1 /**
2 * UGENE - Integrated Bioinformatics Tools.
3 * Copyright (C) 2008-2021 UniPro <ugene@unipro.ru>
4 * http://ugene.net
5 *
6 * This program is free software; you can redistribute it and/or
7 * modify it under the terms of the GNU General Public License
8 * as published by the Free Software Foundation; either version 2
9 * of the License, or (at your option) any later version.
10 *
11 * This program is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program; if not, write to the Free Software
18 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
19 * MA 02110-1301, USA.
20 */
21
22 #include "CloneAssemblyWithReferenceToDbiTask.h"
23
24 #include <QScopedPointer>
25
26 #include <U2Core/AssemblyObject.h>
27 #include <U2Core/CloneObjectTask.h>
28 #include <U2Core/DNASequenceObject.h>
29 #include <U2Core/DocumentModel.h>
30 #include <U2Core/U2AssemblyDbi.h>
31 #include <U2Core/U2DbiUtils.h>
32 #include <U2Core/U2ObjectDbi.h>
33 #include <U2Core/U2SafePoints.h>
34 #include <U2Core/U2SequenceDbi.h>
35
36 namespace U2 {
37
CloneAssemblyWithReferenceToDbiTask(const U2Assembly & assembly,const U2Sequence & reference,const U2DbiRef & srcDbiRef,const U2DbiRef & dstDbiRef,const QVariantMap & hints)38 CloneAssemblyWithReferenceToDbiTask::CloneAssemblyWithReferenceToDbiTask(const U2Assembly &assembly,
39 const U2Sequence &reference,
40 const U2DbiRef &srcDbiRef,
41 const U2DbiRef &dstDbiRef,
42 const QVariantMap &hints)
43 : Task(tr("Clone assembly object to the destination database"), TaskFlags_FOSE_COSC),
44 assembly(assembly),
45 reference(reference),
46 srcDbiRef(srcDbiRef),
47 dstDbiRef(dstDbiRef),
48 dstFolder(hints.value(DocumentFormat::DBI_FOLDER_HINT, U2ObjectDbi::ROOT_FOLDER).toString()),
49 cloneAssemblyTask(nullptr),
50 cloneReferenceTask(nullptr) {
51 SAFE_POINT_EXT(assembly.hasValidId(), setError(tr("Invalid assembly ID")), );
52 SAFE_POINT_EXT(reference.hasValidId(), setError(tr("Invalid assembly ID")), );
53 SAFE_POINT_EXT(srcDbiRef.isValid(), setError(tr("Invalid source database reference")), );
54 SAFE_POINT_EXT(dstDbiRef.isValid(), setError(tr("Invalid destination database reference")), );
55 }
56
prepare()57 void CloneAssemblyWithReferenceToDbiTask::prepare() {
58 AssemblyObject *assemblyObject = new AssemblyObject(assembly.visualName, U2EntityRef(srcDbiRef, assembly.id));
59 cloneAssemblyTask = new CloneObjectTask(assemblyObject, dstDbiRef, dstFolder);
60 addSubTask(cloneAssemblyTask);
61
62 U2SequenceObject *sequenceObject = new U2SequenceObject(reference.visualName, U2EntityRef(srcDbiRef, reference.id));
63 cloneReferenceTask = new CloneObjectTask(sequenceObject, dstDbiRef, dstFolder);
64 addSubTask(cloneReferenceTask);
65 }
66
run()67 void CloneAssemblyWithReferenceToDbiTask::run() {
68 delete cloneAssemblyTask->getSourceObject();
69 delete cloneReferenceTask->getSourceObject();
70
71 QScopedPointer<GObject> clonedObject(cloneAssemblyTask->takeResult());
72 SAFE_POINT_EXT(nullptr != clonedObject, setError(tr("Can't get the cloned object")), );
73 QScopedPointer<AssemblyObject> clonedAssemblyObject(qobject_cast<AssemblyObject *>(clonedObject.data()));
74 SAFE_POINT_EXT(nullptr != clonedAssemblyObject, setError(tr("Unexpected result object: expect AssemblyObject, got %1 object").arg(clonedObject->getGObjectType())), );
75 clonedObject.take();
76
77 clonedObject.reset(cloneReferenceTask->takeResult());
78 SAFE_POINT_EXT(nullptr != clonedObject, setError(tr("Can't get the cloned object")), );
79 QScopedPointer<U2SequenceObject> clonedSequenceObject(qobject_cast<U2SequenceObject *>(clonedObject.data()));
80 SAFE_POINT_EXT(nullptr != clonedSequenceObject, setError(tr("Unexpected result object: expect U2SequenceObject, got %1 object").arg(clonedObject->getGObjectType())), );
81 clonedObject.take();
82
83 DbiConnection con(dstDbiRef, stateInfo);
84 CHECK_OP(stateInfo, );
85
86 U2Assembly clonedAssembly = con.dbi->getAssemblyDbi()->getAssemblyObject(clonedAssemblyObject->getEntityRef().entityId, stateInfo);
87 CHECK_OP(stateInfo, );
88 U2Sequence clonedSequence = con.dbi->getSequenceDbi()->getSequenceObject(clonedSequenceObject->getEntityRef().entityId, stateInfo);
89 CHECK_OP(stateInfo, );
90
91 clonedAssembly.referenceId = clonedSequence.id;
92 con.dbi->getAssemblyDbi()->updateAssemblyObject(clonedAssembly, stateInfo);
93 }
94
95 } // namespace U2
96