Show new fields analysis samples

pyproject.toml

@@ -125,9 +125,11 @@ ignore = [
   "ANN002",  # Too strict for introduction of ANN. # https://docs.astral.sh/ruff/rules/missing-type-args/
   "ANN003",  # Too strict for introduction of ANN. # https://docs.astral.sh/ruff/rules/missing-type-kwargs/
   "ANN204",  # Too strict for introduction of ANN. # https://docs.astral.sh/ruff/rules/missing-return-type-special-method/
-  "ANN401"  # Too strict and too many errors atm. Consider enabling later after more typing is added. Search for `Any` to find unknown types. # https://docs.astral.sh/ruff/rules/any-type/
+  "ANN401",  # Too strict and too many errors atm. Consider enabling later after more typing is added. Search for `Any` to find unknown types. # https://docs.astral.sh/ruff/rules/any-type/
+  "TRY003",  # This doesn't seem too bad. # https://docs.astral.sh/ruff/rules/raise-vanilla-args/
+  "DJ001"  # Nullable string fields does is used a lot in this project. Maybe enable later? # https://docs.astral.sh/ruff/rules/django-nullable-model-string-field/
 ]
-select = ["E", "W", "I", "F", "UP", "S", "B", "A", "COM", "LOG", "PTH", "Q", "PL", "RUF", "ANN"]
+select = ["E", "W", "I", "F", "UP", "S", "B", "A", "COM", "LOG", "PTH", "Q", "PL", "RUF", "ANN", "PIE", "TC", "TRY", "DJ"]
 
 [tool.ruff.lint.flake8-annotations]
 mypy-init-return = true  # https://docs.astral.sh/ruff/settings/#lint_flake8-annotations_mypy-init-return

src/capps/users/adapters.py

@@ -17,7 +17,7 @@ def report(e: Exception | None, error: Any) -> None:
         set_context("oauth error", {"error": str(error)})
         capture_exception(e)
     except Exception:
-        logging.error(traceback.format_exc())  # noqa: LOG015
+        logging.exception(traceback.format_exc())  # noqa: LOG015
 
 
 class AccountAdapter(DefaultAccountAdapter):

src/capps/users/autocomplete.py

@@ -1,8 +1,20 @@
 from dal import autocomplete
+from django.db.models import QuerySet
 
 from .models import User
 
 
 class UserAutocomplete(autocomplete.Select2QuerySetView):
     model = User
     search_fields = ["email", "first_name", "last_name"]
+
+
+class StaffUserAutocomplete(autocomplete.Select2QuerySetView):
+    model = User
+    search_fields = ["email", "first_name", "last_name"]
+
+    def get_queryset(self) -> QuerySet:
+        if not self.request.user.is_authenticated:
+            return User.objects.none()
+
+        return User.objects.filter(groups__name="genlab")

src/capps/users/exceptions.py

@@ -0,0 +1,2 @@
+class NotAuthenticated(Exception):
+    """User is not authenticated when authentication is required."""

src/capps/users/forms.py

@@ -20,7 +20,7 @@ class UserAdminCreationForm(admin_forms.UserCreationForm):
 
     class Meta(admin_forms.UserCreationForm.Meta):  # type: ignore[name-defined]
         model = User
-        fields = ("email",)
+        fields = ["email"]
         field_classes = {"email": EmailField}
         error_messages = {
             "email": {"unique": _("This email has already been taken.")},

src/capps/users/managers.py

@@ -25,7 +25,7 @@ def _create_user(
         user = self.model(email=email, **extra_fields)
         user.password = make_password(password)
         user.save(using=self._db)
-        return user
+        return user  # type: ignore[return-value]
 
     def create_user(
         self: Self,

src/capps/users/views.py

@@ -10,6 +10,7 @@
 
 from capps.ui.views import UIDetailView, UIListView, UIUpdateView
 
+from .exceptions import NotAuthenticated
 from .filters import UserFilterSet
 from .tables import UserTable
 
@@ -32,7 +33,7 @@ class UserUpdateView(LoginRequiredMixin, SuccessMessageMixin, UpdateView):
 
     def get_success_url(self: Self) -> str:
         if not self.request.user.is_authenticated:
-            raise Exception("User is not authenticated")
+            raise NotAuthenticated
         return self.request.user.get_absolute_url()
 
     def get_object(self, queryset: QuerySet | None = None) -> Any:

src/config/autocomplete.py

@@ -1,12 +1,13 @@
 from django.urls import path
 
-from capps.users.autocomplete import UserAutocomplete
+from capps.users.autocomplete import StaffUserAutocomplete, UserAutocomplete
 from genlab_bestilling.autocomplete import (
     AnalysisOrderAutocomplete,
     AreaAutocomplete,
     EquipmentAutocomplete,
     ExtractionOrderAutocomplete,
     GenrequestAutocomplete,
+    IsolationMethodAutocomplete,
     LocationAutocomplete,
     MarkerAutocomplete,
     OrderAutocomplete,
@@ -25,6 +26,7 @@
     path("project/", ProjectAutocomplete.as_view(), name="project"),
     path("marker/", MarkerAutocomplete.as_view(), name="marker"),
     path("user/", UserAutocomplete.as_view(), name="user"),
+    path("staff-user/", StaffUserAutocomplete.as_view(), name="staff-user"),
     path("genrequest/", GenrequestAutocomplete.as_view(), name="genrequest"),
     path("location/", LocationAutocomplete.as_view(), name="location"),
     path("order/", OrderAutocomplete.as_view(), name="order"),
@@ -35,4 +37,9 @@
         ExtractionOrderAutocomplete.as_view(),
         name="extraction-order",
     ),
+    path(
+        "isolation-method/",
+        IsolationMethodAutocomplete.as_view(),
+        name="isolation-method",
+    ),
 ]

src/genlab_bestilling/api/constants.py

@@ -0,0 +1,184 @@
+SAMPLE_CSV_FIELD_LABELS = {
+    "genlab_id": "Genlab ID",
+    "fish_id": "Old Genlab ID",
+    "guid": "GUID",
+    "name": "Name",
+    "species.name": "Species",
+    "location.name": "Location",
+    "order": "EXT_order",
+    "analysis_orders": "ANL_order",
+    "pop_id": "PopID",
+    "type.name": "Sample Type",
+    "gender": "Gender",
+    "length": "Length",
+    "weight": "Weight",
+    "classification": "Classification",
+    "year": "Year",
+    "notes": "Notes",
+    "project": "Project Number",
+    "isolation_method": "Isolation Method",
+    "qiagen_number": "Qiagen#",
+    "is_marked": "Marked",
+    "is_plucked": "Plucked",
+    "is_isolated": "Isolated",
+    "station": "Station",
+    "placement_in_fridge": "Placement in Fridge",
+    "delivered_to_lab": "Delivered to Lab",
+    "fluidigm#": "Fluidigm#",
+    "laksov_species": "LaksOV + Species",
+    "species_date": "Species Date",
+    "pcr": "PCR",
+    "fluidigm": "Fluidigm",
+    "output": "Output",
+    "analysis_note": "Analysis Note",
+    "rerun": "Rerun",
+    "rerun_qiagen": "Rerun Qiagen",
+    "river": "River",
+    "str_date": "STR Date",
+    "rerun_date": "Rerun Date",
+    "watercourse_number": "Watercourse Number",
+    "under_locality": "Sub-locality",
+    "county": "County",
+    "snp_assay_1": "SNP Assay 1",
+    "snp_assay_2": "SNP Assay 2",
+    "str_mixab": "STR Mix AB",
+    "str_mixc": "STR Mix C",
+    "str_mixy": "STR Mix Y",
+    "internal_note": "Internal Note",
+    "bb#": "BB#",
+    "output_bb": "Output",
+    "bba2#": "BBA2#",
+    "output_bba2": "Output",
+    "mixab": "Mix AB",
+    "ab_rep#": "AB Rep#",
+    "mixc": "Mix C",
+    "c_rep#": "C Rep#",
+    "re_extracted_date": "Re-extracted Date",
+    "re_extracted_qiagen#": "Re-extracted Qiagen#",
+    "weight_g_for_diet_analysis": "Weight (g) for Diet Analysis",
+    "position": "Position",
+}
+
+SAMPLE_CSV_FIELDS_BY_AREA = {
+    "Akvatisk": [
+        "name",
+        "genlab_id",
+        "fish_id",
+        "guid",
+        "order",
+        "analysis_orders",
+        "location.name",
+        "watercourse_number",
+        "pop_id",
+        "species.name",
+        "gender",
+        "length",
+        "weight",
+        "classification",
+        "year",
+        "notes",
+        "project",
+        "type.name",
+        "isolation_method",
+        "qiagen_number",
+        "fluidigm#",
+        "laksov_species",
+        "species_date",
+        "is_marked",
+        "is_plucked",
+        "is_isolated",
+        "pcr",
+        "fluidigm",
+        "output",
+        "analysis_note",
+        "rerun",
+        "rerun_date",
+    ],
+    "Elvemusling": [
+        "name",
+        "genlab_id",
+        "fish_id",
+        "guid",
+        "river",
+        "location.name",
+        "under_locality",
+        "watercourse_number",
+        "county",
+        "year",
+        "station",
+        "type.name",
+        "length",
+        "notes",
+        "isolation_method",
+        "qiagen_number",
+        "position",
+        "placement_in_fridge",
+        "is_marked",
+        "is_plucked",
+        "is_isolated",
+        "pcr",
+        "str_date",
+        "output",
+        "analysis_note",
+        "rerun",
+        "rerun_date",
+    ],
+    "Terrestrisk": [
+        "name",
+        "genlab_id",
+        "guid",
+        "type.name",
+        "species.name",
+        "location.name",
+        "delivered_to_lab",
+        "order",
+        "analysis_orders",
+        "notes",
+        "snp_assay_1",
+        "snp_assay_2",
+        "str_mixab",
+        "str_mixc",
+        "str_mixy",
+        "is_marked",
+        "is_plucked",
+        "is_isolated",
+        "isolation_method",
+        "qiagen_number",
+        "internal_note",
+        "bb#",
+        "output_bb",
+        "bba2#",
+        "output_bba2",
+        "mixab",
+        "ab_rep#",
+        "mixc",
+        "c_rep#",
+        "re_extracted_date",
+        "re_extracted_qiagen#",
+        "weight_g_for_diet_analysis",
+    ],
+    "default": [
+        "genlab_id",
+        "guid",
+        "name",
+        "type.name",
+        "species.name",
+        "location.name",
+        "order",
+        "analysis_orders",
+        "notes",
+        "is_marked",
+        "is_plucked",
+        "is_isolated",
+        "isolation_method",
+        "qiagen_number",
+    ],
+}
+
+LABEL_CSV_FIELDS_BY_AREA = {
+    "Akvatisk": ["fish_id", "genlab_id", "guid"],
+    "Elvemusling": ["fish_id", "genlab_id", "guid"],
+    "Terrestrisk": ["genlab_id", "guid", "name"],
+    "MiljøDNA": ["genlab_id", "guid", "name", "location.name"],
+    "default": ["genlab_id", "guid", "name"],
+}