Merge 769ad1d into 7915dea

amgut/handlers/add_sample.py

@@ -2,9 +2,11 @@
 from wtforms import (Form, SelectField, DateField, DateTimeField, TextField,
                      HiddenField, validators)
 from tornado.web import authenticated
+from tornado import escape
 from future.utils import viewitems
 
 from amgut.connections import ag_data
+from amgut.lib.util import survey_vioscreen
 from amgut.handlers.base_handlers import BaseHandler
 from amgut import media_locale
 
@@ -21,6 +23,37 @@ class LogSample(Form):
     notes = TextField('notes')
 
 
+class AddHumanFFQHandler(BaseHandler):
+    @authenticated
+    def post(self):
+        self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
+
+    def get(self):
+        ag_login_id = ag_data.get_user_for_kit(self.current_user)
+        barcode = self.get_secure_cookie('barcode')
+        participant_name = self.get_secure_cookie('participant_name')
+        self.clear_cookie('barcode')
+        self.clear_cookie('participant_name')
+
+        if barcode is None or participant_name is None:
+            self.set_status(404)
+            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
+            return
+        else:
+            barcode = escape.json_decode(barcode)
+            participant_name = escape.json_decode(participant_name)
+
+        new_survey_id = ag_data.get_new_survey_id()
+        ag_data.associate_barcode_to_survey_id(ag_login_id, participant_name,
+                                               barcode, new_survey_id)
+        ag_data.updateVioscreenStatus(new_survey_id, 0)  # 0 -> not started
+        dat = survey_vioscreen(new_survey_id, None, None)
+
+        self.render('human_sample_specific_survey.html',
+                    skid=self.current_user,
+                    surveys=[dat])
+
+
 class AddSample(BaseHandler):
     _sample_sites = []
     page_type = ''
@@ -74,7 +107,14 @@ def post(self):
                                      env_sampled, sample_date,
                                      sample_time, participant_name, notes)
 
-        self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
+        if sample_site is None or self.page_type != 'add_sample_human':
+            self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
+        else:
+            self.set_secure_cookie('participant_name',
+                                   escape.json_encode(participant_name))
+            self.set_secure_cookie('barcode', escape.json_encode(barcode))
+            url = media_locale['SITEBASE'] + '/authed/add_sample_human_ffq/'
+            self.redirect(url)
 
     @authenticated
     def get(self):

amgut/handlers/animal_survey.py

@@ -1,7 +1,5 @@
 from urllib import urlencode
 from json import dumps
-import binascii
-import os
 
 from tornado.web import authenticated
 from tornado.escape import url_escape
@@ -38,16 +36,18 @@ def post(self):
         animal_survey_id = self.get_argument('survey_id', None)
         sitebase = media_locale['SITEBASE']
 
+        form = self.animal_survey()
+        form.process(data=self.request.arguments)
+        data = {'questions': form.data}
+        participant_name = form['Pet_Information_127_0'].data[0]
+
         if not animal_survey_id:
-            animal_survey_id = binascii.hexlify(os.urandom(8))
+            animal_survey_id = ag_data.get_new_survey_id()
+
             new_survey = True
         else:
             new_survey = False
 
-        form = self.animal_survey()
-        form.process(data=self.request.arguments)
-        data = {'questions': form.data}
-        participant_name = form['Pet_Information_127_0'].data[0]
         # If the participant already exists, stop them outright
         if new_survey and \
                 ag_data.check_if_consent_exists(ag_login_id, participant_name):

amgut/handlers/new_participant.py

@@ -1,5 +1,3 @@
-import binascii
-import os
 from json import dumps
 
 from tornado.web import authenticated
@@ -57,7 +55,7 @@ def post(self):
             self.redirect(url)
             return
 
-        human_survey_id = binascii.hexlify(os.urandom(8))
+        human_survey_id = ag_data.get_new_survey_id()
 
         consent = {'participant_name': participant_name,
                    'participant_email': participant_email,

amgut/handlers/secondary_survey.py

@@ -1,8 +1,6 @@
 from urllib import urlencode
 from tornado.escape import url_unescape
 from json import dumps
-import binascii
-import os
 
 from tornado.web import authenticated
 
@@ -54,7 +52,7 @@ def post(self):
         sitebase = media_locale['SITEBASE']
 
         if not survey_id:
-            survey_id = binascii.hexlify(os.urandom(8))
+            survey_id = ag_data.get_new_survey_id()
 
         sec_survey = self.sec_surveys[survey_type]
         survey_class = make_survey_class(sec_survey.groups[0],

amgut/lib/data_access/ag_data_access.py

@@ -19,6 +19,8 @@
 import bcrypt
 import numpy as np
 import pandas as pd
+import random
+import string
 
 from amgut.lib.data_access.sql_connection import TRN
 
@@ -540,10 +542,16 @@ def logParticipantSample(self, ag_login_id, barcode, sample_site,
                              participant_name, notes):
         with TRN:
             if sample_site is not None:
-                # Get survey id
+                # Get non timepoint specific survey IDs.
+                # As of this comment, a non timepoint specific survey is
+                # implicit, and currently limited to vioscreen FFQs
+                # We do not want to associate timepoint specific surveys
+                # with the wrong barcode
                 sql = """SELECT survey_id
                          FROM ag_login_surveys
-                         WHERE ag_login_id = %s AND participant_name = %s"""
+                         WHERE ag_login_id = %s
+                            AND participant_name = %s
+                            AND vioscreen_status is null"""
 
                 TRN.add(sql, (ag_login_id, participant_name))
                 survey_ids = TRN.execute_fetchindex()
@@ -634,6 +642,45 @@ def getHumanParticipants(self, ag_login_id):
             TRN.add(sql, [ag_login_id, 1])
             return TRN.execute_fetchflatten()
 
+    def associate_barcode_to_survey_id(self, ag_login_id, participant_name,
+                                       barcode, survey_id):
+        """Associate a barcode to an existing survey ID
+
+        Parameters
+        ----------
+        ag_login_id : str
+            A valid AG login ID
+        participant_name : str
+            The name of a participant associated with the login
+        barcode : str
+            A valid barcode associated with the login
+        survey_id : str
+            A valid survey ID
+        """
+        with TRN:
+            # first let's sanity check things
+            sql = """SELECT ag_login_id, participant_name, barcode
+                     FROM ag.ag_login_surveys
+                     JOIN ag.source_barcodes_surveys USING(survey_id)
+                     WHERE ag_login_id=%s
+                        AND participant_name=%s
+                        AND barcode=%s"""
+            TRN.add(sql, [ag_login_id, participant_name, barcode])
+            results = TRN.execute_fetchflatten()
+
+            if len(results) == 0:
+                raise ValueError("Unexpected name and ID relation")
+
+            sql = """INSERT INTO ag_login_surveys
+                     (ag_login_id, survey_id, participant_name)
+                     VALUES (%s, %s, %s)"""
+            TRN.add(sql, [ag_login_id, survey_id, participant_name])
+
+            sql = """INSERT INTO ag.source_barcodes_surveys
+                     (survey_id, barcode)
+                     VALUES (%s, %s)"""
+            TRN.add(sql, [survey_id, barcode])
+
     def updateVioscreenStatus(self, survey_id, status):
         with TRN:
             sql = """UPDATE ag_login_surveys
@@ -1102,6 +1149,35 @@ def get_participants_surveys(self, ag_login_id, participant_name,
                 raise ValueError("No survey IDs found!")
             return surveys
 
+    def get_new_survey_id(self):
+        """Return a new unique survey ID
+
+        Notes
+        -----
+        This is *NOT* atomic. At the creation of this method, it is not
+        possible to store a survey ID without first storing consent. That
+        would require a fairly large structural change. This method replaces
+        the existing non-atomic logic, with logic that is much safer but not
+        perfect.
+
+        Returns
+        -------
+        str
+            A unique survey ID
+        """
+        alpha = string.ascii_letters + string.digits
+        with TRN:
+            sql = """SELECT survey_id
+                     FROM ag.ag_login_surveys"""
+            TRN.add(sql)
+            existing = {i[0] for i in TRN.execute()[0]}
+
+            new_id = ''.join([random.choice(alpha) for i in range(16)])
+            while new_id in existing:
+                new_id = ''.join([random.choice(alpha) for i in range(16)])
+
+            return new_id
+
     def get_countries(self):
         """
         Returns

amgut/lib/data_access/test/test_ag_data_access.py

@@ -325,6 +325,16 @@ def test_getConsentNotPresent(self):
         with self.assertRaises(ValueError):
             self.ag_data.getConsent("42")
 
+    def test_get_new_survey_id(self):
+        with TRN:
+            sql = """SELECT survey_id FROM ag.ag_login_surveys"""
+            TRN.add(sql)
+            results = {i[0] for i in TRN.execute()[0]}
+
+        for i in range(100):
+            new_id = self.ag_data.get_new_survey_id()
+            self.assertNotIn(new_id, results)
+
     def test_logParticipantSample_badinfo(self):
         # bad ag_login_id
         with self.assertRaises(ValueError):
@@ -333,6 +343,79 @@ def test_logParticipantSample_badinfo(self):
                 'stool', None, datetime.date(2015, 9, 27),
                 datetime.time(15, 54), 'BADNAME', '')
 
+    @rollback
+    def test_associate_barcode_to_survey_id(self):
+        name = 'Name - öV2NA"+u+$'
+        id_ = '1835e434-b4a4-4f0d-a781-25ba54070c0b'
+        barcode = '000033139'
+
+        with TRN:
+            self.ag_data.associate_barcode_to_survey_id(id_, name, barcode,
+                                                        'xyz')
+            self.ag_data.associate_barcode_to_survey_id(id_, name, barcode,
+                                                        'yzx')
+            self.ag_data.associate_barcode_to_survey_id(id_, name, barcode,
+                                                        'foo')
+            sql = """SELECT survey_id
+                     FROM ag.source_barcodes_surveys
+                     WHERE barcode = %s"""
+
+            TRN.add(sql, [barcode])
+            obs = set(TRN.execute_fetchflatten())
+            exp = {'xyz', 'yzx', 'foo'}
+            self.assertTrue(exp.issubset(obs))
+
+        with self.assertRaises(ValueError):
+            self.ag_data.associate_barcode_to_survey_id(id_, name + 'foo',
+                                                        barcode, 'xyz')
+
+        with self.assertRaises(ValueError):
+            self.ag_data.associate_barcode_to_survey_id(id_, name,
+                                                        '000004216', 'xyz')
+
+    @rollback
+    def test_logParticipantSample_avoid_vios(self):
+        participant_name = 'Name - öV2NA"+u+$'
+        ag_login_id = '1835e434-b4a4-4f0d-a781-25ba54070c0b'
+        barcode = '000033139'
+
+        a = self.ag_data.get_new_survey_id()
+        b = 'not a vios'
+
+        self.ag_data.associate_barcode_to_survey_id(ag_login_id,
+                                                    participant_name,
+                                                    barcode, a)
+
+        with TRN:
+            sql = """INSERT INTO ag_login_surveys
+                     (ag_login_id, survey_id, participant_name)
+                     VALUES (%s, %s, %s)"""
+            TRN.add(sql, [ag_login_id, b, participant_name])
+
+        self.ag_data.updateVioscreenStatus(a, 0)
+
+        with TRN:
+            sql = """SELECT survey_id FROM ag.source_barcodes_surveys
+                     WHERE barcode = %s"""
+            TRN.add(sql, [barcode])
+            obs = set(TRN.execute_fetchflatten())
+            self.assertEqual(len(obs), 2)
+            self.assertTrue(a in obs)
+            self.assertFalse(b in obs)
+
+        self.ag_data.logParticipantSample(
+            ag_login_id, barcode, 'Stool', None, datetime.date(2015, 9, 27),
+            datetime.time(15, 54), participant_name, '')
+
+        with TRN:
+            sql = """SELECT survey_id FROM ag.source_barcodes_surveys
+                     WHERE barcode = %s"""
+            TRN.add(sql, [barcode])
+            obs = set(TRN.execute_fetchflatten())
+            self.assertEqual(len(obs), 3)
+            self.assertTrue(a in obs)
+            self.assertTrue(b in obs)
+
     @rollback
     def test_logParticipantSample_tomultiplesurveys(self):
         ag_login_id = '5a10ea3e-9c7f-4ec3-9e96-3dc42e896668'

amgut/lib/data_access/test/test_survey.py

@@ -245,7 +245,7 @@ def insert_data(self):
         c = ascii_letters + '1234567890'
         notes_test = ''.join([choice(c) for i in range(40)])
 
-        survey_id = '817ff95701f4dd10'
+        survey_id = ag_data.get_new_survey_id()
         survey = Survey(2)
         consent = {
             'login_id': 'eba20873-b7db-33cc-e040-8a80115d392c',

amgut/lib/locale_data/english_gut.py

@@ -962,6 +962,7 @@
 _HUMAN_SURVEY_COMPLETED = {
     'AVAILABLE_SURVEYS': 'Below are a few additional surveys that you may be interested in completing. There is no requirement to take these surveys, and your decision does not affect your involvement in the project in any way.',
     'COMPLETED_HEADER': 'Congratulations!',
+    'COMPLETED_SAMPLE_ASSIGNED_HEADER': 'Thank you for logging your sample!',
     'COMPLETED_TEXT': 'You are now an enrolled participant in the %(PROJECT_TITLE)s! As a reminder, you still need to associate your sample(s) with the survey to complete the process. If your sample(s) are not associated with a survey, we will not be able to process them.' % media_locale,
     'SURVEY_ASD': '<h3 style="text-align: center"><a href="%s" target="_blank">ASD-Cohort survey</a></h3><a href="http://www.anl.gov/contributors/jack-gilbert">Dr. Jack Gilbert</a> is exploring the relationship between gut dysbiosis and Autism Spectrum Disorders, and in conjunction with the {0}, we started an ASD-Cohort study. This additional survey contains questions specific to that cohort, but it is open to any participant to take if they so choose.'.format(AMGUT_CONFIG.project_name),
     'SURVEY_VIOSCREEN': '<h3 style="text-align: center"><a href="%s">Dietary Survey</a></h3>The {0} and its sister projects are very interested in diet. If you\'d like to provide additional detail about your diet, please click above to take a detailed diet survey (known as an Food Frequency Questionnaire). This is a validated FFQ, and is the one used by the Mayo Clinic.'.format(AMGUT_CONFIG.project_name),

amgut/templates/human_sample_specific_survey.html

@@ -0,0 +1,20 @@
+{% extends sitebase.html %}
+{% block content %}
+{% from amgut import text_locale, media_locale %}
+{% set tl = text_locale['human_survey_completed.html'] %}
+<h2>{% raw tl['COMPLETED_SAMPLE_ASSIGNED_HEADER'] %}</h2>
+<div style="text-align: left; padding-left: 10px; padding-right: 10px">
+<p>{% raw tl['AVAILABLE_SURVEYS'] %}</p>
+
+{% for payload in surveys %}
+    <p>{% raw payload %}</p>
+{% end %}
+</div>
+<form action='{% raw media_locale["SITEBASE"] %}/authed/human_survey_completed/' id="human_survey_completed" method="POST">
+    <input type="hidden" name="go_home" value="Done">
+    <input type="submit" value="Back to portal"></td>
+</form>
+<br>
+<br/>
+{% end %}
+

amgut/webserver.py

@@ -30,6 +30,7 @@
 from amgut.handlers.human_survey_completed import HumanSurveyCompletedHandler
 from amgut.handlers.vioscreen import VioscreenPassthroughHandler
 from amgut.handlers.add_sample import (AddHumanSampleHandler,
+                                       AddHumanFFQHandler,
                                        AddGeneralSampleHandler,
                                        AddAnimalSampleHandler)
 from amgut.handlers.new_participant import NewParticipantHandler
@@ -88,6 +89,7 @@ def __init__(self):
              PersonalMicrobiomeOverviewHandler),
             (r"/authed/portal/", PortalHandler),
             (r"/authed/add_sample_human/", AddHumanSampleHandler),
+            (r"/authed/add_sample_human_ffq/", AddHumanFFQHandler),
             (r"/authed/add_sample_animal/", AddAnimalSampleHandler),
             (r"/authed/add_sample_general/", AddGeneralSampleHandler),
             (r"/authed/change_password/", ChangePasswordHandler),