Updating bioassay branch with main

.github/copilot-instructions.md

@@ -0,0 +1,58 @@
+# Health Assessment Workspace Collaborative (HAWC)
+
+HAWC is a web-based platform for capturing, analyzing, and sharing data related to human-health assessments of chemicals and environmental exposures. It supports hazard identification and quantitative risk assessment workflows for researchers and regulatory agencies.
+
+## Folder Structure
+
+- `hawc/`: Python Django backend application
+- `hawc/client/`: Python client package
+- `frontend/`: JavaScript/React frontend application
+- `frontend/tests/`: JavaScript/React tets
+- `compose/`: Docker Compose files and deployment configuration
+- `tests/`: Python backend tests
+- `tests/integration/`: Python integration tests which require the JavaScript code to be compiled. This can be done either in a separate process (via `npm run start`; preferred) or built (via `npm run build`).
+- `docs/`: documentation for development and overall structure of application
+
+## Libraries and Frameworks
+
+- **Backend:** Python 3.13, Django, uv (dependency management), flit (packaging)
+- **Frontend:** React, MobX, Yarn (dependency management), Vite (build tool)
+- **Testing:** Pytest, Coverage.py, Playwright (integration), Jest (JS unit tests)
+
+The HAWC application is a mixture of Django HTML templates for some pages, and then a Django API plus JavaScript application for serving more dynamic pages. We use simpler HTML templates where possible, and only use JavaScript for more complex interactions. We are increasingly using htmx for more complex django HTML template based interactions.
+
+## Code Standards (Linting/Formatting)
+
+- **Python:**
+   - Lint with `poe lint-py` (ruff)
+   - HTML linting with `poe lint-html`
+- **JavaScript:**
+   - Lint with `yarn --cwd ./frontend run lint` (uses biome.js)
+
+## Testing (Python)
+
+Run backend tests: `pytest --record-mode=none`
+
+## Testing (JavaScript)
+
+Run frontend tests: `yarn --cwd ./frontend run test`
+
+## Testing (Integration)
+
+Integration tests require both backend and frontend to be available.  The integration tests are run using Python and the playwright integration to check browser interactions.
+
+Python integration tests which require the JavaScript code to be compiled. To compile:
+
+- **Preferred:** Start the frontend in a separate process: `yarn --cwd ./frontend run`
+- **Alternative:** Build the frontend before running integration tests: `yarn --cwd ./frontend build`
+
+The preferred approach allows for faster development cycles since it doesn't require a compile step.
+
+To run integration tests: `py.test -sv tests/integration/`
+
+## References:
+
+* See GitHub actions in `.github/workflows`
+* See documentation in `docs/`
+* For editing [this file](https://docs.github.com/en/copilot/how-tos/configure-custom-instructions/add-repository-instructions?tool=vscode):
+

.github/workflows/copilot-setup-steps.yml

@@ -0,0 +1,77 @@
+# https://docs.github.com/en/copilot/how-tos/use-copilot-agents/coding-agent/customize-the-agent-environment
+name: "Copilot Setup Steps"
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  schedule:
+    - cron: "14 3 1 */1 *" # At 03:14 on the 1st of every month
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # The job MUST be called `copilot-setup-steps` or it will not be picked up by Copilot.
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    services:
+      postgres:
+        image: postgres:16-alpine
+        env:
+          POSTGRES_USER: hawc
+          POSTGRES_PASSWORD: password
+          POSTGRES_DB: hawc
+        options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
+        ports:
+        - 5432:5432
+      redis:
+        image: redis:6-alpine
+        options: --health-cmd "redis-cli ping" --health-interval 10s --health-timeout 5s --health-retries 5
+        ports:
+        - 6379:6379
+
+    env:
+      DJANGO_DB_NAME: hawc
+      DJANGO_DB_USER: hawc
+      DJANGO_DB_PW: password
+      DJANGO_DB_HOST: localhost
+      DJANGO_CACHE_LOCATION: redis://localhost:6379/0
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 22
+          cache: "yarn"
+          cache-dependency-path: "frontend/yarn.lock"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          cache-dependency-glob: "**/pyproject.toml"
+      - name: install
+        run: |
+          uv pip install --system -e ".[dev,docs]"
+          uv pip install --system -e client
+      - name: install
+        run: |
+          yarn --cwd ./frontend install --frozen-lockfile
+
+      # check environment is setup correctly
+      # - name: test
+      #   run: |
+      #     pytest --record-mode=none
+      #     yarn --cwd ./frontend run test

.github/workflows/main.yml

@@ -66,7 +66,7 @@ jobs:
         if [ "$RUNNER_OS" == "Linux" ]; then
           export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib"
         fi
-        coverage run -m pytest --record-mode=none
+        coverage run -m pytest -v --block-network --allowed-hosts=127.0.0.1,::1 --record-mode=none
         echo "# Python coverage report" >> $GITHUB_STEP_SUMMARY
         coverage report --format=markdown -i >> $GITHUB_STEP_SUMMARY || true
         coverage html -d coverage -i
@@ -162,13 +162,13 @@ jobs:
       id: test
       continue-on-error: true
       run: |
-        uv run py.test -sv tests/integration/
+        uv run py.test -v --block-network --allowed-hosts=127.0.0.1,::1 tests/integration/
     - name: run integration tests (retry)
       if: steps.test.outcome=='failure'
       id: retry
       continue-on-error: true
       run: |
-        uv run py.test -sv --lf tests/integration/
+        uv run py.test -v --block-network --allowed-hosts=127.0.0.1,::1 --lf tests/integration/
     - name: set status
       if: always()
       run: |

.gitignore

@@ -18,6 +18,7 @@ hawc/gitcommit.json
 hawc/main/settings/local.py
 package-lock.json
 uv.lock
+CLAUDE.md
 
 # folders
 *.egg-info/
@@ -28,6 +29,8 @@ uv.lock
 .ruff_cache/
 .venv/
 .vscode/
+.serena/
+.claude/
 /data/
 docs/site
 __pycache__/

client/hawc_client/__init__.py

@@ -16,7 +16,7 @@
 from .summary import SummaryClient
 from .vocab import VocabClient
 
-__version__ = "2024.4"
+__version__ = "2025.1.1"
 __all__ = ["BaseClient", "HawcClient", "HawcClientException", "HawcServerException"]
 
 

compose/app/Dockerfile

@@ -30,7 +30,7 @@ COPY ./dist /app/build/dist
 WORKDIR /app/build
 
 RUN python -m pip install -U pip --root-user-action=ignore && \
-    python -m pip install "$(ls dist/hawc-*.whl | head -1)[prod]" --no-cache-dir && \
+    python -m pip install "$(ls -t dist/hawc-*.whl | head -1)[prod]" --no-cache-dir && \
     mkdir -p /app/logs && \
     python -m pip uninstall -y pip setuptools && \
     rm -rf /app/build && \

compose/example.env

@@ -26,7 +26,7 @@ DJANGO_HTTPS_ONLY=False
 DJANGO_EMAIL_BACKEND=CONSOLE
 ADMIN_URL_PREFIX=c6cbceb2-0592-497b-bd92-5d881a1fae40
 PUBMED_API_KEY=8852fcfa8cc0850a16d7e24d21e23f77
-CCTE_API_KEY=0468d596fe45f2e7b562318d80b11ea2
+EPA_COMPTOX_API_KEY=0468d596fe45f2e7b562318d80b11ea2
 HAWC_SESSION_DURATION=604800
 HAWC_ANYONE_CAN_CREATE_ASSESSMENTS=True
 HAWC_PM_CAN_MAKE_PUBLIC=True

compose/nginx/Dockerfile

@@ -1,4 +1,4 @@
-FROM nginx:stable-alpine
+FROM nginx:alpine-slim
 
 RUN apk update && \
     apk upgrade --available && \

compose/redis/Dockerfile

@@ -1,4 +1,4 @@
-FROM redis:7-alpine
+FROM redis:8-alpine
 
 RUN apk update && \
     apk upgrade --available && \

docs/docs/client.md

@@ -58,26 +58,27 @@ Client tutorials for common operations are below:
 
 ### Changelog
 
-#### [2025-1](https://pypi.org/project/hawc-client/2025.1/) (TBD)
+#### [2025.1](https://pypi.org/project/hawc-client/2025.1/) (TBD)
 
 * Add `unpublished` parameter to bmd dataset download
 * Remove data pivot API endpoints; all behaviors can be accomplished using the visual API
+* Publish package on PyPI using GitHub Actions
 
-#### [2024-4](https://pypi.org/project/hawc-client/2024.4/) (January 2025)
+#### [2024.4](https://pypi.org/project/hawc-client/2024.4/) (January 2025)
 
 * Added assessment team member API endpoint to retrieve assessments a user is a member of
 * Added literature tag API {create, update, delete, move} to modify tags
 
-#### [2024-3](https://pypi.org/project/hawc-client/2024.3/) (October 2024)
+#### [2024.3](https://pypi.org/project/hawc-client/2024.3/) (October 2024)
 
 * Update data pivot and visual output formats to return JSON
 * Add a new BMDS Export to return dose-response data
 
-#### [2024-2](https://pypi.org/project/hawc-client/2024.2/) (July 2024)
+#### [2024.2](https://pypi.org/project/hawc-client/2024.2/) (July 2024)
 
 * Minor documentation and docstring updates
 
-#### [2024-1](https://pypi.org/project/hawc-client/2024.1/) (February 2024)
+#### [2024.1](https://pypi.org/project/hawc-client/2024.1/) (February 2024)
 
 * Add new interactive client for downloading visual and data pivots images
 * Updated study evaluation/risk of bias APIs
@@ -86,20 +87,20 @@ Client tutorials for common operations are below:
 * Add APIs to modify Visuals and Data Pivots
 * Add APIs to modify Assessments, Assessment Values, and Assessment Details
 
-#### [2023-2](https://pypi.org/project/hawc-client/2023.2/) (April 2023)
+#### [2023.2](https://pypi.org/project/hawc-client/2023.2/) (April 2023)
 
 * Add new `login` parameter to `client.set_authentication_token`, and returns  boolean instead of a dict.
     - If `login` is False (default), a token based API session is created. This is consistent with previous behavior.
     - If `login` is True, a django cookie-based session is set instead of a token-based API session. This may be used if using the client to browse the website, however CSRF tokens will be required for API and form requests.
 * Added ``client.lit.reference_user_tags`` - retrieves all user tag for all references for an assessment.
 
-#### [2023-1](https://pypi.org/project/hawc-client/2023.1/) (January 2023)
+#### [2023.1](https://pypi.org/project/hawc-client/2023.1/) (January 2023)
 
 * Added ``client.riskofbias.compare_metrics`` - align metrics when copying across assessments via fuzzy text matching
 * Added ``client.summary.datapivot_list`` - retrieve all data pivots for an assessment
 * Added ``client.summary.table_list`` - retrieve all tables for an assessment
 
-#### [2022-7](https://pypi.org/project/hawc-client/2022.7/) (July 2022)
+#### [2022.7](https://pypi.org/project/hawc-client/2022.7/) (July 2022)
 
 * Added ``client.study.studies`` to return dataframe of studies for an assessment
 * Added new parameter, ``invert``, to the ``client.animal.endpoints``

frontend/animal/AnimalGroupTable/index.js

@@ -1,16 +1,16 @@
 import {Provider} from "mobx-react";
 import React from "react";
-import ReactDOM from "react-dom";
+import {createRoot} from "react-dom/client";
 
 import App from "./App";
 import Store from "./store";
 
 export default function (el, config) {
     const store = new Store(config);
-    ReactDOM.render(
+    const root = createRoot(el);
+    root.render(
         <Provider store={store}>
             <App />
-        </Provider>,
-        el
+        </Provider>
     );
 }

frontend/animal/AnimalGroupTable/store.js

@@ -1,5 +1,5 @@
 import _ from "lodash";
-import {action, computed, observable, toJS} from "mobx";
+import {action, computed, makeObservable, observable, toJS} from "mobx";
 import TableFootnotes from "shared/utils/TableFootnotes";
 
 import Endpoint from "../Endpoint";
@@ -17,6 +17,7 @@ class AnimalGroupTableStore {
     @observable sortValue = 1;
 
     constructor(data) {
+        makeObservable(this);
         this.endpoints = data.endpoints.map(d => new Endpoint(d));
         this.footnotes = new TableFootnotes();
     }

frontend/animal/BMDResult.js

@@ -1,7 +1,8 @@
 import _ from "lodash";
 import PropTypes from "prop-types";
 import React from "react";
-import ReactDOM from "react-dom";
+import {createRoot} from "react-dom/client";
+
 import h from "shared/utils/helpers";
 
 import EndpointCriticalDose from "./EndpointCriticalDose";
@@ -55,7 +56,8 @@ BmdResultComponent.propTypes = {
 
 class BMDResult extends EndpointCriticalDose {
     update() {
-        ReactDOM.render(<BmdResultComponent endpoint={this.endpoint} />, this.span[0]);
+        const root = createRoot(this.span[0]);
+        root.render(<BmdResultComponent endpoint={this.endpoint} />);
     }
 }
 

frontend/animal/DRPlot.js

@@ -545,7 +545,11 @@ class DRPlot extends D3Plot {
         if (this.legend_left) {
             legend_settings.box_l = this.legend_left;
         } else {
-            legend_settings.box_l = 10;
+            let isIncreasing = true;
+            if (Array.isArray(this.values) && this.values.length > 0) {
+                isIncreasing = this.values[0].y < this.values[this.values.length - 1].y;
+            }
+            legend_settings.box_l = isIncreasing ? 10 : this.w - 80;
         }
 
         if (this.legend_top) {

frontend/animal/EndpointForm/index.js

@@ -1,17 +1,17 @@
 import {Provider} from "mobx-react";
 import React from "react";
-import ReactDOM from "react-dom";
+import {createRoot} from "react-dom/client";
 
 import App from "./App";
 import Store from "./store";
 
 export default function (el, config) {
     const store = new Store(config);
 
-    ReactDOM.render(
+    const root = createRoot(el);
+    root.render(
         <Provider store={store}>
             <App />
-        </Provider>,
-        el
+        </Provider>
     );
 }

frontend/animal/EndpointForm/store.js

@@ -1,5 +1,5 @@
 import _ from "lodash";
-import {action, computed, observable} from "mobx";
+import {action, computed, makeObservable, observable} from "mobx";
 import h from "shared/utils/helpers";
 
 import {termUrlLookup} from "./constants";
@@ -11,6 +11,7 @@ class EndpointFormStore {
     @observable useControlledVocabulary = null;
 
     constructor(config) {
+        makeObservable(this);
         this.config = config;
         this.setUseControlledVocabulary();
     }

frontend/animal/EndpointListApp/EndpointListStore.js

@@ -1,5 +1,5 @@
 import _ from "lodash";
-import {action, computed, observable, toJS} from "mobx";
+import {action, computed, makeObservable, observable, toJS} from "mobx";
 import h from "shared/utils/helpers";
 
 const CRITICAL_VALUES = ["noel", "loel", "fel", "bmd", "bmdl"];
@@ -16,6 +16,7 @@ class EndpointListStore {
     @observable criticalValueOptions = null;
 
     constructor(config) {
+        makeObservable(this);
         this.config = config;
         this.getDataset();
     }