From d9fa6f0be45909407715300b8047b9395903b0be Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 24 Jan 2023 12:27:27 +0000
Subject: [PATCH] clean(pipe): remove unused comments
---
src/aliby/pipeline.py | 25 ++++++++++++++-----------
1 file changed, 14 insertions(+), 11 deletions(-)
diff --git a/src/aliby/pipeline.py b/src/aliby/pipeline.py
index b68180f0..72eff003 100644
--- a/src/aliby/pipeline.py
+++ b/src/aliby/pipeline.py
@@ -68,7 +68,6 @@ class PipelineParameters(ParametersABC):
baby={},
extraction={},
postprocessing={},
- # reporting={},
):
expt_id = general.get("expt_id", 19993)
if isinstance(expt_id, PosixPath):
@@ -189,7 +188,6 @@ class Pipeline(ProcessABC):
folder, file_level: str = "INFO", stream_level: str = "WARNING"
):
- # create logger for aliby 'spam_application'
logger = logging.getLogger("aliby")
logger.setLevel(getattr(logging, file_level))
formatter = logging.Formatter(
@@ -283,22 +281,27 @@ class Pipeline(ProcessABC):
return logging.getLogger("aliby")
def run(self):
- # Config holds the general information, use in main
- # Steps holds the description of tasks with their parameters
- # Steps: all holds general tasks
- # steps: strain_name holds task for a given strain
+ """
+ Config holds the general information, use in main
+ 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"])
- print("Searching OMERO")
+ dispatcher = dispatch_dataset(
+ expt_id, **self.general.get("server_info", {})
+ )
+ logging.getLogger("aliby").INFO(
+ f"Fetching data using {dispatcher.__class__.__name__}"
+ )
# Do all all initialisations
- with dispatch_dataset(
- expt_id, **self.general.get("server_info", {})
- ) as conn:
+ with dispatcher as conn:
image_ids = conn.get_images()
directory = self.store or root_dir / conn.unique_name
@@ -526,7 +529,7 @@ class Pipeline(ProcessABC):
self._log("Analysis finished successfully.", "info")
return 1
- except Exception as e: # bug during setup or runtime
+ except Exception as e: # Catch bugs during setup or runtime
logging.exception(
f"{name}: Exception caught.",
exc_info=True,
--
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