def test_item_timestamps(app_client, load_test_data):
"""Test created and updated timestamps (common metadata)"""
test_item = load_test_data("test_item.json")
start_time = datetime.now(timezone.utc)
time.sleep(2)
# Confirm `created` timestamp
resp = app_client.post(f"/collections/{test_item['collection']}/items",
json=test_item)
item = resp.json()
created_dt = parse_datetime(item["properties"]["created"])
assert resp.status_code == 200
assert start_time < created_dt < datetime.now(timezone.utc)
time.sleep(2)
# Confirm `updated` timestamp
item["properties"]["proj:epsg"] = 4326
resp = app_client.put(f"/collections/{test_item['collection']}/items",
json=item)
assert resp.status_code == 200
updated_item = resp.json()
# Created shouldn't change on update
assert item["properties"]["created"] == updated_item["properties"][
"created"]
assert parse_datetime(updated_item["properties"]["updated"]) > created_dt
def end_date(self) -> Optional[datetime]:
values = self.datetime.split("/")
if len(values) == 1:
return parse_datetime(values[0])
if values[1] == "..":
return None
return parse_datetime(values[1])
def end_date(self) -> Optional[datetime]:
"""Extract the end date from the datetime string."""
if not self.datetime:
return
values = self.datetime.split("/")
if len(values) == 1:
return parse_datetime(values[0])
if values[1] == "..":
return None
return parse_datetime(values[1])
async def _run(self, ws):
api = StreamingApi(ws, self._state)
try:
funcs = self._get_handlers(ServiceEventName.startup)
await asyncio.gather(*[Func(func, api)() for func in funcs])
async for msg in ws:
if msg.type == aiohttp.WSMsgType.TEXT:
data = msg.json()
event_name = data['event']
payload = data['payload']
server_time = parse_datetime(data['time'])
if event_name in self.schemas:
data = self.schemas[event_name].parse_obj(payload)
else:
data = payload
await asyncio.gather(*self._call_handlers(
event_name, api, data, server_time))
elif msg.type == aiohttp.WSMsgType.CLOSED:
break
elif msg.type == aiohttp.WSMsgType.ERROR:
break
await self._cleanup(api)
except asyncio.CancelledError:
await self._cleanup(api)
raise
def impl_AllergyIntolerance_1(inst):
assert inst.category == "food"
assert (
inst.extension[0].url ==
"http://hl7.org/fhir/StructureDefinition/allergyintolerance-reasonRefuted"
)
assert inst.extension[0].valueCodeableConcept.coding[0].code == "MED"
assert (inst.extension[0].valueCodeableConcept.coding[0].display ==
"Medical Status Altered")
assert (inst.extension[0].valueCodeableConcept.coding[0].system ==
"http://hl7.org/fhir/v3/ActReason")
assert inst.id == "allergyintolerance-example-refuted"
assert inst.identifier[0].system == "http://acme.com/ids/patients/risks"
assert inst.identifier[0].value == "49476534"
assert inst.patient.reference == "Patient/example"
assert inst.recordedDate == parse_datetime("2014-10-09T14:58:00+11:00")
assert inst.recorder.reference == "Practitioner/example"
assert inst.status == "refuted"
assert inst.substance.coding[0].code == "227493005"
assert inst.substance.coding[0].display == "Cashew nuts"
assert inst.substance.coding[0].system == "http://snomed.info/sct"
assert (
inst.text.div ==
"<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: allergyintolerance-example-refuted</p><p><b>identifier</b>: 49476534</p><p><b>recordedDate</b>: 09/10/2014 2:58:00 PM</p><p><b>recorder</b>: <a>Practitioner/example</a></p><p><b>patient</b>: <a>Patient/example</a></p><p><b>substance</b>: Cashew nuts <span>(Details : {SNOMED CT code '227493005' = '227493005', given as 'Cashew nuts'})</span></p><p><b>status</b>: refuted</p><p><b>category</b>: food</p></div>"
)
assert inst.text.status == "generated"
async def store_click(ctx, *, link_id, ip, ts, user_agent):
cache_key = f'click-{link_id}-{ip}'
with await ctx['redis'] as redis:
v = await redis.incr(cache_key)
if v > 1:
return 'recently_clicked'
await redis.expire(cache_key, 60)
async with ctx['pg'].acquire() as conn:
message_id, target = await conn.fetchrow(
'select message_id, url from links where id=$1', link_id)
extra = {'target': target, 'ip': ip, 'user_agent': user_agent}
if user_agent:
ua_dict = ParseUserAgent(user_agent)
platform = ua_dict['device']['family']
if platform in {'Other', None}:
platform = ua_dict['os']['family']
extra['user_agent_display'] = ((
'{user_agent[family]} {user_agent[major]} on '
'{platform}').format(platform=platform, **ua_dict).strip(' '))
ts = parse_datetime(ts)
status = 'click'
await conn.execute_b(
'insert into events (:values__names) values :values',
values=Values(message_id=message_id,
status=status,
ts=ts,
extra=json.dumps(extra)),
)
def parse_last_modified(cls, value: Any) -> Optional[datetime]:
"""Parse last_modified value."""
if value is None:
return None
if not isinstance(value, str):
raise ValueError("must be a string")
if value.strip() == "-":
return None
try:
parsed_datetime = parse_datetime(value)
if parsed_datetime.tzinfo is None:
parsed_datetime = parsed_datetime.replace(tzinfo=timezone.utc)
return parsed_datetime
except DateTimeError:
# Ignore
pass
try:
date_value = parse_date(value)
return datetime.combine(date_value,
datetime.min.time(),
tzinfo=timezone.utc)
except DateError:
log.error("Unable to parse last_modified value: %s", value)
return None
def impl_Device_5(inst):
assert inst.contact[0].system == "phone"
assert inst.contact[0].value == "ext 4352"
assert inst.id == "example"
assert inst.identifier[0].system == "http://goodcare.org/devices/id"
assert inst.identifier[0].value == "345675"
assert inst.identifier[1].type.coding[0].code == "SNO"
assert (inst.identifier[1].type.coding[0].system ==
"http://hl7.org/fhir/identifier-type")
assert inst.identifier[1].type.text == "Serial Number"
assert inst.identifier[1].value == "AMID-342135-8464"
assert inst.lotNumber == "43453424"
assert inst.manufacturer == "Acme Devices, Inc"
assert inst.model == "AB 45-J"
assert inst.note[0].authorReference.reference == "Practitioner/xcda-author"
assert inst.note[0].text == "QA Checked"
assert inst.note[0].time == parse_datetime("2015-06-28T14:03:32+10:00")
assert inst.status == "available"
assert (
inst.text.div ==
"<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>identifier</b>: 345675, Serial Number = AMID-342135-8464</p><p><b>type</b>: ECG <span>(Details : {SNOMED CT code '86184003' = '86184003', given as 'Electrocardiographic monitor and recorder'})</span></p><p><b>note</b>: QA Checked</p><p><b>status</b>: available</p><p><b>manufacturer</b>: Acme Devices, Inc</p><p><b>model</b>: AB 45-J</p><p><b>lotNumber</b>: 43453424</p><p><b>contact</b>: ph: ext 4352</p></div>"
)
assert inst.text.status == "generated"
assert inst.type.coding[0].code == "86184003"
assert inst.type.coding[
0].display == "Electrocardiographic monitor and recorder"
assert inst.type.coding[0].system == "http://snomed.info/sct"
assert inst.type.text == "ECG"
def impl_DocumentManifest_1(inst):
assert inst.author[0].reference == "#a1"
assert inst.contained[0].id == "a1"
assert inst.contained[0].name.family[0] == "Dopplemeyer"
assert inst.contained[0].name.given[0] == "Sherry"
assert (inst.contained[0].practitionerRole[0].managingOrganization.display
== "Cleveland Clinic")
assert inst.contained[0].practitionerRole[0].role.text == "Primary Surgon"
assert inst.contained[0].practitionerRole[0].specialty[
0].text == "Orthopedic"
assert inst.contained[0].telecom[0].system == "email"
assert inst.contained[0].telecom[
0].value == "*****@*****.**"
assert inst.content[0].pReference.reference == "DocumentReference/example"
assert inst.created == parse_datetime("2004-12-25T23:50:50-05:00")
assert inst.description == "Physical"
assert inst.id == "example"
assert inst.identifier[0].system == "http://example.org/documents"
assert inst.identifier[0].value == "23425234234-2347"
assert inst.masterIdentifier.system == "http://example.org/documents"
assert inst.masterIdentifier.value == "23425234234-2346"
assert inst.recipient[0].reference == "Practitioner/xcda1"
assert inst.related[0].identifier.system == "http://example.org/documents"
assert inst.related[0].identifier.value == "23425234234-9999"
assert inst.related[0].ref.reference == "DocumentReference/example"
assert inst.source == "urn:oid:1.3.6.1.4.1.21367.2009.1.2.1"
assert inst.status == "current"
assert inst.subject.reference == "Patient/xcda"
assert inst.text.div == "<div>Text</div>"
assert inst.text.status == "generated"
assert inst.type.text == "History and Physical"
def impl_Communication_1(inst):
assert inst.category.coding[0].code == "Alert"
assert inst.category.coding[0].system == "http://acme.org/messagetypes"
assert inst.category.text == "Alert"
assert (
inst.extension[0].url ==
"http://hl7.org/fhir/StructureDefinition/communication-reasonNotPerformed"
)
assert inst.extension[0].valueCodeableConcept.coding[0].code == "EIE"
assert (inst.extension[0].valueCodeableConcept.coding[0].display ==
"entered in error")
assert (inst.extension[0].valueCodeableConcept.coding[0].system ==
"http://hl7.org/fhir/v3/ActReason")
assert inst.id == "communication-example"
assert inst.identifier[0].system == "urn:oid:1.3.4.5.6.7"
assert inst.identifier[0].type.text == "Paging System"
assert inst.identifier[0].value == "2345678901"
assert (
inst.payload[0].contentString ==
"Patient 1 has a very high serum potassium value (7.2 mmol/L on 2014-Dec-12 at 5:55 pm)"
)
assert inst.payload[
1].contentReference.reference == "Observation/643666aa12f"
assert inst.recipient[0].reference == "Practitioner/21"
assert inst.sender.reference == "Device/f001"
assert inst.sent == parse_datetime("2014-12-12T18:01:10-08:00")
assert inst.status == "suspended"
assert inst.subject.reference == "Patient/1"
assert inst.text.div == "<div>Patient has very high serum potassium</div>"
assert inst.text.status == "generated"
def validate_datetime(cls, v, values):
if v == "null":
if not values["start_datetime"] and not values["end_datetime"]:
raise ValueError(
"start_datetime and end_datetime must be specified when datetime is null"
)
if isinstance(v, str):
return parse_datetime(v)
return v
def __eq__(self, other):
self.other = other
if not isinstance(other, datetime):
try:
from pydantic.datetime_parse import parse_datetime
except ImportError: # pragma: no cover
raise ImportError('pydantic is required to use CloseToNow, please run `pip install pydantic`')
other = parse_datetime(other)
if other.tzinfo:
self.now = self.now.replace(tzinfo=timezone.utc)
self.match = -self.delta < (self.now - other).total_seconds() < self.delta
return self.match
def convert_to_datetime(val: str) -> datetime:
constants = {
'now': datetime.utcnow(),
'day': datetime.utcnow() - timedelta(days=1),
'week': datetime.utcnow() - timedelta(days=7),
'month': datetime.utcnow() - timedelta(days=31),
'6month': datetime.utcnow() - timedelta(days=31 * 6),
'year': datetime.utcnow() - timedelta(days=365),
}
if val in constants:
return constants[val]
return parse_datetime(val)
async def build(cls, request_body: Union[str, bytes],
http_client: AsyncClient) -> Optional['SesWebhookInfo']:
payload = await sns.verify_webhook(request_body, http_client)
if not payload:
# happens legitimately for subscription confirmation webhooks
return None
try:
message = json.loads(payload.message)
except ValueError:
# this can happen legitimately, e.g. when a new configuration set is setup
logger.warning('invalid JSON in SNS notification',
extra={'data': {
'request': payload.request_data
}})
return None
event_type = message['eventType'].lower()
if event_type not in {
'send', 'delivery', 'open', 'click', 'bounce', 'complaint'
}:
logger.warning('unknown aws webhook event %s',
event_type,
extra={'data': {
'request': payload.request_data
}})
message_id = message['mail']['messageId']
logger.info('%s for message %s', event_type, message_id)
details = message.get(event_type) or {}
mail = message.get('mail') or {}
tags = mail.get('tags') or {}
timestamp = details.get('timestamp') or mail.get('timestamp')
if event_type == 'bounce':
unsubscribe = details.get('bounceType') == 'Permanent'
elif event_type == 'complaint':
unsubscribe = True
else:
unsubscribe = False
return cls(
message_id=message_id,
event_type=event_type,
timestamp=timestamp and parse_datetime(timestamp),
unsubscribe=unsubscribe,
tags={k: v[0]
for k, v in tags.items()},
details=details,
full_message=message,
request_data=payload.request_data,
)
def validate(cls, v: Any) -> datetime:
if isinstance(v, datetime):
d = v
else:
d = parse_datetime(v)
# MongoDB does not store timezone info
# https://docs.python.org/3/library/datetime.html#determining-if-an-object-is-aware-or-naive
if d.tzinfo is not None and d.tzinfo.utcoffset(d) is not None:
raise ValueError("datetime objects must be naive (no timeone info)")
# Round microseconds to the nearest millisecond to comply with Mongo behavior
microsecs = round(d.microsecond / 1000) * 1000
return d.replace(microsecond=microsecs)
def validate_datetime(cls, v):
if "/" in v:
values = v.split("/")
else:
# Single date is interpreted as end date
values = ["..", v]
dates = []
for value in values:
if value == "..":
dates.append(value)
continue
parse_datetime(value)
dates.append(value)
if ".." not in dates:
if parse_datetime(dates[0]) > parse_datetime(dates[1]):
raise ValueError(
"Invalid datetime range, must match format (begin_date, end_date)"
)
return v
def impl_AllergyIntolerance_3(inst):
assert inst.category == "food"
assert inst.id == "fishallergy"
assert inst.identifier[0].system == "http://acme.com/ids/patients/risks"
assert inst.identifier[0].value == "49476535"
assert inst.patient.reference == "Patient/example"
assert inst.recordedDate == parse_datetime("2015-08-06T15:37:31-06:00")
assert inst.recorder.reference == "Practitioner/example"
assert inst.substance.coding[0].code == "227037002"
assert inst.substance.coding[0].display == "Fish - dietary (substance)"
assert inst.substance.coding[0].system == "http://snomed.info/sct"
assert inst.substance.text == "Allergic to fresh fish. Tolerates canned fish"
assert (inst.text.div == """<div>
<p>allergy is to fresh fish. Tolerates canned fish</p>
<p>recordedDate:2015-08-06T00:00:00-06:00</p>
<p>substance:Fish - dietary (substance)</p>
</div>""")
assert inst.text.status == "additional"
def impl_AllergyIntolerance_2(inst):
assert inst.category == "food"
assert inst.criticality == "CRITH"
assert inst.id == "allergyintolerance-example"
assert inst.identifier[0].system == "http://acme.com/ids/patients/risks"
assert inst.identifier[0].value == "49476534"
assert inst.lastOccurence == "2012-06"
assert inst.patient.reference == "Patient/example"
assert inst.reaction[0].certainty == "confirmed"
assert (
inst.reaction[0].description ==
"Challenge Protocol. Severe Reaction to 1/8 cashew. Epinephrine administered"
)
assert inst.reaction[0].manifestation[0].coding[0].code == "39579001"
assert (inst.reaction[0].manifestation[0].coding[0].display ==
"Anaphylactic reaction")
assert (inst.reaction[0].manifestation[0].coding[0].system ==
"http://snomed.info/sct")
assert inst.reaction[0].onset == parse_date("2012-06-12")
assert inst.reaction[0].severity == "severe"
assert inst.reaction[0].substance.coding[0].code == "C3214954"
assert (inst.reaction[0].substance.coding[0].display ==
"cashew nut allergenic extract Injectable Product")
assert (inst.reaction[0].substance.coding[0].system ==
"http://www.nlm.nih.gov/research/umls/rxnorm")
assert inst.reaction[1].certainty == "likely"
assert inst.reaction[1].manifestation[0].coding[0].code == "64305001"
assert inst.reaction[1].manifestation[0].coding[0].display == "Urticaria"
assert (inst.reaction[1].manifestation[0].coding[0].system ==
"http://snomed.info/sct")
assert inst.reaction[1].onset == "2004"
assert inst.reaction[1].severity == "moderate"
assert inst.recordedDate == parse_datetime("2014-10-09T14:58:00+11:00")
assert inst.recorder.reference == "Practitioner/example"
assert inst.status == "confirmed"
assert inst.substance.coding[0].code == "227493005"
assert inst.substance.coding[0].display == "Cashew nuts"
assert inst.substance.coding[0].system == "http://snomed.info/sct"
assert (
inst.text.div ==
"<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: allergyintolerance-example</p><p><b>identifier</b>: 49476534</p><p><b>recordedDate</b>: 09/10/2014 2:58:00 PM</p><p><b>recorder</b>: <a>Practitioner/example</a></p><p><b>patient</b>: <a>Patient/example</a></p><p><b>substance</b>: Cashew nuts <span>(Details : {SNOMED CT code '227493005' = '227493005', given as 'Cashew nuts'})</span></p><p><b>status</b>: confirmed</p><p><b>criticality</b>: CRITH</p><p><b>type</b>: allergy</p><p><b>category</b>: food</p><p><b>lastOccurence</b>: 01/06/2012</p><blockquote><p><b>reaction</b></p><p><b>substance</b>: cashew nut allergenic extract Injectable Product <span>(Details : {RxNorm code 'C3214954' = '??', given as 'cashew nut allergenic extract Injectable Product'})</span></p><p><b>certainty</b>: confirmed</p><p><b>manifestation</b>: Anaphylactic reaction <span>(Details : {SNOMED CT code '39579001' = '39579001', given as 'Anaphylactic reaction'})</span></p><p><b>description</b>: Challenge Protocol. Severe Reaction to 1/8 cashew. Epinephrine administered</p><p><b>onset</b>: 12/06/2012</p><p><b>severity</b>: severe</p></blockquote><blockquote><p><b>reaction</b></p><p><b>certainty</b>: likely</p><p><b>manifestation</b>: Urticaria <span>(Details : {SNOMED CT code '64305001' = '64305001', given as 'Urticaria'})</span></p><p><b>onset</b>: 01/01/2004</p><p><b>severity</b>: moderate</p></blockquote></div>"
)
assert inst.text.status == "generated"
assert inst.type == "allergy"
def validate(cls, value) -> datetime:
""" Validate/parse the datetime """
if isinstance(value, datetime):
# It's already a datetime!
return value
if not isinstance(value, str):
raise ValueError(f"string: str expected not {type(value)}")
match = Datetime.regex.match(value) # type: ignore
if match:
kwargs: Dict[str, Union[int, timezone]] = {
k: int(v)
for k, v in match.groupdict().items()
}
return datetime(tzinfo=timezone.utc, **kwargs) # type: ignore
return datetime_parse.parse_datetime(value)
def test_datetime_parsing(value, result):
if result == errors.DateTimeError:
with pytest.raises(errors.DateTimeError):
parse_datetime(value)
else:
assert parse_datetime(value) == result
def init_osm_update(ctx):
"""
Init osmosis folder with configuration files and
latest state.txt file before .pbf timestamp
"""
logging.info("initializing osm update...")
session = requests.Session()
class OsmState(BaseModel):
"""
ConfigParser uses lowercased keys
"sequenceNumber" from state.txt is renamed to "sequencenumber"
"""
sequencenumber: int
timestamp: datetime
def get_state_url(sequence_number=None):
base_url = ctx.osm_update.replication_url
if sequence_number is None:
# Get last state.txt
return f'{base_url}/state.txt'
else:
return f'{base_url}' \
f'/{sequence_number // 1_000_000 :03d}' \
f'/{sequence_number // 1000 % 1000 :03d}' \
f'/{sequence_number % 1000 :03d}.state.txt'
def get_state(sequence_number=None):
url = get_state_url(sequence_number)
resp = session.get(url)
resp.raise_for_status()
# state file may contain escaped ':' in the timestamp
state_string = resp.text.replace('\:', ':')
c = configparser.ConfigParser()
c.read_string('[root]\n' + state_string)
return OsmState(**c['root'])
# Init osmosis working directory
ctx.run(f'mkdir -p {ctx.update_tiles_dir}')
ctx.run(f'touch {ctx.update_tiles_dir}/download.lock')
raw_osm_datetime = ctx.run(
f'osmconvert {ctx.osm.file} --out-timestamp').stdout
osm_datetime = parse_datetime(raw_osm_datetime)
# Rewind 2 hours as a precaution
osm_datetime -= timedelta(hours=2)
last_state = get_state()
sequence_number = last_state.sequencenumber
sequence_dt = last_state.timestamp
for i in range(ctx.osm_update.max_interations):
if sequence_dt < osm_datetime:
break
sequence_number -= 1
state = get_state(sequence_number)
sequence_dt = state.timestamp
else:
logging.error(
"Failed to init osm update. "
"Could not find a replication sequence before %s",
osm_datetime,
)
return
state_url = get_state_url(sequence_number)
ctx.run(f'wget -q "{state_url}" -O {ctx.update_tiles_dir}/state.txt')
with open(f'{ctx.update_tiles_dir}/configuration.txt', 'w') as conf_file:
conf_file.write(f'baseUrl={ctx.osm_update.replication_url}\n')
conf_file.write(f'maxInterval={ctx.osm_update.max_interval}\n')
async def record_email_event(self, raw_message: str):
"""
record email events
"""
message = json.loads(raw_message)
msg_id = message['mail']['messageId']
r = await self.pg.fetchrow(
'select id, user_id, update_ts from emails where ext_id=$1',
msg_id)
if not r:
return
email_id, user_id, last_updated = r
event_type = message.get('eventType')
extra = None
data = message.get(event_type.lower()) or {}
if event_type == 'Send':
data = message['mail']
elif event_type == 'Delivery':
extra = {
'delivery_time': data.get('processingTimeMillis'),
}
elif event_type == 'Open':
extra = {
'ip': data.get('ipAddress'),
'ua': data.get('userAgent'),
}
elif event_type == 'Click':
extra = {
'link': data.get('link'),
'ip': data.get('ipAddress'),
'ua': data.get('userAgent'),
}
elif event_type == 'Bounce':
extra = {
'bounceType': data.get('bounceType'),
'bounceSubType': data.get('bounceSubType'),
'reportingMTA': data.get('reportingMTA'),
'feedbackId': data.get('feedbackId'),
'unsubscribe': data.get('bounceType') == 'Permanent',
}
elif event_type == 'Complaint':
extra = {
'complaintFeedbackType': data.get('complaintFeedbackType'),
'feedbackId': data.get('feedbackId'),
'ua': data.get('userAgent'),
'unsubscribe': True
}
else:
logger.warning('unknown aws webhooks %s',
event_type,
extra={'data': {
'message': message
}})
values = dict(email=email_id, status=event_type)
ts = None
if data.get('timestamp'):
ts = parse_datetime(data['timestamp'])
values['ts'] = ts
if extra:
values['extra'] = json.dumps({k: v for k, v in extra.items() if v})
async with self.pg.acquire() as conn:
await conn.execute_b(
'insert into email_events (:values__names) values :values',
values=Values(**values))
if not ts:
await conn.execute(
'update emails set status=$1, update_ts=CURRENT_TIMESTAMP where id=$2',
event_type, email_id)
elif last_updated < ts:
await conn.execute(
'update emails set status=$1, update_ts=$2 where id=$3',
event_type, ts, email_id)
if extra and extra.get('unsubscribe'):
await conn.execute(
'update users set receive_emails=false where id=$1',
user_id)
return event_type
def is_datetime(value: Union[datetime, StrBytesIntFloat]) -> bool:
try:
parse_datetime(value)
return isinstance(value, (str, datetime))
except:
return False
def convert_to_datetime(s):
return parse_datetime(s).astimezone()
def replace_data(m):
dt = parse_datetime(m.group())
# WARNING: this means the output is not valid json, but is more readable
return f'{m.group()} ({dt:%a %Y-%m-%d %H:%M})'
def test_datetime_parsing(value, result):
if type(result) == type and issubclass(result, Exception):
with pytest.raises(result):
parse_datetime(value)
else:
assert parse_datetime(value) == result
def impl_DocumentReference_1(inst):
assert inst.authenticator.reference == "Organization/organization-example"
assert inst.author[0].reference == "Practitioner/xcda1"
assert inst.author[1].reference == "#a2"
assert inst.contained[0].id == "a2"
assert inst.contained[0].name.family[0] == "Smitty"
assert inst.contained[0].name.given[0] == "Gerald"
assert (
inst.contained[0].practitionerRole[0].managingOrganization.display
== "Cleveland Clinic"
)
assert inst.contained[0].practitionerRole[0].role.text == "Attending"
assert inst.contained[0].practitionerRole[0].specialty[0].text == "Orthopedic"
assert inst.content[0].attachment.contentType == "application/hl7-v3+xml"
assert inst.content[0].attachment.hash == b"2jmj7l5rSw0yVb/vlWAYkK/YBwk="
assert inst.content[0].attachment.language == "en-US"
assert inst.content[0].attachment.size == 3654
assert (
inst.content[0].attachment.url
== "http://example.org/xds/mhd/Binary/07a6483f-732b-461e-86b6-edb665c45510"
)
assert inst.content[0].format[0].code == "urn:ihe:pcc:handp:2008"
assert inst.content[0].format[0].display == "History and Physical Specification"
assert inst.content[0].format[0].system == "urn:oid:1.3.6.1.4.1.19376.1.2.3"
assert inst.context.encounter.reference == "Encounter/xcda"
assert inst.context.event[0].coding[0].code == "T-D8200"
assert inst.context.event[0].coding[0].display == "Arm"
assert (
inst.context.event[0].coding[0].system
== "http://ihe.net/xds/connectathon/eventCodes"
)
assert inst.context.facilityType.coding[0].code == "Outpatient"
assert inst.context.facilityType.coding[0].display == "Outpatient"
assert (
inst.context.facilityType.coding[0].system
== "http://www.ihe.net/xds/connectathon/healthcareFacilityTypeCodes"
)
assert inst.context.period.end == parse_datetime("2004-12-23T08:01:00+11:00")
assert inst.context.period.start == parse_datetime("2004-12-23T08:00:00+11:00")
assert inst.context.practiceSetting.coding[0].code == "General Medicine"
assert inst.context.practiceSetting.coding[0].display == "General Medicine"
assert (
inst.context.practiceSetting.coding[0].system
== "http://www.ihe.net/xds/connectathon/practiceSettingCodes"
)
assert inst.context.related[0].identifier.system == "urn:ietf:rfc:3986"
assert (
inst.context.related[0].identifier.value
== "urn:oid:1.3.6.1.4.1.21367.2005.3.7.2345"
)
assert inst.context.related[0].ref.reference == "Patient/xcda"
assert inst.context.sourcePatientInfo.reference == "Patient/xcda"
assert inst.created == parse_datetime("2005-12-24T09:35:00+11:00")
assert inst.custodian.reference == "Organization/organization-example"
assert inst.description == "Physical"
assert inst.docStatus.coding[0].code == "preliminary"
assert inst.docStatus.coding[0].display == "preliminary"
assert inst.docStatus.coding[0].system == "http://hl7.org/fhir/composition-status"
assert inst.id == "example"
assert inst.identifier[0].system == "urn:ietf:rfc:3986"
assert inst.identifier[0].value == "urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234"
assert inst.indexed == parse_datetime("2005-12-24T09:43:41+11:00")
assert inst.masterIdentifier.system == "urn:ietf:rfc:3986"
assert inst.masterIdentifier.value == "urn:oid:1.3.6.1.4.1.21367.2005.3.7"
assert inst.relatesTo[0].code == "appends"
assert inst.relatesTo[0].target.reference == "DocumentReference/example"
assert inst.securityLabel[0].coding[0].code == "V"
assert inst.securityLabel[0].coding[0].display == "very restricted"
assert (
inst.securityLabel[0].coding[0].system
== "http://hl7.org/fhir/v3/Confidentiality"
)
assert inst.status == "current"
assert inst.subject.reference == "Patient/xcda"
assert (
inst.text.div
== "<div><p><b>Generated Narrative with Details</b></p><p><b>id</b>: example</p><p><b>contained</b>: </p><p><b>masterIdentifier</b>: urn:oid:1.3.6.1.4.1.21367.2005.3.7</p><p><b>identifier</b>: urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234</p><p><b>subject</b>: <a>Patient/xcda</a></p><p><b>type</b>: Outpatient Note <span>(Details : {LOINC code '34108-1' = 'Outpatient Note', given as 'Outpatient Note'})</span></p><p><b>class</b>: History and Physical <span>(Details : {http://ihe.net/xds/connectathon/classCodes code 'History and Physical' = '??', given as 'History and Physical'})</span></p><p><b>author</b>: <a>Practitioner/xcda1</a>, id: a2; Gerald Smitty </p><p><b>custodian</b>: <a>Organization/organization-example</a></p><p><b>authenticator</b>: <a>Organization/organization-example</a></p><p><b>created</b>: 24/12/2005 9:35:00 AM</p><p><b>indexed</b>: 24/12/2005 9:43:41 AM</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary <span>(Details : {http://hl7.org/fhir/composition-status code 'preliminary' = 'Preliminary', given as 'preliminary'})</span></p><h3>RelatesTos</h3><table><tr><td>-</td><td><b>Code</b></td><td><b>Target</b></td></tr><tr><td>*</td><td>appends</td><td><a>DocumentReference/example</a></td></tr></table><p><b>description</b>: Physical</p><p><b>securityLabel</b>: very restricted <span>(Details : {http://hl7.org/fhir/v3/Confidentiality code 'V' = 'very restricted', given as 'very restricted'})</span></p><h3>Contents</h3><table><tr><td>-</td><td><b>Attachment</b></td><td><b>Format</b></td></tr><tr><td>*</td><td/><td>History and Physical Specification (Details: urn:oid:1.3.6.1.4.1.19376.1.2.3 code urn:ihe:pcc:handp:2008 = '??', stated as 'History and Physical Specification')</td></tr></table><blockquote><p><b>context</b></p><p><b>encounter</b>: <a>Encounter/xcda</a></p><p><b>event</b>: Arm <span>(Details : {http://ihe.net/xds/connectathon/eventCodes code 'T-D8200' = '??', given as 'Arm'})</span></p><p><b>period</b>: 23/12/2004 8:00:00 AM --> 23/12/2004 8:01:00 AM</p><p><b>facilityType</b>: Outpatient <span>(Details : {http://www.ihe.net/xds/connectathon/healthcareFacilityTypeCodes code 'Outpatient' = '??', given as 'Outpatient'})</span></p><p><b>practiceSetting</b>: General Medicine <span>(Details : {http://www.ihe.net/xds/connectathon/practiceSettingCodes code 'General Medicine' = '??', given as 'General Medicine'})</span></p><p><b>sourcePatientInfo</b>: <a>Patient/xcda</a></p><h3>Relateds</h3><table><tr><td>-</td><td><b>Identifier</b></td><td><b>Ref</b></td></tr><tr><td>*</td><td>urn:oid:1.3.6.1.4.1.21367.2005.3.7.2345</td><td><a>Patient/xcda</a></td></tr></table></blockquote></div>"
)
assert inst.text.status == "generated"
assert inst.type.coding[0].code == "34108-1"
assert inst.type.coding[0].display == "Outpatient Note"
assert inst.type.coding[0].system == "http://loinc.org"
async def update_user(
user_data: DotDict,
update_data: Dict[str, Any],
is_new: bool = False,
is_registering: bool = False,
is_admin: bool = False,
is_self: bool = False,
no_registration: bool = False,
):
if 'sub' in update_data or '_id' in update_data or 'picture' in update_data:
raise HTTPException(400, f"Cannot modify 'sub', '_id' or 'picture'")
was_active = user_data.get('active', False)
reset_user_cache = False
if is_new:
assert '_id' not in user_data
user_data['_id'] = generate_token(48)
if 'password' in update_data:
if not isinstance(update_data['password'], str):
raise HTTPException(400, "'password' must be a string")
_validate_property_write('password', is_self, is_admin)
if is_self and not is_registering and user_data.get(
'password') is not None:
if 'old_password' not in update_data:
raise HTTPException(
400, f"Need {repr('old_password')} for setting password")
if not isinstance(update_data['old_password'], str):
raise HTTPException(400,
f"{repr('old_password')} is not a string")
is_valid, _ = verify_and_update(update_data['old_password'],
user_data['password'])
if not is_valid:
raise HTTPException(401, "Old password does not match")
try:
user_data['password'] = create_password(update_data['password'])
del update_data['password']
except PasswordLeakedException:
raise HTTPException(
400,
"Password is leaked and cannot be used. See https://haveibeenpwned.com/"
)
async def send_mail():
pass
if is_registering and update_data.get(
'email', user_data['email']) == user_data['email']:
user_data['email_verified'] = True
elif 'email' in update_data:
if not isinstance(update_data['email'], str):
raise HTTPException(400, "'email' must be a string")
_validate_property_write('email', is_self, is_admin)
if not is_email(update_data['email'], check_dns=True):
raise HTTPException(400, "E-Mail address not accepted")
if await async_user_collection.count_documents(
{'email': update_data['email']}, limit=1) != 0:
raise HTTPException(
400,
"E-Mail address already in use, please use existing account")
new_mail = update_data['email']
locale = update_data.get(
'locale',
user_data.get('locale',
config.oauth2.user.properties['locale'].default))
if locale is None:
locale = 'en_us'
tz = _get_tz(update_data.get('zoneinfo', user_data.get('zoneinfo')))
del update_data['email']
if is_new and not no_registration:
user_data['email'] = new_mail
user_data['email_verified'] = False
token_valid_until = int(time.time() +
config.manager.token_valid.registration)
user_data['registration_token'] = create_token(
user_data['_id'], token_valid_until)
async def send_mail():
await async_send_mail_register(user_data, token_valid_until,
locale, tz)
elif not is_admin:
token_valid_until = int(time.time() +
config.manager.token_valid.email_set)
user_data['email_verification_token'] = create_token(
new_mail, token_valid_until)
if is_registering:
user_data['email'] = new_mail
user_data['email_verified'] = False
async def send_mail():
await async_send_mail_verify(locale, new_mail, user_data,
token_valid_until, tz)
else:
user_data['email'] = new_mail
user_data['email_verified'] = False
if 'access_tokens' in update_data:
if not isinstance(update_data['access_tokens'], list):
raise HTTPException(400, "'access_tokens' must be a list")
try:
access_tokens = [
ValidateAccessToken.validate(val)
for val in update_data['access_tokens']
]
except ValueError as err:
raise HTTPException(400, str(err))
_validate_property_write('access_tokens', is_self, is_admin)
existing_access_tokens = [
UserPasswordAccessToken.validate(access_token)
for access_token in user_data.get('access_tokens', [])
]
existing_access_tokens_by_id = {
existing_access_token.id: existing_access_token
for existing_access_token in existing_access_tokens
}
new_access_tokens = []
for access_token in access_tokens:
if access_token.id is not None:
store_token = existing_access_tokens_by_id.get(access_token.id)
if store_token is None:
raise HTTPException(400,
f"Invalid token ID {access_token.id}")
store_token.description = access_token.description
if access_token.token is not None:
store_token.token = access_token.token
else:
store_token = UserPasswordAccessToken(
id=generate_token(24),
description=access_token.description,
token=access_token.token,
)
new_access_tokens.append(store_token)
del update_data['access_tokens']
user_data['access_tokens'] = [
access_token.dict() for access_token in new_access_tokens
]
if 'groups' in update_data:
if await _update_groups(
user_data,
update_data,
property='groups',
is_self=is_self,
is_admin=is_admin,
existence_check_property=None,
groups_add_property='members',
groups_pull_properties=(
'members',
'email_allowed_forward_members',
'email_forward_members',
'email_postbox_access_members',
),
members_pull_properties=(
'email_allowed_forward_members',
'email_forward_members',
'email_postbox_access_members',
),
):
reset_user_cache = True
if 'email_allowed_forward_groups' in update_data:
await _update_groups(
user_data,
update_data,
property='email_allowed_forward_groups',
is_self=is_self,
is_admin=is_admin,
existence_check_property='groups',
groups_add_property='email_allowed_forward_members',
groups_pull_properties=('email_allowed_forward_members',
'email_forward_members'),
members_pull_properties=('email_forward_members', ))
if 'email_forward_groups' in update_data:
await _update_groups(
user_data,
update_data,
property='email_forward_groups',
is_self=is_self,
is_admin=is_admin,
existence_check_property='email_allowed_forward_groups',
groups_add_property='email_forward_members',
groups_pull_properties=('email_forward_members', ),
)
if 'email_postbox_access_groups' in update_data:
await _update_groups(
user_data,
update_data,
property='email_postbox_access_groups',
is_self=is_self,
is_admin=is_admin,
existence_check_property='groups',
groups_add_property='email_postbox_access_members',
groups_pull_properties=('email_postbox_access_members', ),
)
for key, value in update_data.items():
_validate_property_write(key, is_self, is_admin)
prop = config.oauth2.user.properties[key]
if prop.write_once and user_data.get(key) is not None:
raise HTTPException(400, f"{repr(key)} can only be set once")
if not value and not prop.required and key in user_data:
del user_data[key]
if prop.type in (UserPropertyType.str, UserPropertyType.multistr,
UserPropertyType.token):
if not isinstance(value, str):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a string")
if prop.template is not None:
raise HTTPException(400,
f"{repr(key)}={repr(value)} is generated")
if prop.format is not None:
regex = get_regex(prop.format)
if not regex.fullmatch(value):
raise HTTPException(
400,
f"{repr(key)}={repr(value)} does not match pattern {repr(regex.pattern)}"
)
user_data[key] = value
elif prop.type == UserPropertyType.int:
if isinstance(value, float):
if not value.is_integer():
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not an integer")
value = int(value)
if not isinstance(value, int):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not an integer")
user_data[key] = value
elif prop.type == UserPropertyType.bool:
if not isinstance(value, bool):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a boolean")
user_data[key] = value
elif prop.type == UserPropertyType.datetime:
if not isinstance(value, str):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a datetime string")
try:
parse_datetime(value)
user_data[key] = value
except ValueError:
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a datetime string")
elif prop.type == UserPropertyType.date:
if not isinstance(value, str):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a date string")
try:
parse_date(value)
user_data[key] = value
except ValueError:
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a datetime string")
elif prop.type == UserPropertyType.enum:
if not isinstance(value, str):
raise HTTPException(
400, f"{repr(key)}={repr(value)} is not a string")
assert prop.values is not None
values = [enum_value.value for enum_value in prop.values]
if value not in values:
raise HTTPException(
400,
f"{repr(key)}={repr(value)} is not a valid enum value")
user_data[key] = value
else:
raise NotImplementedError(f"{repr(prop.type)}")
# Set others to default
if is_new or is_registering:
for key, value in config.oauth2.user.properties.items():
if value.default is not None and key not in user_data:
user_data[key] = value.default
# Activate the user after registration
if is_registering:
user_data['active'] = True
# Apply all templates and validate required, when not active
if user_data.get('active', False):
# Validate that all required variables are present
for key, value in config.oauth2.user.properties.items():
if value.required and user_data.get(key) is None:
raise HTTPException(400, f"Missing {repr(key)}")
# Apply templates (they should not be required)
for key, value in config.oauth2.user.properties.items():
if (value.type == UserPropertyType.str
and value.template is not None
and (not value.write_once or not user_data.get(key))):
assert "'''" not in value.template, f"Invalid ''' in template: {value.template}"
user_data[key] = eval(
f"f'''{value.template}'''",
{
'make_username': make_username,
'config': config
},
user_data,
)
user_data['updated_at'] = int(time.time())
User.validate(user_data)
if is_new:
await async_user_collection.insert_one(user_data)
else:
await async_user_collection.replace_one({'_id': user_data['_id']},
user_data)
if user_data.get('active', False):
if reset_user_cache:
await async_client_user_cache_collection.delete_many(
{'user_id': user_data['_id']})
else:
await async_client_user_cache_collection.update_many(
{'user_id': user_data['_id']},
{'$set': {
'last_modified': user_data['updated_at']
}},
)
elif was_active:
await async_client_user_cache_collection.delete_many(
{'user_id': user_data['_id']})
await async_token_collection.delete_many({'user_id': user_data['_id']})
await async_session_collection.delete_many(
{'user_id': user_data['_id']})
await async_authorization_code_collection.delete_many(
{'user_id': user_data['_id']})
elif reset_user_cache:
await async_client_user_cache_collection.delete_many(
{'user_id': user_data['_id']})
# Last: Send the email if there is one
await send_mail()
def datetime_verifier(raw_data):
return parse_datetime(raw_data)
def validate(cls, v: Any) -> datetime:
return datetime.fromtimestamp(parse_datetime(v).timestamp())
