Use pydna classes for external imports and oligonucleotide hybridization #378

manulera · 2025-11-27T11:15:02Z

No description provided.

…ly failing

codecov · 2025-11-27T11:19:58Z

Codecov Report

❌ Patch coverage is 99.62121% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 97.29%. Comparing base (7137e1d) to head (cce8455).
⚠️ Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/opencloning/ncbi_requests.py	98.24%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #378      +/-   ##
==========================================
+ Coverage   96.83%   97.29%   +0.45%     
==========================================
  Files          28       29       +1     
  Lines        1642     1698      +56     
==========================================
+ Hits         1590     1652      +62     
+ Misses         52       46       -6

Flag	Coverage Δ
unittests	`97.29% <99.62%> (+0.45%)`	⬆️

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Copilot

Pull request overview

This pull request refactors external sequence imports and oligonucleotide hybridization functionality to use pydna classes, improving code organization and type safety. The changes centralize external repository handling through catalog-based lookups and delegate hybridization logic to pydna's native implementations.

Key changes:

Introduced catalog system for external plasmid repositories (SEVA, SnapGene, iGEM2024, OpenDNA Collections)
Refactored external import endpoints to use pydna's RepositoryIdSource and other source models
Replaced custom oligonucleotide hybridization with pydna's oligonucleotide_hybridization function
Updated pydna dependency and opencloning-linkml schema version
Improved error handling with consistent use of FastAPI's HTTPException

Reviewed changes

Copilot reviewed 29 out of 31 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/opencloning/catalogs/init.py	New catalog module for loading plasmid repository mappings from YAML/TSV files
src/opencloning/catalogs/*.yaml	New catalog data files for SnapGene, SEVA, iGEM2024, and OpenDNA collections
src/opencloning/dna_functions.py	Refactored repository functions to return Dseqrecord with pydna source models
src/opencloning/ncbi_requests.py	Added genome annotation querying and region extraction with pydna source integration
src/opencloning/endpoints/external_import.py	Simplified endpoint handlers using centralized error handling and pydna models
src/opencloning/endpoints/no_input.py	Replaced custom hybridization with pydna's implementation
src/opencloning/endpoints/endpoint_utils.py	Updated `format_products` to accept source_id and handle pydna sources
scripts/update_catalogs.py	New script for automated catalog updates from upstream sources
tests/*	Updated tests to reflect API changes and new error messages
pyproject.toml	Updated pydna and opencloning-linkml dependencies

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Copilot · 2025-11-28T18:56:36Z

src/opencloning/catalogs/__init__.py

+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_openDNA_collections_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_iGEM2024_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)


Use yaml.safe_load() instead of yaml.load() with FullLoader. The yaml.load() function with FullLoader can execute arbitrary Python code and poses a security risk. yaml.safe_load() is the recommended secure alternative for loading YAML files.

Suggested change

return yaml.load(f, Loader=yaml.FullLoader)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

return yaml.safe_load(f)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

Copilot · 2025-11-28T18:56:37Z

scripts/update_catalogs.py

+        response = await client.get(
+            'https://raw.githubusercontent.com/manulera/SnapGene_crawler/refs/heads/master/index.yaml'
+        )
+        data = yaml.load(response.text, Loader=yaml.FullLoader)


Use yaml.safe_load() instead of yaml.load() with FullLoader. The yaml.load() function with FullLoader can execute arbitrary Python code and poses a security risk. yaml.safe_load() is the recommended secure alternative for loading YAML files.

Suggested change

data = yaml.load(response.text, Loader=yaml.FullLoader)

data = yaml.safe_load(response.text)

Copilot · 2025-11-28T18:56:37Z

src/opencloning/catalogs/__init__.py

+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_openDNA_collections_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_iGEM2024_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)


Use yaml.safe_load() instead of yaml.load() with FullLoader. The yaml.load() function with FullLoader can execute arbitrary Python code and poses a security risk. yaml.safe_load() is the recommended secure alternative for loading YAML files.

Suggested change

return yaml.load(f, Loader=yaml.FullLoader)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

return yaml.safe_load(f)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

Copilot · 2025-11-28T18:56:37Z

src/opencloning/catalogs/__init__.py

+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_openDNA_collections_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)
+
+
+def get_iGEM2024_catalog():
+    catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')
+    with open(catalog_path, 'r') as f:
+        return yaml.load(f, Loader=yaml.FullLoader)


Use yaml.safe_load() instead of yaml.load() with FullLoader. The yaml.load() function with FullLoader can execute arbitrary Python code and poses a security risk. yaml.safe_load() is the recommended secure alternative for loading YAML files.

Suggested change

return yaml.load(f, Loader=yaml.FullLoader)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.load(f, Loader=yaml.FullLoader)

return yaml.safe_load(f)

def get_openDNA_collections_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'openDNA_collections.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

def get_iGEM2024_catalog():

catalog_path = os.path.join(os.path.dirname(__file__), 'igem2024.yaml')

with open(catalog_path, 'r') as f:

return yaml.safe_load(f)

tests/test_endpoints_no_input.py

manulera added 10 commits November 25, 2025 18:26

wip towards simplifying import of external seqs

8c58930

update pydna

1ba5e4f

better addgene

a0a093d

add oligo hybridization and improve common funciton, SEVA tests weird…

64d7513

…ly failing

update SEVA plasmids

8671c0f

test SEVA plasmid that does not have url in data.js

3ab69d5

wip refactor snapgene

bf9ceb8

reformat wekwikgene and snapgene

ee854e5

simplify repository error handling

97ebefb

add support for OpenDNA collections

675c2df

manulera mentioned this pull request Nov 27, 2025

Small changes to adapt to pydna usage OpenCloning/OpenCloning_LinkML#67

Merged

update data model version

3912648

manulera added 9 commits November 27, 2025 11:43

improve test coverage + better handling of errors when parsing files

9e857fa

iGEM support and some fixes

9aff17b

iGEM support and some fixes

a0b28a5

added euroscarg

bc9ac9b

working on genbank endpoint

d5bc03a

improve error handling

5e9fc44

working on genome region, exception handling makes tests fail

09076f4

simplify http error handling

c3ab878

fix error handling + reduce reruns to 2

d062be2

manulera requested a review from Copilot November 28, 2025 18:54

Copilot started reviewing on behalf of manulera November 28, 2025 18:54 View session

Copilot finished reviewing on behalf of manulera November 28, 2025 18:55

Copilot AI reviewed Nov 28, 2025

View reviewed changes

manulera added 3 commits November 28, 2025 19:03

fix vulns suggested by copilot

715f5cd

improve test coverage

ea5fa7b

improve test coverage

cce8455

manulera merged commit e15020e into master Dec 1, 2025
9 checks passed

manulera deleted the wip-better-imports2 branch December 1, 2025 10:02

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	data = yaml.load(response.text, Loader=yaml.FullLoader)
	data = yaml.safe_load(response.text)

Use pydna classes for external imports and oligonucleotide hybridization #378

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