fixinig predefined algorithms constant

cosapweb/api/constants.py

@@ -97,7 +97,7 @@ class VCFHeaders(Enum):
     SAMPLE = "SAMPLE"
 
 class ProjectTypeAlgorithms(Enum):
-    ProjectTypes.SOMATIC.value = {
+    SOMATIC = {
          ProjectAlgorithmKeys.ALIGNER: [
             "BWA2"
         ],
@@ -106,7 +106,7 @@ class ProjectTypeAlgorithms(Enum):
         ],
         ProjectAlgorithmKeys.VARIANT_ANNOTATOR: []
     }
-    ProjectTypes.GERMLINE.value = {
+    GERMLINE = {
         ProjectAlgorithmKeys.ALIGNER: [
             "BWA2"
         ],

cosapweb/api/helpers/project_helpers.py

@@ -191,3 +191,17 @@ def get_or_create_project_summary(project_id):
     project_summary = ProjectSummary.objects.get_or_create(project=project)[0]
 
     return project_summary
+
+def remove_project_data_and_snvs(project_id):
+    """
+    Removes project data and snvs.
+    """
+
+    project = Project.objects.get(id=project_id)
+    project_snvs = ProjectSNVs.objects.get(project=project)
+    project_summary = ProjectSummary.objects.get(project=project)
+    project_snv_data = ProjectSNVData.objects.get(project=project)
+
+    project_snvs.delete()
+    project_summary.delete()
+    project_snv_data.delete()

cosapweb/api/views.py

@@ -36,7 +36,7 @@
 
 from ..common.utils import (convert_file_relative_path_to_absolute_path,
                             create_chonky_filemap)
-from .helpers.project_helpers import get_project_dir
+from .helpers.project_helpers import get_project_dir, remove_project_data_and_snvs
 from .constants import ProjectStatus, ProjectTypeAlgorithms, ProjectTypes
 
 USER = get_user_model()
@@ -258,6 +258,9 @@ def rerun_project(self, request, pk=None):
         project.status = ProjectStatus.PENDING.value
         project.save()
 
+        # Remove project data and snvs
+        remove_project_data_and_snvs(pk)
+
         return HttpResponse(status=status.HTTP_200_OK)
 
     @action(detail=True, methods=["post"])

cosapweb/settings.py

@@ -234,3 +234,5 @@
 #         },
 #     },
 # }
+
+DATA_UPLOAD_MAX_NUMBER_FIELDS = 100000

docker-compose.yaml

@@ -20,7 +20,7 @@ services:
   db:
     image: postgres
     volumes:
-      - postgres-data:/var/lib/postgresql/data
+      - ./data/db:/var/lib/postgresql/data
     environment:
       - POSTGRES_NAME=${COSAP_POSTGRES_NAME}
       - POSTGRES_USER=${COSAP_POSTGRES_USER}