def test_item_separator_false_separate_optional(self):
draft2 = {
"type": [
"null", {
"type": "array",
"items": "string"
}],
"inputBinding": {
"prefix": "-a",
"itemSeparator": None,
"separate": False
}
}
converted = {
"type": [
"null", {
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-a",
"separate": False
}
}]
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl["type"], converted["type"])
self.assertIn("valueFrom", cwl1.cwl["inputBinding"])
self.assertNotIn("default", cwl1.cwl)
def test_doc(self):
draft2 = {
"description": "Some description."
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl['doc'], draft2['description'])
self.assertNotIn('description', cwl1.cwl)
def test_item_separator_true_separate(self):
draft2 = {
"type": [{
"type": "array",
"items": "string"
}],
"inputBinding": {
"prefix": "-a",
"itemSeparator": None,
"separate": True,
"position": 1
}
}
converted = {
"type": [{
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-a",
"separate": True
}
}],
"inputBinding": {
"position": 1,
"shellQuote": False
}
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl["type"], converted["type"])
self.assertIn("valueFrom", cwl1.cwl["inputBinding"])
# Check that default is not added by mistake
self.assertNotIn("default", cwl1.cwl)
def test_delete_cmd_include(self):
draft2 = {
"inputBinding": {
"sbg:cmdInclude": True
}
}
cwl1 = Input(draft2, in_id="input")
self.assertNotIn('sbg:cmdInclude', cwl1.cwl["inputBinding"])
def test_secondary_files_typecheck(self):
draft2 = {
"inputBinding": {
"secondaryFiles": [
7
]
}
}
with self.assertRaises(Exception):
Input(draft2)
def test_optional_type(self):
draft2 = {
"required": False,
"type": [
"File", "null"
]
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl['type'], 'File?')
self.assertNotIn('required', cwl1.cwl)
def test_secondary_files(self):
draft2 = {
"inputBinding": {
"secondaryFiles": [
".bai", ".fai", ".crai"
]
}
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl['secondaryFiles'],
draft2["inputBinding"]["secondaryFiles"])
def test_item_separator_without_prefix(self):
draft2 = {
"type": [{
"type": "array",
"items": "string"
}],
"inputBinding": {
"itemSeparator": 'a'
}
}
cwl1 = Input(draft2)
self.assertNotIn("itemSeparator", cwl1.cwl["inputBinding"])
def test_enum_name_changed(self):
draft2 = {
"id": "#foo",
"type": [
"null",
{
"type": "enum",
"symbols": ["a", "b"],
"name": "null"
}
]
}
cwl1 = Input(draft2, in_id='foo')
self.assertEqual(cwl1.cwl['type'][1]["name"], 'foo')
def test_array_dict_with_no_separator(self):
draft2 = {
"type": {
"type": "array",
"items": "File"
},
"inputBinding": {
"position": 0,
"prefix": "-v",
"separate": True,
}
}
cwl1 = Input(draft2)
self.assertIn("inputBinding", cwl1.cwl["type"])
def test_record_type_position_added(self):
draft2 = {
"required": False,
"type": [
{
"type": "record",
"fields": [
{
"type": [
"File"
],
"inputBinding": {
"position": 1,
"secondaryFiles": []
},
"name": "input_field"
},
{
"type": [
"null",
"string"
],
"inputBinding": {
"position": 1
},
"name": "input_field_1"
}
],
"name": "input"
}
]
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl['type']['type'], 'record')
self.assertEqual(cwl1.cwl['inputBinding']['position'], 1)
self.assertNotIn('required', cwl1.cwl)
def test_item_separator_without_separate(self):
draft2 = {
"type": [{
"type": "array",
"items": "string"
}],
"inputBinding": {
"prefix": "-a",
"itemSeparator": None
}
}
converted = {
"type": [{
"type": "array",
"items": "string",
"inputBinding": {
"prefix": "-a"
}
}]
}
cwl1 = Input(draft2)
self.assertEqual(cwl1.cwl["type"], converted["type"])
self.assertIn("valueFrom", cwl1.cwl["inputBinding"])