diff --git a/README.md b/README.md index 5ee2b5f..985515e 100644 --- a/README.md +++ b/README.md @@ -3,3 +3,5 @@ Sckanner (Beta) is a web based platform to visualize tool and a key component of the SPARC Program is SCKAN. It is a semantic store housing a comprehensive knowledge base of autonomic nervous system (ANS) and peripheral nervous system (PNS) nerve to end organ connectivity. Connectivity information is derived from SPARC experts, SPARC data, literature and textbooks. SCKAN supports reasoning and offers powerful query and visualization capabilities. To read more about how to setup the sckanner locally checkout - [Setup README](./applications/sckanner/README.md) + +To know more about the application and how to use it please checkout the [Sckanner handbook](https://docs.google.com/document/u/3/d/e/2PACX-1vSutrIHER8Ff7k5rEIcP_bH9eAC_pk0U-KKrmSDG0x3lbnY6WXpBqy6stihz4jXXQ93IqrnHHnZ_3tb/pub#h.13iq9hm69tnb) 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;