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Merge pull request #109 from phenomecentre/develop
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Develop
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@carolinesands
carolinesands authored May 15, 2023
2 parents 1fce4e5 + a49f663 commit 60ce19d
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Showing 15 changed files with 1,038 additions and 708 deletions.
5 changes: 4 additions & 1 deletion .gitignore
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@@ -1,3 +1,6 @@
.settings/
.project
.pydevproject
*.mat
*.png
*.pdf
Expand All @@ -18,4 +21,4 @@
/Tests/htmlcov/
*.xml
nPYc.iml
.cache/
.cache/
2 changes: 2 additions & 0 deletions Tests/test_dataset.py
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Expand Up @@ -287,6 +287,8 @@ def test_validateObject(self):
testDataset.intensityDataExcluded.append(testDataset.intensityData[[0, 2], :])
testDataset.featureMetadataExcluded.append(testDataset.featureMetadata)
testDataset.excludedFlag.append('Samples')

#print(testDataset.featureMetadata.to_string())
testDataset.featureMetadataExcluded.append(testDataset.featureMetadata.loc[3, :])
testDataset.intensityDataExcluded.append(testDataset.intensityData[:, 3])
testDataset.sampleMetadataExcluded.append(testDataset.sampleMetadata)
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1,102 changes: 655 additions & 447 deletions Tests/test_targeteddataset.py
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228 changes: 2 additions & 226 deletions Tests/test_utilities.py
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Expand Up @@ -16,6 +16,8 @@
sys.path.append("..")
import nPYc



def L(x, x0, gamma):
""" Return Lorentzian line shape at x with HWHM gamma """
return (1 / numpy.pi) * ((gamma/2) / (((x-x0)**2) + ((gamma/2)**2)))
Expand Down Expand Up @@ -566,232 +568,6 @@ def test_utilities_addReferenceRanges(self):
pandas.testing.assert_frame_equal(expectedFeatureMetadata, featureMetadata, check_dtype=False)


class test_utilities_read_bruker_xml(unittest.TestCase):

def test_utilities_readBrukerXML(self):

from nPYc.utilities._readBrukerXML import readBrukerXML

with self.subTest(msg='BI-LISA type'):
expected = ('UnitTest6_expno10.100000.11r',
'27-Aug-2015 09:59:47',
[{'Feature Name': 'TPTG',
'comment': 'Main Parameters, Triglycerides, TG',
'type': 'prediction',
'value': 134.65,
'lod': '-',
'loq': '-',
'Unit': 'mg/dL',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': 53.45,
'Upper Reference Value': 489.81,
},
{'Feature Name': 'TPCH',
'comment': 'Main Parameters, Cholesterol, Chol',
'type': 'prediction',
'value': 183.95,
'lod': '-',
'loq': '-',
'Unit': 'mg/dL',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': 140.31,
'Upper Reference Value': 341.43},
{'Feature Name': 'LDCH',
'comment': 'Main Parameters, LDL Cholesterol, LDL-Chol',
'type': 'prediction',
'value': 94.57,
'lod': '-',
'loq': '-',
'Unit': 'mg/dL',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': 54.52,
'Upper Reference Value': 226.6},
{'Feature Name': 'HDCH',
'comment': 'Main Parameters, HDL Cholesterol, HDL-Chol',
'type': 'prediction',
'value': 52.22,
'lod': '-',
'loq': '-',
'lodMask': True,
'Unit': 'mg/dL',
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': 34.6,
'Upper Reference Value': 96.25}])
actual = readBrukerXML(os.path.join('..', '..', 'npc-standard-project', 'Derived_Data','bruker_quant_BILISA.xml'))

self.assertEqual(expected, actual)

with self.subTest(msg='Urine Quant type'):
expected = ('UnitTest5_expno840.100000.10r',
'15-Aug-2017 13:06:45',
[{'Feature Name': 'Creatinine',
'comment': '',
'type': 'quantification',
'value': 4.3,
'lod': '-',
'loq': '-',
'Unit': 'mmol/L',
'lodMask': True},
{'Feature Name': 'Dimethylamine',
'comment': '',
'type': 'quantification',
'value': 0.19,
'lod': 0.133,
'loq': '-',
'Unit': 'mmol/L',
'lodMask': True},
{'Feature Name': 'Dimethylamine',
'comment': '',
'type': 'quantification',
'value': 43,
'lod': 31,
'loq': '-',
'Unit': 'mmol/mol Crea',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': '-',
'Upper Reference Value': 54},
{'Feature Name': 'Trimethylamine',
'comment': '',
'type': 'quantification',
'value': 0,
'lod': 0.009,
'loq': '-',
'Unit': 'mmol/L',
'lodMask': False},
{'Feature Name': 'Trimethylamine',
'comment': '',
'type': 'quantification',
'value': 0,
'lod': 2,
'loq': '-',
'Unit': 'mmol/mol Crea',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': '-',
'Upper Reference Value': 3},
{'Feature Name': '1-Methylhistidine',
'comment': '',
'type': 'quantification',
'value': 0,
'lod': 0.065,
'loq': '-',
'Unit': 'mmol/L',
'lodMask': False},
{'Feature Name': '1-Methylhistidine',
'comment': '',
'type': 'quantification',
'value': 0,
'lod': 15,
'loq': '-',
'Unit': 'mmol/mol Crea',
'lodMask': True,
'Lower Reference Bound': 2.5,
'Upper Reference Bound': 97.5,
'Lower Reference Value': '-',
'Upper Reference Value': 15}])

actual = readBrukerXML(os.path.join('..', '..', 'npc-standard-project', 'Derived_Data','bruker_quant_urine.xml'))

self.assertEqual(expected, actual)


def test_utilities_readBrukerXML_warns(self):

from nPYc.utilities._readBrukerXML import importBrukerXML

with tempfile.TemporaryDirectory() as tmpdirname:
tmpfile = os.path.join(tmpdirname, 'malformedxml.xml')

with open(tmpfile, 'w') as tmpf:
tmpf.write('Most definitely not xml <as \n')

self.assertWarnsRegex(UserWarning, 'Error parsing xml in .+?, skipping', importBrukerXML, [tmpfile])


def test_utilities_importBrukerXML(self):

from nPYc.utilities._readBrukerXML import importBrukerXML

path = os.path.join('..', '..', 'npc-standard-project', 'Derived_Data','bruker_quant_urine.xml')

paths = [path, path, path]

expectedIntesityData = numpy.array([[4.3, 0.19, 43., 0., 0., 0., 0.],
[4.3, 0.19, 43., 0., 0., 0., 0.],
[4.3, 0.19, 43., 0., 0., 0., 0.]])

expectedFeatureMetadata = pandas.DataFrame.from_dict({'Feature Name': {0: 'Creatinine', 1: 'Dimethylamine', 2: 'Dimethylamine', 3: 'Trimethylamine',
4: 'Trimethylamine', 5: '1-Methylhistidine',6: '1-Methylhistidine'},
'Lower Reference Bound': {0: numpy.nan, 1: numpy.nan, 2: 2.5, 3: numpy.nan, 4: 2.5, 5: numpy.nan, 6: 2.5},
'Lower Reference Value': {0: numpy.nan, 1: numpy.nan, 2: '-', 3: numpy.nan, 4: '-', 5: numpy.nan, 6: '-'},
'Unit': {0: 'mmol/L', 1: 'mmol/L', 2: 'mmol/mol Crea', 3: 'mmol/L', 4: 'mmol/mol Crea',
5: 'mmol/L', 6: 'mmol/mol Crea'},
'Upper Reference Bound': {0: numpy.nan, 1: numpy.nan, 2: 97.5, 3: numpy.nan, 4: 97.5, 5: numpy.nan, 6: 97.5},
'Upper Reference Value': {0: numpy.nan, 1: numpy.nan, 2: 54.0, 3: numpy.nan, 4: 3.0, 5: numpy.nan, 6: 15.0},
'comment': {0: '', 1: '', 2: '', 3: '', 4: '', 5: '', 6: ''},
'lod': {0: '-', 1: 0.133, 2: 31, 3: 0.009, 4: 2, 5: 0.065, 6: 15},
'lodMask': {0: True, 1: True, 2:True, 3: False, 4: True, 5: False, 6: True},
'loq': {0: '-', 1: '-', 2: '-', 3: '-', 4: '-', 5: '-', 6: '-'},
'type': {0: 'quantification', 1: 'quantification', 2: 'quantification',
3: 'quantification', 4: 'quantification', 5: 'quantification',
6: 'quantification'}})

expectedSampleMetadata = pandas.DataFrame([], columns=['Sample File Name', 'Sample Base Name', 'expno', 'Path', 'Acquired Time', 'Run Order'])
expectedSampleMetadata['Path'] = [path, path, path]
#expectedSampleMetadata['Sample File Name'] = ['UnitTest5_expno840.100000.10r', 'UnitTest5_expno840.100000.10r', 'UnitTest5_expno840.100000.10r'] # change to Sample File Name matching Sample Base Name
expectedSampleMetadata['Sample File Name'] = ['UnitTest5/840', 'UnitTest5/840', 'UnitTest5/840']
expectedSampleMetadata['Sample Base Name'] = ['UnitTest5/840', 'UnitTest5/840', 'UnitTest5/840']
expectedSampleMetadata['Acquired Time'] = [pandas.Timestamp('2017-08-15 13:06:45'), pandas.Timestamp('2017-08-15 13:06:45'), pandas.Timestamp('2017-08-15 13:06:45')]
expectedSampleMetadata['Run Order'] = [0, 1, 2]
expectedSampleMetadata['expno'] = [840, 840, 840]

(intensityData, sampleMetadata, featureMetadata) = importBrukerXML(paths)

numpy.testing.assert_array_equal(intensityData, expectedIntesityData)
pandas.testing.assert_frame_equal(sampleMetadata, expectedSampleMetadata)
pandas.testing.assert_frame_equal(featureMetadata, expectedFeatureMetadata, check_like=True)


def test_utilities_importBrukerXML_fails(self):

from nPYc.utilities._readBrukerXML import importBrukerXML

path = os.path.join('..', '..', 'npc-standard-project', 'Derived_Data','bruker_quant_urine.xml')

with tempfile.TemporaryDirectory() as tmpdirname:
tmpfile = os.path.join(tmpdirname, 'malformedxml.xml')

with open(tmpfile, 'w') as tmpf:
tmpf.write('Most definitely not xml <as \n')

paths = [path, path, tmpfile, path, tmpfile, tmpfile]

with warnings.catch_warnings():
warnings.simplefilter("ignore")
(intensityData, sampleMetadata, featureMetadata) = importBrukerXML(paths)

expectedSampleMetadata = pandas.DataFrame([], columns=['Sample File Name', 'Sample Base Name', 'expno', 'Path', 'Acquired Time', 'Run Order'])
expectedSampleMetadata['Path'] = [path, path, path]
#expectedSampleMetadata['Sample File Name'] = ['UnitTest5_expno840.100000.10r', 'UnitTest5_expno840.100000.10r', 'UnitTest5_expno840.100000.10r'] # change to Sample File Name matching Sample Base Name
expectedSampleMetadata['Sample File Name'] = ['UnitTest5/840', 'UnitTest5/840', 'UnitTest5/840']
expectedSampleMetadata['Sample Base Name'] = ['UnitTest5/840', 'UnitTest5/840', 'UnitTest5/840']
expectedSampleMetadata['Acquired Time'] = [pandas.Timestamp('2017-08-15 13:06:45'), pandas.Timestamp('2017-08-15 13:06:45'), pandas.Timestamp('2017-08-15 13:06:45')]
expectedSampleMetadata['Run Order'] = [0, 1, 2]
expectedSampleMetadata['expno'] = [840, 840, 840]

pandas.testing.assert_frame_equal(sampleMetadata, expectedSampleMetadata)
self.assertEqual(intensityData.shape[0], 3)


class test_utilities_calibratePPMscale(unittest.TestCase):

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4 changes: 4 additions & 0 deletions Tests/test_utilities_extractParams.py
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Expand Up @@ -93,6 +93,10 @@ def test_extractParams_buildFileList(self):
os.path.join('UnitTest1', 'UnitTest1_Urine_Rack1_SLL_270814', '90', 'pdata', '1', '1r'),
os.path.join('UnitTest1', 'UnitTest1_Urine_Rack1_SLL_270814', '70', 'pdata', '1', '1r'),
os.path.join('UnitTest1', 'UnitTest1_Urine_Rack1_SLL_270814', '40', 'pdata', '1', '1r'),

os.path.join('UnitTest2', 'UnitTest2_Plasma_Rack1_SLL_051218', '10', 'pdata', '1', '1r'),
os.path.join('UnitTest2', 'UnitTest2_Plasma_Rack1_SLL_051218', '20', 'pdata', '1', '1r'),

os.path.join('UnitTest3', 'UnitTest3_Serum_Rack01_RCM_190116', '150', 'pdata', '1', '1r'),
os.path.join('UnitTest3', 'UnitTest3_Serum_Rack01_RCM_190116', '161', 'pdata', '1', '1r'),
os.path.join('UnitTest3', 'UnitTest3_Serum_Rack01_RCM_190116', '160', 'pdata', '1', '1r'),
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