def test_1_hsmetrics(self):
"""Run hs metrics"""
self.app = self.make_app(argv=['production', 'hs-metrics', 'J.Doe_00_01', '-f', '120829_SN0001_0001_AA001AAAXX', '--region_file', 'regionfile', '--force', '-n'], extensions=['scilifelab.pm.ext.ext_hs_metrics'])
handler.register(ProductionController)
self._run_app()
hsmetrics_str = "(DRY_RUN): java -Xmx3g -jar {}/CalculateHsMetrics.jar INPUT={}/120829_SN0001_0001_AA001AAAXX/1_120829_AA001AAAXX_nophix_10-sort-dup.bam TARGET_INTERVALS={}/regionfile BAIT_INTERVALS={}/regionfile OUTPUT={}/120829_SN0001_0001_AA001AAAXX/1_120829_AA001AAAXX_nophix_10-sort-dup.hs_metrics VALIDATION_STRINGENCY=SILENT".format(os.getenv("PICARD_HOME"), self.app.config.get("production", "root"), os.path.abspath(os.curdir), os.path.abspath(os.curdir), self.app.config.get("production", "root"))
self.eq(hsmetrics_str, str(self.app._output_data['stderr'].getvalue().split("\n")[0]))
def test_clean(self):
before = glob.glob(os.path.join(intermediate, "120829_AA001AAAXX",
"*"))
self.app = self.make_app(argv=[
'project', 'clean', 'j_doe_00_02', '--pileup', '--intermediate',
'--force'
])
handler.register(ProjectController)
self._run_app()
after = glob.glob(os.path.join(intermediate, "120829_AA001AAAXX", "*"))
diff = [
os.path.basename(x)
for x in list(set(before).difference(set(after)))
]
self.eq(
set(diff),
set([
'1_120829_AA001AAAXX_nophix_12-sort-dup-target.pileup.gz',
'1_120829_AA001AAAXX_nophix_12-sort-dup-target.pileup',
'1_120829_AA001AAAXX_nophix_12-sort-dup-target.crisp_pileup.gz',
'1_120829_AA001AAAXX_nophix_12-sort-dup-target.crisp_pileup',
'1_120829_AA001AAAXX_nophix_10-sort-dup-target.crisp_pileup.gz',
'1_120829_AA001AAAXX_nophix_10-sort-dup-target.crisp_pileup',
'1_120829_AA001AAAXX_nophix_10-sort-dup-target.pileup',
'1_120829_AA001AAAXX_nophix_10-sort-dup-target.pileup.gz'
]))
def load():
"""Called by the framework when the extension is 'loaded'."""
hook.register('post_setup', add_drmaa_option)
hook.register('post_setup', add_sbatch_option)
hook.register('post_setup', add_shared_distributed_options)
hook.register('pre_run', set_distributed_handler)
handler.register(DistributedCommandHandler)
def test_runinfo_yaml(self):
"""Test runinfo yaml list"""
self.app = self.make_app(argv=['archive', 'runinfo', '-f', '120829_SN0001_0001_AA001AAAXX', '--as_yaml'])
handler.register(ArchiveController)
self._run_app()
info = Flowcell(runinfo)
self.eq(self.app._output_data['stdout'].getvalue(), info.as_yaml())
def test_clean_dry(self):
self.app = self.make_app(argv=[
'project', 'clean', 'j_doe_00_02', '--pileup', '-n',
'--intermediate', '--force'
])
handler.register(ProjectController)
self._run_app()
def test_project_run_samplefile(self):
"""Test running project in project folder using a sample file as input."""
self.app = self.make_app(argv = ['project', 'run', 'j_doe_00_04', '--restart', '--amplicon', '--sample', SAMPLEFILE, '--debug', '--force', '--quiet'], extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProjectController)
handler.register(BcbioRunController)
self._run_app()
os.chdir(filedir)
def test_clean_fastqbam(self):
before = glob.glob(
os.path.join(data, "P1_106F_index6/120829_AA001AAAXX/alignments",
"*"))
self.app = self.make_app(argv=[
'project', 'clean', 'j_doe_00_02', '--data', '--fastqbam',
'--force'
])
handler.register(ProjectController)
self._run_app()
after = glob.glob(
os.path.join(data, "P1_106F_index6/120829_AA001AAAXX/alignments",
"*"))
diff = len(before) - len(after)
self.eq(diff, 2)
diff = [
os.path.basename(x)
for x in list(set(before).difference(set(after)))
]
self.eq(
set(diff),
set([
'1_120829_AA001AAAXX_nophix_10_1_fastq-fastq.bam',
'1_120829_AA001AAAXX_nophix_10_2_fastq-fastq.bam'
]))
def test_decompress(self):
"""Test decompression of project data"""
self.app = self.make_app(argv=[
'project', 'decompress', 'j_doe_00_01', '--fastq', '--force'
])
handler.register(ProjectController)
self._run_app()
def test_hsmetrics_empty(self):
"""Run hs metrics when no files present"""
self.app = self.make_app(argv=['production', 'hs-metrics', 'J.Doe_00_02', '-f', '120829_SN0001_0001_AA001AAAXX','--targets', os.path.join(filedir, 'regionfile'), '--force', '-n'], extensions=[])
handler.register(ProductionController)
self._run_app()
## Shouldn't produce any output
self.eq([''], self.app._output_data['stdout'].getvalue().split("\n"))
def test_register_duplicate_handler(self):
from cement.ext import ext_dummy
handler.register(ext_dummy.DummyOutputHandler)
try:
handler.register(DuplicateHandler)
except exc.FrameworkError:
raise
def test_hsmetrics_drmaa(self):
"""Run hs metrics over drmaa"""
self.app = self.make_app(argv=['production', 'hs-metrics', 'J.Doe_00_01', '-f', '120829_SN0001_0001_AA001AAAXX', '--targets', os.path.join(filedir, 'regionfile'), '--force', '-A', 'jobaccount', '--jobname', 'jobname', '--partition', 'node', '--time', '10:00:00', '--drmaa', '-n'], extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProductionController)
self._run_app()
hsmetrics_str = "(DRY_RUN): java -Xmx3g -jar {}/CalculateHsMetrics.jar INPUT={}/120829_SN0001_0001_AA001AAAXX/1_120829_AA001AAAXX_nophix_8-sort-dup.bam TARGET_INTERVALS={}/regionfile BAIT_INTERVALS={}/regionfile OUTPUT={}/120829_SN0001_0001_AA001AAAXX/1_120829_AA001AAAXX_nophix_8-sort-dup.hs_metrics VALIDATION_STRINGENCY=SILENT".format(os.getenv("PICARD_HOME"), self.app.config.get("production", "root"), filedir, filedir, self.app.config.get("production", "root"))
self.eq(hsmetrics_str, str(sorted(self.app._output_data['stderr'].getvalue().rstrip().split("\n"))[-1]))
def load():
"""Called by the framework when the extension is 'loaded'."""
hook.register('post_setup', add_drmaa_option)
hook.register('post_setup', add_sbatch_option)
hook.register('post_setup', add_shared_distributed_options)
hook.register('pre_run', set_distributed_handler)
handler.register(DistributedCommandHandler)
def register_controllers(self):
self.controllers = [
AuthController,
TargetSetController,
TargetGetController,
CreateTeamController,
UpdateTeamController,
ShowTeamController,
DeleteTeamController,
ShowUserController,
TeamAddUserController,
CreateProjectController,
UpdateProjectController,
DeleteProjectController,
TeamRemoveUserController,
ChangePasswordController,
ScheduleLoadTestController,
ListLoadTestController,
InstanceLoadTestController,
TrackLoadTestController,
ShowResultController,
SetDefaultController,
GetDefaultController,
]
for controller in self.controllers:
handler.register(controller)
def test_3_from_pre_to_casava_transfer(self):
"""Test from pre-casava to casava transfer to project directory"""
self.app = self.make_app(argv = ['production', 'transfer', 'J.Doe_00_01', '-f', '120829_SN0001_0001_AA001AAAXX', '--from_pre_casava'])
handler.register(ProductionController)
self._run_app()
res = shell.exec_cmd(["ls", "-1", os.path.join(delivery_dir, "P1_101F_index1", "120829_AA001AAAXX")])
self.eq(['1_120829_AA001AAAXX_barcode', '1_120829_AA001AAAXX_nophix_1-sort-dup.align_metrics', '1_120829_AA001AAAXX_nophix_1-sort-dup.bam', '1_120829_AA001AAAXX_nophix_1-sort-dup.dup_metrics', '1_120829_AA001AAAXX_nophix_1-sort-dup.hs_metrics', '1_120829_AA001AAAXX_nophix_1-sort-dup.insert_metrics', '1_120829_AA001AAAXX_nophix_1-sort.bam', 'P1_101F_index1-bcbb-config.yaml', 'alignments'], res[0].split())
def test_4_from_pre_to_pre_casava_transfer(self):
"""Test pre_casava transfer to project directory"""
self.app = self.make_app(argv = ['production', 'transfer', 'J.Doe_00_01', '-f', '120829_SN0001_0001_AA001AAAXX', '--from_pre_casava', '--to_pre_casava', '--quiet'])
handler.register(ProductionController)
self._run_app()
## Assert data output
res = shell.exec_cmd(["ls", "-1", os.path.join(delivery_dir, "120829_AA001AAAXX", "1_120829_AA001AAAXX_barcode")])
res_files = ['1_120829_AA001AAAXX_nophix_10_1_fastq.txt', '1_120829_AA001AAAXX_nophix_10_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_12_1_fastq.txt','1_120829_AA001AAAXX_nophix_12_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_1_1_fastq.txt','1_120829_AA001AAAXX_nophix_1_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_2_1_fastq.txt','1_120829_AA001AAAXX_nophix_2_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_3_1_fastq.txt','1_120829_AA001AAAXX_nophix_3_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_4_1_fastq.txt','1_120829_AA001AAAXX_nophix_4_2_fastq.txt',
'1_120829_AA001AAAXX_nophix_8_1_fastq.txt','1_120829_AA001AAAXX_nophix_8_2_fastq.txt']
self.eq(set(res_files), set(res[0].split()))
## Assert intermediate delivery output
res = shell.exec_cmd(["ls", "-1", os.path.join(intermediate_delivery_dir, "120829_AA001AAAXX")])
self.eq(['1_120829_AA001AAAXX_nophix_1-sort-dup.align_metrics','1_120829_AA001AAAXX_nophix_1-sort-dup.bam'], res[0].split()[0:2])
self.eq(['1_120829_AA001AAAXX_nophix_8-sort-dup.insert_metrics','1_120829_AA001AAAXX_nophix_8-sort.bam', 'alignments'], res[0].split()[-3:])
## Assert pruned yaml file contents
with open(os.path.join(delivery_dir, "120829_AA001AAAXX", "project_run_info.yaml")) as fh:
runinfo_yaml = yaml.load(fh)
self.eq(runinfo_yaml['details'][0]['multiplex'][0]['name'], 'P1_101F_index1')
self.eq(runinfo_yaml['details'][0]['multiplex'][0]['description'], 'J.Doe_00_01_P1_101F_index1')
self.eq(set(runinfo_yaml['details'][0]['multiplex'][0]['files']), set([os.path.join(delivery_dir,"120829_AA001AAAXX", "1_120829_AA001AAAXX_barcode", os.path.basename(x)) for x in ['1_120829_AA001AAAXX_nophix_1_1_fastq.txt','1_120829_AA001AAAXX_nophix_1_2_fastq.txt']]))
def setup(self):
# Add hooks
hook.register('post_argument_parsing', hooks.pre_run_hook)
# Add controllers
controllers = [
InitController,
CreateController,
EventsController,
LogsController,
PrintEnvController,
DeployController,
StatusController,
TerminateController,
ConfigController,
SwapController,
OpenController,
ConsoleController,
ScaleController,
SSHController,
UseController,
SetEnvController,
ListController,
PlatformController,
CloneController,
UpgradeController,
AbortController,
LabsController,
LocalController,
HealthController,
CodeSourceController,
]
# register all controllers
for c in controllers:
c._add_to_handler(handler)
# Add special controllers
handler.register(CompleterController)
super(EB, self).setup()
#Register global arguments
self.add_arg('-v',
'--verbose',
action='store_true',
help=flag_text['base.verbose'])
self.add_arg('--profile', help=flag_text['base.profile'])
self.add_arg('-r', '--region', help=flag_text['base.region'])
self.add_arg('--endpoint-url', help=SUPPRESS)
self.add_arg('--no-verify-ssl',
action='store_true',
help=flag_text['base.noverify'])
self.add_arg(
'--debugboto', # show debug info for botocore
action='store_true',
help=SUPPRESS)
ebglobals.app = self
def test_1_clean(self):
before = glob.glob(os.path.join(intermediate, "120829_AA001AAAXX", "*"))
self.app = self.make_app(argv = ['project', 'clean', 'j_doe_00_02', '--pileup', '--intermediate', '--force'])
handler.register(ProjectController)
self._run_app()
after = glob.glob(os.path.join(intermediate, "120829_AA001AAAXX", "*"))
diff = [os.path.basename(x) for x in list(set(before).difference(set(after)))]
self.eq(set(diff), set(['1_120829_AA001AAAXX_nophix_12-sort-dup-target.pileup.gz', '1_120829_AA001AAAXX_nophix_12-sort-dup-target.pileup', '1_120829_AA001AAAXX_nophix_12-sort-dup-target.crisp_pileup.gz', '1_120829_AA001AAAXX_nophix_12-sort-dup-target.crisp_pileup', '1_120829_AA001AAAXX_nophix_10-sort-dup-target.crisp_pileup.gz', '1_120829_AA001AAAXX_nophix_10-sort-dup-target.crisp_pileup', '1_120829_AA001AAAXX_nophix_10-sort-dup-target.pileup', '1_120829_AA001AAAXX_nophix_10-sort-dup-target.pileup.gz']))
def test_production(self):
self.app = self.make_app(argv=[
'production', 'run', 'J.Doe_00_04', '--debug', '--force',
'--amplicon', '--restart'
])
handler.register(ProductionController)
self._run_app()
os.chdir(filedir)
def test_3_project_status_ps_map(self):
self.app = self.make_app(argv=[
'report', 'project_status', '--user', self.user, '--password',
self.pw, '--url', self.url, self.examples["project"], '--debug'
],
extensions=['scilifelab.pm.ext.ext_couchdb'])
handler.register(DeliveryReportController)
self._run_app()
def test_1_ls(self):
self.app = self.make_app(argv=['production', 'ls'])
handler.register(ProductionController)
self._run_app()
self.eq(
self.app._output_data['stdout'].getvalue(),
'120829_SN0001_0001_AA001AAAXX\n120829_SN0001_0002_BB001BBBXX\n120924_SN0002_0003_CC003CCCXX\nJ.Doe_00_04\nJ.Doe_00_05\nJ.Doe_00_06'
)
def test_change_platform_args(self):
"""Test that passing --time actually changes platform
arguments. These arguments should have precedence over
whatever is written in the config file."""
self.app = self.make_app(argv = ['production', 'run', 'J.Doe_00_04', '--debug', '--force', '--amplicon', '--restart', '--sample', SAMPLES[1], '--drmaa', '--time', '00:01:00', '-n'], extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProductionController)
self._run_app()
os.chdir(filedir)
def test_rm_analysis_1_dry(self):
"""Test dry removal of one intermediate analysis"""
self.app = self.make_app(argv=[
'project', 'rm', 'j_doe_00_04', 'analysis_1', '-n', '--force'
])
handler.register(ProjectController)
handler.register(ProjectRmController)
self._run_app()
def test_project_status(self):
self.app = self.make_app(
argv=['report', 'project_status', self.examples["project"]],
extensions=['scilifelab.pm.ext.ext_couchdb'])
handler.register(DeliveryReportController)
self._run_app()
data = ast.literal_eval(self.app._output_data['debug'].getvalue())
self.assertEqual(data['param']['project_name'], 'J.Doe_00_01')
self.assertEqual(data['param']['ordered_amount'], 0.1)
def load(app):
# register the plugin class.. this only happens if the plugin is enabled
handler.register(EELogController)
handler.register(EELogShowController)
handler.register(EELogResetController)
handler.register(EELogGzipController)
handler.register(EELogMailController)
# register a hook (function) to run after arguments are parsed.
hook.register('post_argument_parsing', ee_log_hook)
def test_register_invalid_handler_type(self):
self.app.setup()
class BadInterface:
class IMeta:
label = 'bad_interface'
class BadHandler(TestHandler):
class Meta:
interface = BadInterface
handler.register(BadHandler)
def load(app):
# register the plugin class.. this only happens if the plugin is enabled
handler.register(SSSSiteController)
handler.register(SSSSiteCreateController)
handler.register(SSSSiteEditController)
handler.register(SSSSiteDeleteController)
handler.register(SSSSiteListController)
# register a hook (function) to run after arguments are parsed.
hook.register('post_argument_parsing', sss_site_hook)
def main():
app = MyApp()
handler.register(MySecondController)
try:
app.setup()
app.run()
finally:
app.close()
def test_5_quiet(self):
"""Test pre_casava delivery to project directory with quiet flag"""
self.app = self.make_app(argv=[
'production', 'transfer', 'J.Doe_00_01', '-f',
'120829_SN0001_0001_AA001AAAXX', '--from_pre_casava',
'--to_pre_casava', '--quiet'
])
handler.register(ProductionController)
self._run_app()
def main():
app = ArtnetApp()
handler.register(ArtnetScriptController)
try:
app.setup()
app.run()
finally:
app.close()
def load(app):
# register the plugin class.. this only happens if the plugin is enabled
handler.register(SSSSiteController)
handler.register(SSSSiteCreateController)
handler.register(SSSSiteEditController)
handler.register(SSSSiteDeleteController)
handler.register(SSSSiteListController)
# register a hook (function) to run after arguments are parsed.
hook.register('post_argument_parsing', sss_site_hook)
def setUp(self):
super(BaseTest, self).setUp()
self.reset_backend()
self.app = DroopeScan(argv=[],
plugin_config_dir="./plugins.d",
plugin_dir="./plugins")
handler.register(AbstractArgumentController)
self.app.testing = True
self.app.setup()
def load(app):
# register the plugin class.. this only happens if the plugin is enabled
handler.register(EELogController)
handler.register(EELogShowController)
handler.register(EELogResetController)
handler.register(EELogGzipController)
handler.register(EELogMailController)
# register a hook (function) to run after arguments are parsed.
hook.register('post_argument_parsing', ee_log_hook)
def test_rm_analysis_1(self):
"""Test removal of non-existing intermediate analysis"""
self.app = self.make_app(argv = ['project', 'rm', 'j_doe_00_04', 'analysisoe', '--force'])
handler.register(ProjectController)
handler.register(ProjectRmController)
try:
self._run_app()
except:
raise Exception
def main():
app = MyApp()
handler.register(MySecondController)
try:
app.setup()
app.run()
finally:
app.close()
def setUp(self):
super(BaseTest, self).setUp()
self.reset_backend()
self.app = DroopeScan(argv=[],
plugin_config_dir="./plugins.d",
plugin_dir="./plugins")
handler.register(AbstractArgumentController)
self.app.testing = True
self.app.setup()
def test_remove_finished(self):
self.app = self.make_app(argv = ['production', 'touch-finished', 'J.Doe_00_04', '--debug', '--force', '--sample', SAMPLES[1]], extensions=[])
handler.register(ProductionController)
self._run_app()
self.assertTrue(os.path.exists(FINISHED['J.Doe_00_04'][SAMPLES[1]]))
## Remove file, dry
self.app = self.make_app(argv = ['production', 'remove-finished', 'J.Doe_00_04', '--debug', '--force', '-n'], extensions=[])
handler.register(ProductionController)
self._run_app()
def load():
# register hook
hook.register('pre_setup', init_configuration_file)
# register controllers
# handler.define(IRESTApi)
handler.register(P4CMInfoController)
handler.register(P4CMConfigController)
def main(): app = ArtnetApp() handler.register(ArtnetScriptController) try: app.setup() app.run() finally: app.close()
def test_rm_analysis_1_intermediate(self):
"""Test removal of one intermediate analysis"""
self.app = self.make_app(argv = ['project', 'rm', 'j_doe_00_04', 'analysis_1', '--force'])
handler.register(ProjectController)
handler.register(ProjectRmController)
self._run_app()
try:
os.listdir(os.path.join(filedir, "data", "projects", "j_doe_00_04", "intermediate", "analysis_1"))
except:
raise Exception
def load():
"""Called by the framework when the extension is 'loaded'."""
if not os.getenv("DRMAA_LIBRARY_PATH"):
LOG.debug("No environment variable $DRMAA_LIBRARY_PATH: loading {} failed".format(__name__))
return
hook.register('post_setup', add_drmaa_option)
hook.register('post_setup', add_shared_distributed_options)
hook.register('pre_run', set_distributed_handler)
hook.register('post_run', run_batch_command)
handler.register(DistributedCommandHandler)
def test_from_casava_to_casava_custom_transfer(self):
"""Test from casava to casava transfer to custom project directory"""
self.app = self.make_app(argv = ['production', 'transfer', 'J.Doe_00_04', '--transfer_dir', 'j_doe_00_04_custom'])
handler.register(ProductionController)
self._run_app()
delivery_dir = os.path.abspath(os.path.join(filedir, "data", "projects", "j_doe_00_04_custom", "data"))
with open(os.path.join(delivery_dir, "P001_101_index3", "120924_CC003CCCXX", "P001_101_index3-bcbb-config.yaml")) as fh:
runinfo_yaml = yaml.load(fh)
res = shell.exec_cmd(["ls", "-1", os.path.join(delivery_dir, "P001_101_index3", "120924_CC003CCCXX")])
self.eq(len(set(res[0].split())), 22)
def test_batch_submission(self):
"""Test that adding --batch groups commands into a batch submission"""
pp = os.path.join(j_doe_00_04, SAMPLES[1], FLOWCELL, "{}-post_process.yaml".format(SAMPLES[1]))
with open(pp) as fh:
config = yaml.load(fh)
platform_args = config["distributed"]["platform_args"].split()
account = platform_args[platform_args.index("-A")+1]
self.app = self.make_app(argv = ['production', 'compress', 'J.Doe_00_04', '--debug', '--force', '--jobname', 'batchsubmission', '--drmaa', '--batch', '--partition', 'devel', '--time', '01:00:00', '-A', account], extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProductionController)
self._run_app()
def test_2_clean_fastqbam(self):
before = glob.glob(os.path.join(data, "P1_106F_index6/120829_AA001AAAXX/alignments", "*"))
self.app = self.make_app(argv = ['project', 'clean', 'j_doe_00_02', '--data', '--fastqbam', '--force'])
handler.register(ProjectController)
self._run_app()
after = glob.glob(os.path.join(data, "P1_106F_index6/120829_AA001AAAXX/alignments", "*"))
diff = len(before) - len(after)
self.eq(diff, 2)
diff = [os.path.basename(x) for x in list(set(before).difference(set(after)))]
self.eq(set(diff), set(['1_120829_AA001AAAXX_nophix_10_1_fastq-fastq.bam', '1_120829_AA001AAAXX_nophix_10_2_fastq-fastq.bam']))
def main():
app = DigitalOceanApp()
handler.register(ApiController)
hook.register('post_argument_parsing', token_check_hook, weight=0)
hook.register('post_argument_parsing', setup_manager_hook, weight=1)
try:
app.setup()
app.run()
finally:
app.close()
def load():
# Subcontrollers for each functional component
handler.register(cli.cloudlet.NephoCloudletController)
handler.register(cli.blueprint.NephoBlueprintController)
handler.register(cli.stack.NephoStackController)
handler.register(cli.parameter.NephoParameterController)
handler.register(cli.scope.NephoScopeController)
hook.register('post_argument_parsing', cli.hooks.set_scope)
hook.register('post_setup', cli.hooks.process_config)
def test_project_run_only_failed(self):
"""Test running project in project folder on only failed samples. """
psummary = os.path.join(j_doe_00_04, "P001_101_index3", "121015_BB002BBBXX", "project_summary.csv")
if os.path.exists(psummary):
os.unlink(psummary)
self.app = self.make_app(argv = ['project', 'run', 'j_doe_00_04', '-n', '--only_failed', '--debug', '--force', '--quiet'], extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProjectController)
handler.register(BcbioRunController)
self._run_app()
os.chdir(filedir)
def test_production_setup(self):
self.app = self.make_app(
argv=[
'production', 'run', 'J.Doe_00_04', '--debug', '--force',
'--only_setup', '--restart', '--drmaa'
],
extensions=['scilifelab.pm.ext.ext_distributed'])
handler.register(ProductionController)
self._run_app()
os.chdir(filedir)
def test_rm_analysis_1(self):
"""Test removal of non-existing intermediate analysis"""
self.app = self.make_app(
argv=['project', 'rm', 'j_doe_00_04', 'analysisoe', '--force'])
handler.register(ProjectController)
handler.register(ProjectRmController)
try:
self._run_app()
except:
raise Exception
def main():
'Initialise and execute the cement app.'
histogram_app = foundation.CementApp('histogram')
handler.register(HistogramBaseController)
try:
histogram_app.setup()
histogram_app.run()
finally:
histogram_app.close()
def test_2_project_status_custom(self):
"""Test project status note generation with command line customizations"""
self.app = self.make_app(argv=[
'report', 'project_status', '--user', self.user, '--password',
self.pw, '--url', self.url, self.examples["project"], '--debug',
'--customer_reference', 'MyCustomerReference', '--uppnex_id',
'MyUppnexID', '--use_bc_map', '--ordered_million_reads', '1'
],
extensions=['scilifelab.pm.ext.ext_couchdb'])
handler.register(DeliveryReportController)
self._run_app()
def test_nested_controller(self):
app = self.make_app(argv=['nested-controller'])
handler.register(TestController)
handler.register(Nested)
app.setup()
app.run()
check = 'nested-controller' in app.controller._visible_commands
self.ok(check)
self.eq(app.controller._dispatch_command['func_name'], '_dispatch')
