Merge pull request #180 from vreuter/automicro

Initial case and framework for smoketesting the CLI with microtest

.travis.yml

@@ -10,7 +10,7 @@ install:
   - pip install .
   - pip install -r requirements/requirements-dev.txt
   - pip install -r requirements/requirements-test.txt
-script: pytest
+script: pytest --cov=looper
 branches:
   only:
     - dev

requirements/requirements-test.txt

@@ -1,2 +1,4 @@
 coveralls==1.1
 pytest-cov==2.4.0
+pytest-remotedata
+ubiquerg>=0.0.3dev

tests/conftest.py

@@ -186,7 +186,6 @@
 PROJECT_CONFIG_DATA = {"metadata": {SAMPLE_ANNOTATIONS_KEY: "annotations.csv"}}
 
 
-
 def update_project_conf_data(extension):
     """ Updated Project configuration data mapping based on file extension """
     updated = copy.deepcopy(PROJECT_CONFIG_DATA)
@@ -196,15 +195,13 @@ def update_project_conf_data(extension):
     return updated
 
 
-
 def pytest_addoption(parser):
     """ Facilitate command-line test behavior adjustment. """
     parser.addoption("--logging-level",
                      default="WARN",
                      help="Project root logger level to use for tests")
 
 
-
 def pytest_generate_tests(metafunc):
     """ Centralize dynamic test case parameterization. """
     if "empty_collection" in metafunc.fixturenames:

tests/test_with_microtest_as_smoketest.py

@@ -0,0 +1,70 @@
+""" Use microtest for smoketesting the looper CLI. """
+
+import os
+import subprocess
+import pytest
+from ubiquerg import build_cli_extra
+
+__author__ = "Vince Reuter"
+__email__ = "[email protected]"
+
+
+REPO_NAME = "microtest"
+REPO_URL = "https://github.com/databio/{}".format(REPO_NAME)
+SAMPLE_SELECTOR_OPTION = "--selector-attribute"
+INCLUSION_OPTION = "--selector-include"
+
+
+@pytest.mark.remote_data
+@pytest.fixture
+def data_root(tmpdir):
+    """ Clone data repo and return path to it. """
+    tmp = tmpdir.strpath
+    cmd = "git clone {}".format(REPO_URL)
+    try:
+        subprocess.check_call(cmd, cwd=tmp, shell=True)
+    except subprocess.CalledProcessError:
+        raise Exception("Failed to pull data ()".format(cmd))
+    root = os.path.join(tmp, REPO_NAME)
+    assert os.path.isdir(root)
+    return root
+
+
+@pytest.fixture
+def data_conf_file(data_root):
+    """ Clone data repo and return path to project config file. """
+    f = os.path.join(data_root, "config", "microtest_config.yaml")
+    assert os.path.isfile(f), "Contents: {}".format(os.listdir(data_root))
+    return f
+
+
+@pytest.fixture(scope="function")
+def temp_chdir_home(tmpdir):
+    """ Temporarily (for a test case) change home and working directories. """
+    key = "HOME"
+    prev_home = os.environ[key]
+    prev_work = os.environ["PWD"]
+    curr_home = tmpdir.strpath
+    os.environ[key] = curr_home
+    os.chdir(curr_home)
+    yield
+    os.environ[key] = prev_home
+    os.chdir(prev_work)
+    assert os.getcwd() == prev_work
+    assert os.getenv(key) == prev_home
+    assert os.environ[key] == prev_home
+
+
+@pytest.mark.remote_data
+@pytest.mark.usefixtures("temp_chdir_home")
+@pytest.mark.parametrize("cli_extra",
+    [build_cli_extra(**kvs) for kvs in
+     [{SAMPLE_SELECTOR_OPTION: "protocol", INCLUSION_OPTION: "ATAC-seq"}]])
+def test_cli_microtest_smoke(cli_extra, data_conf_file):
+    """ Using microtest as project, test CLI for failure on specific cases. """
+    cmd = "looper run -d {} {}".format(data_conf_file, cli_extra)
+    try:
+        subprocess.check_call(cmd, shell=True)
+    except Exception as e:
+        print("Exception: {}".format(e))
+        pytest.fail("Failed command: {}".format(cmd))