Merge next -> main

.github/workflows/main.yml

@@ -24,10 +24,10 @@ jobs:
     - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
-        repository: shapiromatron/bmds
+        repository: USEPA/bmds-private
         path: venv
         ref: main
-        lfs: true
+        token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
@@ -55,8 +55,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     - name: lint
       run: |
@@ -71,7 +70,6 @@ jobs:
       run: |
         export "LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH"
         coverage run -m pytest --vcr-record=none
-        coverage html -d coverage_report
         echo "# Python coverage report" >> $GITHUB_STEP_SUMMARY
         coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
 
@@ -145,10 +143,10 @@ jobs:
     - name: Checkout bmds@main
       uses: actions/checkout@v3
       with:
-        repository: shapiromatron/bmds
+        repository: USEPA/bmds-private
         path: venv
         ref: main
-        lfs: true
+        token: ${{ secrets.USEPA_BMDS_PRIVATE_PAT }}
     - uses: actions/setup-python@v4
       with:
         python-version: '3.11'
@@ -177,8 +175,7 @@ jobs:
         export "LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib:/usr/lib"
         sudo cp vendor/libnlopt.so /usr/local/lib/libnlopt.so.0
         sudo ln -s /lib/x86_64-linux-gnu/libgsl.so /usr/local/lib/libgsl.so.25
-        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bin/BMDS330/libDRBMD.so"
-        echo $BMD_DLL
+        export "BMD_DLL=$GITHUB_WORKSPACE/venv/bmds/bmdscore.cpython-*-x86_64-linux-gnu.so"
         ldd $BMD_DLL
     # https://github.community/t/how-to-retry-a-failed-step-in-github-actions-workflow/125880
     - name: run integration tests

.gitignore

@@ -9,6 +9,7 @@
 bmds_server/static/bundles/
 build/
 /data/
+coverage_report/
 dist/
 docs/site/
 node_modules/
@@ -20,7 +21,7 @@ venv/
 # files
 *.log
 *.py[cod]
-*.sqlite3
+*.sqlite3*
 *log
 .coverage
 .env

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include bmds_server/ *css *.js *.json *.html *.py
+recursive-include bmds_server/ *css *.js *.json *.html *.md *.py
 recursive-include bmds_server/static *
 recursive-include bmds_server/templates *
 global-exclude .DS_Store .gitkeep __pycache__ *.pyc

Makefile

@@ -56,6 +56,11 @@ test-integration-debug:  ## Run integration tests in debug mode (requires npm ru
 	@playwright install --with-deps chromium
 	@INTEGRATION_TESTS=1 PWDEBUG=1 py.test -sv tests/integration/
 
+coverage: ## Run test coverage
+	coverage run -m pytest
+	coverage html -d coverage_report
+	$(BROWSER) coverage_report/index.html
+
 docs: ## Build documentation
 	cd docs; mkdocs build --strict
 
@@ -75,10 +80,10 @@ lint: lint-py lint-js  ## Check formatting issues
 format: format-py format-js  ## Fix formatting issues where possible
 
 lint-py:  ## Check python formatting issues
-	@black . --check && ruff .
+	@ruff format . --check && ruff .
 
 format-py:  ## Fix python formatting issues where possible
-	@black . && ruff . --fix --show-fixes
+	@ruff format . && ruff . --fix --show-fixes
 
 lint-js:  ## Check javascript formatting issues
 	@npm --prefix ./frontend run lint

README.rst

@@ -5,9 +5,6 @@ BMDS webserver
         :target: https://bmds-server.readthedocs.io/en/master/
         :alt: Documentation Status
 
-.. image:: https://zenodo.org/badge/73124145.svg
-   :target: https://zenodo.org/badge/latestdoi/73124145
-
 Run a webserver that will batch process dose-response data using the US EPA's
 benchmark dose modeling software (`BMDS`_).  Under the hood, this web application
 uses the `BMDS Python interface`_.

bmds_server/analysis/admin.py

@@ -47,3 +47,8 @@ def edit_url(self, obj):
 class Content(VersionAdmin):
     list_display = ("id", "content_type", "subject", "created", "last_updated")
     list_filter = ("content_type",)
+
+
+@admin.register(models.Collection)
+class CollectionAdmin(VersionAdmin):
+    pass

bmds_server/analysis/api.py

@@ -1,20 +1,24 @@
+from bmds.datasets.transforms.polyk import PolyKAdjustment
+from django.conf import settings
 from django.core.exceptions import ValidationError
 from rest_framework import exceptions, mixins, viewsets
-from rest_framework.decorators import action, api_view
+from rest_framework.decorators import action
 from rest_framework.response import Response
 
 from ..common import renderers
+from ..common.renderers import BinaryFile
+from ..common.serializers import UnusedSerializer
 from ..common.task_cache import ReportStatus
 from ..common.utils import get_bool
 from ..common.validation import pydantic_validate
 from . import models, schema, serializers, validators
 from .reporting.cache import DocxReportCache, ExcelReportCache
-from .reporting.docx import add_update_url
+from .reporting.docx import add_update_url, build_polyk_docx
 
 
 class AnalysisViewset(mixins.RetrieveModelMixin, viewsets.GenericViewSet):
     serializer_class = serializers.AnalysisSerializer
-    queryset = models.Analysis.objects.all()
+    queryset = models.Analysis.objects.prefetch_related("collections").all()
 
     @action(detail=False, url_path="default")
     def default(self, request, *args, **kwargs):
@@ -133,7 +137,7 @@ def excel(self, request, *args, **kwargs):
             data = renderers.BinaryFile(data=response.content, filename=instance.slug)
             return Response(data)
 
-        return Response(response.dict(), content_type="application/json")
+        return Response(response.model_dump(), content_type="application/json")
 
     @action(detail=True, renderer_classes=(renderers.DocxRenderer,))
     def word(self, request, *args, **kwargs):
@@ -155,14 +159,71 @@ def word(self, request, *args, **kwargs):
             data = add_update_url(instance, response.content, uri) if edit else response.content
             return Response(renderers.BinaryFile(data=data, filename=instance.slug))
 
-        return Response(response.dict(), content_type="application/json")
+        return Response(response.model_dump(), content_type="application/json")
 
+    @action(detail=True, methods=("post",))
+    def star(self, request, *args, **kwargs):
+        instance = self.get_object()
+
+        # permissions check
+        if instance.password != request.data.get("editKey", ""):
+            raise exceptions.PermissionDenied()
+
+        # flip the star (but don't change last_updated)
+        if settings.IS_DESKTOP:
+            models.Analysis.objects.filter(id=instance.id).update(starred=not instance.starred)
+            instance.refresh_from_db()
+
+        serializer = self.get_serializer(instance)
+        return Response(serializer.data)
+
+    @action(detail=True, methods=("post",))
+    def collections(self, request, *args, **kwargs):
+        instance = self.get_object()
 
-@api_view(["POST"])
-def polyk_transform(request):
-    try:
-        settings = pydantic_validate(request.data, schema.PolyKInput)
-    except ValidationError as err:
-        raise exceptions.ValidationError(err.message)
-    (df, df2) = settings.calculate()
-    return Response({"df": df.to_dict(orient="list"), "df2": df2.to_dict(orient="list")})
+        # permissions check
+        if instance.password != request.data.get("editKey", ""):
+            raise exceptions.PermissionDenied()
+
+        # update collections
+        if settings.IS_DESKTOP:
+            ids = [d for d in request.data.get("collections", []) if isinstance(d, int)]
+            collections = models.Collection.objects.filter(id__in=ids)
+            instance.collections.set(collections)
+
+        serializer = self.get_serializer(instance)
+        return Response(serializer.data)
+
+
+class PolyKViewset(viewsets.GenericViewSet):
+    queryset = models.Analysis.objects.none()
+    serializer_class = UnusedSerializer
+
+    def _run_analysis(self, request) -> PolyKAdjustment:
+        try:
+            settings = pydantic_validate(request.data, schema.PolyKInput)
+        except ValidationError as err:
+            raise exceptions.ValidationError(err.message)
+        return settings.calculate()
+
+    def create(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        return Response(
+            {
+                "df": analysis.adjusted_data.to_dict(orient="list"),
+                "df2": analysis.summary.to_dict(orient="list"),
+            }
+        )
+
+    @action(detail=False, methods=["POST"], renderer_classes=(renderers.XlsxRenderer,))
+    def excel(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        data = BinaryFile(analysis.to_excel(), "polyk-adjustment")
+        return Response(data)
+
+    @action(detail=False, methods=["POST"], renderer_classes=(renderers.DocxRenderer,))
+    def word(self, request, *args, **kwargs):
+        analysis = self._run_analysis(request)
+        f = build_polyk_docx(analysis)
+        data = BinaryFile(f, "polyk-adjustment")
+        return Response(data)

bmds_server/analysis/apps.py

@@ -3,3 +3,6 @@
 
 class Config(AppConfig):
     name = "bmds_server.analysis"
+
+    def ready(self):
+        from .signals import init_command  # noqa: F401