def analyze_seqrun(project, sample, libprep, seqrun, config=None, config_file_path=None):
"""Analyze data at the sequencing run (individual fastq) level.
:param NGIProject project: the project to analyze
:param NGISample sample: the sample to analyzed
:param NGILibraryPrep libprep: The library prep to analyzed
:seqrun NGISeqrun seqrun: The sequencing run to analyzed
:param dict config: The parsed configuration file (optional)
:param str config_file_path: The path to the configuration file (optional)
"""
modules_to_load = ["java/sun_jdk1.7.0_25", "R/2.15.0"]
load_modules(modules_to_load)
for workflow_subtask in get_subtasks_for_level(level="seqrun"):
if not is_seqrun_analysis_running_local(workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name,
libprep_id=libprep.name,
seqrun_id=seqrun.name):
try:
## Temporarily logging to a file until we get ELK set up
log_file_path = create_log_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.name,
sample_id=sample.name,
libprep_id=libprep.name,
seqrun_id=seqrun.name)
rotate_log(log_file_path)
# Store the exit code of detached processes
exit_code_path = create_exit_code_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.name,
sample_id=sample.name,
libprep_id=libprep.name,
seqrun_id=seqrun.name)
build_setup_xml(project, config, sample, libprep.name, seqrun.name)
command_line = build_piper_cl(project, workflow_subtask, exit_code_path, config)
p_handle = launch_piper_job(command_line, project, log_file_path)
try:
record_process_seqrun(project=project, sample=sample, libprep=libprep,
seqrun=seqrun, workflow_subtask=workflow_subtask,
analysis_module_name="piper_ngi",
analysis_dir=project.analysis_dir,
pid=p_handle.pid)
except CharonError as e:
## This is a problem. If the job isn't recorded, we won't
## ever know that it has been run and its results will be ignored.
## I think? Or no I guess if it's relaunched then the results will be there.
## But we will have multiple processes running.
## FIXME fix this
LOG.error("<Could not record ...>")
continue
except (NotImplementedError, RuntimeError) as e:
error_msg = ('Processing project "{}" / sample "{}" / libprep "{}" / '
'seqrun "{}" failed: {}'.format(project, sample, libprep, seqrun,
e.__repr__()))
LOG.error(error_msg)
def analyze_sample(project, sample, config=None, config_file_path=None):
"""Analyze data at the sample level.
:param NGIProject project: the project to analyze
:param NGISample sample: the sample to analyzed
:param dict config: The parsed configuration file (optional)
:param str config_file_path: The path to the configuration file (optional)
"""
modules_to_load = ["java/sun_jdk1.7.0_25", "R/2.15.0"]
load_modules(modules_to_load)
charon_session = CharonSession()
# Determine if we can begin sample-level processing yet.
# Conditions are that the coverage is above 28.9X
# If these conditions become more complex we can create a function for this
sample_total_autosomal_coverage = charon_session.sample_get(project.project_id,
sample.name).get('total_autosomal_coverage')
if sample_total_autosomal_coverage > 28.4:
LOG.info('Sample "{}" in project "{}" is ready for processing.'.format(sample, project))
for workflow_subtask in get_subtasks_for_level(level="sample"):
if not is_sample_analysis_running_local(workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name):
try:
## Temporarily logging to a file until we get ELK set up
log_file_path = create_log_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.name,
sample_id=sample.name)
rotate_log(log_file_path)
# Store the exit code of detached processes
exit_code_path = create_exit_code_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.name,
sample_id=sample.name)
build_setup_xml(project, config, sample)
command_line = build_piper_cl(project, workflow_subtask, exit_code_path, config)
p_handle = launch_piper_job(command_line, project, log_file_path)
try:
record_process_sample(project=project, sample=sample,
workflow_subtask=workflow_subtask,
analysis_module_name="piper_ngi",
analysis_dir=project.analysis_dir,
pid=p_handle.pid)
except RuntimeError as e:
LOG.error(e)
continue
except (NotImplementedError, RuntimeError) as e:
error_msg = ('Processing project "{}" / sample "{}" failed: '
'{}'.format(project, sample, e.__repr__()))
LOG.error(error_msg)
else:
LOG.info('Sample "{}" in project "{}" is not yet ready for '
'processing.'.format(sample, project))
def test_create_log_file_path(self):
got_path = utils.create_log_file_path(self.workflow_subtask,
self.project_base_path,
self.project_name,
self.project_id,
sample_id=self.sample_id,
libprep_id=self.libprep_id,
seqrun_id=self.seqrun_id)
expected_path = '{}/ANALYSIS/P123/piper_ngi/logs/P123-P123_1001-A-seqrun-subtask.log'.format(
self.tmp_dir)
self.assertEqual(got_path, expected_path)
def analyze(project, sample, exec_mode="sbatch", restart_finished_jobs=False,
restart_running_jobs=False, config=None, config_file_path=None):
"""Analyze data at the sample level.
:param NGIProject project: the project to analyze
:param NGISample sample: the sample to analyzed
:param str exec_mode: "sbatch" or "local"
:param dict config: The parsed configuration file (optional)
:param str config_file_path: The path to the configuration file (optional)
:raises ValueError: If exec_mode is an unsupported value
"""
try:
check_for_preexisting_sample_runs(project, sample, restart_running_jobs, restart_finished_jobs)
except RuntimeError as e:
# may want to process anyway.
raise RuntimeError('Aborting processing of project/sample "{}/{}": '
'{}'.format(project, sample, e))
if exec_mode.lower() not in ("sbatch", "local"):
raise ValueError(('"exec_mode" param must be one of "sbatch" or "local" ')
('value was "{}"'.format(exec_mode)))
modules_to_load = ["java/sun_jdk1.7.0_25", "R/2.15.0"]
load_modules(modules_to_load)
LOG.info('Sample "{}" in project "{}" is ready for processing.'.format(sample, project))
for workflow_subtask in workflows.get_subtasks_for_level(level="sample"):
if not is_sample_analysis_running_local(workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name):
try:
log_file_path = create_log_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
setup_xml_cl, setup_xml_path = build_setup_xml(project=project,
sample=sample,
local_scratch_mode=(exec_mode == "sbatch"),
config=config)
piper_cl = build_piper_cl(project=project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=config,
exec_mode=exec_mode)
remove_previous_sample_analyses(project)
if exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample([setup_xml_cl, piper_cl],
workflow_subtask,
project, sample,
restart_finished_jobs=restart_finished_jobs)
for x in xrange(10): # Time delay to let sbatch get its act together (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(project, sample, slurm_job_id))
else:
## FIXME Now this is broken again
raise NotImplementedError("Sorry dude it's a no-go")
slurm_job_id = None
launch_piper_job(setup_xml_cl, project)
process_handle = launch_piper_job(piper_cl, project)
process_id = process_handle.pid
try:
record_process_sample(project=project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error('Could not record process for project/sample '
'{}/{}, workflow {}'.format(project, sample,
workflow_subtask))
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = ('Processing project "{}" / sample "{}" failed: '
'{}'.format(project, sample, e.__repr__()))
LOG.error(error_msg)
def analyze(analysis_object,
level='sample',
config=None,
config_file_path=None):
"""Analyze data at the sample level.
:param NGIAnalysis analysis_object: holds all the parameters for the analysis
:raises ValueError: If exec_mode is an unsupported value
"""
charon_session = CharonSession()
for sample in analysis_object.project:
try:
charon_reported_status = charon_session.sample_get(
analysis_object.project.project_id,
sample).get('analysis_status')
# Check Charon to ensure this hasn't already been processed
do_analyze = handle_sample_status(analysis_object, sample,
charon_reported_status)
if not do_analyze:
continue
except CharonError as e:
LOG.error(e)
continue
if level == "sample":
status_field = "alignment_status"
elif level == "genotype":
status_field = "genotype_status"
else:
LOG.warn('Unknown workflow level: "{}"'.format(level))
status_field = "alignment_status" # Or should we abort?
try:
check_for_preexisting_sample_runs(
analysis_object.project, sample,
analysis_object.restart_running_jobs,
analysis_object.restart_finished_jobs, status_field)
except RuntimeError as e:
raise RuntimeError(
'Aborting processing of project/sample "{}/{}": '
'{}'.format(analysis_object.project, sample, e))
if analysis_object.exec_mode.lower() not in ("sbatch", "local"):
raise ValueError(
'"exec_mode" param must be one of "sbatch" or "local" '
'value was "{}"'.format(analysis_object.exec_mode))
if analysis_object.exec_mode == "local":
modules_to_load = analysis_object.config.get("piper", {}).get(
"load_modules", [])
load_modules(modules_to_load)
for workflow_subtask in workflows.get_subtasks_for_level(level=level):
if level == "genotype":
genotype_status = None # Some records in Charon lack this field, I'm guessing
try:
charon_session = CharonSession()
genotype_status = charon_session.sample_get(
projectid=analysis_object.project.project_id,
sampleid=sample.name).get("genotype_status")
except CharonError as e:
LOG.error(
'Couldn\'t determine genotyping status for project/'
'sample "{}/{}"; skipping analysis.'.format(
analysis_object.project, sample))
continue
if find_previous_genotype_analyses(
analysis_object.project,
sample) or genotype_status == "DONE":
if not analysis_object.restart_finished_jobs:
LOG.info(
'Project/sample "{}/{}" has completed genotype '
'analysis previously; skipping (use flag to force '
'analysis)'.format(analysis_object.project,
sample))
continue
if analysis_object.restart_running_jobs:
# Kill currently-running jobs if they exist
kill_running_sample_analysis(
workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
# This checks the local jobs database
if not is_sample_analysis_running_local(
workflow_subtask=workflow_subtask,
project_id=analysis_object.project.project_id,
sample_id=sample.name):
LOG.info('Launching "{}" analysis for sample "{}" in project '
'"{}"'.format(workflow_subtask, sample,
analysis_object.project))
try:
log_file_path = create_log_file_path(
workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(
workflow_subtask=workflow_subtask,
project_base_path=analysis_object.project.base_path,
project_name=analysis_object.project.dirname,
project_id=analysis_object.project.project_id,
sample_id=sample.name)
if level == "sample":
if not analysis_object.keep_existing_data:
remove_previous_sample_analyses(
analysis_object.project, sample)
default_files_to_copy = None
elif level == "genotype":
if not analysis_object.keep_existing_data:
remove_previous_genotype_analyses(
analysis_object.project)
default_files_to_copy = None
# Update the project to keep only valid fastq files for setup.xml creation
if level == "genotype":
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
restart_finished_jobs=True,
status_field="genotype_status")
else:
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(analysis_object.project,
sample,
analysis_object.restart_finished_jobs,
status_field="alignment_status")
setup_xml_cl, setup_xml_path = build_setup_xml(
project=updated_project,
sample=sample,
workflow=workflow_subtask,
local_scratch_mode=(
analysis_object.exec_mode == "sbatch"),
config=analysis_object.config)
piper_cl = build_piper_cl(
project=analysis_object.project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=analysis_object.config,
exec_mode=analysis_object.exec_mode,
generate_bqsr_bam=analysis_object.generate_bqsr_bam)
if analysis_object.exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample(
[setup_xml_cl, piper_cl],
workflow_subtask,
analysis_object.project,
sample,
restart_finished_jobs=analysis_object.
restart_finished_jobs,
files_to_copy=default_files_to_copy)
for x in xrange(10):
# Time delay to let sbatch get its act together
# (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(analysis_object.project,
sample, slurm_job_id))
else: # "local"
raise NotImplementedError(
'Local execution not currently implemented. '
'I\'m sure Denis can help you with this.')
#slurm_job_id = None
#launch_piper_job(setup_xml_cl, project)
#process_handle = launch_piper_job(piper_cl, project)
#process_id = process_handle.pid
try:
record_process_sample(
project=analysis_object.project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error(e)
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = (
'Processing project "{}" / sample "{}" / workflow "{}" '
'failed: {}'.format(analysis_object.project, sample,
workflow_subtask, e))
LOG.error(error_msg)
def analyze(project, sample,
exec_mode="sbatch",
restart_finished_jobs=False,
restart_running_jobs=False,
keep_existing_data=False,
level="sample",
genotype_file=None,
config=None, config_file_path=None,
generate_bqsr_bam=False):
"""Analyze data at the sample level.
:param NGIProject project: the project to analyze
:param NGISample sample: the sample to analyzed
:param str exec_mode: "sbatch" or "local" (local not implemented)
:param bool restart_finished_jobs: Restart jobs that are already done (have a .done file)
:param bool restart_running_jobs: Kill and restart currently-running jobs
:param str level: The level on which to perform the analysis ("sample" or "genotype")
:param str genotype_file: The path to the genotype file (only relevant for genotype analysis)
:param dict config: The parsed configuration file (optional)
:param str config_file_path: The path to the configuration file (optional)
:raises ValueError: If exec_mode is an unsupported value
"""
if level == "sample":
status_field = "alignment_status"
elif level == "genotype":
status_field = "genotype_status"
else:
LOG.warn('Unknown workflow level: "{}"'.format(level))
status_field = "alignment_status" # Or should we abort?
try:
check_for_preexisting_sample_runs(project, sample, restart_running_jobs,
restart_finished_jobs, status_field)
except RuntimeError as e:
raise RuntimeError('Aborting processing of project/sample "{}/{}": '
'{}'.format(project, sample, e))
if exec_mode.lower() not in ("sbatch", "local"):
raise ValueError('"exec_mode" param must be one of "sbatch" or "local" '
'value was "{}"'.format(exec_mode))
if exec_mode == "local":
modules_to_load = config.get("piper", {}).get("load_modules", [])
load_modules(modules_to_load)
for workflow_subtask in workflows.get_subtasks_for_level(level=level):
if level == "genotype":
genotype_status = None # Some records in Charon lack this field, I'm guessing
try:
charon_session = CharonSession()
genotype_status = charon_session.sample_get(projectid=project.project_id,
sampleid=sample.name).get("genotype_status")
except CharonError as e:
LOG.error('Couldn\'t determine genotyping status for project/'
'sample "{}/{}"; skipping analysis.'.format(project, sample))
continue
if find_previous_genotype_analyses(project, sample) or genotype_status == "DONE":
if not restart_finished_jobs:
LOG.info('Project/sample "{}/{}" has completed genotype '
'analysis previously; skipping (use flag to force '
'analysis)'.format(project, sample))
continue
if restart_running_jobs:
# Kill currently-running jobs if they exist
kill_running_sample_analysis(workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name)
# This checks the local jobs database
if not is_sample_analysis_running_local(workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name):
LOG.info('Launching "{}" analysis for sample "{}" in project '
'"{}"'.format(workflow_subtask, sample, project))
try:
log_file_path = create_log_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
if level == "sample":
if not keep_existing_data:
remove_previous_sample_analyses(project, sample)
default_files_to_copy=None
elif level == "genotype":
if not keep_existing_data:
remove_previous_genotype_analyses(project)
default_files_to_copy=None
# Update the project to keep only valid fastq files for setup.xml creation
if level == "genotype":
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(project,
sample,
restart_finished_jobs=True,
status_field="genotype_status")
else:
updated_project, default_files_to_copy = \
collect_files_for_sample_analysis(project,
sample,
restart_finished_jobs,
status_field="alignment_status")
setup_xml_cl, setup_xml_path = build_setup_xml(project=updated_project,
sample=sample,
workflow=workflow_subtask,
local_scratch_mode=(exec_mode == "sbatch"),
config=config)
piper_cl = build_piper_cl(project=project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=config,
exec_mode=exec_mode,
generate_bqsr_bam=generate_bqsr_bam)
if exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample([setup_xml_cl, piper_cl],
workflow_subtask,
project, sample,
restart_finished_jobs=restart_finished_jobs,
files_to_copy=default_files_to_copy)
for x in xrange(10):
# Time delay to let sbatch get its act together
# (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(project, sample, slurm_job_id))
else: # "local"
raise NotImplementedError('Local execution not currently implemented. '
'I\'m sure Denis can help you with this.')
#slurm_job_id = None
#launch_piper_job(setup_xml_cl, project)
#process_handle = launch_piper_job(piper_cl, project)
#process_id = process_handle.pid
try:
record_process_sample(project=project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error(e)
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = ('Processing project "{}" / sample "{}" / workflow "{}" '
'failed: {}'.format(project, sample,
workflow_subtask,
e))
LOG.error(error_msg)
def analyze(project,
sample,
exec_mode="sbatch",
restart_finished_jobs=False,
restart_running_jobs=False,
config=None,
config_file_path=None):
"""Analyze data at the sample level.
:param NGIProject project: the project to analyze
:param NGISample sample: the sample to analyzed
:param str exec_mode: "sbatch" or "local"
:param dict config: The parsed configuration file (optional)
:param str config_file_path: The path to the configuration file (optional)
:raises ValueError: If exec_mode is an unsupported value
"""
try:
check_for_preexisting_sample_runs(project, sample,
restart_running_jobs,
restart_finished_jobs)
except RuntimeError as e:
# may want to process anyway.
raise RuntimeError('Aborting processing of project/sample "{}/{}": '
'{}'.format(project, sample, e))
if exec_mode.lower() not in ("sbatch", "local"):
raise ValueError(
('"exec_mode" param must be one of "sbatch" or "local" ')(
'value was "{}"'.format(exec_mode)))
modules_to_load = ["java/sun_jdk1.7.0_25", "R/2.15.0"]
load_modules(modules_to_load)
LOG.info('Sample "{}" in project "{}" is ready for processing.'.format(
sample, project))
for workflow_subtask in workflows.get_subtasks_for_level(level="sample"):
if not is_sample_analysis_running_local(
workflow_subtask=workflow_subtask,
project_id=project.project_id,
sample_id=sample.name):
try:
log_file_path = create_log_file_path(
workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
rotate_file(log_file_path)
exit_code_path = create_exit_code_file_path(
workflow_subtask=workflow_subtask,
project_base_path=project.base_path,
project_name=project.dirname,
project_id=project.project_id,
sample_id=sample.name)
setup_xml_cl, setup_xml_path = build_setup_xml(
project=project,
sample=sample,
local_scratch_mode=(exec_mode == "sbatch"),
config=config)
piper_cl = build_piper_cl(project=project,
workflow_name=workflow_subtask,
setup_xml_path=setup_xml_path,
exit_code_path=exit_code_path,
config=config,
exec_mode=exec_mode)
remove_previous_sample_analyses(project)
if exec_mode == "sbatch":
process_id = None
slurm_job_id = sbatch_piper_sample(
[setup_xml_cl, piper_cl],
workflow_subtask,
project,
sample,
restart_finished_jobs=restart_finished_jobs)
for x in xrange(
10
): # Time delay to let sbatch get its act together (takes a few seconds to be visible with sacct)
try:
get_slurm_job_status(slurm_job_id)
break
except ValueError:
time.sleep(2)
else:
LOG.error('sbatch file for sample {}/{} did not '
'queue properly! Job ID {} cannot be '
'found.'.format(project, sample,
slurm_job_id))
else:
## FIXME Now this is broken again
raise NotImplementedError("Sorry dude it's a no-go")
slurm_job_id = None
launch_piper_job(setup_xml_cl, project)
process_handle = launch_piper_job(piper_cl, project)
process_id = process_handle.pid
try:
record_process_sample(project=project,
sample=sample,
analysis_module_name="piper_ngi",
slurm_job_id=slurm_job_id,
process_id=process_id,
workflow_subtask=workflow_subtask)
except RuntimeError as e:
LOG.error('Could not record process for project/sample '
'{}/{}, workflow {}'.format(
project, sample, workflow_subtask))
## Question: should we just kill the run in this case or let it go?
continue
except (NotImplementedError, RuntimeError, ValueError) as e:
error_msg = ('Processing project "{}" / sample "{}" failed: '
'{}'.format(project, sample, e.__repr__()))
LOG.error(error_msg)