CPHEAPM-27 Add ToxRefDB to Update Vocab Endpoint (#1075)

* feat: add ToxRef vocab fixture and migration, create a new vocabulary page * test: create toxref vocab tests * fix: refactor vocab additions * update vocab files for testing and run lint * fix: account for undefined vocab * update: implement toxrefdb in 'update modules' * update the endpoint model to account for ToxRefDB * bump django version minimum * minor edits from code review * fix api endpoint * add staticmethod props * text updates * remove debugging * revise lookups * use a lookup * format --------- Co-authored-by: Zindah, Farha <63080@icf.com> Co-authored-by: Andy Shapiro <shapiromatron@gmail.com>
shapiromatron · Sep 10, 2024 · 3d9a079 · 3d9a079
1 parent 87f9d7f
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diff --git a/frontend/animal/EndpointForm/TermSelector.js b/frontend/animal/EndpointForm/TermSelector.js
@@ -32,7 +32,7 @@ class TermSelector extends Component {
                 store,
                 parentRequired,
             } = this.props,
-            {object, debug, vocabulary_display} = store.config,
+            {object, vocabulary_display} = store.config,
             useControlledVocabulary = store.useControlledVocabulary[termTextField],
             currentId = object[termIdField],
             currentText = object[termTextField],
@@ -50,9 +50,7 @@ class TermSelector extends Component {
                                 style={{maxWidth: 130}}
                                 value={this.state.idLookupValue}
                                 onChange={event =>
-                                    this.setState({
-                                        idLookupValue: parseInt(event.target.value),
-                                    })
+                                    this.setState({idLookupValue: parseInt(event.target.value)})
                                 }
                             />
                             <div className="input-group-append">
@@ -136,13 +134,6 @@ class TermSelector extends Component {
                         className="form-text text-muted"
                         dangerouslySetInnerHTML={{__html: helpText}}></small>
                 ) : null}
-                {debug ? (
-                    <ul>
-                        <li>termId: {currentId}</li>
-                        <li>text: {currentText}</li>
-                        <li>parent: {object[parentIdField]}</li>
-                    </ul>
-                ) : null}
             </div>
         );
     }

diff --git a/frontend/animal/EndpointForm/components/VocabTermFields.js b/frontend/animal/EndpointForm/components/VocabTermFields.js
@@ -19,19 +19,17 @@ class VocabTermFields extends Component {
             rowClass = label.organ ? "col-md-3" : "col-md-4";
         return (
             <>
-                {label.endpoint_name ? (
-                    <TermSelector
-                        name={"name"}
-                        label={label.endpoint_name}
-                        helpText={helpTextName}
-                        popupHelpText={helpText.endpoint_name_popup}
-                        termIdField={"name_term_id"}
-                        termTextField={"name"}
-                        parentIdField={termParent.endpoint_name_parent}
-                        parentRequired={true}
-                        idLookupAction={store.endpointNameLookup}
-                    />
-                ) : null}
+                <TermSelector
+                    name={"name"}
+                    label={label.endpoint_name}
+                    helpText={helpTextName}
+                    popupHelpText={helpText.endpoint_name_popup}
+                    termIdField={"name_term_id"}
+                    termTextField={"name"}
+                    parentIdField={termParent.endpoint_name_parent}
+                    parentRequired={true}
+                    idLookupAction={store.endpointNameLookup}
+                />
 
                 <div className="row">
                     <div className={rowClass}>

diff --git a/frontend/animal/EndpointForm/constants.js b/frontend/animal/EndpointForm/constants.js
@@ -9,6 +9,8 @@ const termUrlLookupMap = {
         "effect_term_id-2": "/vocab/api/toxrefdb/effect/?format=json",
         "effect_subtype_term_id-2": "/vocab/api/toxrefdb/effect_subtype/?format=json",
         "name_term_id-2": "/vocab/api/toxrefdb/endpoint_name/?format=json",
+        "id-lookup-1": "/vocab/api/ehv/:id/endpoint-name-lookup/",
+        "id-lookup-2": "/vocab/api/toxrefdb/:id/endpoint-name-lookup/",
     },
     termUrlLookup = function(term, vocab) {
         return termUrlLookupMap[`${term}-${vocab}`];

diff --git a/frontend/animal/EndpointForm/store.js b/frontend/animal/EndpointForm/store.js
@@ -2,6 +2,8 @@ import _ from "lodash";
 import {action, computed, observable} from "mobx";
 import h from "shared/utils/helpers";
 
+import {termUrlLookup} from "./constants";
+
 const fields = ["system", "organ", "effect", "effect_subtype", "name"];
 
 class EndpointFormStore {
@@ -34,7 +36,7 @@ class EndpointFormStore {
 
     @action.bound
     endpointNameLookup(val) {
-        const url = `/vocab/api/ehv/${val}/endpoint-name-lookup/`;
+        const url = termUrlLookup("id-lookup", this.config.vocabulary).replace(":id", val);
 
         if (!val) {
             return;

diff --git a/frontend/shared/components/AutocompleteTerm.js b/frontend/shared/components/AutocompleteTerm.js
@@ -14,10 +14,6 @@ import {
 } from "./Autocomplete/constants";
 
 class AutocompleteTerm extends Component {
-    /*
-    Autocomplete widget; works with `hawc.apps.vocab.api.EhvTermViewSet`
-    */
-
     constructor(props) {
         super(props);
         this.state = {

diff --git a/hawc/apps/animal/forms.py b/hawc/apps/animal/forms.py
@@ -453,14 +453,9 @@ def helper(self):
         if vocab_enabled:
             vocab_id = self.instance.assessment.vocabulary
             vocab_url = VocabularyNamespace(vocab_id).display_url
-            vocab = f"""&nbsp;The <a href="{vocab_url}">
-                {VocabularyNamespace(vocab_id).display_name}</a> is enabled for this assessment. Browse to view
-                controlled terms, and whenever possible please use these terms."""
+            vocab = f"""The <a href="{vocab_url}">{VocabularyNamespace(vocab_id).display_name}</a> is enabled for this assessment. Browse to view controlled terms, and whenever possible please use these terms."""
         else:
-            vocab = f"""&nbsp;A controlled vocabulary is not enabled for this assessment.
-                However, you can still browse the <a href="{reverse('vocab:ehv-browse')}"></a>
-                  to see if this vocabulary would be a good fit for your
-                assessment. If it is, consider updating the assessment to use this vocabulary."""
+            vocab = f"""A controlled vocabulary is not enabled for this assessment. However, you can still browse the <a href="{reverse('vocab:ehv-browse')}">EHV</a> to see if this vocabulary would be a good fit for your assessment."""
 
         if self.instance.id:
             inputs = {
@@ -471,9 +466,7 @@ def helper(self):
         else:
             inputs = {
                 "legend_text": "Create new endpoint",
-                "help_text": f"""Create a new endpoint. An endpoint may should describe one
-                    measure-of-effect which was measured in the study. It may
-                    or may not contain quantitative data.{vocab}""",
+                "help_text": f"""Create a new endpoint. An endpoint should describe one measure-of-effect in the study. It may or may not contain quantitative data. {vocab}""",
                 "cancel_url": self.instance.animal_group.get_absolute_url(),
             }
 

diff --git a/hawc/apps/animal/managers.py b/hawc/apps/animal/managers.py
@@ -481,13 +481,11 @@ def _validate_update_terms(self, objs: list[dict], assessment: Assessment):
     @transaction.atomic
     def update_terms(self, objs: list[dict], assessment: Assessment) -> list:
         """
-        Updates all of the terms and respective text fields
-        for a list of endpoints based on the given name term.
-        All endpoints must be from the same assessment.
+        Updates all of the terms and respective text fields for a list of endpoints based on the
+        given name term. All endpoints must be from the same assessment.
 
         Args:
-            objs (list[dict]): List of endpoint dicts, where each dict has
-                for keys 'id' and 'name_term_id'
+            objs (list[dict]): Endpoint dicts, where each dict has keys "id" and "name_term_id"
             assessment (Assessment): Assessment for endpoints
 
         Returns:
@@ -500,7 +498,7 @@ def update_terms(self, objs: list[dict], assessment: Assessment) -> list:
         endpoint_id_to_term_id = {obj["id"]: obj["name_term_id"] for obj in objs}
 
         # set endpoint terms
-        terms_df = Term.ehv_dataframe()
+        terms_df = Term.vocab_dataframe(assessment.vocabulary)
         endpoint_ids = [obj["id"] for obj in objs]
         endpoints = self.get_queryset().filter(pk__in=endpoint_ids)
         type_to_text_field = VocabularyTermType.value_to_text_field()

diff --git a/hawc/apps/animal/models.py b/hawc/apps/animal/models.py
@@ -21,6 +21,7 @@
     tryParseInt,
 )
 from ..study.models import Study
+from ..vocab.constants import VocabularyNamespace
 from ..vocab.models import Term
 from . import constants, managers
 
@@ -806,12 +807,11 @@ def unique_items(els):
 
     @classmethod
     def get_vocabulary_settings(cls, assessment: Assessment, form: ModelForm) -> str:
+        vocab = VocabularyNamespace(assessment.vocabulary) if assessment.vocabulary else None
         return json.dumps(
             {
-                "debug": False,
-                "vocabulary": assessment.vocabulary,
-                "vocabulary_url": assessment.get_vocabulary_url(),
-                "vocabulary_display": assessment.get_vocabulary_display(),
+                "vocabulary": vocab.value if vocab else None,
+                "vocabulary_display": vocab.display_name if vocab else None,
                 "object": {
                     "system": form["system"].value() or "",
                     "organ": form["organ"].value() or "",

diff --git a/hawc/apps/assessment/models.py b/hawc/apps/assessment/models.py
@@ -366,15 +366,8 @@ def user_is_project_manager_or_higher(self, user) -> bool:
         perms = self.get_permissions()
         return perms.project_manager_or_higher(user)
 
-    def get_vocabulary_display(self) -> str:
-        # override default method
-        if self.vocabulary:
-            return VocabularyNamespace(self.vocabulary).display_name
-        else:
-            return ""
-
-    def get_vocabulary_url(self) -> str | None:
-        return VocabularyNamespace(self.vocabulary).display_url if self.vocabulary else None
+    def get_vocabulary_display(self) -> str | None:
+        return VocabularyNamespace(self.vocabulary).display_name if self.vocabulary else None
 
     def get_noel_names(self) -> NoelNames:
         if self.noel_name == constants.NoelName.NEL:

diff --git a/hawc/apps/vocab/api.py b/hawc/apps/vocab/api.py
@@ -72,16 +72,19 @@ def endpoint_name(self, request: Request) -> Response:
 
     @action(detail=True, url_path="endpoint-name-lookup")
     def endpoint_name_lookup(self, request: Request, pk: int) -> Response:
-        try:
-            term = models.Term.objects.get(
+        term = (
+            models.Term.objects.filter(
                 id=pk,
                 type=constants.VocabularyTermType.endpoint_name,
                 namespace=self.namespace,
                 deprecated_on__isnull=True,
             )
-        except models.Term.DoesNotExist as err:
-            raise exceptions.NotFound() from err
-        return Response(term.vocab_endpoint_name())
+            .select_related("parent__parent__parent__parent")
+            .first()
+        )
+        if term is None:
+            raise exceptions.NotFound()
+        return Response(term.inheritance())
 
     @action(detail=True, methods=("post",), url_path="related-entity")
     def related_entity(self, request: Request, pk: int | None = None) -> Response:

diff --git a/hawc/apps/vocab/constants.py b/hawc/apps/vocab/constants.py
@@ -1,6 +1,5 @@
 from django.db.models import IntegerChoices
-from django.urls import reverse_lazy
-from django.utils.functional import classproperty
+from django.urls import reverse
 
 
 class VocabularyNamespace(IntegerChoices):
@@ -12,25 +11,25 @@ class VocabularyNamespace(IntegerChoices):
     EHV = 1, "EHV"
     ToxRefDB = 2, "ToxRefDB"
 
-    @classproperty
-    def display_dict(cls) -> dict:
-        return {1: "EPA Environmental health vocabulary", 2: "EPA ToxRefDB vocabulary"}
-
-    @classproperty
-    def display_urls(cls) -> dict:
-        return {1: reverse_lazy("vocab:ehv-browse"), 2: reverse_lazy("vocab:toxrefdb-browse")}
-
     @classmethod
     def display_choices(cls) -> list:
-        return [(key, value) for key, value in cls.display_dict.items()]
+        return [(item, item.display_name) for item in cls]
 
     @property
     def display_url(self) -> str:
-        return self.display_urls[self.value].lower()
+        match self:
+            case self.EHV:
+                return reverse("vocab:ehv-browse")
+            case self.ToxRefDB:
+                return reverse("vocab:toxrefdb-browse")
 
     @property
     def display_name(self) -> str:
-        return self.display_dict[self.value]
+        match self:
+            case self.EHV:
+                return "EPA Environmental health vocabulary"
+            case self.ToxRefDB:
+                return "EPA ToxRefDB vocabulary"
 
 
 class VocabularyTermType(IntegerChoices):

diff --git a/hawc/apps/vocab/models.py b/hawc/apps/vocab/models.py
@@ -35,6 +35,14 @@ def deprecated(self) -> bool:
     def get_admin_edit_url(self) -> str:
         return reverse("admin:vocab_term_change", args=(self.id,))
 
+    @classmethod
+    def vocab_dataframe(cls, namespace: constants.VocabularyNamespace) -> pd.DataFrame:
+        dataframes = {
+            constants.VocabularyNamespace.EHV: cls.ehv_dataframe,
+            constants.VocabularyNamespace.ToxRefDB: cls.toxrefdb_dataframe,
+        }
+        return dataframes[namespace]()
+
     @classmethod
     def ehv_dataframe(cls) -> pd.DataFrame:
         vocab_data = cls.vocab_data(constants.VocabularyNamespace.EHV)
@@ -44,23 +52,21 @@ def ehv_dataframe(cls) -> pd.DataFrame:
             {"df": vocab_data["effect_subtype"], "left_on": "effect_term_id"},
             {"df": vocab_data["endpoint_name"], "left_on": "effect_subtype_term_id"},
         ]
-
         df = cls.merge_data(vocab_data["system"], term_data)
         return df
 
     @classmethod
     def toxrefdb_dataframe(cls) -> pd.DataFrame:
         vocab_data = cls.vocab_data(constants.VocabularyNamespace.ToxRefDB)
-
         term_data = [
             {"df": vocab_data["effect"], "left_on": "system_term_id"},
             {"df": vocab_data["effect_subtype"], "left_on": "effect_term_id"},
             {"df": vocab_data["endpoint_name"], "left_on": "effect_subtype_term_id"},
         ]
-
         df = cls.merge_data(vocab_data["system"], term_data)
         return df
 
+    @staticmethod
     def vocab_data(namespace) -> dict:
         cols = ("id", "type", "parent_id", "name")
         all_df = pd.DataFrame(
@@ -109,6 +115,7 @@ def vocab_data(namespace) -> dict:
 
         return data
 
+    @staticmethod
     def merge_data(df, data):
         # merge df queries based on relevant hierarchy
         for term in data:
@@ -119,19 +126,34 @@ def merge_data(df, data):
         df = df.sort_values(by=[term["left_on"] for term in data]).reset_index(drop=True)
         return df
 
-    def vocab_endpoint_name(self) -> dict:
-        return {
-            "system": self.parent.parent.parent.parent.name,
-            "organ": self.parent.parent.parent.name,
-            "effect": self.parent.parent.name,
-            "effect_subtype": self.parent.name,
-            "name": self.name,
-            "system_term_id": self.parent.parent.parent.parent.id,
-            "organ_term_id": self.parent.parent.parent.id,
-            "effect_term_id": self.parent.parent.id,
-            "effect_subtype_term_id": self.parent.id,
-            "name_term_id": self.id,
-        }
+    def inheritance(self) -> dict:
+        if self.namespace == constants.VocabularyNamespace.EHV:
+            return {
+                "system": self.parent.parent.parent.parent.name,
+                "organ": self.parent.parent.parent.name,
+                "effect": self.parent.parent.name,
+                "effect_subtype": self.parent.name,
+                "name": self.name,
+                "system_term_id": self.parent.parent.parent.parent.id,
+                "organ_term_id": self.parent.parent.parent.id,
+                "effect_term_id": self.parent.parent.id,
+                "effect_subtype_term_id": self.parent.id,
+                "name_term_id": self.id,
+            }
+        elif self.namespace == constants.VocabularyNamespace.ToxRefDB:
+            return {
+                "system": self.parent.parent.parent.name,
+                "organ": None,
+                "effect": self.parent.parent.name,
+                "effect_subtype": self.parent.name,
+                "name": self.name,
+                "system_term_id": self.parent.parent.parent.id,
+                "organ_term_id": None,
+                "effect_term_id": self.parent.parent.id,
+                "effect_subtype_term_id": self.parent.id,
+                "name_term_id": self.id,
+            }
+        raise ValueError(f"Invalid namespace: {self.namespace}")
 
 
 class Entity(models.Model):

diff --git a/pyproject.toml b/pyproject.toml
@@ -18,7 +18,7 @@ classifiers = [
 requires-python = ">=3.12"
 dependencies = [
   # web application
-  "Django~=5.1",
+  "Django~=5.1.1",
   "django-crispy-forms==2.2",
   "crispy-bootstrap4==2024.1",
   "django-filter==24.2",