Merge pull request #285 from biocore/csymons_overhaul_20230823

Reconsent Tweaks & Results Report Content

microsetta_interface/implementation.py

@@ -1079,6 +1079,19 @@ def get_account(*, account_id=None):
     if RECONSENT_DECLINED_KEY in session:
         session.pop(RECONSENT_DECLINED_KEY)
 
+    # Determine if the source/profile has any action items. This framework
+    # will evolve over time.
+    for s in sources:
+        alerts = 0
+
+        need_reconsent_d = check_current_consent(
+            account_id, s[SOURCE_ID], "data"
+        )
+        if need_reconsent_d:
+            alerts += 1
+
+        s['alerts'] = alerts
+
     sources = [translate_source(s) for s in sources]
 
     japan_user = False
@@ -1162,7 +1175,8 @@ def get_consent_page(*, account_id=None):
         return consent_output
 
     form_type = "data"
-    reconsent = False
+    skip_dupe_check = False
+    reconsent = None
 
     return _render_with_defaults(
         'new_participant.jinja2',
@@ -1171,12 +1185,13 @@ def get_consent_page(*, account_id=None):
         duplicate_source_check=duplicate_source_check,
         home_url=home_url,
         form_type=form_type,
-        reconsent=reconsent,
+        skip_dupe_check=skip_dupe_check,
         language_tag=session_locale(),
         account_id=account_id,
         participant_name=None,
         age_range=None,
-        source_id=None
+        source_id=None,
+        reconsent=reconsent
     )
 
 
@@ -1242,11 +1257,19 @@ def post_create_human_source(*, account_id=None, body=None):
             return consent_output
 
         session.pop(SOURCE_ID)
-        return post_claim_samples(
-            account_id=account_id,
-            source_id=source_id,
-            sample_ids=body['sample_ids']
-        )
+        # Yes, "None" is coming through as a string in this instance, not as
+        # an actual None type.
+        if body["sample_ids"] != "None":
+            return post_claim_samples(
+                account_id=account_id,
+                source_id=source_id,
+                sample_ids=body['sample_ids']
+            )
+        else:
+            return redirect(
+                "/accounts/%s/sources/%s/kits" %
+                (account_id, source_id)
+            )
 
 
 @prerequisite([ACCT_PREREQS_MET])
@@ -1362,6 +1385,11 @@ def get_fill_source_survey(*,
             ctr = 0
             trig_ctr = 0
             for field in group['fields']:
+                if need_reconsent:
+                    # If the user has not agreed to the current consent, we
+                    # disable all of the fields.
+                    field['disabled'] = True
+
                 if "triggered_by" in field:
                     field['label'] = str(ctr) + ascii_lowercase[trig_ctr]\
                                      + ". " + field['label']
@@ -1828,6 +1856,13 @@ def get_kits(*, account_id=None, source_id=None, check_survey_date=False):
 
         prompt_survey_update = prompt_response['prompt']
 
+    need_reconsent_data = check_current_consent(
+        account_id, source_id, "data"
+    )
+    need_reconsent_biospecimen = check_current_consent(
+        account_id, source_id, "biospecimen"
+    )
+
     return _render_with_defaults(
         'kits.jinja2',
         account_id=account_id,
@@ -1842,7 +1877,9 @@ def get_kits(*, account_id=None, source_id=None, check_survey_date=False):
         public_endpoint=SERVER_CONFIG['public_api_endpoint'],
         profile_has_samples=profile_has_samples,
         prompt_survey_update=prompt_survey_update,
-        prompt_survey_id=BASIC_INFO_ID
+        prompt_survey_id=BASIC_INFO_ID,
+        need_reconsent_data=need_reconsent_data,
+        need_reconsent_biospecimen=need_reconsent_biospecimen
     )
 
 
@@ -2037,6 +2074,22 @@ def get_consent_view(*, account_id=None, source_id=None, consent_type=None):
     )
 
 
+def get_reconsent(*, account_id, source_id, consent_type):
+    # Let's make sure they actually need to reconsent
+    need_reconsent = check_current_consent(
+        account_id, source_id, consent_type
+    )
+
+    if need_reconsent is False:
+        # User shouldn't be here, send them back to their profile
+        return redirect(
+            "/accounts/%s/sources/%s" %
+            (account_id, source_id)
+        )
+    else:
+        return render_consent_page(account_id, source_id, consent_type)
+
+
 # Note: ideally this would be represented as a DELETE, not as a GET
 # However, it is used as a link, and HTML links do not support a DELETE
 # action
@@ -2054,7 +2107,7 @@ def get_remove_source(*,
     return _refresh_state_and_route_to_sink(account_id)
 
 
-@prerequisite([BIOSPECIMEN_PREREQS_MET])
+@prerequisite([SOURCE_PREREQS_MET, BIOSPECIMEN_PREREQS_MET])
 def get_update_sample(*, account_id=None, source_id=None, sample_id=None):
     has_error, source_output, _ = ApiRequest.get(
         '/accounts/%s/sources/%s' %
@@ -2118,27 +2171,56 @@ def get_update_sample(*, account_id=None, source_id=None, sample_id=None):
         dt = datetime.fromisoformat(sample_output['sample_datetime'])
         # TODO: This might need some flask_babel calls, hmm...
         sample_output['date'] = dt.strftime("%m/%d/%Y")
-        sample_output['time'] = dt.strftime("%I:%M %p")
+        sample_output['time'] = dt.strftime("%-I:%M %p")
     else:
         sample_output['date'] = ""
         sample_output['time'] = ""
 
     profile_has_samples = _check_if_source_has_samples(account_id, source_id)
 
-    return _render_with_defaults('sample.jinja2',
-                                 account_id=account_id,
-                                 source_id=source_id,
-                                 source_name=source_output['source_name'],
-                                 sample=sample_output,
-                                 sample_sites=sample_sites,
-                                 sample_sites_text=sample_site_translations,
-                                 is_environmental=is_environmental,
-                                 profile_has_samples=profile_has_samples)
+    need_reconsent_data = check_current_consent(
+        account_id, source_id, "data"
+    )
+    need_reconsent_biospecimen = check_current_consent(
+        account_id, source_id, "biospecimen"
+    )
+    return _render_with_defaults(
+        'sample.jinja2',
+        account_id=account_id,
+        source_id=source_id,
+        source_name=source_output['source_name'],
+        sample=sample_output,
+        sample_sites=sample_sites,
+        sample_sites_text=sample_site_translations,
+        is_environmental=is_environmental,
+        profile_has_samples=profile_has_samples,
+        need_reconsent_data=need_reconsent_data,
+        need_reconsent_biospecimen=need_reconsent_biospecimen
+    )
 
 
 # TODO: guess we should also rewrite as ajax post for sample vue form?
 @prerequisite([BIOSPECIMEN_PREREQS_MET])
 def post_update_sample(*, account_id=None, source_id=None, sample_id=None):
+    # We hid the submit buttons for users who need to reconsent, but let's
+    # be defensive and make sure someone has current consent for both data
+    # and biospecimen. Admins are allowed to update samples regardless of
+    # consent status.
+    if session.get(ADMIN_MODE_KEY, False) is False:
+        need_reconsent_d = check_current_consent(
+            account_id, source_id, "data"
+        )
+        need_reconsent_b = check_current_consent(
+            account_id, source_id, "biospecimen"
+        )
+        if need_reconsent_d is True or need_reconsent_b is True:
+            # They've seen multiple messages telling them to reconsent, we'll
+            # dump them back at the My Kits page.
+            return redirect(
+                "/accounts/%s/sources/%s/kits" %
+                (account_id, source_id)
+            )
+
     model = {}
     for x in flask.request.form:
         model[x] = flask.request.form[x]
@@ -2441,8 +2523,7 @@ def post_claim_samples(*, account_id=None, source_id=None, body=None,
             account_id,
             source_id,
             "biospecimen",
-            sample_ids=sample_ids,
-            reconsent=True
+            sample_ids=sample_ids
         )
 
     has_error, survey_output, _ = ApiRequest.get(

microsetta_interface/routes.yaml

@@ -479,6 +479,26 @@ paths:
         '302':
           description: Set session variable for declined reconsent and redirect to profile page
 
+  '/accounts/{account_id}/sources/{source_id}/reconsent/{consent_type}':
+    get:
+      operationId: microsetta_interface.implementation.get_reconsent
+      tags:
+        - Source
+      parameters:
+        - $ref: '#/components/parameters/account_id'
+        - $ref: '#/components/parameters/source_id'
+        - $ref: '#/components/parameters/consent_type'
+      responses:
+        '200':
+          description: Interface to agree to the current consent document
+          content:
+            text/html:
+              schema:
+                type: string
+        '302':
+          description: Redirect if the user doesn't need to reconsent
+
+
   '/accounts/{account_id}/sources/{source_id}/consents':
     get:
       operationId: microsetta_interface.implementation.get_consents

microsetta_interface/static/css/minimal_interface.css

@@ -217,6 +217,15 @@ a.breadcrumb-item-profile {
     color: var(--tmi-red);
 }
 
+.btn-orange {
+    background: var(--tmi-orange);
+    border-radius: 50px;
+    font-weight: 700;
+    font-size: 14px;
+    line-height: 22px;
+    color: #ffffff;
+}
+
 .card-header {
     background-color: #ffffff;
     color: #222222;
@@ -380,6 +389,18 @@ p.tmi-content {
     border-bottom: 0px;
 }
 
+.card-profile-alerts {
+    height: 270px;
+    background: linear-gradient(
+        to bottom,
+        var(--tmi-orange) 0px,
+        var(--tmi-orange) 100px,
+        white 100px,
+        white 270px
+    );
+    border-bottom: 0px;
+}
+
 .card-survey {
     height: 310px;
     background-color: white;
@@ -798,6 +819,30 @@ li.active-profile {
     color: var(--tmi-gray-90);
 }
 
+.alert-consent > ul {
+    margin-bottom: 0px;
+}
+
+.alert-consent > ul > li > a {
+    color: var(--tmi-gray-90) !important;
+}
+
+.alert-updates {
+    background: var(--tmi-orange-bg);
+    border-left: 8px solid var(--tmi-orange);
+    border-radius: 12px;
+    color: var(--tmi-gray-90);
+    height: 48px;
+    width: 100%;
+    max-width: 260px;
+    display: flex;
+    align-items: center;
+    justify-content: center;
+    font-weight: 700;
+    font-size: 14px;
+    line-height: 22px;
+}
+
 .blue-bg-card {
     background: var(--tmi-blue-bg);
     box-shadow: none;
@@ -1367,3 +1412,7 @@ input.barcode-checkbox[type=checkbox]:checked+label {
     margin-left: 1rem;
     margin-right: 1rem;
 }
+
+.orange-text {
+    color: var(--tmi-orange);
+}

microsetta_interface/templates/account_overview.jinja2

@@ -52,13 +52,28 @@
     <div class="row mb-5">
         {% for source in sources %}
         <div class="col-md-4 mb-4">
-            <div class="card card-profile">
-                <img src="/static/img/profile_card_icon.png" class="mx-auto card-profile-icon">
-                <h2 class="centered profile-card-h2">{{ source.source_name|e}}</h2>
-                <a class="btn btn-blue-gradient centered" style="width: fit-content;" href="/accounts/{{account.account_id}}/sources/{{ source.source_id|e }}">
-                    {{ _('Go to My Profile') }}
-                </a>
-            </div>
+            {% if source.alerts > 0 %}
+                <div class="card card-profile-alerts">
+                    <img src="/static/img/profile_card_icon.png" class="mx-auto card-profile-icon">
+                    <h2 class="profile-card-h2 mx-auto mt-2 mb-3">{{ source.source_name|e}}</h2>
+                    <div class="alert-updates mx-auto mb-3">
+                        {% if source.alerts > 1 %}
+                            {{ _('You have') }}&nbsp;<span class="orange-text">{{ source.alerts }}</span>&nbsp;{{ _('updates') }}
+                        {% else %}
+                            {{ _('You have') }}&nbsp;<span class="orange-text">{{ source.alerts }}</span>&nbsp;{{ _('update') }}
+                        {% endif %}
+                        <a class="btn btn-orange ms-4" style="width: fit-content;" href="/accounts/{{account.account_id}}/sources/{{ source.source_id|e }}">View</a>
+                    </div>
+                </div>
+            {% else %}
+                <div class="card card-profile">
+                    <img src="/static/img/profile_card_icon.png" class="mx-auto card-profile-icon">
+                    <h2 class="profile-card-h2 mx-auto mt-2 mb-4">{{ source.source_name|e}}</h2>
+                    <a class="btn btn-blue-gradient mx-auto" style="width: fit-content;" href="/accounts/{{account.account_id}}/sources/{{ source.source_id|e }}">
+                        {{ _('Go to My Profile') }}
+                    </a>
+                </div>
+            {% endif %}
         </div>
         {% endfor %}
     </div>

microsetta_interface/templates/kits.jinja2

@@ -201,6 +201,19 @@
             {{ _('Thank you for logging your sample information. It looks like you haven\'t updated your profile recently. Please review') }} <a href="/accounts/{{account_id}}/sources/{{source_id}}/take_survey?survey_template_id={{prompt_survey_id}}">{{ _('your survey responses') }}</a> {{ _('to ensure they\'re as current and complete as possible.') }}
         </div>
         {% endif %}
+        {% if profile_has_samples and (need_reconsent_data or need_reconsent_biospecimen) %}
+            <div id="consent_alert" class="alert alert-consent mt-4" role="alert">
+                {{ _('To update your existing samples or contribute new samples, please review the following:') }}<br />
+                <ul>
+                {% if need_reconsent_data %}
+                    <li><a href="/accounts/{{account_id}}/sources/{{source_id}}/reconsent/data">{{ _('Consent to Act as a Research Subject') }}</a></li>
+                {% endif %}
+                {% if need_reconsent_biospecimen %}
+                    <li><a href="/accounts/{{account_id}}/sources/{{source_id}}/reconsent/biospecimen">{{ _('Consent to Act as a Research Subject - Biospecimen and Future Use Research') }}</a></li>
+                {% endif %}
+                </ul>
+            </div>
+        {% endif %}
         <div class="alert alert-primary alert-profile mt-4" role="alert">
             {{ _('Click on the following link if you would like to contribute to receive a kit') }} - <a href="{{ fundrazr_url }}" target="_blank">{{ _('Get a Kit') }}</a>
         </div>

microsetta_interface/templates/new_participant.jinja2

@@ -217,13 +217,21 @@
             {{ _('We\'ve made some changes to the project since you last logged in, including an update to our consent agreement. To proceed, please provide your updated consent.') }}
         </div>
     {% endif %}
-    {% if age_range != None %}
-        <input type="hidden" name="age-range" value="{{ age_range }}" />
+    {% if form_type == "biospecimen" %}
         <div class="row mb-4">
             <div class="col-12 biospecimen-alert">
                 {{ _('Signature and agreement of this consent form is required to process your sample(s).') }}
             </div>
         </div>
+    {% else %}
+        <div class="row mb-4">
+            <div class="col-12 biospecimen-alert">
+                {{ _('Signature and agreement of this consent form is required to update your information.') }}
+            </div>
+        </div>
+    {% endif %}
+    {% if age_range != None %}
+        <input type="hidden" name="age-range" value="{{ age_range }}" />
     {% else %}
     <div class="row">
         <div class="col-12">