# 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']), [Json2OrphanPerfDB(perf_session_maker, name='convert.from_backend.orphans', commit_interval=1000)])
[Json2CorePerfDB(perf_session_maker, PerfBioconcept, name='convert.from_backend.bioconcept', delete_untouched=True, commit_interval=1000)]) # ------------------------------------------ Bioitem ------------------------------------------ from src.sgd.model.perf.core import Bioitem as PerfBioitem 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)]) # ------------------------------------------ Tag ------------------------------------------ do_conversion(make_backend_starter(nex_backend, 'all_tags', 1000), [Json2CorePerfDB(perf_session_maker, PerfTag, name='convert.from_backend.tag', commit_interval=1000, delete_untouched=True)]) from src.sgd.model.nex import locus_types do_conversion(make_orphan_arg_backend_starter(nex_backend, 'locus_list', locus_types), [Json2OrphanPerfDB(perf_session_maker, name='convert.from_backend.orphans', commit_interval=1000)]) do_conversion(make_orphan_backend_starter(nex_backend, ['tag_list', 'snapshot']), [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) # ------------------------------------------ Disambig ------------------------------------------ do_conversion(make_backend_starter(perf_backend, 'all_disambigs', 1000), [Json2DisambigPerfDB(perf_session_maker, commit_interval=1000)]) # ------------------------------------------ Evelements ------------------------------------------ from src.sgd.model.perf.core import Strain as PerfStrain do_conversion(make_backend_starter(perf_backend, 'all_strains', 1000), [Json2CorePerfDB(perf_session_maker, PerfStrain, name='convert.from_backend.strain', commit_interval=1000, delete_untouched=True)])
nex_backend = SGDBackend(config.NEX_DBTYPE, 'sgd-master-db.stanford.edu:1521', config.NEX_DBNAME, config.NEX_SCHEMA, config.NEX_DBUSER, config.NEX_DBPASS, None) # ------------------------------------------ Perf ------------------------------------------ # ------------------------------------------ Reference ------------------------------------------ from src.sgd.model.perf.core import Reference as PerfReference, Author as PerfAuthor, Bibentry as PerfBibentry do_conversion(make_backend_starter(nex_backend, 'all_references', 1000), [Json2CorePerfDB(perf_session_maker, PerfReference, name='convert.from_backend.reference', delete_untouched=True, commit_interval=1000)]) do_conversion(make_backend_starter(nex_backend, 'all_authors', 1000), [Json2CorePerfDB(perf_session_maker, PerfAuthor, name='convert.from_backend.author', delete_untouched=True, commit_interval=1000)]) do_conversion(make_backend_starter(nex_backend, 'all_bibentries', 1000), [Json2CorePerfDB(perf_session_maker, PerfBibentry, name='convert.from_backend.all_bibentries', commit_interval=1000, delete_untouched=True)]) do_conversion(make_orphan_backend_starter(nex_backend, ['references_this_week']), [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) # ------------------------------------------ Reference ------------------------------------------ from src.sgd.model.perf.core import Reference as PerfReference, Author as PerfAuthor, Bibentry as PerfBibentry do_conversion(make_backend_starter(perf_backend, 'all_references', 1000), [Json2CorePerfDB(perf_session_maker, PerfReference, name='convert.from_backend.reference', delete_untouched=True, commit_interval=1000)]) do_conversion(make_backend_starter(perf_backend, 'all_authors', 1000), [Json2CorePerfDB(perf_session_maker, PerfAuthor, name='convert.from_backend.author', delete_untouched=True, commit_interval=1000)]) do_conversion(make_backend_starter(perf_backend, 'all_bibentries', 1000),