diff --git a/applications/sckanner/backend/requirements.txt b/applications/sckanner/backend/requirements.txt index f4cf39a..d7c95fe 100644 --- a/applications/sckanner/backend/requirements.txt +++ b/applications/sckanner/backend/requirements.txt @@ -2,7 +2,7 @@ pydantic==2.9.2 django-treebeard==4.7.1 django-ninja pyontutils==0.1.38 -neurondm==0.1.8 +neurondm==0.1.10 jsonschema==4.24.0 h11>=0.16.0 # Fix CVE-2025-43859 (HTTP request smuggling vulnerability) setuptools>=78.1.1 # Fix CVE-2025-47273 (path traversal vulnerability) diff --git a/applications/sckanner/backend/sckanner/migrations/data/composer_ingestion_script.py b/applications/sckanner/backend/sckanner/migrations/data/composer_ingestion_script.py index 84592cb..8627341 100644 --- a/applications/sckanner/backend/sckanner/migrations/data/composer_ingestion_script.py +++ b/applications/sckanner/backend/sckanner/migrations/data/composer_ingestion_script.py @@ -123,7 +123,11 @@ def fetch_paginated_data(population_ids: list[str], stdout=None): return detailed_data -def get_statements(version="", stdout=None, a_b_via_c_json_file_path=None): +def get_statements(version="", **kwargs): + # Extract parameters from kwargs with defaults + stdout = kwargs.get('stdout', None) + a_b_via_c_json_file_path = kwargs.get('a_b_via_c_json_file_path', None) + try: # Step 1: Load raw JSON from file or external source if a_b_via_c_json_file_path: diff --git a/applications/sckanner/backend/sckanner/migrations/data/neurondm_ingestion_script.py b/applications/sckanner/backend/sckanner/migrations/data/neurondm_ingestion_script.py index ca83dee..cb2992a 100644 --- a/applications/sckanner/backend/sckanner/migrations/data/neurondm_ingestion_script.py +++ b/applications/sckanner/backend/sckanner/migrations/data/neurondm_ingestion_script.py @@ -1082,7 +1082,11 @@ def refine_statement(statement: Dict) -> Dict: ## Based on: ## https://github.com/tgbugs/pyontutils/blob/30c415207b11644808f70c8caecc0c75bd6acb0a/neurondm/docs/composer.py#L668-L698 -def get_statements(version="", local=False, full_imports=[], label_imports=[]): +def get_statements(version="", **kwargs): + # Extract parameters from kwargs with defaults + local = kwargs.get('local', False) + full_imports = kwargs.get('full_imports', []) + label_imports = kwargs.get('label_imports', []) config = Config('random-merge') g = OntGraph() # load and query graph diff --git a/applications/sckanner/backend/sckanner/services/ingestion/connectivity_statement_adapter.py b/applications/sckanner/backend/sckanner/services/ingestion/connectivity_statement_adapter.py index 7be31d9..03312eb 100644 --- a/applications/sckanner/backend/sckanner/services/ingestion/connectivity_statement_adapter.py +++ b/applications/sckanner/backend/sckanner/services/ingestion/connectivity_statement_adapter.py @@ -40,15 +40,13 @@ def _parse_and_validate_statements( # Get statements from the uploaded module if hasattr(module, "get_statements") and callable(module.get_statements): - # Pass the a_b_via_c_json_file path if available - a_b_via_c_json_file_path = None + # Prepare kwargs to pass to get_statements + kwargs = {} if self.snapshot.a_b_via_c_json_file: - a_b_via_c_json_file_path = self.snapshot.a_b_via_c_json_file.path + kwargs['a_b_via_c_json_file_path'] = self.snapshot.a_b_via_c_json_file.path - statements = module.get_statements( - self.snapshot.version, - a_b_via_c_json_file_path=a_b_via_c_json_file_path - ) + # Call get_statements with version and any additional kwargs + statements = module.get_statements(self.snapshot.version, **kwargs) try: # Validate the statements against the schema current_path = os.path.dirname(os.path.abspath(__file__)) diff --git a/applications/sckanner/backend/setup.py b/applications/sckanner/backend/setup.py index d2eedc9..df99663 100644 --- a/applications/sckanner/backend/setup.py +++ b/applications/sckanner/backend/setup.py @@ -5,7 +5,7 @@ from setuptools import find_packages, setup NAME = "sckanner" -VERSION = "3.1.0" +VERSION = "3.1.1" # To install the library, run the following # diff --git a/applications/sckanner/deploy/values-prod.yaml b/applications/sckanner/deploy/values-prod.yaml index c19d89d..97f0cf1 100644 --- a/applications/sckanner/deploy/values-prod.yaml +++ b/applications/sckanner/deploy/values-prod.yaml @@ -15,7 +15,7 @@ harness: mountpath: /usr/src/app/persistent name: sckanner-ingestion-files auto: true - size: 100Mi + size: 5Gi usenfs: false livenessProbe: {path: /api/live} readinessProbe: {path: /api/ready} diff --git a/applications/sckanner/deploy/values.yaml b/applications/sckanner/deploy/values.yaml index c19d89d..6347302 100644 --- a/applications/sckanner/deploy/values.yaml +++ b/applications/sckanner/deploy/values.yaml @@ -15,7 +15,7 @@ harness: mountpath: /usr/src/app/persistent name: sckanner-ingestion-files auto: true - size: 100Mi + size: 1Gi usenfs: false livenessProbe: {path: /api/live} readinessProbe: {path: /api/ready} diff --git a/applications/sckanner/frontend/package.json b/applications/sckanner/frontend/package.json index 8f1c571..b26fe61 100644 --- a/applications/sckanner/frontend/package.json +++ b/applications/sckanner/frontend/package.json @@ -1,7 +1,7 @@ { "name": "sckan-explorer", "private": true, - "version": "3.1.0", + "version": "3.1.1", "type": "module", "scripts": { "dev": "vite", diff --git a/applications/sckanner/frontend/src/settings.ts b/applications/sckanner/frontend/src/settings.ts index 81d26c5..8c46d35 100644 --- a/applications/sckanner/frontend/src/settings.ts +++ b/applications/sckanner/frontend/src/settings.ts @@ -75,7 +75,7 @@ export const STRINGS_NUMBERS = [ ]; // Get version from Vite environment variable (set at build time) -export const SCKANNER_VERSION = import.meta.env.VITE_APP_VERSION || '3.1.0'; +export const SCKANNER_VERSION = import.meta.env.VITE_APP_VERSION || '3.1.1'; export const COMPOSER_VERSION = '6.0.0'; export const NEURONDM_VERSION = '2025-10-27'; export const KNOWLEDGE_STATEMENTS_BATCH_SIZE = 15;