Merge branch 'dev' into au/event/feature/show_inactive_participants

.env.example

@@ -98,8 +98,6 @@ GCS_SIGNED_URL_LIFETIME_IN_MINUTES=1440
 # GCP Research Environments
 ENABLE_CLOUD_RESEARCH_ENVIRONMENTS="False"
 CLOUD_RESEARCH_ENVIRONMENTS_API_URL="https://example.api"
-CLOUD_RESEARCH_ENVIRONMENTS_API_JWT_SERVICE_ACCOUNT_PATH="environment/api/tests/service_account.json"
-CLOUD_RESEARCH_ENVIRONMENTS_API_JWT_AUDIENCE="https://example.com"
 
 # Site-specific content
 SITE_NAME="DataShare"
@@ -187,7 +185,7 @@ MIN_WORDS_RESEARCH_SUMMARY_CREDENTIALING = 20
 # CITISOAPService API
 # This is the WebServices username and password to access the CITI SOAP Service to obtain users training report details
 # The account can be created at https://webservices.citiprogram.org/login/CreateAccount.aspx
-# The SOAP Service Access can be tested at https://webservices.citiprogram.org/Client/CITISOAPClient_Simple.aspx 
+# The SOAP Service Access can be tested at https://webservices.citiprogram.org/Client/CITISOAPClient_Simple.aspx
 CITI_USERNAME=
 CITI_PASSWORD=
 CITI_SOAP_URL="https://webservices.citiprogram.org/SOAP/CITISOAPService.asmx"

.github/workflows/physionet-build-test.yml

@@ -14,7 +14,7 @@ jobs:
   test:
     name: Test
     runs-on: ubuntu-latest
-    container: debian:11
+    container: ${{ matrix.container }}
     env:
       DJANGO_SETTINGS_MODULE: physionet.settings.settings
       TEST_GCS_INTEGRATION: false
@@ -26,6 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         pip3: ['poetry', 'requirements.txt']
+        container: ['debian:11', 'debian:12']
     steps:
 
       - name: Update packages

.github/workflows/physionet-upgrade-test.yml

@@ -12,7 +12,10 @@ jobs:
   testupgrade:
     name: Upgrade Test
     runs-on: ubuntu-latest
-    container: debian:11
+    container: ${{ matrix.container }}
+    strategy:
+      matrix:
+        container: ['debian:11', 'debian:12']
     steps:
       - name: Install dependencies
         run: |

deploy/README.md

@@ -100,16 +100,16 @@ cd /physionet
 # Copy over the .env file into /physionet/physionet-build
 scp <somewhere>/.env /physionet/physionet-build/
 # The software folder should be owned by the dedicated user. The socket file directory should be accessible by nginx.
-chown -R pn.pn /physionet
-chown pn.www-data /physionet/deploy
+chown -R pn:pn /physionet
+chown pn:www-data /physionet/deploy
 chmod g+w /physionet/deploy
 # Make the static and media roots
 mkdir /data
 mkdir /data/pn-static
 mkdir /data/pn-static/published-projects
 mkdir /data/pn-media
 mkdir /data/pn-media/{active-projects,archived-projects,credential-applications,published-projects,users}
-chown -R pn.pn /data/{pn-media,pn-static}
+chown -R pn:pn /data/{pn-media,pn-static}
 ```
 
 The directory structure for the site's software and files will be:

deploy/test-server/install-pn-test-server

@@ -90,7 +90,7 @@ printf '%s\n%s\n' "$DBPASSWORD" "$DBPASSWORD" |
 su postgres -c 'createdb physionet -O physionet'
 
 mkdir -p /physionet /data/pn-static /data/pn-media
-chown pn.pn /physionet /data/pn-static /data/pn-media
+chown pn:pn /physionet /data/pn-static /data/pn-media
 su pn -c '
    set -e
    umask 0002
@@ -153,17 +153,17 @@ su pn -c '
    yes | python3 manage.py loaddemo
 '
 
-chown www-data.www-data -R /physionet/deploy
-chown www-data.www-data -R /data/pn-media
-chown www-data.www-data -R /data/pn-static/published-projects
+chown www-data:www-data -R /physionet/deploy
+chown www-data:www-data -R /data/pn-media
+chown www-data:www-data -R /data/pn-static/published-projects
 
 rm /etc/nginx/sites-enabled/default
 ln -s ../sites-available/physionet_nginx.conf \
    /etc/nginx/sites-enabled/physionet_nginx.conf
 
 mkdir /data/log /data/log/nginx /data/log/uwsgi /data/log/pn
-chown www-data.root /data/log/uwsgi
-chown pn.root /data/log/pn
+chown www-data:root /data/log/uwsgi
+chown pn:root /data/log/pn
 
 (
     cd /physionet/physionet-build/deploy/common

physionet-django/console/forms.py

@@ -1,10 +1,5 @@
-import pdb
 import re
 
-from django.forms.widgets import RadioSelect
-
-from django.forms.widgets import RadioSelect
-
 from console.utility import generate_doi_payload, register_doi
 from dal import autocomplete
 from django import forms
@@ -27,9 +22,10 @@
     PublishedAffiliation,
     PublishedAuthor,
     PublishedProject,
+    PublishedPublication,
+    SubmissionStatus,
     exists_project_slug,
 )
-from project.projectfiles import ProjectFiles
 from project.validators import MAX_PROJECT_SLUG_LENGTH, validate_doi, validate_slug
 from user.models import CodeOfConduct, CredentialApplication, CredentialReview, User, TrainingQuestion
 
@@ -91,10 +87,12 @@ def __init__(self, *args, **kwargs):
                 .order_by('username')
 
     def clean_project(self):
-        pid = self.cleaned_data['project']
+        pid = self.cleaned_data["project"]
         validate_integer(pid)
-        if ActiveProject.objects.get(id=pid) not in ActiveProject.objects.filter(submission_status=10):
-            raise forms.ValidationError('Incorrect project selected.')
+        if ActiveProject.objects.get(id=pid) not in ActiveProject.objects.filter(
+            submission_status=SubmissionStatus.NEEDS_ASSIGNMENT
+        ):
+            raise forms.ValidationError("Incorrect project selected.")
         return pid
 
 
@@ -230,13 +228,13 @@ def save(self):
                 edit_log = EditLog.objects.get(id=edit_log.id)
             # Resubmit with revisions
             elif edit_log.decision == 1:
-                project.submission_status = 30
+                project.submission_status = SubmissionStatus.NEEDS_RESUBMISSION
                 project.revision_request_datetime = now
                 project.latest_reminder = now
                 project.save()
             # Accept
             else:
-                project.submission_status = 40
+                project.submission_status = SubmissionStatus.NEEDS_COPYEDIT
                 project.editor_accept_datetime = now
                 project.latest_reminder = now
 
@@ -289,7 +287,7 @@ def save(self):
             project = copyedit_log.project
             now = timezone.now()
             copyedit_log.complete_datetime = now
-            project.submission_status = 50
+            project.submission_status = SubmissionStatus.NEEDS_APPROVAL
             project.copyedit_completion_datetime = now
             project.latest_reminder = now
             copyedit_log.save()
@@ -310,12 +308,12 @@ def __init__(self, project, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.project = project
         # No option to set slug if publishing new version
-        if self.project.version_order:
+        if self.project.is_new_version:
             del(self.fields['slug'])
         else:
             self.fields['slug'].initial = project.slug
 
-        if not ProjectFiles().can_make_zip():
+        if not project.files.can_make_zip():
             self.fields['make_zip'].disabled = True
             self.fields['make_zip'].required = False
             self.fields['make_zip'].initial = 0
@@ -705,6 +703,32 @@ def save(self):
         return contact
 
 
+class AddPublishedPublicationForm(forms.ModelForm):
+    class Meta:
+        model = PublishedPublication
+        fields = ('citation', 'url')
+
+    def __init__(self, project, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.project = project
+
+    def clean(self):
+        cleaned_data = super().clean()
+        existing_publication = PublishedPublication.objects.filter(project=self.project).first()
+
+        if existing_publication:
+            raise forms.ValidationError("A publication already exists for this project.")
+
+        return cleaned_data
+
+    def save(self, commit=True):
+        publication = super().save(commit=False)
+        publication.project = self.project
+        if commit:
+            publication.save()
+        return publication
+
+
 class CreateLegacyAuthorForm(forms.ModelForm):
     """
     Create an author for a legacy project.

physionet-django/console/templates/console/console_navbar.html

@@ -123,13 +123,16 @@
               <span class="nav-link-text">Events</span>
             </a>
             <!-- submenu -->
-          {% if events_nav %}
+          {% if nav_event_active or nav_event_archive %}
             <ul class="sidenav-second-level collapse show" id="events">
           {% else  %}
             <ul class="sidenav-second-level collapse" id="events">
           {% endif %}
-              <li class="nav-item {% if events_nav %}active{% endif %}">
-                <a id="nav_events" class="nav-link" href="{% url 'event' %}">Event List</a>
+              <li class="nav-item {% if nav_event_active %}active{% endif %}">
+                <a id="nav_event_active" class="nav-link" href="{% url 'event_active' %}">Active</a>
+              </li>
+              <li class="nav-item {% if nav_event_archive %}active{% endif %}">
+                <a id="nav_event_archive" class="nav-link" href="{% url 'event_archive' %}">Archived</a>
               </li>
             </ul>
         </li>

physionet-django/console/templates/console/copyedit_submission.html

@@ -94,7 +94,7 @@ <h3>Discovery</h3>
 </script>
 
 <script>disableAddButtons();</script>
-{% if project.has_other_versions or project.version_order %}
+{% if project.is_new_version %}
   <script src="{% static 'custom/js/disable-title.js' %}"></script>
 {% endif %}
 

physionet-django/console/templates/console/event.html → physionet-django/console/templates/console/event_active.html

@@ -13,7 +13,7 @@
 {% block content %}
 <div class="card mb-3">
     <div class="card-header">
-        Events <span class="badge badge-pill badge-info">{{ events.paginator.count }}</span> 
+        Active Events <span class="badge badge-pill badge-info">{{ event_active.paginator.count }}</span> 
     </div>
     <div class="card-body">
         <div class="table-responsive">
@@ -32,7 +32,7 @@
                 </tr>
               </thead>
               <tbody>
-              {% for event in events %}
+              {% for event in event_active %}
                 <tr>
                     <td><a href="{% url 'event_detail' event.slug %}">{{ event.title }}</a></td>
                     <td>{{ event.get_category_display|title }}</td>

physionet-django/console/templates/console/event_archive.html

@@ -0,0 +1,55 @@
+{% extends "console/base_console.html" %}
+
+{% load static %}
+
+{% block title %}Archived Events{% endblock %}
+
+{% block local_css %}
+<link rel="stylesheet" type="text/css" href="{% static 'custom/css/pagination.css' %}">
+{% endblock %}
+
+{% load console_templatetags %}
+
+{% block content %}
+<div class="card mb-3">
+    <div class="card-header">
+        Archived Events <span class="badge badge-pill badge-info">{{ event_archive.paginator.count }}</span> 
+    </div>
+    <div class="card-body">
+        <div class="table-responsive">
+            <table class="table table-bordered">
+              <thead>
+                <tr>
+                  <th>Event</th>
+                  <th>Event Type</th>
+                  <th>Host</th>
+                  <th>Created</th>
+                  <th>Started</th>
+                  <th>Ended</th>
+                  <th>Credentialing</th>
+                  <th>Training</th>
+                  <th>Manage</th>
+                </tr>
+              </thead>
+              <tbody>
+              {% for event in event_archive %}
+                <tr>
+                    <td><a href="{% url 'event_detail' event.slug %}">{{ event.title }}</a></td>
+                    <td>{{ event.get_category_display|title }}</td>
+                    <td>{{ event.host }}</td>
+                    <td>{{ event.added_datetime|date }}</td>
+                    <td>{{ event.start_date }}</td>
+                    <td>{{ event.end_date }}</td>
+                    <td><a href = "{% url 'credential_processing' %}?event={{ event.slug }}">View list</a></td>
+                    <td><a href = "{% url 'training_list' status='review' %}?event={{ event.slug }}">View list</a></td>
+                    <td><a href="{% url 'event_management' event.slug %}" class="btn btn-sm btn-primary" role="button">Manage</a></td>
+                </tr>
+              {% endfor %}
+              </tbody>
+            </table>
+            {% include "console/pagination.html" with pagination=events %}
+          </div>           
+    </div>
+</div>
+{% endblock %}
+

physionet-django/console/templates/console/manage_published_project.html

@@ -49,6 +49,7 @@ <h4 class="card-title"><a href="{% url 'published_project' project.slug project.
     </div>
   </div>
 </div>
+
 <!-- legacy project management -->
 {% if project.is_legacy %}
 <div class="card mb-3">
@@ -67,6 +68,28 @@ <h3>Add an author</h3>
 </div>
 {% endif %}
 
+<!-- Associated publication -->
+<div class="card mb-3">
+  <div class="card-header">
+    Associated publication
+  </div>
+  <div class="card-body">
+    {% if project.publications.all %}
+      {% for publication in project.publications.all %}
+        <p><strong>Citation</strong>: {{ publication.citation }}<br />
+          <strong>URL</strong>: {{ publication.url }}</p>
+      {% endfor %}
+    {% else %}
+      <form method="POST" id="publication_form">
+        {% include "inline_form_snippet.html" with form=publication_form %}
+        <button class="btn btn-primary btn-fixed" name="set_publication" type="submit">Add publication</button>
+      </form>
+    {% endif %}
+
+  </div>
+</div>
+
+
 <div class="card mb-3">
     <div class="card-header">
       Contact information

physionet-django/console/templates/console/submission_info_card.html

@@ -22,7 +22,7 @@
         <a class="nav-link {% if passphrase %} active {% endif %}" id="embargo-tab" data-toggle="tab" href="#embargo" role="tab" aria-controls="reassign" aria-selected="false">Embargo</a>
       </li>
       {% endif %}
-      {% if project.submission_status >= 40 %}
+      {% if project.submission_status >= SubmissionStatus.NEEDS_COPYEDIT %}
       <li class="nav-item">
         <a class="nav-link" id="doi-tab" data-toggle="tab" href="#doi" role="tab" aria-controls="timeline" aria-selected="false">DOIs</a>
       </li>
@@ -40,7 +40,7 @@ <h4 class="card-title">{{ project.title }}</h4>
           Created: {{ project.creation_datetime|date }}. Submitted: {{ project.submission_datetime|date }}.<br>
           Storage Used: {{ storage_info.readable_used }} / {{ storage_info.readable_allowance }}<br>
           Version: {{ project.version }}
-          {% if project.version_order %}<br>Latest Published Version: <a href="{% url 'published_project' latest_version.slug latest_version.version %}" target="_blank">{{ latest_version.version }}</a>{% endif %}
+          {% if project.is_new_version %}<br>Latest Published Version: <a href="{% url 'published_project' latest_version.slug latest_version.version %}" target="_blank">{{ latest_version.version }}</a>{% endif %}
           {% if project.latest_reminder %}
             <br>Latest reminder email sent on: {{ project.latest_reminder }}
           {% endif %}