def test_tutorial_init_from_kwds():
"""Test :func:`planemo.training.tutorial.tutorial.init_from_kwds`."""
kwds = {
'tutorial_name': "my_tuto",
'tutorial_title': "Title of tuto",
'hands_on': True,
'slides': True,
'workflow': WF_FP,
'workflow_id': 'id',
'zenodo_link': None,
'datatypes': datatype_fp
}
tuto = Tutorial(
training=training,
topic=topic)
tuto.init_from_kwds(kwds)
assert tuto.name == "my_tuto"
assert tuto.title == "Title of tuto"
assert tuto.zenodo_link == ''
assert "Which biological questions are addressed by the tutorial?" in tuto.questions
assert tuto.hands_on
assert tuto.slides
assert tuto.init_wf_id == 'id'
assert tuto.init_wf_fp == WF_FP
assert tuto.datatype_fp == datatype_fp
assert "my_tuto" in tuto.dir
def test_tutorial_get_tuto_metata():
"""Test :func:`planemo.training.tutorial.tutorial.get_tuto_metata`."""
tuto = Tutorial(
training=training,
topic=topic)
tuto.questions = ['q1', 'q2']
metadata = tuto.get_tuto_metata()
assert 'title: The new tutorial' in metadata
assert '- q1' in metadata
def test_tutorial_exists():
"""Test :func:`planemo.training.tutorial.tutorial.exists`."""
# default
tuto = Tutorial(
training=training,
topic=topic)
assert not tuto.exists()
# after dir creation
os.makedirs(tuto.dir)
assert tuto.exists()
shutil.rmtree("topics")
def test_tutorial_set_dir_name():
"""Test :func:`planemo.training.tutorial.tutorial.set_dir_name`."""
tuto = Tutorial(
training=training,
topic=topic)
tuto.name = "the_tuto"
tuto.set_dir_name()
assert tuto.name in tuto.dir
assert tuto.name in tuto.tuto_fp
assert tuto.name in tuto.slide_fp
assert tuto.name in tuto.data_lib_fp
assert tuto.name in tuto.wf_dir
assert tuto.name in tuto.wf_fp
def test_tutorial_write_hands_on_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.write_hands_on_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
tuto.zenodo_file_links = ["URL1", "URL2"]
tuto.write_hands_on_tutorial()
assert os.path.exists(tuto.tuto_fp)
with open(tuto.tuto_fp, 'r') as tuto_f:
tuto_c = tuto_f.read()
assert 'layout: tutorial_hands_on' in tuto_c
assert '# Introduction' in tuto_c
assert 'URL1' in tuto_c
assert '# Conclusion' in tuto_c
shutil.rmtree("topics")
def test_tutorial_get_files_from_zenodo():
"""Test :func:`planemo.training.tutorial.tutorial.get_files_from_zenodo`."""
tuto = Tutorial(
training=training,
topic=topic,
zenodo_link=zenodo_link)
tuto.datatype_fp = datatype_fp
files, z_record = tuto.get_files_from_zenodo()
assert z_record == "1321885"
# test links
file_link_prefix = "https://zenodo.org/api/files/51a1b5db-ff05-4cda-83d4-3b46682f921f"
assert file_link_prefix in tuto.zenodo_file_links[0]
# test files dict
assert file_link_prefix in files[0]['url']
assert files[0]['src'] == 'url'
assert files[0]['info'] == zenodo_link
assert "# Please add" in files[0]['ext']
assert files[1]['ext'] == 'csv'
def test_tutorial_init_from_existing_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.init_from_existing_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
# non existing tutorial
exp_exception = "The tutorial existing_tutorial does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
tuto.init_from_existing_tutorial('existing_tutorial')
# existing tutorial
create_existing_tutorial('existing_tutorial', tuto_fp, tuto.topic)
tuto.init_from_existing_tutorial('existing_tutorial')
assert tuto.title == 'A tutorial to test'
assert "A learning objective" in tuto.objectives
assert tuto.time_estimation == "1H"
assert 'the_best_contributor' in tuto.contributors
assert '# First section' in tuto.body
shutil.rmtree("topics")
def test_tutorial_has_workflow():
"""Test :func:`planemo.training.tutorial.tutorial.has_workflow`."""
# default
tuto = Tutorial(
training=training,
topic=topic)
assert not tuto.has_workflow()
# with wf filepath
tuto.init_wf_fp = WF_FP
assert tuto.has_workflow()
# with no wf filepah nor wf id
tuto.init_wf_fp = None
tuto.init_wf_id = ''
assert not tuto.has_workflow()
# with wf id
tuto.init_wf_id = 'ID'
assert tuto.has_workflow()
def test_tutorial_create_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.create_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
tuto.init_from_kwds({
'tutorial_name': "my_tuto",
'tutorial_title': "Title of tuto",
'hands_on': True,
'slides': True,
'workflow': WF_FP,
'workflow_id': None,
'zenodo_link': zenodo_link,
'datatypes': datatype_fp
})
tuto.create_tutorial(CTX)
assert os.path.exists(tuto.dir)
assert os.path.exists(tuto.tour_dir)
assert os.path.exists(tuto.wf_dir)
assert os.path.exists(tuto.data_lib_fp)
assert os.path.exists(tuto.tuto_fp)
assert os.path.exists(tuto.slide_fp)
assert 'layout: tutorial_slides' in open(tuto.slide_fp, 'r').read()
shutil.rmtree("topics")
def test_tutorial_init_data_lib():
"""Test :func:`planemo.training.tutorial.tutorial.init_data_lib`."""
tuto = Tutorial(
training=training,
topic=topic)
tuto.init_data_lib()
assert tuto.data_lib['destination']['type'] == 'library'
assert tuto.data_lib['items'][0]['name'] == topic.title
assert tuto.data_lib['items'][0]['items'][0]['name'] == tuto.title
# from existing data library file
os.makedirs(tuto.dir)
tuto.data_lib = {}
tuto.init_data_lib()
assert tuto.data_lib['items'][0]['name'] == topic.title
assert tuto.data_lib['items'][0]['items'][0]['name'] == tuto.title
# other tutorial already there and add the new one
tuto.data_lib['items'][0]['items'][0]['name'] = 'Different tutorial'
save_to_yaml(tuto.data_lib, tuto.data_lib_fp)
tuto.init_data_lib()
assert tuto.data_lib['items'][0]['items'][0]['name'] == 'Different tutorial'
assert tuto.data_lib['items'][0]['items'][1]['name'] == tuto.title
shutil.rmtree("topics")
def test_tutorial_prepare_data_library_from_zenodo():
"""Test :func:`planemo.training.tutorial.tutorial.prepare_data_library_from_zenodo`."""
# without zenodo link
tuto = Tutorial(
training=training,
topic=topic)
tuto.datatype_fp = datatype_fp
os.makedirs(tuto.wf_dir)
tuto.prepare_data_library_from_zenodo()
assert os.path.exists(tuto.data_lib_fp)
assert 'DOI' not in open(tuto.data_lib_fp, 'r').read()
# with zenodo link
tuto.zenodo_link = zenodo_link
tuto.prepare_data_library_from_zenodo()
assert "DOI: 10.5281/zenodo" in open(tuto.data_lib_fp, 'r').read()
shutil.rmtree("topics")
def test_tutorial_export_workflow_file():
"""Test :func:`planemo.training.tutorial.tutorial.export_workflow_file`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
# with worflow fp
tuto.init_wf_fp = WF_FP
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
# with workflow id
tuto.init_wf_fp = None
os.remove(tuto.wf_fp)
assert is_galaxy_engine(**KWDS)
galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_url = galaxy_url
tuto.training.galaxy_api_key = config.user_api_key
tuto.export_workflow_file()
assert os.path.exists(tuto.wf_fp)
shutil.rmtree("topics")
def test_tutorial_init_from_existing_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.init_from_existing_tutorial`."""
tuto = Tutorial(training=training, topic=topic)
# non existing tutorial
exp_exception = "The tutorial existing_tutorial does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
tuto.init_from_existing_tutorial('existing_tutorial')
# existing tutorial
create_existing_tutorial('existing_tutorial', tuto_fp, tuto.topic)
tuto.init_from_existing_tutorial('existing_tutorial')
assert tuto.title == 'A tutorial to test'
assert "A learning objective" in tuto.objectives
assert tuto.time_estimation == "1H"
assert 'the_best_contributor' in tuto.contributors
assert '# First section' in tuto.body
shutil.rmtree("topics")
def test_tutorial_create_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.create_tutorial`."""
tuto = Tutorial(training=training, topic=topic)
tuto.init_from_kwds({
'tutorial_name': "my_tuto",
'tutorial_title': "Title of tuto",
'hands_on': True,
'slides': True,
'workflow': WF_FP,
'workflow_id': None,
'zenodo_link': zenodo_link,
'datatypes': datatype_fp
})
tuto.create_tutorial(CTX)
assert os.path.exists(tuto.dir)
assert os.path.exists(tuto.tour_dir)
assert os.path.exists(tuto.wf_dir)
assert os.path.exists(tuto.data_lib_fp)
assert os.path.exists(tuto.tuto_fp)
assert os.path.exists(tuto.slide_fp)
assert 'layout: tutorial_slides' in open(tuto.slide_fp, 'r').read()
shutil.rmtree("topics")
def test_tutorial_create_hands_on_tutorial():
"""Test :func:`planemo.training.tutorial.tutorial.create_hands_on_tutorial`."""
tuto = Tutorial(
training=training,
topic=topic)
os.makedirs(tuto.wf_dir)
# with init_wf_id and no Galaxy URL
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = None
exp_exception = "No Galaxy URL given"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id and no Galaxy API key
tuto.init_wf_id = 'ID'
tuto.training.galaxy_url = 'http://%s:%s' % (KWDS['host'], KWDS['port'])
tuto.training.galaxy_api_key = None
exp_exception = "No API key to access the given Galaxy instance"
with assert_raises_regexp(Exception, exp_exception):
tuto.create_hands_on_tutorial(CTX)
# with init_wf_id
assert is_galaxy_engine(**KWDS)
with engine_context(CTX, **KWDS) as galaxy_engine:
with galaxy_engine.ensure_runnables_served([RUNNABLE]) as config:
tuto.init_wf_id = config.workflow_id(WF_FP)
tuto.training.galaxy_api_key = config.user_api_key
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
os.remove(tuto.tuto_fp)
# with init_wf_fp
tuto.init_wf_id = None
tuto.init_wf_fp = WF_FP
tuto.create_hands_on_tutorial(CTX)
assert os.path.exists(tuto.tuto_fp)
shutil.rmtree("topics")