NCBI C++ Toolkit Cross Reference

  C++/src/sra/data_loaders/sra/test/test_sra_loader.cpp


/* $Id: test_sra_loader.cpp 67746 2015-06-09 14:51:29Z vasilche $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Eugene Vasilchenko * * File Description: * Unit tests for SRA data loader * * =========================================================================== */ #include <ncbi_pch.hpp> #include <sra/data_loaders/sra/sraloader.hpp> #include <objmgr/scope.hpp> #include <objmgr/bioseq_handle.hpp> #include <corelib/test_boost.hpp> #include <common/test_assert.h> /* This header must go last */ USING_NCBI_SCOPE; USING_SCOPE(objects); BOOST_AUTO_TEST_CASE(FetchSeq1) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eNoTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR000123.1.2"); const TSeqPos seqlen1 = 153; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); } BOOST_AUTO_TEST_CASE(FetchSeq2) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eNoTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR066117.18823.2"); const TSeqPos seqlen1 = 112; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); } BOOST_AUTO_TEST_CASE(FetchSeq3) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eNoTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR066117.1.2"); const TSeqPos seqlen1 = 110; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); } BOOST_AUTO_TEST_CASE(FetchSeq4) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR000123.1.2"); const TSeqPos seqlen1 = 107; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); } BOOST_AUTO_TEST_CASE(FetchSeq5) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR066117.18823.2"); const TSeqPos seqlen1 = 102; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); } BOOST_AUTO_TEST_CASE(FetchSeq6) { CRef<CObjectManager> om = CObjectManager::GetInstance(); string loader_name = CSRADataLoader::RegisterInObjectManager(*om, CSRADataLoader::eTrim) .GetLoader()->GetName(); CScope scope(*om); scope.AddDataLoader(loader_name); CSeq_id seqid1("gnl|SRA|SRR066117.1.2"); const TSeqPos seqlen1 = 100; BOOST_REQUIRE_EQUAL(seqlen1, scope.GetSequenceLength(seqid1)); BOOST_REQUIRE_EQUAL(CSeq_inst::eMol_na, scope.GetSequenceType(seqid1)); CBioseq_Handle handle1 = scope.GetBioseqHandle(seqid1); BOOST_REQUIRE_EQUAL(seqlen1, handle1.GetInst().GetLength()); }

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