hawc 2023-Q1 + hawc-client 2023.2

MANIFEST.in

@@ -1,4 +1,4 @@
-recursive-include hawc *css *.js *.json *.html *.py *.txt
+recursive-include hawc *css *.js *.json *.jsonl *.html *.py *.txt
 recursive-include hawc/refml/nltk_data *
 recursive-include hawc/static *
 recursive-include hawc/templates *

compose/app/Dockerfile

@@ -10,7 +10,6 @@ COPY ./compose/app/sync.sh /app/bin/sync.sh
 COPY ./compose/app/web.sh /app/bin/web.sh
 COPY ./compose/app/workers.sh /app/bin/workers.sh
 COPY ./compose/app/cron.sh /app/bin/cron.sh
-COPY ./vendor/bmds-0.11.0.tar.gz /app/build/vendor/bmds-0.11.0.tar.gz
 
 # used in some dev/staging environments
 COPY ./tests/data/fixtures/db.yaml /app/test-db-fixture.yaml

docs/docs/client.md

@@ -45,12 +45,12 @@ Client tutorials for common operations are below:
 
 ### Changelog
 
-#### [2023-2](https://pypi.org/project/hawc-client/2023.2/) (January 2023)
+#### [2023-2](https://pypi.org/project/hawc-client/2023.2/) (April 2023)
 
-* Add new parameter to `set_authentication_token`, login, and returns  boolean instead of a dict.
-    - If False (default), a token based API session is created. This is consistent with previous behavior.
-    - If 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 would be required for form-based requests.
+* 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)
 

frontend/animal/Endpoint.js

@@ -120,10 +120,6 @@ class Endpoint extends Observee {
             .then(data => cb(new Endpoint(data)));
     }
 
-    static getTagURL(assessment, slug) {
-        return `/ani/assessment/${assessment}/endpoints/tags/${slug}/`;
-    }
-
     static displayAsModal(id, opts) {
         Endpoint.get_object(id, d => d.displayAsModal(opts));
     }
@@ -271,7 +267,10 @@ class Endpoint extends Observee {
                 var div = $("<div>");
                 div.append(
                     tags.map(v => {
-                        const url = Endpoint.getTagURL(assessment_id, v.slug);
+                        const url = h.getUrlWithParameters(
+                            `/ani/assessment/${assessment_id}/endpoints/`,
+                            {tags: v.name}
+                        );
                         return `<a class="btn btn-light" href="${url}">${v.name}</a>`;
                     })
                 );

frontend/shared/utils/helpers.js

@@ -173,6 +173,9 @@ const helpers = {
     getBulkUrl(host, base, ids = null) {
         return `${host}${base}&ids=${ids}`;
     },
+    getUrlWithParameters(path, params) {
+        return `${path}?${new URLSearchParams(params).toString()}`;
+    },
     datetimeFormat(dt) {
         return moment(dt).format("MMMM Do YYYY, h:mm:ss a");
     },

frontend/study/Study.js

@@ -86,7 +86,7 @@ class Study {
         );
         if (this.data.full_text_url)
             tbl.add_tbody_tr(
-                "Full-text link",
+                "Full text URL",
                 `<a href=${this.data.full_text_url}>${this.data.full_text_url}</a>`
             );
         tbl.add_tbody_tr("COI reported", this.data.coi_reported);

hawc/__init__.py

@@ -1,7 +1,7 @@
 import os
 import sys
 
-__version__ = "0.1"
+__version__ = "2023.1"
 
 
 def manage():

hawc/apps/animal/managers.py

@@ -150,23 +150,6 @@ def get_queryset(self):
     def published(self, assessment_id=None):
         return self.get_qs(assessment_id).filter(animal_group__experiment__study__published=True)
 
-    def tag_qs(self, assessment_id, tag_slug=None):
-        AnimalGroup = apps.get_model("animal", "AnimalGroup")
-        Experiment = apps.get_model("animal", "Experiment")
-        Study = apps.get_model("study", "Study")
-        return (
-            self.filter(effects__slug=tag_slug)
-            .select_related("animal_group", "animal_group__dosing_regime")
-            .prefetch_related("animal_group__dosing_regime__doses")
-            .filter(
-                animal_group__in=AnimalGroup.objects.filter(
-                    experiment__in=Experiment.objects.filter(
-                        study__in=Study.objects.get_qs(assessment_id)
-                    )
-                )
-            )
-        )
-
     def optimized_qs(self, **filters):
         return (
             self.filter(**filters)

hawc/apps/animal/urls.py

@@ -121,11 +121,6 @@
         views.EndpointListV2.as_view(),
         name="endpoint_list_v2",
     ),
-    path(
-        "assessment/<int:pk>/endpoints/tags/<slug:tag_slug>/",
-        views.EndpointTags.as_view(),
-        name="assessment_endpoint_taglist",
-    ),
     path(
         "animal-group/<int:pk>/endpoint/create/",
         views.EndpointCreate.as_view(),

hawc/apps/animal/views.py

@@ -437,13 +437,6 @@ def get_app_config(self, context) -> WebappConfig:
         )
 
 
-class EndpointTags(EndpointFilterList):
-    # List of Endpoints associated with an assessment and tag
-
-    def get_queryset(self):
-        return super().get_queryset().tag_qs(self.assessment.pk, self.kwargs["tag_slug"])
-
-
 class EndpointRead(BaseDetail):
     queryset = models.Endpoint.objects.select_related(
         "animal_group",

hawc/apps/assessment/api/helper.py

@@ -2,6 +2,7 @@
 
 from rest_framework import status
 from rest_framework.exceptions import APIException
+from rest_framework.request import Request
 
 from ...common.helper import tryParseInt
 from .. import models
@@ -17,17 +18,19 @@ class InvalidAssessmentID(APIException):
     default_detail = "Assessment does not exist for given `assessment_id`."
 
 
-def get_assessment_id_param(request) -> int:
+def get_assessment_id_param(request: Request) -> int:
     """
     If request doesn't contain an integer-based `assessment_id`, an exception is raised.
     """
-    assessment_id = tryParseInt(request.GET.get("assessment_id"))
+    assessment_id = tryParseInt(
+        request.query_params.get("assessment_id") or request.data.get("assessment_id")
+    )
     if assessment_id is None:
         raise RequiresAssessmentID()
     return assessment_id
 
 
-def get_assessment_from_query(request) -> Optional[models.Assessment]:
+def get_assessment_from_query(request: Request) -> Optional[models.Assessment]:
     """Returns assessment or raises exception if does not exist."""
     assessment_id = get_assessment_id_param(request)
     try:

hawc/apps/assessment/api/viewsets.py

@@ -146,7 +146,6 @@ class AssessmentEditViewset(viewsets.ModelViewSet):
     assessment_filter_args = ""
     permission_classes = (AssessmentLevelPermissions,)
     action_perms = {}
-    parent_model = models.Assessment
     filter_backends = (InAssessmentFilter,)
     lookup_value_regex = re_digits
 

hawc/apps/assessment/forms.py

@@ -279,7 +279,7 @@ def helper(self):
 class AssessmentFilterForm(forms.Form):
     search = forms.CharField(required=False)
 
-    DEFAULT_ORDER_BY = "-last_updated"
+    DEFAULT_ORDER_BY = "-year"
     ORDER_BY_CHOICES = [
         ("name", "Name"),
         ("year", "Year, ascending"),

hawc/apps/assessment/managers.py

@@ -171,10 +171,10 @@ def get_df(self) -> pd.DataFrame:
             "system": "system",
             "value_type": "value_type",
             "value": "value",
-            "value_unit__name": "value_unit",
+            "value_unit": "value_unit",
             "basis": "basis",
             "pod_value": "pod_value",
-            "pod_unit__name": "pod_unit",
+            "pod_unit": "pod_unit",
             "species_studied": "species_studied",
             "duration": "duration",
             "study_id": "study_id",

hawc/apps/assessment/models.py

@@ -455,7 +455,7 @@ def _has_data(self, app: str, model: str, filter: str = "study__assessment") ->
 
     @property
     def has_lit_data(self) -> bool:
-        return self._has_data("lit", "Reference")
+        return self._has_data("lit", "Reference", filter="assessment")
 
     @property
     def has_rob_data(self) -> bool:

hawc/apps/assessment/templates/assessment/assessment_detail.html

@@ -254,7 +254,7 @@ <h3>Assessment details for team members*</h3>
 {% block extrajs %}
 {% if crud == "Read" and object.dtxsids.first %}
 <script type="text/javascript">
-  $(document).on('ready', function () {
+  window.addEventListener("DOMContentLoaded", function () {
     const dtxsids = {{dtxsids|safe}},
       el = document.getElementById('dtxsid-app');
     window.app.startup("assessmentStartup", function(app){

hawc/apps/common/autocomplete/forms.py

@@ -66,6 +66,18 @@ def update_filters(self, filters: dict):
         self.filters.update(filters)
         self.url = self.autocomplete_class.url(**self.filters)
 
+    def filter_choices_to_render(self, selected_choices):
+        """Filter out un-selected choices if choices is a QuerySet.
+
+        patched - see https://github.com/yourlabs/django-autocomplete-light/pull/1321
+        """
+        try:
+            qs = self.choices.queryset.filter(pk__in=[c for c in selected_choices if c])
+        except ValueError:
+            # set queryset to empty set if filters are invalid
+            qs = self.choices.queryset.none()
+        self.choices.queryset = qs
+
 
 class AutocompleteSelectWidget(AutocompleteWidgetMixin, autocomplete.ModelSelect2):
     pass

hawc/apps/common/flavors/help_text.py

@@ -12,13 +12,13 @@
         StudyPopulation=dict(
             design=(
                 "Choose the most specific description of study design. See “Epidemiology Terms Appendix“ for additional guidance: "
-                "<a target='_new' href='https://hawcprd.epa.gov/assessment/100000039/'>https://hawcprd.epa.gov/assessment/100000039/</a>. "
+                "<a target='_new' href='https://hawc.epa.gov/assessment/100000039/'>https://hawc.epa.gov/assessment/100000039/</a>. "
                 "<span class='important-note'>This field is commonly used in HAWC visualizations</span>"
             ),
         ),
         Outcome=dict(
             name=(
-                "Follow “Recommended Terminology for Outcomes/Endpoints“: <a target='_new' href='https://hawcprd.epa.gov/assessment/100000039/'>https://hawcprd.epa.gov/assessment/100000039/</a>. "
+                "Follow “Recommended Terminology for Outcomes/Endpoints“: <a target='_new' href='https://hawc.epa.gov/assessment/100000039/'>https://hawc.epa.gov/assessment/100000039/</a>. "
                 "Use title style (capitalize all words). Ex. Hyperthyroidism <span class='important-note'>This field is commonly used in HAWC visualizations</span>"
             ),
             effects=(
@@ -28,17 +28,17 @@
             ),
             system=(
                 "Enter biological system affected, following “Recommended Terminology for Outcomes/Endpoints“: "
-                "<a target='_new' href='https://hawcprd.epa.gov/assessment/100000039/'>https://hawcprd.epa.gov/assessment/100000039/</a>. "
+                "<a target='_new' href='https://hawc.epa.gov/assessment/100000039/'>https://hawc.epa.gov/assessment/100000039/</a>. "
                 "Use title style (capitalize all words). Ex. Endocrine"
             ),
             effect=(
                 "Enter effect, following “Recommended Terminology for Outcomes/Endpoints“: "
-                "<a target='_new' href='https://hawcprd.epa.gov/assessment/100000039/'>https://hawcprd.epa.gov/assessment/100000039/</a>. "
+                "<a target='_new' href='https://hawc.epa.gov/assessment/100000039/'>https://hawc.epa.gov/assessment/100000039/</a>. "
                 "Use title style (capitalize all words). Ex. Thyroid Hormones "
             ),
             effect_subtype=(
                 "Enter effect subtype, following “Recommended Terminology for Outcomes/Endpoints“: "
-                "<a target='_new' href='https://hawcprd.epa.gov/assessment/100000039/'>https://hawcprd.epa.gov/assessment/100000039/</a>."
+                "<a target='_new' href='https://hawc.epa.gov/assessment/100000039/'>https://hawc.epa.gov/assessment/100000039/</a>."
                 "Use title style (capitalize all words). Ex. Absolute "
                 "<i>This field is not mandatory; often no effect subtype is necessary</i>"
             ),

hawc/apps/common/helper.py

@@ -76,10 +76,6 @@ def strip_entities(value):
     return re.sub(r"&(?:\w+|#\d+);", "", force_str(value))
 
 
-def listToUl(list_):
-    return f"<ul>{''.join(['<li>{0}</li>'.format(d) for d in list_])}</ul>"
-
-
 def tryParseInt(
     value: Any, default: int = None, min_value: int = -inf, max_value: int = inf
 ) -> Optional[int]:

hawc/apps/common/serializers.py

@@ -299,7 +299,7 @@ def create(self, validated_data, *args, **kwargs):
 class FlexibleFieldsMixin:
     """
     Allows manipulation of fields on serializer instances.
-    This mixin is primarily meant for serailization and not deserialization.
+    This mixin is primarily meant for serialization and not deserialization.
 
     Constructor kwargs:
         fields (list[str]): allowlist of field names to include in serializer

hawc/apps/epi/api.py

@@ -512,21 +512,25 @@ def perform_update(self, serializer):
 
 class ComparisonSet(EditPermissionsCheckMixin, AssessmentEditViewset):
     edit_check_keys = ["study_population", "outcome"]
-    assessment_filter_args = "assessment"  # todo: fix
+    assessment_filter_args = "study_population__study__assessment"
     model = models.ComparisonSet
-    serializer_class = serializers.ComparisonSetSerializer
+
+    def get_serializer_class(self):
+        if self.action in ["list"]:
+            return serializers.ComparisonSetLinkSerializer
+        return serializers.ComparisonSetSerializer
 
 
 class GroupNumericalDescriptions(EditPermissionsCheckMixin, AssessmentEditViewset):
     edit_check_keys = ["group"]
-    # assessment_filter_args = "group__assessment"
+    assessment_filter_args = "group__comparison_set__study_population__study__assessment"
     model = models.GroupNumericalDescriptions
     serializer_class = serializers.GroupNumericalDescriptionsSerializer
 
 
 class Group(EditPermissionsCheckMixin, AssessmentEditViewset):
     edit_check_keys = ["comparison_set"]
-    assessment_filter_args = "assessment"  # todo: fix
+    assessment_filter_args = "comparison_set__study_population__study__assessment"
     model = models.Group
     serializer_class = serializers.GroupSerializer
 

hawc/apps/epi/models.py

@@ -984,6 +984,9 @@ def __str__(self):
     def get_assessment(self):
         return self.group.get_assessment()
 
+    def get_absolute_url(self):
+        return self.group.get_absolute_url()
+
 
 class ResultMetric(models.Model):
     objects = managers.ResultMetricManager()

hawc/apps/epi/templates/epi/comparisonset_form.html

@@ -28,7 +28,7 @@
 
 {% block extrajs %}
   <script type="text/javascript">
-    $(document).on('ready', function(){
+    window.addEventListener("DOMContentLoaded", function(){
       new window.app.DynamicFormset($('#gFormset'), 'form', {oneFormRequired: true});
       $('#gFormset').insertBefore($('#gcForm .form-actions'));
     });

hawc/apps/epi/templates/epi/exposure_form.html

@@ -17,7 +17,7 @@
 
 {% block extrajs %}
   <script type="text/javascript">
-    $(document).on('ready', function () {
+    window.addEventListener("DOMContentLoaded", function () {
       new window.app.DynamicFormset($('#ctFormset'), 'form', { oneFormRequired: true });
       $('#ctFormset').insertBefore($('.form-actions'));
     });

hawc/apps/epi/templates/epi/group_form.html

@@ -33,7 +33,7 @@
 
 {% block extrajs %}
   <script type="text/javascript">
-    $(document).on('ready', function(){
+    window.addEventListener("DOMContentLoaded", function(){
       new window.app.DynamicFormset($('#gnFormset'), 'form', {oneFormRequired: true});
       $('#gnFormset').insertBefore($('#gForm .form-actions'));
     });

hawc/apps/epi/templates/epi/result_form.html

@@ -21,7 +21,7 @@
 
 {% block extrajs %}
   <script type="text/javascript">
-    $(document).on('ready', function(){
+    window.addEventListener("DOMContentLoaded", function(){
 
       var printf = window.app.HAWCUtils.printf,
           elFormset = $("#rFormset").insertBefore($('#rForm .form-actions')),

hawc/apps/hawc_admin/api.py

@@ -39,7 +39,7 @@ class ReportsViewset(viewsets.ViewSet):
 
     @action(detail=False, renderer_classes=PandasRenderers)
     def values(self, request):
-        """Gets all value data accross all assessments."""
+        """Gets all value data across all assessments."""
         export = ValuesListExport(
             queryset=AssessmentValue.objects.all(), filename="hawc-assessment-values"
         ).build_export()

hawc/apps/invitro/api.py

@@ -46,13 +46,13 @@ def full_export(self, request, pk):
 
 
 class IVChemical(AssessmentViewset):
-    assessment_filter_args = "assessment"
+    assessment_filter_args = "study__assessment"
     model = models.IVChemical
     serializer_class = serializers.IVChemicalSerializer
 
 
 class IVCellType(AssessmentViewset):
-    assessment_filter_args = "assessment"
+    assessment_filter_args = "study__assessment"
     model = models.IVCellType
     serializer_class = serializers.IVCellTypeSerializer
 

hawc/apps/invitro/templates/invitro/ivendpoint_form.html

@@ -47,7 +47,7 @@
         },
     };
 
-    $(document).on('ready', function(){
+    window.addEventListener("DOMContentLoaded", function(){
         new window.app.DynamicFormset($('#egFormset'), 'form', {oneFormRequired: false});
         $('#egFormset').insertBefore($('#eForm .form-actions'));
         $('#egBenchmarkFormset').insertBefore($('#eForm .form-actions'));