From 64adf7c74aa4d75bff39fbe4bd6ffc9a4e12e418 Mon Sep 17 00:00:00 2001 From: Dario Del Piano Date: Mon, 23 Feb 2026 12:55:24 +0100 Subject: [PATCH 1/4] increasing disk size --- applications/sckanner/deploy/values-prod.yaml | 2 +- applications/sckanner/deploy/values.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/applications/sckanner/deploy/values-prod.yaml b/applications/sckanner/deploy/values-prod.yaml index c19d89d6..97f0cf18 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 c19d89d6..63473023 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} From c5067306c353372d02ac65ccbd5d126ddbfbce11 Mon Sep 17 00:00:00 2001 From: Dario Del Piano Date: Thu, 26 Feb 2026 12:28:48 +0100 Subject: [PATCH 2/4] changing signature to use kwargs --- .../migrations/data/composer_ingestion_script.py | 6 +++++- .../migrations/data/neurondm_ingestion_script.py | 6 +++++- .../ingestion/connectivity_statement_adapter.py | 12 +++++------- 3 files changed, 15 insertions(+), 9 deletions(-) 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 84592cb1..86273411 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 ca83dee2..cb2992ab 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 7be31d91..03312eb0 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__)) From c31cfde62a50d806adcb8be8b3aa972b5a7c692c Mon Sep 17 00:00:00 2001 From: Dario Del Piano Date: Fri, 27 Feb 2026 17:40:40 +0100 Subject: [PATCH 3/4] bumping version up --- applications/sckanner/backend/setup.py | 2 +- applications/sckanner/frontend/package.json | 2 +- applications/sckanner/frontend/src/settings.ts | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/applications/sckanner/backend/setup.py b/applications/sckanner/backend/setup.py index d2eedc9b..df996639 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/frontend/package.json b/applications/sckanner/frontend/package.json index 8f1c5713..b26fe613 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 81d26c59..8c46d359 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; From 715f83a3c661c5081008d098dc6b7c5d4b604280 Mon Sep 17 00:00:00 2001 From: Dario Del Piano Date: Fri, 27 Feb 2026 17:44:08 +0100 Subject: [PATCH 4/4] move to latest neurondm --- applications/sckanner/backend/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/applications/sckanner/backend/requirements.txt b/applications/sckanner/backend/requirements.txt index f4cf39a7..d7c95fec 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)