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test_serializer.py
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test_serializer.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
unit tests for the serializer module
"""
import os
import shutil
import json
from . import (
PlutoTestCase,
CWLFile,
OFile,
ODir
)
class TestSerializer(PlutoTestCase):
def test_cwl_file1(self):
"""
Test case for serializing an output file object
"""
obj = OFile(size = 488, name = 'Sample4_purity.seg', dir = '/tmp/foo', hash = 'e6df130c57ca594578f9658e589cfafc8f40a56c')
expected = {
'basename': 'Sample4_purity.seg',
'checksum': 'sha1$e6df130c57ca594578f9658e589cfafc8f40a56c',
'class': 'File',
'location': 'file:///tmp/foo/Sample4_purity.seg',
'path': '/tmp/foo/Sample4_purity.seg',
'size': 488
}
self.assertDictEqual(obj, expected)
def test_cwl_secondaryFiles1(self):
obj = OFile(
size = 488,
name = 'Sample4_purity.seg',
dir = '/tmp/foo',
hash = 'e6df130c57ca594578f9658e589cfafc8f40a56c',
secondaryFiles = [OFile(name = 'Sample4_purity.seg.tbi', hash = "1234abcd", size = 1, dir = '/tmp/foo')])
expected = {
'basename': 'Sample4_purity.seg',
'checksum': 'sha1$e6df130c57ca594578f9658e589cfafc8f40a56c',
'class': 'File',
'location': 'file:///tmp/foo/Sample4_purity.seg',
'path': '/tmp/foo/Sample4_purity.seg',
'size': 488,
'secondaryFiles': [
{
'class': 'File',
'basename': 'Sample4_purity.seg.tbi',
'checksum': 'sha1$1234abcd',
'location': 'file:///tmp/foo/Sample4_purity.seg.tbi',
'path': '/tmp/foo/Sample4_purity.seg.tbi',
'size': 1
}
]
}
self.assertDictEqual(obj, expected)
def test_cwl_file2(self):
"""
Test case with no 'dir' arg used for OFile; should output just the basename for path
"""
obj = OFile(size = 488, name = 'Sample4_purity.seg', hash = 'e6df130c57ca594578f9658e589cfafc8f40a56c')
expected = {
'basename': 'Sample4_purity.seg',
'checksum': 'sha1$e6df130c57ca594578f9658e589cfafc8f40a56c',
'class': 'File',
'location': 'file://Sample4_purity.seg',
'path': 'Sample4_purity.seg',
'size': 488
}
self.assertDictEqual(obj, expected)
def test_cwl_dir1(self):
"""
Test case for serializing a directory
"""
obj = ODir(name = 'portal', dir = '/tmp/foo', items = [])
expected = {
'basename': 'portal',
'class': 'Directory',
'location': 'file:///tmp/foo/portal',
'path': '/tmp/foo/portal',
'listing': []
}
self.assertDictEqual(obj, expected)
def test_cwl_dir2(self):
"""
Test case for serializing a Directory with a File in it
"""
_file = OFile(size = 488, name = 'Sample4_purity.seg', hash = 'e6df130c57ca594578f9658e589cfafc8f40a56c')
_dir = ODir(name = 'portal', dir = '/tmp/foo', items = [_file])
expected = {
'basename': 'portal',
'class': 'Directory',
'location': 'file:///tmp/foo/portal',
'path': '/tmp/foo/portal',
'listing': [
{
'basename': 'Sample4_purity.seg',
'checksum': 'sha1$e6df130c57ca594578f9658e589cfafc8f40a56c',
'class': 'File',
'location': 'file:///tmp/foo/portal/Sample4_purity.seg',
'path': '/tmp/foo/portal/Sample4_purity.seg',
'size': 488
}
]
}
self.maxDiff = None
self.assertDictEqual(_dir, expected)
def test_cwl_dir3(self):
"""
Test using temp dir to dynamically generate the output paths
"""
_file = OFile(size = 488, name = 'Sample4_purity.seg', hash = 'e6df130c57ca594578f9658e589cfafc8f40a56c')
_dir = ODir(name = 'portal', dir = self.tmpdir, items = [_file])
expected = {
'basename': 'portal',
'class': 'Directory',
'location': 'file://'+ os.path.join(self.tmpdir, 'portal'),
'path': os.path.join(self.tmpdir, 'portal'),
'listing': [
{
'basename': 'Sample4_purity.seg',
'checksum': 'sha1$e6df130c57ca594578f9658e589cfafc8f40a56c',
'class': 'File',
'location': 'file://' + os.path.join(self.tmpdir, 'portal/Sample4_purity.seg'),
'path': os.path.join(self.tmpdir, 'portal/Sample4_purity.seg'),
'size': 488
}
]
}
self.maxDiff = None
self.assertDictEqual(_dir, expected)
# The next test cases are going to run an actual CWL to test against their results
has_cwl_runner = True if shutil.which('cwl-runner') else False
if not has_cwl_runner:
print(">>> skipping tests that require cwl-runner")
class TestSerializeCWLOutput(PlutoTestCase):
"""
Test that CWL output can be represented accurately with the serializer OFile
"""
CWL_DIR = os.path.abspath('cwl')
cwl_file = CWLFile('copy.cwl', CWL_DIR = CWL_DIR)
# @unittest.skipIf(has_cwl_runner!=True, "need cwl runner for this test")
def test_copy1(self):
"""
Test case for using serialized objects in a CWL test case
"""
lines = [
['# comment 1']
]
input = self.write_table(tmpdir = self.tmpdir, filename = 'input.maf', lines = lines)
self.input = {
"input_file": {
"class": "File",
"path": input
},
"output_filename": 'output.maf',
}
output_json, output_dir = self.run_cwl()
expected_output = {
'output_file': OFile(size = 12, name = 'output.maf', dir = output_dir, hash = 'ce7e0e370d46ae73b6478c062dec9f1a2d6bb37e')
}
self.assertCWLDictEqual(output_json, expected_output)
class TestSerializeCWLOutput2(PlutoTestCase):
CWL_DIR = os.path.abspath('cwl')
cwl_file = CWLFile('create_secondaryFiles.cwl', CWL_DIR = CWL_DIR)
def test_make_secondaryFiles(self):
lines = [
['# comment 1']
]
input = self.write_table(tmpdir = self.tmpdir, filename = 'input.maf', lines = lines)
self.input = {
"input_file": {
"class": "File",
"path": input
},
"secondaryFilename": 'input.maf.tbi',
}
output_json, output_dir = self.run_cwl()
expected_output = {
'output_file': OFile(size = 12, name = 'input.maf', dir = output_dir, hash = 'ce7e0e370d46ae73b6478c062dec9f1a2d6bb37e', secondaryFiles = [
OFile(name = "input.maf.tbi", dir = output_dir, hash = 'da39a3ee5e6b4b0d3255bfef95601890afd80709', size = 0)
])
}
self.assertCWLDictEqual(output_json, expected_output)
class TestSerializeCWLDirOutput(PlutoTestCase):
"""
Test cases for using the serializer when output contains directories
"""
CWL_DIR = os.path.abspath('cwl')
cwl_file = CWLFile('put_in_dir.cwl', CWL_DIR = CWL_DIR)
# @unittest.skipIf(has_cwl_runner!=True, "need cwl runner for this test")
def test_put_in_dir1(self):
"""
Test case for dir output object
"""
lines = [
['# comment 1']
]
input = self.write_table(tmpdir = self.tmpdir, filename = 'input.maf', lines = lines)
self.input = {
"item": {"class": "File", "path": input},
"output_directory_name": 'foo_output',
}
output_json, output_dir = self.run_cwl()
expected_output = {
'directory': ODir(name = 'foo_output', dir = output_dir, items = [
OFile(name = 'input.maf', size = 12, hash = 'ce7e0e370d46ae73b6478c062dec9f1a2d6bb37e')
])
}
self.assertCWLDictEqual(output_json, expected_output)
class TestSerializeCWLSubDirOutput(PlutoTestCase):
"""
Test cases for when the output contains subdirectories
"""
CWL_DIR = os.path.abspath('cwl')
cwl_file = CWLFile('create_subdir.cwl', CWL_DIR = CWL_DIR)
# @unittest.skipIf(has_cwl_runner!=True, "need cwl runner for this test")
def test_put_in_subdir(self):
"""
Test case for dir output object with nested subdir
"""
self.input = {}
output_json, output_dir = self.run_cwl(allow_empty_input = True)
expected_output = {
# /.../output/foo
'output_dir': ODir(name = 'foo', dir = output_dir, items = [
OFile(name = 'input.maf', size = 12, hash = 'ce7e0e370d46ae73b6478c062dec9f1a2d6bb37e')
]),
# /.../output/bar/foo
'output_subdir': ODir(name = 'bar', dir = output_dir, items = [
ODir(name = 'foo', items = [
OFile( # /.../output/bar/foo/input.maf
name = 'input.maf', size = 12, hash = 'ce7e0e370d46ae73b6478c062dec9f1a2d6bb37e')
])
])
}
self.assertCWLDictEqual(output_json, expected_output)
class TestRepr(PlutoTestCase):
def test_repr_ofile(self):
"""
Test that we can output a representation of the object that can be used
to recreate the object
"""
# create OFile object with classmethod; this saves the args
f = OFile.init(name = 'input.maf', size = 12, hash = '12345')
# create a string representation of the object
r = f.repr()
# its expected to look like this:
e = """OFile(name='input.maf', size=12, hash='12345')"""
self.assertEqual(r, e)
# use the string repr to create a new copy of the obj
x = eval(r)
# test that the old and new obj's are equivalent
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(f, attr), getattr(x, attr))
self.assertEqual(f.items(), x.items())
f = OFile.init('input.maf', size = 12, hash = '12345')
r = f.repr()
e = """OFile('input.maf', size=12, hash='12345')"""
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(f, attr), getattr(x, attr))
self.assertEqual(f.items(), x.items())
f = OFile.init('input.maf', size = 12, class_label = 'foo')
r = f.repr()
e = """OFile('input.maf', size=12, class_label='foo')"""
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(f, attr), getattr(x, attr))
self.assertEqual(f.items(), x.items())
f = OFile.init('input.maf', None, 12)
r = f.repr()
e = """OFile('input.maf', None, 12)"""
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(f, attr), getattr(x, attr))
self.assertEqual(f.items(), x.items())
def test_repr_odir(self):
"""
Test that we can output a representation of the object that can be used
to recreate the object
"""
# create ODir object with classmethod; this saves the args
d = ODir.init(name = 'output', items = [])
# create a string representation of the object
r = d.repr()
# its expected to look like this:
e = """ODir(name='output', items=[])"""
self.assertEqual(r, e)
# use the string repr to create a new copy of the obj
x = eval(r)
# test that the old and new obj's are equivalent
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(d, attr), getattr(x, attr))
self.assertEqual(d.items(), x.items())
d = ODir.init('output', items = [])
r = d.repr()
e = """ODir('output', items=[])"""
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(d, attr), getattr(x, attr))
self.assertEqual(d.items(), x.items())
d = ODir.init(name = 'foo', dir = '/output', items = [
OFile.init(name = 'input.maf', size = 12, hash ='1234')])
r = d.repr()
e = """ODir(name='foo', dir='/output', items=[OFile(name='input.maf', size=12, hash='1234')])"""
self.maxDiff = None
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(d, attr), getattr(x, attr))
self.assertEqual(d.items(), x.items())
d = ODir.init(name = 'bar', dir = '/output', items = [
ODir.init(name = 'foo', items = [
OFile.init( # /.../output/bar/foo/input.maf
name = 'input.maf', size = 12, hash = '1234')
])
])
r = d.repr()
e = """ODir(name='bar', dir='/output', items=[ODir(name='foo', items=[OFile(name='input.maf', size=12, hash='1234')])])"""
self.assertEqual(r, e)
x = eval(r)
for attr in [ 'path', 'location' ]:
self.assertEqual(getattr(d, attr), getattr(x, attr))
self.assertEqual(d.items(), x.items())
class TestLoadJSON(PlutoTestCase):
def test_load_ofile_from_repr(self):
"""
Initialize OFile objects from a JSON blob
"""
json_str = """{
"location": "file:///output/Sample1.maf",
"basename": "Sample1.maf",
"nameroot": "Sample1",
"nameext": ".maf",
"class": "File",
"checksum": "sha1$12345",
"size": 108887494
}"""
data = json.loads(json_str)
f = OFile.init_dict(data)
ex = {'basename': 'Sample1.maf', 'class': 'File', 'size': 108887494, 'checksum': 'sha1$12345', 'location': 'file:///output/Sample1.maf', 'path': '/output/Sample1.maf'}
self.assertCWLDictEqual(f, ex)
r = f.repr()
ex2 = """OFile(name='Sample1.maf', size=108887494, hash='12345', dir='/output')"""
self.assertEqual(r, ex2)
f2 = eval(r)
self.assertCWLDictEqual(f2, ex)
f = OFile.init_dict(data, in_subdir = True)
ex = {'basename': 'Sample1.maf', 'class': 'File', 'size': 108887494, 'checksum': 'sha1$12345',
'location': 'file://Sample1.maf', 'path': 'Sample1.maf'} # NOTE: location and path here are wrong but this is meant to be overriden by the parent ODir object... should not show up in repr()
self.assertCWLDictEqual(f, ex)
r = f.repr()
ex = """OFile(name='Sample1.maf', size=108887494, hash='12345')"""
self.assertEqual(r, ex)
def test_load_odir_from_repr(self):
"""
Initialize ODir objects from JSON blob
"""
json_str = """{
"class": "Directory",
"basename": "analysis",
"listing": [
{
"location": "file:///output/analysis/cna.txt",
"basename": "cna.txt",
"nameroot": "cna",
"nameext": ".txt",
"class": "File",
"checksum": "sha1$1234",
"size": 6547460
}
],
"location": "file:///output/analysis"
}"""
data = json.loads(json_str)
d = ODir.init_dict(data)
ex = {'basename': 'analysis', 'class': 'Directory', 'location': 'file:///output/analysis', 'path': '/output/analysis', 'listing': [
{'basename': 'cna.txt', 'class': 'File', 'size': 6547460, 'checksum': 'sha1$1234', 'location': 'file:///output/analysis/cna.txt', 'path': '/output/analysis/cna.txt'}
]}
self.assertCWLDictEqual(d, ex)
r = d.repr()
ex2 = """ODir(name='analysis', items=[OFile(name='cna.txt', size=6547460, hash='1234')], dir='/output')"""
self.assertEqual(r, ex2)
d2 = eval(r)
self.assertCWLDictEqual(d2, ex)
# self.assertCWLDictEqual(d2, data)
json_str = """{
"class": "Directory",
"basename": "portal",
"listing": [
{
"location": "file:///output/portal/meta_clinical_sample.txt",
"basename": "meta_clinical_sample.txt",
"nameroot": "meta_clinical_sample",
"nameext": ".txt",
"class": "File",
"checksum": "sha1$1234",
"size": 135
},
{
"class": "Directory",
"basename": "case_lists",
"listing": [
{
"location": "file:///output/portal/case_lists/cases_all.txt",
"basename": "cases_all.txt",
"nameroot": "cases_all",
"nameext": ".txt",
"class": "File",
"checksum": "sha1$4567",
"size": 448
}
],
"location": "file:///output/portal/case_lists"
},
{
"location": "file:///output/portal/report.html",
"basename": "report.html",
"nameroot": "report",
"nameext": ".html",
"class": "File",
"checksum": "sha1$7890",
"size": 1026290
}
],
"location": "file:///output/portal"
}"""
data = json.loads(json_str)
d = ODir.init_dict(data)
ex = {'basename': 'portal', 'class': 'Directory', 'location': 'file:///output/portal', 'path': '/output/portal', 'listing': [
{'basename': 'meta_clinical_sample.txt', 'class': 'File', 'size': 135, 'checksum': 'sha1$1234', 'location': 'file:///output/portal/meta_clinical_sample.txt', 'path': '/output/portal/meta_clinical_sample.txt'},
{'basename': 'case_lists', 'class': 'Directory', 'location': 'file:///output/portal/case_lists', 'path': '/output/portal/case_lists', 'listing': [
{'basename': 'cases_all.txt', 'class': 'File', 'size': 448, 'checksum': 'sha1$4567', 'location': 'file:///output/portal/case_lists/cases_all.txt', 'path': '/output/portal/case_lists/cases_all.txt'}
]},
{'basename': 'report.html', 'class': 'File', 'size': 1026290, 'checksum': 'sha1$7890', 'location': 'file:///output/portal/report.html', 'path': '/output/portal/report.html'}
]}
self.assertCWLDictEqual(d, ex)
r = d.repr()
ex2 = """ODir(name='portal', items=[OFile(name='meta_clinical_sample.txt', size=135, hash='1234'), ODir(name='case_lists', items=[OFile(name='cases_all.txt', size=448, hash='4567')]), OFile(name='report.html', size=1026290, hash='7890')], dir='/output')"""
self.assertEqual(r, ex2)
d2 = eval(r)
self.assertCWLDictEqual(d2, ex)