# Obj2NexDB(nex_session_maker, lambda x: x.query(Alignmentevidence), # name='convert.from_bud.evidence.alignment_evidence', # delete_untouched=True, # commit_interval=1000), # OutputTransformer(1000)]) # ------------------------------------------ Perf ------------------------------------------ from src.sgd.model.perf.bioentity_data import BioentityDetails from src.sgd.model.nex.bioentity import Locus nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] nex_session.close() do_conversion(make_locus_data_backend_starter(nex_backend, 'alignment_bioent', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'ALIGNMENT', locus_ids, name='convert.from_backend.alignment_details', commit_interval=100, sure=True), OutputTransformer(100)]) do_conversion(make_orphan_backend_starter(nex_backend, ['alignments']), [Json2OrphanPerfDB(perf_session_maker, name='convert.from_backend.orphans', commit_interval=1000)]) # ------------------------------------------ Perf2 ------------------------------------------ perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, 'sgd-db2.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) perf_backend = PerfBackend(config.PERF_DBTYPE, 'sgd-db1.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS, None) do_conversion(make_locus_data_backend_starter(perf_backend, 'alignment_bioent', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'ALIGNMENT', locus_ids, name='convert.from_backend.alignment_details', commit_interval=100, sure=True), OutputTransformer(100)]) do_conversion(make_orphan_backend_starter(perf_backend, ['alignments']),
delete_untouched=True, commit_interval=1000, already_deleted=clean_up_orphans(nex_session_maker, Physinteractionevidence, Evidence, 'PHYSINTERACTION'))]) # ------------------------------------------ Perf ------------------------------------------ from src.sgd.model.perf.bioentity_data import BioentityDetails from src.sgd.model.perf.reference_data import ReferenceDetails from src.sgd.model.nex.bioentity import Locus from src.sgd.model.nex.reference import Reference nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] reference_ids = [x.id for x in nex_session.query(Reference).all()] nex_session.close() do_conversion(make_locus_data_backend_starter(nex_backend, 'interaction_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'INTERACTION', locus_ids, name='convert.from_backend.interaction_details', commit_interval=1000)]) do_conversion(make_reference_data_backend_starter(nex_backend, 'interaction_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'INTERACTION', reference_ids, name='convert.from_backend.interaction_details', commit_interval=1000)]) # ------------------------------------------ Perf2 ------------------------------------------ perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, 'sgd-db2.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) perf_backend = PerfBackend(config.PERF_DBTYPE, 'sgd-db1.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS, None) do_conversion(make_locus_data_backend_starter(perf_backend, 'interaction_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'INTERACTION', locus_ids, name='convert.from_backend.interaction_details', commit_interval=1000)]) do_conversion(make_reference_data_backend_starter(perf_backend, 'interaction_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'INTERACTION', reference_ids, name='convert.from_backend.interaction_details', commit_interval=1000)])
from src.sgd.model.nex.bioconcept import Go, ECNumber, Phenotype, Observable from src.sgd.model.nex.bioitem import Domain, Chemical nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] reference_ids = [x.id for x in nex_session.query(Reference).all()] go_ids = [x.id for x in nex_session.query(Go).all()] domain_ids = [x.id for x in nex_session.query(Domain).all()] ecnumber_ids = [x.id for x in nex_session.query(ECNumber).all()] phenotype_ids = [x.id for x in nex_session.query(Phenotype).all()] observable_ids = [x.id for x in nex_session.query(Observable).all()] chemical_ids = [x.id for x in nex_session.query(Chemical).all()] nex_session.close() # ------------------------------------------ GO Perf ------------------------------------------ do_conversion(make_locus_data_backend_starter(nex_backend, 'go_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'GO', locus_ids, name='convert.from_backend.go_details', commit_interval=1000, sure=True)]) do_conversion(make_go_data_backend_starter(nex_backend, 'go_details', go_ids), [Json2DataPerfDB(perf_session_maker, BioconceptDetails, 'GO_LOCUS', go_ids, name='convert.from_backend.go_details', commit_interval=1000, sure=True)]) do_conversion(make_reference_data_backend_starter(nex_backend, 'go_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'GO', reference_ids, name='convert.from_backend.go_details', commit_interval=1000, sure=True)]) do_conversion(make_go_data_with_children_backend_starter(nex_backend, 'go_details', go_ids), [Json2DataPerfDB(perf_session_maker, BioconceptDetails, 'GO_LOCUS_ALL_CHILDREN', go_ids, name='convert.from_backend.go_details', commit_interval=1000, sure=True)]) # ------------------------------------------ Misc Perf ------------------------------------------ do_conversion(make_locus_data_backend_starter(nex_backend, 'ec_number_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'EC_NUMBER', locus_ids, name='convert.from_backend.ec_number_details', commit_interval=1000, sure=True)])
from src.sgd.model.nex.evidence import Posttranslationalevidence, Evidence from src.sgd.convert.from_bud.evidence import make_posttranslational_evidence_starter do_conversion(make_posttranslational_evidence_starter(nex_session_maker), [Json2Obj(Posttranslationalevidence), Evidence2NexDB(nex_session_maker, lambda x: x.query(Posttranslationalevidence), name='convert.from_bud.evidence.posttranslationsl', delete_untouched=True, commit_interval=1000, already_deleted=clean_up_orphans(nex_session_maker, Posttranslationalevidence, Evidence, 'POSTTRANSLATIONAL')), OutputTransformer(1000)]) from src.sgd.model.nex.bioentity import Locus nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] nex_session.close() from src.sgd.model.perf.bioentity_data import BioentityDetails do_conversion(make_locus_data_backend_starter(nex_backend, 'posttranslational_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'POSTTRANSLATIONAL', locus_ids, name='convert.from_backend.posttranslational_details', commit_interval=1000, sure=True), OutputTransformer(1000)]) perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, 'sgd-db2.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) perf_backend = PerfBackend(config.PERF_DBTYPE, 'sgd-db1.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS, None) do_conversion(make_locus_data_backend_starter(nex_backend, 'posttranslational_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'POSTTRANSLATIONAL', locus_ids, name='convert.from_backend.posttranslational_details', commit_interval=1000, sure=True), OutputTransformer(1000)])
from src.sgd.model.nex.bioentity import Locus from src.sgd.model.nex.reference import Reference from src.sgd.model.nex.bioconcept import Go, ECNumber, Phenotype, Observable from src.sgd.model.nex.bioitem import Domain, Chemical nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] reference_ids = [x.id for x in nex_session.query(Reference).all()] phenotype_ids = [x.id for x in nex_session.query(Phenotype).all()] observable_ids = [x.id for x in nex_session.query(Observable).all()] chemical_ids = [x.id for x in nex_session.query(Chemical).all()] nex_session.close() # ------------------------------------------ Literature Perf ------------------------------------------ do_conversion(make_locus_data_backend_starter(nex_backend, 'literature_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'LITERATURE', locus_ids, name='convert.from_backend.literature_details', commit_interval=1000, sure=True)]) do_conversion(make_reference_data_backend_starter(nex_backend, 'literature_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'LITERATURE', reference_ids, name='convert.from_backend.literature_details', commit_interval=1000, sure=True)]) # ------------------------------------------ Phenotype Perf ------------------------------------------ do_conversion(make_locus_data_backend_starter(nex_backend, 'phenotype_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'PHENOTYPE', locus_ids, name='convert.from_backend.phenotype_details', commit_interval=1000, sure=True)]) do_conversion(make_phenotype_data_backend_starter(nex_backend, 'phenotype_details', phenotype_ids), [Json2DataPerfDB(perf_session_maker, BioconceptDetails, 'PHENOTYPE_LOCUS', phenotype_ids, name='convert.from_backend.phenotype_details', commit_interval=1000, sure=True)]) do_conversion(make_reference_data_backend_starter(nex_backend, 'phenotype_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'PHENOTYPE', reference_ids, name='convert.from_backend.phenotype_details', commit_interval=1000, sure=True)])
# # ------------------------------------------ Perf ------------------------------------------ from src.sgd.model.perf.bioentity_data import BioentityDetails from src.sgd.model.perf.bioitem_data import BioitemDetails from src.sgd.model.perf.core import Bioitem as PerfBioitem # from src.sgd.model.perf.core import Strain as PerfStrain # from src.sgd.model.nex.bioentity import Locus from src.sgd.model.nex.bioitem import Contig nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] contig_ids = [x.id for x in nex_session.query(Contig).all()] nex_session.close() do_conversion(make_locus_data_backend_starter(nex_backend, 'neighbor_sequence_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'NEIGHBOR_SEQUENCE', locus_ids, name='convert.from_backend.neighbor_sequence_details', commit_interval=1000)]) do_conversion(make_locus_data_backend_starter(nex_backend, 'sequence_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'SEQUENCE', locus_ids, name='convert.from_backend.sequence_details', commit_interval=1000)]) do_conversion(make_contig_data_backend_starter(nex_backend, 'sequence_details', contig_ids), [Json2DataPerfDB(perf_session_maker, BioitemDetails, 'SEQUENCE', contig_ids, name='convert.from_backend.sequence_details', commit_interval=1000)]) do_conversion(make_backend_starter(nex_backend, 'all_bioitems', 1000), [Json2CorePerfDB(perf_session_maker, PerfBioitem, name='convert.from_backend.bioitem', commit_interval=1000, delete_untouched=True)]) # do_conversion(make_backend_starter(nex_backend, 'all_strains', 1000), # [Json2CorePerfDB(perf_session_maker, PerfStrain, name='convert.from_backend.strain', commit_interval=1000, delete_untouched=True)])
delete_untouched=True, commit_interval=1000, already_deleted=clean_up_orphans(nex_session_maker, Regulationevidence, Evidence, 'REGULATION'))]) # ------------------------------------------ Perf ------------------------------------------ from src.sgd.model.perf.bioentity_data import BioentityDetails, BioentityEnrichment from src.sgd.model.perf.reference_data import ReferenceDetails from src.sgd.model.nex.bioentity import Locus from src.sgd.model.nex.reference import Reference nex_session = nex_session_maker() locus_ids = [x.id for x in nex_session.query(Locus).all()] reference_ids = [x.id for x in nex_session.query(Reference).all()] nex_session.close() do_conversion(make_locus_data_backend_starter(nex_backend, 'regulation_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'REGULATION', locus_ids, name='convert.from_backend.regulation_details', commit_interval=1000)]) do_conversion(make_reference_data_backend_starter(nex_backend, 'regulation_details', reference_ids), [Json2DataPerfDB(perf_session_maker, ReferenceDetails, 'REGULATION', reference_ids, name='convert.from_backend.regulation_details', commit_interval=1000)]) do_conversion(make_locus_data_backend_starter(nex_backend, 'regulation_target_enrichment', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityEnrichment, 'REGULATION', locus_ids, name='convert.from_backend.regulation_target_enrichment', commit_interval=1000)]) # ------------------------------------------ Perf2 ------------------------------------------ perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, 'sgd-db2.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) perf_backend = PerfBackend(config.PERF_DBTYPE, 'sgd-db1.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS, None) do_conversion(make_locus_data_backend_starter(perf_backend, 'regulation_details', locus_ids), [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'REGULATION', locus_ids, name='convert.from_backend.regulation_details', commit_interval=1000)])