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
do_conversion(make_backend_starter(nex_backend, 'all_bioentities', 1000),
[Json2CorePerfDB(perf_session_maker, PerfBioentity, name='convert.from_backend.bioentity', commit_interval=1000, delete_untouched=True)])
do_conversion(make_backend_starter(nex_backend, 'all_locustabs', 1000),
[Json2CorePerfDB(perf_session_maker, PerfLocustab, name='convert.from_backend.all_locustabs', 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)
from src.sgd.model.nex.bioitem import Reservedname
from src.sgd.model.nex.paragraph import Paragraph, Bioentityparagraph, ParagraphReference
from src.sgd.convert.from_bud.paragraph import make_bioentity_paragraph_starter, make_paragraph_reference_starter
do_conversion(make_bioentity_paragraph_starter(bud_session_maker, nex_session_maker),
[Json2Obj(Bioentityparagraph),
Obj2NexDB(nex_session_maker, lambda x: x.query(Bioentityparagraph),
name='convert.from_bud.paragraph.bioentity',
delete_untouched=True,
commit=True,
already_deleted=clean_up_orphans(nex_session_maker, Bioentityparagraph, Paragraph, 'BIOENTITY'))])
do_conversion(make_paragraph_reference_starter(nex_session_maker),
[Json2Obj(ParagraphReference),
Obj2NexDB(nex_session_maker, lambda x: x.query(ParagraphReference),
name='convert.from_bud.paragraph_reference',
delete_untouched=True,
commit=True)])
from src.sgd.model.perf.core import Bioentity as PerfBioentity
do_conversion(make_backend_starter(nex_backend, 'all_bioentities', 1000),
[Json2CorePerfDB(perf_session_maker, PerfBioentity, name='convert.from_backend.bioentity', commit_interval=1000, delete_untouched=True)])
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_backend_starter(perf_backend, 'all_bioentities', 1000),
[Json2CorePerfDB(perf_session_maker, PerfBioentity, name='convert.from_backend.bioentity', commit_interval=1000, delete_untouched=True)])
# ------------------------------------------ Paragraph ------------------------------------------
from src.sgd.model.nex.paragraph import Paragraph, Strainparagraph, ParagraphReference
from src.sgd.convert.from_bud.paragraph import make_strain_paragraph_starter, make_paragraph_reference_starter
do_conversion(make_strain_paragraph_starter(nex_session_maker),
[Json2Obj(Strainparagraph),
Obj2NexDB(nex_session_maker, lambda x: x.query(Strainparagraph),
name='convert.from_bud.paragraph.strain',
delete_untouched=True,
commit=True,
already_deleted=clean_up_orphans(nex_session_maker, Strainparagraph, Paragraph, 'STRAIN'))])
# do_conversion(make_paragraph_reference_starter(nex_session_maker),
# [Json2Obj(ParagraphReference),
# Obj2NexDB(nex_session_maker, lambda x: x.query(ParagraphReference),
# name='convert.from_bud.paragraph_reference',
# delete_untouched=True,
# commit=True)])
# ------------------------------------------ Perf ------------------------------------------
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)])
# ------------------------------------------ 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_backend_starter(perf_backend, 'all_strains', 1000),
[Json2CorePerfDB(perf_session_maker, PerfStrain, name='convert.from_backend.strain', commit_interval=1000, delete_untouched=True)])
__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 ------------------------------------------
# ------------------------------------------ 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)
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)])
# ------------------------------------------ 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, '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(perf_backend, 'sequence_details', locus_ids),
# [Json2DataPerfDB(perf_session_maker, BioentityDetails, 'SEQUENCE', locus_ids, name='convert.from_backend.sequence_details', commit_interval=1000)])
#
