def create_charon_entries_from_project(project, best_practice_analysis="whole_genome_reseq",
sequencing_facility="NGI-S",
force_overwrite=False, delete_existing=False,
retry_on_fail=True):
"""Given a project object, creates the relevant entries in Charon.
This code is remarkably shoddy as I created it in a hurry and then later
it became a part of the pipeline. Use at your own risk! Ha ha.
:param NGIProject project: The NGIProject object
:param str best_practice_analysis: The workflow to assign for this project (default "variant_calling")
:param str sequencing_facility: The facility that did the sequencing
:param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
:param bool delete_existing: Don't just update existing entries, delete them and create new ones (default false)
"""
charon_session = CharonSession()
update_failed=False
try:
status = "OPEN"
LOG.info('Creating project "{}" with status "{}", best practice analysis "{}", '
'and sequencing_facility {}'.format(project, status,
best_practice_analysis,
sequencing_facility))
charon_session.project_create(projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" created in Charon.'.format(project))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}"'.format(project))
charon_session.project_update(projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" updated in Charon.'.format(project))
else:
LOG.info('Project "{}" already exists; moving to samples...'.format(project))
else:
raise
for sample in project:
if delete_existing:
LOG.warn('Deleting existing sample "{}"'.format(sample))
try:
charon_session.sample_delete(projectid=project.project_id,
sampleid=sample.name)
except CharonError as e:
update_failed=True
LOG.error('Could not delete sample "{}": {}'.format(sample, e))
try:
analysis_status = "TO_ANALYZE"
LOG.info('Creating sample "{}" with analysis_status "{}"'.format(sample, analysis_status))
charon_session.sample_create(projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status)
LOG.info('Project/sample "{}/{}" created in Charon.'.format(project, sample))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}"'.format(project, sample))
charon_session.sample_update(projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status)
LOG.info('Project/sample "{}/{}" updated in Charon.'.format(project, sample))
else:
LOG.info('Project "{}" / sample "{}" already exists; moving '
'to libpreps'.format(project, sample))
else:
update_failed=True
LOG.error(e)
continue
for libprep in sample:
if delete_existing:
LOG.warn('Deleting existing libprep "{}"'.format(libprep))
try:
charon_session.libprep_delete(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name)
except CharonError as e:
LOG.warn('Could not delete libprep "{}": {}'.format(libprep, e))
try:
qc = "PASSED"
LOG.info('Creating libprep "{}" with qc status "{}"'.format(libprep, qc))
charon_session.libprep_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(('Project/sample/libprep "{}/{}/{}" created in '
'Charon').format(project, sample, libprep))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}"'.format(project, sample,
libprep))
charon_session.libprep_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(('Project/sample/libprep "{}/{}/{}" updated in '
'Charon').format(project, sample, libprep))
else:
LOG.debug(e)
LOG.info('Project "{}" / sample "{}" / libprep "{}" already '
'exists; moving to libpreps'.format(project, sample, libprep))
else:
update_failed=True
LOG.error(e)
continue
for seqrun in libprep:
if delete_existing:
LOG.warn('Deleting existing seqrun "{}"'.format(seqrun))
try:
charon_session.seqrun_delete(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name)
except CharonError as e:
update_failed=True
LOG.error('Could not delete seqrun "{}": {}'.format(seqrun, e))
try:
alignment_status="NOT_RUNNING"
LOG.info('Creating seqrun "{}" with alignment_status "{}"'.format(seqrun, alignment_status))
charon_session.seqrun_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'created in Charon').format(project, sample,
libprep, seqrun))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}" / '
'seqrun "{}"'.format(project, sample,
libprep, seqrun))
charon_session.seqrun_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'updated in Charon').format(project, sample,
libprep, seqrun))
else:
LOG.info('Project "{}" / sample "{}" / libprep "{}" / '
'seqrun "{}" already exists; next...'.format(project, sample,
libprep, seqrun))
else:
update_failed=True
LOG.error(e)
continue
if update_failed :
if retry_on_fail:
create_charon_entries_from_project(project, best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility,
force_overwrite=force_overwrite, delete_existing=delete_existing,
retry_on_fail=False)
else:
raise CharonError("A network error blocks Charon updating.")
def create_charon_entries_from_project(project, workflow="NGI", force_overwrite=False):
"""Given a project object, creates the relevant entries
in Charon.
:param NGIProject project: The NGIProject object
:param str workflow: The workflow to assign for this project (default NGI)
:param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
"""
charon_session = CharonSession()
try:
status="SEQUENCED"
LOG.info('Creating project "{}" with status "{}" and workflow "{}"'.format(project, status, workflow))
charon_session.project_create(projectid=project.project_id,
name=project.name,
status=status,
pipeline=workflow)
except CharonError:
if force_overwrite:
LOG.warn('Overwriting data for project "{}"'.format(project))
charon_session.project_update(projectid=project.project_id,
name=project.name,
status=status,
pipeline=workflow)
else:
LOG.info('Project "{}" already exists; moving to samples...'.format(project))
for sample in project:
try:
LOG.info('Creating sample "{}"'.format(sample))
charon_session.sample_create(projectid=project.project_id,
sampleid=sample.name,
status="NEW")
except CharonError:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}"'.format(project, sample))
charon_session.sample_update(projectid=project.project_id,
sampleid=sample.name,
status="NEW")
else:
LOG.info('Project "{}" / sample "{}" already exists; moving '
'to libpreps'.format(project, sample))
for libprep in sample:
try:
LOG.info('Creating libprep "{}"'.format(libprep))
charon_session.libprep_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
status="NEW")
except CharonError:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}"'.format(project, sample,
libprep))
charon_session.libprep_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
status="NEW")
else:
LOG.info('Project "{}" / sample "{}" / libprep "{}" already '
'exists; moving to libpreps'.format(project, sample, libprep))
for seqrun in libprep:
try:
LOG.info('Creating seqrun "{}"'.format(seqrun))
charon_session.seqrun_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
total_reads=0,
mean_autosomal_coverage=0,
sequencing_status="DONE",
alignment_status="NEW")
except CharonError as e:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}" / '
'seqrun "{}"'.format(project, sample,
libprep, seqrun))
charon_session.seqrun_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
status="NEW")
else:
LOG.info('Project "{}" / sample "{}" / libprep "{}" / '
'seqrun "{}" already exists; next...'.format(project, sample,
libprep, seqrun))
def create_charon_entries_from_project(project, best_practice_analysis="whole_genome_reseq",
sequencing_facility="NGI-S",
force_overwrite=False, delete_existing=False):
"""Given a project object, creates the relevant entries
in Charon.
:param NGIProject project: The NGIProject object
:param str best_practice_analysis: The workflow to assign for this project (default "variant_calling")
:param str sequencing_facility: The facility that did the sequencing
:param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
:param bool delete_existing: Don't just update existing entries, delete them and create new ones (default false)
"""
charon_session = CharonSession()
try:
status="OPEN"
LOG.info('Creating project "{}" with status "{}", best practice analysis "{}", '
'and sequencing_facility {}'.format(project, status, best_practice_analysis,
sequencing_facility))
charon_session.project_create(projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" created in Charon.'.format(project))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}"'.format(project))
charon_session.project_update(projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" updated in Charon.'.format(project))
else:
LOG.info('Project "{}" already exists; moving to samples...'.format(project))
else:
raise
for sample in project:
if delete_existing:
LOG.warn('Deleting existing sample "{}"'.format(sample))
try:
charon_session.sample_delete(projectid=project.project_id,
sampleid=sample.name)
except CharonError as e:
LOG.error('Could not delete sample "{}": {}'.format(sample, e))
try:
analysis_status = "TO_ANALYZE"
LOG.info('Creating sample "{}" with analysis_status "{}"'.format(sample, analysis_status))
charon_session.sample_create(projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status)
LOG.info('Project/sample "{}/{}" created in Charon.'.format(project, sample))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}"'.format(project, sample))
charon_session.sample_update(projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status)
LOG.info('Project/sample "{}/{}" updated in Charon.'.format(project, sample))
else:
LOG.info('Project "{}" / sample "{}" already exists; moving '
'to libpreps'.format(project, sample))
else:
LOG.error(e)
continue
for libprep in sample:
if delete_existing:
LOG.warn('Deleting existing libprep "{}"'.format(libprep))
try:
charon_session.libprep_delete(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name)
except CharonError as e:
LOG.warn('Could not delete libprep "{}": {}'.format(libprep, e))
try:
qc= "PASSED"
LOG.info('Creating libprep "{}" with qc status "{}"'.format(libprep, qc))
charon_session.libprep_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(('Project/sample/libprep "{}/{}/{}" created in '
'Charon').format(project, sample, libprep))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}"'.format(project, sample,
libprep))
charon_session.libprep_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(('Project/sample/libprep "{}/{}/{}" updated in '
'Charon').format(project, sample, libprep))
else:
LOG.info(e)
LOG.info('Project "{}" / sample "{}" / libprep "{}" already '
'exists; moving to libpreps'.format(project, sample, libprep))
else:
LOG.error(e)
continue
for seqrun in libprep:
if delete_existing:
LOG.warn('Deleting existing seqrun "{}"'.format(seqrun))
try:
charon_session.seqrun_delete(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name)
except CharonError as e:
LOG.error('Could not delete seqrun "{}": {}'.format(seqrun, e))
try:
alignment_status="NOT_RUNNING"
LOG.info('Creating seqrun "{}" with alignment_status "{}"'.format(seqrun, alignment_status))
charon_session.seqrun_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'created in Charon').format(project, sample,
libprep, seqrun))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warn('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}" / '
'seqrun "{}"'.format(project, sample,
libprep, seqrun))
charon_session.seqrun_update(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'updated in Charon').format(project, sample,
libprep, seqrun))
else:
LOG.info('Project "{}" / sample "{}" / libprep "{}" / '
'seqrun "{}" already exists; next...'.format(project, sample,
libprep, seqrun))
else:
LOG.error(e)
continue
def create_charon_entries_from_project(
project,
best_practice_analysis="whole_genome_reseq",
sequencing_facility="NGI-S",
force_overwrite=False,
retry_on_fail=True):
"""Given a project object, creates the relevant entries in Charon.
This code is remarkably shoddy as I created it in a hurry and then later
it became a part of the pipeline. Use at your own risk! Ha ha.
:param NGIProject project: The NGIProject object
:param str best_practice_analysis: The workflow to assign for this project (default "variant_calling")
:param str sequencing_facility: The facility that did the sequencing
:param bool force_overwrite: If this is set to true, overwrite existing entries in Charon (default false)
"""
charon_session = CharonSession()
update_failed = False
try:
status = "OPEN"
LOG.info(
'Creating project "{}" with status "{}", best practice analysis "{}", '
'and sequencing_facility {}'.format(project, status,
best_practice_analysis,
sequencing_facility))
charon_session.project_create(
projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" created in Charon.'.format(project))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warning(
'Overwriting data for project "{}"'.format(project))
charon_session.project_update(
projectid=project.project_id,
name=project.name,
status=status,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility)
LOG.info('Project "{}" updated in Charon.'.format(project))
else:
LOG.info(
'Project "{}" already exists; moving to samples...'.format(
project))
else:
raise
for sample in project:
try:
analysis_status = "TO_ANALYZE"
sample_data_status_value = "STALE"
LOG.info('Creating sample "{}" with analysis_status "{}"'.format(
sample, analysis_status))
charon_session.sample_create(projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status)
LOG.info('Project/sample "{}/{}" created in Charon.'.format(
project, sample))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warning('Overwriting data for project "{}" / '
'sample "{}"'.format(project, sample))
charon_session.sample_update(
projectid=project.project_id,
sampleid=sample.name,
analysis_status=analysis_status,
status=sample_data_status_value)
LOG.info(
'Project/sample "{}/{}" updated in Charon.'.format(
project, sample))
else:
#update the status of the sample to STALE
charon_session.sample_update(
projectid=project.project_id,
sampleid=sample.name,
status=sample_data_status_value)
LOG.info(
'Project "{}" / sample "{}" already exists; moving '
'to libpreps'.format(project, sample))
else:
update_failed = True
LOG.error(e)
continue
for libprep in sample:
try:
qc = "PASSED"
LOG.info('Creating libprep "{}" with qc status "{}"'.format(
libprep, qc))
charon_session.libprep_create(projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(('Project/sample/libprep "{}/{}/{}" created in '
'Charon').format(project, sample, libprep))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warning('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}"'.format(
project, sample, libprep))
charon_session.libprep_update(
projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
qc=qc)
LOG.info(
('Project/sample/libprep "{}/{}/{}" updated in '
'Charon').format(project, sample, libprep))
else:
LOG.debug(e)
LOG.info(
'Project "{}" / sample "{}" / libprep "{}" already '
'exists; moving to libpreps'.format(
project, sample, libprep))
else:
update_failed = True
LOG.error(e)
continue
for seqrun in libprep:
try:
alignment_status = "NOT_RUNNING"
LOG.info('Creating seqrun "{}" with alignment_status "{}"'.
format(seqrun, alignment_status))
charon_session.seqrun_create(
projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(
('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'created in Charon').format(project, sample, libprep,
seqrun))
except CharonError as e:
if e.status_code == 400:
if force_overwrite:
LOG.warning('Overwriting data for project "{}" / '
'sample "{}" / libprep "{}" / '
'seqrun "{}"'.format(
project, sample, libprep, seqrun))
charon_session.seqrun_update(
projectid=project.project_id,
sampleid=sample.name,
libprepid=libprep.name,
seqrunid=seqrun.name,
alignment_status=alignment_status,
total_reads=0,
mean_autosomal_coverage=0)
LOG.info(
('Project/sample/libprep/seqrun "{}/{}/{}/{}" '
'updated in Charon').format(
project, sample, libprep, seqrun))
else:
LOG.info(
'Project "{}" / sample "{}" / libprep "{}" / '
'seqrun "{}" already exists; next...'.format(
project, sample, libprep, seqrun))
else:
update_failed = True
LOG.error(e)
continue
if update_failed:
if retry_on_fail:
create_charon_entries_from_project(
project,
best_practice_analysis=best_practice_analysis,
sequencing_facility=sequencing_facility,
force_overwrite=force_overwrite,
retry_on_fail=False)
else:
raise CharonError("A network error blocks Charon updating.")
