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chore: adding snapshot tests #117

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Jan 15, 2024
Merged

chore: adding snapshot tests #117

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2b9ed1c
chore: adding snapshot tests
sellth Jan 15, 2024
986ea32
portable paths in snapshot tests
holtgrewe Jan 15, 2024
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2 changes: 2 additions & 0 deletions requirements/test.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,5 @@ flake8 >=3.5.0
isort

pyright

syrupy
65 changes: 65 additions & 0 deletions tests/__snapshots__/test_apps.ambr
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Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
# serializer version: 1
# name: test_isatab2isatab
list([
'''
Investigation with only one study contains metadata:
ID: i_minimal
Title: Minimal Investigation
Path: i_minimal.txt
Submission Date:
Public Release Date: None
Prefer recording metadata in the study section.
''',
'''
Assay without platform:
Path: a_minimal.txt
Measurement Type: exome sequencing assay
Technology Type: nucleotide sequencing
Technology Platform:
''',
'No reference headers available for section INVESTIGATION PUBLICATIONS. Applying default order.',
'No reference headers available for section INVESTIGATION CONTACTS. Applying default order.',
'No reference headers available for section STUDY DESIGN DESCRIPTORS. Applying default order.',
'No reference headers available for section STUDY PUBLICATIONS. Applying default order.',
'No reference headers available for section STUDY FACTORS. Applying default order.',
'No reference headers available for section STUDY CONTACTS. Applying default order.',
])
# ---
# name: test_isatab2isatab_input_is_output
'<Result IsaException("Can\'t output ISA-tab files to same directory as as input: /home/runner/work/altamisa/tests/data/i_minimal == /home/runner/work/altamisa/tests/data/i_minimal")>'
# ---
# name: test_isatab_validate
list([
'Incomplete ontology source; found: , Incomplete 1, 1, Incomplete 1, ()',
'Incomplete ontology source; found: Incomplete 2, , 2, Incomplete 2, ()',
'Ontology source name including whitespace(s); found: Incomplete 2, , 2, Incomplete 2, ()',
'Incomplete ontology source; found: Incomplete 3, Incomplete 3, , Incomplete 3, ()',
'Ontology source name including whitespace(s); found: Incomplete 3, Incomplete 3, , Incomplete 3, ()',
'Incomplete ontology source; found: Incomplete 4, Incomplete 4, 4, , ()',
'Ontology source name including whitespace(s); found: Incomplete 4, Incomplete 4, 4, , ()',
'''
Investigation with only one study contains metadata:
ID: i_warnings
Title: Investigation with Warnings
Path: i_warnings.txt
Submission Date:
Public Release Date: None
Prefer recording metadata in the study section.
''',
'Invalid mail address: invalid_mail',
'Invalid phone/fax number: CALL-ME',
'Invalid phone/fax number: FAX-ME',
'Invalid pubmed_id string: not-pubmed',
'Invalid doi string: not-a-doi',
'''
Assay without platform:
Path: a_warnings.txt
Measurement Type: exome sequencing assay
Technology Type: nucleotide sequencing
Technology Platform:
''',
'Assay path used more than once: a_warnings.txt',
"Found samples in assay 'a_warnings.txt' but not in parent study 's_warnings.txt':\\n0815-N2",
"Found samples in assay 'a_warnings.txt' but not in parent study 's_warnings.txt':\\n0815-N2",
])
# ---
15 changes: 9 additions & 6 deletions tests/test_apps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import os.path

import pytest
from syrupy.assertion import SnapshotAssertion
from typer.testing import CliRunner

from altamisa.apps import isatab2dot, isatab2isatab, isatab_validate
Expand All @@ -12,18 +13,18 @@
runner = CliRunner()


def test_isatab_validate():
def test_isatab_validate(snapshot: SnapshotAssertion):
i_file = os.path.join(os.path.dirname(__file__), "data", "i_warnings", "i_warnings.txt")
argv = ["--input-investigation-file", i_file, "--show-duplicate-warnings"]

with pytest.warns(IsaWarning) as record:
result = runner.invoke(isatab_validate.app, argv)
assert result.exit_code == 0

assert 17 == len(record)
assert snapshot == [str(r.message) for r in record]


def test_isatab2isatab(tmpdir):
def test_isatab2isatab(tmpdir, snapshot: SnapshotAssertion):
i_file = os.path.join(os.path.dirname(__file__), "data", "i_minimal", "i_minimal.txt")
argv = [
"--input-investigation-file",
Expand All @@ -38,10 +39,10 @@ def test_isatab2isatab(tmpdir):
result = runner.invoke(isatab2isatab.app, argv)
assert result.exit_code == 0

assert 8 == len(record)
assert snapshot == [str(r.message) for r in record]


def test_isatab2isatab_input_is_output(tmpdir):
def test_isatab2isatab_input_is_output(tmpdir, snapshot: SnapshotAssertion):
i_file = os.path.join(os.path.dirname(__file__), "data", "i_minimal", "i_minimal.txt")
argv = [
"--input-investigation-file",
Expand All @@ -54,7 +55,9 @@ def test_isatab2isatab_input_is_output(tmpdir):

result = runner.invoke(isatab2isatab.app, argv)
assert result.exit_code == 1
assert "Can't output ISA-tab files to same directory as as input" in str(result)
assert snapshot == str(result).replace(
os.path.dirname(__file__), "/home/runner/work/altamisa/tests"
)


def test_isatab2dot(tmpdir):
Expand Down