test(nbia): added test for downloadSeries

tests/test_nbia.py

@@ -1,7 +1,13 @@
 #####
 # pytest -v -n 8
+
+# To run only one of the tests:
+# pytest -v -n 8 tests/test_nbia.py::test_getCollections
+
 import pytest
 from nbiatoolkit import NBIAClient
+from tempfile import TemporaryDirectory
+import os
 
 @pytest.fixture(scope="session")
 def nbia_client():
@@ -25,6 +31,52 @@ def nbia_patients(nbia_client, nbia_collections):
         Collection=nbia_collections[0], Modality = "CT")
     return patients
 
+
+def test_downloadSeries(nbia_client, nbia_collections, nbia_patients):
+    seriesList = nbia_client.getSeries(
+        Collection=nbia_collections[0],
+        PatientID=nbia_patients[0],
+        Modality="CT"
+    )
+    filePattern = '%PatientID/%Modality/%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm'
+    # create a temporary directory
+
+    tempdir = TemporaryDirectory()
+    tempdir = tempdir.name
+
+    nbia_client.downloadSeries(
+        SeriesInstanceUID=seriesList[0]["SeriesInstanceUID"],
+        downloadDir=tempdir,
+        filePattern=filePattern
+    )
+    dir = os.listdir(tempdir)
+
+    assert len(dir) == 1
+    assert dir[0] == nbia_patients[0]
+    assert os.path.isdir(os.path.join(tempdir, dir[0]))
+
+    modality_dir = os.listdir(os.path.join(tempdir, dir[0]))
+    assert len(modality_dir) == 1
+    assert modality_dir[0] == "CT"
+    assert os.path.isdir(os.path.join(tempdir, dir[0], modality_dir[0]))
+
+    series_dir = os.listdir(os.path.join(tempdir, dir[0], modality_dir[0]))
+    assert len(series_dir) == 1
+    # only last 5 digits of SeriesInstanceUID are used
+    assert series_dir[0] == "{}-{}".format(
+        seriesList[0]["SeriesNumber"], seriesList[0]["SeriesInstanceUID"][-5:])
+    assert os.path.isdir(os.path.join(tempdir, dir[0], modality_dir[0], series_dir[0]))
+
+    dicom_dir = os.listdir(os.path.join(
+        tempdir, dir[0], modality_dir[0], series_dir[0]))
+
+    assert len(dicom_dir) == int(seriesList[0]["ImageCount"])
+    for file in dicom_dir:
+        assert file.endswith(".dcm")
+        assert file[:-4].isdigit()
+
+
+
 def test_nbiaclient_access_token(nbia_client):
     assert nbia_client.api_headers is not None
 
@@ -65,7 +117,6 @@ def test_getPatients(nbia_patients):
     assert isinstance(nbia_patients[0], str)
     assert len(nbia_patients[0]) > 0
 
-
 def test_getSeries(nbia_client, nbia_collections, nbia_patients):
     seriesList = nbia_client.getSeries(
         Collection=nbia_collections[0],
@@ -77,7 +128,6 @@ def test_getSeries(nbia_client, nbia_collections, nbia_patients):
     assert len(seriesList) > 0
     assert isinstance(seriesList[0], dict)
 
-
 def test_fail_getSeries(nbia_client, nbia_collections, nbia_patients):
     with pytest.raises(Exception):
         seriesList = nbia_client.getSeries(
@@ -91,3 +141,6 @@ def test_fail_getSeries(nbia_client, nbia_collections, nbia_patients):
         assert len(seriesList) > 0
         assert isinstance(seriesList[0], dict)
 
+
+
+    # nbia_client.downloadSeries(