Merge remote-tracking branch 'biocore/master' into master-overhaul

Author: ayobi

ci/pip_requirements.txt

@@ -1,4 +1,5 @@
 openapi-spec-validator < 0.2.10
+swagger-ui-bundle==0.0.9
 connexion[swagger-ui] < 2.7.1
 jsonschema < 4.0.0
 pyjwt[crypto] < 2.2.0

microsetta_private_api/LEGACY/locale_data/japanese_gut.py

@@ -6,24 +6,24 @@
 _NEW_PARTICIPANT = {
     'ADD_HUMAN_TITLE': '新しいプロフィール情報を追加する',
     'SEL_AGE_RANGE': '参加者の年齢層を選択する:',
-    'AGE_0_6': '',
-    'AGE_7_12': '',
-    'AGE_13_17': '',
+    'AGE_0_6': '3ヶ月 -  6才',
+    'AGE_7_12': '7〜12才',
+    'AGE_13_17': '13〜17年',
     'AGE_18': '18歳以上',
 
     'PARTICIPATION_AGREEMENT': '''''',
 
     'EXHIBIT_A': '''''',
     'BILL_OF_RIGHTS': '''研究被験者の権利章典''',
     'TEXT_I_HAVE_READ_1': '私は同意書を読みました (又は代読してもらいました)。研究試験への参加を求められていることを理解し、この試験への参加に自由意志で同意します。私の個人データが処理される方法、関連した私の権利を理解しており、この同意書に記載されているように私のデータが処理されることに同意します。',
-    'TEXT_I_HAVE_READ_SIMPLIFIED': '',
-    'PERSON_ATTAINING_ASSENT': '',
-    'TEXT_ASSENT_WITNESS': '',
-    'OBTAINER_NAME': '',
-    'TEXT_I_HAVE_READ_PARENT': '',
+    'TEXT_I_HAVE_READ_SIMPLIFIED': 'はい、あなたはこの調査研究に参加します。',
+    'PERSON_ATTAINING_ASSENT': '同意を得る人の署名',
+    'TEXT_ASSENT_WITNESS': '私の判断において、参加者は自発的かつ自主的に同意し、研究に参加する意思を示す法的能力を持っています。',
+    'OBTAINER_NAME': '同意を得る人の名前',
+    'TEXT_I_HAVE_READ_PARENT': '私はこのフォームを読みました（または誰かが代読した）。私は、我が子の調査研究への参加に、同意を求められていることを理解しました。私は自発的に我が子がこの研究に参加することに同意します。我が子の個人データの処理方法、これに関連する権利、そして提供す',
     'PARTICIPANT_NAME': '参加者名',
     'PARTICIPANT_EMAIL': 'Eメール',
-    'PARTICIPANT_PARENT_1': '',
+    'PARTICIPANT_PARENT_1': '親/保護者の名前',
     'PARTICIPANT_PARENT_2': '',
     'PARTICIPANT_DECEASED_PARENTS': '',
     'DATE_SIGNED': 'DATE_SIGNED',

microsetta_private_api/admin/admin_impl.py

@@ -919,3 +919,21 @@ def get_vioscreen_sample_to_user(token_info):
         st_repo = SurveyTemplateRepo(t)
         data = st_repo.get_vioscreen_sample_to_user()
     return jsonify(data), 200
+
+
+def get_perk_fulfillment_state(token_info):
+    validate_admin_access(token_info)
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        pf_state = admin_repo.get_perk_fulfillment_state()
+    return jsonify({"pf_state": pf_state}), 200
+
+
+def update_perk_fulfillment_state(token_info, perk_fulfillment_state):
+    validate_admin_access(token_info)
+    with Transaction() as t:
+        admin_repo = AdminRepo(t)
+        admin_repo.update_perk_fulfillment_state(perk_fulfillment_state)
+        pf_state = admin_repo.get_perk_fulfillment_state()
+        t.commit()
+    return jsonify({"pf_state": pf_state}), 200

microsetta_private_api/admin/email_templates.py

@@ -26,7 +26,7 @@ class EmailMessage(Enum):
         EventSubtype.EMAIL_ACTIVATION
     )
     incorrect_sample_type = (
-        gettext("Your Microsetta Initiative status update: attention needed"),
+        gettext("Microsetta Initiative update: attention needed"),
         "email/incorrect_sample_type.jinja2",
         ("contact_name", "sample_barcode", "recorded_type", "received_type",
          "resolution_url"),
@@ -35,21 +35,21 @@ class EmailMessage(Enum):
     )
     missing_sample_info = (
         gettext(
-            "Your Microsetta Initiative status update: information needed"),
+            "Microsetta Initiative update: information needed"),
         "email/missing_sample_info.jinja2",
         ("contact_name", "sample_barcode", "received_type", "resolution_url"),
         EventType.EMAIL,
         EventSubtype.EMAIL_MISSING_SAMPLE_INFO
     )
     sample_is_valid = (
-        gettext("Your Microsetta Initiative status update and next steps"),
+        gettext("We received your Microsetta Initiative sample"),
         "email/sample_is_valid.jinja2",
         ("contact_name",),
         EventType.EMAIL,
         EventSubtype.EMAIL_SAMPLE_IS_VALID
     )
     no_associated_source = (
-        gettext("Your Microsetta Initiative status update: "
+        gettext("Microsetta Initiative update: "
                 "critical information needed"),
         "email/no_associated_source.jinja2",
         ("contact_name", "sample_barcode", "resolution_url"),
@@ -65,7 +65,7 @@ class EmailMessage(Enum):
     )
     address_invalid = (
         gettext(
-            "Your Microsetta Initiative status update: information needed"),
+            "Microsetta Initiative update: information needed"),
         "email/address_invalid.jinja2",
         ("contact_name", "resolution_url"),
         EventType.EMAIL,
@@ -81,23 +81,23 @@ class EmailMessage(Enum):
     )
     thank_you_with_kit = (
         gettext(
-            "Registration code & kit update!"),
+            "Microsetta Initiative 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!"),
+            "Your Microsetta Initiative 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!"),
+            "Your Microsetta Initiative kit has shipped"),
         "email/kit_tracking_number.jinja2",
         ("first_name", "tracking_number"),
         EventType.EMAIL,

microsetta_private_api/admin/tests/test_admin_repo.py

@@ -1344,3 +1344,43 @@ def test_create_ffq_code(self):
                 )
                 row = cur.fetchone()
                 self.assertEqual(row['registration_code_used'], None)
+
+    def test_get_perk_fulfillment_state(self):
+        with Transaction() as t:
+            admin_repo = AdminRepo(t)
+            with t.cursor() as cur:
+                cur.execute(
+                    "UPDATE ag.settings "
+                    "SET perk_fulfillment_active = TRUE"
+                )
+
+                obs = admin_repo.get_perk_fulfillment_state()
+                self.assertTrue(obs)
+
+                cur.execute(
+                    "UPDATE ag.settings "
+                    "SET perk_fulfillment_active = False"
+                )
+
+                obs = admin_repo.get_perk_fulfillment_state()
+                self.assertFalse(obs)
+
+    def test_update_perk_fulfillment_state(self):
+        with Transaction() as t:
+            with t.cursor() as cur:
+                admin_repo = AdminRepo(t)
+                admin_repo.update_perk_fulfillment_state(True)
+                cur.execute(
+                    "SELECT perk_fulfillment_active "
+                    "FROM ag.settings"
+                )
+                obs = cur.fetchone()
+                self.assertTrue(obs[0])
+
+                admin_repo.update_perk_fulfillment_state(False)
+                cur.execute(
+                    "SELECT perk_fulfillment_active "
+                    "FROM ag.settings"
+                )
+                obs = cur.fetchone()
+                self.assertFalse(obs[0])

microsetta_private_api/api/__init__.py

@@ -18,7 +18,8 @@
 from ._source import (
     create_source, read_source, update_source, read_sources,
     create_human_source_from_consent, check_duplicate_source_name,
-    scrub_source, check_source_ffq_prereqs, check_prompt_survey_update
+    scrub_source, check_source_ffq_prereqs, check_prompt_survey_update,
+    get_external_reports, get_external_report, get_external_report_bytes
 )
 from ._survey import (
     read_survey_template, read_survey_templates, read_answered_survey,
@@ -84,6 +85,9 @@
     'read_source',
     'check_source_ffq_prereqs',
     'check_prompt_survey_update',
+    'get_external_reports',
+    'get_external_report',
+    'get_external_report_bytes',
     'update_source',
     'scrub_source',
     'read_sources',

microsetta_private_api/api/_account.py

@@ -124,6 +124,11 @@ def check_email_match(account_id, token_info):
 def update_account(account_id, body, token_info):
     acc = _validate_account_access(token_info, account_id)
 
+    # Prevent users outside Japan from selecting Japanese
+    if body['language'] == "ja_JP" and\
+            body['address']['country_code'] != "JP":
+        return jsonify(code=422, message="Invalid language selected"), 422
+
     with Transaction() as t:
         acct_repo = AccountRepo(t)
         acc.first_name = body['first_name']

microsetta_private_api/api/_consent.py

@@ -3,11 +3,14 @@
 from microsetta_private_api import localization
 from microsetta_private_api.api._account import \
     _validate_account_access
-from microsetta_private_api.model.consent import ConsentSignature
+from microsetta_private_api.model.consent import ConsentSignature,\
+    HUMAN_CONSENT_AGE_GROUPS
 from microsetta_private_api.repo.consent_repo import ConsentRepo
+from microsetta_private_api.repo.source_repo import SourceRepo
 from microsetta_private_api.repo.transaction import Transaction
 from microsetta_private_api.api.literals import CONSENT_DOC_NOT_FOUND_MSG
 from werkzeug.exceptions import NotFound
+from microsetta_private_api.api.literals import SRC_NOT_FOUND_MSG
 
 
 def render_consent_doc(account_id, language_tag, token_info):
@@ -47,7 +50,12 @@ def check_consent_signature(account_id, source_id, consent_type, token_info):
 
     with Transaction() as t:
         consent_repo = ConsentRepo(t)
-        res = consent_repo.is_consent_required(source_id, consent_type)
+        source_repo = SourceRepo(t)
+        source = source_repo.get_source(account_id, source_id)
+        age_range = source.source_data.age_range
+        res = consent_repo.is_consent_required(
+            source_id, age_range, consent_type
+        )
 
     return jsonify({"result": res}), 200
 
@@ -56,6 +64,54 @@ def sign_consent_doc(account_id, source_id, consent_type, body, token_info):
     _validate_account_access(token_info, account_id)
 
     with Transaction() as t:
+        # Sources are now permitted to update their age range, but only if it
+        # moves the source to an older age group. For this purpose, "legacy"
+        # is treated as younger than "0-6", as they're choosing an age group
+        # for the first time.
+        source_repo = SourceRepo(t)
+        source = source_repo.get_source(account_id, source_id)
+        if source is None:
+            return jsonify(code=404, message=SRC_NOT_FOUND_MSG), 404
+
+        if source.source_data.age_range != body['age_range']:
+            # Let's make sure it's a valid change. First, grab the index of
+            # their current age range.
+            try:
+                cur_age_index = HUMAN_CONSENT_AGE_GROUPS.index(
+                    source.source_data.age_range
+                )
+            except ValueError:
+                # Catch any sources that have a blank, "legacy", or faulty
+                # age_range
+                cur_age_index = -1
+
+            # Next, make sure their new age range is valid
+            try:
+                new_age_index = HUMAN_CONSENT_AGE_GROUPS.index(
+                    body['age_range']
+                )
+            except ValueError:
+                # Shouldn't reach this point, but if we do, reject it
+                return jsonify(
+                    code=403, message="Invalid age_range update"
+                ), 403
+
+            # Finally, make sure the new age_range isn't younger than the
+            # current age_range.
+            if new_age_index < cur_age_index:
+                return jsonify(
+                    code=403, message="Invalid age_range update"
+                ), 403
+
+            update_success = source_repo.update_source_age_range(
+                source_id, body['age_range']
+            )
+            if not update_success:
+                return jsonify(
+                    code=403, message="Invalid age_range update"
+                ), 403
+
+        # Now back to the normal flow of signing a consent document
         consent_repo = ConsentRepo(t)
         sign_id = str(uuid.uuid4())
         consent_sign = ConsentSignature.from_dict(body, source_id, sign_id)

microsetta_private_api/api/_interested_user.py

@@ -7,7 +7,10 @@
 from microsetta_private_api.exceptions import RepoException
 from microsetta_private_api.repo.campaign_repo import CampaignRepo
 from microsetta_private_api.repo.melissa_repo import MelissaRepo
+from microsetta_private_api.repo.perk_fulfillment_repo import\
+    PerkFulfillmentRepo
 from microsetta_private_api.tasks import send_email
+from microsetta_private_api.admin.admin_impl import validate_admin_access
 
 
 def create_interested_user(body):
@@ -105,18 +108,12 @@ def get_interested_user_address_update(interested_user_id, email):
                 else:
                     # We've determined it's a valid user and their address
                     # needs to be fixed, so we return a subset of their info.
-                    # Certain paths into the database allow null address_2
-                    # which causes problems, so we change it to "".
-                    if interested_user.address_2 is None:
-                        interested_user.address_2 = ""
-
                     # We also need to grab the reason(s) that Melissa couldn't
                     # verify the address.
                     melissa_repo = MelissaRepo(t)
                     melissa_result = melissa_repo.check_duplicate(
                         interested_user.address_1,
                         interested_user.address_2,
-                        interested_user.address_3,
                         interested_user.postal_code,
                         interested_user.country
                     )
@@ -146,6 +143,7 @@ def get_interested_user_address_update(interested_user_id, email):
                         state=interested_user.state,
                         postal_code=interested_user.postal_code,
                         country=interested_user.country,
+                        phone=interested_user.phone,
                         error_codes=error_codes
                     ), 200
 
@@ -161,6 +159,14 @@ def put_interested_user_address_update(body):
             message="Invalid user."
         ), 404
     else:
+        required_fields = ['address_1', 'city', 'state', 'postal', 'phone']
+        for f in required_fields:
+            if body.get(f, "") == "":
+                return jsonify(
+                    code=400,
+                    message="Failed to update address due to missing fields."
+                ), 400
+
         with Transaction() as t:
             i_u_repo = InterestedUserRepo(t)
             interested_user = \
@@ -282,3 +288,17 @@ def _validate_user_match(interested_user, email):
         # someone doesn't stumble upon a valid email and/or id.
         # if they don't both match, treat as invalid
         return interested_user.email == email
+
+
+def search_ffq_codes_by_email(email, token_info):
+    validate_admin_access(token_info)
+
+    with Transaction() as t:
+        pfr = PerkFulfillmentRepo(t)
+        ffq_diag = pfr.get_ffq_codes_by_email(email)
+        ffq_codes_obj = {
+            "ffq_codes": ffq_diag
+        }
+        if ffq_diag is None:
+            return jsonify(code=404, message="Email not found"), 404
+        return jsonify(ffq_codes_obj), 200

microsetta_private_api/api/_sample.py

@@ -137,9 +137,13 @@ def update_sample_association(account_id, source_id, sample_id, body,
         except ValueError:
             raise BadRequest("Invalid sample_datetime")
         curdate = datetime.now(sample_datetime.tzinfo)
-        lower_limit = curdate + relativedelta(years=-10)
+        lower_limit = curdate + relativedelta(years=-1)
         upper_limit = curdate + relativedelta(months=+1)
-        if sample_datetime < lower_limit or sample_datetime > upper_limit:
+        is_admin = token_grants_admin_access(token_info)
+
+        # Allow admins to bypass the back-dating/forward-dating limits
+        if (sample_datetime < lower_limit or sample_datetime > upper_limit)\
+                and not is_admin:
             raise BadRequest('Invalid sample date')
         # sample_site will not be present if its environmental. this will
         # default to None if the key is not present
@@ -151,7 +155,6 @@ def update_sample_association(account_id, source_id, sample_id, body,
             body["sample_notes"]
         )
 
-        is_admin = token_grants_admin_access(token_info)
         sample_repo.update_info(account_id, source_id, sample_info,
                                 override_locked=is_admin)