diff --git a/requirements.txt b/requirements.txt
index 67644e195dd3578eaeba9c357afff56d394170f0..50cf9ab36269228d76171803b72a00b358c0eb07 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,4 +12,5 @@ nexmo
django-excel==0.0.9
pyexcel-xls==0.5.0
pyexcel==0.5.3
+pycurl==7.43.0
diff --git a/smash/web/migrations/0049_auto_20170912_1438.py b/smash/web/migrations/0049_auto_20170912_1438.py
new file mode 100644
index 0000000000000000000000000000000000000000..bcca9e64b11c01fc021e79300bf4abb53e8c4f82
--- /dev/null
+++ b/smash/web/migrations/0049_auto_20170912_1438.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.7 on 2017-09-12 12:38
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0048_auto_20170911_1504'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='configurationitem',
+ name='name',
+ field=models.CharField(editable=False, max_length=255, verbose_name=b'Name'),
+ ),
+ ]
diff --git a/smash/web/migrations/0050_configurationitem_redcap_items.py b/smash/web/migrations/0050_configurationitem_redcap_items.py
new file mode 100644
index 0000000000000000000000000000000000000000..b7befcc120fd24a81201e66894516270be98781c
--- /dev/null
+++ b/smash/web/migrations/0050_configurationitem_redcap_items.py
@@ -0,0 +1,33 @@
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, \
+ REDCAP_BASE_URL_CONFIGURATION_TYPE
+
+
+def configuration_item_color_fields(apps, schema_editor):
+ # We can't import the ConfigurationItem model directly as it may be a newer
+ # version than this migration expects. We use the historical version.
+ ConfigurationItem = apps.get_model("web", "ConfigurationItem")
+ cancelled_appointment_color = ConfigurationItem.objects.create()
+ cancelled_appointment_color.type = REDCAP_TOKEN_CONFIGURATION_TYPE
+ cancelled_appointment_color.value = ""
+ cancelled_appointment_color.name = "API Token for RED Cap integration"
+ cancelled_appointment_color.save()
+
+ cancelled_appointment_color = ConfigurationItem.objects.create()
+ cancelled_appointment_color.type = REDCAP_BASE_URL_CONFIGURATION_TYPE
+ cancelled_appointment_color.value = ""
+ cancelled_appointment_color.name = "Base url of RED Cap (ie 'https://pd-redcap.uni.lu/redcap/')"
+ cancelled_appointment_color.save()
+
+
+class Migration(migrations.Migration):
+ dependencies = [
+ ('web', '0049_auto_20170912_1438'),
+ ]
+
+ operations = [
+ migrations.RunPython(configuration_item_color_fields),
+ ]
diff --git a/smash/web/migrations/0051_missingsubject.py b/smash/web/migrations/0051_missingsubject.py
new file mode 100644
index 0000000000000000000000000000000000000000..ee2ac92ab67ef1aa342af2db28daf5759b5e5ea1
--- /dev/null
+++ b/smash/web/migrations/0051_missingsubject.py
@@ -0,0 +1,26 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.7 on 2017-09-12 14:54
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0050_configurationitem_redcap_items'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='MissingSubject',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('ignore', models.BooleanField(default=False, verbose_name=b'Ignore missing subject')),
+ ('redcap_id', models.CharField(blank=True, max_length=255, null=True, verbose_name=b'RED Cap id')),
+ ('redcap_url', models.CharField(blank=True, max_length=255, null=True, verbose_name=b'URL to RED Cap subject')),
+ ('subject', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='web.Subject', verbose_name=b'Subject')),
+ ],
+ ),
+ ]
diff --git a/smash/web/migrations/0052_auto_20170913_0943.py b/smash/web/migrations/0052_auto_20170913_0943.py
new file mode 100644
index 0000000000000000000000000000000000000000..851f4cccb60f063d88f3e5cf8bda22d63a8fee63
--- /dev/null
+++ b/smash/web/migrations/0052_auto_20170913_0943.py
@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.7 on 2017-09-13 07:43
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0051_missingsubject'),
+ ]
+
+ operations = [
+ migrations.CreateModel(
+ name='InconsistentField',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('name', models.CharField(max_length=255, verbose_name=b'Field name')),
+ ('smash_value', models.CharField(max_length=255, verbose_name=b'Smash value')),
+ ('redcap_value', models.CharField(max_length=255, verbose_name=b'RED Cap value')),
+ ],
+ ),
+ migrations.CreateModel(
+ name='InconsistentSubject',
+ fields=[
+ ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+ ('ignore', models.BooleanField(default=False, verbose_name=b'Ignore missing subject')),
+ ('redcap_url', models.CharField(blank=True, max_length=255, null=True, verbose_name=b'URL to RED Cap subject')),
+ ('subject', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='web.Subject', verbose_name=b'Subject')),
+ ],
+ ),
+ migrations.AddField(
+ model_name='inconsistentfield',
+ name='inconsistent_subject',
+ field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='web.InconsistentSubject', verbose_name=b'Invalid fields'),
+ ),
+ ]
diff --git a/smash/web/migrations/0053_auto_20170913_0948.py b/smash/web/migrations/0053_auto_20170913_0948.py
new file mode 100644
index 0000000000000000000000000000000000000000..83284054ea9e7aaa6df6c66e389e86e107d3e3aa
--- /dev/null
+++ b/smash/web/migrations/0053_auto_20170913_0948.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.7 on 2017-09-13 07:48
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0052_auto_20170913_0943'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='subject',
+ name='nd_number',
+ field=models.CharField(blank=True, max_length=25, verbose_name=b'ND number'),
+ ),
+ ]
diff --git a/smash/web/models/__init__.py b/smash/web/models/__init__.py
index 1ec7eb07a74595218e24e585fec0c3724378db43..3b9f8e50c878e0764d4ff6a7bb5c288ca933b56c 100644
--- a/smash/web/models/__init__.py
+++ b/smash/web/models/__init__.py
@@ -21,6 +21,8 @@ from language import Language
from subject import Subject
from contact_attempt import ContactAttempt
from mail_template import MailTemplate
+from missing_subject import MissingSubject
+from inconsistent_subject import InconsistentSubject, InconsistentField
def get_current_year():
@@ -28,4 +30,5 @@ def get_current_year():
__all__ = [FlyingTeam, Appointment, AppointmentType, Availability, Holiday, Item, Language, Location, Room, Subject,
- Visit, Worker, ContactAttempt, ConfigurationItem, MailTemplate, AppointmentTypeLink]
+ Visit, Worker, ContactAttempt, ConfigurationItem, MailTemplate, AppointmentTypeLink, MissingSubject,
+ InconsistentSubject, InconsistentField]
diff --git a/smash/web/models/configuration_item.py b/smash/web/models/configuration_item.py
index 0129315ae6f6b1286471ba903db2b447035bcdd2..37db0488bb25d9b370e567f3acc5445d7ebe2a8e 100644
--- a/smash/web/models/configuration_item.py
+++ b/smash/web/models/configuration_item.py
@@ -12,7 +12,7 @@ class ConfigurationItem(models.Model):
verbose_name='Type',
editable=False
)
- name = models.CharField(max_length=50,
+ name = models.CharField(max_length=255,
verbose_name='Name',
editable=False
)
diff --git a/smash/web/models/constants.py b/smash/web/models/constants.py
index 0ce288687e46156dd99ede9f0d1c76c2610ca193..2dfee4e2c98362f30a49e5f2ac982796b313827a 100644
--- a/smash/web/models/constants.py
+++ b/smash/web/models/constants.py
@@ -71,3 +71,6 @@ WEEKDAY_CHOICES = (
(SATURDAY_AS_DAY_OF_WEEK, 'SATURDAY'),
(SUNDAY_AS_DAY_OF_WEEK, 'SUNDAY'),
)
+
+REDCAP_TOKEN_CONFIGURATION_TYPE = "REDCAP_TOKEN_CONFIGURATION_TYPE"
+REDCAP_BASE_URL_CONFIGURATION_TYPE = "REDCAP_BASE_URL_CONFIGURATION_TYPE"
diff --git a/smash/web/models/inconsistent_subject.py b/smash/web/models/inconsistent_subject.py
new file mode 100644
index 0000000000000000000000000000000000000000..590388fd37b3835fa8adfe6deab63ab459575334
--- /dev/null
+++ b/smash/web/models/inconsistent_subject.py
@@ -0,0 +1,78 @@
+# coding=utf-8
+import logging
+from django.db import models
+
+logger = logging.getLogger(__name__)
+
+
+class InconsistentField(models.Model):
+ name = models.CharField(max_length=255,
+ verbose_name='Field name',
+ null=False,
+ blank=False
+ )
+ smash_value = models.CharField(max_length=255,
+ verbose_name='Smash value'
+ )
+ redcap_value = models.CharField(max_length=255,
+ verbose_name='RED Cap value'
+ )
+ inconsistent_subject = models.ForeignKey("web.InconsistentSubject",
+ verbose_name='Invalid fields',
+ )
+
+ @staticmethod
+ def create(name, smash_value, redcap_value):
+ result = InconsistentField()
+ result.name = name
+ result.smash_value = smash_value
+ if result.smash_value is None:
+ result.smash_value = "[None]"
+ result.redcap_value = redcap_value
+ if result.redcap_value is None:
+ result.redcap_value = "[None]"
+ return result
+
+ def __str__(self):
+ return self.name + ": " + self.smash_value + "; RED Cap: " + self.redcap_value
+
+ def __unicode__(self):
+ return self.name + ": " + self.smash_value + "; RED Cap: " + self.redcap_value
+
+
+class InconsistentSubject(models.Model):
+ class Meta:
+ app_label = 'web'
+
+ ignore = models.BooleanField(
+ default=False,
+ verbose_name='Ignore missing subject'
+ )
+
+ subject = models.ForeignKey("web.Subject",
+ verbose_name='Subject',
+ null=True,
+ blank=True
+ )
+
+ redcap_url = models.CharField(max_length=255,
+ verbose_name='URL to RED Cap subject',
+ null=True,
+ blank=True
+ )
+
+ @staticmethod
+ def create(smash_subject, url=None, fields=None):
+ if fields is None:
+ fields = []
+ result = InconsistentSubject()
+ result.subject = smash_subject
+ result.redcap_url = url
+ result.fields = fields
+ return result
+
+ def __str__(self):
+ return "Subject: " + str(self.subject)
+
+ def __unicode__(self):
+ return "Subject: " + unicode(self.subject)
diff --git a/smash/web/models/missing_subject.py b/smash/web/models/missing_subject.py
new file mode 100644
index 0000000000000000000000000000000000000000..ff7353bbfec9910de716a47575fc90a9d0466782
--- /dev/null
+++ b/smash/web/models/missing_subject.py
@@ -0,0 +1,48 @@
+# coding=utf-8
+from django.db import models
+
+
+class MissingSubject(models.Model):
+ class Meta:
+ app_label = 'web'
+
+ ignore = models.BooleanField(
+ default=False,
+ verbose_name='Ignore missing subject'
+ )
+
+ subject = models.ForeignKey("web.Subject",
+ verbose_name='Subject',
+ null=True,
+ blank=True
+ )
+
+ redcap_id = models.CharField(max_length=255,
+ verbose_name='RED Cap id',
+ null=True,
+ blank=True
+ )
+ redcap_url = models.CharField(max_length=255,
+ verbose_name='URL to RED Cap subject',
+ null=True,
+ blank=True
+ )
+
+ @staticmethod
+ def create(red_cap_subject=None, smash_subject=None, url=None):
+ result = MissingSubject()
+ if red_cap_subject is not None:
+ result.redcap_id = red_cap_subject.nd_number
+ result.subject = smash_subject
+ result.redcap_url = url
+ return result
+
+ def __str__(self):
+ if self.subject is not None:
+ return "Subject: " + str(self.subject)
+ return "RED Cap subject: " + self.redcap_id
+
+ def __unicode__(self):
+ if self.subject is not None:
+ return "Subject: " + str(self.subject)
+ return "RED Cap subject: " + self.redcap_id
diff --git a/smash/web/models/subject.py b/smash/web/models/subject.py
index 38c7470047c8202dd6d80def640c27dd6d95e578..b67ff306635512895eaf7cd398577166c9568332 100644
--- a/smash/web/models/subject.py
+++ b/smash/web/models/subject.py
@@ -118,7 +118,7 @@ class Subject(models.Model):
unique=True,
verbose_name='Screening number', blank=False, null=False
)
- nd_number = models.CharField(max_length=6,
+ nd_number = models.CharField(max_length=25,
blank=True,
verbose_name='ND number'
)
diff --git a/smash/web/redcap_connector.py b/smash/web/redcap_connector.py
new file mode 100644
index 0000000000000000000000000000000000000000..586bd701d372aedee03c5340611d20ef5c589c2d
--- /dev/null
+++ b/smash/web/redcap_connector.py
@@ -0,0 +1,256 @@
+# coding=utf-8
+import logging
+import pycurl, cStringIO
+import certifi
+import json
+
+from web.models.missing_subject import MissingSubject
+from web.models.inconsistent_subject import InconsistentField, InconsistentSubject
+
+from web.models import ConfigurationItem, Subject, Language
+
+from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, \
+ REDCAP_BASE_URL_CONFIGURATION_TYPE, SEX_CHOICES_MALE, SEX_CHOICES_FEMALE
+
+RED_CAP_LANGUAGE_4_FIELD = 'dm_language_4'
+
+RED_CAP_LANGUAGE_3_FIELD = 'dm_language_3'
+
+RED_CAP_LANGUAGE_2_FIELD = 'dm_language_2'
+
+RED_CAP_LANGUAGE_1_FIELD = 'dm_language_1'
+
+RED_CAP_MPOWER_ID_FIELD = 'dm_mpowerid'
+
+RED_CAP_DEAD_FIELD = 'dm_death'
+
+RED_CAP_SEX_FIELD = 'cdisc_dm_sex'
+
+RED_CAP_DATE_BORN_FIELD = 'cdisc_dm_brthdtc'
+
+RED_CAP_ND_NUMBER_FIELD = 'cdisc_dm_usubjd'
+
+logger = logging.getLogger(__name__)
+
+
+class RedcapSubject(object):
+ url = None
+ nd_number = None
+ date_born = None
+ sex = None
+ dead = None
+ languages = None
+ mpower_id = None
+
+ def __init__(self):
+ self.languages = []
+
+ def add_language(self, language):
+ if language is not None:
+ self.languages.append(language)
+
+
+class RedcapConnector(object):
+ def __init__(self):
+ self.token = None
+ self.base_url = None
+ items = ConfigurationItem.objects.filter(type=REDCAP_TOKEN_CONFIGURATION_TYPE)
+ if len(items) > 0:
+ if items[0].value:
+ self.token = items[0].value
+ items = ConfigurationItem.objects.filter(type=REDCAP_BASE_URL_CONFIGURATION_TYPE)
+ if len(items) > 0:
+ if items[0].value:
+ self.base_url = items[0].value
+ self.language_by_name = {}
+ languages = Language.objects.all()
+ for language in languages:
+ self.language_by_name[language.name.lower()] = language
+
+ def find_missing(self):
+ pid = self.get_project_id()
+ redcap_version = self.get_redcap_version()
+
+ red_cap_subjects = self.get_red_cap_subjects()
+ red_cap_subject_by_nd = {}
+ for subject in red_cap_subjects:
+ red_cap_subject_by_nd[subject.nd_number] = subject
+
+ smash_subjects = Subject.objects.exclude(nd_number='')
+ smash_subject_by_nd = {}
+ for subject in smash_subjects:
+ smash_subject_by_nd[subject.nd_number] = subject
+
+ result = []
+ for subject in red_cap_subjects:
+ if getattr(smash_subject_by_nd, subject.nd_number, None) is None:
+ url = self.create_redcap_link(pid, redcap_version, subject)
+ result.append(MissingSubject.create(red_cap_subject=subject, smash_subject=None, url=url))
+
+ for subject in smash_subjects:
+ if getattr(red_cap_subject_by_nd, subject.nd_number, None) is None:
+ result.append(MissingSubject.create(red_cap_subject=None, smash_subject=subject))
+
+ return result
+
+ def find_inconsistent(self):
+ pid = self.get_project_id()
+ redcap_version = self.get_redcap_version()
+
+ red_cap_subjects = self.get_red_cap_subjects()
+ red_cap_subject_by_nd = {}
+ for subject in red_cap_subjects:
+ red_cap_subject_by_nd[subject.nd_number] = subject
+
+ smash_subjects = Subject.objects.exclude(nd_number='')
+
+ result = []
+ for subject in smash_subjects:
+ red_cap_subject = red_cap_subject_by_nd.get(subject.nd_number)
+ if red_cap_subject is not None:
+ url = self.create_redcap_link(pid, redcap_version, subject)
+ subject = self.create_inconsistency_subject(red_cap_subject, subject, url)
+ if subject is not None:
+ result.append(subject)
+
+ return result
+
+ @staticmethod
+ def create_inconsistency_subject(red_cap_subject, subject, url):
+ fields = []
+ if subject.sex != red_cap_subject.sex:
+ field = InconsistentField.create("sex", subject.sex, red_cap_subject.sex)
+ fields.append(field)
+ subject_date_born = ""
+ if subject.date_born is not None:
+ subject_date_born = subject.date_born.strftime('%Y-%m-%d')
+ redcap_subject_date_born = red_cap_subject.date_born
+ if redcap_subject_date_born is None:
+ redcap_subject_date_born = ""
+ if len(redcap_subject_date_born) > 10:
+ redcap_subject_date_born = redcap_subject_date_born[:10]
+ if subject_date_born != redcap_subject_date_born:
+ field = InconsistentField.create("date of birth", subject_date_born, redcap_subject_date_born)
+ fields.append(field)
+ if subject.dead != red_cap_subject.dead:
+ field = InconsistentField.create("dead", str(subject.dead), str(red_cap_subject.dead))
+ fields.append(field)
+ if subject.mpower_id != red_cap_subject.mpower_id:
+ field = InconsistentField.create("mpower id", subject.mpower_id, red_cap_subject.mpower_id)
+ fields.append(field)
+ missing_language = False
+ if len(red_cap_subject.languages) < 4:
+ for language in subject.languages.all():
+ if language not in red_cap_subject.languages:
+ missing_language = True
+ for language in red_cap_subject.languages:
+ if language not in subject.languages.all():
+ missing_language = True
+ if missing_language:
+ subject_languages = ""
+ for language in subject.languages.all():
+ subject_languages += language.name + ", "
+ red_cap_subject_languages = ""
+ for language in red_cap_subject.languages:
+ red_cap_subject_languages += language.name + ", "
+ field = InconsistentField.create("languages", subject_languages, red_cap_subject_languages)
+ fields.append(field)
+ result = None
+ if len(fields) > 0:
+ result = InconsistentSubject.create(smash_subject=subject, url=url, fields=fields)
+ return result
+
+ def create_redcap_link(self, pid, redcap_version, subject):
+ return self.base_url + "/redcap_v" + redcap_version + "/DataEntry/index.php?pid=" + pid + "&id=" + \
+ subject.nd_number + "&page=demographics"
+
+ def get_red_cap_subjects(self):
+ query_data = {
+ 'token': self.token,
+ 'content': 'record',
+ 'format': 'json',
+ 'type': 'flat',
+ 'fields[0]': RED_CAP_DATE_BORN_FIELD,
+ 'fields[1]': RED_CAP_SEX_FIELD,
+ 'fields[2]': RED_CAP_ND_NUMBER_FIELD,
+ 'fields[3]': RED_CAP_DEAD_FIELD,
+ 'fields[4]': RED_CAP_LANGUAGE_1_FIELD,
+ 'fields[5]': RED_CAP_LANGUAGE_2_FIELD,
+ 'fields[6]': RED_CAP_LANGUAGE_3_FIELD,
+ 'fields[7]': RED_CAP_LANGUAGE_4_FIELD,
+ 'fields[8]': RED_CAP_MPOWER_ID_FIELD,
+ 'rawOrLabel': 'label',
+ 'rawOrLabelHeaders': 'raw',
+ 'exportCheckboxLabel': 'false',
+ 'exportSurveyFields': 'false',
+ 'exportDataAccessGroups': 'false',
+ 'returnFormat': 'json'
+ }
+ data = self.execute_query(query_data)
+ result = []
+ for row in data:
+ redcap_subject = RedcapSubject()
+ redcap_subject.nd_number = row[RED_CAP_ND_NUMBER_FIELD]
+ redcap_subject.date_born = row[RED_CAP_DATE_BORN_FIELD]
+ redcap_subject.sex = row[RED_CAP_SEX_FIELD]
+ redcap_subject.dead = (row[RED_CAP_DEAD_FIELD].lower() == "yes")
+ redcap_subject.mpower_id = row[RED_CAP_MPOWER_ID_FIELD]
+ if row[RED_CAP_LANGUAGE_1_FIELD]:
+ redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_1_FIELD]))
+ if row[RED_CAP_LANGUAGE_2_FIELD]:
+ redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_2_FIELD]))
+ if row[RED_CAP_LANGUAGE_3_FIELD]:
+ redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_3_FIELD]))
+ if row[RED_CAP_LANGUAGE_4_FIELD]:
+ redcap_subject.add_language(self.get_language(row[RED_CAP_LANGUAGE_4_FIELD]))
+
+ result.append(redcap_subject)
+ return result
+
+ def get_language(self, name):
+ language = self.language_by_name.get(name.lower())
+ if language is None:
+ logger.warn("Unknown language: " + name)
+ return language
+
+ def execute_query(self, query_data, is_json=True):
+ buf = cStringIO.StringIO()
+ curl_connection = pycurl.Curl()
+ curl_connection.setopt(pycurl.CAINFO, certifi.where())
+ curl_connection.setopt(curl_connection.URL, self.base_url + "/api/")
+ curl_connection.setopt(curl_connection.HTTPPOST, query_data.items())
+ curl_connection.setopt(curl_connection.WRITEFUNCTION, buf.write)
+ curl_connection.perform()
+ curl_connection.close()
+ if is_json:
+ data = json.loads(buf.getvalue())
+ else:
+ data = buf.getvalue()
+ buf.close()
+ return data
+
+ def get_project_id(self):
+ query_data = {
+ 'token': self.token,
+ 'content': 'project',
+ 'format': 'json',
+ 'returnFormat': 'json'
+ }
+ data = self.execute_query(query_data)
+ return data['project_id']
+
+ def get_redcap_version(self):
+ query_data = {
+ 'token': self.token,
+ 'content': 'version'
+ }
+ data = self.execute_query(query_data, is_json=False)
+ return data
+
+ def is_valid(self):
+ if not self.token:
+ return False
+ if not self.base_url:
+ return False
+
+ return True
diff --git a/smash/web/static/AdminLTE/js/bootstrap.min.js b/smash/web/static/AdminLTE/js/bootstrap.min.js
index e79c065134f2cfcf3e44a59cffcb5f090232f98f..0a9ef01e8853e28ef6ca05335601c4ec2f3d36fd 100755
--- a/smash/web/static/AdminLTE/js/bootstrap.min.js
+++ b/smash/web/static/AdminLTE/js/bootstrap.min.js
@@ -4,4 +4,4 @@
* Licensed under the MIT license
*/
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+ d.parent(".dropdown-menu").length&&(d=d.closest("li.dropdown").addClass("active")),d.trigger("activate.bs.scrollspy")},b.prototype.clear=function(){a(this.selector).parentsUntil(this.options.target,".active").removeClass("active")};var d=a.fn.scrollspy;a.fn.scrollspy=c,a.fn.scrollspy.Constructor=b,a.fn.scrollspy.noConflict=function(){return a.fn.scrollspy=d,this},a(window).on("load.bs.scrollspy.data-api",function(){a('[data-spy="scroll"]').each(function(){var b=a(this);c.call(b,b.data())})})}(jQuery),+function(a){"use strict";function b(b){return this.each(function(){var d=a(this),e=d.data("bs.tab");e||d.data("bs.tab",e=new c(this)),"string"==typeof b&&e[b]()})}var c=function(b){this.element=a(b)};c.VERSION="3.3.6",c.TRANSITION_DURATION=150,c.prototype.show=function(){var b=this.element,c=b.closest("ul:not(.dropdown-menu)"),d=b.data("target");if(d||(d=b.attr("href"),d=d&&d.replace(/.*(?=#[^\s]*$)/,"")),!b.parent("li").hasClass("active")){var e=c.find(".active:last a"),f=a.Event("hide.bs.tab",{relatedTarget:b[0]}),g=a.Event("show.bs.tab",{relatedTarget:e[0]});if(e.trigger(f),b.trigger(g),!g.isDefaultPrevented()&&!f.isDefaultPrevented()){var h=a(d);this.activate(b.closest("li"),c),this.activate(h,h.parent(),function(){e.trigger({type:"hidden.bs.tab",relatedTarget:b[0]}),b.trigger({type:"shown.bs.tab",relatedTarget:e[0]})})}}},c.prototype.activate=function(b,d,e){function f(){g.removeClass("active").find("> .dropdown-menu > .active").removeClass("active").end().find('[data-toggle="tab"]').attr("aria-expanded",!1),b.addClass("active").find('[data-toggle="tab"]').attr("aria-expanded",!0),h?(b[0].offsetWidth,b.addClass("in")):b.removeClass("fade"),b.parent(".dropdown-menu").length&&b.closest("li.dropdown").addClass("active").end().find('[data-toggle="tab"]').attr("aria-expanded",!0),e&&e()}var g=d.find("> .active"),h=e&&a.support.transition&&(g.length&&g.hasClass("fade")||!!d.find("> .fade").length);g.length&&h?g.one("bsTransitionEnd",f).emulateTransitionEnd(c.TRANSITION_DURATION):f(),g.removeClass("in")};var d=a.fn.tab;a.fn.tab=b,a.fn.tab.Constructor=c,a.fn.tab.noConflict=function(){return a.fn.tab=d,this};var e=function(c){c.preventDefault(),b.call(a(this),"show")};a(document).on("click.bs.tab.data-api",'[data-toggle="tab"]',e).on("click.bs.tab.data-api",'[data-toggle="pill"]',e)}(jQuery),+function(a){"use strict";function b(b){return this.each(function(){var d=a(this),e=d.data("bs.affix"),f="object"==typeof b&&b;e||d.data("bs.affix",e=new c(this,f)),"string"==typeof b&&e[b]()})}var c=function(b,d){this.options=a.extend({},c.DEFAULTS,d),this.$target=a(this.options.target).on("scroll.bs.affix.data-api",a.proxy(this.checkPosition,this)).on("click.bs.affix.data-api",a.proxy(this.checkPositionWithEventLoop,this)),this.$element=a(b),this.affixed=null,this.unpin=null,this.pinnedOffset=null,this.checkPosition()};c.VERSION="3.3.6",c.RESET="affix affix-top affix-bottom",c.DEFAULTS={offset:0,target:window},c.prototype.getState=function(a,b,c,d){var e=this.$target.scrollTop(),f=this.$element.offset(),g=this.$target.height();if(null!=c&&"top"==this.affixed)return c>e?"top":!1;if("bottom"==this.affixed)return null!=c?e+this.unpin<=f.top?!1:"bottom":a-d>=e+g?!1:"bottom";var h=null==this.affixed,i=h?e:f.top,j=h?g:b;return null!=c&&c>=e?"top":null!=d&&i+j>=a-d?"bottom":!1},c.prototype.getPinnedOffset=function(){if(this.pinnedOffset)return this.pinnedOffset;this.$element.removeClass(c.RESET).addClass("affix");var a=this.$target.scrollTop(),b=this.$element.offset();return this.pinnedOffset=b.top-a},c.prototype.checkPositionWithEventLoop=function(){setTimeout(a.proxy(this.checkPosition,this),1)},c.prototype.checkPosition=function(){if(this.$element.is(":visible")){var b=this.$element.height(),d=this.options.offset,e=d.top,f=d.bottom,g=Math.max(a(document).height(),a(document.body).height());"object"!=typeof d&&(f=e=d),"function"==typeof e&&(e=d.top(this.$element)),"function"==typeof f&&(f=d.bottom(this.$element));var h=this.getState(g,b,e,f);if(this.affixed!=h){null!=this.unpin&&this.$element.css("top","");var i="affix"+(h?"-"+h:""),j=a.Event(i+".bs.affix");if(this.$element.trigger(j),j.isDefaultPrevented())return;this.affixed=h,this.unpin="bottom"==h?this.getPinnedOffset():null,this.$element.removeClass(c.RESET).addClass(i).trigger(i.replace("affix","affixed")+".bs.affix")}"bottom"==h&&this.$element.offset({top:g-b-f})}};var d=a.fn.affix;a.fn.affix=b,a.fn.affix.Constructor=c,a.fn.affix.noConflict=function(){return a.fn.affix=d,this},a(window).on("load",function(){a('[data-spy="affix"]').each(function(){var c=a(this),d=c.data();d.offset=d.offset||{},null!=d.offsetBottom&&(d.offset.bottom=d.offsetBottom),null!=d.offsetTop&&(d.offset.top=d.offsetTop),b.call(c,d)})})}(jQuery);
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diff --git a/smash/web/tests/data/__init__.py b/smash/web/tests/data/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/smash/web/tests/functions.py b/smash/web/tests/functions.py
index 1918e847adc49fbdb271018bb25ed069f4645edc..734738861e371ffc57ecc3b0a1857bce53fa116b 100644
--- a/smash/web/tests/functions.py
+++ b/smash/web/tests/functions.py
@@ -3,6 +3,7 @@ import datetime
import os
from django.contrib.auth.models import User
+from web.redcap_connector import RedcapSubject
from web.models import Location, AppointmentType, Subject, Worker, Visit, Appointment, ConfigurationItem, Language, \
ContactAttempt, FlyingTeam
from web.models.constants import SEX_CHOICES_MALE, SUBJECT_TYPE_CHOICES_CONTROL, CONTACT_TYPES_PHONE
@@ -64,6 +65,12 @@ def create_subject(subject_id=1):
)
+def create_red_cap_subject():
+ result = RedcapSubject()
+ result.nd_number = "123"
+ return result
+
+
def create_user(username=None, password=None):
if username is None:
username = 'piotr'
diff --git a/smash/web/tests/models/__init__.py b/smash/web/tests/models/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/smash/web/tests/models/test_inconsistent_subject.py b/smash/web/tests/models/test_inconsistent_subject.py
new file mode 100644
index 0000000000000000000000000000000000000000..926314158302ac7bb18ed4900a7c2ba1fa0d5216
--- /dev/null
+++ b/smash/web/tests/models/test_inconsistent_subject.py
@@ -0,0 +1,19 @@
+from django.test import TestCase
+
+from web.models.inconsistent_subject import InconsistentSubject, InconsistentField
+from web.tests.functions import create_subject
+
+
+class InconsistentSubjectTests(TestCase):
+ def test_create_with_empty_data(self):
+ subject = create_subject()
+ inconsistent_subject = InconsistentSubject.create(subject)
+ self.assertIsNotNone(str(inconsistent_subject))
+ self.assertIsNotNone(unicode(inconsistent_subject))
+
+
+class InconsistentFieldTests(TestCase):
+ def test_create_with_empty_data(self):
+ inconsistent_field = InconsistentField.create("field name", None, None)
+ self.assertIsNotNone(str(inconsistent_field))
+ self.assertIsNotNone(unicode(inconsistent_field))
diff --git a/smash/web/tests/models/test_missing_subject.py b/smash/web/tests/models/test_missing_subject.py
new file mode 100644
index 0000000000000000000000000000000000000000..37a7f92459ec0ad09ae3ec06203f370712eb95d7
--- /dev/null
+++ b/smash/web/tests/models/test_missing_subject.py
@@ -0,0 +1,19 @@
+from django.test import TestCase
+
+from web.models.missing_subject import MissingSubject
+from web.tests.functions import create_subject, create_red_cap_subject
+
+
+class MissingSubjectTests(TestCase):
+ def test_create_with_empty_redcap_subject(self):
+ subject = create_subject()
+ missing_subject = MissingSubject.create(red_cap_subject=None, smash_subject=subject)
+ self.assertIsNotNone(str(missing_subject))
+ self.assertIsNotNone(unicode(missing_subject))
+
+ def test_create_with_empty_smash_subject(self):
+ red_cap_subject = create_red_cap_subject()
+ missing_subject = MissingSubject.create(red_cap_subject=red_cap_subject, smash_subject=None)
+ self.assertIsNotNone(str(missing_subject))
+ self.assertIsNotNone(unicode(missing_subject))
+
diff --git a/smash/web/tests/test_RedcapConnector.py b/smash/web/tests/test_RedcapConnector.py
new file mode 100644
index 0000000000000000000000000000000000000000..db5b57266dabca14b12fc0d2032956503661870b
--- /dev/null
+++ b/smash/web/tests/test_RedcapConnector.py
@@ -0,0 +1,149 @@
+# coding=utf-8
+
+import logging
+
+from django.test import TestCase
+
+from functions import create_subject
+from web.models import ConfigurationItem, Language
+from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, REDCAP_BASE_URL_CONFIGURATION_TYPE
+from web.redcap_connector import RedcapConnector, RedcapSubject
+from web.views.notifications import get_today_midnight_date
+
+logger = logging.getLogger(__name__)
+
+
+class TestRedcapConnector(TestCase):
+ def test_invalid_configuration(self):
+ redcap_connection = RedcapConnector()
+ self.assertFalse(redcap_connection.is_valid())
+
+ def test_valid_configuration(self):
+ self.prepare_test_redcap_connection()
+
+ redcap_connection = RedcapConnector()
+ self.assertTrue(redcap_connection.is_valid())
+
+ def test_get_invalid_connections(self):
+ self.prepare_test_redcap_connection()
+
+ redcap_connection = RedcapConnector()
+ data = redcap_connection.find_missing()
+ self.assertTrue(len(data) > 0)
+ missing_subject = data[0]
+ self.assertIsNone(missing_subject.subject)
+ self.assertIsNotNone(missing_subject.redcap_id)
+ self.assertIsNotNone(missing_subject.redcap_url)
+ self.assertFalse(missing_subject.ignore)
+
+ def test_get_invalid_connections_for_new_local(self):
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+ subject.nd_number = "123"
+ subject.save()
+
+ redcap_connection = RedcapConnector()
+ data = redcap_connection.find_missing()
+ self.assertTrue(len(data) > 0)
+
+ def test_get_inconsistent_data(self):
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+ # noinspection SpellCheckingInspection
+ subject.nd_number = 'NDtest_external'
+ subject.save()
+
+ redcap_connection = RedcapConnector()
+ data = redcap_connection.find_inconsistent()
+ self.assertTrue(len(data) > 0)
+ inconsistent_subject = data[0]
+ self.assertIsNotNone(inconsistent_subject.subject)
+ self.assertTrue(len(inconsistent_subject.fields))
+
+ def test_create_inconsistent_data_for_date_born(self):
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+
+ redcap_subject = self.create_redcap_subject_from_smash_subject(subject)
+ subject.date_born = get_today_midnight_date()
+
+ self.check_single_inconsistency(redcap_subject, subject)
+
+ def check_single_inconsistency(self, redcap_subject, subject):
+ redcap_connection = RedcapConnector()
+ result = redcap_connection.create_inconsistency_subject(redcap_subject, subject, "")
+ self.assertIsNotNone(result)
+ self.assertEqual(1, len(result.fields), "Invalid number of fields. Found: " + str(result.fields))
+
+ def test_create_inconsistent_data_for_dead(self):
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+
+ redcap_subject = self.create_redcap_subject_from_smash_subject(subject)
+ subject.dead = not subject.dead
+
+ self.check_single_inconsistency(redcap_subject, subject)
+
+ def test_create_inconsistent_data_for_language(self):
+ language = Language.objects.create(name="xx")
+ language.save()
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+
+ redcap_subject = self.create_redcap_subject_from_smash_subject(subject)
+ subject.languages.add(language)
+
+ self.check_single_inconsistency(redcap_subject, subject)
+
+ def test_create_inconsistent_data_for_language2(self):
+ language = Language.objects.create(name="xx")
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+
+ redcap_subject = self.create_redcap_subject_from_smash_subject(subject)
+ redcap_subject.add_language(language)
+
+ self.check_single_inconsistency(redcap_subject, subject)
+
+ def test_create_inconsistent_data_for_mpower_id(self):
+ self.prepare_test_redcap_connection()
+ subject = create_subject()
+
+ redcap_subject = self.create_redcap_subject_from_smash_subject(subject)
+ subject.mpower_id = "105"
+
+ self.check_single_inconsistency(redcap_subject, subject)
+
+ @staticmethod
+ def create_redcap_subject_from_smash_subject(subject):
+ redcap_subject = RedcapSubject()
+ for language in subject.languages.all():
+ redcap_subject.add_language(language)
+ redcap_subject.mpower_id = subject.mpower_id
+ redcap_subject.dead = subject.dead
+ redcap_subject.date_born = subject.date_born
+ redcap_subject.nd_number = subject.nd_number
+ redcap_subject.sex = subject.sex
+ return redcap_subject
+
+ @staticmethod
+ def prepare_test_redcap_connection():
+ Language.objects.create(name="Finnish").save()
+ Language.objects.create(name="Italian").save()
+ token_item = ConfigurationItem.objects.filter(type=REDCAP_TOKEN_CONFIGURATION_TYPE)[0]
+ # noinspection SpellCheckingInspection
+ token_item.value = "5C75EEC3DBDDA5218B6ACC0424B3F695"
+ token_item.save()
+ url_item = ConfigurationItem.objects.filter(type=REDCAP_BASE_URL_CONFIGURATION_TYPE)[0]
+ url_item.value = "https://luxparktest.org/redcap/"
+ url_item.save()
+
+ def test_get_language(self):
+ language = Language.objects.create(name="xx")
+ language.save()
+ self.prepare_test_redcap_connection()
+
+ redcap_connection = RedcapConnector()
+
+ self.assertIsNotNone(redcap_connection.get_language("xx"))
+ self.assertIsNone(redcap_connection.get_language("yy"))