From 5525d30c60fe6643bcb1882ccdfce45af7b2b5b4 Mon Sep 17 00:00:00 2001 From: Dario <37704177+ddelpiano@users.noreply.github.com> Date: Fri, 20 Feb 2026 16:51:57 +0100 Subject: [PATCH 1/5] Update README.md --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 5ee2b5fe..985515e3 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) From 64adf7c74aa4d75bff39fbe4bd6ffc9a4e12e418 Mon Sep 17 00:00:00 2001 From: Dario Del Piano Date: Mon, 23 Feb 2026 12:55:24 +0100 Subject: [PATCH 2/5] 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 3/5] 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 4/5] 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 5/5] 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)