Merge pull request #532 from biocore/master-overhaul

Merge Master-overhaul into Master

ci/conda_requirements.txt

@@ -3,4 +3,4 @@ psycopg2
 flask
 natsort
 pycryptodome
-pandas
+pandas < 2.0.0

microsetta_private_api/LEGACY/locale_data/english_gut.py

@@ -567,10 +567,9 @@
     'TEXT_I_HAVE_READ_SIMPLIFIED': 'Yes, you will be in this research study.',
     'PERSON_ATTAINING_ASSENT': 'Signature Of Person Obtaining Assent',
     'TEXT_ASSENT_WITNESS': 'In my judgment, the participant is voluntarily and knowingly giving assent and possesses the legal capacity to give assent to participate in the study.',
-    'OBTAINER_NAME': 'Name of person obtaining assent',
+    'ASSENT_OBTAINER': 'Name of person obtaining assent',
     'TEXT_I_HAVE_READ_PARENT': 'I have read (or someone has read to me) this form. I am aware that I am being asked to provide consent for my child to be in a research study. I voluntarily agree to allow my child to participate in this study. I understand how my child’s personal data will be processed, my related rights, and that I consent to the processing of my child’s sample and data as provided in this document.',
     'PARTICIPANT_NAME': 'Participant name',
-    'PARTICIPANT_EMAIL': 'Participant email',
     'PARTICIPANT_PARENT_1': 'Parent/Guardian name',
     'PARTICIPANT_PARENT_2': 'Parent/Guardian name of second parent',
     'PARTICIPANT_DECEASED_PARENTS': 'One parent/guardian is deceased or unable to consent',

microsetta_private_api/LEGACY/locale_data/spain_spanish_gut.py

@@ -67,7 +67,7 @@
     'TEXT_I_HAVE_READ_SIMPLIFIED': 'Sí, estarás en este estudio de investigación.',
     'PERSON_ATTAINING_ASSENT': 'Firma de la persona que obtiene el consentimiento',
     'TEXT_ASSENT_WITNESS': 'A mi juicio, el participante está dando su consentimiento voluntaria y conscientemente y posee la capacidad legal de dar su consentimiento para participar en el estudio.',
-    'OBTAINER_NAME': 'Nombre de la persona que obtiene el consentimiento',
+    'ASSENT_OBTAINER': 'Nombre de la persona que obtiene el consentimiento',
     'TEXT_I_HAVE_READ_PARENT': 'He leído (o alguien me ha leído) este formulario. Soy consciente de que se le está pidiendo a mi hijo que participe en un estudio de investigación. Acepto voluntariamente que mi hijo participe en este estudio',
     'PARTICIPANT_NAME': 'Nombre del participante',
     'PARTICIPANT_EMAIL': 'Correo electrónico del participante',

microsetta_private_api/LEGACY/locale_data/spanish_gut.py

@@ -67,10 +67,9 @@
     'TEXT_I_HAVE_READ_SIMPLIFIED': 'Sí, estarás en este estudio de investigación.',
     'PERSON_ATTAINING_ASSENT': 'Firma de la persona que obtiene el consentimiento',
     'TEXT_ASSENT_WITNESS': 'A mi juicio, el participante está dando su consentimiento voluntaria y conscientemente y posee la capacidad legal de dar su consentimiento para participar en el estudio.',
-    'OBTAINER_NAME': 'Nombre de la persona que obtiene el consentimiento',
+    'ASSENT_OBTAINER': 'Nombre de la persona que obtiene el consentimiento',
     'TEXT_I_HAVE_READ_PARENT': 'He leído (o alguien me ha leído) este formulario. Soy consciente de que se le está pidiendo a mi hijo que participe en un estudio de investigación. Acepto voluntariamente que mi hijo participe en este estudio',
     'PARTICIPANT_NAME': 'Nombre del participante',
-    'PARTICIPANT_EMAIL': 'Correo electrónico del participante',
     'PARTICIPANT_PARENT_1': 'Nombre del Padre de Familia / Guardian',
     'PARTICIPANT_PARENT_2': 'Nombre del padre / tutor del segundo padre',
     'PARTICIPANT_DECEASED_PARENTS': 'Uno de los padres / tutor ha fallecido o no puede dar su consentimiento',

microsetta_private_api/admin/admin_impl.py

@@ -35,6 +35,7 @@
 from werkzeug.exceptions import Unauthorized
 from microsetta_private_api.qiita import qclient
 from microsetta_private_api.repo.interested_user_repo import InterestedUserRepo
+from microsetta_private_api.repo.removal_queue_repo import RemovalQueueRepo
 
 
 def search_barcode(token_info, sample_barcode):
@@ -542,6 +543,21 @@ def create_daklapack_orders(body, token_info):
     return response
 
 
+# We need an internal wrapper to create orders based on contributions coming
+# from Fundrazr without authenticating an admin user.
+# Do NOT expose an API endpoint for this.
+def create_daklapack_order_internal(order_dict):
+    # Since we've established the consent dummy as a stable account across
+    # dev, staging, and production, we'll continue to use that internally
+    with Transaction() as t:
+        account_repo = AccountRepo(t)
+        order_dict[SUBMITTER_ACCT_KEY] = account_repo.get_account(
+            SERVER_CONFIG['fulfillment_account_id'])
+
+    result = _create_daklapack_order(order_dict)
+    return result
+
+
 def _create_daklapack_order(order_dict):
     order_dict[ORDER_ID_KEY] = str(uuid.uuid4())
 
@@ -614,6 +630,15 @@ def list_campaigns(token_info):
     return jsonify(campaigns), 200
 
 
+def list_removal_queue(token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        repo = RemovalQueueRepo(t)
+        requests = repo.get_all_account_removal_requests()
+    return jsonify(requests), 200
+
+
 def post_campaign_information(body, token_info):
     validate_admin_access(token_info)
 
@@ -656,6 +681,20 @@ def generate_activation_codes(body, token_info):
     return jsonify(results), 200
 
 
+def generate_ffq_codes(body, token_info):
+    validate_admin_access(token_info)
+
+    quantity = body.get("code_quantity", 1)
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        code_list = []
+        for i in range(quantity):
+            code_list.append(admin_repo.create_ffq_code())
+        t.commit()
+
+    return jsonify(code_list), 200
+
+
 def list_barcode_query_fields(token_info):
     validate_admin_access(token_info)
 
@@ -796,7 +835,6 @@ def delete_account(account_id, token_info):
         src_repo = SourceRepo(t)
         samp_repo = SampleRepo(t)
         sar_repo = SurveyAnswersRepo(t)
-        template_repo = SurveyTemplateRepo(t)
 
         acct = acct_repo.get_account(account_id)
         if acct is None:
@@ -806,8 +844,6 @@ def delete_account(account_id, token_info):
             if acct.account_type == 'deleted':
                 return None, 204
 
-        sample_count = 0
-        account_has_external = False
         sources = src_repo.get_sources_in_account(
             account_id,
             allow_revoked=True
@@ -820,50 +856,61 @@ def delete_account(account_id, token_info):
                 allow_revoked=True
             )
 
-            has_samples = len(samples) > 0
-            sample_count += len(samples)
-            has_external = template_repo.has_external_surveys(account_id,
-                                                              source.id)
-
-            if has_external:
-                account_has_external = True
-
             for sample in samples:
                 # we scrub rather than disassociate in the event that the
                 # sample is in our freezers but not with an up-to-date scan
                 samp_repo.scrub(account_id, source.id, sample.id)
 
             surveys = sar_repo.list_answered_surveys(account_id, source.id)
-            if has_samples or has_external:
-                # if we have samples or external surveys, we need to scrub
-                # survey / source free text
-                for survey_id in surveys:
-                    sar_repo.scrub(account_id, source.id, survey_id)
-
-                # We're including scrubbed sources to detect external surveys
-                # so we need to make sure the source isn't already scrubbed
-                if source.source_data.date_revoked is None:
-                    src_repo.scrub(account_id, source.id)
-
-            if not has_samples and not has_external:
-                # if we do not have associated samples, or external surveys,
-                # then the source is safe to delete
-                for survey_id in surveys:
-                    sar_repo.delete_answered_survey(account_id, survey_id)
-                src_repo.delete_source(account_id, source.id)
-
-        # an account is safe to delete if there are no associated samples
-        # and does not have external surveys
-        if sample_count > 0 or account_has_external:
-            acct_repo.scrub(account_id)
-        else:
-            acct_repo.delete_account(account_id)
+            for survey_id in surveys:
+                sar_repo.scrub(account_id, source.id, survey_id)
+
+            # We're including scrubbed sources to detect external surveys
+            # so we need to make sure the source isn't already scrubbed
+            if source.source_data.date_revoked is None:
+                src_repo.scrub(account_id, source.id)
+
+        acct_repo.scrub(account_id)
 
         t.commit()
 
     return None, 204
 
 
+def ignore_removal_request(account_id, token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        rq_repo = RemovalQueueRepo(t)
+        try:
+            # remove the user from the queue, noting the admin who allowed it
+            # and the time the action was performed.
+            rq_repo.update_queue(account_id, token_info['email'], 'ignored')
+            t.commit()
+        except RepoException as e:
+            raise e
+
+    return None, 204
+
+
+def allow_removal_request(account_id, token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        rq_repo = RemovalQueueRepo(t)
+
+        try:
+            # remove the user from the queue, noting the admin who allowed it
+            # and the time the action was performed.
+            rq_repo.update_queue(account_id, token_info['email'], 'deleted')
+            t.commit()
+        except RepoException as e:
+            raise e
+
+        # delete the user
+        return delete_account(account_id, token_info)
+
+
 def get_vioscreen_sample_to_user(token_info):
     validate_admin_access(token_info)
     with Transaction() as t:

microsetta_private_api/admin/email_templates.py

@@ -79,6 +79,38 @@ class EmailMessage(Enum):
         EventType.EMAIL,
         EventSubtype.EMAIL_SUBMIT_INTEREST_CONFIRMATION
     )
+    thank_you_with_kit = (
+        gettext(
+            "Registration code & kit update!"),
+        "email/thank_you_with_kit.jinja2",
+        ("first_name", "registration_code", "interface_endpoint"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_THANK_YOU_WITH_KIT
+    )
+    thank_you_no_kit = (
+        gettext(
+            "Your questionnaire is ready!"),
+        "email/thank_you_no_kit.jinja2",
+        ("first_name", "registration_code", "interface_endpoint"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_THANK_YOU_NO_KIT
+    )
+    kit_tracking_number = (
+        gettext(
+            "Your kit is on its way!"),
+        "email/kit_tracking_number.jinja2",
+        ("first_name", "tracking_number"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_KIT_TRACKING_NUMBER
+    )
+    subscription_ffq_code = (
+        gettext(
+            "Registration code & kit update!"),
+        "email/subscription_ffq_code.jinja2",
+        ("first_name", "tracking_number", "interface_endpoint"),
+        EventType.EMAIL,
+        EventSubtype.EMAIL_SUBSCRIPTION_FFQ_CODE
+    )
 
     def __init__(self, subject, html, required, event_type, event_sub):
         self.subject = subject

microsetta_private_api/admin/sample_summary.py

@@ -41,12 +41,10 @@ def per_sample(project, barcodes, strip_sampleid):
             source = diag['source']
 
             account_email = None if account is None else account.email
-            source_email = None
             source_type = None if source is None else source.source_type
             vio_id = None
 
             if source is not None and source_type == Source.SOURCE_TYPE_HUMAN:
-                source_email = source.source_data.email
 
                 vio_id = template_repo.get_vioscreen_id_if_exists(account.id,
                                                                   source.id,
@@ -75,7 +73,6 @@ def per_sample(project, barcodes, strip_sampleid):
                 "project": project,
                 "source-type": source_type,
                 "site-sampled": sample_site,
-                "source-email": source_email,
                 "account-email": account_email,
                 "vioscreen_username": vio_id,
                 "ffq-taken": ffq_taken,