pass server info as kwarg

aliby/io/omero.py

@@ -31,8 +31,8 @@ class Argo:
 
 
 class Dataset(Argo):
-    def __init__(self, expt_id):
-        super().__init__()
+    def __init__(self, expt_id, **server_info):
+        super().__init__(**server_info)
         self.expt_id = expt_id
         self._files = None
 
@@ -87,8 +87,8 @@ class Dataset(Argo):
 
 
 class Image(Argo):
-    def __init__(self, image_id):
-        super().__init__()
+    def __init__(self, image_id, **server_info):
+        super().__init__(**server_info)
         self.image_id = image_id
         self._image_wrap = None
 

aliby/pipeline.py

@@ -57,7 +57,7 @@ class PipelineParameters(ParametersABC):
         """
         expt_id = general.get("expt_id", 19993)
         directory = Path(general.get("directory", "../data"))
-        with Dataset(int(expt_id)) as conn:
+        with Dataset(int(expt_id), **general.get("server_info")) as conn:
             directory = directory / conn.unique_name
             if not directory.exists():
                 directory.mkdir(parents=True)
@@ -132,7 +132,7 @@ class Pipeline(ProcessABC):
 
         print("Searching OMERO")
         # Do all initialis
-        with Dataset(int(expt_id)) as conn:
+        with Dataset(int(expt_id), **self.general["server_info"]) as conn:
             image_ids = conn.get_images()
             directory = root_dir / conn.unique_name
             if not directory.exists():
@@ -165,7 +165,7 @@ class Pipeline(ProcessABC):
         earlystop = general_config["earlystop"]
         try:
             directory = general_config["directory"]
-            with Image(image_id) as image:
+            with Image(image_id, **self.general['server_info']) as image:
                 filename = f"{directory}/{image.name}.h5"
                 try:
                     os.remove(filename)