Merge branch 'MIT-LCP:dev' into au/training/feature/create_training_b…

…asics__implement_training_user

.env.example

@@ -144,6 +144,17 @@ SOURCE_CODE_REPOSITORY_LINK='https://github.com/MIT-LCP/physionet-build'
 # These variables are used to set the theme colors for the site
 DARK='#343A40'
 PRIMARY='#002A5C'
+SECONDARY='#6D247A'
+SUCCESS='#8DBF2E'
+INFO='#6FC7EA'
+WARNING='#F1C500'
+DANGER='#DC4633'
+LIGHT='#007FA3'
+
+## Gradient colors on homepage
+
+GRADIENT_60 = 'rgba(42, 47, 52, 0.6)'
+GRADIENT_85 = 'rgba(42, 47, 52, 0.85)'
 
 # Users settings
 # maximum number of emails that can be associated to a user model
@@ -172,3 +183,16 @@ DEFAULT_NUMBER_OF_APPLICATIONS_TO_REMIND = 5
 
 # minimum number of word needed for research_summary field for Credentialing Model.
 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 
+CITI_USERNAME=
+CITI_PASSWORD=
+CITI_SOAP_URL="https://webservices.citiprogram.org/SOAP/CITISOAPService.asmx"
+
+# Django configuration for file upload
+# See https://docs.djangoproject.com/en/4.2/ref/settings/
+DATA_UPLOAD_MAX_NUMBER_FILES=1000
+DATA_UPLOAD_MAX_MEMORY_SIZE=2621440

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

@@ -37,6 +37,7 @@ jobs:
                   build-essential \
                   flake8 \
                   git \
+                  libcap-dev \
                   libffi-dev \
                   libflac-dev \
                   libpq-dev \

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

@@ -21,6 +21,7 @@ jobs:
                   build-essential \
                   flake8 \
                   git \
+                  libcap-dev \
                   libffi-dev \
                   libflac-dev \
                   libpq-dev \

.gitignore

@@ -148,4 +148,5 @@ physionet-django/static/bootstrap/scss/theme.scss
 physionet-django/static/bootstrap/css/bootstrap-grid.css
 physionet-django/static/bootstrap/css/bootstrap-reboot.css
 physionet-django/static/bootstrap/css/bootstrap.css
-physionet-django/static/bootstrap/css/theme.css
+physionet-django/static/bootstrap/css/theme.css
+physionet-django/static/custom/css/home.css

Dockerfile

@@ -2,7 +2,7 @@ FROM python:3.9-bullseye
 
 RUN apt-get update -y \
     && apt-get upgrade -y \
-    && apt-get install build-essential libflac-dev libseccomp-dev libpq-dev libpcre3-dev postgresql-client wget zip -y --no-install-recommends \
+    && apt-get install build-essential libcap-dev libflac-dev libseccomp-dev libpq-dev libpcre3-dev postgresql-client wget zip -y --no-install-recommends \
     && rm -rf /var/lib/apt/lists/*
 
 RUN wget https://github.com/bemoody/wfdb/archive/10.7.0.tar.gz -O wfdb.tar.gz \

README.md

@@ -114,8 +114,25 @@ If the migration behavior interacts with other changes that have been applied to
 
 #### Theming instructions
 
-The PRIMARY and DARK environment variables can be configured in the .env file.
- * The management command "compilestatic" generates a theme.scss file and compiles the CSS.
+The theme of the deployed website can be configured by changing the following environment variables:
+
+  * DARK
+  * PRIMARY
+  * SECONDARY
+  * SUCCESS
+  * INFO
+  * WARNING
+  * DANGER
+  * LIGHT
+
+
+  The management command "compilestatic" generates a theme.scss file and compiles the following CSS files.
+
+   *  static/custom/css/home.css
+   *  static/bootstrap/css/bootstrap.css
+
+**Note:** The css files above are not tracked by git and are generated only when you run compilestatic command.
+
 
 #### Setting Up Cronjobs
 

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

@@ -48,7 +48,7 @@ apt-get install -y \
         `# Python application server` \
         virtualenv python3-dev libpq-dev libffi-dev \
         `# Requirements for building LightWAVE` \
-        build-essential libflac-dev libseccomp-dev \
+        build-essential libcap-dev libflac-dev libseccomp-dev \
         `# Other tools required by PhysioNet` \
         zip unzip xfsprogs \
         `# Development and administration tools` \

physionet-django/console/templates/console/rejected_submissions.html → physionet-django/console/templates/console/archived_submissions.html

@@ -2,7 +2,7 @@
 
 {% load static %}
 
-{% block title %}Rejected Projects{% endblock %}
+{% block title %}Archived Projects{% endblock %}
 
 {% block local_css %}
 <link rel="stylesheet" type="text/css" href="{% static 'custom/css/pagination.css' %}">
@@ -11,7 +11,7 @@
 {% block content %}
 <div class="card mb-3">
   <div class="card-header">
-    Rejected Projects <span class="badge badge-pill badge-info">{{ projects.paginator.count }}</span>
+    Archived Projects <span class="badge badge-pill badge-info">{{ projects.paginator.count }}</span>
   </div>
   <div class="card-body">
     <div class="table-responsive">
@@ -24,14 +24,14 @@
             <th>Submitting Author</th>
             <th>Editor</th>
             <th>Creation Date</th>
-            <th>Rejection Date</th>
+            <th>Archived Date</th>
           </tr>
         </thead>
         <tbody>
         {% for project in projects %}
           <tr>
             <td>{{ project.title }}</td>
-            <td><a href="{% url 'rejected_submission_history' project.slug %}">View History</a></td>
+            <td><a href="{% url 'archived_submission_history' project.slug %}">View History</a></td>
             <td>{{ project.version }}</td>
             <td>{% if project.submitting_author %}
               <a href="{% url 'user_management' project.submitting_author.user.username %}">{{ project.submitting_author }}</a>

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

@@ -32,7 +32,7 @@
       <!-- projects -->
       {% if perms.project.change_publishedproject %}
         <li class="nav-item" data-toggle="tooltip" data-placement="right">
-        {% if project_info_nav or submitted_projects_nav or unsubmitted_projects_nav or published_projects_nav or rejected_projects_nav %}
+        {% if project_info_nav or submitted_projects_nav or unsubmitted_projects_nav or published_projects_nav or archived_projects_nav %}
           <a id="nav_projects_dropdown" class="nav-link nav-link-collapse drop" data-toggle="collapse" href="#projectComponents" data-parent="#sideAccordion" aria-expanded="true">
         {% else %}
           <a id="nav_projects_dropdown" class="nav-link nav-link-collapse drop collapsed" data-toggle="collapse" href="#projectComponents" data-parent="#sideAccordion" aria-expanded="false">
@@ -41,7 +41,7 @@
             <span class="nav-link-text">Projects</span>
           </a>
           <!-- submenu -->
-        {% if project_info_nav or submitted_projects_nav or unsubmitted_projects_nav or published_projects_nav or rejected_projects_nav %}
+        {% if project_info_nav or submitted_projects_nav or unsubmitted_projects_nav or published_projects_nav or archived_projects_nav %}
           <ul class="sidenav-second-level collapse show" id="projectComponents" style="">
         {% else %}
           <ul class="sidenav-second-level collapse" id="projectComponents">
@@ -55,8 +55,8 @@
             <li class="nav-item {% if published_projects_nav %}active{% endif %}">
               <a id="nav_published_projects" class="nav-link" href="{% url 'published_projects' %}">Published</a>
             </li>
-            <li class="nav-item {% if rejected_projects_nav %}active{% endif %}">
-              <a id="nav_rejected_submissions" class="nav-link" href="{% url 'rejected_submissions' %}">Rejected</a>
+            <li class="nav-item {% if archived_projects_nav %}active{% endif %}">
+              <a id="nav_archived_submissions" class="nav-link" href="{% url 'archived_submissions' %}">Archived</a>
             </li>          
           </ul>
         </li>

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

@@ -35,6 +35,30 @@ <h3>Profile</h3>
       {{ subject.is_credentialed }}
     </div>
   </div>
+  <div class="row mb-1">
+    <div class="col-md-3">
+      Amazon ID
+    </div>
+    <div class="col-md-9">
+      {% if aws_info %}
+        {{ aws_info }}
+      {% else %}
+        Not provided.
+      {% endif %}
+    </div>
+  </div>
+  <div class="row mb-1">
+    <div class="col-md-3">
+      Google Cloud ID:
+    </div>
+    <div class="col-md-9">
+      {% if gcp_info %}
+        {{ gcp_info }}
+      {% else %} 
+        Not provided.
+      {% endif %}
+    </div>
+  </div>
 
     <div class="row mb-1">
       <div class="col-md-3">
@@ -48,6 +72,18 @@ <h3>Profile</h3>
         {% endif %}
       </div>
     </div>
+    <div class="row mb-1">
+      <div class="col-md-3">
+        Personal Website:
+      </div>
+      <div class="col-md-9">
+        {% if profile.website %}
+        <a href="{{ profile.website }}" rel="nofollow">{{ profile.website }}</a>
+        {% else %}
+         Not provided.
+        {% endif %}
+      </div>
+    </div>
 
   {% if profile.location %}
     <div class="row mb-1">
@@ -75,17 +111,6 @@ <h3>Profile</h3>
     </div>
   {% endfor %}
 
-  {% if profile.website %}
-    <div class="row mb-1">
-      <div class="col-md-3">
-        Website:
-      </div>
-      <div class="col-md-9">
-        <a href="{{ profile.website }}" rel="nofollow">{{ profile.website }}</a>
-      </div>
-    </div>
-  {% endif %}
-
   {% if groups %}
       <div class="row mb-1">
         <div class="col-md-3">
@@ -116,7 +141,7 @@ <h4>{{ status }} projects</h4>
           <li><a href="{% url 'submission_info' project.slug %}">{{ project.title }}
             </a> (v{{ project.version }})</li>
         {% elif status == "Archived" %}
-          <li><a href="{% url 'rejected_submission_history' project.slug %}">{{ project.title }}
+          <li><a href="{% url 'archived_submission_history' project.slug %}">{{ project.title }}
             </a> (v{{ project.version }})</li>
         {% elif status == "Published" %}
           <li><a href="{% url 'manage_published_project' project.slug project.version %}">{{ project.title }}

physionet-django/console/urls.py

@@ -14,8 +14,7 @@
         name='submitted_projects'),
     path('published-projects/', views.published_projects,
         name='published_projects'),
-    path('rejected-submissions/', views.rejected_submissions,
-        name='rejected_submissions'),
+    path('archived-submissions/', views.archived_submissions, name='archived_submissions'),
     path('project-access-manage/<pid>/', views.project_access_manage,
         name='project_access_manage'),
     path('published-projects/<project_slug>/<version>/',

physionet-django/console/views.py

@@ -1,6 +1,7 @@
 import csv
 import logging
 import os
+import re
 from collections import OrderedDict
 from datetime import datetime
 from itertools import chain
@@ -54,6 +55,7 @@
     Topic,
     exists_project_slug,
 )
+from project.authorization.access import can_view_project_files
 from project.projectfiles import ProjectFiles
 from project.utility import readable_size
 from project.validators import MAX_PROJECT_SLUG_LENGTH
@@ -67,7 +69,8 @@
     Training,
     TrainingType,
     TrainingQuestion,
-    CodeOfConduct
+    CodeOfConduct,
+    CloudInformation
 )
 from physionet.enums import LogCategory
 from console import forms, utility, services
@@ -1003,14 +1006,14 @@ def gcp_bucket_management(request, project, user):
 
 
 @permission_required('project.change_archivedproject', raise_exception=True)
-def rejected_submissions(request):
+def archived_submissions(request):
     """
-    List of rejected submissions
+    List of archived submissions
     """
-    projects = ArchivedProject.objects.filter(archive_reason=3).order_by('archive_datetime')
+    projects = ArchivedProject.objects.all().order_by('archive_datetime')
     projects = paginate(request, projects, 50)
-    return render(request, 'console/rejected_submissions.html',
-                  {'projects': projects, 'rejected_projects_nav': True})
+    return render(request, 'console/archived_submissions.html',
+                  {'projects': projects, 'archived_projects_nav': True})
 
 
 @permission_required('user.view_user', raise_exception=True)
@@ -1070,6 +1073,14 @@ def user_management(request, username):
     Admin page for managing an individual user account.
     """
     user = get_object_or_404(User, username__iexact=username)
+    try:
+        aws_info = CloudInformation.objects.get(user=user).aws_id
+    except CloudInformation.DoesNotExist:
+        aws_info = None
+    try:
+        gcp_info = CloudInformation.objects.get(user=user).gcp_email
+    except CloudInformation.DoesNotExist:
+        gcp_info = None
 
     _training = Training.objects.select_related('training_type').filter(user=user).order_by('-status')
 
@@ -1107,7 +1118,9 @@ def user_management(request, username):
                                                             'emails': emails,
                                                             'projects': projects,
                                                             'training_list': training,
-                                                            'credentialing_app': credentialing_app})
+                                                            'credentialing_app': credentialing_app,
+                                                            'aws_info': aws_info,
+                                                            'gcp_info': gcp_info})
 
 
 @permission_required('user.view_user', raise_exception=True)
@@ -1125,7 +1138,10 @@ def users_search(request, group):
 
         users = User.objects.filter(Q(username__icontains=search_field)
                                     | Q(profile__first_names__icontains=search_field)
-                                    | Q(email__icontains=search_field))
+                                    | Q(profile__last_name__icontains=search_field)
+                                    | Q(email__icontains=search_field)
+                                    | Q(associated_emails__email__icontains=search_field)
+                                    ).distinct()
 
         if 'inactive' in group:
             users = users.filter(is_active=False)
@@ -1152,15 +1168,13 @@ def users_aws_access_list_json(request):
     2022).  Don't rely on this function; it will go away.
     """
     projects_datathon = [
-        "mimiciv-0.3",
-        "mimiciv-0.4",
-        "mimiciv-1.0",
-        "mimiciv-2.0"
+        "mimiciv-2.2"
     ]
     published_projects = PublishedProject.objects.all()
     users_with_awsid = User.objects.filter(cloud_information__aws_id__isnull=False)
     datasets = {}
     datasets['datasets'] = []
+    aws_id_pattern = r"\b\d{12}\b"
 
     for project in published_projects:
         dataset = {}
@@ -1169,8 +1183,9 @@ def users_aws_access_list_json(request):
             dataset['name'] = project_name
             dataset['accounts'] = []
             for user in users_with_awsid:
-                if project.can_view_files(user):
-                    dataset['accounts'].append(user.cloud_information.aws_id)
+                if can_view_project_files(project, user):
+                    if re.search(aws_id_pattern, user.cloud_information.aws_id):
+                        dataset['accounts'].append(user.cloud_information.aws_id)
             datasets['datasets'].append(dataset)
 
     return JsonResponse(datasets)

physionet-django/events/models.py

@@ -224,6 +224,7 @@ def is_accessible(self):
 
     def has_access(self, user):
         """
+        Deprecated: use projects.authorization.access.has_access_to_event_dataset instead
         Checks if the user has access to this EventDataset.
         This does not check if the associated dataset(PublishedProject) is accessible
         """

physionet-django/events/templates/events/event_entries.html

@@ -15,7 +15,7 @@
             <td>{{ participant.user.username }}</td>
             <td>{{ participant.user.get_full_name }}</td>
             <td>{{ participant.user.email }}</td>
-            <td>{{ participant.user.is_credentialed }}</td>
+            <td>{{ participant.user.get_credentialing_status }}</td>
             <td>
                 {% if participant.is_cohost %}
                     <input type="checkbox" name="toggle-cohost-status"  event-slug="{{ event.slug }}" value="{{ participant.id }}" disabled checked>