Package org.apache.airavata.gfac.core.handler

Examples of org.apache.airavata.gfac.core.handler.GFacHandlerException

220
221
222
223
224
225
226
227
228
229
230
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
                try {
                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
                } catch (ApplicationSettingsException e) {
                    log.error(e.getMessage());
                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
                }
            }
            delegateToMonitorHandlers(jobExecutionContext, (GsisshHostType) host, jobId);
        } catch (GFacHandlerException e) {
            throw new GFacProviderException("Error delegating already ran job to Monitoring", e);
View Full Code Here
47
48
49
50
51
52
53
54
55
56
57
58
59
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
            }
        } catch (ApplicationSettingsException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        } catch (GFacException e) {
          throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        }

        log.info("Setup SSH job directorties");
        super.invoke(jobExecutionContext);
        makeDirectory(jobExecutionContext);
View Full Code Here
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
  }
  private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
                try {
        Cluster cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
        if (cluster == null) {
            throw new GFacHandlerException("Security context is not set properly");
        } else {
            log.info("Successfully retrieved the Security Context");
        }
        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();

            String workingDirectory = app.getScratchWorkingDirectory();
            cluster.makeDirectory(workingDirectory);
            cluster.makeDirectory(app.getScratchWorkingDirectory());
            cluster.makeDirectory(app.getInputDataDirectory());
            cluster.makeDirectory(app.getOutputDataDirectory());
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            status.setTransferState(TransferState.DIRECTORY_SETUP);
            detail.setTransferStatus(status);
            detail.setTransferDescription("Working directory = " + workingDirectory);

            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
        } catch (Exception e) {
            DataTransferDetails detail = new DataTransferDetails();
            TransferStatus status = new TransferStatus();
            detail.setTransferDescription(e.getLocalizedMessage());
            status.setTransferState(TransferState.FAILED);
            detail.setTransferStatus(status);
            try {
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error executing the Handler: " + GSISSHDirectorySetupHandler.class, e);
        }
  }
View Full Code Here
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
                try {
                    GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
                } catch (ApplicationSettingsException e) {
                    log.error(e.getMessage());
                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
                }
            }
            log.info("Invoking SCPInputHandler");

            MessageContext input = jobExecutionContext.getInMessageContext();
            Set<String> parameters = input.getParameters().keySet();
            for (String paramName : parameters) {
                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
                String paramValue = MappingFactory.toString(actualParameter);
                //TODO: Review this with type
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(jobExecutionContext, paramValue);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
                    List<String> newFiles = new ArrayList<String>();
                    for (String paramValueEach : split) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            String stageInputFiles = stageInputFiles(jobExecutionContext, paramValueEach);
                            status.setTransferState(TransferState.UPLOAD);
                            detail.setTransferStatus(status);
                            detail.setTransferDescription("Input Data Staged: " + stageInputFiles);
                            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            newFiles.add(stageInputFiles);
                        }

                    }
                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                }
                inputNew.getParameters().put(paramName, actualParameter);
            }
        } catch (Exception e) {
            log.error(e.getMessage());
            status.setTransferState(TransferState.FAILED);
            detail.setTransferDescription(e.getLocalizedMessage());
            detail.setTransferStatus(status);
            try {
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
        jobExecutionContext.setInMessageContext(inputNew);
    }
View Full Code Here
168
169
170
171
172
173
174
175
                paramValue = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
            }
            cluster.scpTo(targetFile, paramValue);
            return targetFile;
        } catch (SSHApiException e) {
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
    }
View Full Code Here
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
            if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
                try {
                    GFACSSHUtils.addSecurityContext(jobExecutionContext);
                } catch (ApplicationSettingsException e) {
                    log.error(e.getMessage());
                    throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
                }
            }
            ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                    .getApplicationDeploymentDescription().getType();

            AuthenticationInfo authenticationInfo = null;
            if (password != null) {
                authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
            } else {
                authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
                        this.passPhrase);
            }
            // Server info
            ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
            Cluster pbsCluster = null;
            // here doesn't matter what the job manager is because we are only doing some file handling
            // not really dealing with monitoring or job submission, so we pa
            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, CommonUtils.getPBSJobManager("/opt/torque/torque-4.2.3.1/bin/"));
            String parentPath = inputPath + File.separator + jobExecutionContext.getExperimentID() + File.separator + jobExecutionContext.getTaskData().getTaskID();
            if (index < oldIndex) {
                parentPath = oldFiles.get(index);
                data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
            } else {
                (new File(parentPath)).mkdirs();
                StringBuffer temp = new StringBuffer(data.append(parentPath).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }
            MessageContext input = jobExecutionContext.getInMessageContext();
            Set<String> parameters = input.getParameters().keySet();
            for (String paramName : parameters) {
                ActualParameter actualParameter = (ActualParameter) input.getParameters().get(paramName);
                String paramValue = MappingFactory.toString(actualParameter);
                //TODO: Review this with type
                if ("URI".equals(actualParameter.getType().getType().toString())) {
                    if (index < oldIndex) {
                        log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                        ((URIParameterType) actualParameter.getType()).setValue(oldFiles.get(index));
                        data.append(oldFiles.get(index++)).append(","); // we get already transfered file and increment the index
                    } else {
                        String s = stageInputFiles(pbsCluster, paramValue, parentPath);
                        ((URIParameterType) actualParameter.getType()).setValue(s);
                        StringBuffer temp = new StringBuffer(data.append(s).append(",").toString());
                        GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                    }
                } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                    List<String> split = Arrays.asList(StringUtil.getElementsFromString(paramValue));
                    List<String> newFiles = new ArrayList<String>();
                    for (String paramValueEach : split) {
                        if (index < oldIndex) {
                            log.info("Input File: " + paramValue + " is already transfered, so we skip this operation !!!");
                            newFiles.add(oldFiles.get(index));
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            String stageInputFiles = stageInputFiles(pbsCluster, paramValueEach, parentPath);
                            StringBuffer temp = new StringBuffer(data.append(stageInputFiles).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                            newFiles.add(stageInputFiles);
                        }
                    }
                    ((URIArrayType) actualParameter.getType()).setValueArray(newFiles.toArray(new String[newFiles.size()]));
                }
                inputNew.getParameters().put(paramName, actualParameter);
            }
        } catch (Exception e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while input File Staging", e, e.getLocalizedMessage());
        }
        jobExecutionContext.setInMessageContext(inputNew);
    }
View Full Code Here
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
                TaskDetails taskData = null;
                try {
                    taskData = (TaskDetails) jobExecutionContext.getRegistry().get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
                } catch (RegistryException e) {
                    log.error("Error retrieving job details from Registry");
                    throw new GFacHandlerException("Error retrieving job details from Registry", e);
                }
                JobDetails jobDetails = taskData.getJobDetailsList().get(0);
                String jobDescription = jobDetails.getJobDescription();
                if (jobDescription != null) {
                    JobDescriptor jobDescriptor = null;
                    try {
                        jobDescriptor = JobDescriptor.fromXML(jobDescription);
                    } catch (XmlException e1) {
                        e1.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
                    applicationDeploymentDescription.getType().setScratchWorkingDirectory(
                            jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
                    applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
                    applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
                    applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
                    applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
                }
            }
        }
        try {
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {

                GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
            }
        } catch (ApplicationSettingsException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        } catch (GFacException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        }
        DataTransferDetails detail = new DataTransferDetails();
        TransferStatus status = new TransferStatus();

        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();
        try {
            Cluster cluster = null;
            if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            } else {
                cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
            }
            if (cluster == null) {
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }

            // Get the Stdouts and StdErrs
            String pluginData = GFacUtils.getPluginData(jobExecutionContext, this.getClass().getName());
            if (pluginData != null) {
                try {
                    oldIndex = Integer.parseInt(pluginData.split("\\|")[0].trim());
                    oldFiles = Arrays.asList(pluginData.split("\\|")[1].split(","));
                    if (oldIndex == oldFiles.size()) {
                        log.info("Old data looks good !!!!");
                    } else {
                        oldIndex = 0;
                        oldFiles.clear();
                    }
                } catch (NumberFormatException e) {
                    log.error("Previously stored data " + pluginData + " is wrong so we continue the operations");
                }
            }

            String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());

            TaskDetails taskData = jobExecutionContext.getTaskData();
            String outputDataDir = null;
            File localStdOutFile;
            File localStdErrFile;

            if (taskData.getAdvancedOutputDataHandling() != null) {
                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
            }
            if (outputDataDir == null) {
                outputDataDir = File.separator + "tmp";
            }
            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
            (new File(outputDataDir)).mkdirs();


            if (index < oldIndex) {
                localStdOutFile = new File(oldFiles.get(index));
                data.append(oldFiles.get(index++)).append(",");
            } else {
                localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
                cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
                Thread.sleep(1000);
                StringBuffer temp = new StringBuffer(data.append(localStdOutFile.getAbsolutePath()).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }
            if (index < oldIndex) {
                localStdErrFile = new File(oldFiles.get(index));
                data.append(oldFiles.get(index++)).append(",");
            } else {
                localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
                cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
                Thread.sleep(1000);
                StringBuffer temp = new StringBuffer(data.append(localStdErrFile.getAbsolutePath()).append(",").toString());
                GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
            }

            String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDOUT:" + stdOutStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDERR:" + stdErrStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            //todo this is a mess we have to fix this
            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {

                    List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
                    if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for (String key : strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if ("URI".equals(actualParameter1.getType().getType().toString())) {
                                String downloadFile = MappingFactory.toString(actualParameter1);
                                String localFile;
                                if (index < oldIndex) {
                                    localFile = oldFiles.get(index);
                                    data.append(oldFiles.get(index++)).append(",");
                                } else {
                                    cluster.scpFrom(downloadFile, outputDataDir);
                                    String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar) + 1, downloadFile.length());
                                    localFile = outputDataDir + File.separator + fileName;
                                    StringBuffer temp = new StringBuffer(data.append(localFile).append(",").toString());
                                    GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                                }
                                jobExecutionContext.addOutputFile(localFile);
                                MappingFactory.fromString(actualParameter1, localFile);
                                DataObjectType dataObjectType = new DataObjectType();
                                dataObjectType.setValue(localFile);
                                dataObjectType.setKey(key);
                                dataObjectType.setType(DataType.URI);
                                outputArray.add(dataObjectType);
                            }
                        }
                        break;
                    } else {
                        String valueList = outputList.get(0);
                        String outputFile;
                        if (index < oldIndex) {
                            outputFile = oldFiles.get(index);
                            data.append(oldFiles.get(index++)).append(",");
                        } else {
                            cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
                            outputFile = outputDataDir + File.separator + valueList;
                            jobExecutionContext.addOutputFile(outputFile);
                            StringBuffer temp = new StringBuffer(data.append(outputFile).append(",").toString());
                            GFacUtils.savePluginData(jobExecutionContext, temp.insert(0, ++index), this.getClass().getName());
                        }
                        jobExecutionContext.addOutputFile(outputFile);
                        DataObjectType dataObjectType = new DataObjectType();
                        dataObjectType.setValue(valueList);
                        dataObjectType.setKey(paramName);
                        dataObjectType.setType(DataType.URI);
                        outputArray.add(dataObjectType);
                    }
                } else {
                    OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr, outputArray);
                    break;
                }
            }
            if (outputArray == null || outputArray.isEmpty()) {
                throw new GFacHandlerException(
                        "Empty Output returned from the Application, Double check the application"
                                + "and ApplicationDescriptor output Parameter Names"
                );
            }
            app.setStandardError(localStdErrFile.getAbsolutePath());
            app.setStandardOutput(localStdOutFile.getAbsolutePath());
            app.setOutputDataDirectory(outputDataDir);
            status.setTransferState(TransferState.DOWNLOAD);
            detail.setTransferStatus(status);
            detail.setTransferDescription(outputDataDir);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
            registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
        } catch (XmlException e) {
            throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
        } catch (ConnectionException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (TransportException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (IOException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (Exception e) {
            try {
                status.setTransferState(TransferState.FAILED);
                detail.setTransferStatus(status);
                detail.setTransferDescription(e.getLocalizedMessage());
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error in retrieving results", e);
        }

    }
View Full Code Here
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
                TaskDetails taskData = null;
                try {
                    taskData = (TaskDetails) registry.get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
                } catch (RegistryException e) {
                    log.error("Error retrieving job details from Registry");
                    throw new GFacHandlerException("Error retrieving job details from Registry", e);
                }
                JobDetails jobDetails = taskData.getJobDetailsList().get(0);
                String jobDescription = jobDetails.getJobDescription();
                if (jobDescription != null) {
                    JobDescriptor jobDescriptor = null;
                    try {
                        jobDescriptor = JobDescriptor.fromXML(jobDescription);
                    } catch (XmlException e1) {
                        e1.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
                    }
                    applicationDeploymentDescription.getType().setScratchWorkingDirectory(
                            jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
                    applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
                    applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
                    applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
                    applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
                }
            }
        }

        try {
            if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {

                GFACSSHUtils.addSecurityContext(jobExecutionContext);
            }
        } catch (ApplicationSettingsException e) {
            log.error(e.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
        } catch (GFacException e1) {
            log.error(e1.getMessage());
            throw new GFacHandlerException("Error while creating SSHSecurityContext", e1, e1.getLocalizedMessage());
        }

        super.invoke(jobExecutionContext);
        DataTransferDetails detail = new DataTransferDetails();
        TransferStatus status = new TransferStatus();

        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
                .getApplicationDeploymentDescription().getType();
        try {
            Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
            if (cluster == null) {
                throw new GFacProviderException("Security context is not set properly");
            } else {
                log.info("Successfully retrieved the Security Context");
            }

            // Get the Stdouts and StdErrs
            String timeStampedServiceName = GFacUtils.createUniqueNameForService(jobExecutionContext.getServiceName());

            TaskDetails taskData = jobExecutionContext.getTaskData();
            String outputDataDir = null;
            File localStdOutFile;
            File localStdErrFile;

            if (taskData.getAdvancedOutputDataHandling() != null) {
                outputDataDir = taskData.getAdvancedOutputDataHandling().getOutputDataDir();
            }
            if (outputDataDir == null) {
                outputDataDir = File.separator + "tmp";
            }
            outputDataDir = outputDataDir + File.separator + jobExecutionContext.getExperimentID() + "-" + jobExecutionContext.getTaskData().getTaskID();
            (new File(outputDataDir)).mkdirs();


            localStdOutFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stdout");
            localStdErrFile = new File(outputDataDir + File.separator + timeStampedServiceName + "stderr");
//            cluster.makeDirectory(outputDataDir);
            cluster.scpFrom(app.getStandardOutput(), localStdOutFile.getAbsolutePath());
            Thread.sleep(1000);
            cluster.scpFrom(app.getStandardError(), localStdErrFile.getAbsolutePath());
            Thread.sleep(1000);

            String stdOutStr = GFacUtils.readFileToString(localStdOutFile.getAbsolutePath());
            String stdErrStr = GFacUtils.readFileToString(localStdErrFile.getAbsolutePath());
            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDOUT:" + stdOutStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());

            status.setTransferState(TransferState.COMPLETE);
            detail.setTransferStatus(status);
            detail.setTransferDescription("STDERR:" + stdErrStr);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());


            List<DataObjectType> outputArray = new ArrayList<DataObjectType>();
            Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
            Set<String> keys = output.keySet();
            for (String paramName : keys) {
                ActualParameter actualParameter = (ActualParameter) output.get(paramName);
                if ("URI".equals(actualParameter.getType().getType().toString())) {

                    List<String> outputList = cluster.listDirectory(app.getOutputDataDirectory());
                    if (outputList.size() == 0 || outputList.get(0).isEmpty()) {
                        OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr,outputArray);
                        Set<String> strings = output.keySet();
                        outputArray.clear();
                        for (String key : strings) {
                            ActualParameter actualParameter1 = (ActualParameter) output.get(key);
                            if ("URI".equals(actualParameter1.getType().getType().toString())) {
                                String downloadFile = MappingFactory.toString(actualParameter1);
                              cluster.scpFrom(downloadFile, outputDataDir);
                              String fileName = downloadFile.substring(downloadFile.lastIndexOf(File.separatorChar)+1, downloadFile.length());
                              String localFile = outputDataDir +  File.separator +fileName;
                jobExecutionContext.addOutputFile(localFile);
                MappingFactory.fromString(actualParameter1, localFile);
                DataObjectType dataObjectType = new DataObjectType();
                                dataObjectType.setValue(localFile);
                                dataObjectType.setKey(key);
                                dataObjectType.setType(DataType.URI);
                                outputArray.add(dataObjectType);
                            }
                        }
                   
                        break;
                    } else {
                        String valueList = outputList.get(0);
                        cluster.scpFrom(app.getOutputDataDirectory() + File.separator + valueList, outputDataDir);
                        jobExecutionContext.addOutputFile(outputDataDir + File.separator + valueList);
                        DataObjectType dataObjectType = new DataObjectType();
                        dataObjectType.setValue(valueList);
                        dataObjectType.setKey(paramName);
                        dataObjectType.setType(DataType.URI);
                        outputArray.add(dataObjectType);
                    }
                } else {
                    OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr,outputArray);
                }
            }
            if (outputArray == null || outputArray.isEmpty()) {
                throw new GFacHandlerException(
                        "Empty Output returned from the Application, Double check the application"
                                + "and ApplicationDescriptor output Parameter Names");
            }
            app.setStandardError(localStdErrFile.getAbsolutePath());
            app.setStandardOutput(localStdOutFile.getAbsolutePath());
            app.setOutputDataDirectory(outputDataDir);
            status.setTransferState(TransferState.DOWNLOAD);
            detail.setTransferStatus(status);
            detail.setTransferDescription(outputDataDir);
            registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
            registry.add(ChildDataType.EXPERIMENT_OUTPUT, outputArray, jobExecutionContext.getExperimentID());
           
        } catch (XmlException e) {
            throw new GFacHandlerException("Cannot read output:" + e.getMessage(), e);
        } catch (ConnectionException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (TransportException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (IOException e) {
            throw new GFacHandlerException(e.getMessage(), e);
        } catch (Exception e) {
            try {
                status.setTransferState(TransferState.FAILED);
                detail.setTransferStatus(status);
                registry.add(ChildDataType.DATA_TRANSFER_DETAIL, detail, jobExecutionContext.getTaskData().getTaskID());
                GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.FILE_SYSTEM_FAILURE);
            } catch (Exception e1) {
                throw new GFacHandlerException("Error persisting status", e1, e1.getLocalizedMessage());
            }
            throw new GFacHandlerException("Error in retrieving results", e);
        }

    }
View Full Code Here
78
79
80
81
82
83
84
85
86
87
88
        if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
            try {
                GFACSSHUtils.addSecurityContext(jobExecutionContext);
            } catch (ApplicationSettingsException e) {
                log.error(e.getMessage());
                throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
            }
        }
        taskID = jobExecutionContext.getTaskData().getTaskID();

        if (!((SSHHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource()) {
View Full Code Here
1112
1113
1114
1115
1116
1117
1118
1119
        Stat exists = zk.exists(expZnodeHandlerPath, false);
        zk.setData(expZnodeHandlerPath, data.toString().getBytes(),
            exists.getVersion());
      }
    } catch (Exception e) {
      throw new GFacHandlerException(e);
    }
  }
View Full Code Here
TOP

Related Classes of org.apache.airavata.gfac.core.handler.GFacHandlerException

  • org.apache.airavata.gfac.core.utils.GFacUtils
  • org.apache.airavata.gfac.core.utils.OutputUtils
  • org.apache.airavata.gfac.gram.handler.GramDirectorySetupHandler
  • org.apache.airavata.gfac.gram.handler.GridFTPInputHandler
  • org.apache.airavata.gfac.gram.handler.GridFTPOutputHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHDirectorySetupHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHInputHandler
  • org.apache.airavata.gfac.gsissh.handler.GSISSHOutputHandler
  • org.apache.airavata.gfac.gsissh.provider.impl.GSISSHProvider
  • org.apache.airavata.gfac.hadoop.handler.HadoopDeploymentHandler
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.