Merge branch 'main' into rob-id-debug

README.rst

@@ -1,9 +1,6 @@
 Health Assessment Workspace Collaborative
 =========================================
 
-.. image:: https://zenodo.org/badge/25273569.svg
-   :target: https://zenodo.org/badge/latestdoi/25273569
-
 .. image:: https://readthedocs.org/projects/hawc/badge/
         :target: https://hawc.readthedocs.io
         :alt: Documentation Status

compose/app/sync.sh

@@ -7,14 +7,9 @@ manage clearsessions
 manage collectstatic --noinput
 manage migrate --noinput
 
-if [[ $HAWC_LOAD_TEST_DB == "2" ]]; then
+if [[ $HAWC_LOAD_TEST_DB == "1" ]]; then
     echo "loading fixture database..."
     manage load_test_db
-elif [[ $HAWC_LOAD_TEST_DB == "1" ]]; then
-    echo "loading fixture database (if empty)..."
-    manage load_test_db --ifempty
-else
-    echo "not modifying database..."
 fi
 
 # drop/rebuild materialized views

compose/example.env

@@ -33,6 +33,7 @@ HAWC_PM_CAN_MAKE_PUBLIC=True
 HAWC_LOAD_TEST_DB=0
 HAWC_FEATURE_FLAGS='{}'
 HAWC_CSRF_TRUSTED_ORIGINS=https://hawc.com
+WAGTAILADMIN_BASE_URL=https://hawc.com
 
 # google tag manager
 GTM_ID=GTM-0000000

docs/docs/deployment.md

@@ -79,7 +79,7 @@ For configurable parameters, we use environment variables which are loaded in th
     - The "django" authentication provider means accounts can be created in hawc and passwords are managed in hawc
     - The "external" authentication provider assumes an upstream server handles authentication and returns appropriate user metadata for integration via `/user/login/wam/`.  If used, `hawc.apps.myuser.views.ExternalAuth.get_user_metadata` requires a custom implementation.
 - `HAWC_LOGOUT_REDIRECT` [str, optional]. URL to redirect to after logout. Defaults to the homepage of hawc; this may need to be modified with some authentication providers.
-- `HAWC_LOAD_TEST_DB` [0/1/2; default 0]. Load a test database with pre-populated fake data: always (2), if empty (1), or never (0; default). This setting is only used in staging and production django settings.
+- `HAWC_LOAD_TEST_DB` [0/1; default 0]. Load a test database with pre-populated fake data (1), or never ( default). This setting is only used in staging and production django settings.
 
 ### Feature flags
 

docs/docs/development.md

@@ -482,7 +482,7 @@ A few major revisions were made to the compiled USWDS assets, most notably:
 
 ### Updating EPA.gov style
 
-THere are multiple styles available when using HAWC; and the EPA style has to be updated periodically for the same look at feel as the EPA website. The following steps describe how to update HAWC styling with the EPA theme:
+There are multiple styles available when using HAWC; and the EPA style has to be updated periodically for the same look at feel as the EPA website. The following steps describe how to update HAWC styling with the EPA theme:
 
 1.  In your browser, go to the [EPA Template](https://www.epa.gov/themes/epa_theme/pattern-lab/patterns/pages-standalone-template/pages-standalone-template.rendered.html) site. We recommend Firefox or Internet Explorer.
 2.  Right click the page and select "Save As" to download the page as an .html file.

docs/docs/index.md

@@ -7,5 +7,4 @@ The Health Assessment Workspace Collaborative (HAWC) is a website designed to ca
 The public website is currently available on <https://hawcproject.org>, though there are additional versions available in other locations, including private deployments.
 
 [![Website](https://img.shields.io/website?url=https%3A%2F%2Fhawcproject.org)](https://hawcproject.org)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1414622.svg)](https://doi.org/10.5281/zenodo.1414622)
 [![Github](https://img.shields.io/github/last-commit/shapiromatron/hawc.svg)](https://github.com/shapiromatron/hawc)

frontend/lit/components/Reference.js

@@ -74,14 +74,15 @@ class Reference extends Component {
             </div>
         );
 
-        if (data.searches.length) {
+        if (!expanded && data.searches.length) {
             nodes.push(
                 <div
                     style={{minWidth: 85}}
                     className="d-flex dropdown flex-shrink-0"
                     key={h.randomString()}>
                     <a
                         className={`btn dropdown-toggle ${btn_size} outline-btn`}
+                        title="HAWC Searches/Imports"
                         data-toggle="dropdown"
                         aria-haspopup="true"
                         aria-expanded="false">
@@ -90,7 +91,7 @@ class Reference extends Component {
                     </a>
                     <div className="dropdown-menu dropdown-menu-right">
                         {data.searches.map((d, i) => (
-                            <a className="dropdown-item small" key={h.randomString()} href={d.url}>
+                            <a className="dropdown-item small" key={d.url} href={d.url}>
                                 {d.title}
                             </a>
                         ))}
@@ -207,6 +208,16 @@ class Reference extends Component {
                         ))}
                     </p>
                 ) : null}
+                {expanded && data.searches.length > 0 ? (
+                    <div>
+                        <label>Searches/imports:&nbsp;</label>
+                        {data.searches.map((d, i) => (
+                            <a className="btn btn-light mr-1 mb-2" key={d.url} href={d.url}>
+                                {d.title}
+                            </a>
+                        ))}
+                    </div>
+                ) : null}
                 {showHr ? <hr className="my-4" /> : null}
             </div>
         );

frontend/shared/utils/HAWCUtils.js

@@ -302,7 +302,12 @@ class HAWCUtils {
             handleChange = () => {
                 const selector = `#detail-${$selectEl.val()}`,
                     clone = $insertItems.find(selector).clone();
-                $insertEl.fadeOut(() => $insertEl.html(clone).fadeIn());
+                $insertEl.fadeOut(() =>
+                    $insertEl
+                        .html(clone)
+                        .trigger("select:change")
+                        .fadeIn()
+                );
             };
         $selectEl.on("change", handleChange).trigger("change");
     }
@@ -328,5 +333,18 @@ class HAWCUtils {
             })
             .trigger("change");
     }
+
+    static addAnchorLinks(parent, selector) {
+        $(parent)
+            .find(selector)
+            .each(function(index) {
+                const id = $(this).attr("id");
+                if (id) {
+                    $(this).append(
+                        `<a href="#${id}" class="ml-2 anchor-link" title="Section link"><span class="fa fa-fw fa-chain"></span></a>`
+                    );
+                }
+            });
+    }
 }
 export default HAWCUtils;

hawc/apps/common/diagnostics.py

@@ -43,6 +43,12 @@ def diagnostic_cache(modeladmin, request, queryset):
     modeladmin.message_user(request, message)
 
 
+def clear_cache(modeladmin, request, queryset):
+    cache.clear()
+    message = "Cache cleared successfully"
+    modeladmin.message_user(request, message)
+
+
 def diagnostic_email(modeladmin, request, queryset):
     to_email = request.user.email
     send_mail(

hawc/apps/common/management/commands/dump_test_db.py

@@ -24,6 +24,15 @@ def handle(self, *args, **options):
 
         call_command("dumpdata", "sites", **shared_kwargs)
         call_command("dumpdata", "contenttypes", **shared_kwargs)
+        call_command("dumpdata", "wagtailcore", **shared_kwargs)
+        call_command("dumpdata", "wagtailadmin", **shared_kwargs)
+        call_command("dumpdata", "wagtaildocs", **shared_kwargs)
+        call_command("dumpdata", "wagtailembeds", **shared_kwargs)
+        call_command("dumpdata", "wagtailforms", **shared_kwargs)
+        call_command("dumpdata", "wagtailimages", **shared_kwargs)
+        call_command("dumpdata", "wagtailredirects", **shared_kwargs)
+        call_command("dumpdata", "wagtailsearch", **shared_kwargs)
+        call_command("dumpdata", "wagtailusers", **shared_kwargs)
         call_command("dumpdata", "myuser", **shared_kwargs)
         call_command("dumpdata", "vocab", **shared_kwargs)
         call_command(
@@ -40,6 +49,7 @@ def handle(self, *args, **options):
         call_command("dumpdata", "invitro", **shared_kwargs)
         call_command("dumpdata", "epimeta", **shared_kwargs)
         call_command("dumpdata", "summary", **shared_kwargs)
+        call_command("dumpdata", "docs", **shared_kwargs)
         call_command("dumpdata", "mgmt", **shared_kwargs)
 
         Path(settings.TEST_DB_FIXTURE).parent.mkdir(exist_ok=True, parents=True)

hawc/apps/common/management/commands/load_test_db.py

@@ -1,10 +1,13 @@
+import sys
 from pathlib import Path
 
 import pandas as pd
 from django.conf import settings
-from django.contrib.auth import get_user_model
 from django.core.management import call_command
 from django.core.management.base import BaseCommand, CommandError
+from django.core.management.commands import migrate
+from django.db.backends.base import creation
+from django.test.utils import setup_databases
 
 from hawc.apps.common.signals import ignore_signals
 
@@ -15,17 +18,23 @@ def load_iris_dataset() -> pd.DataFrame:
     )
 
 
+class DisableMigrations:
+    def __contains__(self, item: str) -> bool:
+        return True
+
+    def __getitem__(self, item: str) -> None:
+        return None
+
+
+class MigrateSilentCommand(migrate.Command):
+    def handle(self, *args, **kwargs):
+        kwargs["verbosity"] = 0
+        return super().handle(*args, **kwargs)
+
+
 class Command(BaseCommand):
     help = """Load the test database from a fixture."""
 
-    def add_arguments(self, parser) -> None:
-        parser.add_argument(
-            "--ifempty",
-            action="store_true",
-            dest="ifempty",
-            help="Only flush/load if database is empty",
-        )
-
     def write_media_files(self):
         """
         Sync filesystem with database.
@@ -50,29 +59,40 @@ def write_media_files(self):
                 fn.parent.mkdir(parents=True, exist_ok=True)
                 df.to_excel(fn, index=False)
 
+    def setup_environment(self) -> None:
+        """Disable migrations like pytest-django does, but outside of pytest-django."""
+        creation.TEST_DATABASE_PREFIX = ""
+        migrate.Command = MigrateSilentCommand
+        settings.MIGRATION_MODULES = DisableMigrations()
+        self.stdout.write(self.style.HTTP_INFO("Migrating database schema..."))
+        setup_databases(verbosity=0, interactive=False, keepdb=True)
+        self.stdout.write(self.style.HTTP_INFO("Loading database fixture..."))
+        call_command("loaddata", str(settings.TEST_DB_FIXTURE), verbosity=0)
+        settings.MIGRATION_MODULES = {}
+        self.stdout.write(self.style.HTTP_INFO("Writing migrations (fake)..."))
+        call_command("migrate", verbosity=0, fake=True)
+
+    def setup_test_environment(self) -> None:
+        """Setup test environment within pytest environment."""
+        self.stdout.write(self.style.HTTP_INFO("Migrating database schema..."))
+        call_command("migrate", verbosity=0)
+        self.stdout.write(self.style.HTTP_INFO("Flushing data..."))
+        call_command("flush", verbosity=0, interactive=False)
+        self.stdout.write(self.style.HTTP_INFO("Loading database fixture..."))
+        call_command("loaddata", str(settings.TEST_DB_FIXTURE), verbosity=0)
+
     def handle(self, *args, **options):
-        if not any(_ in settings.DATABASES["default"]["NAME"] for _ in ["fixture", "test"]):
+        db_name = settings.DATABASES["default"]["NAME"]
+        if not any(_ in db_name for _ in ["fixture", "test"]):
             raise CommandError("Must be using a test database to execute.")
-
         with ignore_signals():
-            self.stdout.write(self.style.HTTP_INFO("Migrating database schema..."))
-            call_command("migrate", verbosity=0)
-
-            if options["ifempty"] and get_user_model().objects.count() > 0:
-                message = "Migrations complete; fixture not loaded (db not empty)"
+            if "pytest" in sys.modules:
+                self.setup_test_environment()
             else:
-                self.stdout.write(self.style.HTTP_INFO("Flushing data..."))
-                call_command("flush", verbosity=0, interactive=False)
-
-                self.stdout.write(self.style.HTTP_INFO("Loading database fixture..."))
-                call_command("loaddata", str(settings.TEST_DB_FIXTURE), verbosity=1)
-
-                self.stdout.write(self.style.HTTP_INFO("Loading database views..."))
-                call_command("recreate_views", verbosity=1)
-
-                self.stdout.write(self.style.HTTP_INFO("Creating files..."))
-                self.write_media_files()
+                self.setup_environment()
 
-                message = "Migrations complete; fixture (re)applied"
+            self.stdout.write(self.style.HTTP_INFO("Recreating database views..."))
+            call_command("recreate_views", verbosity=0)
 
-            self.stdout.write(self.style.SUCCESS(message))
+            self.stdout.write(self.style.HTTP_INFO("Creating files..."))
+            self.write_media_files()

hawc/apps/common/signals.py

@@ -1,6 +1,10 @@
 from contextlib import contextmanager
+from itertools import chain
 
-from django.db.models.signals import m2m_changed, post_delete, post_save, pre_delete, pre_save
+from django.db.models import signals as dsignals
+from django.dispatch import Signal
+from wagtail import signals as wts
+from wagtail.admin import signals as wtas
 
 
 @contextmanager
@@ -10,7 +14,15 @@ def ignore_signals():
 
     Originally taken from: https://www.cameronmaske.com/muting-django-signals-with-a-pytest-fixture/
     """
-    signals = [pre_save, post_save, pre_delete, post_delete, m2m_changed]
+    signals = [
+        signal
+        for signal in chain(
+            dsignals.__dict__.values(),
+            wts.__dict__.values(),
+            wtas.__dict__.values(),
+        )
+        if isinstance(signal, Signal)
+    ]
     restore = {}
     for signal in signals:
         restore[signal] = signal.receivers

hawc/apps/common/templates/common/analytics_plot.html

@@ -0,0 +1,7 @@
+<div class="card box-shadow">
+    <div class="card-body">
+        <h3 class="text-center">{{ title }}</h3>
+        <div>{% plotly plot event="htmx" resizable="True" %}</div>
+        <p class="text-muted text-center"> {{ caption }}</p>
+    </div>
+</div>

hawc/apps/common/templatetags/bs4.py

@@ -6,6 +6,7 @@
 from uuid import uuid4
 
 from django import template
+from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 from plotly.graph_objs._figure import Figure
 
@@ -47,6 +48,11 @@ def bs4_fullrow(text: str, tr_attrs: str = "") -> str:
     )
 
 
+@register.simple_tag()
+def icon(name: str):
+    return format_html('<span class="fa fa-fw {} mr-1" aria-hidden="true"></span>', name)
+
+
 @register.tag(name="alert")
 def bs4_alert(parser, token):
     args = token.contents.split()
@@ -124,3 +130,17 @@ def add_class(value, css_class):
     else:
         return mark_safe(string.replace(">", f' class="{css_class}">'))
     return value
+
+
+@register.simple_tag
+def analytics_card(value, label):
+    return mark_safe(
+        f"""
+        <div class="card box-shadow">
+            <div class="card-body">
+                <h2 class="m-0 mt-1">{ value }</h2>
+                <p class="small">{ label }</p>
+            </div>
+        </div>
+        """
+    )

hawc/apps/docs/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class DocsConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "hawc.apps.docs"

hawc/apps/docs/constants.py

@@ -0,0 +1,15 @@
+RICH_TEXT_FEATURES = [
+    "anchor-identifier",
+    "h3",
+    "h4",
+    "h5",
+    "h6",
+    "bold",
+    "italic",
+    "link",
+    "ol",
+    "ul",
+    "hr",
+    "image",
+    "document-link",
+]