Adding new/updated copick_project_from_dataportal_0.2.1

cellcanvas · Oct 3, 2024 · 26f555b · 26f555b
1 parent d0c8b20
commit 26f555b
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Showing 4 changed files with 20 additions and 3 deletions.
diff --git a/album_catalog_index.db b/album_catalog_index.db
diff --git a/solutions/copick/project_from_dataportal/CHANGELOG.md b/solutions/copick/project_from_dataportal/CHANGELOG.md
@@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [0.2.1] - 2024-10-03
-Use dict instead of CopickConfig for initial json
+Add retry mechanism when downloading add more logging
 
 ## [0.2.0] - 2024-10-03
 Improve metadata retention and download segmentations

diff --git a/solutions/copick/project_from_dataportal/solution.py b/solutions/copick/project_from_dataportal/solution.py
@@ -17,6 +17,7 @@
     - cryoet-data-portal
     - copick
     - ndjson
+    - tenacity    
 """
 
 def generate_unique_colors(n):
@@ -39,6 +40,22 @@ def run():
     from cryoet_data_portal import Client, Run, AnnotationFile, Tomogram, TiltSeries
     import copick
     from copick.models import CopickPoint, CopickConfig
+    from tenacity import retry, wait_fixed, stop_after_attempt, RetryError
+    import logging
+
+    # Configure logging
+    logging.basicConfig(level=logging.INFO, format='%(asctime)s %(levelname)s ~ %(message)s')
+    logger = logging.getLogger(__name__)
+
+    @retry(wait=wait_fixed(5), stop=stop_after_attempt(3))
+    def safe_query_run(annotation, run):
+        try:
+            if annotation.annotation.tomogram_voxel_spacing.run_id != run.id:
+                return False
+            return True
+        except Exception as e:
+            logger.error(f"Error during query: {e}")
+            raise e
 
     args = get_args()
     dataset_id = args.dataset_id

diff --git a/solutions/copick/project_from_dataportal/solution.yml b/solutions/copick/project_from_dataportal/solution.yml
@@ -20,7 +20,7 @@ args:
   name: static_root
   required: false
   type: string
-changelog: Use dict instead of CopickConfig for initial json
+changelog: Add retry mechanism when downloading add more logging
 cite:
 - text: Cellcanvas and Copick teams
   url: https://cellcanvas.org
@@ -36,6 +36,6 @@ tags:
 - deep learning
 - tomography
 - cryoET
-timestamp: '2024-10-03T11:24:23.511772'
+timestamp: '2024-10-03T12:57:04.006288'
 title: Fetch Data from CryoET Data Portal and Integrate with Copick
 version: 0.2.1