Chore/hawc-1169 merge bioassay branch

client/hawc_client/animal.py

@@ -152,6 +152,30 @@ def bmds_endpoints(self, assessment_id: int, unpublished: bool = False) -> pd.Da
         response_json = self.session.get(url, params=params).json()
         return pd.DataFrame(response_json)
 
+    def update_endpoint(self, endpoint_id: int, data: dict) -> dict:
+        """
+        Update an existing endpoint via PATCH.
+
+        Args:
+            endpoint_id (int): Endpoint ID
+            data (dict): fields to update
+
+        Returns:
+            dict: The resulting object, if update was successful
+        """
+        url = f"{self.session.root_url}/ani/api/endpoint/{endpoint_id}/"
+        return self.session.patch(url, data).json()
+
+    def delete_endpoint(self, endpoint_id: int) -> None:
+        """
+        Delete an endpoint.
+
+        Args:
+            endpoint_id (int): Endpoint ID
+        """
+        url = f"{self.session.root_url}/ani/api/endpoint/{endpoint_id}/"
+        self.session.delete(url)
+
     def metadata(self) -> dict:
         """
         Retrieves field choices for all animal models.

client/hawc_client/assessment.py

@@ -107,6 +107,125 @@ def delete(self, assessment_id: int) -> Response:
         url = f"{self.session.root_url}/assessment/api/assessment/{assessment_id}/"
         return self.session.delete(url)
 
+    def list_species(self) -> list[dict]:
+        """
+        List all species.
+
+        Returns:
+            list[dict]: Species data
+        """
+        url = f"{self.session.root_url}/assessment/api/species/"
+        return self.session.get(url).json()
+
+    def create_species(self, data: dict) -> dict:
+        """
+        Create a new species.
+
+        Args:
+            data (dict): required metadata (name)
+
+        Returns:
+            dict: The created species
+        """
+        url = f"{self.session.root_url}/assessment/api/species/"
+        return self.session.post(url, data).json()
+
+    def update_species(self, species_id: int, data: dict) -> dict:
+        """
+        Update an existing species.
+
+        Args:
+            species_id (int): species ID
+            data (dict): fields to update
+
+        Returns:
+            dict: The updated species
+        """
+        url = f"{self.session.root_url}/assessment/api/species/{species_id}/"
+        return self.session.patch(url, data).json()
+
+    def delete_species(self, species_id: int) -> Response:
+        """
+        Delete a species.
+
+        Args:
+            species_id (int): species ID
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/assessment/api/species/{species_id}/"
+        return self.session.delete(url)
+
+    def list_strains(self, species_id: int | None = None) -> list[dict]:
+        """
+        List all strains, optionally filtered by species.
+
+        Args:
+            species_id (int, optional): Filter by species ID
+
+        Returns:
+            list[dict]: Strain data
+        """
+        url = f"{self.session.root_url}/assessment/api/strain/"
+        params = {}
+        if species_id is not None:
+            params["species"] = species_id
+        return self.session.get(url, params=params).json()
+
+    def create_strain(self, data: dict) -> dict:
+        """
+        Create a new strain.
+
+        Args:
+            data (dict): required metadata (name, species)
+
+        Returns:
+            dict: The created strain
+        """
+        url = f"{self.session.root_url}/assessment/api/strain/"
+        return self.session.post(url, data).json()
+
+    def update_strain(self, strain_id: int, data: dict) -> dict:
+        """
+        Update an existing strain.
+
+        Args:
+            strain_id (int): strain ID
+            data (dict): fields to update
+
+        Returns:
+            dict: The updated strain
+        """
+        url = f"{self.session.root_url}/assessment/api/strain/{strain_id}/"
+        return self.session.patch(url, data).json()
+
+    def delete_strain(self, strain_id: int) -> Response:
+        """
+        Delete a strain.
+
+        Args:
+            strain_id (int): strain ID
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/assessment/api/strain/{strain_id}/"
+        return self.session.delete(url)
+
+    def create_dose_units(self, name: str) -> dict:
+        """
+        Create a new dose unit.
+
+        Args:
+            name (str): Name of the dose unit
+
+        Returns:
+            dict: The created dose unit
+        """
+        url = f"{self.session.root_url}/ani/api/dose-units/"
+        return self.session.post(url, {"name": name}).json()
+
     def effect_tag_create(self, name: str, slug: str) -> dict:
         """Create an effect tag.
 

client/hawc_client/literature.py

@@ -36,6 +36,20 @@ def _import(
         url = f"{self.session.root_url}/lit/api/search/"
         return self.session.post(url, payload).json()
 
+    def create_reference(self, data: dict) -> dict:
+        """
+        Create a manual reference (no external ID required).
+
+        Args:
+            data (dict): Reference data. Required: assessment, title.
+                Optional: authors_short, authors, year, journal, abstract, full_text_url.
+
+        Returns:
+            dict: The created reference
+        """
+        url = f"{self.session.root_url}/lit/api/reference/"
+        return self.session.post(url, data).json()
+
     def import_hero(self, assessment_id: int, title: str, description: str, ids: list[int]) -> dict:
         """
         Imports a list of HERO IDs as literature references for the given assessment.

client/hawc_client/vocab.py

@@ -1,3 +1,5 @@
+from requests import Response
+
 from .client import BaseClient
 
 
@@ -32,6 +34,112 @@ def bulk_update(self, terms: list[dict]) -> list[dict]:
         url = f"{self.session.root_url}/vocab/api/term/bulk-update/"
         return self.session.patch(url, terms).json()
 
+    def list_guidelines(self) -> list[dict]:
+        """
+        List all guidelines.
+
+        Returns:
+            list[dict]: Guideline data
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline/"
+        return self.session.get(url).json()
+
+    def create_guideline(self, data: dict) -> dict:
+        """
+        Create a new guideline.
+
+        Args:
+            data (dict): required metadata
+
+        Returns:
+            dict: The created guideline
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline/"
+        return self.session.post(url, data).json()
+
+    def update_guideline(self, guideline_id: int, data: dict) -> dict:
+        """
+        Update an existing guideline.
+
+        Args:
+            guideline_id (int): guideline ID
+            data (dict): fields to update
+
+        Returns:
+            dict: The updated guideline
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline/{guideline_id}/"
+        return self.session.patch(url, data).json()
+
+    def delete_guideline(self, guideline_id: int) -> Response:
+        """
+        Delete a guideline.
+
+        Args:
+            guideline_id (int): guideline ID
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline/{guideline_id}/"
+        return self.session.delete(url)
+
+    def list_guideline_profiles(self, guideline_id: int | None = None) -> list[dict]:
+        """
+        List all guideline profiles, optionally filtered by guideline.
+
+        Args:
+            guideline_id (int, optional): Filter by guideline ID
+
+        Returns:
+            list[dict]: GuidelineProfile data
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline-profile/"
+        params = {}
+        if guideline_id is not None:
+            params["guideline"] = guideline_id
+        return self.session.get(url, params=params).json()
+
+    def create_guideline_profile(self, data: dict) -> dict:
+        """
+        Create a new guideline profile.
+
+        Args:
+            data (dict): required metadata
+
+        Returns:
+            dict: The created guideline profile
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline-profile/"
+        return self.session.post(url, data).json()
+
+    def update_guideline_profile(self, profile_id: int, data: dict) -> dict:
+        """
+        Update an existing guideline profile.
+
+        Args:
+            profile_id (int): guideline profile ID
+            data (dict): fields to update
+
+        Returns:
+            dict: The updated guideline profile
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline-profile/{profile_id}/"
+        return self.session.patch(url, data).json()
+
+    def delete_guideline_profile(self, profile_id: int) -> Response:
+        """
+        Delete a guideline profile.
+
+        Args:
+            profile_id (int): guideline profile ID
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/vocab/api/guideline-profile/{profile_id}/"
+        return self.session.delete(url)
+
     def uids(self) -> list[tuple[int, int]]:
         """
         Get all term ids and uids.

docs/docs/database.md

@@ -18,6 +18,11 @@ The HAWC database is a [PostgreSQL](https://www.postgresql.org/) database. See d
 
 ## Animal bioassay schema
 
+<figure markdown>
+  ![HAWC animal bioassay v2 data schema](./static/img/hawc-schema-animalv2.png)
+  <figcaption>Animal bioassay v2 schema. The image is very large; please save/or open in another tab.</figcaption>
+</figure>
+
 <figure markdown>
   ![HAWC animal bioassay data schema](./static/img/hawc-schema-animal.png)
   <figcaption>Animal bioassay schema. The image is very large; please save/or open in another tab.</figcaption>
@@ -84,6 +89,7 @@ pip install -U pydot
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-lit.png lit study
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-study.png study riskofbias
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-animal.png animal
+manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-animalv2.png animalv2
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-bmd.png bmd
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-epi.png epi
 manage graph_models -g --pydot -o ./docs/docs/static/img/hawc-schema-epiv2.png epiv2

docs/docs/development.md

@@ -44,6 +44,10 @@ uv pip install -e client
 # create a PostgreSQL database and superuser
 createuser --superuser --no-password hawc
 createdb -E UTF-8 -U hawc hawc
+
+# create test databases (required for running unit tests)
+createdb -T template0 -E UTF8 hawc-fixture
+createdb -T template0 -E UTF8 hawc-test
 ```
 
 For Windows, using Anaconda or Miniconda is preferred for additional dependencies:
@@ -76,9 +80,12 @@ pg_ctl -D pgdata initdb
 mkdir pgdata\logs
 pg_ctl -D pgdata -l pgdata\logs\logfile start
 
-:: create our superuser and main/test databases
+:: create a PostgreSQL database and superuser
 createuser --superuser --no-password hawc
 createdb -T template0 -E UTF8 hawc
+
+:: create test databases (required for running unit tests)
+createdb -T template0 -E UTF8 hawc-fixture
 createdb -T template0 -E UTF8 hawc-test
 ```
 

frontend/animal/EndpointForm/constants.js

@@ -62,14 +62,14 @@ const termUrlLookupMap = {
             endpoint_name_parent: "effect_subtype_term_id",
         },
         helpText: {
-            system_popup: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. "Multi-system" is an option for widespread effects. If the Endpoint is measured in Blood, Urine, or biological media other than the affected system, extract the media term in the Effect Subtype field.`,
+            system_popup: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. 'System' maps to 'endpoint_category' in ToxRefDB as the broadest descriptive term for an endpoint. Possible endpoint categories include: systemic, developmental, reproductive, and cholinesterase.`,
             system: `The health effect category/biological system an endpoint/outcome or group of related endpoints/outcomes within a health effect category. Please use a controlled vocabulary term if possible.`,
-            effect_popup: `A group of related outcomes considered as a health effect category and/or unit of analysis typically considered together during evidence synthesis.`,
+            effect_popup: `A group of related outcomes considered as a health effect category and/or unit of analysis typically considered together during evidence synthesis. 'Effect' maps to 'endpoint_type' in ToxRefDB as a subcategory for endpoint_category, which is more descriptive for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive performance, etc.`,
             effect: `Related outcomes (e.g., unit of analysis) considered together during evidence synthesis. Please use a controlled vocabulary term if possible.`,
-            effect_subtype_popup: `An outcome or measurement within an effect.`,
+            effect_subtype_popup: `An outcome or measurement within an effect. 'Effect_subtype' maps to 'Endpoint_target' in ToxRefDB indicating where or how the sample was collected to supply data for a particular endpoint. Typically describes an organ/tissue or metabolite/protein measured.`,
             effect_subtype: `Please use a controlled vocabulary term if possible.`,
             endpoint_name_popup: `An observable or measurable biological change used as an index of a potential health effect of an exposure. Endpoint may also be referred to as effect, outcome, or event. Search for the best match based on the author reported term. Use the field "Diagnostic (as reported)" to capture as reported by study authors. If no existing term matches, deselect use EHV for endpoint and enter the name as reported. Do not include units. If an endpoint is a repeated measure, indicate the time in parentheses, [e.g., running wheel activity (6 wk)], using the abbreviated format: seconds = sec, minutes = min, hours = h, days = d, weeks = wk, months = mon, years = y.`,
-            endpoint_name: `An observable or measurable biological change used as an index of a potential health effect of an exposure. Endpoint may also be referred to as effect or outcome. For a searchable list of ToxRefDB Vocabulary terms, see the <a href="/vocab/toxrefdb/">ToxRefDB.</a> Enter the term ID and all relationships to this term will automatically populate. Please use a controlled vocabulary term if possible.`,
+            endpoint_name: `An observable or measurable biological change used as an index of a potential health effect of an exposure. 'Endpoint_name' maps to 'Effect_desc' in ToxRefDB, detailing a specific condition associated with an endpoint_target (e.g. dysplasia, atrophy, necrosis, etc.`,
         },
     },
     defaultHelpText = {

frontend/animal/VocabBrowser/ToxRefDBBrowser/Table.js

@@ -44,28 +44,28 @@ class Table extends Component {
                         <thead>
                             <tr>
                                 <th>
-                                    Endpoint Category
+                                    System
                                     <HelpTextPopup
                                         title="Endpoint Category"
                                         content={helpText.system_popup}
                                     />
                                 </th>
                                 <th>
-                                    Endpoint Type
+                                    Effect
                                     <HelpTextPopup
                                         title="Endpoint Type"
                                         content={helpText.effect_popup}
                                     />
                                 </th>
                                 <th>
-                                    Endpoint Target
+                                    Effect Subtype
                                     <HelpTextPopup
                                         title="Endpoint Target"
                                         content={helpText.effect_subtype_popup}
                                     />
                                 </th>
                                 <th>
-                                    Effect Description
+                                    Endpoint/Outcome
                                     <HelpTextPopup
                                         title="Effect Description"
                                         content={helpText.endpoint_name_popup}