def assertNewJobInputHash(self, cmd_snippet, arguments_hash):
cmd = "dx-jobutil-new-job entrypointname " + cmd_snippet + " --test"
expected_job_input = {"function": "entrypointname", "input": {}}
env = override_environment(DX_JOB_ID="job-000000000000000000000001", DX_WORKSPACE_ID=self.project)
output = run(cmd, env=env)
expected_job_input.update(arguments_hash)
self.assertEqual(json.loads(output), expected_job_input)
def assertNewJobInputHash(self, cmd_snippet, arguments_hash):
cmd = "dx-jobutil-new-job entrypointname " + cmd_snippet + " --test"
expected_job_input = {"function": "entrypointname", "input": {}}
env = override_environment(DX_JOB_ID="job-000000000000000000000001",
DX_WORKSPACE_ID=self.project)
output = run(cmd, env=env)
expected_job_input.update(arguments_hash)
self.assertEqual(json.loads(output), expected_job_input)
def test_build_asset_help(self):
env = override_environment(DX_SECURITY_CONTEXT=None,
DX_APISERVER_HOST=None,
DX_APISERVER_PORT=None,
DX_APISERVER_PROTOCOL=None)
run("dx build_asset -h", env=env)
def assertNewJobError(self, cmd_snippet, exit_code):
cmd = "dx-jobutil-new-job entrypointname " + cmd_snippet + " --test"
env = override_environment(DX_JOB_ID="job-000000000000000000000001",
DX_WORKSPACE_ID=self.project)
with self.assertSubprocessFailure(exit_code=exit_code):
run(cmd, env=env)
def test_build_asset_help(self):
env = override_environment(DX_SECURITY_CONTEXT=None, DX_APISERVER_HOST=None,
DX_APISERVER_PORT=None, DX_APISERVER_PROTOCOL=None)
run("dx build_asset -h", env=env)
def assertNewJobError(self, cmd_snippet, exit_code):
cmd = "dx-jobutil-new-job entrypointname " + cmd_snippet + " --test"
env = override_environment(DX_JOB_ID="job-000000000000000000000001", DX_WORKSPACE_ID=self.project)
with self.assertSubprocessFailure(exit_code=exit_code):
run(cmd, env=env)
def test_dx_jobutil_new_job(self):
first_record = dxpy.new_dxrecord(name="first_record")
second_record = dxpy.new_dxrecord(name="second_record")
dxpy.new_dxrecord(name="duplicate_name_record")
dxpy.new_dxrecord(name="duplicate_name_record")
# In a different project...
third_record = dxpy.new_dxrecord(name="third_record", project=self.aux_project.get_id())
test_cases = (
# string
("-ifoo=input_string", {"foo": "input_string"}),
# string that looks like a {job,analysis} ID
("-ifoo=job-012301230123012301230123", {"foo": "job-012301230123012301230123"}),
("-ifoo=analysis-012301230123012301230123", {"foo": "analysis-012301230123012301230123"}),
# int
("-ifoo=24", {"foo": 24}),
# float
("-ifoo=24.5", {"foo": 24.5}),
# json
('-ifoo=\'{"a": "b"}\'', {"foo": {"a": "b"}}),
('-ifoo=\'["a", "b"]\'', {"foo": ["a", "b"]}),
# objectName
("-ifoo=first_record", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
# objectId
("-ifoo=" + first_record.get_id(), {"foo": dxpy.dxlink(first_record.get_id())}),
# project:objectName
("-ifoo=" + self.aux_project.get_id() + ":third_record",
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# project:objectId
("-ifoo=" + self.aux_project.get_id() + ":" + third_record.get_id(),
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# same, but wrong project is specified
("-ifoo=" + self.project + ":" + third_record.get_id(),
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# glob
("-ifoo=first*", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
# JBOR
("-ifoo=job-012301230123012301230123:outputfield",
{"foo": {"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}}}),
# order of inputs is preserved from command line to API call
("-ifoo=first* -ifoo=second_record -ifoo=job-012301230123012301230123:outputfield",
{"foo": [dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project),
{"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}}]}),
("-ifoo=job-012301230123012301230123:outputfield -ifoo=first_record -ifoo=second_*",
{"foo": [{"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}},
dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project)]}),
# if there is any ambiguity, the name is left unresolved
("-ifoo=duplicate_name_record", {"foo": "duplicate_name_record"}),
("-ifoo=*record", {"foo": "*record"}),
# Override class
("-ifoo:int=24", {"foo": 24}),
("-ifoo:string=24", {"foo": "24"}),
("-ifoo:string=first_record", {"foo": "first_record"}),
('-ifoo:hash=\'{"a": "b"}\'', {"foo": {"a": "b"}}),
('-ifoo:hash=\'["a", "b"]\'', {"foo": ["a", "b"]}),
("-ifoo:file=first_record", None), # Error
("-ifoo:int=foo", None), # Error
("-ifoo:int=24.5", None), # Error
# Array inputs
# implicit array notation
("-ifoo=24 -ifoo=25", {"foo": [24, 25]}),
("-ifoo=25 -ibar=1 -ifoo=24", {"foo": [25, 24], "bar": 1}),
("-ifoo=first_record -ifoo=second_record",
{"foo": [dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project)]}),
# different types (unusual, but potentially meaningful if
# foo is a json input)
("-ifoo=24 -ifoo=bar", {"foo": [24, "bar"]}),
# explicit array notation is NOT respected (in contexts with
# no inputSpec such as this one)
("-ifoo:array:int=24", {"foo": 24}),
("-ifoo:array:record=first_record", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
)
env = override_environment(DX_JOB_ID="job-000000000000000000000001",
DX_WORKSPACE_ID=self.project)
for cmd_snippet, expected_input_hash in test_cases:
cmd = "dx-jobutil-new-job " + cmd_snippet + " entrypointname --test"
if expected_input_hash is None:
with self.assertSubprocessFailure(exit_code=1):
run(cmd, env=env)
else:
output = run(cmd, env=env)
self.assertEqual(json.loads(output), {"input": expected_input_hash, "function": "entrypointname"})
def test_dx_jobutil_new_job(self):
first_record = dxpy.new_dxrecord(name="first_record")
second_record = dxpy.new_dxrecord(name="second_record")
dxpy.new_dxrecord(name="duplicate_name_record")
dxpy.new_dxrecord(name="duplicate_name_record")
# In a different project...
third_record = dxpy.new_dxrecord(name="third_record", project=self.aux_project.get_id())
test_cases = (
# string
("-ifoo=input_string", {"foo": "input_string"}),
# string that looks like a {job,analysis} ID
("-ifoo=job-012301230123012301230123", {"foo": "job-012301230123012301230123"}),
("-ifoo=analysis-012301230123012301230123", {"foo": "analysis-012301230123012301230123"}),
# int
("-ifoo=24", {"foo": 24}),
# float
("-ifoo=24.5", {"foo": 24.5}),
# json
('-ifoo=\'{"a": "b"}\'', {"foo": {"a": "b"}}),
('-ifoo=\'["a", "b"]\'', {"foo": ["a", "b"]}),
# objectName
("-ifoo=first_record", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
# objectId
("-ifoo=" + first_record.get_id(), {"foo": dxpy.dxlink(first_record.get_id())}),
# project:objectName
("-ifoo=" + self.aux_project.get_id() + ":third_record",
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# project:objectId
("-ifoo=" + self.aux_project.get_id() + ":" + third_record.get_id(),
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# same, but wrong project is specified
("-ifoo=" + self.project + ":" + third_record.get_id(),
{"foo": dxpy.dxlink(third_record.get_id(), self.aux_project.get_id())}),
# glob
("-ifoo=first*", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
# JBOR
("-ifoo=job-012301230123012301230123:outputfield",
{"foo": {"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}}}),
# order of inputs is preserved from command line to API call
("-ifoo=first* -ifoo=second_record -ifoo=job-012301230123012301230123:outputfield",
{"foo": [dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project),
{"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}}]}),
("-ifoo=job-012301230123012301230123:outputfield -ifoo=first_record -ifoo=second_*",
{"foo": [{"$dnanexus_link": {"job": "job-012301230123012301230123", "field": "outputfield"}},
dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project)]}),
# if there is any ambiguity, the name is left unresolved
("-ifoo=duplicate_name_record", {"foo": "duplicate_name_record"}),
("-ifoo=*record", {"foo": "*record"}),
# Override class
("-ifoo:int=24", {"foo": 24}),
("-ifoo:string=24", {"foo": "24"}),
("-ifoo:string=first_record", {"foo": "first_record"}),
('-ifoo:hash=\'{"a": "b"}\'', {"foo": {"a": "b"}}),
('-ifoo:hash=\'["a", "b"]\'', {"foo": ["a", "b"]}),
("-ifoo:file=first_record", None), # Error
("-ifoo:int=foo", None), # Error
("-ifoo:int=24.5", None), # Error
# Array inputs
# implicit array notation
("-ifoo=24 -ifoo=25", {"foo": [24, 25]}),
("-ifoo=25 -ibar=1 -ifoo=24", {"foo": [25, 24], "bar": 1}),
("-ifoo=first_record -ifoo=second_record",
{"foo": [dxpy.dxlink(first_record.get_id(), self.project),
dxpy.dxlink(second_record.get_id(), self.project)]}),
# different types (unusual, but potentially meaningful if
# foo is a json input)
("-ifoo=24 -ifoo=bar", {"foo": [24, "bar"]}),
# explicit array notation is NOT respected (in contexts with
# no inputSpec such as this one)
("-ifoo:array:int=24", {"foo": 24}),
("-ifoo:array:record=first_record", {"foo": dxpy.dxlink(first_record.get_id(), self.project)}),
)
env = override_environment(DX_JOB_ID="job-000000000000000000000001",
DX_WORKSPACE_ID=self.project)
for cmd_snippet, expected_input_hash in test_cases:
cmd = "dx-jobutil-new-job " + cmd_snippet + " entrypointname --test"
if expected_input_hash is None:
with self.assertSubprocessFailure(exit_code=1):
run(cmd, env=env)
else:
output = run(cmd, env=env)
self.assertEqual(json.loads(output), {"input": expected_input_hash, "function": "entrypointname"})
