Arc schema

.github/workflows/get_schema_on_tag.yml

@@ -0,0 +1,42 @@
+name: Run Python Script on Tag
+
+on:
+  push:
+    tags:
+      - '*'  # Trigger on all tags
+
+permissions:
+  contents: write
+
+jobs:
+  run-script:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: Run script with tag
+        run: |
+          TAG_NAME=${GITHUB_REF#refs/tags/}
+          echo "Running script with tag: $TAG_NAME"
+          python schemas/isaric_schema.py "$TAG_NAME"
+
+      - name: Commit and push changes
+        run: |
+            git config --global user.name "github-actions[bot]"
+            git config --global user.email "github-actions[bot]@users.noreply.github.com"
+            git add arc_$TAG_NAME_isaric_long_schema.json
+            git commit -m "Add generated schema for tag $TAG_NAME" || echo "No changes to commit"
+            git push
+        env:
+            TAG_NAME: ${GITHUB_REF#refs/tags/}

.gitignore

@@ -0,0 +1,6 @@
+.venv
+.vscode/
+.DS_Store
+
+__pycache__/
+*.pyc

CHANGELOG.md

@@ -12,3 +12,50 @@ ARC v1.1.3 delivers significant updates to support dengue research and harmonisa
 - Restructured **Dengue ARChetype CRF**, aligning variable definitions with current WHO classification.  
 - Introduced **recommended outcomes for Dengue**, enabling more standardised reporting across studies.  
 
+## ARC v1.1.1 (02 Jul 2025)
+
+### Overview
+In ARC v1.1.1, variables in the ONSET & PRESENTATION section were updated to use the prefix pres_ instead of date_ to better reflect their meaning..
+
+### Variable‑Level Updates
+Prefix change in ONSET & PRESENTATION section: Variables previously using the date_ prefix were renamed to pres_ (e.g., date_adm, → pres_adm).
+
+### Interoperability
+Standardised term code lists have been revised to align with SNOMED‑CT, LOINC, and UMLS.
+
+## ARC v1.1.0 (09 May 2025)
+
+### Overview
+ARC v1.1.0 delivers a substantial expansion of the data model, introduces a dedicated **Acute Respiratory Infection (ARI)** preset, and separates **signs** from **symptoms** to improve semantic clarity and analytic power.
+
+### Column / Preset Changes
+| Category | Details |
+|---|---|
+| **New presets / columns (1)** | `preset_ARChetype Syndromic CRF_ARI` **(new)** |
+| **Renamed / (4)** | `preset_ARChetype CRF_Covid` → `preset_ARChetype Disease CRF_Covid`<br>`preset_ARChetype CRF_Dengue` → `preset_ARChetype Disease CRF_Dengue`<br>`preset_ARChetype CRF_Mpox` → `preset_ARChetype Disease CRF_Mpox`<br>`preset_ARChetype CRF_H5Nx` → `preset_ARChetype Disease CRF_H5Nx`|
+
+### Variable‑Level Updates
+- **Added variables**: 472 (e.g., `adsym_blurryvis`, `adsym_cough_type`).
+- **Removed variables**: 303 (e.g., `adasses_bacsi_oth`, `adasses_lymph`).
+- **Field‑type changes**: 84 variables.
+- **List updates**: 652 variables.
+- **Answer‑choice updates**: 68 variables.
+- **Signs vs Symptoms**: Clinical **signs** are now represented by brand‑new `sign_*` variables and no longer stored in `sympt_*`, clearly separating objective observations from patient‑reported symptoms.
+
+### Interoperability
+Standardised term code lists have been revised to align with **SNOMED‑CT**, **LOINC**, and **UMLS**.
+
+## ARC v1.0.4  (04 Mar 2025)
+
+### Overview  
+The changes in ARC v1.0.4 are designed to enhance the system’s usability and ensure a more coherent structure for data entry and analysis. Users are encouraged to review their workflows and adjust any scripts or processes to reflect the updated variable names and group structures.
+
+### Key Updates  
+
+**Renaming of Presets**  
+   - The preset "disease" has been renamed to "ARChetype CRF" in the principal ARC CSV and in the lists.
+
+**Updates to Answer Choices**  
+   - The test_biospecimentype variable has been changed to a userlist.
+
+---

schemas/isaric-core.json

@@ -0,0 +1,113 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "title": "ISARIC Core Wide Schema",
+    "type": "object",
+    "properties": {
+        "subjid": {
+            "type": "string",
+            "description": "Patient Identification Number (PIN). May not uniquely identify a patient."
+        },
+        "siteid": {
+            "type": "string",
+            "description": "Site ID that collected the data for the patient."
+        },
+        "dataset_id": {
+            "type": "string",
+            "description": "Dataset ID that patient belongs to."
+        },
+        "dataset_disease": {
+            "type": "string",
+            "description": "Disease or syndrome corresponding to the primary reason for the data collection (same for each patient in the dataset)."
+        },
+        "demog_sex": {
+            "type": "string",
+            "enum": [
+                "male",
+                "female",
+                "other"
+            ],
+            "description": "Sex at birth"
+        },
+        "demog_age_days": {
+            "type": "integer",
+            "minimum": 0,
+            "description": "Age in days"
+        },
+        "demog_country_iso3": {
+            "type": "string",
+            "pattern": "^[A-Z]{3}$",
+            "description": "ISO 3166-1 alpha-3 country code"
+        },
+        "pres_adm": {
+            "type": "string",
+            "description": "Admitted to hospital",
+            "enum": [
+                "unknown",
+                "yes",
+                "no"
+            ]
+        },
+        "pres_date": {
+            "type": "string",
+            "anyOf": [
+                {
+                    "format": "date-time"
+                },
+                {
+                    "format": "date"
+                },
+                {
+                    "pattern": "^[0-9]{4}-[0-9]{2}$"
+                },
+                {
+                    "pattern": "^[0-9]{4}$"
+                }
+            ],
+            "description": "Most recent presentation/admission date at this facility"
+        },
+        "outco_outcome": {
+            "type": "string",
+            "enum": [
+                "discharged_alive",
+                "still_hospitalised",
+                "transfer_to_other_facility",
+                "death",
+                "palliative_care",
+                "discharged_against_medical_advice",
+                "alive_not_admitted"
+            ],
+            "description": "Outcome"
+        },
+        "outco_date": {
+            "type": "string",
+            "anyOf": [
+                {
+                    "format": "date-time"
+                },
+                {
+                    "format": "date"
+                },
+                {
+                    "pattern": "^[0-9]{4}-[0-9]{2}$"
+                },
+                {
+                    "pattern": "^[0-9]{4}$"
+                }
+            ],
+            "description": "Outcome date"
+        }
+    },
+    "required": [
+        "subjid",
+        "siteid",
+        "dataset_id",
+        "dataset_disease",
+        "demog_sex",
+        "demog_age_days",
+        "demog_country_iso3",
+        "pres_adm",
+        "pres_date",
+        "outco_outcome",
+        "outco_date"
+    ]
+}