-
Notifications
You must be signed in to change notification settings - Fork 167
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #2 from odysseusinc/temp-vulnerability-fixes
Updating to 2.2
- Loading branch information
Showing
93 changed files
with
4,029 additions
and
1,027 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| *application.properties | ||
| .idea/ | ||
| .metadata/ | ||
| *.iml | ||
| sandbox/ | ||
| /target/ | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
122 changes: 122 additions & 0 deletions
122
src/main/java/org/ohdsi/webapi/cohortdefinition/GenerationJobExecutionListener.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
| /* | ||
| * Copyright 2017 cknoll1. | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
| package org.ohdsi.webapi.cohortdefinition; | ||
|
|
||
| import java.util.Calendar; | ||
| import java.util.Collection; | ||
| import java.util.Date; | ||
| import java.util.Map; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.ohdsi.sql.SqlRender; | ||
| import org.ohdsi.sql.SqlTranslate; | ||
| import org.ohdsi.webapi.GenerationStatus; | ||
| import org.springframework.batch.core.BatchStatus; | ||
| import org.springframework.batch.core.JobExecution; | ||
| import org.springframework.batch.core.JobExecutionListener; | ||
| import org.springframework.batch.core.JobParameters; | ||
| import org.springframework.jdbc.core.JdbcTemplate; | ||
| import org.springframework.transaction.TransactionDefinition; | ||
| import org.springframework.transaction.TransactionStatus; | ||
| import org.springframework.transaction.support.DefaultTransactionDefinition; | ||
| import org.springframework.transaction.support.TransactionTemplate; | ||
|
|
||
| /** | ||
| * | ||
| * @author cknoll1 | ||
| */ | ||
| public class GenerationJobExecutionListener implements JobExecutionListener { | ||
|
|
||
| private final CohortDefinitionRepository cohortDefinitionRepository; | ||
| private final TransactionTemplate transactionTemplate; | ||
| private final JdbcTemplate sourceTemplate; | ||
|
|
||
| public GenerationJobExecutionListener(CohortDefinitionRepository cohortDefinitionRepository, | ||
| TransactionTemplate transactionTemplate, | ||
| JdbcTemplate sourceTemplate) | ||
| { | ||
| this.cohortDefinitionRepository = cohortDefinitionRepository; | ||
| this.transactionTemplate = transactionTemplate; | ||
| this.sourceTemplate = sourceTemplate; | ||
| } | ||
|
|
||
| private CohortGenerationInfo findBySourceId(Collection<CohortGenerationInfo> infoList, Integer sourceId) | ||
| { | ||
| for (CohortGenerationInfo info : infoList) { | ||
| if (info.getId().getSourceId().equals(sourceId)) | ||
| return info; | ||
| } | ||
| return null; | ||
| } | ||
|
|
||
| @Override | ||
| public void afterJob(JobExecution je) { | ||
|
|
||
| JobParameters jobParams = je.getJobParameters(); | ||
| Integer defId = Integer.valueOf(jobParams.getString("cohort_definition_id")); | ||
| Integer sourceId = Integer.valueOf(jobParams.getString("source_id")); | ||
| String targetDialect = jobParams.getString("target_dialect"); | ||
| String cohortTable = jobParams.getString("target_database_schema") + "." + jobParams.getString("target_table"); | ||
|
|
||
| DefaultTransactionDefinition completeTx = new DefaultTransactionDefinition(); | ||
| completeTx.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW); | ||
| TransactionStatus completeStatus = this.transactionTemplate.getTransactionManager().getTransaction(completeTx); | ||
| CohortDefinition df = this.cohortDefinitionRepository.findOne(defId); | ||
| CohortGenerationInfo info = findBySourceId(df.getGenerationInfoList(), sourceId); | ||
| info.setExecutionDuration((int)(je.getEndTime().getTime() - je.getStartTime().getTime())); | ||
| info.setStatus(GenerationStatus.COMPLETE); | ||
|
|
||
| if (je.getStatus() == BatchStatus.FAILED) { | ||
| info.setIsValid(false); | ||
| info.setRecordCount(null); | ||
| info.setPersonCount(null); | ||
| info.setFailMessage(StringUtils.left(je.getAllFailureExceptions().get(0).getMessage(),2000)); | ||
| } else { | ||
| info.setIsValid(true); | ||
| info.setFailMessage(null); | ||
|
|
||
| // query summary results from source | ||
| String statsQuery = "SELECT count(distinct subject_id) as person_count, count(*) as record_count from @cohort_table where cohort_definition_id = @cohort_definition_id"; | ||
| String statsSql = SqlTranslate.translateSql(statsQuery, targetDialect, null, null); | ||
| String renderedSql = SqlRender.renderSql(statsSql, new String[]{"cohort_table", "cohort_definition_id"}, new String[]{cohortTable, defId.toString()}); | ||
| Map<String, Object> stats = this.sourceTemplate.queryForMap(renderedSql); | ||
| info.setPersonCount(Long.parseLong(stats.get("person_count").toString())); | ||
| info.setRecordCount(Long.parseLong(stats.get("record_count").toString())); | ||
| } | ||
|
|
||
| this.cohortDefinitionRepository.save(df); | ||
| this.transactionTemplate.getTransactionManager().commit(completeStatus); | ||
|
|
||
| } | ||
|
|
||
| @Override | ||
| public void beforeJob(JobExecution je) { | ||
| Date startTime = Calendar.getInstance().getTime(); | ||
| JobParameters jobParams = je.getJobParameters(); | ||
| Integer defId = Integer.valueOf(jobParams.getString("cohort_definition_id")); | ||
| Integer sourceId = Integer.valueOf(jobParams.getString("source_id")); | ||
|
|
||
| DefaultTransactionDefinition initTx = new DefaultTransactionDefinition(); | ||
| initTx.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRES_NEW); | ||
| TransactionStatus initStatus = this.transactionTemplate.getTransactionManager().getTransaction(initTx); | ||
| CohortDefinition df = this.cohortDefinitionRepository.findOne(defId); | ||
| CohortGenerationInfo info = findBySourceId(df.getGenerationInfoList(), sourceId); | ||
| info.setIsValid(false); | ||
| info.setStartTime(startTime); | ||
| info.setStatus(GenerationStatus.RUNNING); | ||
| this.cohortDefinitionRepository.save(df); | ||
| this.transactionTemplate.getTransactionManager().commit(initStatus); | ||
| } | ||
| } |
Oops, something went wrong.