Adds data upload and sharing agreement template to the project files page.

physionet-django/console/test_views.py

@@ -53,22 +53,25 @@ def test_assign_editor(self):
         response = self.client.post(reverse(
             'submitted_projects'), data={'project':project.id,
             'editor':editor.id})
+        self.assertEqual(response.status_code, 200)
         project = ActiveProject.objects.get(title='MIT-BIH Arrhythmia Database')
         self.assertTrue(project.editor, editor)
         self.assertEqual(project.submission_status, 20)
 
+
     def test_reassign_editor(self):
         """
         Assign an editor, then reassign it
         """
         # Submit project
         project = ActiveProject.objects.get(title='MIT-BIH Arrhythmia Database')
         project.submit(author_comments='')
-        # Assign editor
+        # Assign editorgi
         self.client.login(username='admin', password='Tester11!')
         editor = User.objects.get(username='cindyehlert')
         response = self.client.post(reverse('submitted_projects'), data={
             'project': project.id, 'editor': editor.id})
+        self.assertEqual(response.status_code, 200)
         project = ActiveProject.objects.get(title='MIT-BIH Arrhythmia Database')
         self.assertTrue(project.editor, editor)
         self.assertEqual(project.submission_status, 20)
@@ -77,9 +80,11 @@ def test_reassign_editor(self):
         editor = User.objects.get(username='amitupreti')
         response = self.client.post(reverse('submission_info',
             args=(project.slug,)), data={'editor': editor.id})
+        self.assertEqual(response.status_code, 200)
         project = ActiveProject.objects.get(title='MIT-BIH Arrhythmia Database')
         self.assertTrue(project.editor, editor)
 
+
     def test_edit_reject(self):
         """
         Edit a project, rejecting it.
@@ -212,8 +217,8 @@ def test_copyedit(self):
         # Recomplete copyedit
         response = self.client.post(reverse(
             'copyedit_submission', args=(project.slug,)),
-            data={'complete_copyedit':'', 'made_changes':1,
-            'changelog_summary':'Removed your things'})
+            data={'complete_copyedit': '', 'made_changes': 1,
+                  'changelog_summary': 'Removed your things'})
         project = ActiveProject.objects.get(id=project.id)
         self.assertFalse(project.copyeditable())
 
@@ -261,15 +266,15 @@ def get_project():
         # Complete copyedit
         response = self.client.post(reverse(
             'copyedit_submission', args=(project.slug,)),
-            data={'complete_copyedit':'', 'made_changes':0})
+            data={'complete_copyedit': '', 'made_changes': 0})
         self.assertEqual(get_project().modified_datetime, timestamp)
 
         # Approve publication
         self.assertFalse(ActiveProject.objects.get(id=project.id).is_publishable())
         self.client.login(username='rgmark', password='Tester11!')
         response = self.client.post(reverse(
             'project_submission', args=(project.slug,)),
-            data={'approve_publication':''})
+            data={'approve_publication': ''})
         self.assertEqual(get_project().modified_datetime, timestamp)
 
         self.assertTrue(ActiveProject.objects.get(id=project.id).is_publishable())
@@ -300,16 +305,14 @@ def test_publish(self):
         # publish_submission ignores the slug parameter)
         if not project.is_new_version:
             taken_slug = PublishedProject.objects.all().first().slug
-            response = self.client.post(reverse(
-                'publish_submission', args=(project.slug,)),
-                data={'slug':taken_slug, 'doi': False, 'make_zip':1})
-            self.assertTrue(bool(ActiveProject.objects.filter(
-                slug=project_slug)))
+            response = self.client.post(reverse('publish_submission', args=(project.slug,)),
+                                        data={'slug': taken_slug, 'doi': False, 'make_zip': 1})
+            self.assertTrue(bool(ActiveProject.objects.filter(slug=project_slug)))
 
         # Publish with a valid custom slug
-        response = self.client.post(reverse(
-            'publish_submission', args=(project.slug,)),
-            data={'slug':custom_slug, 'doi': False, 'make_zip':1})
+        response = self.client.post(reverse('publish_submission',
+                                    args=(project.slug,)), data={
+                                        'slug': custom_slug, 'doi': False, 'make_zip': 1})
 
         # Run background tasks
         self.assertTrue(bool(tasks.run_next_task()))
@@ -321,8 +324,7 @@ def test_publish(self):
         project = PublishedProject.objects.get(slug=custom_slug,
                                                version=project.version)
         # Access the published project's page and its (open) files
-        response = self.client.get(reverse('published_project',
-            args=(project.slug, project.version)))
+        response = self.client.get(reverse('published_project', args=(project.slug, project.version)))
         self.assertEqual(response.status_code, 200)
         response = self.client.get(reverse('serve_published_project_file', args=(
             project.slug, project.version, 'subject-100/100.atr')))
@@ -332,8 +334,7 @@ def test_publish(self):
         self.assertEqual(response.status_code, 200)
         # Access the submission log as the author
         self.client.login(username='rgmark', password='Tester11!')
-        response = self.client.get(reverse('published_submission_history',
-            args=(project.slug, project.version,)))
+        response = self.client.get(reverse('published_submission_history', args=(project.slug, project.version,)))
         self.assertEqual(response.status_code, 200)
 
         # The internal links should now point to published files
@@ -382,11 +383,16 @@ def test_publish_with_versions(self):
         for version in versions[1:]:
             self.client.login(username=self.AUTHOR,
                               password=self.AUTHOR_PASSWORD)
-            response = self.client.post(
-                reverse('new_project_version', args=(self.PROJECT_SLUG,)),
-                data={'version': version})
+            response = self.client.post(reverse('new_project_version', args=(self.PROJECT_SLUG,)),
+                                        data={'version': version})
+            self.assertEqual(response.status_code, 302)
+            project = ActiveProject.objects.get(title='MIT-BIH Arrhythmia Database')
+            self.client.post(reverse('project_files', args=(project.slug,)), data={
+                'has_copy_right_permission': '0', 'has_human_subject_data': '0',
+                'has_phi': '0', 'submit_upload_agreement': 'submitbutton'})
             self.test_publish()
 
+
         # Sort the list of version numbers
         sorted_versions = []
         for version in versions:

physionet-django/project/fixtures/demo-project.json

@@ -2249,5 +2249,16 @@
     "responder": null,
     "responder_comments": ""
   }
+},
+{
+  "model": "project.datauploadagreement",
+  "pk": 1,
+  "fields": {
+    "project": 1,
+    "has_copy_right_permission":0,
+    "has_human_subject_data":0,
+    "has_phi":0
+  }
 }
 ]
+

physionet-django/project/forms.py

@@ -39,6 +39,7 @@
     Topic,
     exists_project_slug,
     UploadedDocument,
+    DataUploadAgreement
 )
 from project.projectfiles import ProjectFiles
 from user.models import User, TrainingType
@@ -1175,3 +1176,22 @@ def __init__(self, *args, **kwargs):
             "Statements on ethics approval should appear here. "
             "Your statement will be included in the public project description."
         )
+
+
+class UploadedAgreementDataForm(forms.ModelForm):
+    class Meta:
+        model = DataUploadAgreement
+        fields = (
+            'has_copy_right_permission',
+            'has_human_subject_data',
+            'has_phi')
+        labels = {
+            'has_copy_right_permission': 'Are you the original creator, or copyright holder, or have\
+            permission from the creators and copyright holders to share these files?',
+            'has_human_subject_data': 'Does this project contain data collected from human subjects?',
+            'has_phi': 'Do these files contain any personally identifiable information (information\
+            that could identify individual human subjects)?'}
+
+    def __init__(self, project, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.project = project

physionet-django/project/migrations/0068_datauploadagreement.py

@@ -0,0 +1,25 @@
+# Generated by Django 3.1.14 on 2022-11-29 18:54
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('project', '0067_alter_activeproject_core_project_and_more'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='DataUploadAgreement',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('has_copy_right_permission', models.PositiveSmallIntegerField(choices=[(0, 'Yes'), (1, 'No')])),
+                ('has_human_subject_data', models.PositiveSmallIntegerField(choices=[(0, 'Yes'), (1, 'No')])),
+                ('has_phi', models.PositiveSmallIntegerField(choices=[(0, 'Yes'), (1, 'No'), (2, 'NA')])),
+                ('project', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE,
+                                                 to='project.activeproject')),
+            ],
+        ),
+    ]

physionet-django/project/modelcomponents/activeproject.py

@@ -26,7 +26,7 @@
     UploadedDocument,
 )
 from project.modelcomponents.publishedproject import PublishedProject
-from project.modelcomponents.submission import CopyeditLog, EditLog, SubmissionInfo
+from project.modelcomponents.submission import CopyeditLog, EditLog, SubmissionInfo, DataUploadAgreement
 from project.modelcomponents.unpublishedproject import UnpublishedProject
 from project.projectfiles import ProjectFiles
 from project.validators import validate_subdir
@@ -329,6 +329,14 @@ def check_integrity(self):
                         f'Corresponding author {author.user.username} '
                         'has not set a corresponding email')
 
+        # Data Upload Agreement
+        try:
+            data_upload = DataUploadAgreement.objects.get(project_id=self.id)
+            if data_upload.has_phi == 0:
+                self.integrity_errors.append('Please remove any Personal Health Information from your data')
+        except DataUploadAgreement.DoesNotExist:
+            self.integrity_errors.append('Missing required field: Data Upload Agreement')
+
         # Metadata
         for attr in ActiveProject.REQUIRED_FIELDS[self.resource_type.id]:
             value = getattr(self, attr)

physionet-django/project/modelcomponents/submission.py

@@ -255,3 +255,21 @@ def quota_manager(self):
             creation_time=self.creation_datetime)
         quota_manager.set_limits(bytes_hard=limit, bytes_soft=limit)
         return quota_manager
+
+
+class DataUploadAgreement(models.Model):
+    """This model is used to store the responses from the data use agreement for the project."""
+    RESPONSE_CHOICES_1_and_2 = (
+        (0, 'Yes'),
+        (1, 'No'),
+    )
+    RESPONSE_CHOICES_3 = (
+        (0, 'Yes'),
+        (1, 'No'),
+        (2, 'NA'),
+    )
+
+    project = models.OneToOneField('project.ActiveProject', on_delete=models.CASCADE)
+    has_copy_right_permission = models.PositiveSmallIntegerField(choices=RESPONSE_CHOICES_1_and_2)
+    has_human_subject_data = models.PositiveSmallIntegerField(choices=RESPONSE_CHOICES_1_and_2)
+    has_phi = models.PositiveSmallIntegerField(choices=RESPONSE_CHOICES_3)

physionet-django/project/templates/project/project_files.html

@@ -19,6 +19,7 @@
 {% block main_content %}
 <h2 class="form-signin-heading">6. Project Files</h2>
 <hr>
+{% include "project/upload_data_agreement.html" %}
 {% include "about/files.html" %}
 <br>
 

physionet-django/project/templates/project/upload_data_agreement.html

@@ -0,0 +1,42 @@
+<h4> Data Upload and Sharing Agreement</h4>
+{% if not project.datauploadagreement %}
+  <div class="alert alert-warning">
+   Please complete the project data upload agreement form below before uploading the project files.
+  </div>
+{% elif project.datauploadagreement.has_phi == 0 %}
+  <div class="alert alert-warning">
+      You are unable to submit your project for review, because you have not removed Personal Health Information from your project files.
+  </div>
+{% else %}
+  <div class="alert alert-info">
+      Please don't include any Personal Health Information within your uploaded project files.
+  </div>
+{% endif %}
+        <button id="upload-agreement-button" type="button" class="btn btn-primary" data-toggle="modal" data-target="#upload-agreement-modal">
+        <i class="fa fa-handshake"></i> Data Upload Agreement
+        </button>
+        <p></p>
+        <div class="modal fade" id="upload-agreement-modal" tabindex="-1" role="dialog" aria-labelledby="upload-agreement-modal" aria-hidden="true">
+          <div class="modal-dialog" role="document">
+            <div class="modal-content">
+              <div class="modal-header">
+                <h5 class="modal-title">Data Upload Agreement</h5>
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close">
+                  <span aria-hidden="true">&times;</span>
+                </button>
+              </div>
+              <form action="" method="post" enctype="multipart/form-data">
+                <div class="modal-body">
+                  {% csrf_token %}
+                  <p>Your responses to the following questions will be shared with the editor, but will not be published.</p>
+                  {{upload_agreement_form}}
+                  <p>By clicking “I agree” and uploading files to {{SITE_NAME}}, you agree that the above information is accurate.</p>
+                  </div>
+                <div class="modal-footer">
+                  <button class="btn btn-primary" name="submit_upload_agreement" type="submit"><i class="fa fa-thumbs-up"></i> I agree</button>
+                  <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
+                </div>
+              </form>
+            </div>
+          </div>
+        </div>

physionet-django/project/views.py

@@ -49,6 +49,7 @@
     StorageRequest,
     Topic,
     UploadedDocument,
+    DataUploadAgreement
 )
 from project.projectfiles import ProjectFiles
 from project.validators import validate_filename, validate_gcs_bucket_object
@@ -1036,6 +1037,19 @@ def project_files(request, project_slug, subdir='', **kwargs):
             if storage_request:
                 storage_request.get().delete()
                 messages.success(request, 'Your storage request has been cancelled.')
+        elif 'submit_upload_agreement' in request.POST:
+            try:
+                agreement = DataUploadAgreement.objects.get(project=project)
+            except DataUploadAgreement.DoesNotExist:
+                agreement = None
+            upload_agreement_form = forms.UploadedAgreementDataForm(project=project,
+                                                                    data=request.POST, instance=agreement)
+            if upload_agreement_form.is_valid():
+                upload_agreement_form.instance.project = project
+                upload_agreement_form.save()
+                messages.success(request, 'Your upload agreement has been received.')
+            else:
+                messages.error(request, utility.get_form_errors(upload_agreement_form))
         else:
             # process the file manipulation post
             subdir = process_files_post(request, project)
@@ -1048,8 +1062,7 @@ def project_files(request, project_slug, subdir='', **kwargs):
     if settings.SYSTEM_MAINTENANCE_NO_UPLOAD:
         maintenance_message = settings.SYSTEM_MAINTENANCE_MESSAGE or (
             "The site is currently undergoing maintenance, and project "
-            "files cannot be edited.  Please try again later."
-        )
+            "files cannot be edited.  Please try again later.")
         files_editable = False
     else:
         maintenance_message = None
@@ -1061,6 +1074,14 @@ def project_files(request, project_slug, subdir='', **kwargs):
     storage_request_form = (
         forms.StorageRequestForm(project=project) if (not storage_request and is_submitting) else None
     )
+    try:
+        agreement = DataUploadAgreement.objects.get(project=project)
+        if agreement.has_phi == 0:
+            files_editable = False
+    except DataUploadAgreement.DoesNotExist:
+        agreement = None
+        files_editable = False
+    upload_agreement_form = forms.UploadedAgreementDataForm(project=project, instance=agreement)
 
     (display_files, display_dirs, dir_breadcrumbs, parent_dir,
      file_error) = get_project_file_info(project=project, subdir=subdir)
@@ -1096,6 +1117,7 @@ def project_files(request, project_slug, subdir='', **kwargs):
             'maintenance_message': maintenance_message,
             'is_lightwave_supported': ProjectFiles().is_lightwave_supported(),
             'storage_type': settings.STORAGE_TYPE,
+            'upload_agreement_form': upload_agreement_form,
         },
     )