def test_query_dates():
"""Date parameters should be passed in proper format"""
query = MintQuery(
minStudyDate=datetime(year=2019, month=1, day=2),
maxStudyDate=datetime(year=2020, month=3, day=1),
patientBirthDate=date(year=1983, month=8, day=11),
)
assert query.as_parameters()["minStudyDate"] == "20190102"
assert query.as_parameters()["maxStudyDate"] == "20200301"
assert query.as_parameters()["patientBirthDate"] == "19830811"
def test_search_error_500(a_mint, requests_mock):
"""Internal errors in the mint server might be communicated by plain html
instead mint format. This should be handled
"""
set_mock_response(requests_mock, MINT_SEARCH_STUDY_LEVEL_ERROR_500)
with pytest.raises(DICOMTrolleyError) as e:
a_mint.find_studies(query=MintQuery(patientName="B*"))
assert "Could not parse" in str(e)
from datetime import datetime
from os import environ
from dicomtrolley.mint import Mint, MintQuery, QueryLevels
from dicomtrolley.servers import VitreaConnection
# Log in to get an authenticated session
session = VitreaConnection(environ["LOGIN_URL"]).log_in(
environ["USER"], environ["PASSWORD"], environ["REALM"])
# Using mint for search
mint = Mint(session, environ["MINT_URL"])
print("Quick search for some studies")
studies = mint.find_studies(
MintQuery(patientName="B*", includeFields=["PatientBirthDate"]))
print(f"Found {len(studies)} studies")
print("More extensive search")
studies = mint.find_studies(
MintQuery(
patientName="B*", # wildcards can be used
modalitiesInStudy="CT*", # more parameters can be found
patientSex="M", # in dicomtrolley.mint.MintQuery
minStudyDate=datetime(year=2015, month=3, day=1),
maxStudyDate=datetime(year=2020, month=3, day=1),
includeFields=[
"PatientBirthDate", # which fields to get back.
"SOPClassesInStudy",
], # see dicomtrolley.fields for options
queryLevel=QueryLevels.
from dicomtrolley.trolley import Trolley
from dicomtrolley.wado import Wado
print("logging in")
session = VitreaConnection(environ["LOGIN_URL"]).log_in(
environ["USER"], environ["PASSWORD"], environ["REALM"])
trolley = Trolley(
searcher=Mint(session, environ["MINT_URL"]),
wado=Wado(session, environ["WADO_URL"]),
)
print("Quick search for studies")
studies = trolley.find_studies(
MintQuery(patientName="B*",
includeFields=["NumberOfStudyRelatedInstances"]))
print(f"Found {len(studies)} studies. Taking one with least instances")
studies.sort(key=lambda x: int(x.data.NumberOfStudyRelatedInstances))
study = studies[1]
print(f"Getting slice info for {study}")
studies_full = trolley.find_studies(
MintQuery(studyInstanceUID=study.uid, queryLevel=QueryLevels.INSTANCE)
) # queryLevel=INSTANCE will return all instances inside each study
print(f"Saving datasets to {environ['DOWNLOAD_PATH']}")
trolley.download(studies_full, environ["DOWNLOAD_PATH"], use_async=False)
print("Done")
def test_trolley_find(a_trolley, some_mint_studies):
a_trolley.searcher.find_studies = Mock(return_value=some_mint_studies)
assert a_trolley.find_studies(query=MintQuery()) == some_mint_studies
def test_query_validation_error(query_params):
"""These queries should fail validation"""
with pytest.raises(ValueError):
MintQuery(**query_params)
def test_find_study_exception(a_mint, some_mint_studies):
"""Using a find_study query that returns multiple studies is not allowed"""
a_mint.find_studies = Mock(return_value=some_mint_studies)
with pytest.raises(DICOMTrolleyError):
a_mint.find_study(MintQuery())
def test_search_instance_level(a_mint, mock_mint_responses):
"""Instance query level returns series per study and also instances per study"""
response = a_mint.find_studies(
query=MintQuery(patientName="B*", queryLevel=QueryLevels.INSTANCE))
assert len(response[0].series[1].instances) == 13
def test_search_series_level(a_mint, mock_mint_responses):
"""Series query level will populate studies with series"""
response = a_mint.find_studies(
query=MintQuery(patientName="B*", queryLevel=QueryLevels.SERIES))
assert len(response[1].series) == 2
def test_search_study_level(a_mint, mock_mint_responses):
"""Default query level receives info in study only"""
response = a_mint.find_studies(query=MintQuery(patientName="B*"))
assert response[2].series == []
def test_query_should_pass(query_params):
"""These queries should pass validation"""
MintQuery(**query_params)