SACGF/variantgrid_private#3689 provide a page that up time robot can …

…check that checks more

eventlog/middleware.py

@@ -5,7 +5,7 @@
 from django.http.response import HttpResponseRedirectBase
 from django.urls import resolve
 
-from auth.session_refresh import VariantGridSessionRefresh
+from oidc_auth.session_refresh import VariantGridSessionRefresh
 from eventlog.models import ViewEvent
 
 IGNORE_SEGMENTS = {"api", "datatable", "citations_json"}  # this should be mostly redundant to is_ajax call

library/keycloak.py

@@ -38,6 +38,16 @@ def __init__(self, connector: Optional[ServerAuth] = None):
         self.connector = connector
         self.realm = settings.KEY_CLOAK_REALM
 
+    def ping(self):
+        full_url = self.connector.url(f'/auth/admin/realms/{self.realm}/clients')
+        print(full_url)
+        response = requests.get(
+            auth=self.connector.auth,
+            url=self.connector.url(f'/auth/admin/realms/{self.realm}/clients'),
+            timeout=MINUTE_SECS,
+        )
+        response.raise_for_status()
+
     def change_password(self, user: User):
         user_settings = UserSettings.get_for_user(user)
         if not user_settings.oauth_sub:

library/uptime_check.py

@@ -0,0 +1,78 @@
+from dataclasses import dataclass
+from enum import Enum, IntEnum
+from functools import cached_property
+from typing import Optional
+import django
+from django.contrib.auth.models import User
+
+from library.utils import text_utils
+
+
+###
+# Uptime Check is similar to health check but
+# The results is to be displayed to a public web page, so it needs to not show sensitive information
+# The results are more about if critical systems are currently working or not, so we can get an alert from uptime robot if they're not
+###
+
+class UptimeCheckStatus(IntEnum):
+    OKAY = 1
+    NON_CRITICAL_FAILURE = 2
+    CRITICAL_FAILURE = 3
+    EXCEPTION_WHEN_CHECKING = 4
+
+    @property
+    def pretty_label(self):
+        return text_utils.pretty_label(self.name)
+
+    def severity(self) -> str:
+        match self:
+            case UptimeCheckStatus.OKAY: return "S"
+            case UptimeCheckStatus.NON_CRITICAL_FAILURE: return "E"
+            case _: return "C"
+
+@dataclass
+class UptimeCheckResponse:
+    name: str
+    status: UptimeCheckStatus
+    note: Optional[str] = None
+
+
+@dataclass
+class UptimeCheckOverall:
+    uptime_checks: list[UptimeCheckResponse]
+
+    @cached_property
+    def status(self) -> UptimeCheckStatus:
+        return max(uc.status for uc in self.uptime_checks)
+
+
+uptime_check_signal = django.dispatch.Signal()
+
+
+def retrieve_uptime_response():
+    all_uptimes = []
+
+    status = UptimeCheckStatus.OKAY
+    try:
+        # note that it's quite likely if the database is down, something well before this will cause an exception
+        # but feels dishonest to say the database is okay without checking anything
+        User.objects.first()
+    except:
+        status = UptimeCheckStatus.CRITICAL_FAILURE
+    all_uptimes.append(UptimeCheckResponse(
+        name="Database",
+        status=status
+    ))
+
+    for caller, result in uptime_check_signal.send_robust(sender=None):
+        if result:
+            if isinstance(result, Exception):
+                all_uptimes.append(UptimeCheckResponse(
+                    name=str(caller),
+                    status=UptimeCheckStatus.EXCEPTION_WHEN_CHECKING,
+                    note=f"Exception generating health check by {caller}: {result}"
+                ))
+            else:
+                all_uptimes.append(result)
+
+    return UptimeCheckOverall(uptime_checks=all_uptimes)

oidc_auth/apps.py

@@ -0,0 +1,14 @@
+from django.apps import AppConfig
+
+# TODO rename to OIDCAuth
+
+# noinspection PyUnresolvedReferences
+class OIDCAuthConfig(AppConfig):
+    name = 'oidc_auth'
+
+    # noinspection PyUnresolvedReferences
+    def ready(self):
+        # pylint: disable=import-outside-toplevel
+        # imported to activate receivers
+        from oidc_auth.signals import keycloak_uptime_check  # pylint: disable=unused-import
+        # pylint: enable=import-outside-toplevel

oidc_auth/signals/keycloak_uptime_check.py

@@ -0,0 +1,28 @@
+from typing import Optional
+
+from django.dispatch import receiver
+from django.conf import settings
+
+from library.keycloak import Keycloak
+from library.uptime_check import uptime_check_signal, UptimeCheckResponse, UptimeCheckStatus
+
+
+@receiver(signal=uptime_check_signal)
+def keycloak_uptime_check(sender, **kwargs):
+    if not settings.KEYCLOAK_SYNC_DETAILS:
+        return None
+
+    status = UptimeCheckStatus.OKAY
+    note: Optional[str] = None
+    try:
+        Keycloak().ping()
+    except Exception as ex:
+        print(str(ex))
+        status = UptimeCheckStatus.CRITICAL_FAILURE
+        note = str(ex)
+
+    return UptimeCheckResponse(
+        name="KeyCloak",
+        status=status,
+        note=note
+    )

snpdb/templates/snpdb/uptime_check.html

@@ -0,0 +1,30 @@
+{% extends "uicore/page/base_external.html" %}
+{% load ui_utils %}
+{% block content %}
+    <div class="container mt-4">
+        <div class="jumbotron">
+            <h1>Uptime Status</h1>
+            <table class="table">
+                <thead>
+                    <tr>
+                        <th>System</th>
+                        <th>Status</th>
+                    </tr>
+                </thead>
+                <tbody>
+                {% for uptime_check in uptime_response.uptime_checks %}
+                    <tr>
+                        <td>{{ uptime_check.name }}</td>
+                        <td>{{ uptime_check.status.severity | severity_icon }}{{ uptime_check.status.pretty_label }}</td>
+                    </tr>
+                {% endfor %}
+                </tbody>
+            </table>
+            {% if uptime_response.status == 1 %}
+                <div class="alert alert-success">Everything is OKAY</div>
+            {% else %}
+                <div class="alert alert-danger">{{ uptime_response.status.severity | severity_icon }}Overall Status {{ uptime_response.status.pretty_label }}</div>
+            {% endif %}
+        </div>
+    </div>
+{% endblock %}

snpdb/urls.py

@@ -134,9 +134,12 @@
     perm_path('autocomplete/Lab/', views_autocomplete.LabAutocompleteView.as_view(), name='lab_autocomplete'),
     perm_path('autocomplete/VCF/', views_autocomplete.VCFAutocompleteView.as_view(), name='vcf_autocomplete'),
 
-    #Previews
+    # Previews
     perm_path('preview/<str:db>/<str:idx>', preview_view, name='preview_data'),
 
+    # For Uptime Robot
+    perm_path('uptime_check', views.view_uptime, name='uptime_check'),
+
     # Debug dev help
     perm_path('ajax_hello_world/<str:data>', views.ajax_hello_world, name='ajax_hello_world'),
 ]

snpdb/views/views.py

@@ -45,6 +45,7 @@
 from genes.custom_text_gene_list import create_custom_text_gene_list
 from genes.forms import CustomGeneListForm, UserGeneListForm, GeneAndTranscriptForm
 from genes.models import GeneListCategory, CustomTextGeneList, GeneList
+from library import uptime_check
 from library.constants import WEEK_SECS, HOUR_SECS
 from library.django_utils import add_save_message, get_model_fields, set_form_read_only, require_superuser, \
     get_field_counts
@@ -1668,3 +1669,9 @@ def view_contig(request, contig_accession):
         "genome_build": genome_build,
     }
     return render(request, "snpdb/genomics/view_contig.html", context)
+
+
+@login_not_required
+def view_uptime(request):
+    uptime_response = uptime_check.retrieve_uptime_response()
+    return render(request, "snpdb/uptime_check.html", {"uptime_response": uptime_response})

variantgrid/settings/env/shariantcommon.py

@@ -53,16 +53,17 @@
 ]
 
 # Keycloak
+INSTALLED_APPS = ["oidc_auth"] + INSTALLED_APPS
 
 AUTHENTICATION_BACKENDS = (
-    'auth.backend.VariantGridOIDCAuthenticationBackend',
+    'oidc_auth.backend.VariantGridOIDCAuthenticationBackend',
     'django.contrib.auth.backends.ModelBackend',  # default
     'guardian.backends.ObjectPermissionBackend',
 )
 
 MIDDLEWARE += (
-    'auth.session_refresh.VariantGridSessionRefresh',
-    'auth.oidc_error_handler.HandleOIDC400Middleware',
+    'oidc_auth.session_refresh.VariantGridSessionRefresh',
+    'oidc_auth.oidc_error_handler.HandleOIDC400Middleware',
 )
 
 REST_FRAMEWORK = {

variantopedia/templates/variantopedia/view_allele.html

@@ -50,7 +50,25 @@
     {% settings_value 'CLINGEN_ALLELE_REGISTRY_DOMAIN' as clingen_url %}
 
     <div class="container">
-        {% page_help page_id='variantdetails/view_allele_help' title='Allele' %}
+        {% page_help_embedded title='Allele' %}
+            <p>
+            An allele is a genetic change independent of a genome builds. Variants from different builds link to the same allele.
+            </p>
+
+            <p>
+            Variant classifications are compared across alleles, so classification differences can be detected regardless of what build it was originally classified against. Classifying a variant will create an allele, and linked variants for all genome builds supported by the server.
+            </p>
+
+            <p>
+            Alleles generally have 1 (and only 1) ClinGen Allele ID, from the <a href="http://reg.clinicalgenome.org">ClinGen Allele Registry</a>, which we use to perform liftover between builds.
+            </p>
+            {% settings_value "LIFTOVER_BCFTOOLS_ENABLED" as bcftools_enabled %}
+            {% if bcftools_enabled %}
+                <p>
+                If ClinGen fails, we use <a href="https://samtools.github.io/bcftools/">BCF tools</a>.
+                </p>
+            {% endif %}
+        {% end_page_help_embedded %}
 
         {% labelled label="Internal Allele ID" %}
             {{ allele_card.allele.pk }} {% admin_link allele_card.allele %}