1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158
|
From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Cleanup test output
Forwarded: https://github.com/common-workflow-language/cwltool/pull/1024
--- cwltool.orig/tests/test_docker.py
+++ cwltool/tests/test_docker.py
@@ -8,9 +8,9 @@
from .util import get_data, get_main_output, needs_docker, needs_singularity
@needs_docker
-def test_docker_workflow():
+def test_docker_workflow(tmpdir):
result_code, _, stderr = get_main_output(
- ['--default-container', 'debian',
+ ['--default-container', 'debian', '--outdir', str(tmpdir),
get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
assert "completed success" in stderr
assert result_code == 0
--- cwltool.orig/tests/test_ext.py
+++ cwltool/tests/test_ext.py
@@ -54,7 +54,7 @@
assert main([get_data('tests/wf/listing_v1_1.cwl'), get_data('tests/listing-job.yml')]) != 0
@needs_docker
-def test_double_overwrite():
+def test_double_overwrite(tmpdir):
try:
tmp = tempfile.mkdtemp()
tmp_name = os.path.join(tmp, "value")
@@ -64,7 +64,8 @@
with open(tmp_name, "w") as f:
f.write(before_value)
- assert main(["--enable-ext", get_data('tests/wf/mut2.cwl'), "-a", tmp_name]) == 0
+ assert main(["--enable-ext", "--outdir", str(tmpdir),
+ get_data('tests/wf/mut2.cwl'), "-a", tmp_name]) == 0
with open(tmp_name, "r") as f:
actual_value = f.read()
@@ -192,8 +193,8 @@
assert main(["--enable-ext", get_data('tests/wf/networkaccess-fail.cwl')]) != 0
@needs_docker
-def test_require_prefix_workreuse():
- assert main(["--enable-ext", get_data('tests/wf/workreuse.cwl')]) == 0
+def test_require_prefix_workreuse(tmpdir):
+ assert main(["--enable-ext", '--outdir', str(tmpdir), get_data('tests/wf/workreuse.cwl')]) == 0
assert main([get_data('tests/wf/workreuse.cwl')]) != 0
assert main(["--enable-ext", get_data('tests/wf/workreuse-fail.cwl')]) != 0
--- cwltool.orig/tests/test_relax_path_checks.py
+++ cwltool/tests/test_relax_path_checks.py
@@ -25,7 +25,7 @@
'''
@needs_docker
-def test_spaces_in_input_files():
+def test_spaces_in_input_files(tmpdir):
try:
script_file = NamedTemporaryFile(mode='w', delete=False)
script_file.write(script)
@@ -35,7 +35,7 @@
spaces = NamedTemporaryFile(prefix="test with spaces", delete=False)
spaces.close()
- params = ["--debug", script_file.name, '--input', spaces.name]
+ params = ["--debug", "--outdir", str(tmpdir), script_file.name, '--input', spaces.name]
assert main(params) == 1
assert main(["--relax-path-checks"] + params) == 0
finally:
--- cwltool.orig/tests/test_toolargparse.py
+++ cwltool/tests/test_toolargparse.py
@@ -78,13 +78,15 @@
@needs_docker
@pytest.mark.parametrize('name,script_contents,params', scripts_argparse_params)
-def test_argparse(name, script_contents, params):
+def test_argparse(name, script_contents, params, tmpdir):
try:
script = NamedTemporaryFile(mode='w', delete=False)
script.write(script_contents)
script.close()
- assert main(params(script.name)) == 0, name
+ my_params = ["--outdir", str(tmpdir)]
+ my_params.extend(params(script.name))
+ assert main(my_params) == 0, name
except SystemExit as err:
assert err.code == 0, name
--- cwltool.orig/tests/test_examples.py
+++ cwltool/tests/test_examples.py
@@ -786,11 +786,11 @@
@needs_docker
-def test_wf_without_container():
+def test_wf_without_container(tmpdir):
test_file = "hello-workflow.cwl"
with temp_dir("cwltool_cache") as cache_dir:
error_code, _, stderr = get_main_output(
- ["--cachedir", cache_dir,
+ ["--cachedir", cache_dir, "--outdir", str(tmpdir),
get_data("tests/wf/" + test_file),
"--usermessage",
"hello"]
@@ -832,11 +832,12 @@
@needs_docker
-def test_no_compute_checksum():
+def test_no_compute_chcksum(tmpdir):
test_file = "tests/wf/wc-tool.cwl"
job_file = "tests/wf/wc-job.json"
error_code, stdout, stderr = get_main_output(
- ["--no-compute-checksum", get_data(test_file), get_data(job_file)])
+ ["--no-compute-checksum", "--outdir", str(tmpdir),
+ get_data(test_file), get_data(job_file)])
assert "completed success" in stderr
assert error_code == 0
assert "checksum" not in stdout
--- cwltool.orig/tests/test_pack.py
+++ cwltool/tests/test_pack.py
@@ -123,7 +123,7 @@
@needs_docker
@pytest.mark.parametrize('wf_path,job_path,namespaced', cwl_to_run)
-def test_packed_workflow_execution(wf_path, job_path, namespaced):
+def test_packed_workflow_execution(wf_path, job_path, namespaced, tmpdir):
load_tool.loaders = {}
document_loader, workflowobj, uri = fetch_document(
@@ -143,8 +143,8 @@
normal_output = StringIO()
packed_output = StringIO()
- normal_params = [get_data(wf_path), get_data(job_path)]
- packed_params = ['--debug', get_data(wf_packed_path), get_data(job_path)]
+ normal_params = ['--outdir', str(tmpdir), get_data(wf_path), get_data(job_path)]
+ packed_params = ['--outdir', str(tmpdir), '--debug', get_data(wf_packed_path), get_data(job_path)]
assert main(normal_params, stdout=normal_output) == 0
assert main(packed_params, stdout=packed_output) == 0
--- cwltool.orig/tests/test_parallel.py
+++ cwltool/tests/test_parallel.py
@@ -8,11 +8,12 @@
@windows_needs_docker
-def test_sequential_workflow():
+def test_sequential_workflow(tmpdir):
load_tool.loaders = {}
test_file = "tests/wf/count-lines1-wf.cwl"
executor = MultithreadedJobExecutor()
runtime_context = RuntimeContext()
+ runtime_context.outdir = str(tmpdir)
runtime_context.select_resources = executor.select_resources
factory = get_windows_safe_factory(
executor=executor, runtime_context=runtime_context)
|