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Fixing issue #9 #48

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Fixing issue #9 #48

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7bec852
Fixing issue #9
odbz Feb 14, 2024
004a5ea
fix v2 issue #9
odbz Feb 20, 2024
2816f5b
applying suggestion using Hibernate native query via EntityManager fo…
odbz Feb 28, 2024
1dcd14e
applying suggested changes
odbz Feb 29, 2024
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63 changes: 32 additions & 31 deletions ...node/src/main/java/com/odysseusinc/arachne/datanode/controller/admin/AdminController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -142,20 +142,20 @@ public Page<SubmissionDTO> list(@PageableDefault(value = DEFAULT_PAGE_SIZE, sort
direction = Sort.Direction.DESC) Pageable pageable) {

Pageable p;
if (!isCustomSort(pageable)) {
p = pageable;
} else {
p = buildPageRequest(pageable);
}
String sortField = isFinishedSort(pageable) ? "finished" : isSubmittedSort(pageable) ? "submitted" : (isStatusSort(pageable) ? "status" : "");
Page<Analysis> analyses;
if (isFinishedSort(pageable)) {
analyses = analysisRepository.findAllPagedOrderByFinished(p);
} else if (isSubmittedSort(pageable)) {
analyses = analysisRepository.findAllPagedOrderBySubmitted(p);
} else if (isStatusSort(pageable)) {
analyses = analysisRepository.findAllPagedOrderByState(p);
} else {
if ("".equals(sortField)) {
if (!isCustomSort(pageable)) {
p = pageable;
} else {
p = buildPageRequest(pageable);
}
analyses = analysisRepository.findAll(p);
}else{
analyses =analysisRepository
.findAllPagingSortingByCalculateFields(pageable.getSort().get().findFirst().get().getDirection().name(),
sortField,
PageRequest.of(pageable.getPageNumber(), pageable.getPageSize()));
}
return analyses.map(analysis -> analysisToSubmissionDTO.convert(analysis));
}
Expand Down Expand Up @@ -222,25 +222,26 @@ private boolean isSortOf(final Pageable pageable, Function<String, Boolean> pred
return false;
}

protected void initProps() {

propertiesMap.put("author.fullName", p -> {
p.add("author.firstName");
p.add("author.lastName");
});
propertiesMap.put("fullName", p -> {
p.add("author.firstName");
p.add("author.lastName");
});
propertiesMap.put("analysis", p -> p.add("title"));
propertiesMap.put("study", p -> p.add("studyTitle"));
propertiesMap.put("status", p -> p.add("journal.state"));
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Why is this line removed?

}
protected void initProps() {

private class EngineStatusResponse {
public EngineStatusResponse(final ExecutionEngineStatus status) {
this.status = status;
}
public ExecutionEngineStatus status;
propertiesMap.put("author.fullName", p -> {
p.add("author.firstName");
p.add("author.lastName");
});
propertiesMap.put("fullName", p -> {
p.add("author.firstName");
p.add("author.lastName");
});
propertiesMap.put("analysis", p -> p.add("title"));
propertiesMap.put("study", p -> p.add("studyTitle"));
}

private class EngineStatusResponse {

public EngineStatusResponse(final ExecutionEngineStatus status) {
this.status = status;
}

public ExecutionEngineStatus status;
}
}
115 changes: 37 additions & 78 deletions datanode/src/main/java/com/odysseusinc/arachne/datanode/repository/AnalysisRepository.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,6 @@
package com.odysseusinc.arachne.datanode.repository;

import com.odysseusinc.arachne.datanode.model.analysis.Analysis;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
Expand All @@ -26,79 +24,40 @@
import java.util.List;
import java.util.Optional;

public interface AnalysisRepository extends JpaRepository<Analysis, Long> {

Optional<Analysis> findById(Long id);

@Query(nativeQuery = true, value =
"SELECT analyses.* FROM analyses WHERE analyses.id = :id AND analyses.callback_password = :password")
Optional<Analysis> findOneExecuting(@Param("id") Long id, @Param("password") String password);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ "FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state = :state AND analyses.central_id IS NOT NULL")
List<Analysis> findAllByState(@Param("state") String state);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ "FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state NOT IN (:states)")
List<Analysis> findAllByNotStateIn(@Param("states") List<String> states);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ " FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state = :state AND journal.date < :time")
List<Analysis> findAllExecutingMoreThan(@Param("state") String state, @Param("time") Date time);

@Query(nativeQuery = true, value =
"select a.* from analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id"
+ " \n--#pageable\n",
countQuery = "select count(a.*) from analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id")
Page<Analysis> findAllPagedOrderByState(Pageable pageable);

@Query(nativeQuery = true, value =
"select a.* from analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, min(date) AS submitted FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS SUB ON journal.date = SUB.submitted AND journal.analysis_id=SUB.analysis_id"
+ " \n--#pageable\n",
countQuery = "select count(a.*) from analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, min(date) AS submitted FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS SUB ON journal.date = SUB.submitted AND journal.analysis_id=SUB.analysis_id")
Page<Analysis> findAllPagedOrderBySubmitted(Pageable pageable);

@Query(nativeQuery = true, value =
"select a.*, "
+ "case journal.state "
+ " when 'EXECUTING' then null "
+ " when 'CREATED' then null"
+ " else journal.date "
+ "end as finished FROM analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, max(date) AS finished FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS SUB ON journal.date = SUB.finished AND journal.analysis_id=SUB.analysis_id"
+ " \n--#pageable\n",
countQuery = "select count(a.*) from analyses a "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = a.id "
+ " JOIN (SELECT analysis_id, max(date) AS finished FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS SUB ON journal.date = SUB.finished AND journal.analysis_id=SUB.analysis_id")
Page<Analysis> findAllPagedOrderByFinished(Pageable pageable);
}
public interface AnalysisRepository extends JpaRepository<Analysis, Long>,
AnalysisRepositoryExtended {

Optional<Analysis> findById(Long id);

@Query(nativeQuery = true, value =
"SELECT analyses.* FROM analyses WHERE analyses.id = :id AND analyses.callback_password = :password")
Optional<Analysis> findOneExecuting(@Param("id") Long id, @Param("password") String password);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ "FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state = :state AND analyses.central_id IS NOT NULL")
List<Analysis> findAllByState(@Param("state") String state);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ "FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state NOT IN (:states)")
List<Analysis> findAllByNotStateIn(@Param("states") List<String> states);

@Query(nativeQuery = true, value =
"SELECT analyses.* "
+ " FROM analyses "
+ " JOIN analysis_state_journal AS journal ON journal.analysis_id = analyses.id "
+ " JOIN (SELECT analysis_id, max(date) AS latest FROM analysis_state_journal "
+ " GROUP BY analysis_id) AS FOO ON journal.date = FOO.latest AND journal.analysis_id=FOO.analysis_id "
+ " WHERE journal.state = :state AND journal.date < :time")
List<Analysis> findAllExecutingMoreThan(@Param("state") String state, @Param("time") Date time);

}
9 changes: 9 additions & 0 deletions ...src/main/java/com/odysseusinc/arachne/datanode/repository/AnalysisRepositoryExtended.java
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@@ -0,0 +1,9 @@
package com.odysseusinc.arachne.datanode.repository;

import com.odysseusinc.arachne.datanode.model.analysis.Analysis;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;

public interface AnalysisRepositoryExtended {
Page<Analysis> findAllPagingSortingByCalculateFields(String direction, String sortField, Pageable pageable);
}
59 changes: 59 additions & 0 deletions ...va/com/odysseusinc/arachne/datanode/repository/implementation/AnalysisRepositoryImpl.java
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@@ -0,0 +1,59 @@
package com.odysseusinc.arachne.datanode.repository.implementation;

import java.util.List;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.Query;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageImpl;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.stereotype.Repository;
import com.odysseusinc.arachne.datanode.model.analysis.Analysis;
import com.odysseusinc.arachne.datanode.repository.AnalysisRepositoryExtended;

@Repository
public class AnalysisRepositoryImpl implements AnalysisRepositoryExtended {
@PersistenceContext
private EntityManager entityManager;
@Override
public Page<Analysis> findAllPagingSortingByCalculateFields(String direction,
String sortField, Pageable pageable) {
String queryString = "SELECT \n" +
" a.* \n" +
"FROM \n" +
" analyses a \n" +
" JOIN analysis_state_journal AS J ON J.analysis_id = a.id \n" +
" JOIN (\n" +
" SELECT \n" +
" J.analysis_id, \n" +
" MAX(J.date) AS finished, \n" +
" MIN(J.date) AS submitted \n" +
" FROM \n" +
" analysis_state_journal J \n" +
" GROUP BY \n" +
" J.analysis_id\n" +
" ) JS ON J.analysis_id = JS.analysis_id \n" +
" AND J.date = JS.finished \n" +
"ORDER BY \n";

if(sortField.equals("finished")){
queryString = queryString + "CASE WHEN J.state IN('EXECUTING', 'CREATED') THEN null ELSE JS.finished END ";
}else if(sortField.equals("status")){
queryString = queryString + "CASE WHEN J.state = 'ABORT_FAILURE' THEN 'Failed to Abort' WHEN J.state = 'EXECUTION_FAILURE' THEN 'Failed' ELSE J.state END ";
}else if(sortField.equals("submitted")){
queryString = queryString + "JS.submitted ";
}
queryString = queryString + direction + " NULLS LAST";

Query query = entityManager.createNativeQuery(queryString, Analysis.class);
query.setFirstResult(pageable.getPageNumber() * pageable.getPageSize());
query.setMaxResults(pageable.getPageSize());
List<Analysis> content = query.getResultList();

Query countQuery = entityManager.createNativeQuery("SELECT COUNT(*) FROM analyses");
Long countResult = ((Number)countQuery.getSingleResult()).longValue();

return new PageImpl<>(content, PageRequest.of(pageable.getPageNumber(), pageable.getPageSize()), countResult);
}
}