Merge branch 'master' of github.com:mskcc/beagle into feature/nucleo_snv

.github/workflows/github-actions.yml

@@ -0,0 +1,56 @@
+on: push
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres:latest
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: github_actions
+        ports:
+          - 5432:5432
+        # needed because the postgres container does not provide a healthcheck
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.8
+    - name: python ldap
+      run: sudo apt-get install libsasl2-dev python3-dev libldap2-dev libssl-dev #adding package for python ldap error 
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        python -m pip install python-ldap
+        pip install -r requirements-dev.txt
+    - name: Run migrations
+      run: python manage.py migrate
+      env:
+          BEAGLE_DB_NAME: github_actions
+          BEAGLE_DB_PASSWORD: postgres
+          BEAGLE_DB_USERNAME: postgres
+    - name: Run test
+      run: |
+        python manage.py test
+      env:
+          BEAGLE_DB_NAME: github_actions
+          BEAGLE_DB_PASSWORD: postgres
+          BEAGLE_DB_USERNAME: postgres
+          BEAGLE_DB_PORT: 5432
+          BEAGLE_NOTIFIER_ACTIVE: False
+          TMPDIR: /tmp
+          BEAGLE_SHARED_TMPDIR: $TMPDIR
+          ENVIRONMENT: 'dev'
+          BEAGLE_PRIMARY_ID_REGEX: "^(0\\d{4}|[1-9]\\d{4,})(|_[B-Z]|_[A-Z]{2,})_\\d+$"
+    - name: Black check
+      uses: psf/black@stable
+      with:
+        options: "--check"
+        version: "22.3.0"

beagle/__init__.py

@@ -1 +1 @@
-__version__ = "1.88.0"
+__version__ = "1.91.2"

beagle_etl/fixtures/beagle_etl.operator.json

@@ -251,5 +251,16 @@
       "version": "v1.2.0",
       "slug": "ArgosBamOperator_v1_0_0"
     }
+  },
+  {
+    "model": "beagle_etl.operator",
+    "pk": 25,
+    "fields": {
+      "active": true,
+      "recipes": "[\"None\"]",
+      "class_name": "runner.operator.copy_outputs_operator.v2_1_0.copy_outputs_operator.CopyOutputsOperator",
+      "version": "v2.1.0",
+      "slug": "CopyOutputsOperator_v2.1.0"
+    }
   }
 ]

file_system/helper/access_helper.py

@@ -81,8 +81,14 @@ def construct_csv(self):
         """
 
         # get fastq metadata for a given request
-        fastqs = File.objects.filter(file_group__slug="lims", request_id__in=self.request_ids)
-        fastq_metadata = [fastq.filemetadata_set.values()[0]["metadata"] for fastq in fastqs]
+        files = FileRepository.filter(
+            file_group=settings.IMPORT_FILE_GROUP,
+            metadata={settings.IGO_COMPLETE_METADATA_KEY: True},
+            filter_redact=True,
+        ).all()
+        fastqs = files.filter(metadata__igoRequestId__in=self.request_ids)
+        fastq_metadata = [fastq.metadata for fastq in fastqs]
+        fastq_metadata = sorted(fastq_metadata, key=lambda d: d["cmoSampleName"])
         cmoPatientId = set([fastq["cmoPatientId"] for fastq in fastq_metadata])
         # get DMP BAM file group
         dmp_bams = FileRepository.filter(file_group=settings.DMP_BAM_FILE_GROUP)