def test_files(self):
resolwe = MagicMock()
data = Data(id=123, resolwe=resolwe)
data._get_dir_files = MagicMock(
side_effect=[['first_dir/file1.txt'], ['fastq_dir/file2.txt']])
data.output = {
'list': [{'file': "element.gz"}],
'dir_list': [{'dir': "first_dir"}],
'fastq': {'file': "file.fastq.gz"},
'fastq_archive': {'file': "archive.gz"},
'fastq_dir': {'dir': "fastq_dir"},
}
data.process = Process(resolwe=resolwe, output_schema=[
{'name': 'list', 'label': 'List', 'type': 'list:basic:file:'},
{'name': 'dir_list', 'label': 'Dir_list', 'type': 'list:basic:dir:'},
{'name': 'fastq', 'label': 'Fastq', 'type': 'basic:file:fastq:'},
{'name': 'fastq_archive', 'label': 'Fastq_archive', 'type': 'basic:file:'},
{'name': 'fastq_dir', 'label': 'Fastq_dir', 'type': 'basic:dir:'},
])
file_list = data.files()
self.assertCountEqual(file_list, [
'element.gz',
'archive.gz',
'file.fastq.gz',
'first_dir/file1.txt',
'fastq_dir/file2.txt'
])
file_list = data.files(file_name='element.gz')
self.assertEqual(file_list, ['element.gz'])
file_list = data.files(field_name='output.fastq')
self.assertEqual(file_list, ['file.fastq.gz'])
data.output = {
'list': [{'no_file_field_here': "element.gz"}],
}
data.process.output_schema = [
{'name': 'list', 'label': 'List', 'type': 'list:basic:file:'},
]
with self.assertRaisesRegex(KeyError, "does not contain 'file' key."):
data.files()
data = Data(resolwe=MagicMock(), id=None)
with self.assertRaisesRegex(ValueError, "must be saved before"):
data.files()
def test_files(self):
data = Data(id=123, resolwe=MagicMock())
data._get_dir_files = MagicMock(
side_effect=[['first_dir/file1.txt'], ['fastq_dir/file2.txt']])
data.output = {
'list': [{'file': "element.gz"}],
'dir_list': [{'dir': "first_dir"}],
'fastq': {'file': "file.fastq.gz"},
'fastq_archive': {'file': "archive.gz"},
'fastq_dir': {'dir': "fastq_dir"},
}
data.process_output_schema = [
{'name': 'list', 'label': 'List', 'type': 'list:basic:file:'},
{'name': 'dir_list', 'label': 'Dir_list', 'type': 'list:basic:dir:'},
{'name': 'fastq', 'label': 'Fastq', 'type': 'basic:file:fastq:'},
{'name': 'fastq_archive', 'label': 'Fastq_archive', 'type': 'basic:file:'},
{'name': 'fastq_dir', 'label': 'Fastq_dir', 'type': 'basic:dir:'},
]
file_list = data.files()
self.assertCountEqual(file_list, [
'element.gz',
'archive.gz',
'file.fastq.gz',
'first_dir/file1.txt',
'fastq_dir/file2.txt'
])
file_list = data.files(file_name='element.gz')
self.assertEqual(file_list, ['element.gz'])
file_list = data.files(field_name='output.fastq')
self.assertEqual(file_list, ['file.fastq.gz'])
data.output = {
'list': [{'no_file_field_here': "element.gz"}],
}
data.process_output_schema = [
{'name': 'list', 'label': 'List', 'type': 'list:basic:file:'},
]
with self.assertRaisesRegex(KeyError, "does not contain 'file' key."):
data.files()
data = Data(resolwe=MagicMock(), id=None)
with self.assertRaisesRegex(ValueError, "must be saved before"):
data.files()
def test_files(self):
resolwe = MagicMock()
data = Data(id=123, resolwe=resolwe)
data._get_dir_files = MagicMock(
side_effect=[["first_dir/file1.txt"], ["fastq_dir/file2.txt"]])
data.output = {
"list": [{
"file": "element.gz"
}],
"dir_list": [{
"dir": "first_dir"
}],
"fastq": {
"file": "file.fastq.gz"
},
"fastq_archive": {
"file": "archive.gz"
},
"fastq_dir": {
"dir": "fastq_dir"
},
}
data.process = Process(
resolwe=resolwe,
output_schema=[
{
"name": "list",
"label": "List",
"type": "list:basic:file:"
},
{
"name": "dir_list",
"label": "Dir_list",
"type": "list:basic:dir:"
},
{
"name": "fastq",
"label": "Fastq",
"type": "basic:file:fastq:"
},
{
"name": "fastq_archive",
"label": "Fastq_archive",
"type": "basic:file:",
},
{
"name": "fastq_dir",
"label": "Fastq_dir",
"type": "basic:dir:"
},
],
)
file_list = data.files()
self.assertCountEqual(
file_list,
[
"element.gz",
"archive.gz",
"file.fastq.gz",
"first_dir/file1.txt",
"fastq_dir/file2.txt",
],
)
file_list = data.files(file_name="element.gz")
self.assertEqual(file_list, ["element.gz"])
file_list = data.files(field_name="output.fastq")
self.assertEqual(file_list, ["file.fastq.gz"])
data.output = {
"list": [{
"no_file_field_here": "element.gz"
}],
}
data.process.output_schema = [
{
"name": "list",
"label": "List",
"type": "list:basic:file:"
},
]
with self.assertRaisesRegex(KeyError, "does not contain 'file' key."):
data.files()
data = Data(resolwe=MagicMock(), id=None)
with self.assertRaisesRegex(ValueError, "must be saved before"):
data.files()