def get_handler_from_desc(desc):
if desc['class'] == 'applet':
return dxpy.DXApplet(desc['id'], project=desc['project'])
elif desc['class'] == 'app':
return dxpy.DXApp(dxid=desc['id'])
else:
return dxpy.DXWorkflow(desc['id'], project=desc['project'])
def once():
try:
desc = test_files[tname]
if tname in test_defaults:
inputs = {}
elif desc.dx_input is None:
inputs = {}
else:
inputs = read_json_file(desc.dx_input)
project.new_folder(test_folder, parents=True)
if desc.kind == "workflow":
exec_obj = dxpy.DXWorkflow(project=project.get_id(), dxid=oid)
elif desc.kind == "applet":
exec_obj = dxpy.DXApplet(project=project.get_id(), dxid=oid)
else:
raise RuntimeError("Unknown kind {}".format(desc.kind))
run_kwargs = {}
if debug_flag:
run_kwargs = {
"debug": {"debugOn": ['AppError', 'AppInternalError', 'ExecutionError'] },
"allow_ssh" : [ "*" ]
}
if delay_workspace_destruction:
run_kwargs["delay_workspace_destruction"] = True
return exec_obj.run(inputs,
project=project.get_id(),
folder=test_folder,
name="{} {}".format(desc.name, git_revision),
instance_type="mem1_ssd1_x4",
**run_kwargs)
except Exception as e:
print("exception message={}".format(e))
return None
def main():
inputs_file = open("inputs_stats.txt", 'w')
print sys.argv[2]
workflow = dxpy.DXWorkflow(sys.argv[2].split(":")[-1])
fh = dxpy.DXFile(sys.argv[1].split(":")[-1])
if "/Results" in fh.describe()['folder']:
return
app_id = sys.argv[3]
if "applet" in app_id:
app = dxpy.DXApplet(app_id)
else:
app = dxpy.DXApp(app_id)
w_id = sys.argv[1].split(":")[1]
existing_inputs = []
for item in workflow.describe()['stages'][0]['input']:
existing_inputs.append(item)
print existing_inputs
for x in app.describe()['inputSpec']:
print x
if x['class'] == 'file' and x['name'] not in existing_inputs:
inputs_file.write(x['name'] + "\n")
inputs_file.close()
def test_duplicate_outputs(self):
"""
If bax files are converted to BAM or FASTA, the output will be of the
format: [prefix].[part_number].[ext]
Since these are grouped together in mapping, we want to make sure
output files don't all have the name [prefix].mapped.bam
"""
job_input = self.base_input
# these are 40MB files
job_input["reads"] = [{
"$dnanexus_link": "file-BXqbQx803GZK2FBqzb40yvQ1"
}, {
"$dnanexus_link": "file-BXqbV1j03GZFyYv3zk4BjZxZ"
}]
job_input["datatype"] = "PacBio"
job_input["chunk_size"] = 1
job = dxpy.DXApplet(self.applet_id).run(job_input,
folder=self.tempdirdx,
name=self.testname,
project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(), )
try:
job.wait_on_done()
output = job.describe()["output"]
# check that 2 files are output
mappings_files = output["bam_files"]
# check that both files don't have the same name
self.assertTrue(len(mappings_files) == 2)
filename1 = dxpy.DXFile(mappings_files[0]).describe()['name']
filename2 = dxpy.DXFile(mappings_files[1]).describe()['name']
self.assertTrue(filename1 != filename2)
except Exception:
DX_PROJ_OBJ.move_folder(self.tempdirdx, ARTIFACTS_FOLDER)
raise
def test_datatype_compatbility(self):
"""
Tests the app with a basic input.
"""
job_input = self.base_input
# this is a subreads.bam file
job_input["reads"] = [
{"$dnanexus_link": "file-FPY0BY80pbJvg49Z3k4zZp71"},
{"$dnanexus_link": "file-FPY0BX802J4jybZVJf0gy272"}
]
job_input["reads_indices"] = [
{"$dnanexus_link": "file-FPY096j0VvqbBk3Y5367XbJp"},
{"$dnanexus_link": "file-FPY096j0G03Gg49Z3k4zZg1Q"}
]
# this is an incompatible datatype
job_input["datatype"] = "ONT"
job = dxpy.DXApplet(self.applet_id).run(job_input, folder=self.tempdirdx, name=self.testname, project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(),)
try:
job.wait_on_done()
print json.dumps(job.describe()["output"])
# if job continued, fail this test
raise Exception("Job should have failed with DXAppError")
except dxpy.exceptions.AppError:
pass
def test_alignment_count(applet_id, project_id, folder, tmpdir):
"""Run BWA on a FASTQ file and verify that the number of
alignments produced is correct.
"""
# Recall that applet_id is set in the associated conftest.py, which either
# gets it from the command line or builds the applet and retrieves its id.
# And tmpdir is some pytest magic. It's type is py.path.local.LocalPath.
# It's strpath property just returns a string.
applet = dxpy.DXApplet(applet_id)
input_dict = {
"fastq": dxpy.dxlink(SAMPLE_FASTQ),
"genomeindex_targz": dxpy.dxlink(HS37D5_BWA_INDEX)
}
job = applet.run(input_dict,
instance_type="mem1_ssd1_x16",
folder=folder,
project=project_id)
job.wait_on_done()
output_bam_dxfile = dxpy.DXFile(job.describe()["output"]["bam"])
local_filename = os.path.join(tmpdir.strpath, "test.bam")
dxpy.download_dxfile(output_bam_dxfile.get_id(), local_filename)
count_alignments_cmd = "samtools view {bam} | wc -l".format(
bam=local_filename)
num_alignments = int(
subprocess.check_output(count_alignments_cmd, shell=True))
assert num_alignments == 1951476
def test_base_input(self):
"""
Tests the app with a basic input.
"""
job = dxpy.DXApplet(self.applet_id).run(self.base_input)
print "Waiting for %s to complete" % (job.get_id(), )
job.wait_on_done()
print json.dumps(job.describe()["output"])
def test_post(self):
"""
Tests the app with a basic input, skipping validation
"""
job = dxpy.DXApplet(self.applet_id).run(self.bed_input)
print "Waiting for %s to complete" % (job.get_id(),)
job.wait_on_done()
outp = job.describe()["output"]
print json.dumps(outp)
bb_input = self.bb_input
bb_input['file_meta'].update({'derived_from': [ outp['accession'] ]})
djob = dxpy.DXApplet(self.applet_id).run(bb_input)
print "Waiting for %s to complete" % (djob.get_id(),)
djob.wait_on_done()
outp = djob.describe()["output"]
print json.dumps(outp)
def build_applet():
"""Build the dxWDL applet."""
dx_applet_id = dxpy.api.applet_new({
"name":
APPLET_NAME,
"title":
"WES dxWDL Runner",
"dxapi":
dxpy.API_VERSION,
"project":
dxpy.PROJECT_CONTEXT_ID,
"properties": {
"version": APPLET_VERSION
},
"inputSpec": [{
"name": "workflow_descriptor",
"class": "string"
}, {
"name": "workflow_params",
"class": "string"
}, {
"name": "workflow_dependencies",
"class": "string",
"optional": True
}, {
"name": "project",
"class": "string"
}, {
"name": "wes_id",
"class": "string"
}],
"outputSpec": [],
"runSpec": {
"code":
APPLET_CODE,
"interpreter":
"python2.7",
"systemRequirements": {
"*": {
"instanceType": "mem1_ssd1_x4"
}
},
"execDepends": [{
"name": "openjdk-8-jre-headless",
}, {
"name": "dx-toolkit"
}]
},
"access": {
"network": ["*"],
"project": "CONTRIBUTE"
},
"release":
"14.04"
})
return dxpy.DXApplet(dx_applet_id["id"])
def test_dx_build_app_locally_using_app_builder(self):
appdir = create_app_dir()
print("Setting current project to", self.project)
dxpy.WORKSPACE_ID = self.project
dxpy.PROJECT_CONTEXT_ID = self.project
bundled_resources = dxpy.app_builder.upload_resources(appdir)
applet_id, _ignored_applet_spec = dxpy.app_builder.upload_applet(appdir, bundled_resources, overwrite=True, dx_toolkit_autodep=False)
app_obj = dxpy.DXApplet(applet_id)
self.assertEqual(app_obj.describe()['id'], app_obj.get_id())
def test_skip(self):
"""
Tests the app skipping validation.
"""
skip_input = self.base_input
skip_input.update({'skipvalidate': True})
job = dxpy.DXApplet(self.applet_id).run(skip_input)
print "Waiting for %s to complete" % (job.get_id(),)
job.wait_on_done()
print json.dumps(job.describe()["output"])
def test_applet_completion(self):
dxapplet = dxpy.DXApplet()
dxapplet.new(runSpec={"code": "placeholder", "interpreter": "bash"},
dxapi="1.0.0",
name="my applet")
self.assert_completion("dx ls my", "my applet ")
self.assert_completion("dx ls", "ls ")
self.assert_completion("dx run my", "my applet ")
self.assert_completion("dx ls ", "my applet ")
def get_project_id(project_id_, applet_id_):
"""Return the project_id to use for the tests.
If project_id is specified, just use that. If not, use the
the project that contains the applet.
"""
if project_id_:
return project_id_
applet = dxpy.DXApplet(applet_id_)
return applet.describe()['project']
def lookup_applet(name, project, folder):
wfgen = dxpy.bindings.search.find_data_objects(name= name,
folder= folder,
project= project.get_id(),
limit= 1)
objs = [item for item in wfgen]
if len(objs) == 0:
raise RuntimeError("applet {} not found in folder {}".format(name, folder))
if len(objs) == 1:
oid = objs[0]['id']
return dxpy.DXApplet(project=project.get_id(), dxid=oid)
raise RuntimeError("sanity")
def build_applet():
"""Build the file localizer applet on dnanexus."""
dx_applet_id = dxpy.api.applet_new({
"name":
APPLET_NAME,
"title":
"WES URL Localizer",
"dxapi":
dxpy.API_VERSION,
"project":
dxpy.PROJECT_CONTEXT_ID,
"properties": {
"version": APPLET_VERSION
},
"inputSpec": [{
"name": "url",
"class": "string"
}, {
"name": "project",
"class": "string"
}, {
"name": "folder",
"class": "string"
}],
"outputSpec": [{
"name": "localized_file",
"class": "file"
}],
"runSpec": {
"code":
APPLET_CODE,
"interpreter":
"python2.7",
"systemRequirements": {
"*": {
"instanceType": "mem1_ssd1_x2"
}
},
"execDepends": [{
"name": "google-cloud-storage",
"package_manager": "pip"
}]
},
"access": {
"network": ["*"],
"project": "UPLOAD"
},
"release":
"14.04"
})
return dxpy.DXApplet(dx_applet_id["id"])
def test_build_and_use_asset(self):
asset_spec = {
"name": "asset library name with space",
"title": "A human readable name",
"description": "A detailed description about the asset",
"version": "0.0.1",
"distribution": "Ubuntu",
"release": "14.04"
}
asset_dir = self.write_asset_directory("build_and_use_asset",
json.dumps(asset_spec),
"resources")
run("mkdir -p " + os.path.join(asset_dir, "resources/usr/local/bin"))
with open(
os.path.join(asset_dir, "resources/usr/local/bin", 'test.sh'),
'wb') as manifest:
manifest.write("echo 'hi'".encode())
run("chmod +x " +
os.path.join(asset_dir, "resources/usr/local/bin", 'test.sh'))
asset_bundle_id = json.loads(run('dx build_asset --json ' +
asset_dir))['id']
code_str = """#!/bin/bash
main(){
test.sh
}
"""
app_spec = {
"name": "asset_depends",
"dxapi": "1.0.0",
"runSpec": {
"code": code_str,
"interpreter": "bash",
"distribution": "Ubuntu",
"release": "14.04",
"assetDepends": [{
"id": asset_bundle_id
}]
},
"inputSpec": [],
"outputSpec": [],
"version": "1.0.0"
}
app_dir = self.write_app_directory("asset_depends",
json.dumps(app_spec))
asset_applet_id = json.loads(
run("dx build --json {app_dir}".format(app_dir=app_dir)))["id"]
asset_applet = dxpy.DXApplet(asset_applet_id)
applet_job = asset_applet.run({})
applet_job.wait_on_done()
self.assertEqual(applet_job.describe()['state'], 'done')
def main(project, folder, name):
# Build the applet
app_id, app_desc = upload_applet('.', None)
app_handler = dxpy.DXApplet(app_id)
# Build a workflow that uses that applet
workflow = dxpy.new_dxworkflow(name=name, project=project, folder=folder)
workflow.add_stage(app_id)
# Delete the applet, to break the workflow
app_handler.remove()
return workflow.get_id()
def test_ont_input(self):
"""
Tests the app with a basic input.
"""
job_input = self.base_input
job_input["reads"] = [{"$dnanexus_link": "file-FPXx7v00x99J3b743k9z93x8"}]
job_input["datatype"] = "ONT"
job = dxpy.DXApplet(self.applet_id).run(job_input, folder=self.tempdirdx, name=self.testname, project=DX_PROJECT_ID)
try:
job.wait_on_done()
print json.dumps(job.describe()["output"])
except Exception:
DX_PROJ_OBJ.move_folder(self.tempdirdx, ARTIFACTS_FOLDER)
raise
def test_dx_run_app_locally_and_compare_results(self):
appdir = create_app_dir()
print("Setting current project to", self.project)
dxpy.WORKSPACE_ID = self.project
dxpy.PROJECT_CONTEXT_ID = self.project
applet_id = dx_build_app.build_and_upload_locally(appdir,
mode='applet',
overwrite=True,
dx_toolkit_autodep=False,
return_object_dump=True)['id']
remote_job = dxpy.DXApplet(applet_id).run({"in1": 8})
print("Waiting for", remote_job, "to complete")
remote_job.wait_on_done()
result = remote_job.describe()
self.assertEqual(result["output"]["out1"], 140)
def test_build_asset_inside_job(self):
asset_spec = {
"name": "asset library name with space",
"title": "A human readable name",
"description": " A detailed description about the asset",
"version": "0.0.1",
"distribution": "Ubuntu",
"release": "14.04"
}
asset_dir = self.write_asset_directory("test_build_asset_inside_job",
json.dumps(asset_spec))
asset_conf_file_id = run("dx upload " +
os.path.join(asset_dir, "dxasset.json") +
" --brief --wait").strip()
code_str = """#!/bin/bash
main(){
dx download "${asset_conf}" -o dxasset.json
dx build_asset
}
"""
app_spec = {
"name": "run_build_asset",
"dxapi": "1.0.0",
"runSpec": {
"code": code_str,
"interpreter": "bash",
"distribution": "Ubuntu",
"release": "14.04"
},
"inputSpec": [{
"name": "asset_conf",
"class": "file"
}],
"outputSpec": [],
"version": "1.0.0"
}
app_dir = self.write_app_directory("run_build_asset",
json.dumps(app_spec))
asset_applet_id = json.loads(
run("dx build --json {app_dir}".format(app_dir=app_dir)))["id"]
asset_applet = dxpy.DXApplet(asset_applet_id)
applet_job = asset_applet.run(
{"asset_conf": {
"$dnanexus_link": asset_conf_file_id
}})
applet_job.wait_on_done()
self.assertEqual(applet_job.describe()['state'], 'done')
def test_pacb_input(self):
"""
Tests the app with a basic input.
"""
job_input = self.base_input
job_input["reads"] = [{"$dnanexus_link": "file-FPY0BY80pbJvg49Z3k4zZp71"}]
job_input["reads_indices"] = [{"$dnanexus_link": "file-FPY096j0VvqbBk3Y5367XbJp"}]
job_input["datatype"] = "PacBio"
job = dxpy.DXApplet(self.applet_id).run(job_input, folder=self.tempdirdx, name=self.testname, project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(),)
try:
job.wait_on_done()
print json.dumps(job.describe()["output"])
except Exception:
DX_PROJ_OBJ.move_folder(self.tempdirdx, ARTIFACTS_FOLDER)
raise
def test_pacb_subjobs(self):
"""
Make sure PacBio format subjobs work as expected by running the app
with multiple file inputs
"""
job_input = self.base_input
# these are 10GB files
job_input["reads"] = [{
"$dnanexus_link": "file-FPY0BY80pbJvg49Z3k4zZp71"
}, {
"$dnanexus_link": "file-FPY0BX802J4jybZVJf0gy272"
}]
job_input["reads_indices"] = [{
"$dnanexus_link":
"file-FPY096j0VvqbBk3Y5367XbJp"
}, {
"$dnanexus_link":
"file-FPY096j0G03Gg49Z3k4zZg1Q"
}]
job_input["datatype"] = "PacBio"
job_input["chunk_size"] = 9
job = dxpy.DXApplet(self.applet_id).run(job_input,
folder=self.tempdirdx,
name=self.testname,
project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(), )
try:
job.wait_on_done()
output = job.describe()["output"]
# check that 2 chunks were run and 2 files are output
mappings_files = output["bam_files"]
self.assertTrue(len(mappings_files) > 1)
# check that two subjobs named "map_reads_pbmm2" were run
subjobs = dxpy.find_jobs(parent_job=job.id)
subjob_names = [
dxpy.DXJob(subjob['id']).name for subjob in subjobs
]
subjob_names = [s.split(':')[-1] for s in subjob_names]
mapping_jobs = [
s for s in subjob_names
if s.split(':')[-1] == 'map_reads_pbmm2'
]
self.assertTrue(len(mapping_jobs) == 2)
except Exception:
DX_PROJ_OBJ.move_folder(self.tempdirdx, ARTIFACTS_FOLDER)
raise
def run_map_sample(project_id,
output_folder,
fastq_files,
genome_fasta_file,
genome_index_file,
mapper,
applet_id,
applet_project,
fastq_files2=None,
mark_duplicates=False,
sample_name=None,
properties=None):
mapper_applet = dxpy.DXApplet(dxid=applet_id, project=applet_project)
print 'Running map_sample'
mapper_input = {
"project_id": project_id,
"output_folder": output_folder,
"fastq_files": fastq_files,
"genome_fasta_file": dxpy.dxlink(genome_fasta_file),
"genome_index_file": dxpy.dxlink(genome_index_file),
"mapper": mapper,
"sample_name": sample_name,
"mark_duplicates": mark_duplicates,
"properties": properties
}
if fastq_files2:
mapper_input['fastq_files2'] = fastq_files2
map_sample_job = mapper_applet.run(mapper_input)
mapper_output = {
"bam": {
"job": map_sample_job.get_id(),
"field": "bam"
},
"bai": {
"job": map_sample_job.get_id(),
"field": "bai"
},
"tools_used": {
"job": map_sample_job.get_id(),
"field": "tools_used"
}
}
return mapper_output
def test_post_and_valid(self):
"""
Tests validation for quantification bams (4 types)
"""
jobs = []
for bam in self.qbams_input:
# start 4 jobs.
jobs.append(dxpy.DXApplet(self.applet_id).run(bam))
print "Waiting for %s to complete" % (jobs[-1].get_id(),)
for job in jobs:
job.wait_on_done()
print "Job %s done" % (job.get_id(),)
# should wait until all 4 are done
for job in jobs:
outp = job.describe()["output"]
print json.dumps(outp)
def test_applet_completion(self):
dxapplet = dxpy.DXApplet()
run_spec = {"code": "placeholder", "interpreter": "bash",
"distribution": "Ubuntu", "release": "14.04"}
dxapplet.new(runSpec=run_spec,
dxapi="1.0.0",
name="my applet")
self.assert_completion("dx ls my", "my applet ")
self.assert_completion("dx ls", "ls ")
self.assert_completion("dx run my", "my applet ")
self.assert_completion("dx ls ", "my applet ")
# not available to run when hidden
dxapplet.new(runSpec=run_spec,
dxapi="1.0.0",
name="hidden",
hidden=True)
self.assert_completion("dx ls hid", "hidden ")
self.assert_no_completions("dx run hid")
def test_ont_subjobs(self):
job_input = self.base_input
# these are 40MB files
job_input["reads"] = [
{"$dnanexus_link": "file-FPXx7v00x99J3b743k9z93x8"},
{"$dnanexus_link": "file-FPXxJXQ0zYzGg49Z3k4zKFP7"}
]
job_input["datatype"] = "ONT"
job_input["chunk_size"] = 1
job = dxpy.DXApplet(self.applet_id).run(job_input, folder=self.tempdirdx,
name=self.testname, project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(),)
try:
job.wait_on_done()
output = job.describe()["output"]
# check that 2 chunks were run and 2 files are output
mappings_files = output["mapped_reads"]
self.assertTrue(len(mappings_files) > 1)
except dxpy.exceptions.AppError:
DX_PROJ_OBJ.move_folder(self.tempdirdx, ARTIFACTS_FOLDER)
raise
def test_base_input(self):
"""
Tests the app with a basic input.
Verify files are in S3
"""
try:
job = dxpy.DXApplet(self.applet_id).run(
self.base_input,
folder="/aws_transfer/aws_platform_to_s3_file_transfer")
print "Waiting for %s to complete" % (job.get_id())
job.wait_on_done()
except dxpy.exceptions.DXJobFailureError as e:
print "Job failed. Review message for error type"
self.fail(msg=e.message)
else:
print json.dumps(job.describe()["output"])
# Verify files are on S3
prefix = "s3://{0}/{1}".format(self.base_input["target_s3"],
self.awsfolder)
full_filenames = _get_full_filenames(self.base_input["f_ids"],
prefix)
aws_ls_cmds = [
"aws s3 ls \"{0}\"".format(filename)
for filename in full_filenames
]
verify_fail = []
for name, cmd in zip(full_filenames, aws_ls_cmds):
try:
print 'Verifying: {0}'.format(name)
_run_cmd(cmd)
except CalledProcessError:
verify_fail.append(name)
if verify_fail:
self.fail(
"Following uploads are not present on S3: {0}".format(
str(verify_fail)))
def build_applets():
applets = [
"fpfilter-tool", "muse-tool", "pindel-tool", "radia-tool",
"samtools-pileup-tool", "somaticsniper-tool", "tcga-vcf-filter-tool",
"varscan-tool", "mutect-tool", "tcga-vcf-reheader"
]
# Build applets for assembly workflow in [args.folder]/applets/ folder
project.new_folder(applets_folder, parents=True)
for applet in applets:
print "building {}...".format(applet),
sys.stdout.flush()
build_out = subprocess.check_output([
"dx", "build", "--destination",
args.project + ":" + applets_folder + "/", applet
])
# take just the last line, ignore other output that makefile generates
applet_dxid = json.loads(build_out.rstrip().split('\n')[-1])["id"]
print applet_dxid
applet = dxpy.DXApplet(applet_dxid, project=project.get_id())
applet.set_properties({"git_revision": git_revision})
def once():
try:
desc = test_files[tname]
if tname in test_defaults:
inputs = {}
else:
inputs = read_json_file_maybe_empty(desc.dx_input)
project.new_folder(test_folder, parents=True)
if desc.kind == "workflow":
exec_obj = dxpy.DXWorkflow(project=project.get_id(), dxid=oid)
elif desc.kind == "applet":
exec_obj = dxpy.DXApplet(project=project.get_id(), dxid=oid)
else:
raise RuntimeError("Unknown kind {}".format(desc.kind))
return exec_obj.run(
inputs,
project=project.get_id(),
folder=test_folder,
name="{} {}".format(desc.name, git_revision),
delay_workspace_destruction=delay_workspace_destruction,
instance_type="mem1_ssd1_x4")
except Exception, e:
print("exception message={}".format(e))
return None
def test_datatype_compatbility(self):
"""
Make sure the app fails when the input reads are in BAM format but
the datatype is specified as ONT
"""
job_input = self.base_input
# this is a subreads.bam file
job_input["reads"] = [{
"$dnanexus_link": "file-FPY0BY80pbJvg49Z3k4zZp71"
}, {
"$dnanexus_link": "file-FPY0BX802J4jybZVJf0gy272"
}]
job_input["reads_indices"] = [{
"$dnanexus_link":
"file-FPY096j0VvqbBk3Y5367XbJp"
}, {
"$dnanexus_link":
"file-FPY096j0G03Gg49Z3k4zZg1Q"
}]
# this is an incompatible datatype
job_input["datatype"] = "ONT"
job = dxpy.DXApplet(self.applet_id).run(job_input,
folder=self.tempdirdx,
name=self.testname,
project=DX_PROJECT_ID)
print "Waiting for %s to complete" % (job.get_id(), )
# check that the job failed
try:
job.wait_on_done()
print json.dumps(job.describe()["output"])
# if job continued, fail this test
raise Exception("Job should have failed with DXAppError")
except dxpy.exceptions.DXJobFailureError:
# confirm that error is an AppError and not something else
failureReason = job.describe()["failureReason"]
self.assertTrue(failureReason == "AppError")