Mercurial > repos > davidvanzessen > shm_csr

comparison tests/test_shm_csr.py @ 98:d714f5ea83d7 draft default tip

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planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
author rhpvorderman
date Wed, 10 Jan 2024 12:32:47 +0000
parents 84e9e5c8c101
children
comparison
equal deleted inserted replaced
97:fbc6307dd83b 98:d714f5ea83d7
47 "Ignore virtualenv and git directories to prevent massive tmp folders" 47 "Ignore virtualenv and git directories to prevent massive tmp folders"
48 if os.path.basename(src) in (".venv", ".git"): 48 if os.path.basename(src) in (".venv", ".git"):
49 return files 49 return files
50 return () 50 return ()
51 51
52 @pytest.fixture(scope="module") 52
53 def shm_csr_result(): 53 def run_shm_csr(
54 input=str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2),
55 infile_name = "input_data",
56 functionality = "productive",
57 unique = "Sequence.ID",
58 naive_output = "no",
59 naive_output_ca = "None",
60 naive_output_cg = "None",
61 naive_output_cm = "None",
62 naive_output_ce = "None",
63 naive_output_all = "None",
64 naive_output_igm_naive = "None",
65 naive_output_igm_naive_memory = "None",
66 filter_unique = "remove",
67 filter_unique_count = '2',
68 class_filter = '70_70',
69 empty_region_filter = 'FR1',
70 # Skip baseline and changeo by default. These tools cannot be modified
71 # anyway and take most of the test time to execute. The environment
72 # variable can be set to "no" on the CI so the code path is tested
73 # at the time a PR is ready.
74 run_changeo = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
75 run_baseline = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no",
76 ):
54 temp_dir = Path(tempfile.mkdtemp()) 77 temp_dir = Path(tempfile.mkdtemp())
55 tool_dir = temp_dir / "shm_csr" 78 tool_dir = temp_dir / "shm_csr"
56 shutil.copytree( 79 shutil.copytree(
57 GIT_ROOT, tool_dir, 80 GIT_ROOT, tool_dir,
58 # Ignore .venv and .git directories. 81 # Ignore .venv and .git directories.
60 working_dir = temp_dir / "working" 83 working_dir = temp_dir / "working"
61 working_dir.mkdir(parents=True) 84 working_dir.mkdir(parents=True)
62 output_dir = temp_dir / "outputs" 85 output_dir = temp_dir / "outputs"
63 output_dir.mkdir(parents=True) 86 output_dir.mkdir(parents=True)
64 wrapper = str(tool_dir / "wrapper.sh") 87 wrapper = str(tool_dir / "wrapper.sh")
65 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
66 out_files_path = output_dir / "results" 88 out_files_path = output_dir / "results"
67 out_file = out_files_path / "result.html" 89 out_file = out_files_path / "result.html"
68 infile_name = "input_data"
69 functionality = "productive"
70 unique = "Sequence.ID"
71 naive_output = "no"
72 naive_output_ca = "None"
73 naive_output_cg = "None"
74 naive_output_cm = "None"
75 naive_output_ce = "None"
76 naive_output_all = "None"
77 naive_output_igm_naive = "None"
78 naive_output_igm_naive_memory = "None"
79 filter_unique = "remove"
80 filter_unique_count = '2'
81 class_filter = '70_70'
82 empty_region_filter = 'FR1'
83 # Skip baseline and changeo by default. These tools cannot be modified
84 # anyway and take most of the test time to execute. The environment
85 # variable can be set to "no" on the CI so the code path is tested
86 # at the time a PR is ready.
87 fast = os.environ.get("SHM_CSR_FAST", "yes")
88 cmd = [ 90 cmd = [
89 "bash", 91 "bash",
90 wrapper, 92 wrapper,
91 input, 93 input,
92 "custom", 94 "custom",
106 naive_output_igm_naive_memory, 108 naive_output_igm_naive_memory,
107 filter_unique, 109 filter_unique,
108 filter_unique_count, 110 filter_unique_count,
109 class_filter, 111 class_filter,
110 empty_region_filter, 112 empty_region_filter,
111 fast 113 run_changeo,
114 run_baseline
112 ] 115 ]
113 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}", 116 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
114 "--rm", # Remove container after running 117 "--rm", # Remove container after running
115 "-v", f"{input}:{input}", 118 "-v", f"{input}:{input}",
116 "-w", str(working_dir), 119 "-w", str(working_dir),
126 ] + cmd 129 ] + cmd
127 with open(temp_dir / "stderr", "wt") as stderr_file: 130 with open(temp_dir / "stderr", "wt") as stderr_file:
128 with open(temp_dir / "stdout", "wt") as stdout_file: 131 with open(temp_dir / "stdout", "wt") as stdout_file:
129 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file, 132 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
130 stderr=stderr_file, check=True) 133 stderr=stderr_file, check=True)
131 yield Path(out_files_path) 134 return Path(out_files_path)
135
136
137 @pytest.fixture(scope="module")
138 def shm_csr_result():
139 yield run_shm_csr()
132 140
133 141
134 def test_check_output(shm_csr_result): 142 def test_check_output(shm_csr_result):
135 assert shm_csr_result.exists() 143 assert shm_csr_result.exists()
136 144
155 ) as result_h: 163 ) as result_h:
156 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt") 164 with open(Path(TEST_DIR, "sequence_overview", "ntoverview.txt")
157 ) as validate_h: 165 ) as validate_h:
158 for line in result_h: 166 for line in result_h:
159 assert line == validate_h.readline() 167 assert line == validate_h.readline()
168
169
170 def test_baseline_succeeds():
171 run_shm_csr(
172 functionality="unproductive",
173 empty_region_filter="None",
174 filter_unique="no",
175 unique="VGene,DGene,JGene,CDR3.IMGT.seq",
176 class_filter="101_101_IGA",
177 naive_output="yes",
178 run_baseline="yes",
179 run_changeo="yes",
180 )