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.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(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.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')