def test_multi_scanner_multi_accession_list(self, tmpdir):
"""This test generates a single Sectra style PACS directory structure
with 4 modality sub-directories (CR, CT, MG, MR) generating a random
number of accession numbers and image directories within each of the
modality sub-directory"""
# Generate the temporary Sectra style directory structure
nAcc = [random.randint(1, 99) for x in range(4)]
accList, nImDirs = self._gen_dirs(tmpdir, nAcc=nAcc)
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(tmpdir.strpath,
dirDataBase=tmpdir.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories
tmpdir.remove()
# Perform three tests: (1) only one accession number has been found and
# (2) that all accession numbers generated exist in the data frame, (3)
# that the number of image directories matches the number that were
# generated automatically
assert (obj.data.loc[:, 'Accession'].size == len(accList))
for acc in accList:
assert (obj.data.Accession.isin([acc]).any())
def test_single_scanner_multi_accession_list(self, tmpdir):
"""This test generates a single Sectra style PACS directory structure
with a single modality sub-directory (CT) containing a multiple
accession number sub-directories"""
# Generate the temporary Sectra style directory structure
nAcc = [0, random.randint(1, 10), 0, 0]
accList, nImDirs = self._gen_dirs(tmpdir, nAcc=nAcc)
# Remove all of the sub-directories except that one for CT
tmpdir.join('folders', 'CR').remove()
tmpdir.join('folders', 'MG').remove()
tmpdir.join('folders', 'MR').remove()
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(tmpdir.strpath,
dirDataBase=tmpdir.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories
tmpdir.remove()
# Perform three tests: (1) only one accession number has been found and
# (2) that accession number matches the auto-generated one, (3) that
# the number of image directories matches the number that were
# generated automatically
assert (obj.data.loc[:, 'Accession'].size == len(accList))
for acc in accList:
assert (obj.data.Accession.isin([acc]).any())
def test_multi_scanner_single_accession_list(self, tmpdir):
"""This test generates a single Sectra style PACS directory structure
with 4 modality sub-directories (CR, CT, MG, MR) generating a random
number of accession numbers and image directories within the CT
modality sub-directory"""
# Generate the temporary Sectra style directory structure
accList, nImDirs = self._gen_dirs(tmpdir)
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(tmpdir.strpath,
dirDataBase=tmpdir.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories
tmpdir.remove()
# Perform three tests: (1) only one accession number has been found and
# (2) that accession number matches the auto-generated one, (3) that
# the number of image directories matches the number that were
# generated automatically
assert (obj.data.loc[:, 'Accession'].size == 1)
assert (obj.data.loc[0, 'Accession'] == accList[0])
assert (len(obj.data.loc[0, 'Series']) == nImDirs[1][0])
def test_single_scanner_no_accession_list(self, tmpdir):
"""This test generates a single Sectra style PACS directory structure
with a single modality sub-directory (CT) containing a single
accession number"""
# Generate the temporary Sectra style directory structure
accList, nImDirs = self._gen_dirs(tmpdir, [0] * 4)
# Remove all of the sub-directories except that one for CT
tmpdir.join('folders', 'CR').remove()
tmpdir.join('folders', 'MG').remove()
tmpdir.join('folders', 'MR').remove()
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(tmpdir.strpath,
dirDataBase=tmpdir.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories
tmpdir.remove()
# Perform a test to ensure that no accession numbers were found
assert (obj.data.loc[:, 'Accession'].size == 0)
def test_pacstools_storage_path_auto_gen_no_input(self):
"""This test checks the auto-generated user directory that is used in
lieu of a user-defined directory for storing files (e.g., databases)
generated by PACSTOOLS"""
# The code here was copied from PACSTOOLS as there is no way to
# generate the local path name without creating the directory
# Get the user's home directory and determine which paths
dirUser = os.path.expanduser("~")
if (os.name == 'nt'):
dirUser = os.path.join(dirUser, 'AppData')
else:
strErr = ('Unable to determine the local user directory. Either '
'the case hasn'
't been programmed or the appropriate '
'system environment variable doesn'
't exist.')
raise NotImplementedError(strErr)
# Concatenate the unique directory name
dirLocalStorage = os.path.join(dirUser, "PACSimport")
if os.path.isdir(dirLocalStorage):
pytest.skip(f'The local storage directory "{dirLocalStorage}" '
'already exists. Unable to test the auto-generate'
'feature.')
# Create a SECTRALISTENER object without using a user-defined directory
# and ensure that the above path exists
pacstools.SectraListener()
assert (os.path.isdir(dirLocalStorage))
# Since we made the directory, remove it
py.path.local(dirLocalStorage).remove()
def test_no_folders_directory_failure(self, tmpdir):
"""This test generates a directory - "folder" - instead of "folders"
to ensure that the SectraListener initialization will raise an
error - NotADirectoryError"""
# Generate a directory that should cause a failure
dirFolder = tmpdir.mkdir('folder').strpath
with pytest.raises(NotADirectoryError):
pacstools.SectraListener(dirFolder)
# Perform the clean-up
tmpdir.remove()
def test_unc_path_multi_scanner_multi_accession(self):
"""This test attempts to test the UNC path capabilities. When the test
file path is convertable to a UNC path, the tests from method
'test_multi_scanner_multi_accession' are run"""
#TODO: the following code will raise an error (2250) when the path is a
# on a local drive. I have tested that the following code works,
# but the generic EXCEPTION is used in the TRY/EXCEPT statement
# below. I'd like to replace this with somethin less general
# Get the current file's absolute path
try:
d = win32wnet.WNetGetUniversalName(py.path.local(__file__).dirname)
except Exception:
pytest.skip('Unable to generate a UNC path with the current' +
'configuration')
d = py.path.local(d)
# Generate the directories as in the multi-scanner, multi-accession
# number test
nAcc = [random.randint(1, 10) for x in range(4)]
accList, nImDirs = self._gen_dirs(d, nAcc=nAcc)
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(d.strpath, dirDataBase=d.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories. Note
# that the 'folders' path must be added because the parent
# directory 'tests' must not be removed!
d.join('folders').remove()
# Perform three tests: (1) only one accession number has been found
# and (2) that all accession numbers generated exist in the data
# frame, (3) that the number of image directories matches the
# number that were generated automatically
assert (obj.data.loc[:, 'Accession'].size == len(accList))
for acc in accList:
assert (obj.data.Accession.isin([acc]).any())
def test_multi_scanner_no_accession_list(self, tmpdir):
"""This test generates a single Sectra style PACS directory structure
with 4 empty modality sub-directories (CR, CT, MG, MR) to check the
case where a PACS directory with no accession numbers"""
# Generate the temporary Sectra style directory structure
accList, nImDirs = self._gen_dirs(tmpdir, [0] * 4)
# Instantiate a SectraListener object, walk the directory structure,
# and validate that a single accession folder was found. Use the same
# temporary directory to house the database to ensure that another
# database is not loaded
obj = pacstools.SectraListener(tmpdir.strpath,
dirDataBase=tmpdir.strpath)
obj.walk_dirs()
# Before asserting the test results, clean-up the directories
tmpdir.remove()
# Perform a test to ensure that no accession numbers were found
assert (obj.data.loc[:, 'Accession'].size == 0)
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 2 00:43:29 2018
@author: Ryan
"""
from context import pacstools
import pacstools_path_test
import py
obj = pacstools_path_test.TestAccessionPathWalk()
# Generate the local path object
d = py.path.local()
accs, nIms = obj._gen_dirs(d)
# Generate the the Sectra object
obj = pacstools.SectraListener(d.strpath, dirDataBase=d.strpath)
obj.walk_dirs()
# Remove the temporary path
d.join('folders').remove()