From 8cbe776ce8d97db7074896bbaa02f778b36ef43b Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Wed, 14 Aug 2024 09:35:41 +0200
Subject: [PATCH] add some diagnostics

---
 src/depiction_targeted_preprocbatch/executor.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/depiction_targeted_preprocbatch/executor.py b/src/depiction_targeted_preprocbatch/executor.py
index 983e970..3dbda67 100644
--- a/src/depiction_targeted_preprocbatch/executor.py
+++ b/src/depiction_targeted_preprocbatch/executor.py
@@ -19,6 +19,7 @@
 from depiction_targeted_preprocbatch.batch_dataset import BatchDataset
 from depiction_targeted_preprocbatch.job_export_results import JobExportResults
 from depiction_targeted_preprocbatch.job_prepare_inputs import JobPrepareInputs
+from loguru import logger
 
 
 @dataclass
@@ -81,13 +82,16 @@ def run_job(self, job: BatchJob) -> None:
         sample_dir.mkdir(parents=True, exist_ok=True)
 
         # stage input
+        logger.debug(f"Preparing inputs for {job}")
         JobPrepareInputs.prepare(job=job, sample_dir=sample_dir)
 
         # invoke the pipeline
+        logger.debug(f"Running pipeline for {job}")
         result_files = self._determine_result_files(job_dir=job_dir)
         SnakemakeInvoke().invoke(work_dir=job_dir, result_files=result_files)
 
         # export the results
+        logger.debug(f"Exporting results for {job}")
         # TODO do not hardcode id
         output_storage = Storage.find(id=2, client=self._client)
         JobExportResults.export(