From 5b44e9abea7ee65edf1cc6bc2813fb0074570e16 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 14 Feb 2018 14:37:03 -0600
Subject: [PATCH] Fix acceptance test to integration tests.
---
.gitlab-ci.yml | 7 +------
workflow/tests/test_call_peaks_macs.py | 4 ++--
workflow/tests/test_convert_reads.py | 2 +-
workflow/tests/test_experiment_design.py | 4 ++--
workflow/tests/test_experiment_qc.py | 4 ++--
workflow/tests/test_map_qc.py | 3 ++-
workflow/tests/test_map_reads.py | 4 ++--
workflow/tests/test_overlap_peaks.py | 4 ++--
workflow/tests/test_pool_and_psuedoreplicate.py | 4 ++--
workflow/tests/test_trim_reads.py | 4 ++--
workflow/tests/test_xcor.py | 4 ++--
11 files changed, 20 insertions(+), 24 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9aebbda..7542f3c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,7 +7,6 @@ before_script:
stages:
- unit
- integration
- - acceptance
user_configuration:
stage: unit
@@ -18,8 +17,4 @@ single_end_mouse:
stage: integration
script:
- nextflow run workflow/main.nf
-
-single_end_acceptance:
- stage: acceptance
- script:
- - pytest -m acceptance
+ - pytest -m integration
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index 62ec2e3..6182f24 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/callPeaksMACS/'
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_call_peaks_macs_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
@@ -16,7 +16,7 @@ def test_call_peaks_macs_singleend():
assert utils.count_lines(peak_file) == 210349
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_call_peaks_macs_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index bae2ff2..1067547 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/convertReads/'
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_convert_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
diff --git a/workflow/tests/test_experiment_design.py b/workflow/tests/test_experiment_design.py
index 7dca74c..51ada86 100644
--- a/workflow/tests/test_experiment_design.py
+++ b/workflow/tests/test_experiment_design.py
@@ -30,7 +30,7 @@ def test_check_update_controls_tag(design_tag):
assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_experiment_design_single_end():
design_file = os.path.join(test_output_path, 'ENCSR238SGC.tsv')
assert os.path.exists(design_file)
@@ -38,7 +38,7 @@ def test_experiment_design_single_end():
assert design_df.shape[0] == 2
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_experiment_qc.py b/workflow/tests/test_experiment_qc.py
index d9ab346..875aea6 100644
--- a/workflow/tests/test_experiment_qc.py
+++ b/workflow/tests/test_experiment_qc.py
@@ -30,7 +30,7 @@ def test_check_update_controls(design_bam):
assert new_design.loc[0, 'control_reads'] == "B_1.bam"
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
@@ -38,7 +38,7 @@ def test_experiment_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_experiment_qc_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 9255e20..a882e53 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/filterReads/'
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_map_qc_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bam.bai'))
@@ -23,6 +23,7 @@ def test_map_qc_singleend():
assert df_library_complexity["PBC2"].iloc[0] == 13.706885
+@pytest.mark.integration
def test_map_qc_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 1bcf609..5c2ff2b 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -7,7 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/alignReads/'
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_map_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.srt.bam'))
aligned_reads_report = test_output_path + 'ENCFF646LXU.srt.bam.flagstat.qc'
@@ -16,7 +16,7 @@ def test_map_reads_singleend():
assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_map_reads_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index 52fa0e5..f75ebcd 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -33,14 +33,14 @@ def test_check_update_design(design_diff):
assert new_design.loc[0, 'peak_caller'] == "bed"
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_overlap_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
assert utils.count_lines(peak_file) == 150302
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_call_peaks_macs_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index de6f94e..6c30f7e 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -60,7 +60,7 @@ def test_check_controls_single(design_experiment_3):
assert no_controls == 1
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_pool_and_psuedoreplicate_single_end():
design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
assert os.path.exists(design_file)
@@ -68,7 +68,7 @@ def test_pool_and_psuedoreplicate_single_end():
assert design_df.shape[0] == 5
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_experiment_design_paired_end():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index ad90935..92f4716 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -10,7 +10,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_trim_reads_pairedend():
# Do the same thing for paired end data
pass
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index d1ccead..cf48408 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -8,7 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/crossReads/'
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_convert_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
@@ -18,7 +18,7 @@ def test_convert_reads_singleend():
assert df_xcor[9].iloc[0] == 1.266678
-@pytest.mark.acceptance
+@pytest.mark.integration
def test_map_qc_pairedend():
# Do the same thing for paired end data
pass
--
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