def add_if_missing(parameterset, name, string_value=None,
numerical_value=None, datetime_value=None):
try:
ExperimentParameter.objects.get(
name__name=name, parameterset=parameterset)
except ExperimentParameter.DoesNotExist:
param_name = ParameterName.objects.get(
name=name, schema=parameterset.schema)
param = ExperimentParameter(name=param_name,
parameterset=parameterset)
param.string_value = string_value
param.numerical_value = numerical_value
param.datetime_value = datetime_value
param.save()
def add_if_missing(parameterset,
name,
string_value=None,
numerical_value=None,
datetime_value=None):
try:
ExperimentParameter.objects.get(name__name=name,
parameterset=parameterset)
except ExperimentParameter.DoesNotExist:
param_name = ParameterName.objects.get(name=name,
schema=parameterset.schema)
param = ExperimentParameter(name=param_name,
parameterset=parameterset)
param.string_value = string_value
param.numerical_value = numerical_value
param.datetime_value = datetime_value
param.save()
def populate_pdb_pub_records():
PUB_SCHEMA = getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT)
PUB_SCHEMA_DRAFT = getattr(settings, 'PUBLICATION_DRAFT_SCHEMA',
default_settings.PUBLICATION_DRAFT_SCHEMA)
PDB_SCHEMA = getattr(settings, 'PDB_PUBLICATION_SCHEMA_ROOT',
default_settings.PDB_PUBLICATION_SCHEMA_ROOT)
publications = Experiment.objects \
.filter(experimentparameterset__schema__namespace=PDB_SCHEMA) \
.filter(experimentparameterset__schema__namespace=PUB_SCHEMA) \
.exclude(experimentparameterset__schema__namespace=PUB_SCHEMA_DRAFT) \
.distinct()
last_update_parameter_name = ParameterName.objects.get(
name='pdb-last-sync',
schema__namespace=PUB_SCHEMA)
def add_if_missing(parameterset, name, string_value=None,
numerical_value=None, datetime_value=None):
try:
ExperimentParameter.objects.get(
name__name=name, parameterset=parameterset)
except ExperimentParameter.DoesNotExist:
param_name = ParameterName.objects.get(
name=name, schema=parameterset.schema)
param = ExperimentParameter(name=param_name,
parameterset=parameterset)
param.string_value = string_value
param.numerical_value = numerical_value
param.datetime_value = datetime_value
param.save()
for pub in publications:
try:
# try to get the last update time for the PDB data
pdb_last_update_parameter = ExperimentParameter.objects.get(
parameterset__schema__namespace=PUB_SCHEMA,
name=last_update_parameter_name,
parameterset__experiment=pub
)
last_update = pdb_last_update_parameter.datetime_value
needs_update = last_update + \
getattr(settings,
'PDB_REFRESH_INTERVAL',
default_settings.PDB_REFRESH_INTERVAL) \
< timezone.now()
except ExperimentParameter.DoesNotExist:
# if the PDB last update time parameter doesn't exist,
# we definitely need to update the data and create a last
# update entry
needs_update = True
pdb_last_update_parameter = None
# If an update needs to happen...
if needs_update:
# 1. get the PDB info
pdb_parameter_set = ExperimentParameterSet.objects.get(
schema__namespace=getattr(
settings,
'PDB_PUBLICATION_SCHEMA_ROOT',
default_settings.PDB_PUBLICATION_SCHEMA_ROOT),
experiment=pub)
pdb = ExperimentParameter.objects.get(
name__name='pdb-id',
parameterset=pdb_parameter_set)
pdb_id = pdb.string_value
# 1a. cosmetic change of case for PDB ID, if entered incorrectly
if pdb_id != pdb_id.upper():
pdb.string_value = pdb_id.upper()
pdb.save()
try:
# 2. fetch the info from pdb.org
pdb = PDBCifHelper(pdb_id)
# 3. insert all standard pdb parameters
add_if_missing(pdb_parameter_set, 'title',
string_value=pdb.get_pdb_title())
add_if_missing(pdb_parameter_set, 'url',
string_value=pdb.get_pdb_url())
try:
add_if_missing(pdb_parameter_set, 'resolution',
numerical_value=pdb.get_resolution())
except ValueError:
logger.error(
'PDB field "resolution" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
try:
add_if_missing(pdb_parameter_set, 'r-value',
numerical_value=pdb.get_obs_r_value())
except ValueError:
logger.error(
'PDB field "r-value" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
try:
add_if_missing(pdb_parameter_set, 'r-free',
numerical_value=pdb.get_free_r_value())
except ValueError:
logger.error(
'PDB field "r-free" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
add_if_missing(pdb_parameter_set, 'space-group',
string_value=pdb.get_spacegroup())
add_if_missing(pdb_parameter_set, 'unit-cell',
string_value=pdb.get_unit_cell())
# 4. insert sequence info (lazy checking)
pdb_seq_parameter_sets = ExperimentParameterSet.objects.filter(
schema__namespace=getattr(
settings,
'PDB_SEQUENCE_PUBLICATION_SCHEMA',
default_settings.PDB_SEQUENCE_PUBLICATION_SCHEMA),
experiment=pub)
if pdb_seq_parameter_sets.count() == 0:
# insert seqences
for seq in pdb.get_sequence_info():
seq_ps_namespace = getattr(
settings,
'PDB_SEQUENCE_PUBLICATION_SCHEMA',
default_settings.PDB_SEQUENCE_PUBLICATION_SCHEMA)
seq_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(
namespace=seq_ps_namespace),
experiment=pub)
seq_parameter_set.save()
add_if_missing(seq_parameter_set, 'organism',
string_value=seq['organism'])
add_if_missing(seq_parameter_set, 'expression-system',
string_value=seq['expression_system'])
add_if_missing(seq_parameter_set, 'sequence',
string_value=seq['sequence'])
# 5. insert/update citation info (aggressive)
ExperimentParameterSet.objects.filter(
schema__namespace=getattr(
settings,
'PDB_CITATION_PUBLICATION_SCHEMA',
default_settings.PDB_CITATION_PUBLICATION_SCHEMA),
experiment=pub).delete()
for citation in pdb.get_citations():
cit_ps_namespace = getattr(
settings,
'PDB_CITATION_PUBLICATION_SCHEMA',
default_settings.PDB_CITATION_PUBLICATION_SCHEMA)
cit_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(namespace=cit_ps_namespace),
experiment=pub)
cit_parameter_set.save()
add_if_missing(cit_parameter_set, 'title',
string_value=citation['title'])
add_if_missing(cit_parameter_set, 'authors',
string_value='; '.join(citation['authors']))
add_if_missing(cit_parameter_set, 'journal',
string_value=citation['journal'])
add_if_missing(cit_parameter_set, 'volume',
string_value=citation['volume'])
add_if_missing(cit_parameter_set, 'page-range',
string_value='-'.join(
[citation['page_first'],
citation['page_last']]))
add_if_missing(cit_parameter_set, 'doi',
string_value='http://dx.doi.org/' +
citation['doi'])
# 6. Remove the PDB embargo if set, since the update has
# occurred and therefore the PDB must have been relased.
try:
ExperimentParameter.objects.get(
name__name='pdb-embargo',
parameterset__schema__namespace=getattr(
settings,
'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT)).delete()
except ExperimentParameter.DoesNotExist:
pass
# 7. Set the last update parameter to be now
if pdb_last_update_parameter is None:
pub_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(namespace=PUB_SCHEMA),
experiment=pub)
pub_parameter_set.save()
pdb_last_update_parameter = ExperimentParameter(
name=last_update_parameter_name,
parameterset=pub_parameter_set,
datetime_value=timezone.now())
else:
pdb_last_update_parameter.datetime_value = timezone.now()
pdb_last_update_parameter.save()
except CifFile.StarError:
# PDB is either unavailable or invalid
# (maybe notify the user somehow?)
continue
def populate_pdb_pub_records():
PUB_SCHEMA = getattr(settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT)
PUB_SCHEMA_DRAFT = getattr(settings, 'PUBLICATION_DRAFT_SCHEMA',
default_settings.PUBLICATION_DRAFT_SCHEMA)
PDB_SCHEMA = getattr(settings, 'PDB_PUBLICATION_SCHEMA_ROOT',
default_settings.PDB_PUBLICATION_SCHEMA_ROOT)
publications = Experiment.objects \
.filter(experimentparameterset__schema__namespace=PDB_SCHEMA) \
.filter(experimentparameterset__schema__namespace=PUB_SCHEMA) \
.exclude(experimentparameterset__schema__namespace=PUB_SCHEMA_DRAFT) \
.distinct()
last_update_parameter_name = ParameterName.objects.get(
name='pdb-last-sync', schema__namespace=PUB_SCHEMA)
def add_if_missing(parameterset,
name,
string_value=None,
numerical_value=None,
datetime_value=None):
try:
ExperimentParameter.objects.get(name__name=name,
parameterset=parameterset)
except ExperimentParameter.DoesNotExist:
param_name = ParameterName.objects.get(name=name,
schema=parameterset.schema)
param = ExperimentParameter(name=param_name,
parameterset=parameterset)
param.string_value = string_value
param.numerical_value = numerical_value
param.datetime_value = datetime_value
param.save()
for pub in publications:
try:
# try to get the last update time for the PDB data
pdb_last_update_parameter = ExperimentParameter.objects.get(
parameterset__schema__namespace=PUB_SCHEMA,
name=last_update_parameter_name,
parameterset__experiment=pub)
last_update = pdb_last_update_parameter.datetime_value
needs_update = last_update + \
getattr(settings,
'PDB_REFRESH_INTERVAL',
default_settings.PDB_REFRESH_INTERVAL) \
< timezone.now()
except ExperimentParameter.DoesNotExist:
# if the PDB last update time parameter doesn't exist,
# we definitely need to update the data and create a last
# update entry
needs_update = True
pdb_last_update_parameter = None
# If an update needs to happen...
if needs_update:
# 1. get the PDB info
pdb_parameter_set = ExperimentParameterSet.objects.get(
schema__namespace=getattr(
settings, 'PDB_PUBLICATION_SCHEMA_ROOT',
default_settings.PDB_PUBLICATION_SCHEMA_ROOT),
experiment=pub)
pdb = ExperimentParameter.objects.get(
name__name='pdb-id', parameterset=pdb_parameter_set)
pdb_id = pdb.string_value
# 1a. cosmetic change of case for PDB ID, if entered incorrectly
if pdb_id != pdb_id.upper():
pdb.string_value = pdb_id.upper()
pdb.save()
try:
# 2. fetch the info from pdb.org
pdb = PDBCifHelper(pdb_id)
# 3. insert all standard pdb parameters
add_if_missing(pdb_parameter_set,
'title',
string_value=pdb.get_pdb_title())
add_if_missing(pdb_parameter_set,
'url',
string_value=pdb.get_pdb_url())
try:
add_if_missing(pdb_parameter_set,
'resolution',
numerical_value=pdb.get_resolution())
except ValueError:
logger.error('PDB field "resolution" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
try:
add_if_missing(pdb_parameter_set,
'r-value',
numerical_value=pdb.get_obs_r_value())
except ValueError:
logger.error('PDB field "r-value" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
try:
add_if_missing(pdb_parameter_set,
'r-free',
numerical_value=pdb.get_free_r_value())
except ValueError:
logger.error('PDB field "r-free" could not be set for '
'publication Id %i \n %s' %
(pub.id, traceback.format_exc()))
add_if_missing(pdb_parameter_set,
'space-group',
string_value=pdb.get_spacegroup())
add_if_missing(pdb_parameter_set,
'unit-cell',
string_value=pdb.get_unit_cell())
# 4. insert sequence info (lazy checking)
pdb_seq_parameter_sets = ExperimentParameterSet.objects.filter(
schema__namespace=getattr(
settings, 'PDB_SEQUENCE_PUBLICATION_SCHEMA',
default_settings.PDB_SEQUENCE_PUBLICATION_SCHEMA),
experiment=pub)
if pdb_seq_parameter_sets.count() == 0:
# insert seqences
for seq in pdb.get_sequence_info():
seq_ps_namespace = getattr(
settings, 'PDB_SEQUENCE_PUBLICATION_SCHEMA',
default_settings.PDB_SEQUENCE_PUBLICATION_SCHEMA)
seq_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(
namespace=seq_ps_namespace),
experiment=pub)
seq_parameter_set.save()
add_if_missing(seq_parameter_set,
'organism',
string_value=seq['organism'])
add_if_missing(seq_parameter_set,
'expression-system',
string_value=seq['expression_system'])
add_if_missing(seq_parameter_set,
'sequence',
string_value=seq['sequence'])
# 5. insert/update citation info (aggressive)
ExperimentParameterSet.objects.filter(
schema__namespace=getattr(
settings, 'PDB_CITATION_PUBLICATION_SCHEMA',
default_settings.PDB_CITATION_PUBLICATION_SCHEMA),
experiment=pub).delete()
for citation in pdb.get_citations():
cit_ps_namespace = getattr(
settings, 'PDB_CITATION_PUBLICATION_SCHEMA',
default_settings.PDB_CITATION_PUBLICATION_SCHEMA)
cit_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(namespace=cit_ps_namespace),
experiment=pub)
cit_parameter_set.save()
add_if_missing(cit_parameter_set,
'title',
string_value=citation['title'])
add_if_missing(cit_parameter_set,
'authors',
string_value='; '.join(citation['authors']))
add_if_missing(cit_parameter_set,
'journal',
string_value=citation['journal'])
add_if_missing(cit_parameter_set,
'volume',
string_value=citation['volume'])
add_if_missing(cit_parameter_set,
'page-range',
string_value='-'.join([
citation['page_first'],
citation['page_last']
]))
add_if_missing(cit_parameter_set,
'doi',
string_value='http://dx.doi.org/' +
citation['doi'])
# 6. Remove the PDB embargo if set, since the update has
# occurred and therefore the PDB must have been relased.
try:
ExperimentParameter.objects.get(
name__name='pdb-embargo',
parameterset__schema__namespace=getattr(
settings, 'PUBLICATION_SCHEMA_ROOT',
default_settings.PUBLICATION_SCHEMA_ROOT)).delete(
)
except ExperimentParameter.DoesNotExist:
pass
# 7. Set the last update parameter to be now
if pdb_last_update_parameter is None:
pub_parameter_set = ExperimentParameterSet(
schema=Schema.objects.get(namespace=PUB_SCHEMA),
experiment=pub)
pub_parameter_set.save()
pdb_last_update_parameter = ExperimentParameter(
name=last_update_parameter_name,
parameterset=pub_parameter_set,
datetime_value=timezone.now())
else:
pdb_last_update_parameter.datetime_value = timezone.now()
pdb_last_update_parameter.save()
except CifFile.StarError:
# PDB is either unavailable or invalid
# (maybe notify the user somehow?)
continue
