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 "WorkflowCMDLineTasks.h"
23
24 #include <QFile>
25
26 #include <U2Core/AppContext.h>
27 #include <U2Core/CMDLineCoreOptions.h>
28 #include <U2Core/CMDLineRegistry.h>
29 #include <U2Core/CMDLineUtils.h>
30 #include <U2Core/Counter.h>
31 #include <U2Core/L10n.h>
32 #include <U2Core/Log.h>
33 #include <U2Core/Settings.h>
34
35 #include <U2Lang/URLAttribute.h>
36 #include <U2Lang/WorkflowEnv.h>
37 #include <U2Lang/WorkflowManager.h>
38 #include <U2Lang/WorkflowRunTask.h>
39 #include <U2Lang/WorkflowUtils.h>
40
41 #include "WorkflowDesignerPlugin.h"
42
43 #define WORKFLOW_CMDLINE_TASK_LOG_CAT "Workflow cmdline tasks"
44
45 namespace U2 {
46
47 /*******************************************
48 * WorkflowRunFromCMDLineBase
49 *******************************************/
WorkflowRunFromCMDLineBase()50 WorkflowRunFromCMDLineBase::WorkflowRunFromCMDLineBase()
51 : Task(tr("Workflow run from cmdline"), TaskFlag_None),
52 schema(nullptr),
53 optionsStartAt(-1),
54 loadTask(nullptr),
55 workflowRunTask(nullptr) {
56 GCOUNTER(cvar, "workflow_run_from_cmdline");
57
58 CMDLineRegistry *cmdLineRegistry = AppContext::getCMDLineRegistry();
59
60 // try to process schema without 'task' option (it can only be the first one)
61 QStringList pureValues = CMDLineRegistryUtils::getPureValues();
62 if (!pureValues.isEmpty()) {
63 QString schemaName = pureValues.first();
64 processLoadSchemaTask(schemaName, 1); // because after program name
65 }
66 if (loadTask != nullptr) {
67 addSubTask(loadTask);
68 return;
69 }
70
71 // process schema with 'task' option
72 int taskOptionIdx = CMDLineRegistryUtils::getParameterIndex(WorkflowDesignerPlugin::RUN_WORKFLOW);
73 if (taskOptionIdx != -1) {
74 processLoadSchemaTask(cmdLineRegistry->getParameterValue(WorkflowDesignerPlugin::RUN_WORKFLOW, taskOptionIdx), taskOptionIdx);
75 }
76 if (loadTask == nullptr) {
77 setError(tr("no task to run"));
78 return;
79 }
80 addSubTask(loadTask);
81 }
82
processLoadSchemaTask(const QString & schemaNameCandidate,int optionIdx)83 void WorkflowRunFromCMDLineBase::processLoadSchemaTask(const QString &schemaNameCandidate, int optionIdx) {
84 loadTask = prepareLoadSchemaTask(schemaNameCandidate);
85 if (loadTask != nullptr) {
86 schemaName = schemaNameCandidate;
87 optionsStartAt = optionIdx + 1;
88 }
89 }
90
prepareLoadSchemaTask(const QString & schemaName)91 LoadWorkflowTask *WorkflowRunFromCMDLineBase::prepareLoadSchemaTask(const QString &schemaName) {
92 QString pathToSchema = WorkflowUtils::findPathToSchemaFile(schemaName);
93 if (pathToSchema.isEmpty()) {
94 coreLog.error(tr("Cannot find workflow: %1").arg(schemaName));
95 return nullptr;
96 }
97
98 schema = QSharedPointer<Schema>::create();
99 schema->setDeepCopyFlag(true);
100 return new LoadWorkflowTask(schema, nullptr, pathToSchema);
101 }
102
setSchemaCMDLineOptions(Schema * schema,int optionsStartAtIdx)103 static void setSchemaCMDLineOptions(Schema *schema, int optionsStartAtIdx) {
104 assert(schema != nullptr && optionsStartAtIdx > 0);
105
106 QList<StrStrPair> parameters = AppContext::getCMDLineRegistry()->getParameters();
107 int sz = parameters.size();
108 for (int i = optionsStartAtIdx; i < sz; ++i) {
109 const StrStrPair ¶m = parameters.at(i);
110 if (param.first.isEmpty()) { // TODO: unnamed parameters not supported yet
111 continue;
112 }
113
114 QString paramAlias = param.first;
115 QString paramName;
116 Actor *actor = WorkflowUtils::findActorByParamAlias(schema->getProcesses(), paramAlias, paramName);
117 if (actor == nullptr) {
118 assert(paramName.isEmpty());
119 coreLog.details(WorkflowRunFromCMDLineBase::tr("alias '%1' not set in workflow").arg(paramAlias));
120 continue;
121 }
122
123 Attribute *attr = actor->getParameter(paramName);
124 if (attr == nullptr) {
125 coreLog.error(WorkflowRunFromCMDLineBase::tr("actor parameter '%1' not found").arg(paramName));
126 continue;
127 }
128
129 DataTypeValueFactory *valueFactory = WorkflowEnv::getDataTypeValueFactoryRegistry()->getById(attr->getAttributeType()->getId());
130 if (valueFactory == nullptr) {
131 coreLog.error(WorkflowRunFromCMDLineBase::tr("cannot parse value from '%1'").arg(param.second));
132 continue;
133 }
134
135 ActorId id = actor->getId();
136 bool isOk;
137 QVariant value = valueFactory->getValueFromString(param.second, &isOk);
138 if (!isOk) {
139 coreLog.error(WorkflowRunFromCMDLineBase::tr("Incorrect value for '%1', null or default value passed to workflow").arg(param.first));
140 continue;
141 }
142 attr->setAttributeValue(value);
143 }
144 }
145
onSubTaskFinished(Task * subTask)146 QList<Task *> WorkflowRunFromCMDLineBase::onSubTaskFinished(Task *subTask) {
147 assert(subTask != nullptr);
148 QList<Task *> res;
149
150 propagateSubtaskError();
151 if (hasError() || isCanceled()) {
152 return res;
153 }
154 assert(!hasError()); // if error, we won't be here
155
156 if (loadTask == subTask) {
157 const QSharedPointer<Schema> schema = loadTask->getSchema();
158 assert(schema != nullptr);
159 remapping = loadTask->getRemapping();
160
161 setSchemaCMDLineOptions(schema.get(), optionsStartAt);
162 if (schema->getDomain().isEmpty()) {
163 QList<QString> domainsId = WorkflowEnv::getDomainRegistry()->getAllIds();
164 assert(!domainsId.isEmpty());
165 if (!domainsId.isEmpty()) {
166 schema->setDomain(domainsId.first());
167 }
168 }
169
170 QStringList l;
171 bool good = WorkflowUtils::validate(*schema, l);
172 if (!good) {
173 QString schemaHelpStr = QString("\n\nsee 'ugene --help=%1' for details").arg(schemaName);
174 setError("\n\n" + l.join("\n\n") + schemaHelpStr);
175 return res;
176 }
177
178 workflowRunTask = getWorkflowRunTask();
179 res << workflowRunTask;
180 }
181 return res;
182 }
183
run()184 void WorkflowRunFromCMDLineBase::run() {
185 CMDLineRegistry *cmdLineRegistry = AppContext::getCMDLineRegistry();
186 SAFE_POINT(nullptr != cmdLineRegistry, "CMDLineRegistry is NULL", );
187 CHECK(nullptr != workflowRunTask, );
188
189 const QString reportFilePath = cmdLineRegistry->getParameterValue(CmdlineTaskRunner::REPORT_FILE_ARG);
190 CHECK(!reportFilePath.isEmpty(), );
191
192 QFile reportFile(reportFilePath);
193 const bool opened = reportFile.open(QIODevice::WriteOnly);
194 CHECK_EXT(opened, setError(L10N::errorOpeningFileWrite(reportFilePath)), );
195
196 reportFile.write(workflowRunTask->generateReport().toLocal8Bit());
197 }
198
199 /*******************************************
200 * WorkflowRunFromCMDLineTask
201 *******************************************/
getWorkflowRunTask() const202 Task *WorkflowRunFromCMDLineTask::getWorkflowRunTask() const {
203 return new WorkflowRunTask(*schema, remapping);
204 }
205
206 } // namespace U2
207