Overhaul

microsetta_private_api/admin/admin_impl.py

@@ -681,6 +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)
 

microsetta_private_api/api/__init__.py

@@ -12,7 +12,8 @@
 from ._consent import (
     render_consent_doc,
     check_consent_signature,
-    sign_consent_doc
+    sign_consent_doc,
+    get_signed_consents
 )
 from ._source import (
     create_source, read_source, update_source, delete_source,
@@ -45,7 +46,7 @@
     get_vioscreen_dietary_scores_descriptions,
     get_vioscreen_food_components_by_code,
     get_vioscreen_food_components_descriptions,
-    get_vioscreen_sessions
+    get_vioscreen_sessions, get_vioscreen_registry_entries, check_ffq_code
 )
 
 from ._campaign import (
@@ -89,6 +90,7 @@
     'create_human_source_from_consent',
     'check_consent_signature',
     'sign_consent_doc',
+    'get_signed_consents',
     'read_survey_template',
     'read_survey_templates',
     'read_answered_survey',
@@ -124,7 +126,9 @@
     'create_interested_user',
     'get_interested_user_address_update',
     'put_interested_user_address_update',
+    'get_vioscreen_sessions',
+    'get_vioscreen_registry_entries',
+    'check_ffq_code',
     'get_opt_out',
-    'put_opt_out',
-    'get_vioscreen_sessions'
+    'put_opt_out'
 ]

microsetta_private_api/api/_account.py

@@ -118,7 +118,8 @@ def update_account(account_id, body, token_info):
             body['address']['city'],
             body['address']['state'],
             body['address']['post_code'],
-            body['address']['country_code']
+            body['address']['country_code'],
+            body['address']['street2']
         )
         acc.language = body['language']
 

microsetta_private_api/api/_consent.py

@@ -52,7 +52,6 @@ def check_consent_signature(account_id, source_id, consent_type, token_info):
 
 
 def sign_consent_doc(account_id, source_id, consent_type, body, token_info):
-
     _validate_account_access(token_info, account_id)
 
     with Transaction() as t:
@@ -62,12 +61,60 @@ def sign_consent_doc(account_id, source_id, consent_type, body, token_info):
         try:
             consent_repo.sign_consent(account_id, consent_sign)
             t.commit()
-        except Exception:
-            return jsonify(code=404, message=CONSENT_DOC_NOT_FOUND_MSG), 404
+        except Exception as e:
+            raise Exception(e)
+            return jsonify(code=404, message=e), 404
 
     response = jsonify({"result": True})
     response.status_code = 201
     response.headers['Location'] = '/api/accounts/%s' % \
         (account_id)
 
     return response
+
+
+def get_signed_consents(account_id, source_id, token_info):
+    _validate_account_access(token_info, account_id)
+
+    ret_val = {}
+    with Transaction() as t:
+        consent_repo = ConsentRepo(t)
+        survey_consent = consent_repo.get_latest_signed_consent(
+            source_id,
+            "data"
+        )
+        if survey_consent is None:
+            ret_val['survey'] = None
+        else:
+            survey_consent = survey_consent.to_api()
+            survey_doc = consent_repo.get_consent_document(
+                survey_consent['consent_id']
+            )
+            survey_consent['consent_content'] = survey_doc.consent_content
+            if survey_consent['assent_id'] is not None:
+                assent_doc = consent_repo.get_consent_document(
+                    survey_consent['assent_id']
+                )
+                survey_consent['assent_content'] = assent_doc.consent_content
+            ret_val['survey'] = survey_consent
+
+        sample_consent = consent_repo.get_latest_signed_consent(
+            source_id,
+            "biospecimen"
+        )
+        if sample_consent is None:
+            ret_val['sample'] = None
+        else:
+            sample_consent = sample_consent.to_api()
+            sample_doc = consent_repo.get_consent_document(
+                sample_consent['consent_id']
+            )
+            sample_consent['consent_content'] = sample_doc.consent_content
+            if sample_consent['assent_id'] is not None:
+                assent_doc = consent_repo.get_consent_document(
+                    sample_consent['assent_id']
+                )
+                sample_consent['assent_content'] = assent_doc.consent_content
+            ret_val['sample'] = sample_consent
+
+    return jsonify(ret_val), 200

microsetta_private_api/api/_source.py

@@ -199,16 +199,12 @@ def create_human_source_from_consent(account_id, body, token_info):
         }
     }
 
-    deceased_parent_key = 'deceased_parent'
-    child_keys = {'parent_1_name', 'parent_2_name', deceased_parent_key,
-                  'obtainer_name'}
+    child_keys = {'parent_1_name', 'obtainer_name'}
 
     intersection = child_keys.intersection(body)
     if intersection:
         source['consent']['child_info'] = {}
         for key in intersection:
-            if key == deceased_parent_key:
-                body[deceased_parent_key] = body[deceased_parent_key] == 'true'
             source['consent']['child_info'][key] = body[key]
 
     # NB: Don't expect to handle errors 404, 422 in this function; expect to

microsetta_private_api/api/_survey.py

@@ -1,6 +1,7 @@
 import flask
 from flask import jsonify, make_response
 from werkzeug.exceptions import NotFound
+from flask_babel import format_datetime, force_locale
 
 from microsetta_private_api.api._account import \
     _validate_account_access
@@ -38,23 +39,22 @@ def read_survey_templates(account_id, source_id, language_tag, token_info):
         template_repo = SurveyTemplateRepo(t)
         if source.source_type == Source.SOURCE_TYPE_HUMAN:
             return jsonify([template_repo.get_survey_template_link_info(x)
-                           for x in [1, 3, 4, 5, 6, 7,
-                                     SurveyTemplateRepo.VIOSCREEN_ID,
-                                     SurveyTemplateRepo.MYFOODREPO_ID,
-                                     SurveyTemplateRepo.POLYPHENOL_FFQ_ID,
-                                     SurveyTemplateRepo.SPAIN_FFQ_ID,
-                                     SurveyTemplateRepo.BASIC_INFO_ID,
-                                     SurveyTemplateRepo.AT_HOME_ID,
-                                     SurveyTemplateRepo.LIFESTYLE_ID,
-                                     SurveyTemplateRepo.GUT_ID,
-                                     SurveyTemplateRepo.GENERAL_HEALTH_ID,
-                                     SurveyTemplateRepo.HEALTH_DIAG_ID,
-                                     SurveyTemplateRepo.ALLERGIES_ID,
-                                     SurveyTemplateRepo.DIET_ID,
-                                     SurveyTemplateRepo.DETAILED_DIET_ID,
-                                     SurveyTemplateRepo.MIGRAINE_ID,
-                                     SurveyTemplateRepo.SURFERS_ID,
-                                     SurveyTemplateRepo.COVID19_ID]]), 200
+                           for x in [
+                                SurveyTemplateRepo.VIOSCREEN_ID,
+                                SurveyTemplateRepo.POLYPHENOL_FFQ_ID,
+                                SurveyTemplateRepo.SPAIN_FFQ_ID,
+                                SurveyTemplateRepo.BASIC_INFO_ID,
+                                SurveyTemplateRepo.AT_HOME_ID,
+                                SurveyTemplateRepo.LIFESTYLE_ID,
+                                SurveyTemplateRepo.GUT_ID,
+                                SurveyTemplateRepo.GENERAL_HEALTH_ID,
+                                SurveyTemplateRepo.HEALTH_DIAG_ID,
+                                SurveyTemplateRepo.ALLERGIES_ID,
+                                SurveyTemplateRepo.DIET_ID,
+                                SurveyTemplateRepo.DETAILED_DIET_ID,
+                                SurveyTemplateRepo.COVID19_ID,
+                                SurveyTemplateRepo.OTHER_ID
+                            ]]), 200
         elif source.source_type == Source.SOURCE_TYPE_ANIMAL:
             return jsonify([template_repo.get_survey_template_link_info(x)
                            for x in [2]]), 200
@@ -259,22 +259,65 @@ def read_survey_template(account_id, source_id, survey_template_id,
                 if field.id in client_side_validation:
                     field.set(**client_side_validation[field.id])
 
-        results, percent_comp = st_repo.migrate_responses(source_id,
-                                                          survey_template_id)
+        date_last_taken = st_repo.get_date_survey_last_taken(
+            source_id,
+            survey_template_id
+        )
+        if date_last_taken is not None:
+            with force_locale(language_tag):
+                date_last_taken = format_datetime(
+                    date_last_taken, "MMM d, yyyy"
+                )
+        info.date_last_taken = date_last_taken
+
+        results = st_repo.migrate_responses(source_id, survey_template_id)
         if results:
             # modify info with previous results before returning to client.
             for group in info.survey_template_text.groups:
                 for field in group.fields:
                     previous_response = results[field.inputName]
                     if previous_response:
                         field.default = previous_response
-            info.percentage_completed = "{0:.2f}%".format(percent_comp * 100)
+            info.percentage_completed = _calculate_completion_percentage(
+                info.survey_template_text
+            )
         else:
-            info.percentage_completed = '0.00%'
+            info.percentage_completed = 0
 
         return jsonify(info), 200
 
 
+def _calculate_completion_percentage(survey_model):
+    visible_questions = 0
+    answered_questions = 0
+    answers = {}
+
+    for group in survey_model.groups:
+        for field in group.fields:
+            answers[field.id] = field.default
+            if hasattr(field, 'triggered_by'):
+                q_is_visible = False
+                for trigger_q in field.triggered_by:
+                    if answers[trigger_q['q_id']] == trigger_q['response']:
+                        q_is_visible = True
+                        break
+
+                if q_is_visible is True:
+                    visible_questions += 1
+                    if _is_question_answered(field.default):
+                        answered_questions += 1
+            else:
+                visible_questions += 1
+                if _is_question_answered(field.default):
+                    answered_questions += 1
+
+    return answered_questions / visible_questions
+
+
+def _is_question_answered(response):
+    return (response is not None and response != '' and response != [])
+
+
 def read_answered_surveys(account_id, source_id, language_tag, token_info):
     _validate_account_access(token_info, account_id)
 

microsetta_private_api/api/_vioscreen.py

@@ -289,7 +289,9 @@ def get_vioscreen_food_components_descriptions(token_info):
         return jsonify(descriptions)
 
 
-def get_vioscreen_sessions(account_id, source_id):
+def get_vioscreen_sessions(account_id, source_id, token_info):
+    _validate_has_account(token_info)
+
     """Obtain vioscreen sessions if it exists"""
     with Transaction() as t:
         vio_session = VioscreenRepo(t)
@@ -299,3 +301,26 @@ def get_vioscreen_sessions(account_id, source_id):
             return jsonify(code=404, message="No vioscreens found"), 404
         else:
             return jsonify({"vioscreens": vioscreen_session})
+
+
+def check_ffq_code(ffq_code, token_info):
+    _validate_has_account(token_info)
+
+    with Transaction() as t:
+        vio_repo = VioscreenRepo(t)
+        unused_code = vio_repo.get_unused_code(ffq_code)
+        if unused_code is None:
+            return jsonify(code=404, message="No unused code found"), 404
+        return jsonify({"unused_code": True}), 200
+
+
+def get_vioscreen_registry_entries(account_id, source_id, token_info):
+    _validate_has_account(token_info)
+
+    with Transaction() as t:
+        vio_repo = VioscreenRepo(t)
+        vio_registry_entries = vio_repo.get_registry_entries_by_source(
+            account_id,
+            source_id
+        )
+    return jsonify(vio_registry_entries), 200