def test_files(self, data_mock):
data_annotation = {
'output.list': {
'value': [{
'file': "element.gz"
}],
'type': 'list:basic:file:'
},
'output.fastq': {
'value': {
'file': "file.fastq.gz"
},
'type': 'basic:file:fastq'
},
'output.fastq_archive': {
'value': {
'file': "archive.gz"
},
'type': 'basic:file:'
},
'input.fastq_url': {
'value': {
'file': "blah"
},
'type': 'basic:url:'
},
'input.blah': {
'value': "blah.gz",
'type': 'basic:file:'
}
}
bad_data_annotation = {
'output.list': {
'value': [{
'no_file_field_here': "element.gz"
}],
'type': 'list:basic:file:'
},
}
data_mock.configure_mock(annotation=data_annotation)
file_list = Data.files(data_mock)
self.assertEqual(set(file_list),
set(['element.gz', 'archive.gz', 'file.fastq.gz']))
file_list = Data.files(data_mock, file_name='element.gz')
self.assertEqual(file_list, ['element.gz'])
file_list = Data.files(data_mock, field_name='output.fastq')
self.assertEqual(file_list, ['file.fastq.gz'])
data_mock.configure_mock(annotation=bad_data_annotation)
message = r"Item .* does not contain 'file' key."
with six.assertRaisesRegex(self, KeyError, message):
Data.files(data_mock)
def test_files(self, data_mock):
data_annotation = {
'output.fastq': {'value': {'file': "file.fastq.gz"}, 'type': 'basic:file:fastq'},
'output.fastq_archive': {'value': {'file': "archive.gz"}, 'type': 'basic:file:'},
'input.fastq_url': {'value': {'file': "blah"}, 'type': 'basic:url:'},
'input.blah': {'value': "blah.gz", 'type': 'basic:file:'}
}
data_mock.configure_mock(annotation=data_annotation)
file_list = Data.files(data_mock)
self.assertEqual(set(file_list), set(['archive.gz', 'file.fastq.gz']))
file_list = Data.files(data_mock, file_name='archive.gz')
self.assertEqual(file_list, ['archive.gz'])
file_list = Data.files(data_mock, field_name='output.fastq')
self.assertEqual(file_list, ['file.fastq.gz'])
def test_add_output(self, data_mock):
data_mock.configure_mock(
annotation={
'output.fastq': {
'type': 'basic:file:',
'value': {
'file': 'reads.fq'
}
},
'output.fasta': {
'type': 'basic:file:',
'value': {
'file': 'genome.fa'
}
}
})
files_list = Data.files(data_mock, field_name="output.fastq")
self.assertEqual(files_list, ['reads.fq'])
files_list = Data.files(data_mock, field_name="fastq")
self.assertEqual(files_list, ['reads.fq'])
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):
data = Data(id=123, resolwe=MagicMock())
data._get_dir_files = MagicMock(
side_effect=[['first_dir/file1.txt'], ['fastq_dir/file2.txt']])
data.annotation = {
'output.list': {'value': [{'file': "element.gz"}], 'type': 'list:basic:file:'},
'output.dir_list': {'value': [{'dir': "first_dir"}], 'type': 'list:basic:dir:'},
'output.fastq': {'value': {'file': "file.fastq.gz"}, 'type': 'basic:file:fastq'},
'output.fastq_archive': {'value': {'file': "archive.gz"}, 'type': 'basic:file:'},
'output.fastq_dir': {'value': {'dir': "fastq_dir"}, 'type': 'basic:dir:'},
'input.fastq_url': {'value': {'file': "blah"}, 'type': 'basic:url:'},
'input.blah': {'value': "blah.gz", 'type': 'basic:file:'}
}
file_list = data.files()
six.assertCountEqual(self, 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.annotation = {
'output.list': {'value': [{'no_file_field_here': "element.gz"}],
'type': 'list:basic:file:'},
}
with six.assertRaisesRegex(self, KeyError, "does not contain 'file' key."):
data.files()
data = Data(resolwe=MagicMock(), id=None)
with six.assertRaisesRegex(self, 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.annotation = {
'output.list': {
'value': [{
'file': "element.gz"
}],
'type': 'list:basic:file:'
},
'output.dir_list': {
'value': [{
'dir': "first_dir"
}],
'type': 'list:basic:dir:'
},
'output.fastq': {
'value': {
'file': "file.fastq.gz"
},
'type': 'basic:file:fastq'
},
'output.fastq_archive': {
'value': {
'file': "archive.gz"
},
'type': 'basic:file:'
},
'output.fastq_dir': {
'value': {
'dir': "fastq_dir"
},
'type': 'basic:dir:'
},
'input.fastq_url': {
'value': {
'file': "blah"
},
'type': 'basic:url:'
},
'input.blah': {
'value': "blah.gz",
'type': 'basic:file:'
}
}
file_list = data.files()
six.assertCountEqual(self, 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.annotation = {
'output.list': {
'value': [{
'no_file_field_here': "element.gz"
}],
'type': 'list:basic:file:'
},
}
with six.assertRaisesRegex(self, KeyError,
"does not contain 'file' key."):
data.files()
data = Data(resolwe=MagicMock(), id=None)
with six.assertRaisesRegex(self, 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()