def test_topic_create_topic_structure():
"""Test :func:`planemo.training.topic.Topic.create_topic_structure`."""
topic = Topic()
topic.create_topic_structure()
topic_name = "new_topic"
topic_title = "The new topic"
# check the folder and its structure
assert topic.exists()
assert os.path.exists(topic.img_folder)
assert os.path.exists(topic.tuto_folder)
# create the index.md and the topic name
assert os.path.exists(topic.index_fp)
assert topic_name in open(topic.index_fp, 'r').read()
# create the README.md and the topic name
assert os.path.exists(topic.readme_fp)
assert topic_title in open(topic.readme_fp, 'r').read()
# check metadata content
assert os.path.exists(topic.metadata_fp)
metadata = load_yaml(topic.metadata_fp)
assert metadata['name'] == topic_name
# check dockerfile
assert os.path.exists(topic.dockerfile_fp)
assert topic_name in open(topic.dockerfile_fp, 'r').read()
assert topic_title in open(topic.dockerfile_fp, 'r').read()
# check introduction slide
assert os.path.exists(topic.intro_slide_fp)
assert topic_title in open(topic.intro_slide_fp, 'r').read()
# check in metadata directory
assert os.path.exists(os.path.join("metadata", "%s.yaml" % topic_name))
# clean
shutil.rmtree(topic.parent_dir)
shutil.rmtree("metadata")
def test_topic_create_topic_structure():
"""Test :func:`planemo.training.topic.Topic.create_topic_structure`."""
topic = Topic()
topic.create_topic_structure()
topic_name = "new_topic"
topic_title = "The new topic"
# check the folder and its structure
assert topic.exists()
assert os.path.exists(topic.img_folder)
assert os.path.exists(topic.tuto_folder)
# create the index.md and the topic name
assert os.path.exists(topic.index_fp)
assert topic_name in open(topic.index_fp, 'r').read()
# create the README.md and the topic name
assert os.path.exists(topic.readme_fp)
assert topic_title in open(topic.readme_fp, 'r').read()
# check metadata content
assert os.path.exists(topic.metadata_fp)
metadata = load_yaml(topic.metadata_fp)
assert metadata['name'] == topic_name
# check dockerfile
assert os.path.exists(topic.dockerfile_fp)
assert topic_name in open(topic.dockerfile_fp, 'r').read()
assert topic_title in open(topic.dockerfile_fp, 'r').read()
# check introduction slide
assert os.path.exists(topic.intro_slide_fp)
assert topic_title in open(topic.intro_slide_fp, 'r').read()
# check in metadata directory
assert os.path.exists(os.path.join("metadata", "%s.yaml" % topic_name))
# clean
shutil.rmtree(topic.parent_dir)
shutil.rmtree("metadata")
def test_topic_exists():
"""Test :func:`planemo.training.topic.Topic.exists`."""
topic = Topic()
assert not topic.exists()
os.makedirs(topic.dir)
assert topic.exists()
shutil.rmtree(topic.parent_dir)
def test_topic_exists():
"""Test :func:`planemo.training.topic.Topic.exists`."""
topic = Topic()
assert not topic.exists()
os.makedirs(topic.dir)
assert topic.exists()
shutil.rmtree(topic.parent_dir)
def test_topic_init_from_metadata():
"""Test :func:`planemo.training.topic.Topic.init_from_metadata`."""
topic = Topic()
os.makedirs(topic.dir)
shutil.copy(os.path.join(TEST_DATA_DIR, 'training_metadata.yaml'), topic.metadata_fp)
topic.init_from_metadata()
assert topic.name == 'test'
assert topic.title == 'Test'
assert topic.summary == 'Summary'
assert topic.requirements[0].title == 'Galaxy introduction'
assert 'maintainer1' in topic.maintainers
shutil.rmtree(topic.parent_dir)
def test_topic_export_metadata_to_ordered_dict():
"""Test :func:`planemo.training.topic.Topic.export_metadata_to_ordered_dict`."""
topic = Topic()
metadata = topic.export_metadata_to_ordered_dict()
assert 'name' in metadata
assert metadata['name'] == "new_topic"
assert 'type' in metadata
assert 'title' in metadata
assert 'summary' in metadata
assert 'requirements' in metadata
assert 'docker_image' in metadata
assert 'maintainers' in metadata
def test_topic_export_metadata_to_ordered_dict():
"""Test :func:`planemo.training.topic.Topic.export_metadata_to_ordered_dict`."""
topic = Topic()
metadata = topic.export_metadata_to_ordered_dict()
assert 'name' in metadata
assert metadata['name'] == "new_topic"
assert 'type' in metadata
assert 'title' in metadata
assert 'summary' in metadata
assert 'requirements' in metadata
assert 'docker_image' in metadata
assert 'maintainers' in metadata
assert 'references' in metadata
def test_topic_init_from_metadata():
"""Test :func:`planemo.training.topic.Topic.init_from_metadata`."""
topic = Topic()
os.makedirs(topic.dir)
shutil.copy(os.path.join(TEST_DATA_DIR, 'training_metadata.yaml'), topic.metadata_fp)
topic.init_from_metadata()
assert topic.name == 'test'
assert topic.title == 'Test'
assert topic.summary == 'Summary'
assert topic.requirements[0].topic_name == 'introduction'
assert topic.requirements[0].tutorials == ['peaks2genes']
assert 'maintainer1' in topic.maintainers
shutil.rmtree(topic.parent_dir)
def test_topic_set_paths():
"""Test :func:`planemo.training.topic.Topic.set_paths`."""
new_name = 'the_new_name'
topic = Topic()
topic.name = new_name
topic.set_paths()
assert new_name in topic.dir
assert new_name in topic.img_folder
assert new_name in topic.tuto_folder
assert new_name in topic.index_fp
assert new_name in topic.readme_fp
assert new_name in topic.metadata_fp
assert new_name in topic.docker_folder
assert new_name in topic.dockerfile_fp
assert new_name in topic.slides_folder
def test_topic_set_paths():
"""Test :func:`planemo.training.topic.Topic.set_paths`."""
new_name = 'the_new_name'
topic = Topic()
topic.name = new_name
topic.set_paths()
assert new_name in topic.dir
assert new_name in topic.img_folder
assert new_name in topic.tuto_folder
assert new_name in topic.index_fp
assert new_name in topic.readme_fp
assert new_name in topic.metadata_fp
assert new_name in topic.docker_folder
assert new_name in topic.dockerfile_fp
assert new_name in topic.slides_folder
def test_topic_init_from_kwds():
"""Test :func:`planemo.training.topic.Topic.init_from_kwds`."""
topic = Topic()
topic.init_from_kwds({
'topic_name': "topic",
'topic_title': "New topic",
'topic_target': "admin",
'topic_summary': "Topic summary"
})
assert topic.name == "topic"
assert topic.type == "admin"
assert topic.title == "New topic"
assert topic.summary == "Topic summary"
assert topic.dir == "topics/topic"
assert len(topic.requirements) == 0
def test_topic_init_from_kwds():
"""Test :func:`planemo.training.topic.Topic.init_from_kwds`."""
topic = Topic()
topic.init_from_kwds({
'topic_name': "topic",
'topic_title': "New topic",
'topic_target': "admin",
'topic_summary': "Topic summary"
})
assert topic.name == "topic"
assert topic.type == "admin"
assert topic.title == "New topic"
assert topic.summary == "Topic summary"
assert topic.dir == "topics/topic"
assert len(topic.requirements) == 0
assert len(topic.references) == 0
def test_topic_get_references():
"""Test :func:`planemo.training.topic.Topic.get_references`."""
topic = Topic()
refs = topic.get_references()
assert len(refs) == 1
assert 'authors' in refs[0]
def test_topic_get_requirements():
"""Test :func:`planemo.training.topic.Topic.get_requirements`."""
topic = Topic()
reqs = topic.get_requirements()
assert len(reqs) == 1
assert 'title' in reqs[0]
def test_topic_get_references():
"""Test :func:`planemo.training.topic.Topic.get_references`."""
topic = Topic()
refs = topic.get_references()
assert len(refs) == 1
assert 'authors' in refs[0]
def test_topic_get_requirements():
"""Test :func:`planemo.training.topic.Topic.get_requirements`."""
topic = Topic()
reqs = topic.get_requirements()
assert len(reqs) == 1
assert 'topic_name' in reqs[0]