Merge pull request #629 from hms-dbmi/development

Development

app/contact/views.py

@@ -46,10 +46,10 @@ def contact_form(request, project_key=None):
                 if project.project_supervisors != '' and project.project_supervisors is not None:
                     recipients = project.project_supervisors.split(',')
                 else:
-                    recipients = settings.CONTACT_FORM_RECIPIENTS.split(',')
+                    recipients = settings.CONTACT_FORM_RECIPIENTS
 
             except ObjectDoesNotExist:
-                recipients = settings.CONTACT_FORM_RECIPIENTS.split(',')
+                recipients = settings.CONTACT_FORM_RECIPIENTS
 
             # Send it out.
             success = email_send(subject='DBMI Portal - Contact Inquiry Received',
@@ -116,7 +116,8 @@ def email_send(subject=None, recipients=None, email_template=None, extra=None):
     try:
         msg = EmailMultiAlternatives(subject=subject,
                                      body=msg_plain,
-                                     from_email=settings.DEFAULT_FROM_EMAIL,
+                                     from_email=settings.EMAIL_FROM_ADDRESS,
+                                     reply_to=(settings.EMAIL_REPLY_TO_ADDRESS, ),
                                      to=recipients)
         msg.attach_alternative(msg_html, "text/html")
         msg.send()

app/hypatio/settings.py

@@ -135,8 +135,8 @@
 SSL_SETTING = "https"
 VERIFY_REQUESTS = True
 
-CONTACT_FORM_RECIPIENTS="[email protected]"
-DEFAULT_FROM_EMAIL="[email protected]"
+# Pass a list of email addresses
+CONTACT_FORM_RECIPIENTS = environment.get_list('CONTACT_FORM_RECIPIENTS', required=True)
 
 RECAPTCHA_KEY = environment.get_str('RECAPTCHA_KEY', required=True)
 RECAPTCHA_CLIENT_ID = environment.get_str('RECAPTCHA_CLIENT_ID', required=True)
@@ -146,6 +146,7 @@
 S3_BUCKET = environment.get_str('S3_BUCKET', required=True)
 
 DEFAULT_FILE_STORAGE = 'storages.backends.s3boto3.S3Boto3Storage'
+AWS_S3_SIGNATURE_VERSION = 's3v4'
 AWS_STORAGE_BUCKET_NAME = environment.get_str('S3_BUCKET', required=True)
 AWS_LOCATION = 'upload'
 
@@ -240,21 +241,29 @@
 
 # Determine email backend
 EMAIL_BACKEND = environment.get_str("EMAIL_BACKEND", required=True)
+if EMAIL_BACKEND == "django.core.mail.backends.smtp.EmailBackend":
 
-# SMTP Email configuration
-EMAIL_SMTP = EMAIL_BACKEND == "django.core.mail.backends.smtp.EmailBackend"
-EMAIL_USE_SSL = environment.get_bool("EMAIL_USE_SSL", default=EMAIL_SMTP)
-EMAIL_HOST = environment.get_str("EMAIL_HOST", required=EMAIL_SMTP)
-EMAIL_HOST_USER = environment.get_str("EMAIL_HOST_USER", required=False)
-EMAIL_HOST_PASSWORD = environment.get_str("EMAIL_HOST_PASSWORD", required=False)
-EMAIL_PORT = environment.get_str("EMAIL_PORT", required=EMAIL_SMTP)
-
-# AWS SES Email configuration
-EMAIL_SES = EMAIL_BACKEND == "django_ses.SESBackend"
-AWS_SES_SOURCE_ARN=environment.get_str("DBMI_SES_IDENTITY", required=EMAIL_SES)
-AWS_SES_FROM_ARN=environment.get_str("DBMI_SES_IDENTITY", required=EMAIL_SES)
-AWS_SES_RETURN_PATH_ARN=environment.get_str("DBMI_SES_IDENTITY", required=EMAIL_SES)
-USE_SES_V2 = True
+    # SMTP Email configuration
+    EMAIL_USE_SSL = environment.get_bool("EMAIL_USE_SSL", default=True)
+    EMAIL_HOST = environment.get_str("EMAIL_HOST", required=True)
+    EMAIL_HOST_USER = environment.get_str("EMAIL_HOST_USER", required=False)
+    EMAIL_HOST_PASSWORD = environment.get_str("EMAIL_HOST_PASSWORD", required=False)
+    EMAIL_PORT = environment.get_str("EMAIL_PORT", required=True)
+
+elif EMAIL_BACKEND == "django_ses.SESBackend":
+
+    # AWS SES Email configuration
+    AWS_SES_SOURCE_ARN = environment.get_str("DBMI_SES_IDENTITY", required=True)
+    AWS_SES_FROM_ARN = environment.get_str("DBMI_SES_IDENTITY", required=True)
+    AWS_SES_RETURN_PATH_ARN = environment.get_str("DBMI_SES_IDENTITY", required=True)
+    USE_SES_V2 = True
+
+else:
+    raise SystemError(f"Email backend '{EMAIL_BACKEND}' is not supported for this application")
+
+# Set default from address
+EMAIL_FROM_ADDRESS = environment.get_str("EMAIL_FROM_ADDRESS", required=True)
+EMAIL_REPLY_TO_ADDRESS = environment.get_str("EMAIL_REPLY_TO_ADDRESS", default=EMAIL_FROM_ADDRESS)
 
 #####################################################################################
 

app/manage/forms.py

@@ -79,3 +79,7 @@ def __init__(self, *args, **kwargs):
             # Limit agreement form choices to those related to the passed project
             if project_key:
                 self.fields['agreement_form'].queryset = DataProject.objects.get(project_key=project_key).agreement_forms.all()
+
+
+class UploadSignedAgreementFormFileForm(forms.Form):
+    file = forms.FileField(label="Signed Agreement Form PDF", required=True)

app/manage/urls.py

@@ -8,6 +8,7 @@
 from manage.views import ProjectPendingParticipants
 from manage.views import team_notification
 from manage.views import UploadSignedAgreementFormView
+from manage.views import UploadSignedAgreementFormFileView
 
 from manage.api import set_dataproject_details
 from manage.api import set_dataproject_registration_status
@@ -62,6 +63,7 @@
     re_path(r'^get-project-participants/(?P<project_key>[^/]+)/$', ProjectParticipants.as_view(), name='get-project-participants'),
     re_path(r'^get-project-pending-participants/(?P<project_key>[^/]+)/$', ProjectPendingParticipants.as_view(), name='get-project-pending-participants'),
     re_path(r'^upload-signed-agreement-form/(?P<project_key>[^/]+)/(?P<user_email>[^/]+)/$', UploadSignedAgreementFormView.as_view(), name='upload-signed-agreement-form'),
+    re_path(r'^upload-signed-agreement-form-file/(?P<signed_agreement_form_id>[^/]+)/$', UploadSignedAgreementFormFileView.as_view(), name='upload-signed-agreement-form-file'),
     re_path(r'^(?P<project_key>[^/]+)/$', DataProjectManageView.as_view(), name='manage-project'),
     re_path(r'^(?P<project_key>[^/]+)/(?P<team_leader>[^/]+)/$', manage_team, name='manage-team'),
 ]

app/manage/views.py

@@ -19,13 +19,15 @@
 from django.core.mail import EmailMultiAlternatives
 from django.template.loader import render_to_string
 from dbmi_client import fileservice
+from django.shortcuts import get_object_or_404
 
 from hypatio.sciauthz_services import SciAuthZ
 from hypatio.scireg_services import get_user_profile, get_distinct_countries_participating
 
 from manage.forms import NotificationForm
 from manage.models import ChallengeTaskSubmissionExport
 from manage.forms import UploadSignedAgreementFormForm
+from manage.forms import UploadSignedAgreementFormFileForm
 from projects.models import AgreementForm, ChallengeTaskSubmission
 from projects.models import DataProject
 from projects.models import Participant
@@ -603,7 +605,8 @@ def team_notification(request, project_key=None):
             try:
                 msg = EmailMultiAlternatives(subject=subject,
                                             body=msg_plain,
-                                            from_email=settings.DEFAULT_FROM_EMAIL,
+                                            from_email=settings.EMAIL_FROM_ADDRESS,
+                                            reply_to=(settings.EMAIL_REPLY_TO_ADDRESS, ),
                                             to=[team.team_leader.email])
                 msg.attach_alternative(msg_html, "text/html")
                 msg.send()
@@ -908,3 +911,87 @@ def post(self, request, project_key, user_email, *args, **kwargs):
         response['X-IC-Script'] += "$('#page-modal').modal('hide');"
 
         return response
+
+
+@method_decorator([user_auth_and_jwt], name='dispatch')
+class UploadSignedAgreementFormFileView(View):
+    """
+    View to upload signed agreement form files for participants.
+
+    * Requires token authentication.
+    * Only admin users are able to access this view.
+    """
+    def get(self, request, signed_agreement_form_id, *args, **kwargs):
+        """
+        Return the upload form template
+        """
+        user = request.user
+        user_jwt = request.COOKIES.get("DBMI_JWT", None)
+
+        signed_agreement_form = get_object_or_404(SignedAgreementForm, id=signed_agreement_form_id)
+
+        sciauthz = SciAuthZ(user_jwt, user.email)
+        is_manager = sciauthz.user_has_manage_permission(signed_agreement_form.project.project_key)
+
+        if not is_manager:
+            logger.debug('User {email} does not have MANAGE permissions for item {project_key}.'.format(
+                email=user.email,
+                project_key=signed_agreement_form.project.project_key
+            ))
+            return HttpResponse(403)
+
+        # Return file upload form
+        form = UploadSignedAgreementFormFileForm()
+
+        # Set context
+        context = {
+            "form": form,
+            "signed_agreement_form_id": signed_agreement_form_id,
+        }
+
+        # Render html
+        return render(request, "manage/upload-signed-agreement-form-file.html", context)
+
+    def post(self, request, signed_agreement_form_id, *args, **kwargs):
+        """
+        Process the form
+        """
+        user = request.user
+        user_jwt = request.COOKIES.get("DBMI_JWT", None)
+
+        signed_agreement_form = get_object_or_404(SignedAgreementForm, id=signed_agreement_form_id)
+
+        sciauthz = SciAuthZ(user_jwt, user.email)
+        is_manager = sciauthz.user_has_manage_permission(signed_agreement_form.project.project_key)
+
+        if not is_manager:
+            logger.debug('User {email} does not have MANAGE permissions for item {project_key}.'.format(
+                email=user.email,
+                project_key=signed_agreement_form.project.project_key
+            ))
+            return HttpResponse(403)
+
+        # Assembles the form and run validation.
+        form = UploadSignedAgreementFormFileForm(data=request.POST, files=request.FILES)
+        if not form.is_valid():
+            logger.warning('Form failed: {}'.format(form.errors.as_json()))
+            return HttpResponse(status=400)
+
+        logger.debug(f"[upload_signed_agreement_form_file] Data -> {form.cleaned_data}")
+
+        # Set the file and save
+        signed_agreement_form.upload = form.cleaned_data['file']
+        signed_agreement_form.save()
+
+        # Create the response.
+        response = HttpResponse(status=201)
+
+        # Setup the script run.
+        response['X-IC-Script'] = "notify('{}', '{}', 'glyphicon glyphicon-{}');".format(
+            "success", "Signed agreement form file successfully uploaded", "thumbs-up"
+        )
+
+        # Close the modal
+        response['X-IC-Script'] += "$('#page-modal').modal('hide');"
+
+        return response

app/projects/migrations/0102_agreementform_skippable.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.4 on 2023-09-12 16:20
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('projects', '0101_challengetask_submission_instructions'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='agreementform',
+            name='skippable',
+            field=models.BooleanField(default=False, help_text='Allow participants to skip this step in instances where they have submitted the agreement form via email or some other means. They will be required to include the name and contact information of the person who they submitted their signed agreement form to.'),
+        ),
+    ]

app/projects/migrations/0103_dataproject_commercial_only.py

@@ -0,0 +1,18 @@
+# Generated by Django 4.2.1 on 2023-06-28 10:32
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('projects', '0102_agreementform_skippable'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='dataproject',
+            name='commercial_only',
+            field=models.BooleanField(default=False, help_text='Commercial only projects are for commercial entities only'),
+        ),
+    ]

app/projects/models.py

@@ -253,6 +253,12 @@ class AgreementForm(models.Model):
     order = models.IntegerField(default=50, help_text="Indicate an order (lowest number = first listing) for how the Agreement Forms should be listed during registration workflows.")
     content = models.TextField(blank=True, null=True, help_text="If Agreement Form type is set to 'MODEL', the HTML set here will be rendered for the user")
     internal = models.BooleanField(default=False, help_text="Internal agreement forms are never presented to participants and are only submitted by administrators on behalf of participants")
+    skippable = models.BooleanField(
+        default=False,
+        help_text="Allow participants to skip this step in instances where they have submitted the agreement form via"
+                  " email or some other means. They will be required to include the name and contact information of"
+                  " the person who they submitted their signed agreement form to."
+    )
 
     # Meta
     created = models.DateTimeField(auto_now_add=True)
@@ -323,6 +329,9 @@ class DataProject(models.Model):
     )
     teams_source_message = models.TextField(default="Teams approved there will be automatically added to this project but will need still need approval for this project.", blank=True, null=True, verbose_name="Teams Source Message")
 
+    # Set this to show badging to indicate that only commercial entities should apply for access
+    commercial_only = models.BooleanField(default=False, blank=False, null=False, help_text="Commercial only projects are for commercial entities only")
+
     show_jwt = models.BooleanField(default=False, blank=False, null=False)
 
     order = models.IntegerField(blank=True, null=True, help_text="Indicate an order (lowest number = highest order) for how the DataProjects should be listed.")

app/static/js/portal.js

@@ -0,0 +1,12 @@
+
+/**
+ * Finds all 'button' elements contained in a form and toggles their 'disabled' proeprty.
+ * @param  {String} formSelector  The jQuery selector of the form to disable buttons for.
+ */
+function toggleFormButtons(formSelector) {
+
+    // Toggle disabled state of all buttons in form
+    $(formSelector).find("button").each(function() {
+        $(this).prop("disabled", !$(this).prop("disabled"));
+    });
+}

app/templates/base.html

@@ -47,6 +47,9 @@
         <script type='text/javascript' src="{% static 'plugins/bootstrap-notify/bootstrap-notify.min.js' %}"></script>
         <script type="text/javascript" src="{% static 'plugins/intercooler/intercooler.min.js' %}"></script>
 
+        <!-- Include portal specific Javascript -->
+        <script type='text/javascript' src="{% static 'js/portal.js' %}"></script>
+
         <title>{% block tab_name %}DBMI Portal{% endblock %}</title>
 
         <script type="application/javascript">
@@ -226,12 +229,14 @@
                                 <a class="dropdown-toggle" data-toggle="dropdown" href="#" id="download">{{ request.user.email }}<span class="caret"></span></a>
                                 <ul class="dropdown-menu" aria-labelledby="downloadn">
                                     <li><a class="nav-link" href="{% url 'profile:profile' %}">Profile <span class="fas fa-sm fa-user"></span></a></li>
-
                                     {% is_project_manager request as is_manager %}
                                     {% if is_manager %}
-                                        <li><a class="nav-link" href="{% url 'manage:manage-projects' %}">Manage Projects</a></li>
+                                    <li><a class="nav-link" href="{% url 'manage:manage-projects' %}">Manage Projects</a></li>
                                     {% endif %}
-
+                                    {% if dbmiuser and dbmiuser.jwt %}
+                                    <li><a id="jwt-copy" class="nav-link clipboard-copy" data-clipboard-text="{{ dbmiuser.jwt|default:"<empty>" }}" data-toggle="tooltip" style="cursor: pointer;" title="Copy API Key" data-tooltip-title="Copy API Key">API Key <i class="fa fa-wrench" aria-hidden="true"></i>
+                                    {% endif %}
+                                    </a></li>
                                     <li><a class="nav-link" href="{% url 'profile:signout' %}">Sign Out</a></li>
                                 </ul>
                             </li>
@@ -255,4 +260,45 @@
 
     {# Allow for some javascript to be added per page #}
     {% block javascript %}{% endblock %}
+
+    <script type="text/javascript" src="{% static 'js/clipboard.min.js' %}"></script>
+    <script type="application/javascript">
+      $(document).ready(function(){
+
+        // Initialize tooltips
+        $('[data-toggle="tooltip"]').tooltip();
+
+        // Reset tooltips
+        $('[data-toggle="tooltip"][data-tooltip-title]').on('hidden.bs.tooltip', function(){
+            $(this).attr('data-original-title', $(this).attr('data-tooltip-title'));
+        });
+
+        // Setup copy button
+        var clipboards = new ClipboardJS(".clipboard-copy");
+        clipboards.on('success', function(e) {
+
+            // Update tooltip
+            $(e.trigger).attr('data-original-title', "Copied!")
+                .tooltip('fixTitle')
+                .tooltip('setContent')
+                .tooltip('show');
+
+            e.clearSelection();
+        });
+
+        clipboards.on('error', function(e) {
+
+            // Update tooltip
+            $(e.trigger).attr('data-original-title', "Error!")
+                .tooltip('fixTitle')
+                .tooltip('setContent')
+                .tooltip('show');
+
+            // Log it
+            console.log('Copy error:' + e.toString());
+
+            e.clearSelection();
+        });
+      });
+  </script>
 </html>

app/templates/manage/upload-signed-agreement-form-file.html

@@ -0,0 +1,23 @@
+{% load bootstrap3 %}
+
+<form id="upload-signed-agreement-form-file-form" class="file-upload-form" method="post" enctype="multipart/form-data"
+      ic-post-to="{% url 'manage:upload-signed-agreement-form-file' signed_agreement_form_id %}"
+      ic-on-beforeSend="toggleFormButtons('#upload-signed-agreement-form-file-form')"
+      ic-on-complete="toggleFormButtons('#upload-signed-agreement-form-file-form')">
+    <div class="modal-header modal-header-primary">
+        <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+        <h3 class="modal-title">Signed Agreement Form File Upload</h3>
+    </div>
+    <div class="modal-body">
+        {% csrf_token %}
+        {% bootstrap_form form inline=True %}
+    </div>
+    <div class="modal-footer">
+        {% buttons %}
+            <button id="file-upload-close-button" type="button" class="btn btn-default" data-dismiss="modal">Close</button>
+            <button id="file-upload-submit-button" type="submit" class="btn btn-primary">Submit
+                <span id="file-upload-form-indicator" style="display: none; margin-left: 5px;" class="ic-indicator fa fa-spinner fa-spin"></span>
+            </button>
+        {% endbuttons %}
+    </div>
+</form>