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 "ClustalOWorker.h"
23
24 #include <U2Core/AppContext.h>
25 #include <U2Core/AppResources.h>
26 #include <U2Core/AppSettings.h>
27 #include <U2Core/Log.h>
28 #include <U2Core/UserApplicationsSettings.h>
29
30 #include <U2Designer/DelegateEditors.h>
31
32 #include <U2Lang/ActorPrototypeRegistry.h>
33 #include <U2Lang/BaseActorCategories.h>
34 #include <U2Lang/BasePorts.h>
35 #include <U2Lang/BaseSlots.h>
36 #include <U2Lang/BaseTypes.h>
37 #include <U2Lang/IntegralBusModel.h>
38 #include <U2Lang/NoFailTaskWrapper.h>
39 #include <U2Lang/WorkflowEnv.h>
40
41 #include "ClustalOSupport.h"
42 #include "TaskLocalStorage.h"
43
44 namespace U2 {
45 namespace LocalWorkflow {
46
47 /****************************
48 * ClustalOWorkerFactory
49 ****************************/
50 const QString ClustalOWorkerFactory::ACTOR_ID("ClustalO");
51
52 static const QString NUM_ITERATIONS("num-iterations");
53 static const QString MAX_GT_ITERATIONS("max-guidetree-iterations");
54 static const QString MAX_HMM_ITERATIONS("max-hmm-iterations");
55 static const QString SET_AUTO("set-auto");
56 static const QString EXT_TOOL_PATH("path");
57 static const QString TMP_DIR_PATH("temp-dir");
58
init()59 void ClustalOWorkerFactory::init() {
60 QList<PortDescriptor *> p;
61 QList<Attribute *> a;
62 Descriptor ind(BasePorts::IN_MSA_PORT_ID(), ClustalOWorker::tr("Input MSA"), ClustalOWorker::tr("Input MSA to process."));
63 Descriptor oud(BasePorts::OUT_MSA_PORT_ID(), ClustalOWorker::tr("ClustalO result MSA"), ClustalOWorker::tr("The result of the ClustalO alignment."));
64
65 QMap<Descriptor, DataTypePtr> inM;
66 inM[BaseSlots::MULTIPLE_ALIGNMENT_SLOT()] = BaseTypes::MULTIPLE_ALIGNMENT_TYPE();
67 p << new PortDescriptor(ind, DataTypePtr(new MapDataType("clustal.in.msa", inM)), true /*input*/);
68 QMap<Descriptor, DataTypePtr> outM;
69 outM[BaseSlots::MULTIPLE_ALIGNMENT_SLOT()] = BaseTypes::MULTIPLE_ALIGNMENT_TYPE();
70 p << new PortDescriptor(oud, DataTypePtr(new MapDataType("clustal.out.msa", outM)), false /*input*/, true /*multi*/);
71
72 Descriptor ni(NUM_ITERATIONS, ClustalOWorker::tr("Number of iterations"), ClustalOWorker::tr("Number of (combined guide-tree/HMM) iterations."));
73 Descriptor ngti(MAX_GT_ITERATIONS, ClustalOWorker::tr("Number of guidetree iterations"), ClustalOWorker::tr("Maximum number guidetree iterations."));
74 Descriptor nhmmi(MAX_HMM_ITERATIONS, ClustalOWorker::tr("Number of HMM iterations"), ClustalOWorker::tr("Maximum number of HMM iterations."));
75 Descriptor sa(SET_AUTO, ClustalOWorker::tr("Set auto options"), ClustalOWorker::tr("Set options automatically (might overwrite some of your options)."));
76
77 Descriptor etp(EXT_TOOL_PATH, ClustalOWorker::tr("Tool path"), ClustalOWorker::tr("Path to the ClustalO tool."
78 "<p>The default path can be set in the UGENE application settings."));
79
80 Descriptor tdp(TMP_DIR_PATH, ClustalOWorker::tr("Temporary folder"), ClustalOWorker::tr("Folder to store temporary files."));
81
82 a << new Attribute(ni, BaseTypes::NUM_TYPE(), false, QVariant(1));
83 a << new Attribute(ngti, BaseTypes::NUM_TYPE(), false, QVariant(0));
84 a << new Attribute(nhmmi, BaseTypes::NUM_TYPE(), false, QVariant(0));
85 a << new Attribute(sa, BaseTypes::BOOL_TYPE(), false, QVariant(false));
86
87 a << new Attribute(etp, BaseTypes::STRING_TYPE(), true, QVariant("Default"));
88 a << new Attribute(tdp, BaseTypes::STRING_TYPE(), true, QVariant("Default"));
89
90 Descriptor desc(ACTOR_ID, ClustalOWorker::tr("Align with ClustalO"), ClustalOWorker::tr("Aligns multiple sequence alignments (MSAs) supplied with ClustalO."
91 "<p>ClustalO is a general purpose multiple sequence alignment program for proteins."
92 "Visit <a href=\"http://www.clustal.org/omega\">http://www.clustal.org/omega</a> to learn more about it."));
93
94 ActorPrototype *proto = new IntegralBusActorPrototype(desc, p, a);
95
96 QMap<QString, PropertyDelegate *> delegates;
97
98 {
99 QVariantMap m;
100 m["minimum"] = int(1);
101 m["maximum"] = int(1000);
102 delegates[NUM_ITERATIONS] = new SpinBoxDelegate(m);
103 }
104 {
105 QVariantMap m;
106 m["minimum"] = int(0);
107 m["maximum"] = int(1000);
108 delegates[MAX_GT_ITERATIONS] = new SpinBoxDelegate(m);
109 }
110 {
111 QVariantMap m;
112 m["minimum"] = int(0);
113 m["maximum"] = int(1000);
114 delegates[MAX_HMM_ITERATIONS] = new SpinBoxDelegate(m);
115 }
116
117 delegates[EXT_TOOL_PATH] = new URLDelegate("", "executable", false, false, false);
118 delegates[TMP_DIR_PATH] = new URLDelegate("", "TmpDir", false, true);
119
120 proto->setEditor(new DelegateEditor(delegates));
121 proto->setPrompter(new ClustalOPrompter());
122 proto->setIconPath(":external_tool_support/images/clustalo.png");
123 proto->addExternalTool(ClustalOSupport::ET_CLUSTALO_ID, EXT_TOOL_PATH);
124 WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_ALIGNMENT(), proto);
125
126 DomainFactory *localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
127 localDomain->registerEntry(new ClustalOWorkerFactory());
128 }
129
130 /****************************
131 * ClustalOPrompter
132 ****************************/
ClustalOPrompter(Actor * p)133 ClustalOPrompter::ClustalOPrompter(Actor *p)
134 : PrompterBase<ClustalOPrompter>(p) {
135 }
composeRichDoc()136 QString ClustalOPrompter::composeRichDoc() {
137 IntegralBusPort *input = qobject_cast<IntegralBusPort *>(target->getPort(BasePorts::IN_MSA_PORT_ID()));
138 Actor *producer = input->getProducer(BasePorts::IN_MSA_PORT_ID());
139 QString producerName = producer ? tr(" from %1").arg(producer->getLabel()) : "";
140 QString doc = tr("Aligns each MSA supplied <u>%1</u> with \"<u>ClustalO</u>\".")
141 .arg(producerName);
142
143 return doc;
144 }
145 /****************************
146 * ClustalOWorker
147 ****************************/
ClustalOWorker(Actor * a)148 ClustalOWorker::ClustalOWorker(Actor *a)
149 : BaseWorker(a), input(nullptr), output(nullptr) {
150 }
151
init()152 void ClustalOWorker::init() {
153 input = ports.value(BasePorts::IN_MSA_PORT_ID());
154 output = ports.value(BasePorts::OUT_MSA_PORT_ID());
155 }
156
tick()157 Task *ClustalOWorker::tick() {
158 if (input->hasMessage()) {
159 Message inputMessage = getMessageAndSetupScriptValues(input);
160 if (inputMessage.isEmpty()) {
161 output->transit();
162 return nullptr;
163 }
164 cfg.numIterations = actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context);
165 cfg.maxGuideTreeIterations = actor->getParameter(MAX_GT_ITERATIONS)->getAttributeValue<int>(context);
166 cfg.maxHMMIterations = actor->getParameter(MAX_HMM_ITERATIONS)->getAttributeValue<int>(context);
167 cfg.setAutoOptions = actor->getParameter(SET_AUTO)->getAttributeValue<bool>(context);
168 cfg.numberOfProcessors = AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount();
169
170 QString path = actor->getParameter(EXT_TOOL_PATH)->getAttributeValue<QString>(context);
171 if (QString::compare(path, "default", Qt::CaseInsensitive) != 0) {
172 AppContext::getExternalToolRegistry()->getById(ClustalOSupport::ET_CLUSTALO_ID)->setPath(path);
173 }
174 path = actor->getParameter(TMP_DIR_PATH)->getAttributeValue<QString>(context);
175 if (QString::compare(path, "default", Qt::CaseInsensitive) != 0) {
176 AppContext::getAppSettings()->getUserAppsSettings()->setUserTemporaryDirPath(path);
177 }
178 QVariantMap qm = inputMessage.getData().toMap();
179 SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
180 QScopedPointer<MultipleSequenceAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
181 SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", nullptr);
182 const MultipleSequenceAlignment msa = msaObj->getMultipleAlignment();
183
184 if (msa->isEmpty()) {
185 algoLog.error(tr("An empty MSA '%1' has been supplied to ClustalO.").arg(msa->getName()));
186 return nullptr;
187 }
188 ClustalOSupportTask *supportTask = new ClustalOSupportTask(msa, GObjectReference(), cfg);
189 supportTask->addListeners(createLogListeners());
190 Task *t = new NoFailTaskWrapper(supportTask);
191 connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
192 return t;
193 } else if (input->isEnded()) {
194 setDone();
195 output->setEnded();
196 }
197 return nullptr;
198 }
199
sl_taskFinished()200 void ClustalOWorker::sl_taskFinished() {
201 auto wrapper = qobject_cast<NoFailTaskWrapper *>(sender());
202 CHECK(wrapper->isFinished(), );
203 auto clustalOTask = qobject_cast<ClustalOSupportTask *>(wrapper->originalTask());
204 if (clustalOTask->isCanceled()) {
205 return;
206 }
207 if (clustalOTask->hasError()) {
208 coreLog.error(clustalOTask->getError());
209 return;
210 }
211
212 SAFE_POINT(output != nullptr, "NULL output!", );
213 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(clustalOTask->getResultAlignment());
214 QVariantMap msgData;
215 msgData[BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()] = qVariantFromValue<SharedDbiDataHandler>(msaId);
216 output->put(Message(BaseTypes::MULTIPLE_ALIGNMENT_TYPE(), msgData));
217 algoLog.info(tr("Aligned %1 with ClustalO").arg(clustalOTask->getResultAlignment()->getName()));
218 }
219
cleanup()220 void ClustalOWorker::cleanup() {
221 }
222
ClustalOWorkerFactory()223 ClustalOWorkerFactory::ClustalOWorkerFactory()
224 : DomainFactory(ACTOR_ID) {
225 }
226
createWorker(Actor * actor)227 Worker *ClustalOWorkerFactory::createWorker(Actor *actor) {
228 return new ClustalOWorker(actor);
229 }
230
231 } //namespace LocalWorkflow
232 } //namespace U2
233
