Merge pull request #98 from Clinical-Genomics/update_mongodb

Unfreeze pymongo and add integration test with MongoDB v7

.github/workflows/integration_test.yml

@@ -0,0 +1,39 @@
+name: Integration tests
+on: [pull_request]
+jobs:
+  integration_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        mongodb-version: ['7']
+
+    steps:
+      - name: Start MongoDB
+        uses: supercharge/mongodb-github-action@1.10.0
+        with:
+          mongodb-version: ${{ matrix.mongodb-version }}
+
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Conda and install python
+        uses: s-weigand/setup-conda@v1
+        with:
+          activate-conda: true
+          python-version: 3.11
+
+      - name: Download Picard
+        uses: wei/wget@v1
+        with:
+          args: -O picard.jar https://github.com/broadinstitute/picard/releases/download/2.26.6/picard.jar
+
+      - name: Install repo and its dependencies
+        run: |
+          pip install -r requirements.txt
+          pip install -e .
+
+      - name: Test run pipeline
+        run: |
+          mutacc --root-dir . extract --picard-executable picard.jar --padding 600 -c mutacc/resources/case.yaml
+          mutacc --root-dir . db import imports/demo_trio_import_mutacc.json
+          mutacc --root-dir . db export --all-variants --member child --proband --sample-name child

CHANGELOG.md

@@ -2,11 +2,14 @@
 All notable changes to this project will be documented in this file.
 
 ## [unreleased]
+### Added
+- Integration test with MongoDB v7 
 ### Changed
 - Moved tests and coverage from Travis to GitHub actions
 - Updated python version and versions of some GitHub actions
 - Unfreeze cyvcf2 lib to be able to install the software with Python>=3.8
 - Installation instructions on README page to install mutacc using Python 3.8
+- Unfreeze pymongo requirement and removed deprecated pymongo code to support latest version of MongoDB
 ### Fixed
 - Badge on Readme page
 - GitHub action to push the right image to Docker Hub

mutacc/mutaccDB/db_adapter.py

@@ -68,20 +68,10 @@ def add_case(self, case):
 
         self.cases_collection.insert_one(case)
 
-    def case_exists(self, case_id):
-        """
-            Check if collection with field 'case_id': case_id exists.
-
-            Args:
-                case_id(str): name of case
-            Returns:
-                exists(bool): True if exists, else False
-        """
-
-        if self.cases_collection.find({"case_id": case_id}).count() > 0:
-            return True
+    def case_exists(self, case_id: str) ->  bool:
+        """Check if collection with field 'case_id': case_id exists."""
 
-        return False
+        return self.cases_collection.count_documents({"case_id": case_id}) > 0
 
     def find_cases(self, query):
 

requirements.txt

@@ -6,4 +6,4 @@ cyvcf2
 mongo_adapter>=0.3.3
 ped_parser
 PyYaml>=5.1
-pymongo<4.0
+pymongo