class TestTxtDevApp(pbcommand.testkit.PbTestApp):
DRIVER_BASE = "python -m pbcommand.cli.examples.dev_txt_app "
# XXX using default args, so the emit/resolve drivers are automatic
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
TASK_OPTIONS = {"pbcommand.task_options.dev_max_nlines": 27}
RESOLVED_TASK_OPTIONS = {"pbcommand.task_options.dev_max_nlines": 27}
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_gather_tool_contract(tc, self.INPUT_FILES, d, d, self.MAX_NPROC, self.TOOL_OPTIONS, self.CHUNK_KEY)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedGatherToolContractTask)
self.assertEqual(rtc.task.chunk_key, self.CHUNK_KEY)
class TestQuickCustomTxtCustomOuts(pbcommand.testkit.PbTestApp):
"""Runs dev_qhello_world """
DRIVER_EMIT = "python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_custom_outs "
DRIVER_RESOLVE = "python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc "
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
def test_01(self):
file_name = "resolved_tool_contract_dev_app.json"
rtc = load_resolved_tool_contract_from(get_data_file(file_name))
self.assertIsInstance(rtc, ResolvedToolContract)
d = get_temp_dir("rtc-app")
f = get_temp_file("-resolved-tool-contract.avro", d)
write_resolved_tool_contract_avro(rtc, f)
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_scatter_tool_contract(tc, self.INPUT_FILES, d, d, self.MAX_NPROC, self.TOOL_OPTIONS, self.MAX_NCHUNKS, self.CHUNK_KEYS, False)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedScatteredToolContractTask)
self.assertEqual(rtc.task.max_nchunks, 7)
self.assertEqual(rtc.task.is_distributed, False)
def test_01(self):
file_name = "resolved_tool_contract_dev_app.json"
rtc = load_resolved_tool_contract_from(get_data_file(file_name))
self.assertIsInstance(rtc, ResolvedToolContract)
d = get_temp_dir("rtc-app")
f = get_temp_file("-resolved-tool-contract.avro", d)
write_resolved_tool_contract_avro(rtc, f)
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_gather_tool_contract(tc, self.INPUT_FILES, d, d,
self.MAX_NPROC, self.TOOL_OPTIONS,
self.CHUNK_KEY)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedGatherToolContractTask)
self.assertEqual(rtc.task.chunk_key, self.CHUNK_KEY)
class TestOptionTypes(pbcommand.testkit.PbTestApp):
DRIVER_BASE = "python -m pbcommand.cli.examples.dev_mixed_app"
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
TASK_OPTIONS = {
"pbcommand.task_options.alpha": 50,
"pbcommand.task_options.beta": 9.876,
"pbcommand.task_options.gamma": False
}
class TestQuickTxt(pbcommand.testkit.PbTestApp):
"""Runs dev_qhello_world """
DRIVER_EMIT = "python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_hello "
DRIVER_RESOLVE = "python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc "
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
IS_DISTRIBUTED = True
RESOLVED_IS_DISTRIBUTED = False # XXX is_distributed=False in task TC!
class TestQuickDevHelloWorld(PbTestApp):
"""Runs dev_qhello_world """
DRIVER_EMIT = "python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_qhello_world "
DRIVER_RESOLVE = "python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc "
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
IS_DISTRIBUTED = True
RESOLVED_IS_DISTRIBUTED = True
def test_tc_no_inputs(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
tc.task.input_file_types = []
def _run():
return tc.to_dict()
self.assertRaises(MalformedToolContractError, _run)
def test_tc_no_inputs(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
tc.task.input_file_types = []
def _run():
return tc.to_dict()
self.assertRaises(MalformedToolContractError, _run)
def test_sanity(self):
d = get_temp_dir("resolved-tool-contract")
tc = load_tool_contract_from(get_data_file(self.FILE_NAME))
rtc = resolve_scatter_tool_contract(tc, self.INPUT_FILES, d, d,
self.MAX_NPROC, self.TOOL_OPTIONS,
self.MAX_NCHUNKS, self.CHUNK_KEYS,
False)
self.assertIsInstance(rtc, ResolvedToolContract)
self.assertIsInstance(rtc.task, ResolvedScatteredToolContractTask)
self.assertEqual(rtc.task.max_nchunks, 7)
self.assertEqual(rtc.task.is_distributed, False)
def test_01(self):
name = "dev_example_tool_contract.json"
p = get_data_file(name)
tc = load_tool_contract_from(p)
input_files = ["/tmp/file.txt"]
root_output_dir = "/tmp"
root_tmp_dir = root_output_dir
max_nproc = 2
rtc = resolve_tool_contract(tc, input_files, root_output_dir, root_tmp_dir, max_nproc, {})
log.info(pprint.pformat(rtc))
self.assertIsNotNone(rtc)
self.assertEqual(os.path.basename(rtc.task.output_files[0]),
"output.txt")
def test_01(self):
name = "dev_example_tool_contract.json"
p = get_data_file(name)
tc = load_tool_contract_from(p)
input_files = ["/tmp/file.txt"]
root_output_dir = "/tmp"
root_tmp_dir = root_output_dir
max_nproc = 2
rtc = resolve_tool_contract(tc, input_files, root_output_dir,
root_tmp_dir, max_nproc, {})
log.info(pprint.pformat(rtc))
self.assertIsNotNone(rtc)
self.assertEqual(os.path.basename(rtc.task.output_files[0]),
"output.txt")
class TestQuickOptionTypes(PbTestApp):
DRIVER_EMIT = "python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_test_options"
DRIVER_RESOLVE = "python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc "
INPUT_FILES = [get_data_file("example.txt")]
TASK_OPTIONS = {
"pbcommand.task_options.alpha": 50,
"pbcommand.task_options.beta": 9.876,
"pbcommand.task_options.gamma": False,
"pbcommand.task_options.ploidy": "diploid"
}
RESOLVED_TASK_OPTIONS = {
"pbcommand.task_options.alpha": 50,
"pbcommand.task_options.beta": 9.876,
"pbcommand.task_options.gamma": False,
"pbcommand.task_options.ploidy": "diploid",
"pbcommand.task_options.delta": 1,
"pbcommand.task_options.epsilon": 0.01
}
class TestOptionTypes(PbTestApp):
DRIVER_BASE = "python -m pbcommand.cli.examples.dev_mixed_app"
REQUIRES_PBCORE = False
INPUT_FILES = [get_data_file("example.txt")]
TASK_OPTIONS = {
"pbcommand.task_options.alpha": 50,
"pbcommand.task_options.beta": 9.876,
"pbcommand.task_options.gamma": False,
"pbcommand.task_options.ploidy": "diploid"
}
RESOLVED_TASK_OPTIONS = {
"pbcommand.task_options.alpha": 50,
"pbcommand.task_options.beta": 9.876,
"pbcommand.task_options.gamma": False,
"pbcommand.task_options.ploidy": "diploid",
"pbcommand.task_options.delta": 1,
"pbcommand.task_options.epsilon": 0.1
}
def test_01(self):
name = "dev_example_dev_txt_app_tool_contract.json"
p = get_data_file(name)
tc = load_tool_contract_from(p)
input_files = ["/tmp/file.txt"]
root_output_dir = "/tmp"
root_tmp_dir = root_output_dir
tmp_file = tempfile.NamedTemporaryFile().name
max_nproc = 2
tool_options = {}
rtc = resolve_tool_contract(tc, input_files, root_output_dir, root_tmp_dir, max_nproc, tool_options, False)
log.info(pprint.pformat(rtc))
self.assertIsNotNone(rtc)
self.assertEqual(os.path.basename(rtc.task.output_files[0]),
"output.txt")
# Validate Resolved Resource Types
log.debug("Resources {t}".format(t=rtc.task.resources))
self.assertEqual(len(rtc.task.tmpdir_resources), 1)
self.assertEqual(len(rtc.task.tmpfile_resources), 2)
def test_01(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
self.assertIsInstance(tc, ToolContract)
def test_01(self):
path = get_data_file("dev_example_resolved_tool_contract.json")
rtc = load_resolved_tool_contract_from(path)
log.info(rtc)
self.assertIsNotNone(rtc)
class TestRunDevApp(pbcommand.testkit.PbTestApp):
DRIVER_BASE = "python -m pbcommand.cli.examples.dev_app "
REQUIRES_PBCORE = True
INPUT_FILES = [get_data_file("example.fasta")]
TASK_OPTIONS = {"pbcommand.task_options.dev_read_length": 27}
def test_sanity(self):
path = get_data_file(self.FILE_NAME)
tool_contract = self._to_object(path)
self.assertIsNotNone(tool_contract)
def test_01(self):
file_name = "dev_example_tool_contract.json"
path = get_data_file(file_name)
tc = load_tool_contract_from(path)
self.assertIsInstance(tc, ToolContract)