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 "GenericReadActor.h"
23 #include <limits.h>
24
25 #include <QFileInfo>
26
27 #include <U2Core/AppContext.h>
28 #include <U2Core/DNAInfo.h>
29 #include <U2Core/DNASequenceObject.h>
30 #include <U2Core/DocumentModel.h>
31 #include <U2Core/GObjectTypes.h>
32
33 #include <U2Designer/DelegateEditors.h>
34
35 #include <U2Gui/DialogUtils.h>
36 #include <U2Gui/GUIUtils.h>
37
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/CoreLibConstants.h>
44 #include <U2Lang/URLAttribute.h>
45 #include <U2Lang/WorkflowEnv.h>
46
47 #include "CoreLib.h"
48 #include "DocActors.h"
49 #include "util/DatasetValidator.h"
50
51 /* TRANSLATOR U2::Workflow::SeqReadPrompter */
52 /* TRANSLATOR U2::Workflow::CoreLib */
53
54 namespace U2 {
55 namespace Workflow {
56
57 /************************************************************************/
58 /* GenericReadDocProto */
59 /************************************************************************/
GenericReadDocProto(const Descriptor & desc)60 GenericReadDocProto::GenericReadDocProto(const Descriptor &desc)
61 : ReadDbObjActorPrototype(desc) {
62 {
63 attrs << new URLAttribute(BaseAttributes::URL_IN_ATTRIBUTE(),
64 BaseTypes::URL_DATASETS_TYPE(),
65 true);
66 }
67
68 setEditor(new DelegateEditor(QMap<QString, PropertyDelegate *>()));
69
70 if (AppContext::isGUIMode()) {
71 setIcon(QIcon(":/U2Designer/images/blue_circle.png"));
72 }
73
74 setValidator(new DatasetValidator());
75 }
76
77 const QString GenericSeqActorProto::MODE_ATTR("mode");
78 const QString GenericSeqActorProto::GAP_ATTR("merge-gap");
79 const QString GenericSeqActorProto::ACC_ATTR("accept-accession");
80 const QString GenericSeqActorProto::LIMIT_ATTR("sequence-count-limit");
81
82 const QString GenericSeqActorProto::TYPE("generic.seq");
83 const QString GenericMAActorProto::TYPE("generic.ma");
84
GenericSeqActorProto()85 GenericSeqActorProto::GenericSeqActorProto()
86 : GenericReadDocProto(CoreLibConstants::GENERIC_READ_SEQ_PROTO_ID) {
87 setCompatibleDbObjectTypes(QSet<GObjectType>() << GObjectTypes::SEQUENCE);
88
89 setDisplayName(U2::Workflow::CoreLib::tr("Read Sequence"));
90 desc = U2::Workflow::CoreLib::tr("Input one or several files with nucleotide or protein sequences."
91 " A file may also contain annotations. Any format, supported by UGENE, is allowed (GenBank, FASTA, etc.)."
92 " The element outputs message(s) with the sequence and annotations data.");
93 QMap<Descriptor, DataTypePtr> m;
94 m[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
95 m[BaseSlots::DATASET_SLOT()] = BaseTypes::STRING_TYPE();
96 m[BaseSlots::DNA_SEQUENCE_SLOT()] = BaseTypes::DNA_SEQUENCE_TYPE();
97 m[BaseSlots::ANNOTATION_TABLE_SLOT()] = BaseTypes::ANNOTATION_TABLE_TYPE();
98
99 DataTypePtr seqTypeset(new MapDataType(Descriptor(TYPE), m));
100 bool treg = WorkflowEnv::getDataTypeRegistry()->registerEntry(seqTypeset);
101 Q_UNUSED(treg);
102 assert(treg);
103
104 ports << new PortDescriptor(Descriptor(BasePorts::OUT_SEQ_PORT_ID(), U2::Workflow::CoreLib::tr("Sequence"), U2::Workflow::CoreLib::tr("A sequence of any type (nucleotide, protein).")),
105 seqTypeset,
106 false,
107 true);
108 {
109 Descriptor md(GenericSeqActorProto::MODE_ATTR, SeqReadPrompter::tr("Mode"), SeqReadPrompter::tr("If the file contains more than one sequence, <i>Split</i> mode sends them \"as is\" to the output, "
110 "while <i>Merge</i> appends all the sequences and outputs the sole merged sequence."));
111 Descriptor gd(GenericSeqActorProto::GAP_ATTR, SeqReadPrompter::tr("Merging gap"), SeqReadPrompter::tr("In <i>Merge</i> mode, the specified number of gaps are inserted between the original sequences. "
112 "This is helpful, for example, to avoid finding false positives at the merge boundaries."));
113 Descriptor acd(GenericSeqActorProto::ACC_ATTR, SeqReadPrompter::tr("Accession filter"), SeqReadPrompter::tr("Reports only sequences containing the specified regular expression."
114 "<p><i>Leave it empty to switch off this filter. Use <b>*</b> to mask many symbol and use <b>?</b> to mask one symbol.</i></p>"));
115 Descriptor ld(LIMIT_ATTR, SeqReadPrompter::tr("Sequence count limit"), SeqReadPrompter::tr("<i>Split mode</i> only."
116 "<p>Read only first N sequences from each file."
117 "<br>Set 0 value for reading all sequences.</p>"));
118
119 attrs << new Attribute(md, BaseTypes::NUM_TYPE(), true, SPLIT);
120 attrs << new Attribute(gd, BaseTypes::NUM_TYPE(), false, 10);
121 attrs << new Attribute(ld, BaseTypes::NUM_TYPE(), false, 0);
122 attrs << new Attribute(acd, BaseTypes::STRING_TYPE(), false, QString());
123 }
124
125 QMap<QString, PropertyDelegate *> delegates;
126 {
127 QVariantMap modeMap;
128 QString splitStr = SeqReadPrompter::tr("Split");
129 QString mergeStr = SeqReadPrompter::tr("Merge");
130 modeMap[splitStr] = SPLIT;
131 modeMap[mergeStr] = MERGE;
132 getEditor()->addDelegate(new ComboBoxDelegate(modeMap), MODE_ATTR);
133 }
134 {
135 QVariantMap minMaxMap;
136 minMaxMap["minimum"] = 0;
137 minMaxMap["maximum"] = INT_MAX;
138 getEditor()->addDelegate(new SpinBoxDelegate(minMaxMap), GAP_ATTR);
139 getEditor()->addDelegate(new SpinBoxDelegate(minMaxMap), LIMIT_ATTR);
140 }
141 setPrompter(new ReadDocPrompter(U2::Workflow::CoreLib::tr("Reads sequence(s) from <u>%1</u>.")));
142
143 QString seqSlotId = BasePorts::OUT_SEQ_PORT_ID() + "." + BaseSlots::DNA_SEQUENCE_SLOT().getId();
144 QString annsSlotId = BasePorts::OUT_SEQ_PORT_ID() + "." + BaseSlots::ANNOTATION_TABLE_SLOT().getId();
145 }
146
GenericMAActorProto()147 GenericMAActorProto::GenericMAActorProto()
148 : GenericReadDocProto(CoreLibConstants::GENERIC_READ_MA_PROTO_ID) {
149 setCompatibleDbObjectTypes(QSet<GObjectType>() << GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT);
150
151 setDisplayName(U2::Workflow::CoreLib::tr("Read Alignment"));
152 desc = U2::Workflow::CoreLib::tr("Input one or several files in one of the multiple sequence alignment formats, supported by UGENE (ClustalW, FASTA, etc.)."
153 " The element outputs message(s) with the alignment data.");
154
155 QMap<Descriptor, DataTypePtr> m;
156 m[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
157 m[BaseSlots::DATASET_SLOT()] = BaseTypes::STRING_TYPE();
158 m[BaseSlots::MULTIPLE_ALIGNMENT_SLOT()] = BaseTypes::MULTIPLE_ALIGNMENT_TYPE();
159 DataTypePtr blockTypeset(new MapDataType(Descriptor(TYPE), m));
160 bool treg = WorkflowEnv::getDataTypeRegistry()->registerEntry(blockTypeset);
161 Q_UNUSED(treg);
162 assert(treg);
163
164 ports << new PortDescriptor(Descriptor(BasePorts::OUT_MSA_PORT_ID(), U2::Workflow::CoreLib::tr("Multiple sequence alignment"), ""),
165 blockTypeset,
166 false,
167 true);
168
169 setPrompter(new ReadDocPrompter(U2::Workflow::CoreLib::tr("Reads MSA(s) from <u>%1</u>.")));
170
171 if (AppContext::isGUIMode()) {
172 setIcon(QIcon(":/U2Designer/images/blue_circle.png"));
173 }
174 }
175
isAcceptableDrop(const QMimeData * md,QVariantMap * params) const176 bool GenericMAActorProto::isAcceptableDrop(const QMimeData *md, QVariantMap *params) const {
177 QList<DocumentFormat *> fs;
178 QString url = WorkflowUtils::getDropUrl(fs, md);
179 foreach (DocumentFormat *f, fs) {
180 if (f->getSupportedObjectTypes().contains(GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT)) {
181 if (params != nullptr) {
182 params->insert(BaseAttributes::URL_IN_ATTRIBUTE().getId(), url);
183 }
184 return true;
185 }
186 }
187 /*DocumentFormatConstraints sc;
188 sc.supportedObjectTypes.append(GObjectTypes::SEQUENCE);
189 foreach(DocumentFormat* f, fs) {
190 if (f->checkConstraints(sc)) {
191 if (params) {
192 params->insert(CoreLib::URL_ATTR_ID, url);
193 }
194 return true;
195 }
196 }*/
197 if (QFileInfo(url).isDir()) {
198 if (params) {
199 params->insert(BaseAttributes::URL_IN_ATTRIBUTE().getId(), url + "/*");
200 }
201 return true;
202 }
203
204 return false;
205 }
206
isAcceptableDrop(const QMimeData * md,QVariantMap * params) const207 bool GenericSeqActorProto::isAcceptableDrop(const QMimeData *md, QVariantMap *params) const {
208 QList<DocumentFormat *> fs;
209 const GObjectMimeData *gomd = qobject_cast<const GObjectMimeData *>(md);
210 if (gomd && params) {
211 const U2SequenceObject *obj = qobject_cast<const U2SequenceObject *>(gomd->objPtr.data());
212 if (obj) {
213 params->insert(BaseAttributes::URL_IN_ATTRIBUTE().getId(), obj->getDocument()->getURLString());
214 QString acc = obj->getStringAttribute(DNAInfo::ACCESSION);
215 if (acc.isEmpty()) {
216 acc = obj->getSequenceName();
217 }
218 params->insert(ACC_ATTR, acc);
219 }
220 }
221
222 QString url = WorkflowUtils::getDropUrl(fs, md);
223 foreach (DocumentFormat *f, fs) {
224 if (f->getSupportedObjectTypes().contains(GObjectTypes::SEQUENCE)) {
225 if (params) {
226 params->insert(BaseAttributes::URL_IN_ATTRIBUTE().getId(), url);
227 }
228 return true;
229 }
230 }
231 if (QFileInfo(url).isDir()) {
232 if (params) {
233 params->insert(BaseAttributes::URL_IN_ATTRIBUTE().getId(), url + "/*");
234 }
235 return true;
236 }
237
238 return false;
239 }
240
composeRichDoc()241 QString SeqReadPrompter::composeRichDoc() {
242 // TODO finish
243 // BusPort* input = qobject_cast<BusPort*>(target->getPort(CoreLib::DATA_PORT_ID));
244 QString url = getURL(BaseAttributes::URL_IN_ATTRIBUTE().getId());
245 return QString("%1").arg(url);
246 }
247
248 } // namespace Workflow
249 } // namespace U2
250
