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PEPPER-1388 remove angio from pancan redirect #2933
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84 changes: 84 additions & 0 deletions
84
...main/java/org/broadinstitute/ddp/studybuilder/task/pancan/PancanAngioRedirectRemoval.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| package org.broadinstitute.ddp.studybuilder.task.pancan; | ||
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| import com.typesafe.config.Config; | ||
| import lombok.extern.slf4j.Slf4j; | ||
| import org.broadinstitute.ddp.db.DBUtils; | ||
| import org.broadinstitute.ddp.db.dao.JdbiUmbrellaStudy; | ||
| import org.broadinstitute.ddp.exception.DDPException; | ||
| import org.broadinstitute.ddp.studybuilder.task.CustomTask; | ||
| import org.jdbi.v3.core.Handle; | ||
| import org.jdbi.v3.sqlobject.SqlObject; | ||
| import org.jdbi.v3.sqlobject.customizer.Bind; | ||
| import org.jdbi.v3.sqlobject.statement.SqlQuery; | ||
| import org.jdbi.v3.sqlobject.statement.SqlUpdate; | ||
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| import java.nio.file.Path; | ||
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| @Slf4j | ||
| public class PancanAngioRedirectRemoval implements CustomTask { | ||
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| private Path cfgPath; | ||
| private Config studyCfg; | ||
| private Config varsCfg; | ||
| private SqlHelper sqlHelper; | ||
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| @Override | ||
| public void init(Path cfgPath, Config studyCfg, Config varsCfg) { | ||
| this.cfgPath = cfgPath; | ||
| this.studyCfg = studyCfg; | ||
| this.varsCfg = varsCfg; | ||
| } | ||
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| @Override | ||
| public void run(Handle handle) { | ||
| var studyDto = handle.attach(JdbiUmbrellaStudy.class).findByStudyGuid(studyCfg.getString("study.guid")); | ||
| if (!studyDto.getGuid().equals("cmi-pancan")) { | ||
| throw new DDPException("This task is only for the pancan study!"); | ||
| } | ||
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| sqlHelper = handle.attach(SqlHelper.class); | ||
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| //find and delete the ANGIO study redirect workflow transition | ||
| long workflowTransitionId = sqlHelper.findPancanAngioStudyRedirectWorkflowId(); | ||
| DBUtils.checkDelete(1, sqlHelper.updatePancanAngioRedirectPex(workflowTransitionId)); | ||
| log.info("Deleted workflow transition with ID: {}", workflowTransitionId); | ||
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| //update pex expressions to remove ANGIO (C_SARCOMAS_ANGIOSARCOMA) | ||
| int rowCount = sqlHelper.updatePancanAngioRedirectPex(); | ||
| log.info("Updated {} rows in expression table", rowCount); | ||
| } | ||
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| private interface SqlHelper extends SqlObject { | ||
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| @SqlQuery("select trans.workflow_transition_id " | ||
| + " from workflow_transition as trans " | ||
| + " join umbrella_study as s on s.umbrella_study_id = trans.umbrella_study_id " | ||
| + " join workflow_state as next_state on next_state.workflow_state_id = trans.next_state_id " | ||
| + " join workflow_state_type as next_state_type on next_state_type.workflow_state_type_id " | ||
| + " = next_state.workflow_state_type_id " | ||
| + " left join workflow_activity_state as next_act_state on next_act_state.workflow_state_id " | ||
| + " = next_state.workflow_state_id " | ||
| + " left join expression as expr on expr.expression_id = trans.precondition_expression_id " | ||
| + " left join workflow_study_redirect_state as next_redirect_state on " | ||
| + " next_redirect_state.workflow_state_id = next_state.workflow_state_id " | ||
| + " where s.guid = 'cmi-pancan' " | ||
| + " and trans.is_active " | ||
| + " and next_state_type.workflow_state_type_code = 'STUDY_REDIRECT' " | ||
| + " and study_guid = 'ANGIO'") | ||
| long findPancanAngioStudyRedirectWorkflowId(); | ||
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| @SqlUpdate("delete workflow_transition " | ||
| + "from workflow_transition " | ||
| + "where workflow_transition_id = :workflowTransitionId") | ||
| int updatePancanAngioRedirectPex(@Bind("workflowTransitionId") long workflowTransitionId); | ||
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| @SqlUpdate("update expression " | ||
| + "set expression_text = REPLACE(expression_text, '\"C_SARCOMAS_ANGIOSARCOMA\",', '') " | ||
| + "where expression_text like '%hasOptionStartsWith(\"C_SARCOMAS_ANGIOSARCOMA\", \"C_GASTRO_ESOPHAGEAL_CANCER\"%' ") | ||
| int updatePancanAngioRedirectPex(); | ||
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| } | ||
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| } |
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This file changes are just to keep config in sync with what patch is doing and patch doest use this file.