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 "ConvertSnpeffVariationsToAnnotationsWorker.h"
23
24 #include <U2Core/AnnotationTableObject.h>
25 #include <U2Core/AppContext.h>
26 #include <U2Core/BaseDocumentFormats.h>
27 #include <U2Core/Formatters.h>
28 #include <U2Core/GUrlUtils.h>
29 #include <U2Core/L10n.h>
30 #include <U2Core/TaskSignalMapper.h>
31 #include <U2Core/U2SafePoints.h>
32
33 #include <U2Designer/DelegateEditors.h>
34
35 #include <U2Formats/ConvertSnpeffVariationsToAnnotationsTask.h>
36
37 #include <U2Lang/ActorPrototypeRegistry.h>
38 #include <U2Lang/BaseActorCategories.h>
39 #include <U2Lang/BaseAttributes.h>
40 #include <U2Lang/BasePorts.h>
41 #include <U2Lang/BaseSlots.h>
42 #include <U2Lang/BaseTypes.h>
43 #include <U2Lang/URLAttribute.h>
44 #include <U2Lang/WorkflowEnv.h>
45 #include <U2Lang/WorkflowMonitor.h>
46
47 namespace U2 {
48 namespace LocalWorkflow {
49
50 static const QString IN_VARIATIONS_URL_PORT_ID = "in-variations-url";
51
ConvertSnpeffVariationsToAnnotationsPrompter(Actor * actor)52 ConvertSnpeffVariationsToAnnotationsPrompter::ConvertSnpeffVariationsToAnnotationsPrompter(Actor *actor)
53 : PrompterBase<ConvertSnpeffVariationsToAnnotationsPrompter>(actor) {
54 }
55
composeRichDoc()56 QString ConvertSnpeffVariationsToAnnotationsPrompter::composeRichDoc() {
57 IntegralBusPort *input = qobject_cast<IntegralBusPort *>(target->getPort(IN_VARIATIONS_URL_PORT_ID));
58 SAFE_POINT(nullptr != input, "No input port", "");
59 const Actor *producer = input->getProducer(BaseSlots::URL_SLOT().getId());
60 const QString unsetStr = "<font color='red'>" + tr("unset") + "</font>";
61 const QString producerName = (nullptr != producer) ? producer->getLabel() : unsetStr;
62 return tr("Parses information in variations from <u>%1</u> into annotations.").arg(producerName);
63 }
64
65 const QString ConvertSnpeffVariationsToAnnotationsFactory::ACTOR_ID = "convert-snpeff-variations-to-annotations";
66
ConvertSnpeffVariationsToAnnotationsFactory()67 ConvertSnpeffVariationsToAnnotationsFactory::ConvertSnpeffVariationsToAnnotationsFactory()
68 : DomainFactory(ACTOR_ID) {
69 }
70
createWorker(Actor * actor)71 Worker *ConvertSnpeffVariationsToAnnotationsFactory::createWorker(Actor *actor) {
72 return new ConvertSnpeffVariationsToAnnotationsWorker(actor);
73 }
74
init()75 void ConvertSnpeffVariationsToAnnotationsFactory::init() {
76 QList<PortDescriptor *> ports;
77 {
78 Descriptor inDesc(IN_VARIATIONS_URL_PORT_ID,
79 ConvertSnpeffVariationsToAnnotationsWorker::tr("Input URL"),
80 ConvertSnpeffVariationsToAnnotationsWorker::tr("Input variation file URL."));
81
82 QMap<Descriptor, DataTypePtr> inType;
83 inType[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
84
85 ports << new PortDescriptor(inDesc, DataTypePtr(new MapDataType(ACTOR_ID + "-in", inType)), true /*input*/);
86 }
87
88 DocumentFormatConstraints constraints;
89 constraints.supportedObjectTypes.insert(GObjectTypes::ANNOTATION_TABLE);
90 constraints.addFlagToSupport(DocumentFormatFlag_SupportWriting);
91 constraints.addFlagToExclude(DocumentFormatFlag_CannotBeCreated);
92 QList<DocumentFormatId> supportedFormats = AppContext::getDocumentFormatRegistry()->selectFormats(constraints);
93
94 QList<Attribute *> attributes;
95 {
96 attributes << new Attribute(BaseAttributes::URL_OUT_ATTRIBUTE(), BaseTypes::STRING_TYPE(), false, "");
97
98 const DocumentFormatId format = (supportedFormats.contains(BaseDocumentFormats::PLAIN_GENBANK) ? BaseDocumentFormats::PLAIN_GENBANK : supportedFormats.first());
99 Attribute *documentFormatAttribute = new Attribute(BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE(), BaseTypes::STRING_TYPE(), false, format);
100 documentFormatAttribute->addRelation(new FileExtensionRelation(BaseAttributes::URL_OUT_ATTRIBUTE().getId()));
101 attributes << documentFormatAttribute;
102 }
103
104 Descriptor desc(ACTOR_ID,
105 ConvertSnpeffVariationsToAnnotationsWorker::tr("Convert SnpEff Variations to Annotations"),
106 ConvertSnpeffVariationsToAnnotationsWorker::tr("Parses information, added to variations by SnpEff, into standard annotations."));
107 ActorPrototype *proto = new IntegralBusActorPrototype(desc, ports, attributes);
108 proto->setPrompter(new ConvertSnpeffVariationsToAnnotationsPrompter(nullptr));
109 WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_VARIATION_ANALYSIS(), proto);
110
111 QMap<QString, PropertyDelegate *> delegates;
112 {
113 DelegateTags tags;
114 tags.set(DelegateTags::PLACEHOLDER_TEXT, ConvertSnpeffVariationsToAnnotationsWorker::tr("Produced from the input file name"));
115 delegates[BaseAttributes::URL_OUT_ATTRIBUTE().getId()] = new URLDelegate(tags, "", "");
116
117 QVariantMap map;
118 for (const DocumentFormatId &formatId : qAsConst(supportedFormats)) {
119 map[formatId] = formatId;
120 }
121 auto formatDelegate = new ComboBoxDelegate(map);
122 formatDelegate->setItemTextFormatter(QSharedPointer<StringFormatter>(new DocumentNameByIdFormatter()));
123 formatDelegate->setSortFlag(true);
124 delegates[BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE().getId()] = formatDelegate;
125 }
126 proto->setEditor(new DelegateEditor(delegates));
127
128 DomainFactory *localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
129 localDomain->registerEntry(new ConvertSnpeffVariationsToAnnotationsFactory());
130 }
131
ConvertSnpeffVariationsToAnnotationsWorker(Actor * actor)132 ConvertSnpeffVariationsToAnnotationsWorker::ConvertSnpeffVariationsToAnnotationsWorker(Actor *actor)
133 : BaseWorker(actor),
134 input(nullptr) {
135 }
136
init()137 void ConvertSnpeffVariationsToAnnotationsWorker::init() {
138 input = ports.value(IN_VARIATIONS_URL_PORT_ID);
139 }
140
tick()141 Task *ConvertSnpeffVariationsToAnnotationsWorker::tick() {
142 if (input->hasMessage()) {
143 return createTask(getMessageAndSetupScriptValues(input));
144 } else if (input->isEnded()) {
145 setDone();
146 }
147 return nullptr;
148 }
149
cleanup()150 void ConvertSnpeffVariationsToAnnotationsWorker::cleanup() {
151 }
152
sl_taskFinished(Task * task)153 void ConvertSnpeffVariationsToAnnotationsWorker::sl_taskFinished(Task *task) {
154 LoadConvertAndSaveSnpeffVariationsToAnnotationsTask *convertTask = qobject_cast<LoadConvertAndSaveSnpeffVariationsToAnnotationsTask *>(task);
155 SAFE_POINT(nullptr != convertTask, L10N::nullPointerError("LoadConvertAndSaveSnpeffVariationsToAnnotationsTask"), );
156 CHECK(!convertTask->hasError() && !convertTask->isCanceled(), );
157 monitor()->addOutputFile(convertTask->getResultUrl(), getActorId());
158 }
159
createTask(const Message & message)160 Task *ConvertSnpeffVariationsToAnnotationsWorker::createTask(const Message &message) {
161 QVariantMap data = message.getData().toMap();
162 const QString variationsFileurl = data[BaseSlots::URL_SLOT().getId()].toString();
163 const QString formatId = actor->getParameter(BaseAttributes::DOCUMENT_FORMAT_ATTRIBUTE().getId())->getAttributeValue<QString>(context);
164 QString annotationsFileUrl = actor->getParameter(BaseAttributes::URL_OUT_ATTRIBUTE().getId())->getAttributeValue<QString>(context);
165 if (annotationsFileUrl.isEmpty()) {
166 annotationsFileUrl = context->getMetadataStorage().get(message.getMetadataId()).getFileUrl();
167 const GUrl sourceUrl = GUrlUtils::changeFileExt(annotationsFileUrl, formatId);
168 annotationsFileUrl = GUrlUtils::rollFileName(context->workingDir() + sourceUrl.baseFileName() + "_variants." + sourceUrl.completeFileSuffix(), "_");
169 }
170 Task *task = new LoadConvertAndSaveSnpeffVariationsToAnnotationsTask(variationsFileurl, context->getDataStorage()->getDbiRef(), annotationsFileUrl, formatId);
171 connect(new TaskSignalMapper(task), SIGNAL(si_taskFinished(Task *)), SLOT(sl_taskFinished(Task *)));
172 return task;
173 }
174
175 } // namespace LocalWorkflow
176 } // namespace U2
177