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Updated pipeline and formatted code
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Pipeline now looks for correct unit test file
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Harrison Deng 2023-06-27 14:15:03 +00:00
parent 58adf3efe8
commit 8cd09bfb41
3 changed files with 24 additions and 8 deletions
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2
Jenkinsfile vendored
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@ -9,7 +9,7 @@ pipeline {
} }
stage("unit tests") { stage("unit tests") {
steps { steps {
sh returnStatus: true, script: "python -m pytest --junitxml=unit_tests.xml --cov-report xml:test_coverage.xml --cov=modvcfsamples" sh returnStatus: true, script: "python -m pytest --junitxml=test_results.xml --cov-report xml:test_coverage.xml --cov=modvcfsamples"
xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)] xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results.xml', stopProcessingIfError: true)]
cobertura autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'test_coverage.xml', failUnhealthy: false, failUnstable: false, maxNumberOfBuilds: 64, lineCoverageTargets: '50, 0, 0', methodCoverageTargets: '50, 0, 0', onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false cobertura autoUpdateHealth: false, autoUpdateStability: false, coberturaReportFile: 'test_coverage.xml', failUnhealthy: false, failUnstable: false, maxNumberOfBuilds: 64, lineCoverageTargets: '50, 0, 0', methodCoverageTargets: '50, 0, 0', onlyStable: false, sourceEncoding: 'ASCII', zoomCoverageChart: false
} }

26
tests/modvcfsamples/test_sample.py
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@ -1,14 +1,24 @@
from modvcfsamples.sample import keep_specific_call_data, get_records_from_vcf, normalize_gt_to_length from modvcfsamples.sample import (
keep_specific_call_data,
get_records_from_vcf,
normalize_gt_to_length,
)
import os import os
def test_filter_all_sample_datatypes_not_empty(): def test_filter_all_sample_datatypes_not_empty():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf")) records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened.vcf")
)
filter_for = ["GT"] filter_for = ["GT"]
modified_records, header = keep_specific_call_data(records, header, *filter_for) modified_records, header = keep_specific_call_data(records, header, *filter_for)
assert len(modified_records) == 11 assert len(modified_records) == 11
def test_filter_all_sample_datatypes_filtered(): def test_filter_all_sample_datatypes_filtered():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened.vcf")) records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened.vcf")
)
filter_for = ["GT"] filter_for = ["GT"]
modified_records, header = keep_specific_call_data(records, header, *filter_for) modified_records, header = keep_specific_call_data(records, header, *filter_for)
for modified_record in modified_records: for modified_record in modified_records:
@ -17,13 +27,19 @@ def test_filter_all_sample_datatypes_filtered():
for key, _ in call.data.items(): for key, _ in call.data.items():
assert key in filter_for assert key in filter_for
def test_normalize_gt_to_length_not_empty(): def test_normalize_gt_to_length_not_empty():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")) records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
)
modified_records, _ = normalize_gt_to_length(records, header, 4) modified_records, _ = normalize_gt_to_length(records, header, 4)
assert len(modified_records) > 0 assert len(modified_records) > 0
def test_normalize_gt_to_length_gt_normalized(): def test_normalize_gt_to_length_gt_normalized():
records, header = get_records_from_vcf(os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")) records, header = get_records_from_vcf(
os.path.abspath("tests/resources/test_files_shortened_haploid.vcf")
)
modified_records, _ = normalize_gt_to_length(records, header, 4) modified_records, _ = normalize_gt_to_length(records, header, 4)
for modified_record in modified_records: for modified_record in modified_records:
for call in modified_record.calls: for call in modified_record.calls: