From 3282d60d17f0ce8d6c3cebdfa786e8caca0d89a6 Mon Sep 17 00:00:00 2001
From: Megan Henning <meganhenning@flywheel.io>
Date: Wed, 10 May 2017 18:27:34 -0500
Subject: [PATCH] Ensure subject age is int
---
bin/database.py | 20 ++++++++++++-
raml/schemas/definitions/subject.json | 2 +-
.../python/test_containers.py | 29 +++++++++++++++++++
3 files changed, 49 insertions(+), 2 deletions(-)
diff --git a/bin/database.py b/bin/database.py
index 55126e04..497c20c1 100755
--- a/bin/database.py
+++ b/bin/database.py
@@ -19,7 +19,7 @@ from api.jobs.jobs import Job
from api.jobs import gears
from api.types import Origin
-CURRENT_DATABASE_VERSION = 27 # An int that is bumped when a new schema change is made
+CURRENT_DATABASE_VERSION = 28 # An int that is bumped when a new schema change is made
def get_db_version():
@@ -93,6 +93,7 @@ def process_cursor(cursor, closure):
# pool.close()
# pool.join()
+ logging.info('Proccessing {} items in cursor ...'.format(cursor.count()))
failed = False
for document in cursor:
@@ -990,6 +991,21 @@ def upgrade_to_27():
config.db.projects.update_one({'_id': p['_id']}, {'$set': {'template': template}})
storage.recalc_sessions_compliance(project_id=str(p['_id']))
+def upgrade_to_28():
+ """
+ Fixes session.subject.age sometimes being a floating-point rather than integer.
+ """
+
+ sessions = config.db.sessions.find({'subject.age': {'$type': 'double'}})
+ logging.info('Fixing {} subjects with age stored as double ...'.format(sessions.count()))
+ for x in sessions:
+ try:
+ int_age = int(x['subject']['age'])
+ except:
+ int_age = None
+
+ config.db.sessions.update({'_id': x['_id']}, {'$set': {'subject.age': int_age}})
+
def upgrade_schema():
"""
@@ -1003,7 +1019,9 @@ def upgrade_schema():
while db_version < CURRENT_DATABASE_VERSION:
db_version += 1
upgrade_script = 'upgrade_to_'+str(db_version)
+ logging.info('Upgrading to version {} ...'.format(db_version))
globals()[upgrade_script]()
+ logging.info('Upgrade to version {} complete.'.format(db_version))
except KeyError as e:
logging.exception('Attempted to upgrade using script that does not exist: {}'.format(e))
sys.exit(1)
diff --git a/raml/schemas/definitions/subject.json b/raml/schemas/definitions/subject.json
index a71d3aaa..7218d203 100644
--- a/raml/schemas/definitions/subject.json
+++ b/raml/schemas/definitions/subject.json
@@ -7,7 +7,7 @@
"firstname_hash": { "type": ["string", "null"] },
"lastname_hash": { "type": ["string", "null"] },
- "age": { "type": ["number", "null"] },
+ "age": { "type": ["integer", "null"] },
"sex": { "enum": ["male", "female", "other", "unknown", null] },
"race": { "enum": ["American Indian or Alaska Native", "Asian", "Native Hawaiian or Other Pacific Islander", "Black or African American", "White", "More Than One Race", "Unknown or Not Reported", null] },
"ethnicity": { "enum": ["Not Hispanic or Latino", "Hispanic or Latino", "Unknown or Not Reported", null] },
diff --git a/test/integration_tests/python/test_containers.py b/test/integration_tests/python/test_containers.py
index 9e61f029..05fb1f94 100644
--- a/test/integration_tests/python/test_containers.py
+++ b/test/integration_tests/python/test_containers.py
@@ -285,3 +285,32 @@ def test_put_container(data_builder, as_admin):
'subject': {'_id': '000000000000000000000000'}
})
assert r.ok
+
+def test_subject_age_must_be_int(data_builder, as_admin):
+ # Ensure subject age can only be set as int (and None)
+ # Found old data that had subject age stored as float
+
+ session = data_builder.create_session()
+
+ subject_age = 123.2
+
+ # Attempt to send age as float
+ r = as_admin.put('/sessions/' + session, json={
+ 'subject': {
+ 'age': subject_age
+ }
+ })
+ assert r.status_code == 400
+
+ subject_age = 123
+
+ # Ensure subject age set as int works correctly
+ r = as_admin.put('/sessions/' + session, json={
+ 'subject': {
+ 'age': subject_age
+ }
+ })
+ assert r.ok
+
+ r = as_admin.get('/sessions/' + session)
+ assert subject_age == r.json['subject']['age']
--
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