Release 1.9.0

backend/README.md

@@ -311,6 +311,12 @@ python3 -m venv python-env
 ```
 When pushing to production please create a new 'Release' on gitHub describing the changes that were rolled out.
 
+Currently we are using a separate repository for deployment: star-drive-dist. To prepare this for deployment, you should have a
+copy of star-drive-dist in the same directory as your local copy of star-drive. Your local star-drive should be on master, 
+up to date with all the changes for the release. Once this is ready, run the ```prepare_for_deploy.sh``` script in 
+star-drive-dist to prepare the release. Commit these changes referencing the release number and push them up. 
+
+
 
 
 

backend/app/data_loader.py

@@ -85,7 +85,7 @@ class DataLoader:
                 db.session.commit()
 
                 for i in range(17, 25):
-                    if row[i] and row[i] is not '':
+                    if row[i] and row[i] != '':
                         category = self.get_category_by_name(row[i].strip())
                         event_id = event.id
                         category_id = category.id
@@ -125,7 +125,7 @@ class DataLoader:
                 db.session.commit()
 
                 for i in range(19, 28):
-                    if row[i] and row[i] is not '':
+                    if row[i] and row[i] != '':
                         category = self.get_category_by_name(row[i].strip())
                         location_id = location.id
                         category_id = category.id
@@ -159,7 +159,7 @@ class DataLoader:
                     db.session.commit()
 
                 for i in range(7, 14):
-                    if row[i] and row[i] is not '':
+                    if row[i] and row[i] != '':
                         category = self.get_category_by_name(row[i].strip())
                         resource_id = resource.id
                         category_id = category.id
@@ -199,7 +199,7 @@ class DataLoader:
                 self.__increment_id_sequence(Study)
 
                 for i in range(24, 31):
-                    if row[i] and row[i] is not '':
+                    if row[i] and row[i] != '':
                         category = self.get_category_by_name(row[i].strip())
                         study_id = study.id
                         category_id = category.id

backend/app/elastic_index.py

@@ -157,7 +157,7 @@ class ElasticIndex:
         for cat in document.categories:
             doc.category.extend(cat.category.all_search_paths())
 
-        if document.__tablename__ is 'study':
+        if document.__tablename__ == 'study':
             doc.title = document.short_title
             doc.description = document.short_description
 
@@ -211,7 +211,7 @@ class ElasticIndex:
             elastic_search = elastic_search.filter('range', **{"date": {"gte": search.date}})
         else:
             elastic_search = elastic_search.filter('bool', **{"should": [
-                {"range": {"date": {"gte": datetime.datetime.now()}}},  # Future events OR
+                {"range": {"date": {"gte": datetime.datetime.utcnow()}}},  # Future events OR
                 {"bool": {"must_not": {"exists": {"field": "date"}}}}   # Date field is empty
             ]})
 
@@ -277,7 +277,7 @@ class ElasticIndex:
 
         # Filter out past events
         elastic_search = elastic_search.filter('bool', **{"should": [
-            {"range": {"date": {"gte": datetime.datetime.now()}}},  # Future events OR
+            {"range": {"date": {"gte": datetime.datetime.utcnow()}}},  # Future events OR
             {"bool": {"must_not": {"exists": {"field": "date"}}}}  # Date field is empty
         ]})
 

backend/app/export_service.py

@@ -206,11 +206,13 @@ class ExportService:
         return meta_relationed
 
     @staticmethod
-    # this evil method recurses down through the metadata, removing items that have a
-    # RELATIONSHIP_REQUIRED, if the relationship isn't there and selecting the right
-    # content from a list, if RELATIONSHIP_SPECIFIC provides an array content for each
-    # possible type of relationship.
     def _recursive_relationship_changes(meta, relationship):
+        """
+        This evil method recurses down through the metadata, removing items that have a
+        RELATIONSHIP_REQUIRED, if the relationship isn't there and selecting the right
+        content from a list, if RELATIONSHIP_SPECIFIC provides an array content for each
+        possible type of relationship.
+        """
         meta_copy = {}
         for k, v in meta.items():
             if type(v) is dict:
@@ -240,12 +242,13 @@ class ExportService:
 
     @staticmethod
     def send_alert_if_exports_not_running():
-        """If more than 30 minutes pass without an export from the Public Mirror to the
-        Private Mirror, an email will be sent to an administrative email address.
-         Emails to this address will occur every two (2) hours for the first 24 hours
-          and every four hours after that until the fault is corrected or the system taken down.
-            After 24 hours, the PI will also be emailed notifications every 8 hours until
-             the fault is corrected or the system taken down."""
+        """
+        If more than 30 minutes pass without an export from the Public Mirror to the Private Mirror, an email will be
+        sent to an administrative email address. Emails to this address will occur every two (2) hours for the first
+        24 hours and every four hours after that until the fault is corrected or the system taken down. After 24
+        hours, the PI will also be emailed notifications every 8 hours until the fault is corrected or the system
+        taken down.
+        """
         alert_principal_investigator = False
         last_log = db.session.query(DataTransferLog).filter(DataTransferLog.type == 'export')\
             .order_by(desc(DataTransferLog.last_updated)).limit(1).first()
@@ -257,7 +260,8 @@ class ExportService:
         else:
             msg = None
             subject = "Autism DRIVE: Error - "
-            time_difference = datetime.datetime.now(tz=UTC) - last_log.last_updated
+            now = datetime.datetime.utcnow().replace(tzinfo=datetime.timezone.utc)  # Make date timezone aware
+            time_difference = now - last_log.last_updated
             hours = int(time_difference.total_seconds()/3600)
             minutes = int(time_difference.total_seconds()/60)
             if hours >= 24 and hours% 4 == 0 and last_log.alerts_sent < (hours / 4 + 12):

backend/app/export_xls_service.py

@@ -108,8 +108,8 @@ class ExportXlsService:
         # Add output to response
         response.data = output.read()
 
-        # Set filname
-        file_name = 'export_{}_{}.xlsx'.format(name, datetime.now())
+        # Set filename
+        file_name = 'export_{}_{}.xlsx'.format(name, datetime.utcnow())
 
         # HTTP headers for forcing file download
         response_headers = Headers({

backend/app/import_service.py

@@ -31,7 +31,7 @@ class ImportService:
         self.import_interval_minutes = app.config['IMPORT_INTERVAL_MINUTES']
 
     def run_backup(self, load_admin=True, full_backup=False):
-        date_started = datetime.datetime.now()
+        date_started = datetime.datetime.utcnow()
         exportables = self.get_export_list(full_backup)
         # Note:  We request data THEN create the next log.  We depend on this order to get data since
         # the last log was recorded, but besure and set the start date from the moment this was called.

backend/app/model/questionnaires/evaluation_history_mixin.py

@@ -1,6 +1,5 @@
 import datetime
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 from sqlalchemy.ext.declarative import declared_attr
 

backend/app/model/questionnaires/home_mixin.py

@@ -1,6 +1,5 @@
 import datetime
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 from sqlalchemy.ext.declarative import declared_attr
 

backend/app/model/resource_category.py

@@ -1,6 +1,5 @@
 import datetime
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 
 from app import db

backend/app/model/study.py

@@ -1,7 +1,6 @@
 import datetime
 import enum
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 
 from app import db

backend/app/model/study_category.py

@@ -1,6 +1,5 @@
 import datetime
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 
 from app import db

backend/app/model/study_investigator.py

@@ -1,6 +1,5 @@
 import datetime
 
-from dateutil.tz import tzutc
 from sqlalchemy import func
 
 from app import db

backend/app/model/user.py

@@ -44,7 +44,9 @@ class User(db.Model):
 
     def get_self_participant(self):
         if len(self.participants) > 0:
-            return next(p for p in self.participants if "self" in p.relationship.name)
+            for p in self.participants:
+                if "self" in p.relationship.name:
+                    return p
 
     def self_registration_complete(self):
         if self.get_self_participant() is not None:
@@ -113,3 +115,16 @@ class User(db.Model):
         for p in self.participants:
             if p.contact:
                 return {'name': p.get_name(), 'relationship': p.relationship.name, 'contact': p.contact}
+
+    def created_password(self):
+        return self.password is not None
+
+    def identity(self):
+        if len(self.participants) > 0:
+            return self.get_self_participant().relationship.name
+        else:
+            return 'Not set'
+
+    def percent_self_registration_complete(self):
+        if len(self.participants) > 0:
+            return self.get_self_participant().get_percent_complete()

backend/app/resources/AdminNoteEndpoint.py

@@ -34,7 +34,7 @@ class AdminNoteEndpoint(flask_restful.Resource):
         instance = db.session.query(AdminNote).filter_by(id=id).first()
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         return self.schema.dump(updated)

backend/app/resources/Auth.py

@@ -49,7 +49,7 @@ def login_password():
             auth_token = user.encode_auth_token().decode()
             g.user = user
             user.token = auth_token
-            user.last_login = datetime.datetime.now()
+            user.last_login = datetime.datetime.utcnow()
             db.session.add(user)
             db.session.commit()
             return schema.jsonify(user)
@@ -101,7 +101,7 @@ def reset_password():
     user.token_url = ''
     user.email_verified = True
     user.password = password
-    user.last_login = datetime.datetime.now()
+    user.last_login = datetime.datetime.utcnow()
     db.session.add(user)
     db.session.commit()
     auth_token = user.encode_auth_token().decode()

backend/app/resources/EventEndpoint.py

@@ -52,7 +52,7 @@ class EventEndpoint(flask_restful.Resource):
             request_data['longitude'] = geocode['lng']
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         elastic_index.update_document(updated, 'Event', latitude=updated.latitude, longitude=updated.longitude)

backend/app/resources/ExportEndpoint.py

@@ -19,6 +19,8 @@ def get_date_arg():
     after_date = None
     if date_arg:
         after_date = datetime.datetime.strptime(date_arg, ExportService.DATE_FORMAT)
+
+    print('after_date', after_date)
     return after_date
 
 
@@ -48,7 +50,7 @@ class ExportListEndpoint(flask_restful.Resource):
     @requires_roles(Role.admin)
     def get(self):
 
-        date_started = datetime.datetime.now()
+        date_started = datetime.datetime.utcnow()
         info_list = ExportService.get_table_info(get_date_arg())
 
         # Remove items that are not exportable, or that are identifying
@@ -71,7 +73,7 @@ class ExportListEndpoint(flask_restful.Resource):
             log = db.session.query(DataTransferLog).filter(DataTransferLog.type == 'export')\
                 .order_by(desc(DataTransferLog.last_updated)).limit(1).first()
             if log is None: log = DataTransferLog(type="export", total_records=0)
-            log.last_updated = datetime.datetime.now()
+            log.last_updated = datetime.datetime.utcnow()
         db.session.add(log)
         db.session.commit()
 

backend/app/resources/FlowEndpoint.py

@@ -79,7 +79,7 @@ class FlowQuestionnaireEndpoint(flask_restful.Resource):
                       flow=flow.name,
                       participant_id=questionnaire.participant_id,
                       user_id=g.user.id,
-                      date_completed=datetime.datetime.now(),
+                      date_completed=datetime.datetime.utcnow(),
                       time_on_task_ms=questionnaire.time_on_task_ms)
         db.session.add(log)
         db.session.commit()

backend/app/resources/InvestigatorEndpoint.py

@@ -30,7 +30,7 @@ class InvestigatorEndpoint(flask_restful.Resource):
         instance = db.session.query(Investigator).filter_by(id=id).first()
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         return self.schema.dump(updated)

backend/app/resources/LocationEndpoint.py

@@ -54,7 +54,7 @@ class LocationEndpoint(flask_restful.Resource):
             request_data['longitude'] = geocode['lng']
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         elastic_index.update_document(updated, 'Location', latitude=updated.latitude, longitude=updated.longitude)

backend/app/resources/ParticipantEndpoint.py

@@ -39,7 +39,7 @@ class ParticipantEndpoint(flask_restful.Resource):
             raise RestException(RestException.UNRELATED_PARTICIPANT)
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         return self.schema.dump(updated)

backend/app/resources/QuestionnaireEndpoint.py

@@ -2,7 +2,6 @@ import datetime
 import flask_restful
 import os
 
-from dateutil.tz import tzutc
 from flask import request
 from sqlalchemy.exc import IntegrityError
 from app import app, db, RestException, auth
@@ -59,7 +58,7 @@ class QuestionnaireEndpoint(flask_restful.Resource):
 
         if errors:
             raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now(tz=tzutc())
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         return schema.dump(updated)

backend/app/resources/ResourceEndpoint.py

@@ -56,7 +56,7 @@ class ResourceEndpoint(flask_restful.Resource):
         instance = db.session.query(Resource).filter_by(id=id).first()
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         elastic_index.update_document(updated, 'Resource')

backend/app/resources/SearchEndpoint.py

@@ -76,7 +76,7 @@ class SearchEndpoint(flask_restful.Resource):
             category = Category(name="Topics")
             category.children = db.session.query(Category)\
                 .filter(Category.parent_id == None)\
-                .order_by(Category.name)\
+                .order_by(Category.name.desc())\
                 .all()
         else:
             c = category

backend/app/resources/StudyEndpoint.py

@@ -37,7 +37,7 @@ class StudyEndpoint(flask_restful.Resource):
         instance = db.session.query(Study).filter_by(id=id).first()
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         elastic_index.update_document(updated, 'Study')

backend/app/resources/Tracking.py

@@ -14,7 +14,7 @@ def logo(user_id, code):
     email_log = EmailLog.query.filter_by(user_id=user_id, tracking_code=code).first()
     if email_log:
         email_log.viewed = True
-        email_log.date_viewed = datetime.datetime.now()
+        email_log.date_viewed = datetime.datetime.utcnow()
         db.session.add(email_log)
         db.session.commit()
     return send_file("static/UVA_STAR-logo.png", mimetype='image/png')

backend/app/resources/UserEndpoint.py

@@ -50,7 +50,7 @@ class UserEndpoint(flask_restful.Resource):
         instance = db.session.query(User).filter_by(id=id).first()
         updated, errors = self.schema.load(request_data, instance=instance)
         if errors: raise RestException(RestException.INVALID_OBJECT, details=errors)
-        updated.last_updated = datetime.datetime.now()
+        updated.last_updated = datetime.datetime.utcnow()
         db.session.add(updated)
         db.session.commit()
         return self.schema.dump(updated)

backend/app/schema/schema.py

@@ -398,7 +398,8 @@ class UserSchema(ModelSchema):
     class Meta:
         model = User
         fields = ('id', 'last_updated', 'registration_date', 'last_login', 'email', 'password', 'role',
-                  'permissions', 'participants', 'token', 'token_url', 'user_favorites', 'participant_count')
+                  'permissions', 'participants', 'token', 'token_url', 'user_favorites', 'participant_count',
+                  'created_password', 'identity', 'percent_self_registration_complete')
     password = fields.String(load_only=True)
     participants = fields.Nested(ParticipantSchema, dump_only=True, many=True)
     participant_count = fields.Integer(required=False, allow_none=True)
@@ -406,6 +407,7 @@ class UserSchema(ModelSchema):
     id = fields.Integer(required=False, allow_none=True)
     role = EnumField(Role)
     permissions = fields.Method('get_permissions', dump_only=True)
+    percent_self_registration_complete = fields.Integer(required=False, allow_none=True)
 
     def get_permissions(self, obj):
         permissions = []

backend/app/templates/complete_registration_email.html

@@ -1,14 +1,13 @@
 {% extends "base_email.html" %}
 {% block content %}
     <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
-        Welcome to Autism DRIVE.
+        Welcome to Autism DRIVE. There are few more steps to complete your profile.
     </p>
 
     <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
-        There are few more steps to complete your profile. Once you provide more information about yourself,
-        we will use this information to contact you about upcoming studies and emerging resources that may be of
-        interest based on details you provided. You will have additional opportunities to create profiles for your
-        children or dependents.
+        Once you provide more information about yourself, we will use this information to contact you about upcoming
+        studies and emerging resources that may be of interest based on details you provided. You will have additional
+        opportunities to create profiles for your children or dependents.
     </p>
     <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
         To complete your profile, continue <a href="{{ profile_url }}">here.</a>

backend/app/templates/confirm_email.html

@@ -1,13 +1,13 @@
 {% extends "base_email.html" %}
 {% block content %}
     <p style="font-family: sans-serif; font-size: 24px; font-weight: bold; margin: 0; Margin-bottom: 15px;">
-        You have a new account on the Autism DRIVE.
+        Welcome to Autism DRIVE. Now you have a new account.
     </p>
 
     <p style="font-family: sans-serif; font-size: 14px; font-weight: normal; margin: 0; Margin-bottom: 15px;">
-        Someone recently created an account for you on the Autism DRIVE. please click the button below to confirm your email
-        address and create your password. Please note that this password-setting link will expire in 24 hours. If that
-        happens you can set your password by requesting a password reset <a href="{{ forgot_pass_url }}">here.</a>
+        Please click the button below to confirm your email address and create your password. Please note that this
+        password-setting link will expire in 24 hours. If that happens you can set your password by requesting a
+        password reset <a href="{{ forgot_pass_url }}">here.</a>
     </p>
 
     <table border="0" cellpadding="0" cellspacing="0">

backend/app/templates/confirm_email.txt

@@ -1,8 +1,7 @@
-You have a new account on the Autism DRIVE.
+Welcome to Autism DRIVE. Now you have a new account.
 
-Someone recently created an account for you on the Autism DRIVE. To create your profile,
-please place the following url in your browser to confirm your email address:
-{{confirm_url}}
+To create your profile, please place the following url in your browser to confirm your
+email address: {{confirm_url}}
 
 Please note that this password-setting link will expire in 24 hours. If that happens you can
 set your password by requesting a password reset at: {{ forgot_pass_url }}

backend/requirements.txt

@@ -6,7 +6,7 @@ marshmallow_sqlalchemy==0.13.2
 Flask-Migrate==2.1.1
 Werkzeug==0.16.1
 # DO NOT use pyscopg2-binary, it will seg fault in the worst possible way in production.
-psycopg2==2.7.5
+psycopg2==2.8.6
 flask-bcrypt==0.7.1
 flask-cors==3.0.3
 flask-httpauth==3.2.4

frontend/3rdpartylicenses.txt

@@ -154,6 +154,8 @@ THE SOFTWARE.
 
 @angular/material/dialog
 
+@angular/material/divider
+
 @angular/material/expansion
 
 @angular/material/form-field

frontend/index.html

@@ -32,6 +32,6 @@
 
 <body>
   <app-root></app-root>
-<script src="runtime-es2015.858f8dd898b75fe86926.js" type="module"></script><script src="polyfills-es2015.696ad2b135b52dd9855f.js" type="module"></script><script src="runtime-es5.741402d1d47331ce975c.js" nomodule></script><script src="polyfills-es5.6ba1fc6238374eb32f77.js" nomodule></script><script src="main-es2015.21f1728e983bb93565b7.js" type="module"></script><script src="main-es5.ef0da0f86e6d77858e01.js" nomodule></script></body>
+<script src="runtime-es2015.858f8dd898b75fe86926.js" type="module"></script><script src="polyfills-es2015.b119ee49bbbfb46089bb.js" type="module"></script><script src="runtime-es5.741402d1d47331ce975c.js" nomodule></script><script src="polyfills-es5.8b864a0703dc82fe4e63.js" nomodule></script><script src="main-es2015.41b2160c0dfceb047dbd.js" type="module"></script><script src="main-es5.ca6c55fbe0110fd2ec82.js" nomodule></script></body>
 
 </html>