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jmchiltonjmchilton
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Run dependency script tests in isolated directories.
Otherwise files get written in Planemo's directory directly. Also cleanup some environment handling TODOs now that we have abandoned Python 2.6.
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‎tests/test_dependency_script.py‎

Lines changed: 61 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
import glob
22
import os
3+
import shutil
34
import tempfile
45

56
from .test_utils import (
@@ -9,25 +10,31 @@
910
)
1011

1112

12-
# This is a bit of a hack, but having failed to get the test
13-
# script to see $INSTALL_DIR and $DOWNLOAD_CACHE set via
14-
# .travis.yml this is an alternative.
15-
temp_dir = tempfile.mkdtemp()
16-
for env_var, default in [
17-
("INSTALL_DIR", os.path.join(temp_dir, "install_dir")),
18-
("DOWNLOAD_CACHE", os.path.join(temp_dir, "download_cache")),
19-
]:
20-
if env_var not in os.environ:
21-
os.environ[env_var] = default
22-
os.makedirs(default)
23-
value = os.environ[env_var]
24-
print("Using $%s=%s" % (env_var, value))
25-
assert os.path.isdir(value), value
26-
# TODO - Once drop Python 2.6, create and remove temp_dir via
27-
# setUpClass and tearDownClass methos
13+
class DependencyScriptTestCase(CliTestCase):
2814

15+
@classmethod
16+
def setUpClass(clazz):
17+
# This is a bit of a hack, but having failed to get the test
18+
# script to see $INSTALL_DIR and $DOWNLOAD_CACHE set via
19+
# .travis.yml this is an alternative.
20+
temp_dir = tempfile.mkdtemp()
21+
clazz.install_dir = os.path.join(temp_dir, "install_dir")
22+
clazz.download_cache = os.path.join(temp_dir, "download_cache")
2923

30-
class DependencyScriptTestCase(CliTestCase):
24+
for env_var, default in [
25+
("INSTALL_DIR", clazz.install_dir),
26+
("DOWNLOAD_CACHE", clazz.download_cache),
27+
]:
28+
if env_var not in os.environ:
29+
os.environ[env_var] = default
30+
os.makedirs(default)
31+
value = os.environ[env_var]
32+
assert os.path.isdir(value), value
33+
34+
@classmethod
35+
def tearDownClass(clazz):
36+
shutil.rmtree(clazz.install_dir)
37+
shutil.rmtree(clazz.download_cache)
3138

3239
def setUp(self):
3340
# Pass to base-class
@@ -40,53 +47,61 @@ def setUp(self):
4047
self.repo_list = repo_list
4148

4249
def test_empty_file(self):
43-
# Using empty file repos/fastqc/tool_dependencies.xml
44-
ds_cmd = ["dependency_script",
45-
os.path.join(TEST_REPOS_DIR, "fastqc")]
46-
self._check_exit_code(ds_cmd, 1)
50+
with self._isolate():
51+
# Using empty file repos/fastqc/tool_dependencies.xml
52+
ds_cmd = ["dependency_script",
53+
os.path.join(TEST_REPOS_DIR, "fastqc")]
54+
self._check_exit_code(ds_cmd, 1)
4755

4856
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
4957
def test_samtools_example(self):
50-
# Also checking the --download_cache option
51-
ds_cmd = ["dependency_script",
52-
"--download_cache", os.environ["DOWNLOAD_CACHE"],
53-
os.path.join(TEST_REPOS_DIR, "package_1")]
54-
self._check_exit_code(ds_cmd, 0)
58+
with self._isolate():
59+
# Also checking the --download_cache option
60+
ds_cmd = ["dependency_script",
61+
"--download_cache", os.environ["DOWNLOAD_CACHE"],
62+
os.path.join(TEST_REPOS_DIR, "package_1")]
63+
self._check_exit_code(ds_cmd, 0)
5564

5665
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
5766
def test_cd_hit_auxtools(self):
58-
ds_cmd = ["dependency_script",
59-
os.path.join(TEST_REPOS_DIR, "bad_repo_name")]
60-
self._check_exit_code(ds_cmd, 0)
67+
with self._isolate():
68+
ds_cmd = ["dependency_script",
69+
os.path.join(TEST_REPOS_DIR, "bad_repo_name")]
70+
self._check_exit_code(ds_cmd, 0)
6171

6272
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
6373
def test_good_examples(self):
64-
ds_cmd = ["dependency_script",
65-
os.path.join(TEST_REPOS_DIR, "package_1"),
66-
os.path.join(TEST_REPOS_DIR, "bad_package_category/"),
67-
os.path.join(TEST_REPOS_DIR, "bad_repo_name")]
68-
self._check_exit_code(ds_cmd, 0)
74+
with self._isolate():
75+
ds_cmd = ["dependency_script",
76+
os.path.join(TEST_REPOS_DIR, "package_1"),
77+
os.path.join(TEST_REPOS_DIR, "bad_package_category/"),
78+
os.path.join(TEST_REPOS_DIR, "bad_repo_name")]
79+
self._check_exit_code(ds_cmd, 0)
6980

7081
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
7182
def test_repos_recurse(self):
72-
# At least one will fail
73-
ds_cmd = ["dependency_script", "-r", TEST_REPOS_DIR]
74-
self._check_exit_code(ds_cmd, 1)
83+
with self._isolate():
84+
# At least one will fail
85+
ds_cmd = ["dependency_script", "-r", TEST_REPOS_DIR]
86+
self._check_exit_code(ds_cmd, 1)
7587

7688
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
7789
def test_repos_recurse_fast(self):
78-
# At least one will fail
79-
ds_cmd = ["dependency_script", "--fail_fast", "-r", TEST_REPOS_DIR]
80-
self._check_exit_code(ds_cmd, 1)
90+
with self._isolate():
91+
# At least one will fail
92+
ds_cmd = ["dependency_script", "--fail_fast", "-r", TEST_REPOS_DIR]
93+
self._check_exit_code(ds_cmd, 1)
8194

8295
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
8396
def test_repos_list(self):
84-
# At least one will fail
85-
ds_cmd = ["dependency_script"] + self.repo_list
86-
self._check_exit_code(ds_cmd, 1)
97+
with self._isolate():
98+
# At least one will fail
99+
ds_cmd = ["dependency_script"] + self.repo_list
100+
self._check_exit_code(ds_cmd, 1)
87101

88102
@skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
89103
def test_repos_list_fast(self):
90-
# At least one will fail
91-
ds_cmd = ["dependency_script", "--fail_fast"] + self.repo_list
92-
self._check_exit_code(ds_cmd, 1)
104+
with self._isolate():
105+
# At least one will fail
106+
ds_cmd = ["dependency_script", "--fail_fast"] + self.repo_list
107+
self._check_exit_code(ds_cmd, 1)

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