Add ELN collection export #1371
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BenjaminCharmes
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Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #1371 +/- ##
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- Coverage 80.10% 79.95% -0.15%
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Files 70 74 +4
Lines 4759 4965 +206
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+ Hits 3812 3970 +158
- Misses 947 995 +48
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| Committer | Ben Charmes |
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ml-evs
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Oct 17, 2025
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This looks fantastic, thanks @BenjaminCharmes!
Just writing a couple of points here that we can discuss:
- configuring amount of resources APScheduler is allowed to use
- using pydantic models rather than direct database queries to create items etc.
- a few bits of permissions we need to be careful with
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| collection_exists = flask_mongo.db.collections.find_one({"collection_id": collection_id}) | ||
| if not collection_exists: | ||
| return jsonify({"status": "error", "message": "Collection not found"}), 404 | ||
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|
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| collection_with_perms = flask_mongo.db.collections.find_one( | ||
| {"collection_id": collection_id, **get_default_permissions(user_only=True)} | ||
| ) | ||
| if not collection_with_perms: | ||
| return jsonify({"status": "error", "message": "Access denied"}), 403 |
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Suggested change
| collection_exists = flask_mongo.db.collections.find_one({"collection_id": collection_id}) | |
| if not collection_exists: | |
| return jsonify({"status": "error", "message": "Collection not found"}), 404 | |
| collection_with_perms = flask_mongo.db.collections.find_one( | |
| {"collection_id": collection_id, **get_default_permissions(user_only=True)} | |
| ) | |
| if not collection_with_perms: | |
| return jsonify({"status": "error", "message": "Access denied"}), 403 | |
| collection_with_perms = flask_mongo.db.collections.find_one( | |
| {"collection_id": collection_id, **get_default_permissions(user_only=True)} | |
| ) | |
| if not collection_with_perms: | |
| return jsonify({"status": "error", "message": "Collection not found"}), 404 |
Better not to leak IDs that exist but the user does not have permission for, so just treat missing ID as 404
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Can probably also set user_only=False
ml-evs
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Oct 17, 2025
| source_path = Path(file_data["location"]) | ||
| if source_path.exists(): | ||
| dest_file = item_folder / file_data["name"] | ||
| shutil.copy2(source_path, dest_file) |
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Somehow the actual raw data files are not making it into the .eln file when I try to export them
ml-evs
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Oct 28, 2025
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Thanks @BenjaminCharmes -- will test locally then merge.
Potential next steps:
- adding the same button for 1 sample
- building on 1, "Export" button that opens a modal for a sample, where the user can export a graph of related samples, and potentially automatically create a collection for it
First attempt export as ELN
Use APScheduler Use APScheduler Use APScheduler Use APScheduler Use APScheduler Use APScheduler
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Closes #1332 & #1046
Implements a new API endpoint and background process to export full collections as .eln files