Merge branch 'main' into bulk-publish-labels

.github/workflows/main.yml

@@ -78,7 +78,7 @@ jobs:
         fi
         coverage run -m pytest --record-mode=none
         echo "# Python coverage report" >> $GITHUB_STEP_SUMMARY
-        coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
+        coverage report --format=markdown -i >> $GITHUB_STEP_SUMMARY || true
         coverage html -d coverage -i
     - name: loc
       run: |
@@ -99,7 +99,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-node@v4
       with:
-        node-version: 20
+        node-version: 22
         cache: 'yarn'
         cache-dependency-path: 'frontend/yarn.lock'
     - name: install

client/hawc_client/literature.py

@@ -1,4 +1,5 @@
 import pandas as pd
+from requests import Response
 
 from .client import BaseClient
 
@@ -303,3 +304,60 @@ def update_references_from_hero(self, assessment_id: int) -> None:
         """
         url = f"{self.session.root_url}/lit/api/assessment/{assessment_id}/update-reference-metadata-from-hero/"
         self.session.post(url)
+
+    def create_tag(self, data: dict) -> dict:
+        """
+        Create a tag.
+
+        Args:
+            data (dict): required metadata for creation
+
+        Returns:
+            dict: The resulting object, if create was successful.
+        """
+        url = f"{self.session.root_url}/lit/api/tags/"
+        response = self.session.post(url, data)
+        return response.json()
+
+    def update_tag(self, tag_id: int, data: dict) -> dict:
+        """
+        Update an existing tag.
+
+        Args:
+            tag_id (int): Tag ID
+            data (dict): fields to update in tag
+
+        Returns:
+            dict: The resulting object, if update was successful.
+        """
+        url = f"{self.session.root_url}/lit/api/tags/{tag_id}/"
+        response = self.session.patch(url, data)
+        return response.json()
+
+    def delete_tag(self, tag_id: int) -> Response:
+        """
+        Delete a tag.
+
+        Args:
+            tag_id (int): Tag ID
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/lit/api/tags/{tag_id}/"
+        return self.session.delete(url)
+
+    def move_tag(self, tag_id: int, new_index: int) -> dict:
+        """
+        Change the order of a tag within its tagtree.
+
+        Args:
+            tag_id (int): Tag ID
+            new_index: Index to place this tag in relation to its siblings in the tagtree
+
+        Returns:
+            Response: The response object.
+        """
+        url = f"{self.session.root_url}/lit/api/tags/{tag_id}/move/"
+        body = {"newIndex": new_index}
+        return self.session.patch(url, body)

docs/docs/client.md

@@ -58,6 +58,10 @@ Client tutorials for common operations are below:
 
 ### Changelog
 
+#### NEXT (TBD)
+
+* Added literature tag API {create, update, delete, move}
+
 #### [2024-3](https://pypi.org/project/hawc-client/2024.3/) (October 2024)
 
 * Update data pivot and visual output formats to return JSON

docs/docs/development.md

@@ -6,7 +6,7 @@ following applications installed on your local development system:
 
 - [Git](https://git-scm.com/)
 - [Python](https://www.python.org/) == 3.12
-- [Node.js](https://nodejs.org)
+- [Node.js](https://nodejs.org) LTS v22
 - [Yarn](https://yarnpkg.com/) < 2
 - [PostgreSQL](https://www.postgresql.org/) >= 16
 

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

@@ -19,7 +19,7 @@ <h2>{{object}}{% debug_badge object.id %}</h2>
           {% endif %}
           <a class="dropdown-item" href="{{ object.get_clear_cache_url }}">Clear assessment cache</a>
           <a class="dropdown-item" href="{{ object.get_assessment_logs_url }}">View change logs</a>
-          <a class="dropdown-item" hx-get="{% url 'assessment:attachment-htmx' object.pk 'create' %}" hx-trigger="click" hx-target="#attach-tbody" hx-swap="beforeend" href="/">Add an attachment</a>
+          <a class="dropdown-item" hx-get="{% url 'assessment:attachment-htmx' object.pk 'create' %}" hx-trigger="click" hx-target=".attachment-edit-row.create-row" hx-swap="outerHTML" href="/">Add an attachment</a>
           <a class="dropdown-item" href="{% url 'assessment:dataset_create' object.pk %}">Add a dataset</a>
           <a class="dropdown-item" href="{% url 'assessment:values-create' object.pk %}">Add a value</a>
           <a class="dropdown-item" href="{% url 'assessment:manage-labels' object.pk %}">Manage labels</a>

hawc/apps/assessment/templates/assessment/fragments/attachment_edit_row.html

@@ -1,5 +1,5 @@
 
-<tr hx-target="this" hx-swap="outerHTML" class="attachment-edit-row">
+<tr hx-target="this" hx-swap="outerHTML" class="attachment-edit-row {% if form and not form.instance.id %} create-row {% endif %}">
   {% if form %}
     <td colspan="3" class="bg-lightblue">
       <form class="attachment-form pad-form p-3" method="post" enctype="multipart/form-data">
@@ -24,7 +24,7 @@
             </button>
             <button class="btn btn-light"
                     type='button'
-                    onclick="window.app.HAWCUtils.hideElement($(this).closest('.attachment-edit-row'), true)">
+                    onclick="window.app.HAWCUtils.hideElement($(this).closest('.attachment-edit-row'), false)">
               Cancel
             </button>
           {% endif %}

hawc/apps/assessment/templates/assessment/fragments/attachment_list.html

@@ -1,7 +1,7 @@
 <div class="hide-empty-tbody">
   <h2>Attachments</h2>
   <table class="table table-sm table-striped">
-    {% if canEdit %}
+    {% if canEdit or permissions.edit %}
       {% bs4_colgroup '25,50,25' %}
       {% bs4_thead 'Attachment,Description,Editing' %}
     {% else %}
@@ -12,6 +12,7 @@ <h2>Attachments</h2>
       {% for object in object_list %}
         {% include "assessment/fragments/attachment_row.html" %}
       {% endfor %}
+      {% include "common/fragments/_create_row.html" with model="attachment" first=True %}
     </tbody>
   </table>
 </div>

hawc/apps/assessment/templates/assessment/fragments/attachment_row.html

@@ -37,3 +37,4 @@
     </td>
   {% endif %}
 </tr>
+{% include "common/fragments/_create_row.html" %}

hawc/apps/assessment/templates/assessment/fragments/label_edit_row.html

@@ -1,5 +1,5 @@
 
-<div hx-target="this" hx-swap="outerHTML" class="label-edit-row list-group-item d-flex {% if action == 'delete' %} bg-pink {% else %} bg-lightblue {% endif %}">
+<div hx-target="this" hx-swap="outerHTML" class="label-edit-row list-group-item d-flex {% if action == 'delete' %} bg-pink {% else %} bg-lightblue {% endif %}{% if form and not form.instance.id %} create-row {% endif %}">
   <form method="post" class="d-flex align-items-center p-1 w-100">
     <div class="col-md-auto flex-fill pl-0 py-2">
       {% crispy form %}
@@ -62,7 +62,7 @@
         <button class="btn btn-light px-3 py-2 ml-2"
                 id="binding-cancel"
                 type='button'
-                onclick="window.app.HAWCUtils.hideElement($(this).closest('.label-edit-row'), true)">
+                onclick="window.app.HAWCUtils.hideElement($(this).closest('.label-edit-row'), false)">
           Cancel
         </button>
       {% endif %}

hawc/apps/assessment/templates/assessment/fragments/label_row.html

@@ -19,3 +19,6 @@
     </div>
   </div>
 </div>
+{% if action == 'create' %}
+  <div class="create-row hidden"></div>
+{% endif %}

hawc/apps/assessment/templates/assessment/label_list.html

@@ -5,8 +5,8 @@
     <h2 class="mb-0">Labels</h2>
     <button class="btn btn-primary ml-2 ml-auto align-self-start flex-shrink-0"
             hx-get="{% url 'assessment:label-htmx' assessment.pk 'create' %}"
-            hx-target="#label-listgroup"
-            hx-swap="beforeend">
+            hx-target=".create-row"
+            hx-swap="outerHTML">
       <i class="fa fa-fw fa-save"></i>&nbsp;
       Create label
     </button>
@@ -17,6 +17,7 @@ <h2 class="mb-0">Labels</h2>
         {% include "assessment/fragments/label_row.html" with canEdit=True %}
       {% endfor %}
       <div class="alert alert-info text-center show-only-child my-0">No labels created (yet).</div>
+      <div class="create-row hidden"></div>
     </div>
   </div>
 {% endblock content %}

hawc/apps/common/autocomplete/registry.py

@@ -1,5 +1,6 @@
-from django.core.exceptions import BadRequest, FieldError, ValidationError
+from django.core.exceptions import FieldError, ValidationError
 from django.http import Http404
+from django.http.response import HttpResponseBadRequest
 from django.utils.encoding import force_str
 from django.utils.module_loading import autodiscover_modules
 
@@ -50,8 +51,8 @@ def get_autocomplete(request, autocomplete_name):
         raise Http404(f"Autocomplete {autocomplete_name} not found") from err
     try:
         return autocomplete_cls.as_view()(request)
-    except (ValueError, ValidationError, FieldError) as err:
-        raise BadRequest(str(err)) from None
+    except (ValueError, ValidationError, FieldError):
+        return HttpResponseBadRequest("Bad request.")
 
 
 def autodiscover():

hawc/apps/common/templates/common/fragments/_create_card.html

@@ -1,3 +1,3 @@
 <h3 class="card-title">{{title}}
-  <button id="{{model}}-create" class="btn btn-sm btn-primary float-right" hx-get="{{hx_get}}" hx-target="{{hx_target}}" hx-swap="beforeend"><i class="fa fa-plus fa-fw"></i>&nbsp;{{btn_text}}</button>
+  <button id="{{model}}-create" class="btn btn-sm btn-primary float-right" hx-get="{{hx_get}}" hx-target="{{hx_target}}" hx-swap="outerHTML"><i class="fa fa-plus fa-fw"></i>&nbsp;{{btn_text}}</button>
 </h3>

hawc/apps/common/templates/common/fragments/_create_row.html

@@ -0,0 +1,3 @@
+{% if action == 'create' or action == 'clone' or first == True %}
+  <tr class="{{model}}-edit-row create-row hidden"></tr>
+{% endif %}

hawc/apps/common/templates/common/fragments/_object_edit_row.html

@@ -1,4 +1,4 @@
-<tr hx-target="this" hx-swap="outerHTML swap:0s" class="{{app}}-edit-row {{model}}-edit-row">
+<tr hx-target="this" hx-swap="outerHTML swap:0s" class="{{app}}-edit-row {{model}}-edit-row {% if form and not form.instance.id %} create-row {% endif %}">
   {% if form %}
     <td colspan="100%" class="p-3">
       <form method="post" class="border p-2 pb-4 edit-form-background rounded pad-form form-{{model}}">
@@ -18,7 +18,7 @@
               Save
             </button>
             <button id="{{model}}-cancel" class="btn btn-sm btn-light mx-2 py-2" type='button' style="width: 8rem; padding: 0.7rem;"
-                    onclick="window.app.HAWCUtils.hideElement($(this).closest('.{{app}}-edit-row'), true)"><i
+                    onclick="window.app.HAWCUtils.hideElement($(this).closest('.{{app}}-edit-row'), false)"><i
               class="fa fa-fw fa-times mr-1"></i>
               Cancel</button>
           {% endif %}

hawc/apps/common/templates/common/fragments/_object_row.html

@@ -20,7 +20,7 @@
     <button id="{{model}}-delete" class="btn btn-sm btn-danger" hx-get="{% crud_url app model 'delete' object.pk %}">
       <i class="fa fa-trash" aria-hidden="true"></i></button>
     <button id="{{model}}-clone" class="btn btn-sm btn-secondary" hx-post="{% crud_url app model 'clone' object.pk %}"
-            hx-target="#{{model}}-tbody" hx-swap="beforeend">
+            hx-target=".{{model}}-edit-row.create-row" hx-swap="outerHTML">
       <i class="fa fa-clone" aria-hidden="true"></i></button>
   </td>
 {% endif %}

hawc/apps/eco/templates/eco/design_update.html

@@ -13,15 +13,16 @@ <h2 class="d-inline-block">{{object.name}}</h2>
   <div class="card my-4 mx-2">
     <div class="card-body">
       {% url 'eco:cause-htmx' object.pk 'create' as cause_create %}
-      {% include "common/fragments/_create_card.html" with title="Causes" hx_get=cause_create hx_target="#cause-tbody" model="cause" btn_text="Create" %}
+      {% include "common/fragments/_create_card.html" with title="Causes" hx_get=cause_create hx_target=".cause-edit-row.create-row" model="cause" btn_text="Create" %}
       <table class="table table-sm table-striped-invert">
         {% bs4_colgroup '10,15,15,15,15,15,15' %}
         {% bs4_thead 'Name,Term,Species,Level,Level Units,Comment,Edit' %}
         <tbody id="cause-tbody">
-          {% include "common/fragments/_create_one.html" with text="No effects. Create one?" %}
           {% for object in causes %}
             {% include "eco/fragments/cause_row.html" %}
           {% endfor %}
+          {% include "common/fragments/_create_one.html" with text="No causes. Create one?" %}
+          {% include "common/fragments/_create_row.html" with model="cause" first=True %}
         </tbody>
       </table>
     </div>
@@ -30,15 +31,16 @@ <h2 class="d-inline-block">{{object.name}}</h2>
   <div class="card my-4 mx-2">
     <div class="card-body">
       {% url 'eco:effect-htmx' object.pk 'create' as effect_create %}
-      {% include "common/fragments/_create_card.html" with title="Effects" hx_get=effect_create hx_target="#effect-tbody" model="effect" btn_text="Create" %}
+      {% include "common/fragments/_create_card.html" with title="Effects" hx_get=effect_create hx_target=".effect-edit-row.create-row" model="effect" btn_text="Create" %}
       <table class="table table-sm table-striped-invert">
         {% bs4_colgroup '10,15,15,15,15,15,15' %}
         {% bs4_thead 'Name,Term,Species,Units,As Reported,Comment,Edit' %}
         <tbody id="effect-tbody">
-          {% include "common/fragments/_create_one.html" with text="No effects. Create one?" %}
           {% for object in effects %}
             {% include "eco/fragments/effect_row.html" %}
           {% endfor %}
+          {% include "common/fragments/_create_one.html" with text="No effects. Create one?" %}
+          {% include "common/fragments/_create_row.html" with model="effect" first=True %}
         </tbody>
       </table>
     </div>
@@ -47,15 +49,16 @@ <h2 class="d-inline-block">{{object.name}}</h2>
   <div class="card my-4 mx-2">
     <div class="card-body">
       {% url 'eco:result-htmx' object.pk 'create' as result_create %}
-      {% include "common/fragments/_create_card.html" with title="Results" hx_get=result_create hx_target="#result-tbody" model="result" btn_text="Create" %}
+      {% include "common/fragments/_create_card.html" with title="Results" hx_get=result_create hx_target=".result-edit-row.create-row" model="result" btn_text="Create" %}
       <table class="table table-sm table-striped-invert">
         {% bs4_colgroup '15,15,15,10,15,15,15' %}
         {% bs4_thead 'Name,Cause,Effect,Relationship Direction,Modifying Factors,Value,Edit' %}
         <tbody id="result-tbody">
-          {% include "common/fragments/_create_one.html" with text="No effects. Create one?" %}
           {% for object in results %}
             {% include "eco/fragments/result_row.html" %}
           {% endfor %}
+          {% include "common/fragments/_create_one.html" with text="No results. Create one?" %}
+          {% include "common/fragments/_create_row.html" with model="result" first=True %}
         </tbody>
       </table>
     </div>

hawc/apps/eco/templates/eco/fragments/cause_row.html

@@ -7,3 +7,4 @@
   <td>{{object.comments }}</td>
   {% include "common/fragments/_object_row.html" with app="eco" model="cause" %}
 </tr>
+{% include "common/fragments/_create_row.html" with model="cause" %}

hawc/apps/eco/templates/eco/fragments/effect_row.html

@@ -7,3 +7,4 @@
   <td>{{object.comments }}</td>
   {% include "common/fragments/_object_row.html" with app="eco" model="effect" %}
 </tr>
+{% include "common/fragments/_create_row.html" with model="effect" %}

hawc/apps/eco/templates/eco/fragments/result_row.html

@@ -12,3 +12,4 @@
   <td>{{object.derived_value }}</td>
   {% include "common/fragments/_object_row.html" with app="eco" model="result" %}
 </tr>
+{% include "common/fragments/_create_row.html" with model="result" %}

hawc/apps/epi/api.py

@@ -274,7 +274,7 @@ def handle_dtxsid(self, request):
         if dtxsid := request.data.get("dtxsid"):
             try:
                 DSSTox.objects.get(dtxsid=dtxsid)
-            except DSSTox.DoesNotExist as err:
+            except (DSSTox.DoesNotExist, ValueError) as err:
                 raise ValidationError(f"{dtxsid} does not exist in HAWC") from err
 
     @transaction.atomic