyan> ║ "
+    "<level>{message}</level>"
+)
+logger.remove()
+logger.add(sys.stderr, format=logger_format)
+
+class ChrisClient(BaseClient):
+    def __init__(self, url: str, username: str, password: str):
+        self.cl = client.Client(url, username, password)
+        self.cl.pacs_series_url = f"{url}pacs/series/"
+        self.req = PACSClient(self.cl.pacs_series_url,username,password)
+
+    def create_con(self,params:dict):
+        return self.cl
+
+    def health_check(self):
+        return self.cl.get_chris_instance()
+
+    def pacs_pull(self):
+        pass
+    def pacs_push(self):
+        pass
+
+    def anonymize(self, dicom_dir: str, tag_struct: str, 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"})
+        pl_dcm_id = self.__get_plugin_id({"name": "pl-orthanc_push", "version": "1.2.7"})
+
+        # 1) Run dircopy
+        # empty directory check
+        if len(dicom_dir) == 0:
+            LOG(f"No directory found in CUBE containing files for search : {tag_struct}")
+            return
+        pv_in_id = self.__create_feed(pl_id, {"previous_id": pv_id, 'dir': dicom_dir})
+
+        # 2) Run anonymization
+        data = {"previous_id": pv_in_id, "tagStruct": tag_struct, 'fileFilter': '.dcm'}
+        tag_sub_id = self.__create_feed(pl_sub_id, data)
+
+        # 3) Push results
+        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"]
+        }
+        pl_inst_id = self.__create_feed(pl_dcm_id, dir_send_data)
+
+    def __create_feed(self, plugin_id: str,params: dict):
+        response = self.cl.create_plugin_instance(plugin_id, params)
+        return response['id']
+
+    def __get_plugin_id(self, params: dict):
+        response = self.cl.get_plugins(params)
+        if response['total'] > 0:
+            return response['data'][0]['id']
+        raise Exception(f"No plugin found with matching search criteria {params}")
+
+
+

chris_pacs_service.py

@@ -1,10 +1,27 @@
-from chrisclient import client
+import requests
+from chrisclient import client, request
+from loguru import logger
+import sys
+
+LOG = logger.debug
+
+logger_format = (
+    "<green>{time:YYYY-MM-DD HH:mm:ss}</green> │ "
+    "<level>{level: <5}</level> │ "
+    "<yellow>{name: >28}</yellow>::"
+    "<cyan>{function: <30}</cyan> @"
+    "<cyan>{line: <4}</cyan> ║ "
+    "<level>{message}</level>"
+)
+logger.remove()
+logger.add(sys.stderr, format=logger_format)
 
 
 class PACSClient(object):
     def __init__(self, url: str, username: str, password: str):
         self.cl = client.Client(url, username, password)
         self.cl.pacs_series_url = f"{url}pacs/series/"
+        self.req = request.Request(username, password)
 
     def get_pacs_registered(self, params: dict):
         """
@@ -15,3 +32,17 @@ def get_pacs_registered(self, params: dict):
         if response:
             return response['total']
         raise Exception(f"No PACS details with matching search criteria {params}")
+
+    def get_pacs_files(self, params: dict):
+        """
+        Get PACS folder path
+        """
+        l_dir_path = set()
+        resp = self.req.get(f"{self.cl.pacs_series_url}search", params)
+        for item in resp.items:
+            for link in item.links:
+                folder = self.req.get(link.href)
+                for item_folder in folder.items:
+                    path = item_folder.data.path.value
+                    l_dir_path.add(path)
+        return ','.join(l_dir_path)

reg_chxr.py

@@ -5,6 +5,7 @@
 from chris_pacs_service import PACSClient
 from loguru import logger
 from chris_plugin import chris_plugin, PathMapper
+from chrisClient import ChrisClient
 import time
 import json
 import copy
@@ -44,6 +45,11 @@
     default="http://localhost:8000/api/v1/",
     help="CUBE URL"
 )
+parser.add_argument(
+    "--pluginInstanceID",
+    default="",
+    help="plugin instance ID from which to start analysis",
+)
 parser.add_argument(
     "--CUBEuser",
     default="chris",
@@ -60,7 +66,12 @@
     type=str,
     help='JSON file containing DICOM data to be retrieved'
 )
-
+parser.add_argument(
+    '--tagStruct',
+    default='',
+    type=str,
+    help='directive to use to anonymize DICOMs'
+)
 parser.add_argument('-V', '--version', action='version',
                     version=f'%(prog)s {__version__}')
 
@@ -97,10 +108,12 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     #
     # Refer to the documentation for more options, examples, and advanced uses e.g.
     # adding a progress bar and parallelism.
+    if not health_check(options): return
 
     cube_cl = PACSClient(options.CUBEurl, options.CUBEuser, options.CUBEpassword)
     mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.inputJSONfile)
     for input_file, output_file in mapper:
+
         # Open and read the JSON file
         with open(input_file, 'r') as file:
             data = json.load(file)
@@ -128,6 +141,11 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
                 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.")
+                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)
 
 
 def sanitize_for_cube(series: dict) -> dict:
@@ -139,6 +157,24 @@ def sanitize_for_cube(series: dict) -> dict:
     params["StudyInstanceUID"] = series["StudyInstanceUID"]
     return params
 
+def health_check(options) -> bool:
+    """
+    check if connections to pfdcm, orthanc, and CUBE is valid
+    """
+    try:
+        if not options.pluginInstanceID:
+            options.pluginInstanceID = os.environ['CHRIS_PREV_PLG_INST_ID']
+    except Exception as ex:
+        LOG(ex)
+        return False
+    try:
+        # create connection object
+        cube_con = ChrisClient(options.CUBEurl, options.CUBEuser, options.CUBEpassword)
+        cube_con.health_check()
+    except Exception as ex:
+        LOG(ex)
+        return False
+    return True
 
 
 if __name__ == '__main__':

setup.py

@@ -25,7 +25,7 @@ def get_version(rel_path: str) -> str:
     author='FNNDSC',
     author_email='[email protected]',
     url='https://github.com/FNNDSC/pl-reg_',
-    py_modules=['reg_chxr','chris_pacs_service'],
+    py_modules=['reg_chxr','chris_pacs_service','base_client','chrisClient'],
     install_requires=['chris_plugin'],
     license='MIT',
     entry_points={