Add support for Onbarding Reports

dashboard_viewer/dashboard_viewer/settings.py

@@ -345,6 +345,23 @@ def locks_make_key(key, key_prefix, version):  # noqa
         "Css for the img tag displaying the app logo",
         str,
     ),
+    "ALLOW_ONBOARDING_UPLOAD" :(
+        False,
+        "If Onboarding reports are allowed to be uploaded, which shows a button in the uploader page if true to allow these kind of files",
+        bool,
+    ),
+    "CAPTION_ONBOARDING" :(
+        "Drug Exposure Diagnostics results for selected ingredients. Executed with minCellCount = 5, sample = 1e+06, "
+        "earliestStartDate = 2010-01-01. # = Number of records. Type (n,%) = Frequency and percentage of available drug types."
+        "Route (n,%) = Frequency and percentage of available routes. Dose Form present n (%) = Frequency and percentage with dose form present."
+        "Fixed amount dose form n (%) = Frequency and percentage of missing denominator unit concept id. Amount distrib. [null or missing] = Distribution of amount (median q05-q95),"
+        "frequency and percentage of null or missing amount. Quantity distrib. [null or missing] = Distribution of quantity (median q05-q95), frequency and percentage of null or missing quantity."
+        "Exposure days distrib. [null or missing] = Distribution of exposure days (median q05-q95), frequency and percentage of null days_supply or missing exposure dates."
+        "Neg. Days n (%) = Frequency and percentage of negative exposure days.",
+        "Caption Text for the table in the Onboarding Report Page",
+        "markdown",
+    ),
+
 }
 
 CONSTANCE_CONFIG_FIELDSETS = OrderedDict(
@@ -356,9 +373,10 @@ def locks_make_key(key, key_prefix, version):  # noqa
                 "UPLOADER_EXECUTE_EXPORT_PACKAGE",
                 "UPLOADER_UPLOAD",
                 "UPLOADER_AUTO_UPDATE",
+                "CAPTION_ONBOARDING"
             ),
         ),
-        ("Uploader Settings", ("UPLOADER_ALLOW_EDIT_DRAFT_STATUS",)),
+        ("Uploader Settings", ("UPLOADER_ALLOW_EDIT_DRAFT_STATUS", "ALLOW_ONBOARDING_UPLOAD")),
         (
             "Superset",
             ("SUPERSET_HOST", "DATABASE_DASHBOARD_IDENTIFIER", "DATABASE_FILTER_ID"),

dashboard_viewer/uploader/forms.py

@@ -33,4 +33,10 @@ class Meta(SourceForm.Meta):
 
 
 class AchillesResultsForm(forms.Form):
-    results_file = forms.FileField()
+    if constance.config.ALLOW_ONBOARDING_UPLOAD:
+        results_file = forms.FileField(required=False, label='Catalogue Export File')
+    else:
+        results_file = forms.FileField()
+
+class OnboardingReportForm(forms.Form):
+    onboarding_results_file = forms.FileField(required=False, label='Onboarding Report file (Optional)')

dashboard_viewer/uploader/migrations/0014_onboardingreport.py

@@ -0,0 +1,26 @@
+# Generated by Django 3.2.13 on 2024-03-27 12:05
+
+from django.db import migrations, models
+import django.db.models.deletion
+import uploader.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('uploader', '0013_auto_20210721_1715'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='OnBoardingReport',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uploaded_file', models.FileField(null=True, upload_to=uploader.models.onboarding_folder)),
+                ('data_source', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='uploader.datasource')),
+            ],
+            options={
+                'db_table': 'onboarding_report',
+            },
+        ),
+    ]

dashboard_viewer/uploader/migrations/0015_onboardingreport_upload_date.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.2.13 on 2024-03-28 12:35
+
+from django.db import migrations, models
+import django.utils.timezone
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('uploader', '0014_onboardingreport'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='onboardingreport',
+            name='upload_date',
+            field=models.DateTimeField(auto_now_add=True, default=django.utils.timezone.now),
+            preserve_default=False,
+        ),
+    ]

dashboard_viewer/uploader/models.py

@@ -175,6 +175,15 @@ def success_data_source_directory(instance, filename):
 
     return datetime.datetime.now().strftime(file_path)
 
+def onboarding_folder(instance, filename):
+    file_path = os.path.join(
+        settings.ACHILLES_RESULTS_STORAGE_PATH,
+        instance.data_source.hash,
+        "onboarding",
+        "%Y%m%d%H%M%S%f" + "".join(pathlib.Path(filename).suffixes),
+    )
+    return datetime.datetime.now().strftime(file_path)
+
 
 class UploadHistory(models.Model):
     """
@@ -266,3 +275,16 @@ class Meta:
     p25_value = models.FloatField(null=True)
     p75_value = models.FloatField(null=True)
     p90_value = models.FloatField(null=True)
+
+class OnboardingReport(models.Model):
+    class Meta:
+        db_table = "onboarding_report"
+
+    data_source = models.ForeignKey(DataSource, on_delete=models.CASCADE)
+    upload_date = models.DateTimeField(auto_now_add=True)
+    uploaded_file = models.FileField(
+        null=True, upload_to=onboarding_folder
+    )
+
+    def get_status(self):
+        return "Done"

dashboard_viewer/uploader/static/js/uploader.js

@@ -26,8 +26,10 @@ document.addEventListener("DOMContentLoaded", () => {
         const tbody = tbodys[0];
 
         for (const tr of tbody.children) {
-            const status_td = tr.children[5];
-
+            const numberOfColumns = tr.children.length;
+            const status_td = tr.children[numberOfColumns-1];
+
+
             if (status_td.dataset.failed === "yes") {
                 add_failure_message_popup(status_td, status_td.dataset.failureMsg);
             }
@@ -37,10 +39,10 @@ document.addEventListener("DOMContentLoaded", () => {
                         .then(r => r.json())
                         .then(r => {
                             if (r.status === "Done") {
-                                tr.children[1].innerText = r.data.r_package_version;
-                                tr.children[2].innerText = r.data.generation_date;
-                                tr.children[3].innerText = r.data.cdm_version;
-                                tr.children[4].innerText = r.data.vocabulary_version;
+                                tr.children[numberOfColumns - 5].innerText = r.data.r_package_version;
+                                tr.children[numberOfColumns - 4].innerText = r.data.generation_date;
+                                tr.children[numberOfColumns - 3].innerText = r.data.cdm_version;
+                                tr.children[numberOfColumns - 2].innerText = r.data.vocabulary_version;
 
                                 update_upload_status(status_td, "Done", "fas fa-check", "status-done");
 

dashboard_viewer/uploader/templates/onboarding_report.html

@@ -0,0 +1,80 @@
+{% extends 'base.html' %}
+{% load static %}
+{% load bootstrap4 %}
+{% load markdownify %}
+
+{% block head_tail %}
+    {{ form.media.css }}
+    <link rel="stylesheet" href='{% static "pages.css" %}' >
+    <link rel="stylesheet" href='{% static "header.css" %}' >
+    <link rel="stylesheet" href='{% static "css/uploader.css" %}' >
+{% endblock %}
+
+
+{% block content %}
+<div>
+    {% include "header.html" %}
+
+    {# Achilles resutls file form #}
+    <div class="content-container" >
+        <div class="row">
+            <h3 class="col">Data Source: {{ obj_data_source.name }}</h3>
+        </div>
+        <div class="row">
+            <div class="col">
+                <p><b>Database type:</b> {{ obj_data_source.database_type }}</p>
+            </div>
+            <div class="col">
+                <p><b>Country:</b> {{ obj_data_source.country }}</p>
+            </div>
+            <div class="col-auto">
+                <p><b>Release date:</b> {{ obj_data_source.release_date }}</p>
+            </div>
+        </div>
+
+        <hr/>
+        <h3 style="margin-top: 15px;">Onboarding Report</h3>
+        <div style="margin-top: 15px;text-align: center;">
+            {% if body|length > 0 %}
+                <table class="table center table-stripped" style="font-size: 14px;margin-top: 20px;width: 95%;">
+                    <caption style="text-align:left"> {{ constance_config.CAPTION_ONBOARDING|markdownify  }}</caption>
+                    <thead style="background-color: #023E8a;color: white">
+                        <tr>
+                            {% for header in headers %}
+                            <th> {{ header }}</th>
+                            {% endfor %}
+                        </tr>
+                    </thead>
+                    <tbody style="background-color: #f5fbff;">
+                    {% for list in body %}
+                        <tr>
+                            {% for el in list %}
+                                <td>{{ el }}</td>
+                            {% endfor %}
+                        </tr>
+                    {% endfor %}
+                    </tbody>
+                </table>
+            {% else %}
+                <p>Onboarding report is not available.</p>
+            {% endif %}
+        </div>
+    </div>
+</div>
+{% endblock %}
+{% block body_before_bootstrap %}
+<style>
+    table
+    {        
+        margin-left: auto;
+        margin-right: auto;
+        border-collapse : collapse;  
+    }
+    caption { caption-side:top; }
+    table td, table th  
+    {         
+        max-width: 100px;
+        word-wrap: break-word;
+    }
+  </style>
+{% endblock %}

dashboard_viewer/uploader/templates/upload_achilles_results.html

@@ -29,7 +29,7 @@ <h3>Upload new database characteristics</h3>
         For more information see the CatalogueExport R-package
         <a href="https://github.com/EHDEN/CatalogueExport">
             <i class="fas fa-link"></i>
-        </a>
+        </a> {%if constance_config.ALLOW_ONBOARDING_UPLOAD %}<br> You can also upload an Onboarding Report {% endif %}
     </span>
 
 {% endblock %}
@@ -43,6 +43,9 @@ <h3>Upload history</h3>
             <table class="table">
                 <thead>
                     <tr>
+                        {% if constance_config.ALLOW_ONBOARDING_UPLOAD %}
+                        <th>Type</th>
+                        {% endif %}
                         <th>Upload Date</th>
                         <th>R Package Version</th>
                         <th>Generation Date</th>
@@ -52,8 +55,11 @@ <h3>Upload history</h3>
                     </tr>
                 </thead>
                 <tbody>
-                {% for up_hi, status in upload_history %}
+                {% for up_hi, status, type in upload_history %}
                     <tr>
+                        {% if constance_config.ALLOW_ONBOARDING_UPLOAD %}
+                        <td>{{ type }}</td>
+                        {% endif %}
                         <td>{{ up_hi.upload_date }}</td>
                         <td>{% if up_hi.r_package_version %}{{ up_hi.r_package_version }}{% else %}--{% endif %}</td>
                         <td>{% if up_hi.generation_date %}{{ up_hi.generation_date }}{% else %}--{% endif %}</td>

dashboard_viewer/uploader/templates/uploader_base.html

@@ -36,7 +36,18 @@
             {% block title %}{% endblock %}
 
             <form id="uploadForm" method="POST" enctype="multipart/form-data">
-                {% bootstrap_form form %}
+                {% if constance_config.ALLOW_ONBOARDING_UPLOAD and onboarding_form %}
+                    <div class="row">
+                        <div class="col-6 col-sm-3">
+                            {% bootstrap_form form %}
+                        </div>
+                        <div class="col-6 col-sm-3">
+                            {% bootstrap_form onboarding_form %}
+                        </div>
+                    </div>
+                {% else %}
+                    {% bootstrap_form form %}
+                {% endif %}
 
                 {% buttons %}
                     <button type="submit" class="btn btn-primary btn-sm-lg" >

dashboard_viewer/uploader/urls.py

@@ -23,4 +23,9 @@
         views.data_source_dashboard,
         name="data_source_dashboard",
     ),
+    path(
+        "<str:data_source>/OnboardingReport/",
+        views.show_onboarding_csv,
+        name="show_onboarding_csv"
+    )
 ]