from src.sgd.model import bud, nex from src.sgd.convert import prepare_schema_connection, config, clean_up_orphans from src.sgd.convert.transformers import do_conversion, Json2Obj, Evidence2NexDB __author__ = 'kpaskov' if __name__ == "__main__": bud_session_maker = prepare_schema_connection(bud, config.BUD_DBTYPE, 'pastry.stanford.edu:1521', config.BUD_DBNAME, config.BUD_SCHEMA, config.BUD_DBUSER, config.BUD_DBPASS) nex_session_maker = prepare_schema_connection(nex, config.NEX_DBTYPE, 'sgd-master-db.stanford.edu:1521', config.NEX_DBNAME, config.NEX_SCHEMA, config.NEX_DBUSER, config.NEX_DBPASS) from src.sgd.model.nex.evidence import Evidence, Goevidence, Literatureevidence, Domainevidence, ECNumberevidence, \ Proteinexperimentevidence, Phenotypeevidence, Historyevidence, Pathwayevidence, Goslimevidence, Posttranslationalevidence from src.sgd.convert.from_bud.evidence import make_go_evidence_starter, make_literature_evidence_starter, \ make_domain_evidence_starter, make_protein_experiment_evidence_starter, \ make_ecnumber_evidence_starter, make_protein_experiment_evidence_starter, make_go_slim_evidence_starter, \ make_phenotype_evidence_starter, make_history_evidence_starter, make_pathway_evidence_starter, make_posttranslational_evidence_starter from src.sgd.convert.from_bud.auxiliary import make_bioconcept_count_starter do_conversion(make_go_evidence_starter(bud_session_maker, nex_session_maker), [Json2Obj(Goevidence), Evidence2NexDB(nex_session_maker, lambda x: x.query(Goevidence), name='convert.from_bud.evidence.go', delete_untouched=True, commit_interval=1000, already_deleted=clean_up_orphans(nex_session_maker, Goevidence, Evidence, 'GO'))]) do_conversion(make_go_slim_evidence_starter(nex_session_maker), [Json2Obj(Goslimevidence), Evidence2NexDB(nex_session_maker, lambda x: x.query(Goslimevidence), name='convert.from_bud.evidence.goslim',
from src.sgd.model import nex, perf from src.sgd.backend.nex import SGDBackend from src.sgd.backend.perf import PerfBackend from src.sgd.convert import prepare_schema_connection, config from src.sgd.convert.transformers import do_conversion, \ make_backend_starter, Json2CorePerfDB, Json2OrphanPerfDB, Json2DisambigPerfDB, make_orphan_arg_backend_starter, \ make_orphan_backend_starter __author__ = 'kpaskov' if __name__ == "__main__": nex_session_maker = prepare_schema_connection(nex, config.NEX_DBTYPE, 'sgd-master-db.stanford.edu:1521', config.NEX_DBNAME, config.NEX_SCHEMA, config.NEX_DBUSER, config.NEX_DBPASS) perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, 'sgd-db1.stanford.edu:1521', config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) 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 ------------------------------------------ # ------------------------------------------ Disambig ------------------------------------------ do_conversion(make_backend_starter(nex_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(nex_backend, 'all_strains', 1000), [Json2CorePerfDB(perf_session_maker, PerfStrain, name='convert.from_backend.strain', commit_interval=1000, delete_untouched=True)]) # ------------------------------------------ Bioentity ------------------------------------------ from src.sgd.model.perf.core import Bioentity as PerfBioentity, Locustab as PerfLocustab, Locusentry as PerfLocusentry, Tag as PerfTag
#import xlrd import json from src.sgd.elastic_search.index_mapping import mapping import requests CLIENT_ADDRESS = 'http://52.41.106.165:9200/'# cluster alpha INDEX_NAME = 'searchable_items_blue' DOC_TYPE = 'searchable_item' RESET_INDEX = False es = Elasticsearch(CLIENT_ADDRESS, retry_on_timeout=True) # prep session #nex_session_maker = prepare_schema_connection(nex, config.NEX_DBTYPE, config.NEX_DBHOST, config.NEX_DBNAME, config.NEX_SCHEMA, config.NEX_DBUSER, config.NEX_DBPASS) #perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, config.PERF_DBHOST, config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) nex_session_maker = prepare_schema_connection(nex, config.NEX_DBTYPE, config.NEX_HOST, config.NEX_DBNAME, config.NEX_SCHEMA, config.NEX_DBUSER, config.NEX_DBPASS) perf_session_maker = prepare_schema_connection(perf, config.PERF_DBTYPE, config.PERF_HOST, config.PERF_DBNAME, config.PERF_SCHEMA, config.PERF_DBUSER, config.PERF_DBPASS) from src.sgd.model.nex.bioentity import Bioentity, Locus from src.sgd.model.perf.core import Bioentity as PerfBioentity from src.sgd.model.perf.core import Reference as PerfReference from src.sgd.model.perf.bioentity_data import BioentityDetails as PerfBioentityDetails from src.sgd.model.perf.bioconcept_data import BioconceptDetails as PerfBioconceptDetails from src.sgd.model.perf.reference_data import ReferenceDetails from src.sgd.model.nex.reference import Author from src.sgd.model.nex.misc import Strain, Alias from src.sgd.model.nex.bioconcept import Go from src.sgd.model.nex.bioconcept import Phenotype from src.sgd.model.nex.bioconcept import Observable from src.sgd.model.nex.reference import Reference from src.sgd.model.nex.bioitem import Contig