def test_validate_params(self):
inputs = {
"reads_tuple": [
{
"input_reads_label": "reads file 1",
"input_reads_obj": "rhodobacterium.art.q20.int.PE.reads",
"input_reads_metadata": {
"key1": "value1"
},
},
{
"input_reads_label": "reads file 2",
"input_reads_obj": "rhodobacterium.art.q10.PE.reads",
"input_reads_metadata": {
"key2": "value2"
},
},
],
"output_object":
"MyReadsSet",
"description":
"New Reads Set",
}
app_id = "NarrativeTest/test_create_set"
tag = "dev"
prev_ws_id = os.environ.get("KB_WORKSPACE_ID")
os.environ["KB_WORKSPACE_ID"] = self.public_ws
sm = specmanager.SpecManager()
spec = sm.get_spec(app_id, tag=tag)
(params,
ws_inputs) = app_util.validate_parameters(app_id, tag,
sm.app_params(spec), inputs)
self.assertDictEqual(params, inputs)
self.assertIn("12345/8/1", ws_inputs)
self.assertIn("12345/7/1", ws_inputs)
if prev_ws_id is None:
del os.environ["KB_WORKSPACE_ID"]
else:
os.environ["KB_WORKSPACE_ID"] = prev_ws_id
def test_input_mapping(self):
self.maxDiff = None
inputs = {
"reads_tuple": [{
"input_reads_label": "reads file 1",
"input_reads_obj": "rhodobacterium.art.q20.int.PE.reads",
"input_reads_metadata": {
"key1": "value1"
}
}, {
"input_reads_label": "reads file 2",
"input_reads_obj": "rhodobacterium.art.q10.PE.reads",
"input_reads_metadata": {
"key2": "value2"
}
}],
"output_object":
"MyReadsSet",
"description":
"New Reads Set"
}
app_id = "NarrativeTest/test_create_set"
tag = "dev"
ws_name = self.public_ws
prev_ws_id = os.environ.get('KB_WORKSPACE_ID', None)
os.environ['KB_WORKSPACE_ID'] = ws_name
sm = specmanager.SpecManager()
spec = sm.get_spec(app_id, tag=tag)
spec_params = sm.app_params(spec)
spec_params_map = dict((spec_params[i]['id'], spec_params[i])
for i in range(len(spec_params)))
mapped_inputs = self.am._map_inputs(
spec['behavior']['kb_service_input_mapping'], inputs,
spec_params_map)
expected = [{
u'output_object_name': 'MyReadsSet',
u'data': {
u'items': [{
u'label': 'reads file 1',
u'metadata': {
'key1': 'value1'
},
u'ref': '12345/7/1'
}, {
u'label': 'reads file 2',
u'metadata': {
'key2': 'value2'
},
u'ref': '12345/8/1'
}],
u'description':
'New Reads Set'
},
u'workspace': ws_name
}]
self.assertDictEqual(expected[0], mapped_inputs[0])
ref_path = ws_name + '/MyReadsSet; ' + ws_name + "/rhodobacterium.art.q10.PE.reads"
ret = app_util.transform_param_value("resolved-ref", ref_path, None)
self.assertEqual(ret, ws_name + '/MyReadsSet;18836/5/1')
if prev_ws_id is None:
del (os.environ['KB_WORKSPACE_ID'])
else:
os.environ['KB_WORKSPACE_ID'] = prev_ws_id
def test_input_mapping(self):
self.maxDiff = None
inputs = {
"reads_tuple": [
{
"input_reads_label": "reads file 1",
"input_reads_obj": "rhodobacterium.art.q20.int.PE.reads",
"input_reads_metadata": {
"key1": "value1"
},
},
{
"input_reads_label": "reads file 2",
"input_reads_obj": "rhodobacterium.art.q10.PE.reads",
"input_reads_metadata": {
"key2": "value2"
},
},
],
"output_object":
"MyReadsSet",
"description":
"New Reads Set",
}
app_id = "NarrativeTest/test_create_set"
tag = "dev"
ws_name = self.public_ws
prev_ws_id = os.environ.get("KB_WORKSPACE_ID", None)
os.environ["KB_WORKSPACE_ID"] = ws_name
sm = specmanager.SpecManager()
spec = sm.get_spec(app_id, tag=tag)
spec_params = sm.app_params(spec)
spec_params_map = dict((spec_params[i]["id"], spec_params[i])
for i in range(len(spec_params)))
mapped_inputs = self.am._map_inputs(
spec["behavior"]["kb_service_input_mapping"], inputs,
spec_params_map)
expected = [{
"output_object_name": "MyReadsSet",
"data": {
"items": [
{
"label": "reads file 1",
"metadata": {
"key1": "value1"
},
"ref": "12345/7/1",
},
{
"label": "reads file 2",
"metadata": {
"key2": "value2"
},
"ref": "12345/8/1",
},
],
"description":
"New Reads Set",
},
"workspace": ws_name,
}]
self.assertDictEqual(expected[0], mapped_inputs[0])
ref_path = (ws_name + "/MyReadsSet; " + ws_name +
"/rhodobacterium.art.q10.PE.reads")
ret = app_util.transform_param_value("resolved-ref", ref_path, None)
self.assertEqual(ret, ws_name + "/MyReadsSet;18836/5/1")
if prev_ws_id is None:
del os.environ["KB_WORKSPACE_ID"]
else:
os.environ["KB_WORKSPACE_ID"] = prev_ws_id