CTX,
datatype_fp,
KWDS,
RUNNABLE,
tuto_fp,
wf,
WF_FP,
wf_param_values,
zenodo_link
)
from .test_utils import (
skip_if_environ,
)
topic = Topic()
training = Training(KWDS)
def test_get_galaxy_datatype():
"""Test :func:`planemo.training.tutorial.get_galaxy_datatype`."""
assert get_galaxy_datatype("csv", datatype_fp) == "csv"
assert get_galaxy_datatype("test", datatype_fp) == "strange_datatype"
assert "# Please add" in get_galaxy_datatype("unknown", datatype_fp)
def test_get_zenodo_record():
"""Test :func:`planemo.training.tutorial.get_zenodo_record`."""
z_record, req_res = get_zenodo_record(zenodo_link)
file_link_prefix = "https://zenodo.org/api/files/51a1b5db-ff05-4cda-83d4-3b46682f921f"
assert z_record == "1321885"
assert 'files' in req_res
def test_generate_tuto_from_wf():
"""Test :func:`planemo.training.generate_tuto_from_wf`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
# no workflow
train.kwds['workflow'] = None
exp_exception = "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided"
with assert_raises_regexp(Exception, exp_exception):
train.generate_tuto_from_wf(CTX)
# with workflow
train.kwds['workflow'] = WF_FP
train.generate_tuto_from_wf(CTX)
with open(train.tuto.tuto_fp, 'r') as fh:
assert '**FastQC** {% icon tool %} with the following parameters:' in fh.read(
)
assert os.path.exists(train.tuto.wf_fp)
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def cli(ctx, uris, **kwds):
"""Create tutorial skeleton from workflow."""
kwds["no_dependency_resolution"] = True
training = Training(kwds)
training.generate_tuto_from_wf(ctx)
def test_training_check_topic_init_tuto():
"""Test :func:`planemo.training.Training.check_topic_init_tuto`."""
train = Training(KWDS)
# no topic
exp_exception = "The topic my_new_topic does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
train.check_topic_init_tuto()
# add topic
train.kwds['tutorial_name'] = None
train.kwds['slides'] = None
train.kwds['workflow'] = None
train.kwds['workflow_id'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
train.check_topic_init_tuto()
assert train.tuto.name == train.kwds['tutorial_name']
assert train.tuto.datatype_fp
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_fill_data_library():
"""Test :func:`planemo.training.fill_data_library`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.kwds['hands_on'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_wo_zenodo_fp,
train.topic)
# no Zenodo link
train.kwds['zenodo_link'] = None
exp_exception = "A Zenodo link should be provided either in the metadata file or as argument of the command"
with assert_raises_regexp(Exception, exp_exception):
train.fill_data_library(CTX)
# with a given Zenodo link and no Zenodo in metadata
train.kwds['zenodo_link'] = zenodo_link
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1321885' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % zenodo_link in fh.read()
# with a given Zenodo link and Zenodo in metadata
new_z_link = 'https://zenodo.org/record/1324204'
train.kwds['zenodo_link'] = new_z_link
train.tuto = None
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1324204' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % new_z_link in fh.read()
# with no given Zenodo link
train.kwds['zenodo_link'] = None
train.fill_data_library(CTX)
with open(train.tuto.data_lib_fp, 'r') as fh:
assert 'DOI: 10.5281/zenodo.1324204' in fh.read()
with open(train.tuto.tuto_fp, 'r') as fh:
assert 'zenodo_link: %s' % new_z_link in fh.read()
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_training_init():
"""Test :func:`planemo.training.Training.init`."""
train = Training(KWDS)
assert train.topics_dir == "topics"
assert train.topic is not None
assert train.tuto is None
def test_training_init_training():
"""Test :func:`planemo.training.Training.init_training`."""
train = Training(KWDS)
# new topic, nothing else
train.kwds['tutorial_name'] = None
train.kwds['slides'] = None
train.kwds['workflow'] = None
train.kwds['workflow_id'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
assert os.path.exists(train.topic.dir)
assert not os.listdir(os.path.join(train.topic.dir, 'tutorials'))
# no new topic, no tutorial name but hands-on
train.kwds['slides'] = True
exp_exception = "A tutorial name is needed to create the skeleton of a tutorial slide deck"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, no tutorial name but workflow
train.kwds['workflow'] = WF_FP
train.kwds['slides'] = False
exp_exception = "A tutorial name is needed to create the skeleton of the tutorial from a workflow"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, no tutorial name but zenodo
train.kwds['workflow'] = None
train.kwds['zenodo_link'] = zenodo_link
exp_exception = "A tutorial name is needed to add Zenodo information"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, new tutorial
train.kwds['tutorial_name'] = "new_tuto"
train.kwds['workflow'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
assert os.path.exists(train.tuto.dir)
assert os.path.exists(train.tuto.tuto_fp)
with open(train.tuto.tuto_fp, 'r') as fh:
assert train.kwds['tutorial_title'] in fh.read()
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_generate_tuto_from_wf():
"""Test :func:`planemo.training.generate_tuto_from_wf`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
# no workflow
train.kwds['workflow'] = None
exp_exception = "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided"
with assert_raises_regexp(Exception, exp_exception):
train.generate_tuto_from_wf(CTX)
# with workflow
train.kwds['workflow'] = WF_FP
train.generate_tuto_from_wf(CTX)
assert_file_contains(
train.tuto.tuto_fp,
"{% tool [FastQC](toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71) %} with the following parameters:",
)
assert os.path.exists(train.tuto.wf_fp)
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def cli(ctx, uris, **kwds):
"""Build training template from workflow."""
kwds["no_dependency_resolution"] = True
training = Training(kwds)
training.init_training(ctx)
def generate(tuto):
'''Generate skeleton of a tutorial'''
shutil.rmtree('topics', ignore_errors=True)
shutil.rmtree('metadata', ignore_errors=True)
kwds = {
'topic_name': 'topic',
'topic_title': "New topic",
'topic_target': "use",
'topic_summary': "Topic summary",
'tutorial_name': tuto['name'],
'tutorial_title': tuto['title'],
'hands_on': True,
'slides': False,
'workflow_id': tuto['workflow_id'],
'zenodo_link': tuto['zenodo'],
'galaxy_url': tuto['galaxy_url'],
'galaxy_api_key': tuto['api_key'],
'workflow': None,
'datatypes': None
}
train = Training(kwds)
ctx = cli.PlanemoCliContext()
ctx.planemo_directory = "/tmp/planemo-test-workspace"
error = None
try:
train.init_training(ctx)
except bioblend.ConnectionError as connect_error:
print(connect_error)
if "Malformed id" in connect_error.body:
error = ("The id of the workflow is malformed "
"for the given Galaxy instance. "
"Please check it before trying again.")
elif "not owned by or shared with current user" in connect_error.body:
error = ("The workflow is not shared publicly "
"on the given Galaxy instance. "
"Please share it before trying again.")
else:
error = connect_error.body
tuto_dp = topic_dp / Path("%s" % tuto['name'])
tuto_fp = tuto_dp / Path('tutorial.md')
if error is None and not tuto_fp.is_file():
error = ("The tutorial file was not generated. "
"The workflow may have some errors. "
"Please check it before trying again.")
if error is None:
zip_fn = "%s" % (tuto['uuid'])
shutil.make_archive(Path(zip_fn), 'zip', tuto_dp)
zip_fp = Path('static') / Path("%s.zip" % zip_fn)
shutil.move("%s.zip" % zip_fn, Path('ptdk') / zip_fp)
shutil.rmtree('topics', ignore_errors=True)
shutil.rmtree('metadata', ignore_errors=True)
return zip_fp
return error
def test_generate_tuto_from_wf():
"""Test :func:`planemo.training.generate_tuto_from_wf`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
# no workflow
train.kwds['workflow'] = None
exp_exception = "A path to a local workflow or the id of a workflow on a running Galaxy instance should be provided"
with assert_raises_regexp(Exception, exp_exception):
train.generate_tuto_from_wf(CTX)
# with workflow
train.kwds['workflow'] = WF_FP
train.generate_tuto_from_wf(CTX)
assert '**FastQC** {% icon tool %} with the following parameters:' in open(train.tuto.tuto_fp, 'r').read()
assert os.path.exists(train.tuto.wf_fp)
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_fill_data_library():
"""Test :func:`planemo.training.fill_data_library`."""
train = Training(KWDS)
train.kwds['tutorial_name'] = None
train.kwds['slides'] = False
train.kwds['hands_on'] = False
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_wo_zenodo_fp, train.topic)
# no Zenodo link
train.kwds['zenodo_link'] = None
exp_exception = "A Zenodo link should be provided either in the metadata file or as argument of the command"
with assert_raises_regexp(Exception, exp_exception):
train.fill_data_library(CTX)
# with a given Zenodo link and no Zenodo in metadata
train.kwds['zenodo_link'] = zenodo_link
train.fill_data_library(CTX)
assert 'DOI: 10.5281/zenodo.1321885' in open(train.tuto.data_lib_fp, 'r').read()
assert 'zenodo_link: %s' % zenodo_link in open(train.tuto.tuto_fp, 'r').read()
# with a given Zenodo link and Zenodo in metadata
new_z_link = 'https://zenodo.org/record/1324204'
train.kwds['zenodo_link'] = new_z_link
train.tuto = None
train.fill_data_library(CTX)
assert 'DOI: 10.5281/zenodo.1324204' in open(train.tuto.data_lib_fp, 'r').read()
assert 'zenodo_link: %s' % new_z_link in open(train.tuto.tuto_fp, 'r').read()
# with no given Zenodo link
train.kwds['zenodo_link'] = None
train.fill_data_library(CTX)
assert 'DOI: 10.5281/zenodo.1324204' in open(train.tuto.data_lib_fp, 'r').read()
assert 'zenodo_link: %s' % new_z_link in open(train.tuto.tuto_fp, 'r').read()
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_training_check_topic_init_tuto():
"""Test :func:`planemo.training.Training.check_topic_init_tuto`."""
train = Training(KWDS)
# no topic
exp_exception = "The topic my_new_topic does not exists. It should be created"
with assert_raises_regexp(Exception, exp_exception):
train.check_topic_init_tuto()
# add topic
train.kwds['tutorial_name'] = None
train.kwds['slides'] = None
train.kwds['workflow'] = None
train.kwds['workflow_id'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
train.kwds['tutorial_name'] = 'existing_tutorial'
create_existing_tutorial('existing_tutorial', tuto_fp, train.topic)
train.check_topic_init_tuto()
assert train.tuto.name == train.kwds['tutorial_name']
assert train.tuto.datatype_fp
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
def test_training_init_training():
"""Test :func:`planemo.training.Training.init_training`."""
train = Training(KWDS)
# new topic, nothing else
train.kwds['tutorial_name'] = None
train.kwds['slides'] = None
train.kwds['workflow'] = None
train.kwds['workflow_id'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
assert os.path.exists(train.topic.dir)
assert not os.listdir(os.path.join(train.topic.dir, 'tutorials'))
# no new topic, no tutorial name but hands-on
train.kwds['slides'] = True
exp_exception = "A tutorial name is needed to create the skeleton of a tutorial slide deck"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, no tutorial name but workflow
train.kwds['workflow'] = WF_FP
train.kwds['slides'] = False
exp_exception = "A tutorial name is needed to create the skeleton of the tutorial from a workflow"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, no tutorial name but zenodo
train.kwds['workflow'] = None
train.kwds['zenodo_link'] = zenodo_link
exp_exception = "A tutorial name is needed to add Zenodo information"
with assert_raises_regexp(Exception, exp_exception):
train.init_training(CTX)
# no new topic, new tutorial
train.kwds['tutorial_name'] = "new_tuto"
train.kwds['workflow'] = None
train.kwds['zenodo_link'] = None
train.init_training(CTX)
assert os.path.exists(train.tuto.dir)
assert os.path.exists(train.tuto.tuto_fp)
assert train.kwds['tutorial_title'] in open(train.tuto.tuto_fp, 'r').read()
# clean after
shutil.rmtree(train.topics_dir)
shutil.rmtree("metadata")
