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updated test cases
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@sellth
sellth committed Jul 28, 2023
1 parent 15e1954 commit e983b67
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12 changes: 6 additions & 6 deletions tests/data/i_small/s_small.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Source Name Characteristics[organism] Term Source REF Term Accession Number Characteristics[age] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[instrument] Performer Date Sample Name Characteristics[status] Factor Value[treatment]
0814 Mus musculus;Homo sapiens NCBITAXON;NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090;http://purl.bioontology.org/ontology/NCBITAXON/9606 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0814-N1 0 yes
0815 Mus musculus NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0815-N1 0 yes
0815 Mus musculus NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel type A;scalpel type B John Doe 2018-02-02 0815-T1 2
0816 Mus musculus day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0816-T1 1 yes
0817 150 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02
Source Name Characteristics[organism] Term Source REF Term Accession Number Characteristics[age] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[instrument] Performer Date Sample Name Characteristics[status] Factor Value[treatment] Term Source REF Term Accession Number
0814 Mus musculus;Homo sapiens NCBITAXON;NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090;http://purl.bioontology.org/ontology/NCBITAXON/9606 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0814-N1 0 vaccine;yes OBI; http://purl.obolibrary.org/obo/VO_0000001;
0815 Mus musculus NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0815-N1 0 yes
0815 Mus musculus NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/10090 90 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel type A;scalpel type B John Doe 2018-02-02 0815-T1 2
0816 Mus musculus day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02 0816-T1 1 yes
0817 150 day UO http://purl.obolibrary.org/obo/UO_0000033 sample collection scalpel John Doe 2018-02-02
78 changes: 69 additions & 9 deletions tests/test_parse_study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file

# Create new row reader and check read headers (+ string representation)
row_reader = StudyRowReader.from_stream("S1", small_study_file)
assert 13 == len(row_reader.header)
assert 14 == len(row_reader.header)
rep0 = "ColumnHeader(column_type='Source Name', col_no=0, span=1)"
rep1 = "LabeledColumnHeader(column_type='Characteristics', col_no=1, span=1, label='organism')"
assert rep0 == repr(row_reader.header[0])
Expand Down Expand Up @@ -181,6 +181,8 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
table_headers.SAMPLE_NAME,
table_headers.CHARACTERISTICS + "[status]",
table_headers.FACTOR_VALUE + "[treatment]",
table_headers.TERM_SOURCE_REF,
table_headers.TERM_ACCESSION_NUMBER,
]

unit = models.OntologyTermRef(
Expand Down Expand Up @@ -262,14 +264,30 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
headers_collection,
)
assert expected == second_row[1]

factor_treatment2 = (
models.FactorValue(
name="treatment",
value=[models.OntologyTermRef("yes", None, None)],
unit=None,
),
)
factor_treatment3 = (
models.FactorValue(
name="treatment",
value=[models.OntologyTermRef(None, None, None)],
unit=None,
),
)

expected = models.Material(
"Sample Name",
"S1-sample-0815-N1",
"0815-N1",
None,
(models.Characteristics("status", ["0"], None),),
(),
(models.FactorValue("treatment", ["yes"], None),),
factor_treatment2,
None,
headers_sample,
)
Expand Down Expand Up @@ -310,7 +328,7 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
None,
(models.Characteristics("status", ["2"], None),),
(),
(models.FactorValue("treatment", [""], None),),
factor_treatment3,
None,
headers_sample,
)
Expand All @@ -329,15 +347,15 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):

# Create new row reader and check read headers
reader = StudyReader.from_stream("S1", small_study_file)
assert 13 == len(reader.header)
assert 14 == len(reader.header)

# Read study
study = reader.read()
StudyValidator(investigation, investigation.studies[0], study).validate()

# Check results
assert os.path.normpath(str(study.file)).endswith(os.path.normpath("data/i_small/s_small.txt"))
assert 13 == len(study.header)
assert 14 == len(study.header)
assert 9 == len(study.materials)
assert 5 == len(study.processes)
assert 10 == len(study.arcs)
Expand All @@ -362,6 +380,8 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
table_headers.SAMPLE_NAME,
table_headers.CHARACTERISTICS + "[status]",
table_headers.FACTOR_VALUE + "[treatment]",
table_headers.TERM_SOURCE_REF,
table_headers.TERM_ACCESSION_NUMBER,
]

unit = models.OntologyTermRef(
Expand Down Expand Up @@ -394,6 +414,34 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
),
models.Characteristics(name="age", value=["150"], unit=unit),
)
factor_treatment1 = (
models.FactorValue(
name="treatment",
value=[
models.OntologyTermRef(
name="vaccine",
accession="http://purl.obolibrary.org/obo/VO_0000001",
ontology_name="OBI",
),
models.OntologyTermRef("yes", None, None)
],
unit=None,
),
)
factor_treatment2 = (
models.FactorValue(
name="treatment",
value=[models.OntologyTermRef("yes", None, None)],
unit=None,
),
)
factor_treatment3 = (
models.FactorValue(
name="treatment",
value=[models.OntologyTermRef(None, None, None)],
unit=None,
),
)

expected = models.Material(
"Source Name",
Expand Down Expand Up @@ -431,14 +479,26 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
headers_source,
)
assert expected == study.materials["S1-source-0817"]
expected = models.Material(
"Sample Name",
"S1-sample-0814-N1",
"0814-N1",
None,
(models.Characteristics("status", ["0"], None),),
(),
factor_treatment1,
None,
headers_sample,
)
assert expected == study.materials["S1-sample-0814-N1"]
expected = models.Material(
"Sample Name",
"S1-sample-0815-N1",
"0815-N1",
None,
(models.Characteristics("status", ["0"], None),),
(),
(models.FactorValue("treatment", ["yes"], None),),
factor_treatment2,
None,
headers_sample,
)
Expand All @@ -450,7 +510,7 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
None,
(models.Characteristics("status", ["2"], None),),
(),
(models.FactorValue("treatment", [""], None),),
factor_treatment3,
None,
headers_sample,
)
Expand All @@ -462,7 +522,7 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
None,
(models.Characteristics("status", ["1"], None),),
(),
(models.FactorValue("treatment", ["yes"], None),),
factor_treatment2,
None,
headers_sample,
)
Expand All @@ -474,7 +534,7 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
None,
(models.Characteristics("status", [""], None),),
(),
(models.FactorValue("treatment", [""], None),),
factor_treatment3,
None,
headers_sample,
)
Expand Down

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