feat/publish upload updates

dashboard_viewer/dashboard_viewer/routers.py

@@ -9,7 +9,7 @@ class AchillesRouter:
      achilles database. The rest will be stored on the default database
     """
 
-    achilles_apps = ["uploader", "materialized_queries_manager"]
+    achilles_apps = ["uploader", "materialized_queries_manager", "updates"]
     achilles_db = "achilles"
 
     def db_for_read(self, model, **_):

dashboard_viewer/dashboard_viewer/settings.py

@@ -79,6 +79,7 @@
     "martor",
     "rest_framework",
     "sass_processor",
+    "updates",
     "materialized_queries_manager",
     "tabsManager",
     "uploader",

dashboard_viewer/docker-init.sh

@@ -7,7 +7,7 @@ wait-for-it "$POSTGRES_ACHILLES_HOST:$POSTGRES_ACHILLES_PORT"
 
 # Apply django migrations
 python manage.py migrate
-python manage.py migrate --database=achilles uploader
+python manage.py migrate --database=achilles
 python manage.py populate_countries
 
 # Create an user for the admin app

dashboard_viewer/requirements.txt

@@ -10,6 +10,7 @@ django-redis==4.12.1                      # acess redis through a programmatic A
 django-sass-processor==0.8.2              # automate scss devolopment
 django==2.2.17
 djangorestframework==3.12.2               # expose tabs content through an API
+Jinja2==2.11.3                            # to render custom code to publish upload updates
 libsass==0.20.1                           # to compile scss files into css
 gunicorn==20.0.4                          # for production deployment
 martor==1.5.8                             # markdown editor in admin app
@@ -36,6 +37,7 @@ django-appconf==1.0.4
 idna==2.10
 kombu==5.0.2
 Markdown==3.3.3
+MarkupSafe==1.1.1
 numpy==1.20.0
 packaging==20.9
 prompt-toolkit==3.0.14

dashboard_viewer/updates/admin.py

@@ -0,0 +1,41 @@
+from django import forms
+from django.contrib import admin
+
+from . import models
+
+
+@admin.register(models.RequestsGroupLog)
+class RequestGroupLogAdmin(admin.ModelAdmin):
+    list_display = ("group", "trigger_upload", "success_count", "time")
+
+    def has_add_permission(self, request):
+        return False
+
+    def has_change_permission(self, request, obj=None):
+        return False
+
+
+@admin.register(models.RequestLog)
+class RequestLogAdmin(admin.ModelAdmin):
+    list_display = ("group", "request", "success")
+
+    def has_add_permission(self, request):
+        return False
+
+    def has_change_permission(self, request, obj=None):
+        return False
+
+
+admin.site.register(models.RequestsGroup)
+
+
+class RequestAdminForm(forms.ModelForm):
+    class Meta:
+        model = models.Request
+        fields = "__all__"
+
+
+@admin.register(models.Request)
+class RequestAdmin(admin.ModelAdmin):
+    list_display = ("group", "order")
+    form = RequestAdminForm

dashboard_viewer/updates/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig
+
+
+class UpdatesConfig(AppConfig):
+    name = "updates"

dashboard_viewer/updates/fixtures/achilles_results_dist.csv

@@ -0,0 +1,4 @@
+analysis_id,stratum_1,stratum_2,stratum_3,stratum_4,stratum_5,count_value,min_value,max_value,avg_value,stdev_value,median_value,p10_value,p25_value,p75_value,p90_value
+0,test,NULL,NULL,NULL,NULL,1171,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL
+2000000,0.151157 secs,NULL,NULL,NULL,NULL,6,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL
+103,NULL,NULL,NULL,NULL,NULL,1171,0,61,14.1289496157131,12.4272078334908,14,0,2,21,32

dashboard_viewer/updates/fixtures/active.json

@@ -0,0 +1,28 @@
+[
+{
+    "model": "updates.requestsgroup",
+    "pk": 1,
+    "fields": {
+        "name": "test",
+        "active": true
+    }
+},
+{
+    "model": "updates.request",
+    "pk": 1,
+    "fields": {
+        "group": 1,
+        "request_arguments_template": "{\"url\": \"http://localhost:8383\",\"method\": \"get\",\"data\": {\"patient_count\": \"{{ achilles_results.0.0.count_value }}\"}}",
+        "order": 1
+    }
+},
+{
+    "model": "updates.request",
+    "pk": 2,
+    "fields": {
+        "group": 1,
+        "request_arguments_template": "{\"url\": \"https://stackoverflow.com?response={{ responses|last|attr(\"text\") }}\",\"method\": \"GET\"}",
+        "order": 2
+    }
+}
+]

dashboard_viewer/updates/fixtures/base.json

@@ -0,0 +1,24 @@
+[
+{
+    "model": "uploader.country",
+    "pk": 1,
+    "fields": {
+        "country": "test",
+        "continent": "test"
+    }
+},
+{
+    "model": "uploader.datasource",
+    "pk": 1,
+    "fields": {
+        "name": "test",
+        "acronym": "test",
+        "release_date": null,
+        "database_type": "test",
+        "country": 1,
+        "latitude": 35.0524837066247,
+        "longitude": -103.095703125,
+        "link": ""
+    }
+}
+]

dashboard_viewer/updates/fixtures/data.json

@@ -0,0 +1,84 @@
+[
+  {
+    "model": "uploader.uploadhistory",
+    "pk": 1,
+    "fields": {
+      "data_source": 1,
+      "upload_date": "2021-05-10T14:46:11.609Z",
+      "r_package_version": "nan",
+      "generation_date": "nan",
+      "cdm_release_date": null,
+      "cdm_version": null,
+      "vocabulary_version": null
+    }
+  },
+  {
+    "model": "uploader.achillesresults",
+    "pk": 1,
+    "fields": {
+      "data_source": 1,
+      "analysis_id": 0,
+      "stratum_1": "test",
+      "stratum_2": null,
+      "stratum_3": null,
+      "stratum_4": null,
+      "stratum_5": null,
+      "count_value": 1171,
+      "min_value": null,
+      "max_value": null,
+      "avg_value": null,
+      "stdev_value": null,
+      "median_value": null,
+      "p10_value": null,
+      "p25_value": null,
+      "p75_value": null,
+      "p90_value": null
+    }
+  },
+  {
+    "model": "uploader.achillesresults",
+    "pk": 2,
+    "fields": {
+      "data_source": 1,
+      "analysis_id": 2000000,
+      "stratum_1": "0.151157 secs",
+      "stratum_2": null,
+      "stratum_3": null,
+      "stratum_4": null,
+      "stratum_5": null,
+      "count_value": 6,
+      "min_value": null,
+      "max_value": null,
+      "avg_value": null,
+      "stdev_value": null,
+      "median_value": null,
+      "p10_value": null,
+      "p25_value": null,
+      "p75_value": null,
+      "p90_value": null
+    }
+  },
+  {
+    "model": "uploader.achillesresults",
+    "pk": 3,
+    "fields": {
+      "data_source": 1,
+      "analysis_id": 103,
+      "stratum_1": null,
+      "stratum_2": null,
+      "stratum_3": null,
+      "stratum_4": null,
+      "stratum_5": null,
+      "count_value": 1171,
+      "min_value": 0,
+      "max_value": 61,
+      "avg_value": 14.1289496157,
+      "stdev_value": 12.4272078335,
+      "median_value": 14,
+      "p10_value": 0,
+      "p25_value": 2,
+      "p75_value": 21,
+      "p90_value": 32
+    }
+  }
+]

dashboard_viewer/updates/fixtures/not_active.json

@@ -0,0 +1,28 @@
+[
+{
+    "model": "updates.requestsgroup",
+    "pk": 1,
+    "fields": {
+        "name": "test",
+        "active": false
+    }
+},
+{
+    "model": "updates.request",
+    "pk": 1,
+    "fields": {
+        "group": 1,
+        "request_arguments_template": "{\"url\": \"http://localhost:8383\",\"method\": \"get\",\"data\": {\"patient_count\": \"{{ achilles_results.0.0.count_value }}\"}}",
+        "order": 1
+    }
+},
+{
+    "model": "updates.request",
+    "pk": 2,
+    "fields": {
+        "group": 1,
+        "request_arguments_template": "{\"url\": \"https://stackoverflow.com?response={{ responses|last|attr(\"text\") }}\",\"method\": \"GET\"}",
+        "order": 2
+    }
+}
+]