def add_bio_feature_reporter_data(self, name, description, *args,
**kwargs):
if len(self.bio_feature_reporter_buffer
) >= self.bio_feature_reporter_buffer_size:
saved = False
while not saved:
try:
init_parsing_database_connections(self.db)
parsing_plt = ParsingPlatform.objects.using(
self.db).get(platform_fk=self.plt_id)
with transaction.atomic(using=self.db):
for rep, values in self.bio_feature_reporter_buffer:
rep.platform = parsing_plt
rep.save(using=self.db)
for value in values:
value.bio_feature_reporter = rep
value.save(using=self.db)
self.bio_feature_reporter_buffer.clear()
saved = True
except OperationalError as e:
time.sleep(2)
else:
reporter = ParsingBioFeatureReporter(name=name,
description=description)
values = []
for field, value in kwargs.items():
reporter_field_value = ParsingBioFeatureReporterValues(
bio_feature_reporter_field=field, value=value)
values.append(reporter_field_value)
self.bio_feature_reporter_buffer.append((reporter, values))
def __init__(self, plt, db):
self.db = db
self.platform_access_id = None
self.platform_name = None
self.description = None
self.platform_type = None
self.plt_id = plt.id
self.bio_feature_reporter_buffer = []
self.bio_feature_reporter_buffer_size = 2000
init_parsing_database_connections(self.db)
try:
parsing_plt = ParsingPlatform.objects.using(
self.db).get(platform_fk=self.plt_id)
except Exception as e:
parsing_plt = ParsingPlatform()
parsing_plt.platform_access_id = plt.platform_access_id
parsing_plt.platform_name = plt.platform_name
parsing_plt.description = plt.description
parsing_plt.platform_fk = plt.id
parsing_plt.platform_type = plt.platform_type.name if plt.platform_type is not None else None
saved = False
while not saved:
try:
parsing_plt.save(using=self.db)
saved = True
except OperationalError as e:
time.sleep(2)
saved = False
while not saved:
try:
parsing_plt.parsingbiofeaturereporter_set.all().delete()
saved = True
except OperationalError as e:
time.sleep(2)
def __init__(self, smp, db):
self.db = db
self.sample_name = None
self.description = None
self.smp_id = smp.id
self.buffer = []
self.buffer_size = 2000
init_parsing_database_connections(self.db)
try:
self.parsing_smp = ParsingSample.objects.using(
self.db).get(sample_fk=self.smp_id)
except Exception as e:
self.parsing_smp = ParsingSample()
self.parsing_smp.sample_name = smp.sample_name
self.parsing_smp.description = smp.description
self.parsing_smp.reporter_platform = self.parsing_smp.platform.reporter_platform
saved = False
while not saved:
try:
self.parsing_smp.save(using=self.db)
saved = True
except OperationalError as e:
time.sleep(2)
saved = False
while not saved:
try:
self.parsing_smp.parsingrawdata_set.all().delete()
saved = True
except OperationalError as e:
time.sleep(2)
def save_sample_object(self):
saved = False
while not saved:
try:
init_parsing_database_connections(self.db)
parsing_smp = ParsingSample.objects.using(
self.db).get(sample_fk=self.smp_id)
parsing_smp.sample_name = self.sample_name if self.sample_name is not None else parsing_smp.sample_name
parsing_smp.description = self.description if self.description is not None else parsing_smp.description
parsing_smp.sample_fk = self.smp_id
parsing_smp.save(using=self.db)
with transaction.atomic(using=self.db):
ParsingRawData.objects.using(self.db).bulk_create(
self.buffer)
saved = True
except OperationalError as e:
time.sleep(2)
def add_raw_data(self, bio_feature_reporter, value):
if len(self.buffer) >= self.buffer_size:
saved = False
while not saved:
try:
init_parsing_database_connections(self.db)
with transaction.atomic(using=self.db):
ParsingRawData.objects.using(self.db).bulk_create(
self.buffer)
self.buffer.clear()
saved = True
except OperationalError as e:
time.sleep(2)
else:
self.buffer.append(
ParsingRawData(sample=self.parsing_smp,
bio_feature_reporter_name=bio_feature_reporter,
value=value))
def save_experiment_object(self):
init_parsing_database_connections(self.db)
try:
parsing_exp = ParsingExperiment.objects.using(
self.db).get(experiment_fk=self.exp_id)
except Exception as e:
parsing_exp = ParsingExperiment()
saved = False
while not saved:
try:
parsing_exp.organism = self.organism if self.organism is not None else parsing_exp.organism
parsing_exp.experiment_access_id = self.experiment_access_id if self.experiment_access_id is not None else parsing_exp.experiment_access_id
parsing_exp.experiment_name = self.experiment_name if self.experiment_name is not None else parsing_exp.experiment_name
parsing_exp.scientific_paper_ref = self.scientific_paper_accession_base_link + self.scientific_paper_ref \
if self.scientific_paper_ref is not None else parsing_exp.scientific_paper_ref
parsing_exp.description = self.description if self.description is not None else parsing_exp.description
parsing_exp.experiment_fk = self.exp_id
parsing_exp.save(using=self.db)
saved = True
except OperationalError as e:
time.sleep(2)
def save_platform_object(self):
saved = False
while not saved:
try:
init_parsing_database_connections(self.db)
parsing_plt = ParsingPlatform.objects.using(
self.db).get(platform_fk=self.plt_id)
parsing_plt.platform_access_id = self.platform_access_id if self.platform_access_id is not None else parsing_plt.platform_access_id
parsing_plt.platform_name = self.platform_name if self.platform_name is not None else parsing_plt.platform_name
parsing_plt.description = self.description if self.description is not None else parsing_plt.description
parsing_plt.platform_fk = self.plt_id
parsing_plt.platform_type = self.platform_type
parsing_plt.save(using=self.db)
with transaction.atomic(using=self.db):
for rep, values in self.bio_feature_reporter_buffer:
rep.platform = parsing_plt
rep.save(using=self.db)
for value in values:
value.bio_feature_reporter = rep
value.save(using=self.db)
saved = True
except OperationalError as e:
time.sleep(2)