def assertDictSubsetOf(self, subset_dict, containing_dict):
mm_items = []
mm_missing = []
for (key, value) in subset_dict.items():
if key in containing_dict:
if value != containing_dict[key]:
mm_items.append(key)
else:
mm_missing.append(key)
err_items = len(mm_items) > 0
err_missing = len(mm_missing) > 0
if err_items or err_missing:
subset_json = self._dictToPPJSON(subset_dict)
containing_json = self._dictToPPJSON(containing_dict)
error_string = "Expected the following:\n"
error_string += "{}\n\nto be a subset of\n\n{}\n\n".format(subset_json,
containing_json)
if err_items:
m = ", ".join(map(lambda x: str(x), mm_items))
error_string += "Field value mismatch at keys: {}\n".format(m)
if err_missing:
m = ", ".join(map(lambda x: str(x), mm_missing))
error_string += "Keys missing from superset: {}\n".format(m)
self.assertFalse(True, error_string)
def assertDictSubsetOf(self, subset_dict, containing_dict):
mm_items = []
mm_missing = []
for (key, value) in list(subset_dict.items()):
if key in containing_dict:
if value != containing_dict[key]:
mm_items.append(key)
else:
mm_missing.append(key)
err_items = len(mm_items) > 0
err_missing = len(mm_missing) > 0
if err_items or err_missing:
subset_json = self._dictToPPJSON(subset_dict)
containing_json = self._dictToPPJSON(containing_dict)
error_string = "Expected the following:\n"
error_string += "{}\n\nto be a subset of\n\n{}\n\n".format(
subset_json, containing_json)
if err_items:
m = ", ".join([str(x) for x in mm_items])
error_string += "Field value mismatch at keys: {}\n".format(m)
if err_missing:
m = ", ".join([str(x) for x in mm_missing])
error_string += "Keys missing from superset: {}\n".format(m)
self.assertFalse(True, error_string)
def tearDown(self):
try:
dxpy.api.project_destroy(self.project, {"terminateJobs": True})
except Exception as e:
print("Failed to remove test project:", str(e))
if 'DX_PROJECT_CONTEXT_ID' in dxpy.config:
del dxpy.config['DX_PROJECT_CONTEXT_ID']
if 'DX_CLI_WD' in dxpy.config:
del dxpy.config['DX_CLI_WD']
def tearDown(self):
try:
subprocess.check_call(u"dx rmproject --yes --quiet {p}".format(p=self.project), shell=True)
except Exception as e:
print("Failed to remove test project:", str(e))
if 'DX_PROJECT_CONTEXT_ID' in os.environ:
del os.environ['DX_PROJECT_CONTEXT_ID']
if 'DX_CLI_WD' in os.environ:
del os.environ['DX_CLI_WD']
def tearDown(self):
try:
dxpy.api.project_destroy(self.project, {"terminateJobs": True})
except Exception as e:
print("Failed to remove test project:", str(e))
if 'DX_PROJECT_CONTEXT_ID' in dxpy.config:
del dxpy.config['DX_PROJECT_CONTEXT_ID']
if 'DX_CLI_WD' in dxpy.config:
del dxpy.config['DX_CLI_WD']
def exit_with_error(msg):
'''
:param msg: string message to print before exiting
Print the error message, as well as a blurb on where to find the
job workspaces
'''
msg += '\n'
msg += 'Local job workspaces can be found in: ' + str(environ.get('DX_TEST_JOB_HOMEDIRS'))
sys.exit(msg)
def tearDown(self):
if "DX_USER_CONF_DIR" in os.environ:
os.environ.pop("DX_USER_CONF_DIR")
try:
dxpy.api.project_destroy(self.project, {"terminateJobs": True})
except Exception as e:
print("Failed to remove test project:", str(e))
if 'DX_PROJECT_CONTEXT_ID' in dxpy.config:
del dxpy.config['DX_PROJECT_CONTEXT_ID']
if 'DX_CLI_WD' in dxpy.config:
del dxpy.config['DX_CLI_WD']
def exit_with_error(msg):
'''
:param msg: string message to print before exiting
Print the error message, as well as a blurb on where to find the
job workspaces
'''
msg += '\n'
msg += 'Local job workspaces can be found in: ' + str(
environ.get('DX_TEST_JOB_HOMEDIRS'))
sys.exit(msg)
def tearDown(self):
if "DX_USER_CONF_DIR" in os.environ:
os.environ.pop("DX_USER_CONF_DIR")
try:
dxpy.api.project_destroy(self.project, {"terminateJobs": True})
except Exception as e:
print("Failed to remove test project:", str(e))
if 'DX_PROJECT_CONTEXT_ID' in dxpy.config:
del dxpy.config['DX_PROJECT_CONTEXT_ID']
if 'DX_CLI_WD' in dxpy.config:
del dxpy.config['DX_CLI_WD']
def queue_entry_point(function, input_hash, depends_on=[], name=None):
'''
:param function: function to run
:param input_hash: input to new job
:param depends_on: list of data object IDs and/or job IDs (local or remote) to wait for before the job can be run
:type depends_on: list of strings
:param name: job name (optional)
:returns: new local job ID
This function should only be called by a locally running job, so
all relevant DX_TEST_* environment variables should be set.
This function will set up the home directory for the job, add an
entry in job_outputs.json, and append the job information to the
job_queue.json file. (Both files found in
$DX_TEST_JOB_HOMEDIRS.)
'''
ensure_env_vars()
all_job_outputs_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'],
'job_outputs.json')
with open(all_job_outputs_path, 'r') as fd:
all_job_outputs = json.load(fd,
object_pairs_hook=collections.OrderedDict)
job_id = 'localjob-' + str(len(all_job_outputs))
with open(all_job_outputs_path, 'wb') as fd:
all_job_outputs[job_id] = None
json.dump(all_job_outputs, fd, indent=4)
fd.write(b'\n')
job_homedir = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
os.mkdir(job_homedir)
job_queue_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'],
'job_queue.json')
with open(job_queue_path, 'r') as fd:
job_queue = json.load(fd)
job_entry = {
"id": job_id,
"function": function,
"input_hash": input_hash,
"depends_on": depends_on
}
if name is not None:
job_entry['name'] = name
job_queue.append(job_entry)
with open(job_queue_path, 'wb') as fd:
json.dump(job_queue, fd, indent=4)
fd.write(b'\n')
return job_id
def make_apps(self, num_apps, name_prefix, bill_to=None):
apps = []
app_spec = dict(self.base_app_spec)
for i in range(num_apps):
app_spec["name"] = name_prefix + "_" + str(i)
if bill_to is not None:
app_spec["billTo"] = bill_to
app_dir = self.write_app_directory("minimal_åpp",
json.dumps(app_spec), "code.py")
app = json.loads(run("dx build --create-app --json " + app_dir))
apps.append(app)
return apps
def make_apps(self, num_apps, name_prefix, bill_to=None):
apps = []
app_spec = dict(self.base_app_spec)
for i in range(num_apps):
app_spec["name"] = name_prefix + "_" + str(i)
if bill_to is not None:
app_spec["billTo"] = bill_to
app_dir = self.write_app_directory("minimal_åpp",
json.dumps(app_spec),
"code.py")
app = json.loads(run("dx build --create-app --json " + app_dir))
apps.append(app)
return apps
def queue_entry_point(function, input_hash, depends_on=[], name=None):
'''
:param function: function to run
:param input_hash: input to new job
:param depends_on: list of data object IDs and/or job IDs (local or remote) to wait for before the job can be run
:type depends_on: list of strings
:param name: job name (optional)
:returns: new local job ID
This function should only be called by a locally running job, so
all relevant DX_TEST_* environment variables should be set.
This function will set up the home directory for the job, add an
entry in job_outputs.json, and append the job information to the
job_queue.json file. (Both files found in
$DX_TEST_JOB_HOMEDIRS.)
'''
ensure_env_vars()
all_job_outputs_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json')
with open(all_job_outputs_path, 'r') as fd:
all_job_outputs = json.load(fd, object_pairs_hook=collections.OrderedDict)
job_id = 'localjob-' + str(len(all_job_outputs))
with open(all_job_outputs_path, 'wb') as fd:
all_job_outputs[job_id] = None
json.dump(all_job_outputs, fd, indent=4)
fd.write(b'\n')
job_homedir = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
os.mkdir(job_homedir)
job_queue_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_queue.json')
with open(job_queue_path, 'r') as fd:
job_queue = json.load(fd)
job_entry = {"id": job_id,
"function": function,
"input_hash": input_hash,
"depends_on": depends_on}
if name is not None:
job_entry['name'] = name
job_queue.append(job_entry)
with open(job_queue_path, 'wb') as fd:
json.dump(job_queue, fd, indent=4)
fd.write(b'\n')
return job_id
def resolve_job_ref(jbor, job_outputs={}, should_resolve=True):
'''
:param jbor: a dict that is a valid job-based object reference
:type jbor: dict
:param job_outputs: a dict of finished local jobs to their output hashes
:type job_outputs: :class:`collections.OrderedDict`
:returns: the referenced value if present
:raises: :exc:`Exception` if the job-based object reference cannot be resolved
TODO: Support metadata references
'''
ref_job_id = get_job_from_jbor(jbor)
ref_job_field = get_field_from_jbor(jbor)
ref_job_index = get_index_from_jbor(jbor)
def resolve_from_hash(output_hash):
if ref_job_index is None:
return output_hash[ref_job_field]
else:
return output_hash[ref_job_field][ref_job_index]
if is_localjob_id(ref_job_id):
if job_outputs.get(ref_job_id) is None:
if should_resolve:
raise Exception('Job ' + ref_job_id +
' not found in local finished jobs')
else:
return jbor
if ref_job_field not in job_outputs[ref_job_id]:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id +
' because field "' + ref_job_field +
'" was not found in its output')
return resolve_from_hash(job_outputs[ref_job_id])
else:
dxjob = dxpy.DXJob(ref_job_id)
try:
dxjob.wait_on_done()
except Exception as e:
raise Exception('Could not wait for ' + ref_job_id +
' to finish: ' + str(e))
job_desc = dxjob.describe()
if ref_job_field not in job_desc['output']:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id +
' because field "' + ref_job_field +
'" was not found in its output')
return resolve_from_hash(job_desc['output'])
def wait_for_depends_on(depends_on, all_job_outputs):
# Wait for depends_on and any data objects in the input to close
if len(depends_on) > 0:
print(fill('Processing dependsOn and any DNAnexus links to closing objects in the input'))
for an_id in depends_on:
try:
print(' Waiting for ' + an_id + '...')
if an_id.startswith('localjob'):
if all_job_outputs.get(an_id) is None:
raise Exception('Job ' + an_id + ' could not be found in local finished jobs')
elif an_id.startswith('job'):
dxjob = dxpy.DXJob(an_id)
dxjob.wait_on_done()
else:
handler = dxpy.get_handler(an_id)
desc = handler.describe()
handler._wait_on_close()
except Exception as e:
raise Exception('Could not wait for ' + an_id + ': ' + str(e))
def make_apps(self, num_apps, name_prefix, bill_to=None):
apps = []
app_spec = {
"dxapi": "1.0.0",
"runSpec": {"file": "code.py", "interpreter": "python2.7"},
"inputSpec": [],
"outputSpec": [],
"version": "1.0.0",
}
for i in range(num_apps):
app_spec["name"] = name_prefix + "_" + str(i)
if bill_to is not None:
app_spec["billTo"] = bill_to
app_dir = self.write_app_directory("minimal_åpp", json.dumps(app_spec), "code.py")
app = json.loads(run("dx build --create-app --json " + app_dir))
apps.append(app)
return apps
def resolve_job_ref(jbor, job_outputs={}, should_resolve=True):
'''
:param jbor: a dict that is a valid job-based object reference
:type jbor: dict
:param job_outputs: a dict of finished local jobs to their output hashes
:type job_outputs: :class:`collections.OrderedDict`
:returns: the referenced value if present
:raises: :exc:`Exception` if the job-based object reference cannot be resolved
TODO: Support metadata references
'''
ref_job_id = get_job_from_jbor(jbor)
ref_job_field = get_field_from_jbor(jbor)
ref_job_index = get_index_from_jbor(jbor)
def resolve_from_hash(output_hash):
if ref_job_index is None:
return output_hash[ref_job_field]
else:
return output_hash[ref_job_field][ref_job_index]
if is_localjob_id(ref_job_id):
if job_outputs.get(ref_job_id) is None:
if should_resolve:
raise Exception('Job ' + ref_job_id + ' not found in local finished jobs')
else:
return jbor
if ref_job_field not in job_outputs[ref_job_id]:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id + ' because field "' + ref_job_field + '" was not found in its output')
return resolve_from_hash(job_outputs[ref_job_id])
else:
dxjob = dxpy.DXJob(ref_job_id)
try:
dxjob.wait_on_done()
except Exception as e:
raise Exception('Could not wait for ' + ref_job_id + ' to finish: ' + str(e))
job_desc = dxjob.describe()
if ref_job_field not in job_desc['output']:
raise Exception('Cannot resolve a JBOR with job ID ' + ref_job_id + ' because field "' + ref_job_field + '" was not found in its output')
return resolve_from_hash(job_desc['output'])
def make_apps(self, num_apps, name_prefix, bill_to=None):
apps = []
app_spec = {
"dxapi": "1.0.0",
"runSpec": {
"file": "code.py",
"interpreter": "python2.7"
},
"inputSpec": [],
"outputSpec": [],
"version": "1.0.0",
}
for i in range(num_apps):
app_spec["name"] = name_prefix + "_" + str(i)
if bill_to is not None:
app_spec["billTo"] = bill_to
app_dir = self.write_app_directory("minimal_åpp",
json.dumps(app_spec), "code.py")
app = json.loads(run("dx build --create-app --json " + app_dir))
apps.append(app)
return apps
def wait_for_depends_on(depends_on, all_job_outputs):
# Wait for depends_on and any data objects in the input to close
if len(depends_on) > 0:
print(
fill(
'Processing dependsOn and any DNAnexus links to closing objects in the input'
))
for an_id in depends_on:
try:
print(' Waiting for ' + an_id + '...')
if an_id.startswith('localjob'):
if all_job_outputs.get(an_id) is None:
raise Exception(
'Job ' + an_id +
' could not be found in local finished jobs')
elif an_id.startswith('job'):
dxjob = dxpy.DXJob(an_id)
dxjob.wait_on_done()
else:
handler = dxpy.get_handler(an_id)
desc = handler.describe()
handler._wait_on_close()
except Exception as e:
raise Exception('Could not wait for ' + an_id + ': ' + str(e))
def run_one_entry_point(job_id,
function,
input_hash,
run_spec,
depends_on,
name=None):
'''
:param job_id: job ID of the local job to run
:type job_id: string
:param function: function to run
:type function: string
:param input_hash: input for the job (may include job-based object references)
:type input_hash: dict
:param run_spec: run specification from the dxapp.json of the app
:type run_spec: dict
Runs the specified entry point and retrieves the job's output,
updating job_outputs.json (in $DX_TEST_JOB_HOMEDIRS) appropriately.
'''
print('======')
job_homedir = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
job_env = environ.copy()
job_env['HOME'] = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
all_job_outputs_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'],
'job_outputs.json')
with open(all_job_outputs_path, 'r') as fd:
all_job_outputs = json.load(fd,
object_pairs_hook=collections.OrderedDict)
if isinstance(name, basestring):
name += ' (' + job_id + ':' + function + ')'
else:
name = job_id + ':' + function
job_name = BLUE() + BOLD() + name + ENDC()
print(job_name)
# Resolve local job-based object references
try:
resolve_job_references(input_hash, all_job_outputs)
except Exception as e:
exit_with_error(job_name + ' ' + JOB_STATES('failed') +
' when resolving input:\n' + fill(str(e)))
# Get list of non-closed data objects in the input that appear as
# DNAnexus links; append to depends_on
if depends_on is None:
depends_on = []
get_implicit_depends_on(input_hash, depends_on)
try:
wait_for_depends_on(depends_on, all_job_outputs)
except Exception as e:
exit_with_error(job_name + ' ' + JOB_STATES('failed') +
' when processing depends_on:\n' + fill(str(e)))
# Save job input to job_input.json
with open(os.path.join(job_homedir, 'job_input.json'), 'wb') as fd:
json.dump(input_hash, fd, indent=4)
fd.write(b'\n')
print(
job_output_to_str(input_hash,
title=(BOLD() + 'Input: ' + ENDC()),
title_len=len("Input: ")).lstrip())
if run_spec['interpreter'] == 'bash':
# Save job input to env vars
env_path = os.path.join(job_homedir, 'environment')
with open(env_path, 'w') as fd:
job_input_file = os.path.join(job_homedir, 'job_input.json')
var_defs_hash = file_load_utils.gen_bash_vars(
job_input_file, job_homedir=job_homedir)
for key, val in var_defs_hash.iteritems():
fd.write("{}={}\n".format(key, val))
print(BOLD() + 'Logs:' + ENDC())
start_time = datetime.datetime.now()
if run_spec['interpreter'] == 'bash':
script = '''
cd hotexamples_com;
. {env_path};
. {code_path};
if [[ $(type -t {function}) == "function" ]];
then {function};
else echo "$0: Global scope execution complete. Not invoking entry point function {function} because it was not found" 1>&2;
fi'''.format(homedir=pipes.quote(job_homedir),
env_path=pipes.quote(
os.path.join(job_env['HOME'], 'environment')),
code_path=pipes.quote(environ['DX_TEST_CODE_PATH']),
function=function)
invocation_args = ['bash', '-c', '-e'] + (
['-x'] if environ.get('DX_TEST_X_FLAG') else []) + [script]
elif run_spec['interpreter'] == 'python2.7':
script = '''#!/usr/bin/env python
import os
os.chdir(hotexamples_com)
{code}
import dxpy, json
if dxpy.utils.exec_utils.RUN_COUNT == 0:
dxpy.run()
'''.format(homedir=repr(job_homedir), code=run_spec['code'])
job_env['DX_TEST_FUNCTION'] = function
invocation_args = ['python', '-c', script]
if USING_PYTHON2:
invocation_args = [
arg.encode(sys.stdout.encoding) for arg in invocation_args
]
env = {k: v.encode(sys.stdout.encoding) for k, v in job_env.items()}
else:
env = job_env
fn_process = subprocess.Popen(invocation_args, env=env)
fn_process.communicate()
end_time = datetime.datetime.now()
if fn_process.returncode != 0:
exit_with_error(job_name + ' ' + JOB_STATES('failed') +
', exited with error code ' +
str(fn_process.returncode) + ' after ' +
str(end_time - start_time))
# Now updating job output aggregation file with job's output
job_output_path = os.path.join(job_env['HOME'], 'job_output.json')
if os.path.exists(job_output_path):
try:
with open(job_output_path, 'r') as fd:
job_output = json.load(
fd, object_pairs_hook=collections.OrderedDict)
except Exception as e:
exit_with_error('Error: Could not load output of ' + job_name +
':\n' + fill(str(e.__class__) + ': ' + str(e)))
else:
job_output = {}
print(job_name + ' -> ' + GREEN() + 'finished running' + ENDC() +
' after ' + str(end_time - start_time))
print(
job_output_to_str(job_output,
title=(BOLD() + "Output: " + ENDC()),
title_len=len("Output: ")).lstrip())
with open(
os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json'),
'r') as fd:
all_job_outputs = json.load(fd,
object_pairs_hook=collections.OrderedDict)
all_job_outputs[job_id] = job_output
# Before dumping, see if any new jbors should be resolved now
for other_job_id in all_job_outputs:
if all_job_outputs[other_job_id] is None:
# Skip if job is not done yet (true for ancestor jobs)
continue
resolve_job_references(all_job_outputs[other_job_id],
all_job_outputs,
should_resolve=False)
with open(
os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json'),
'wb') as fd:
json.dump(all_job_outputs, fd, indent=4)
fd.write(b'\n')
def run_one_entry_point(job_id, function, input_hash, run_spec, depends_on, name=None):
'''
:param job_id: job ID of the local job to run
:type job_id: string
:param function: function to run
:type function: string
:param input_hash: input for the job (may include job-based object references)
:type input_hash: dict
:param run_spec: run specification from the dxapp.json of the app
:type run_spec: dict
Runs the specified entry point and retrieves the job's output,
updating job_outputs.json (in $DX_TEST_JOB_HOMEDIRS) appropriately.
'''
print('======')
job_homedir = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
job_env = environ.copy()
job_env['HOME'] = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], job_id)
all_job_outputs_path = os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json')
with open(all_job_outputs_path, 'r') as fd:
all_job_outputs = json.load(fd, object_pairs_hook=collections.OrderedDict)
if isinstance(name, basestring):
name += ' (' + job_id + ':' + function + ')'
else:
name = job_id + ':' + function
job_name = BLUE() + BOLD() + name + ENDC()
print(job_name)
# Resolve local job-based object references
try:
resolve_job_references(input_hash, all_job_outputs)
except Exception as e:
exit_with_error(job_name + ' ' + JOB_STATES('failed') + ' when resolving input:\n' + fill(str(e)))
# Get list of non-closed data objects in the input that appear as
# DNAnexus links; append to depends_on
if depends_on is None:
depends_on = []
get_implicit_depends_on(input_hash, depends_on)
try:
wait_for_depends_on(depends_on, all_job_outputs)
except Exception as e:
exit_with_error(job_name + ' ' + JOB_STATES('failed') + ' when processing depends_on:\n' + fill(str(e)))
# Save job input to job_input.json
with open(os.path.join(job_homedir, 'job_input.json'), 'wb') as fd:
json.dump(input_hash, fd, indent=4)
fd.write(b'\n')
print(job_output_to_str(input_hash, title=(BOLD() + 'Input: ' + ENDC()),
title_len=len("Input: ")).lstrip())
if run_spec['interpreter'] == 'bash':
# Save job input to env vars
env_path = os.path.join(job_homedir, 'environment')
with open(env_path, 'w') as fd:
# Following code is what is used to generate env vars on the remote worker
fd.write("\n".join(["export {k}=( {vlist} )".format(k=k, vlist=" ".join([pipes.quote(vitem if isinstance(vitem, basestring) else json.dumps(vitem)) for vitem in v])) if isinstance(v, list) else "export {k}={v}".format(k=k, v=pipes.quote(v if isinstance(v, basestring) else json.dumps(v))) for k, v in input_hash.items()]))
print(BOLD() + 'Logs:' + ENDC())
start_time = datetime.datetime.now()
if run_spec['interpreter'] == 'bash':
script = '''
cd hotexamples_com;
. {env_path};
. {code_path};
if [[ $(type -t {function}) == "function" ]];
then {function};
else echo "$0: Global scope execution complete. Not invoking entry point function {function} because it was not found" 1>&2;
fi'''.format(homedir=pipes.quote(job_homedir),
env_path=pipes.quote(os.path.join(job_env['HOME'], 'environment')),
code_path=pipes.quote(environ['DX_TEST_CODE_PATH']),
function=function)
invocation_args = ['bash', '-c', '-e'] + (['-x'] if environ.get('DX_TEST_X_FLAG') else []) + [script]
elif run_spec['interpreter'] == 'python2.7':
script = '''#!/usr/bin/env python
import os
os.chdir(hotexamples_com)
{code}
import dxpy, json
if dxpy.utils.exec_utils.RUN_COUNT == 0:
dxpy.run()
'''.format(homedir=repr(job_homedir),
code=run_spec['code'])
job_env['DX_TEST_FUNCTION'] = function
invocation_args = ['python', '-c', script]
if USING_PYTHON2:
invocation_args = [arg.encode(sys.stdout.encoding) for arg in invocation_args]
env = {k: v.encode(sys.stdout.encoding) for k, v in job_env.items()}
else:
env = job_env
fn_process = subprocess.Popen(invocation_args, env=env)
fn_process.communicate()
end_time = datetime.datetime.now()
if fn_process.returncode != 0:
exit_with_error(job_name + ' ' + JOB_STATES('failed') + ', exited with error code ' + str(fn_process.returncode) + ' after ' + str(end_time - start_time))
# Now updating job output aggregation file with job's output
job_output_path = os.path.join(job_env['HOME'], 'job_output.json')
if os.path.exists(job_output_path):
try:
with open(job_output_path, 'r') as fd:
job_output = json.load(fd, object_pairs_hook=collections.OrderedDict)
except Exception as e:
exit_with_error('Error: Could not load output of ' + job_name + ':\n' + fill(str(e.__class__) + ': ' + str(e)))
else:
job_output = {}
print(job_name + ' -> ' + GREEN() + 'finished running' + ENDC() + ' after ' + str(end_time - start_time))
print(job_output_to_str(job_output, title=(BOLD() + "Output: " + ENDC()),
title_len=len("Output: ")).lstrip())
with open(os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json'), 'r') as fd:
all_job_outputs = json.load(fd, object_pairs_hook=collections.OrderedDict)
all_job_outputs[job_id] = job_output
# Before dumping, see if any new jbors should be resolved now
for other_job_id in all_job_outputs:
if all_job_outputs[other_job_id] is None:
# Skip if job is not done yet (true for ancestor jobs)
continue
resolve_job_references(all_job_outputs[other_job_id], all_job_outputs, should_resolve=False)
with open(os.path.join(environ['DX_TEST_JOB_HOMEDIRS'], 'job_outputs.json'), 'wb') as fd:
json.dump(all_job_outputs, fd, indent=4)
fd.write(b'\n')
def generate_unique_username_email():
r = random.randint(0, 255)
username = "******" + str(int(time.time())) + "_" + str(r)
email = username + "@example.com"
return username, email
def generate_unique_username_email():
r = random.randint(0, 255)
username = "******" + str(int(time.time())) + "_" + str(r)
email = username + "@example.com"
return username, email
