def get_vcf_comments(vcf_id):
"""Return all user comments in the following format:
{
"comments": {
"<row_key STRING>": [<comment_fields>, ...],
"<row_key STRING>": [...], ...
}
}
"""
def _row_key(comment, table):
cols = ['contig', 'position', 'reference', 'alternates', 'sample_name']
return ':'.join([str(comment[col]) for col in cols])
with tables(db.engine, 'user_comments') as (conn, user_comments):
cols = user_comments.c
stmt = select(cols.values()).where(cols.vcf_id == vcf_id)
results = conn.execute(stmt)
results_map = defaultdict(list)
for comment in (dict(c) for c in results):
row_key = _row_key(comment, user_comments)
comment['last_modified'] = to_epoch(comment['last_modified'])
comment['created'] = to_epoch(comment['created'])
comment = camelcase_dict(comment)
results_map[row_key].append(comment)
return {'comments': results_map}
def test_delete_with_out_of_date_timestamp(self):
comment = create_comment_with_text(self.run['id'], 'some text')
now = datetime.datetime.now()
r = self.delete('/api/runs/{}/comments/{}'.format(self.run['id'], comment['id']),
data={'lastModified': to_epoch(now)})
assert r.status_code == 409
assert 'out of date' in json.loads(r.data)['message']
def test_delete_comment(self):
comment = create_comment_with_text(self.run['id'], 'some text')
r = self.delete('/api/runs/{}/comments/{}'.format(self.run['id'], comment['id']),
data={'lastModified': to_epoch(comment['last_modified'])})
assert r.status_code == 200
assert json.loads(r.data)['id'] == comment['id']
r = self.get('/api/runs/{}/comments/{}'.format(self.run['id'], comment['id']))
assert r.status_code == 404
def _ensure_not_out_of_date(comment, last_modified):
"""Assert that the comment has the same last_modified time,
otherwise abort(409).
"""
current_time = to_epoch(comment['last_modified'])
if current_time != last_modified:
abort(409, message=('Comment id={} is out of date.'
.format(comment['id'])),
current_time=current_time)
def test_update_with_out_of_date_timestamp(self):
comment = create_comment_with_text(self.run["id"], "some text")
now = datetime.datetime.now()
r = self.put(
"/api/runs/{}/comments/{}".format(self.run["id"], comment["id"]),
data={"commentText": "blah", "lastModified": to_epoch(now)},
)
assert r.status_code == 409
assert "out of date" in json.loads(r.data)["message"]
def test_delete_comment(self):
comment = create_comment_with_text(self.run["id"], "some text")
r = self.delete(
"/api/runs/{}/comments/{}".format(self.run["id"], comment["id"]),
data={"lastModified": to_epoch(comment["last_modified"])},
)
assert r.status_code == 200
assert json.loads(r.data)["id"] == comment["id"]
r = self.get("/api/runs/{}/comments/{}".format(self.run["id"], comment["id"]))
assert r.status_code == 404
def test_update_comment(self):
new_text = 'NEW TEXT!'
new_author = 'NEW AUTHOR!'
comment = create_comment_with_text(self.run['id'], 'some text')
r = self.put('/api/runs/{}/comments/{}'.format(self.run['id'], comment['id']),
data={'commentText': new_text,
'last_modified': to_epoch(comment['last_modified'])})
assert r.status_code == 200
assert json.loads(r.data)['id'] == comment['id']
assert json.loads(r.data)['commentText'] == new_text
def test_update_comment(self):
new_text = "NEW TEXT!"
new_author = "NEW AUTHOR!"
comment = create_comment_with_text(self.run["id"], "some text")
r = self.put(
"/api/runs/{}/comments/{}".format(self.run["id"], comment["id"]),
data={
"commentText": new_text,
"authorName": new_author,
"last_modified": to_epoch(comment["last_modified"]),
},
)
assert r.status_code == 200
assert json.loads(r.data)["id"] == comment["id"]
assert json.loads(r.data)["commentText"] == new_text
assert json.loads(r.data)["authorName"] == new_author
def epochify_comments(comments):
"""Sets `lastModified` and `created` to be epoch time instead of iso8061."""
for c in comments:
c['lastModified'] = to_epoch(c['lastModified'])
c['created'] = to_epoch(c['created'])
return comments
def format(self, value):
return to_epoch(value)