def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.chemical')
log.info('begin')
convert_allele(old_session_maker, new_session_maker)
convert_chemical(old_session_maker, new_session_maker)
def convert(new_session_maker):
log = set_up_logging('convert.binding')
log.info('begin')
convert_evidence(new_session_maker, 10000)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.protein')
log.info('begin')
convert_domain(new_session_maker, 5000)
convert_domain_evidence(new_session_maker, 5000)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.bioentity')
log.info('begin')
convert_locus(old_session_maker, new_session_maker)
convert_protein(old_session_maker, new_session_maker)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.physical_interaction')
log.info('begin')
convert_physical_interevidence(old_session_maker, new_session_maker, 10000)
from model_new_schema.interaction import Physinteractionevidence
get_bioent_ids_f = lambda x: [x.bioentity1_id, x.bioentity2_id]
convert_bioentity_reference(new_session_maker, Physinteractionevidence, 'PHYSINTERACTION', 'convert.physical_interaction.bioentity_reference', 10000, get_bioent_ids_f)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.bioentity_in_depth')
log.info('begin')
convert_alias(old_session_maker, new_session_maker)
convert_url(old_session_maker, new_session_maker, 1000)
convert_qualifier_evidence(old_session_maker, new_session_maker)
convert_bioentitytabs(new_session_maker)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.evelements')
log.info('begin')
convert_experiment(old_session_maker, new_session_maker)
convert_experiment_alias(old_session_maker, new_session_maker)
convert_experiment_relation(old_session_maker, new_session_maker)
convert_strain(old_session_maker, new_session_maker)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.reference')
requests_log = logging.getLogger("requests")
requests_log.setLevel(logging.WARNING)
log.info('begin')
convert_journal(old_session_maker, new_session_maker)
convert_book(old_session_maker, new_session_maker)
convert_reference(old_session_maker, new_session_maker, 3000)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.go')
log.info('begin')
#convert_go(old_session_maker, new_session_maker)
convert_evidence(old_session_maker, new_session_maker, 10000)
from model_new_schema.go import Goevidence
get_bioent_ids_f = lambda x: [x.bioentity_id]
convert_bioentity_reference(new_session_maker, Goevidence, 'GO', 'convert.go.bioentity_reference', 10000, get_bioent_ids_f)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.phenotype')
log.info('begin')
convert_phenotype(old_session_maker, new_session_maker)
convert_evidence(old_session_maker, new_session_maker, 10000)
convert_evidence_chemical(old_session_maker, new_session_maker, 10000)
from model_new_schema.phenotype import Phenotypeevidence
get_bioent_ids_f = lambda x: [x.bioentity_id]
convert_bioentity_reference(new_session_maker, Phenotypeevidence, 'PHENOTYPE', 'convert.phenotype.bioentity_reference', 10000, get_bioent_ids_f)
log.info('complete')
def convert(new_session_maker):
log = set_up_logging('convert.regulation')
log.info('begin')
convert_evidence(new_session_maker, 10000)
from model_new_schema.regulation import Regulationevidence
get_bioent_ids_f = lambda x: [x.bioentity1_id, x.bioentity2_id]
convert_paragraph(new_session_maker)
convert_paragraph_reference(new_session_maker)
convert_bioentity_reference(new_session_maker, Regulationevidence, 'REGULATION', 'convert.regulation.bioentity_reference', 10000, get_bioent_ids_f)
log.info('complete')
def convert(new_session_maker):
log = set_up_logging('convert.interaction_families')
log.info('begin')
from model_new_schema.interaction import Physinteractionevidence
convert_interaction(new_session_maker, Physinteractionevidence, 'PHYSINTERACTION', 'convert.physical_interaction.interaction', 10000, False)
from model_new_schema.interaction import Geninteractionevidence
convert_interaction(new_session_maker, Geninteractionevidence, 'GENINTERACTION', 'convert.genetic_interaction.interaction', 10000, False)
convert_interaction_family(new_session_maker, 100)
from model_new_schema.regulation import Regulationevidence
convert_interaction(new_session_maker, Regulationevidence, 'REGULATION', 'convert.interaction.regulation_interaction', 10000, True)
convert_regulation_family(new_session_maker, 100)
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.literature')
log.info('begin')
convert_litevidence(old_session_maker, new_session_maker, 100000)
from model_new_schema.literature import Literatureevidence
get_bioent_ids_f = lambda x: [x.bioentity_id]
convert_bioentity_reference(new_session_maker, Literatureevidence, 'PRIMARY_LITERATURE', 'convert.literature.primary_bioentity_reference',
100000, get_bioent_ids_f, filter_f = lambda x: x.topic=='Primary Literature')
convert_bioentity_reference(new_session_maker, Literatureevidence, 'ADDITIONAL_LITERATURE', 'convert.literature.additional_bioentity_reference',
100000, get_bioent_ids_f, filter_f = lambda x: x.topic=='Additional Literature')
convert_bioentity_reference(new_session_maker, Literatureevidence, 'OMICS_LITERATURE', 'convert.literature.omics_bioentity_reference',
100000, get_bioent_ids_f, filter_f = lambda x: x.topic=='Omics')
convert_bioentity_reference(new_session_maker, Literatureevidence, 'REVIEW_LITERATURE', 'convert.literature.review_bioentity_reference',
100000, get_bioent_ids_f, filter_f = lambda x: x.topic=='Reviews')
log.info('complete')
def convert(old_session_maker, new_session_maker):
log = set_up_logging("convert.genetic_interaction")
log.info("begin")
convert_genetic_interevidence(old_session_maker, new_session_maker, 10000)
from model_new_schema.interaction import Geninteractionevidence
get_bioent_ids_f = lambda x: [x.bioentity1_id, x.bioentity2_id]
convert_bioentity_reference(
new_session_maker,
Geninteractionevidence,
"GENINTERACTION",
"convert.genetic_interaction.bioentity_reference",
10000,
get_bioent_ids_f,
)
log.info("complete")
def convert(old_session_maker, new_session_maker):
log = set_up_logging('convert.reference_in_depth')
requests_log = logging.getLogger("requests")
requests_log.setLevel(logging.WARNING)
log.info('begin')
convert_abstract(old_session_maker, new_session_maker, 3000)
convert_author(old_session_maker, new_session_maker, 10000)
convert_author_reference(old_session_maker, new_session_maker, 10000)
convert_reftype(old_session_maker, new_session_maker)
convert_reference_relation(old_session_maker, new_session_maker)
convert_alias(old_session_maker, new_session_maker, 3000)
convert_url(new_session_maker, 3000)
convert_bibentry(new_session_maker, 3000)
log.info('complete')
convert_evelements, convert_chemical, set_up_logging
from convert_evidence import convert_literature, \
convert_regulation, convert_phenotype, convert_go, convert_protein, \
convert_bioentity_in_depth, convert_reference_in_depth, convert_binding, \
convert_genetic_interaction, convert_physical_interaction
from schema_conversion import new_config, old_config, prepare_schema_connection
from threading import Thread
import model_new_schema
import model_old_schema
import sys
if __name__ == "__main__":
old_session_maker = prepare_schema_connection(model_old_schema, old_config)
new_session_maker = prepare_schema_connection(model_new_schema, new_config)
log = set_up_logging('convert')
log.info('begin')
################# Core Converts ###########################
#Evelement
try:
convert_evelements.convert(old_session_maker, new_session_maker)
except Exception:
log.exception( "Unexpected error:" + str(sys.exc_info()[0]) )
#Reference
try:
convert_reference.convert(old_session_maker, new_session_maker)
except Exception:
log.exception( "Unexpected error:" + str(sys.exc_info()[0]) )