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How to use g_importer method in autotest

Best Python code snippet using autotest_python

mock.py

Source:mock.py

...1188    arguments will be applied to *all* patches done by `patch.multiple`.1189    When used as a class decorator `patch.multiple` honours `patch.TEST_PREFIX`1190    for choosing which methods to wrap.1191    """1192    def g_importer():1193        return _importer(target)1194    def g_target():1195        return target1196    if type(target) in (unicode, str):1197        getter = g_importer1198    else:1199        getter = g_target1200    if not kwargs:1201        raise ValueError(1202            'Must supply at least one keyword argument with patch.multiple'1203        )1204    # need to wrap in a list for python 3, where items is a view1205    items = list(kwargs.items())1206    attribute, new = items[0]...

Transfer.py

Source:Transfer.py

1ï»¿#!/usr/bin/env python2# -*- coding: utf-8 -*-3import pudb4import datetime5import argparse6import time7from taxamerger.TaxonomiesMerger import TaxonomiesMerger8from CopyResultDB import CopyResultDB9from runSolrIndexer import runSolrIndexer10from GlobalConfig import ConfigReader11from TempDB import TempDB12from lib.logTransfer import TransferLog13from DBConnectors.MSSQLConnector import MSSQLConnector14from lib.Datasources import Datasources15from lib.SpecimenTransfer.DCGetter import DCGetter16from lib.SpecimenTransfer.DCSpecimenGetter import DCSpecimenGetter17from lib.SpecimenTransfer.InsertSpecimen import InsertSpecimen18from lib.SpecimenTransfer.DCProjectGetter import DCProjectGetter19from lib.SpecimenTransfer.InsertProject import InsertProject20from lib.SpecimenTransfer.DCProjectUserGetter import DCProjectUserGetter21from lib.SpecimenTransfer.InsertProjectUser import InsertProjectUser22from lib.SpecimenTransfer.DCCollectionProjectGetter import DCCollectionProjectGetter23from lib.SpecimenTransfer.InsertCollectionProject import InsertCollectionProject24from lib.SpecimenTransfer.DCInstituteGetter import DCInstituteGetter25from lib.SpecimenTransfer.InsertInstitute import InsertInstitute26from lib.SpecimenTransfer.DCSpecimenDataGetter import DCSpecimenDataGetter27from lib.SpecimenTransfer.InsertSpecimenData import InsertSpecimenData28from lib.SpecimenTransfer.DCMediaGetter import DCMediaGetter29from lib.SpecimenTransfer.InsertMedia import InsertMedia30from lib.SpecimenTransfer.DCGeoGetter import DCGeoGetter31from lib.SpecimenTransfer.InsertGeo import InsertGeo32from lib.SpecimenTransfer.DCBarcodeGetter import DCBarcodeGetter33from lib.SpecimenTransfer.InsertBarcode import InsertBarcode34from lib.SpecimenTransfer.DCBarcodeReadsGetter import DCBarcodeReadsGetter35from lib.SpecimenTransfer.InsertBarcodeReads import InsertBarcodeReads36from lib.TaxaMatcher.TaxaMatcher import TaxaMatcher37from lib.CopyMatchedTaxa.CopyMatchedTaxa import CopyMatchedTaxa38from lib.CopyMatchedTaxa.CopyCommonNamesToTargetTable import CopyCommonNamesToTargetTable39from lib.CopyMatchedTaxa.CopyRedListToTargetTable import CopyRedListToTargetTable40from lib.CopyMatchedTaxa.CopyTaxonomySources import CopyTaxonomySources41from lib.CopyMatchedTaxa.CopyTaxonomicRanksEnum import CopyTaxonomicRanksEnum42from lib.CopyMatchedTaxa.NestedSetGenerator import NestedSetGenerator43from lib.CopyMatchedTaxa.FlatTaxaTable import FlatTaxaTable44from lib.Statistics.CalculateStatistics import CalculateStatistics45from lib.Statistics.SpecimenCompleteness import SpecimenCompleteness46import pudb47from configparser import ConfigParser48config = ConfigParser()49config.read('config.ini')50import logging, logging.config51if __name__ == "__main__":52	logging.config.fileConfig('config.ini', defaults={'logfilename': 'sync_dwb2portal.log'}, disable_existing_loggers=False)53logger = logging.getLogger('sync_webportal')54if __name__ == "__main__":55	usage = "Transfer.py [--skip taxamerger]"56	parser = argparse.ArgumentParser(prog="Transfer.py", usage=usage, description='Arguments for Transfer.py')57	parser.add_argument('--skip', metavar = 'taxamerger')58	args = parser.parse_args()59	60	61	logger.info("\n\n======= S t a r t - {:%Y-%m-%d %H:%M:%S} ======".format(datetime.datetime.now()))62	63	globalconfig = ConfigReader(config)64	65	if args.skip == 'taxamerger':66		pass67	else:68		taxonomiesmerger = TaxonomiesMerger(globalconfig)69		taxonomiesmerger.mergeTaxonomies()70	71	72	tempdb = TempDB(globalconfig)73	transfer_log = TransferLog(globalconfig)74	transfer_log.start()75	76	for datasource in globalconfig.data_sources:77		78		#time.sleep(60)79		80		datasourcename = datasource.data_source_name81		dstable = Datasources(globalconfig)82		dstable.addDatasource(datasourcename)83		datasourceid = dstable.getDatasourceID(datasourcename)84		85		dc_db = MSSQLConnector(connectionstring=datasource.source_database)86		87		dcgetter = DCGetter(dc_db, datasourcename, globalconfig, datasourceid)88		dcgetter.create_transfer_ids_temptable()89		90		logger.info("Transfer Specimens {0}".format(datasourcename.upper()))91		sp_getter = DCSpecimenGetter(dc_db, datasourcename, globalconfig, datasourceid)92		sp_importer = InsertSpecimen(globalconfig, sp_getter)93		94		logger.info("Transfer institutes {0}".format(datasourcename.upper()))95		inst_getter = DCInstituteGetter(dc_db, datasourcename, globalconfig, datasourceid)96		inst_importer = InsertInstitute(globalconfig, inst_getter)97		98		logger.info("Transfer Projects {0}".format(datasourcename.upper()))99		p_getter = DCProjectGetter(dc_db, datasourcename, globalconfig, datasourceid)100		p_importer = InsertProject(globalconfig, p_getter)101		102		logger.info("Transfer ProjectUser {0}".format(datasourcename.upper()))103		pu_getter = DCProjectUserGetter(dc_db, datasourcename, globalconfig, datasourceid)104		pu_importer = InsertProjectUser(globalconfig, pu_getter)105		106		logger.info("Transfer Collection Projects {0}".format(datasourcename.upper()))107		cp_getter = DCCollectionProjectGetter(dc_db, datasourcename, globalconfig, datasourceid)108		cp_importer = InsertCollectionProject(globalconfig, cp_getter)109		110		# import specimen data111		tables = ['specimendata', 'biology', 'event', 'agent', 'part', 'collection']112		for table in tables:113			logger.info("Transfer Specimen Data {0} {1}".format(datasourcename.upper(), table))114			d_getter = DCSpecimenDataGetter(dc_db, datasourcename, globalconfig, table, datasourceid)115			d_importer = InsertSpecimenData(globalconfig, d_getter)116		117		118		logger.info("Transfer Media {0}".format(datasourcename.upper()))119		md_getter = DCMediaGetter(dc_db, datasourcename, globalconfig, datasourceid)120		md_importer = InsertMedia(globalconfig, md_getter)121		122		logger.info("Transfer Coordinates {0}".format(datasourcename.upper()))123		g_getter = DCGeoGetter(dc_db, datasourcename, globalconfig, datasourceid)124		g_importer = InsertGeo(globalconfig, g_getter)125		126		logger.info("Transfer Barcodes {0}".format(datasourcename.upper()))127		b_getter = DCBarcodeGetter(dc_db, datasourcename, globalconfig, datasourceid)128		b_importer = InsertBarcode(globalconfig, b_getter)129		130		logger.info("Transfer Barcode Reads {0}".format(datasourcename.upper()))131		br_getter = DCBarcodeReadsGetter(dc_db, datasourcename, globalconfig, datasourceid)132		br_importer = InsertBarcodeReads(globalconfig, br_getter)133		134		transfer_log.update(datasourcename)135		dc_db.closeConnection()136	137	transfer_log.finished()138	139	taxamatcher = TaxaMatcher(globalconfig)140	141	copytaxa = CopyMatchedTaxa(globalconfig)142	143	copycommonnames = CopyCommonNamesToTargetTable(globalconfig)144	145	copyredlist = CopyRedListToTargetTable(globalconfig)146	147	copytaxonomysources = CopyTaxonomySources(globalconfig)148	149	copytaxranks = CopyTaxonomicRanksEnum(globalconfig)150	151	nestedgen = NestedSetGenerator(globalconfig)152	153	flattaxatable = FlatTaxaTable(globalconfig)154	155	calcstats = CalculateStatistics(globalconfig)156	157	spcompletenes = SpecimenCompleteness(globalconfig)158	159	dbcopy = CopyResultDB(globalconfig)160	dbcopy.copy_db()161	162	runSolrIndexer()...

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