From 1ac94283733f07cf05895d17c52571c588cb8547 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 18:22:09 +0000
Subject: [PATCH] fix(pipe): update calls to server_info data
---
src/aliby/pipeline.py | 40 +++++++++++++++++-----------------------
1 file changed, 17 insertions(+), 23 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index 3924715b..2977cada 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -76,7 +76,10 @@ class PipelineParameters(ParametersABC):
directory = Path(general.get("directory", "../data"))
- with dispatch_dataset(expt_id, **get_server_info(general)) as conn:
+ with dispatch_dataset(
+ expt_id,
+ **{k: general.get(k) for k in ("host", "username", "password")},
+ ) as conn:
directory = directory / conn.unique_name
if not directory.exists():
directory.mkdir(parents=True)
@@ -286,15 +289,16 @@ class Pipeline(ProcessABC):
"""
config = self.parameters.to_dict()
- general = config["general"]
- expt_id = general["id"]
- distributed = general["distributed"]
- pos_filter = general["filter"]
- root_dir = Path(general["directory"])
-
- dispatcher = dispatch_dataset(
- expt_id, **self.general.get("server_info", {})
- )
+ expt_id = config["general"]["id"]
+ distributed = config["general"]["distributed"]
+ pos_filter = config["general"]["filter"]
+ root_dir = Path(config["general"]["directory"])
+ self.server_info = {
+ k: config["general"].get(k)
+ for k in ("host", "username", "password")
+ }
+
+ dispatcher = dispatch_dataset(expt_id, **self.server_info)
logging.getLogger("aliby").info(
f"Fetching data using {dispatcher.__class__.__name__}"
)
@@ -313,7 +317,7 @@ class Pipeline(ProcessABC):
# Modify to the configuration
self.parameters.general["directory"] = str(directory)
- general["directory"] = directory
+ config["general"]["directory"] = directory
self.setLogger(directory)
@@ -399,7 +403,7 @@ class Pipeline(ProcessABC):
min_process_from = min(process_from.values())
with get_image_class(image_id)(
- image_id, **get_server_info(self.general)
+ image_id, **self.server_info
) as image:
# Initialise Steps
@@ -652,9 +656,7 @@ class Pipeline(ProcessABC):
directory = general_config["directory"]
trackers_state: t.List[np.ndarray] = []
- with get_image_class(image_id)(
- image_id, **get_server_info(general_config)
- ) as image:
+ with get_image_class(image_id)(image_id, **self.server_info) as image:
filename = Path(f"{directory}/{image.name}.h5")
meta = MetaData(directory, filename)
@@ -730,11 +732,3 @@ 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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