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
