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 /** Set of wrappers for typical workflow tasks */
23 
24 #ifndef _SIMPLE_WORKFLOW_TASK_H_
25 #define _SIMPLE_WORKFLOW_TASK_H_
26 
27 #include <QTemporaryFile>
28 
29 #include <U2Core/DocumentModel.h>
30 #include <U2Core/DocumentProviderTask.h>
31 #include <U2Core/MultipleSequenceAlignment.h>
32 #include <U2Core/SaveDocumentTask.h>
33 #include <U2Core/Task.h>
34 
35 #include <U2Lang/Schema.h>
36 #include <U2Lang/WorkflowIOTasks.h>
37 
38 namespace U2 {
39 
40 using namespace Workflow;
41 
42 class CmdlineTaskRunner;
43 class LoadDocumentTask;
44 class MultipleSequenceAlignmentObject;
45 
46 class U2LANG_EXPORT SimpleInOutWorkflowTaskConfig {
47 public:
48     SimpleInOutWorkflowTaskConfig();
49     QList<GObject *> objects;
50     DocumentFormatId inFormat;
51     QVariantMap inDocHints;
52     DocumentFormatId outFormat;
53     QVariantMap outDocHints;
54     QStringList extraArgs;
55     QString schemaName;
56     bool emptyResultPossible;
57 };
58 
59 /**
60     Runs workflow in a separate process and handles in-out parameters.
61     The result is output document.
62     If problems occur during the workflow execution, only the first error is detected and warnings are skipped.
63 */
64 class U2LANG_EXPORT SimpleInOutWorkflowTask : public DocumentProviderTask {
65     Q_OBJECT
66 public:
67     SimpleInOutWorkflowTask(const SimpleInOutWorkflowTaskConfig &conf);
68     void prepare();
69     virtual QList<Task *> onSubTaskFinished(Task *subTask);
70 
71 private:
72     void prepareTmpFile(QTemporaryFile &tmpFile, const QString &tmpl);
73 
74     SimpleInOutWorkflowTaskConfig conf;
75 
76     Document *inDoc;
77 
78     SaveDocumentTask *saveInputTask;
79     QTemporaryFile inputTmpFile;
80 
81     CmdlineTaskRunner *runWorkflowTask;
82 
83     QTemporaryFile resultTmpFile;
84     LoadDocumentTask *loadResultTask;
85 
86     QString schemaPath;
87 };
88 
89 class SimpleMSAWorkflowTaskConfig {
90 public:
91     QString schemaName;
92     QStringList schemaArgs;
93     QVariantMap resultDocHints;
94 };
95 
96 class U2LANG_EXPORT SimpleMSAWorkflow4GObjectTask : public Task {
97     Q_OBJECT
98 
99 public:
100     SimpleMSAWorkflow4GObjectTask(const QString &taskName, MultipleSequenceAlignmentObject *maObj, const SimpleMSAWorkflowTaskConfig &conf);
101 
102     void prepare();
103     ReportResult report();
104     MultipleSequenceAlignment getResult();
105 
106 private:
107     QPointer<MultipleSequenceAlignmentObject> msaObjectPointer;
108     QString docName;
109     SimpleMSAWorkflowTaskConfig conf;
110     SimpleInOutWorkflowTask *runWorkflowTask;
111     QPointer<StateLock> msaObjectLock;
112 };
113 
114 }  // namespace U2
115 
116 #endif  // #ifndef _RUN_SCHEMA_FOR_TASK_H_
117