From c49dae8a6647da64a41af336411bf99ef7d22129 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Mon, 23 Jan 2023 17:39:37 +0000
Subject: [PATCH] change(pipe): move server_info params one lvl up
---
src/aliby/pipeline.py | 31 ++++++++++++++++++-------------
1 file changed, 18 insertions(+), 13 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 26e9b9dc..586453f6 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -75,9 +75,7 @@ class PipelineParameters(ParametersABC):
directory = Path(general.get("directory", "../data"))
- with dispatch_dataset(
- expt_id, **general.get("server_info", {})
- ) as conn:
+ with dispatch_dataset(expt_id, **get_server_info(general)) as conn:
directory = directory / conn.unique_name
if not directory.exists():
directory.mkdir(parents=True)
@@ -286,17 +284,16 @@ class Pipeline(ProcessABC):
# Steps: all holds general tasks
# steps: strain_name holds task for a given strain
config = self.parameters.to_dict()
- expt_id = config["general"]["id"]
- distributed = config["general"]["distributed"]
- pos_filter = config["general"]["filter"]
- root_dir = Path(config["general"]["directory"])
+ general = config["general"]
+ expt_id = general["id"]
+ distributed = general["distributed"]
+ pos_filter = general["filter"]
+ root_dir = Path(general["directory"])
print("Searching OMERO")
# Do all all initialisations
- with dispatch_dataset(
- expt_id, **self.general.get("server_info", {})
- ) as conn:
+ with dispatch_dataset(expt_id, **get_server_info(general)) as conn:
image_ids = conn.get_images()
directory = self.store or root_dir / conn.unique_name
@@ -309,7 +306,7 @@ class Pipeline(ProcessABC):
# Modify to the configuration
self.parameters.general["directory"] = str(directory)
- config["general"]["directory"] = directory
+ general["directory"] = directory
self.setLogger(directory)
@@ -395,7 +392,7 @@ class Pipeline(ProcessABC):
min_process_from = min(process_from.values())
with get_image_class(image_id)(
- image_id, **self.general.get("server_info", {})
+ image_id, **get_server_info(self.general)
) as image:
# Initialise Steps
@@ -649,7 +646,7 @@ class Pipeline(ProcessABC):
trackers_state: t.List[np.ndarray] = []
with get_image_class(image_id)(
- image_id, **self.general.get("server_info", {})
+ image_id, **get_server_info(general_config)
) as image:
filename = Path(f"{directory}/{image.name}.h5")
meta = MetaData(directory, filename)
@@ -724,3 +721,11 @@ class Pipeline(ProcessABC):
def _close_session(session):
if session:
session.close()
+
+
+def get_server_info(general: dict) -> t.Dict[str, int or str]:
+ return {
+ k: general[k]
+ for k in ("host", "username", "password")
+ if general.get(k)
+ }
--
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