From bad714b483c24d6341cf2ff89f3a3278c13ddadc Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 14 Feb 2018 10:15:13 -0600
Subject: [PATCH] Update testing setup.

---
 .gitlab-ci.yml                                | 21 ++++++++++++++++---
 workflow/tests/test_call_peaks_macs.py        |  2 ++
 workflow/tests/test_check_design.py           |  8 +++++++
 workflow/tests/test_convert_reads.py          |  2 ++
 workflow/tests/test_experiment_design.py      |  3 +++
 workflow/tests/test_experiment_qc.py          |  4 +++-
 workflow/tests/test_map_qc.py                 |  1 +
 workflow/tests/test_map_reads.py              |  2 ++
 workflow/tests/test_overlap_peaks.py          |  5 ++++-
 .../tests/test_pool_and_psuedoreplicate.py    |  6 ++++++
 workflow/tests/test_trim_reads.py             |  3 +++
 workflow/tests/test_utils.py                  |  6 ++++++
 workflow/tests/test_xcor.py                   |  2 ++
 13 files changed, 60 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index bc3e9e8..5b68a72 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,22 @@ before_script:
   - module load nextflow/0.24.1-SNAPSHOT
   - ln -s /project/shared/bicf_workflow_ref/workflow_testdata/chipseq/*fastq.gz test_data/
 
-test:
+stages:
+  - unit
+  - integration
+  - acceptance
+
+user_configuration:
+  stage: unit
+  script:
+  - pytest -m unit
+
+single_end_mouse:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf
+
+single_end_acceptance:
+  stage: unit
   script:
-  - nextflow run workflow/main.nf 
-  - pytest
+  - pytest -m acceptance
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index aba3570..62ec2e3 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -8,6 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/callPeaksMACS/'
 
 
+@pytest.mark.acceptance
 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'))
@@ -15,6 +16,7 @@ def test_call_peaks_macs_singleend():
     assert utils.count_lines(peak_file) == 210349
 
 
+@pytest.mark.acceptance
 def test_call_peaks_macs_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_check_design.py b/workflow/tests/test_check_design.py
index 23575ec..517c53c 100644
--- a/workflow/tests/test_check_design.py
+++ b/workflow/tests/test_check_design.py
@@ -70,6 +70,7 @@ def fastq_files_1(fastq_files):
     return fastq_df
 
 
+@pytest.mark.unit
 def test_check_headers_singleend(design_1):
     paired = False
     with pytest.raises(Exception) as excinfo:
@@ -77,6 +78,7 @@ def test_check_headers_singleend(design_1):
     assert str(excinfo.value) == "Missing column headers: ['fastq_read1']"
 
 
+@pytest.mark.unit
 def test_check_headers_pairedend(design):
     paired = True
     with pytest.raises(Exception) as excinfo:
@@ -84,12 +86,14 @@ def test_check_headers_pairedend(design):
     assert str(excinfo.value) == "Missing column headers: ['fastq_read2']"
 
 
+@pytest.mark.unit
 def test_check_controls(design_2):
     with pytest.raises(Exception) as excinfo:
         check_design.check_controls(design_2)
     assert str(excinfo.value) == "Missing control experiments: ['B_1']"
 
 
+@pytest.mark.unit
 def test_check_files_missing_files(design, fastq_files_1):
     paired = False
     with pytest.raises(Exception) as excinfo:
@@ -97,18 +101,22 @@ def test_check_files_missing_files(design, fastq_files_1):
     assert str(excinfo.value) == "Missing files from design file: ['B_2.fastq.gz']"
 
 
+@pytest.mark.unit
 def test_check_files_output_singleend(design, fastq_files):
     paired = False
     new_design = check_design.check_files(design, fastq_files, paired)
     assert new_design.loc[0, 'fastq_read1'] == "/path/to/file/A_1.fastq.gz"
 
 
+@pytest.mark.unit
 def test_check_files_output_pairedend(design_3, fastq_files):
     paired = True
     new_design = check_design.check_files(design_3, fastq_files, paired)
     assert new_design.loc[0, 'fastq_read2'] == "/path/to/file/A_2.fastq.gz"
 
 
+
+@pytest.mark.unit
 def test_check_replicates(design_4):
     paired = False
     with pytest.raises(Exception) as excinfo:
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index 4ee7ee1..bae2ff2 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -7,11 +7,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/convertReads/'
 
 
+@pytest.mark.acceptance
 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'))
 
 
+@pytest.mark.integration
 def test_map_qc_pairedend():
     # Do the same thing for paired end data
     # Also check that bedpe exists
diff --git a/workflow/tests/test_experiment_design.py b/workflow/tests/test_experiment_design.py
index bfbd3c0..7dca74c 100644
--- a/workflow/tests/test_experiment_design.py
+++ b/workflow/tests/test_experiment_design.py
@@ -24,11 +24,13 @@ def design_tag():
     return design_df
 
 
+@pytest.mark.unit
 def test_check_update_controls_tag(design_tag):
     new_design = experiment_design.update_controls(design_tag)
     assert new_design.loc[0, 'control_tag_align'] == "B_1.tagAlign.gz"
 
 
+@pytest.mark.acceptance
 def test_experiment_design_single_end():
     design_file = os.path.join(test_output_path, 'ENCSR238SGC.tsv')
     assert os.path.exists(design_file)
@@ -36,6 +38,7 @@ def test_experiment_design_single_end():
     assert design_df.shape[0] == 2
 
 
+@pytest.mark.acceptance
 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 16f6b00..d9ab346 100644
--- a/workflow/tests/test_experiment_qc.py
+++ b/workflow/tests/test_experiment_qc.py
@@ -24,11 +24,13 @@ def design_bam():
     return design_df
 
 
+@pytest.mark.unit
 def test_check_update_controls(design_bam):
     new_design = experiment_qc.update_controls(design_bam)
     assert new_design.loc[0, 'control_reads'] == "B_1.bam"
 
 
+@pytest.mark.acceptance
 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'))
@@ -36,7 +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
 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 ebc2cd5..9255e20 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -8,6 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/filterReads/'
 
 
+@pytest.mark.acceptance
 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'))
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 04ffd08..1bcf609 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -7,6 +7,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/alignReads/'
 
 
+@pytest.mark.acceptance
 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'
@@ -15,6 +16,7 @@ def test_map_reads_singleend():
     assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
 
 
+@pytest.mark.acceptance
 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 db22fb8..52fa0e5 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -25,6 +25,7 @@ def design_diff():
     return design_df
 
 
+@pytest.mark.unit
 def test_check_update_design(design_diff):
     new_design = overlap_peaks.update_design(design_diff)
     assert new_design.shape[0] == 2
@@ -32,12 +33,14 @@ def test_check_update_design(design_diff):
     assert new_design.loc[0, 'peak_caller'] == "bed"
 
 
+@pytest.mark.acceptance
 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) == 150096
+    assert utils.count_lines(peak_file) == 150302
 
 
+@pytest.mark.acceptance
 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 b7a351d..de6f94e 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -36,26 +36,31 @@ def design_experiment_3(design_experiment):
     return design_experiment
 
 
+@pytest.mark.unit
 def test_check_replicates(design_experiment):
     no_reps = pool_and_psuedoreplicate.check_replicates(design_experiment)
     assert no_reps == 2
 
 
+@pytest.mark.unit
 def test_check_replicates_single(design_experiment_2):
     no_reps = pool_and_psuedoreplicate.check_replicates(design_experiment_2)
     assert no_reps == 1
 
 
+@pytest.mark.unit
 def test_check_controls(design_experiment):
     no_controls = pool_and_psuedoreplicate.check_controls(design_experiment)
     assert no_controls == 2
 
 
+@pytest.mark.unit
 def test_check_controls_single(design_experiment_3):
     no_controls = pool_and_psuedoreplicate.check_controls(design_experiment_3)
     assert no_controls == 1
 
 
+@pytest.mark.acceptance
 def test_pool_and_psuedoreplicate_single_end():
     design_file = os.path.join(test_output_path, 'ENCSR238SGC_ppr.tsv')
     assert os.path.exists(design_file)
@@ -63,6 +68,7 @@ def test_pool_and_psuedoreplicate_single_end():
     assert design_df.shape[0] == 5
 
 
+@pytest.mark.acceptance
 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 7ca0375..ad90935 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -9,6 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/trimReads/'
 
 
+
+@pytest.mark.acceptance
 def test_trim_reads_singleend():
     raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
     trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
@@ -19,6 +21,7 @@ def test_trim_reads_singleend():
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
 
 
+@pytest.mark.acceptance
 def test_trim_reads_pairedend():
     # Do the same thing for paired end data
     pass
diff --git a/workflow/tests/test_utils.py b/workflow/tests/test_utils.py
index 0abba1b..66b9c11 100644
--- a/workflow/tests/test_utils.py
+++ b/workflow/tests/test_utils.py
@@ -29,6 +29,7 @@ def steps_2(steps_1):
     return steps_1
 
 
+@pytest.mark.unit
 def test_run_one_step(steps_1, capsys):
     check_output = 'ENCLB144FDT\tENCSR238SGC\tlimb\tH3K4me1\tNone\t1\tENCLB304SBJ\tENCFF833BLU.fastq.gz'.encode('UTF-8')
     out, err = utils.run_pipe(steps_1)
@@ -37,6 +38,7 @@ def test_run_one_step(steps_1, capsys):
     assert check_output in out
 
 
+@pytest.mark.unit
 def test_run_two_step(steps_2, capsys):
     check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'.encode('UTF-8')
     out, err = utils.run_pipe(steps_2)
@@ -45,6 +47,7 @@ def test_run_two_step(steps_2, capsys):
     assert check_output in out
 
 
+@pytest.mark.unit
 def test_run_last_step_file(steps_2, capsys, tmpdir):
     check_output = 'ENCFF833BLU.fastq.gz\nENCFF646LXU.fastq.gz'
     tmp_outfile = tmpdir.join('output.txt')
@@ -54,16 +57,19 @@ def test_run_last_step_file(steps_2, capsys, tmpdir):
     assert check_output in tmp_outfile.read()
 
 
+@pytest.mark.unit
 def test_strip_extensions():
     filename = utils.strip_extensions('ENCFF833BLU.fastq.gz', STRIP_EXTENSIONS)
     assert filename == 'ENCFF833BLU'
 
 
+@pytest.mark.unit
 def test_strip_extensions_not_valid():
     filename = utils.strip_extensions('ENCFF833BLU.not.valid', STRIP_EXTENSIONS)
     assert filename == 'ENCFF833BLU.not.valid'
 
 
+@pytest.mark.unit
 def test_strip_extensions_missing_basename():
     filename = utils.strip_extensions('.fastq.gz', STRIP_EXTENSIONS)
     assert filename == '.fastq'
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index b0eafa3..d1ccead 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -8,6 +8,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/crossReads/'
 
 
+@pytest.mark.acceptance
 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")
@@ -17,6 +18,7 @@ def test_convert_reads_singleend():
     assert df_xcor[9].iloc[0] == 1.266678
 
 
+@pytest.mark.acceptance
 def test_map_qc_pairedend():
     # Do the same thing for paired end data
     pass
-- 
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