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Merge pull request #469 from sanger/biorisk
x1210 Support bio risk (block registration)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| package uk.ac.sanger.sccp.stan.model; | ||
|
|
||
| import javax.persistence.*; | ||
| import java.util.Objects; | ||
|
|
||
| import static uk.ac.sanger.sccp.utils.BasicUtils.describe; | ||
|
|
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| /** | ||
| * Biological risk assessment number. | ||
| * @author dr6 | ||
| */ | ||
| @Entity | ||
| public class BioRisk implements HasIntId, HasEnabled { | ||
| @Id | ||
| @GeneratedValue(strategy = GenerationType.IDENTITY) | ||
| private Integer id; | ||
| private String code; | ||
| private boolean enabled = true; | ||
|
|
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| public BioRisk() {} // required no-arg constructor | ||
|
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| public BioRisk(Integer id, String code, boolean enabled) { | ||
| this.id = id; | ||
| this.code = code; | ||
| this.enabled = enabled; | ||
| } | ||
|
|
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| public BioRisk(Integer id, String code) { | ||
| this(id, code, true); | ||
| } | ||
|
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| public BioRisk(String code) { | ||
| this(null, code, true); | ||
| } | ||
|
|
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| /** Primary key */ | ||
| @Override | ||
| public Integer getId() { | ||
| return this.id; | ||
| } | ||
|
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| public void setId(Integer id) { | ||
| this.id = id; | ||
| } | ||
|
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| /** The alphanumeric code representing this risk assessment. */ | ||
| public String getCode() { | ||
| return this.code; | ||
| } | ||
|
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| public void setCode(String code) { | ||
| this.code = code; | ||
| } | ||
|
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| @Override | ||
| public boolean isEnabled() { | ||
| return this.enabled; | ||
| } | ||
|
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| @Override | ||
| public void setEnabled(boolean enabled) { | ||
| this.enabled = enabled; | ||
| } | ||
|
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| @Override | ||
| public String toString() { | ||
| return describe(this) | ||
| .add("id", id) | ||
| .add("code", code) | ||
| .add("enabled", enabled) | ||
| .reprStringValues() | ||
| .toString(); | ||
| } | ||
|
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| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) return true; | ||
| if (o == null || o.getClass() != this.getClass()) return false; | ||
| BioRisk that = (BioRisk) o; | ||
| return (this.enabled == that.enabled | ||
| && Objects.equals(this.id, that.id) | ||
| && Objects.equals(this.code, that.code) | ||
| ); | ||
| } | ||
|
|
||
| @Override | ||
| public int hashCode() { | ||
| return (id != null ? id.hashCode() : code !=null ? code.hashCode() : 0); | ||
| } | ||
| } |
96 changes: 96 additions & 0 deletions
96
src/main/java/uk/ac/sanger/sccp/stan/repo/BioRiskRepo.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,96 @@ | ||
| package uk.ac.sanger.sccp.stan.repo; | ||
|
|
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| import org.springframework.data.jpa.repository.Modifying; | ||
| import org.springframework.data.jpa.repository.Query; | ||
| import org.springframework.data.repository.CrudRepository; | ||
| import uk.ac.sanger.sccp.stan.model.BioRisk; | ||
| import uk.ac.sanger.sccp.stan.model.Sample; | ||
|
|
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| import javax.persistence.EntityNotFoundException; | ||
| import java.util.*; | ||
|
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| import static java.util.stream.Collectors.toMap; | ||
| import static java.util.stream.Collectors.toSet; | ||
| import static uk.ac.sanger.sccp.utils.BasicUtils.*; | ||
|
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| /** Repo for {@link BioRisk} */ | ||
| public interface BioRiskRepo extends CrudRepository<BioRisk, Integer> { | ||
| /** Finds the bio risk with the given code, if it exists. */ | ||
| Optional<BioRisk> findByCode(String code); | ||
|
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| /** | ||
| * Gets the bio risk with the given code. | ||
| * @param code the code of the bio risk to get | ||
| * @return the bio risk with the given code | ||
| * @exception EntityNotFoundException if no such bio risk exists | ||
| */ | ||
| default BioRisk getByCode(String code) throws EntityNotFoundException { | ||
| return findByCode(code).orElseThrow(() -> new EntityNotFoundException("Unknown bio risk code: "+repr(code))); | ||
| } | ||
|
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| List<BioRisk> findAllByCodeIn(Collection<String> codes); | ||
|
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| /** Finds all bio risks matching the given value for enabled. */ | ||
| List<BioRisk> findAllByEnabled(boolean enabled); | ||
|
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| @Query(value = "select bio_risk_id from sample_bio_risk where sample_id=?", nativeQuery = true) | ||
| Integer loadBioRiskIdForSampleId(int sampleId); | ||
|
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| @Query(value = "select sample_id, bio_risk_id from sample_bio_risk where sample_id in (?1)", nativeQuery = true) | ||
| int[][] _loadBioRiskIdsForSampleIds(Collection<Integer> sampleIds); | ||
|
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| /** Loads the bio risk (if any) linked to the specified sample */ | ||
| default Optional<BioRisk> loadBioRiskForSampleId(int sampleId) { | ||
| Integer bioRiskId = loadBioRiskIdForSampleId(sampleId); | ||
| return bioRiskId == null ? Optional.empty() : findById(bioRiskId); | ||
| } | ||
|
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| /** | ||
| * Loads the bio risk ids linked to the given sample ids | ||
| * @param sampleIds sample ids | ||
| * @return a map of sample id to bio risk id, omitting missing values | ||
| */ | ||
| default Map<Integer, Integer> loadBioRiskIdsForSampleIds(Collection<Integer> sampleIds) { | ||
| int[][] sambr = _loadBioRiskIdsForSampleIds(sampleIds); | ||
| if (sambr == null || sambr.length==0) { | ||
| return Map.of(); | ||
| } | ||
| return Arrays.stream(sambr) | ||
| .collect(toMap(arr -> arr[0], arr -> arr[1])); | ||
| } | ||
|
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| /** | ||
| * Loads the bio risks linked to the given sample ids | ||
| * @param sampleIds sample ids | ||
| * @return a map of sample id to bio risk, omitting missing values | ||
| */ | ||
| default Map<Integer, BioRisk> loadBioRisksForSampleIds(Collection<Integer> sampleIds) { | ||
| int[][] sambr = _loadBioRiskIdsForSampleIds(sampleIds); | ||
| if (sambr==null || sambr.length==0) { | ||
| return Map.of(); | ||
| } | ||
| Set<Integer> bioRiskIds = Arrays.stream(sambr) | ||
| .map(arr -> arr[1]) | ||
| .collect(toSet()); | ||
| Map<Integer, BioRisk> idBioRisks = stream(findAllById(bioRiskIds)) | ||
| .collect(inMap(BioRisk::getId)); | ||
| return Arrays.stream(sambr) | ||
| .collect(toMap(arr -> arr[0], arr -> idBioRisks.get(arr[1]))); | ||
| } | ||
|
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| /** | ||
| * Records the given bio risk id against the given sample id and operation id | ||
| * @param sampleId sample id | ||
| * @param bioRiskId bio risk id | ||
| * @param opId operation id | ||
| */ | ||
| @Modifying | ||
| @Query(value = "insert INTO sample_bio_risk (sample_id, bio_risk_id, operation_id) " + | ||
| "values (?, ?, ?)", nativeQuery = true) | ||
| void recordBioRisk(int sampleId, int bioRiskId, Integer opId); | ||
|
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| /** Links the given bio risk to the given sample and operation */ | ||
| default void recordBioRisk(Sample sample, BioRisk bioRisk, int opId) { | ||
| recordBioRisk(sample.getId(), bioRisk.getId(), opId); | ||
| } | ||
| } |
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