def test_remap_job():
job = TEMPLATE_JOB
tool = from_url(join(dirname(__file__), 'bwa-mem.json#tool'))
context = init_context(tool)
app = context.from_dict(tool)
input_file = from_url(join(dirname(__file__), 'inputs.json'))
startdir = './'
def test_invalid_json_schema():
ctx = init_context()
no_type = {
"properties": {
"a": {
"type": "integer"
}
}
}
assert_raises(RabixError, JsonSchema, ctx, no_type)
not_object = {
"type": "int",
"properties": {
"a": {
"type": "integer"
}
}
}
assert_raises(RabixError, JsonSchema, ctx, not_object)
no_properties = {
"type": "object",
}
assert_raises(RabixError, JsonSchema, ctx, no_properties)
def test_workflow():
path = abspath(join(__file__, '../../test_runtime/wf_tests.yaml'))
context = init_context()
doc = from_url(path)
tests = doc['tests']
for test_name, test in six.iteritems(tests):
features = test.get('requiresFeatures', [])
if 'map' not in features:
fix_types(test['job']['app'])
yield assert_execution, context.from_dict(test['job']), test['outputs']
def test_workflow():
path = abspath(join(__file__, '../../test_runtime/wf_tests.yaml'))
doc = from_url(path)
tests = doc['tests']
for test_name, test in six.iteritems(tests):
context = init_context(test['job'])
job = Job.from_dict(context, test['job'])
for inp in job.app.inputs:
construct_files(job.inputs.get(inp.id), inp.validator)
yield assert_execution, job, test['outputs']
def test_simple_json_schema():
schema = {
"type": "object",
"properties": {
"a": {
"type": "integer"
}
}
}
js = JsonSchema(init_context(), schema)
a = next(iter(js))
assert_equal(a.id, 'a')
assert_equal(a.constructor.name, 'integer')
assert_false(a.required)
to_dict = js.to_dict()
for k, v in six.iteritems(schema):
assert_equal(to_dict[k], v)
