x1514 Change sample.section (and all related fields) to be a string

src/main/java/uk/ac/sanger/sccp/stan/config/FieldValidation.java

@@ -19,6 +19,12 @@
  */
 @Configuration
 public class FieldValidation {
+    @Bean
+    public Validator<String> sectionValidator() {
+        Set<CharacterType> charTypes = EnumSet.of(CharacterType.ALPHA, CharacterType.DIGIT);
+        return new StringValidator("Section", 1, 16, charTypes, false, Pattern.compile("[1-9][0-9]*[a-z]*", Pattern.CASE_INSENSITIVE));
+    }
+
     @Bean
     public Validator<String> cellClassValidator() {
         Set<CharacterType> charTypes = EnumSet.of(

src/main/java/uk/ac/sanger/sccp/stan/model/CytassistOverview.java

@@ -15,7 +15,7 @@ public class CytassistOverview {
     private Integer id;
     private String workNumber;
     private Integer sampleId;
-    private Integer section;
+    private String section;
     private String sourceBarcode;
     private String sourceSlotAddress;
     private String sourceLabwareType;
@@ -73,11 +73,11 @@ public void setSampleId(Integer sampleId) {
         this.sampleId = sampleId;
     }
 
-    public Integer getSection() {
+    public String getSection() {
         return this.section;
     }
 
-    public void setSection(Integer section) {
+    public void setSection(String section) {
         this.section = section;
     }
 

src/main/java/uk/ac/sanger/sccp/stan/model/PlanAction.java

@@ -1,10 +1,10 @@
 package uk.ac.sanger.sccp.stan.model;
 
-import com.google.common.base.MoreObjects;
-
 import javax.persistence.*;
 import java.util.Objects;
 
+import static uk.ac.sanger.sccp.utils.BasicUtils.describe;
+
 /**
  * A planned action inside a planned operation.
  * @author dr6
@@ -26,7 +26,7 @@ public class PlanAction {
     private Slot destination;
     @ManyToOne
     private Sample sample;
-    private Integer newSection;
+    private String newSection;
     private String sampleThickness;
     @ManyToOne
     private BioState newBioState;
@@ -38,7 +38,7 @@ public PlanAction(Integer id, Integer planOperationId, Slot source, Slot destina
     }
 
     public PlanAction(Integer id, Integer planOperationId, Slot source, Slot destination, Sample sample,
-                      Integer newSection, String sampleThickness, BioState newBioState) {
+                      String newSection, String sampleThickness, BioState newBioState) {
         this.id = id;
         this.planOperationId = planOperationId;
         this.source = source;
@@ -89,11 +89,11 @@ public void setSample(Sample sample) {
         this.sample = sample;
     }
 
-    public Integer getNewSection() {
+    public String getNewSection() {
         return this.newSection;
     }
 
-    public void setNewSection(Integer section) {
+    public void setNewSection(String section) {
         this.newSection = section;
     }
 
@@ -135,13 +135,13 @@ public int hashCode() {
 
     @Override
     public String toString() {
-        return MoreObjects.toStringHelper(this)
+        return describe(this)
                 .add("id", id)
                 .add("planOperationId", planOperationId)
                 .add("source", source)
                 .add("destination", destination)
                 .add("sample", sample)
-                .add("newSection", newSection)
+                .addRepr("newSection", newSection)
                 .add("sampleThickness", sampleThickness)
                 .add("newBioState", newBioState)
                 .toString();

src/main/java/uk/ac/sanger/sccp/stan/model/Sample.java

@@ -1,10 +1,10 @@
 package uk.ac.sanger.sccp.stan.model;
 
-import com.google.common.base.MoreObjects;
-
 import javax.persistence.*;
 import java.util.Objects;
 
+import static uk.ac.sanger.sccp.utils.BasicUtils.describe;
+
 /**
  * A sample is a piece of some tissue that has some particular state and can be located inside slots in labware,
  * and used in operations.
@@ -15,15 +15,15 @@ public class Sample {
     @Id
     @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Integer id;
-    private Integer section;
+    private String section;
     @ManyToOne
     private Tissue tissue;
     @ManyToOne
     private BioState bioState;
 
     public Sample() {}
 
-    public Sample(Integer id, Integer section, Tissue tissue, BioState bioState) {
+    public Sample(Integer id, String section, Tissue tissue, BioState bioState) {
         this.id = id;
         this.section = section;
         this.tissue = tissue;
@@ -38,11 +38,11 @@ public void setId(Integer id) {
         this.id = id;
     }
 
-    public Integer getSection() {
+    public String getSection() {
         return this.section;
     }
 
-    public void setSection(Integer section) {
+    public void setSection(String section) {
         this.section = section;
     }
 
@@ -80,9 +80,9 @@ public int hashCode() {
 
     @Override
     public String toString() {
-        return MoreObjects.toStringHelper(this)
+        return describe(this)
                 .add("id", id)
-                .add("section", section)
+                .addRepr("section", section)
                 .add("tissue", tissue)
                 .add("bioState", bioState)
                 .toString();

src/main/java/uk/ac/sanger/sccp/stan/repo/PlanActionRepo.java

@@ -8,22 +8,9 @@
 import java.util.OptionalInt;
 
 public interface PlanActionRepo extends CrudRepository<PlanAction, Integer> {
-    @Query("SELECT MAX(a.newSection) FROM PlanAction a WHERE a.sample.tissue.id=?1")
-    Integer _findMaxPlannedSectionForTissueId(int tissueId);
-
-    @Query("SELECT MAX(a.newSection) FROM PlanAction a WHERE a.source.id=?1")
+    @Query(value = "SELECT MAX(CAST(a.new_section AS UNSIGNED)) FROM plan_action a WHERE a.source_slot_id=?1", nativeQuery = true)
     Integer _findMaxPlannedSectionFromSlotId(int sourceSlotId);
 
-    /**
-     * Finds the maximum section for planned actions for particular tissue
-     * @param tissueId the id of tissue
-     * @return the highest section number of any planned action on a sample with that tissue id
-     */
-    default OptionalInt findMaxPlannedSectionForTissueId(int tissueId) {
-        Integer maxInteger = _findMaxPlannedSectionForTissueId(tissueId);
-        return (maxInteger==null ? OptionalInt.empty() : OptionalInt.of(maxInteger));
-    }
-
     /**
      * Finds the maximum section for planned actions from a particular slot
      * @param sourceSlotId the id of the source slot

src/main/java/uk/ac/sanger/sccp/stan/repo/SampleRepo.java

@@ -1,32 +1,16 @@
 package uk.ac.sanger.sccp.stan.repo;
 
-import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import uk.ac.sanger.sccp.stan.model.Sample;
 
 import javax.persistence.EntityNotFoundException;
 import java.util.*;
 
 public interface SampleRepo extends CrudRepository<Sample, Integer> {
-    @Query("SELECT MAX(section) FROM Sample WHERE tissue.id=?1")
-    Integer _findMaxSectionForTissueId(int tissueId);
-
     List<Sample> findAllByIdIn(Collection<Integer> ids);
 
     List<Sample> findAllByTissueIdIn(Collection<Integer> tissueIds);
 
-    /**
-     * Finds the maximum section for particular tissue
-     *
-     * @param tissueId the id of tissue
-     * @return the highest section number of any section with that tissue id
-     * @deprecated no current use case
-     */
-    default OptionalInt findMaxSectionForTissueId(int tissueId) {
-        Integer maxInteger = _findMaxSectionForTissueId(tissueId);
-        return maxInteger == null ? OptionalInt.empty() : OptionalInt.of(maxInteger);
-    }
-
     /**
      * Gets the samples with the given ids
      * @param ids the ids to find

src/main/java/uk/ac/sanger/sccp/stan/request/confirm/CancelPlanAction.java

@@ -13,20 +13,16 @@
 public class CancelPlanAction {
     private Address destinationAddress;
     private Integer sampleId;
-    private Integer newSection;
+    private String newSection;
 
     public CancelPlanAction() {}
 
-    public CancelPlanAction(Address destinationAddress, Integer sampleId, Integer newSection) {
+    public CancelPlanAction(Address destinationAddress, Integer sampleId, String newSection) {
         this.destinationAddress = destinationAddress;
         this.sampleId = sampleId;
         this.newSection = newSection;
     }
 
-    public CancelPlanAction(PlanAction planAction) {
-        this(planAction.getDestination().getAddress(), planAction.getSample().getId(), planAction.getNewSection());
-    }
-
     public Address getDestinationAddress() {
         return this.destinationAddress;
     }
@@ -43,11 +39,11 @@ public void setSampleId(Integer sampleId) {
         this.sampleId = sampleId;
     }
 
-    public Integer getNewSection() {
+    public String getNewSection() {
         return this.newSection;
     }
 
-    public void setNewSection(Integer newSection) {
+    public void setNewSection(String newSection) {
         this.newSection = newSection;
     }
 
@@ -71,7 +67,7 @@ public String toString() {
         return BasicUtils.describe("CancelPlanAction")
                 .add("destinationAddress", destinationAddress)
                 .add("sampleId", sampleId)
-                .add("newSection", newSection)
+                .addRepr("newSection", newSection)
                 .toString();
     }
 

src/main/java/uk/ac/sanger/sccp/stan/request/confirm/ConfirmSection.java

@@ -16,26 +16,26 @@
 public class ConfirmSection {
     private List<Address> destinationAddresses = List.of();
     private Integer sampleId;
-    private Integer newSection;
+    private String newSection;
     private List<Integer> commentIds = List.of();
     private String thickness;
 
     public ConfirmSection() {}
 
-    public ConfirmSection(List<Address> destinationAddresses, Integer sampleId, Integer newSection,
+    public ConfirmSection(List<Address> destinationAddresses, Integer sampleId, String newSection,
                           List<Integer> commentIds) {
         setDestinationAddress(destinationAddresses);
         setSampleId(sampleId);
         setNewSection(newSection);
         setCommentIds(commentIds);
     }
 
-    public ConfirmSection(Address destinationAddress, Integer sampleId, Integer newSection,
+    public ConfirmSection(Address destinationAddress, Integer sampleId, String newSection,
                           List<Integer> commentIds) {
         this(destinationAddress==null ? null : List.of(destinationAddress), sampleId, newSection, commentIds);
     }
 
-    public ConfirmSection(Address destinationAddress, Integer sampleId, Integer newSection) {
+    public ConfirmSection(Address destinationAddress, Integer sampleId, String newSection) {
         this(destinationAddress, sampleId, newSection, null);
     }
 
@@ -55,11 +55,11 @@ public void setSampleId(Integer sampleId) {
         this.sampleId = sampleId;
     }
 
-    public Integer getNewSection() {
+    public String getNewSection() {
         return this.newSection;
     }
 
-    public void setNewSection(Integer newSection) {
+    public void setNewSection(String newSection) {
         this.newSection = newSection;
     }
 
@@ -102,7 +102,7 @@ public String toString() {
         return BasicUtils.describe("ConfirmSection")
                 .add("destinationAddresses", destinationAddresses)
                 .add("sampleId", sampleId)
-                .add("newSection", newSection)
+                .addRepr("newSection", newSection)
                 .add("commentIds", commentIds)
                 .addRepr("thickness", thickness)
                 .toString();

src/main/java/uk/ac/sanger/sccp/stan/request/register/SectionRegisterContent.java

@@ -23,7 +23,7 @@ public class SectionRegisterContent {
     private String replicateNumber;
     private String fixative;
     private String medium;
-    private Integer sectionNumber;
+    private String sectionNumber;
     private String sectionThickness;
     private String region;
     private LocalDate dateSectioned;
@@ -126,11 +126,11 @@ public void setMedium(String medium) {
         this.medium = medium;
     }
 
-    public Integer getSectionNumber() {
+    public String getSectionNumber() {
         return this.sectionNumber;
     }
 
-    public void setSectionNumber(Integer sectionNumber) {
+    public void setSectionNumber(String sectionNumber) {
         this.sectionNumber = sectionNumber;
     }
 

src/main/java/uk/ac/sanger/sccp/stan/service/graph/GraphServiceImp.java

@@ -8,13 +8,16 @@
 import uk.ac.sanger.sccp.stan.request.history.HistoryGraph.Link;
 import uk.ac.sanger.sccp.stan.request.history.HistoryGraph.Node;
 import uk.ac.sanger.sccp.stan.service.releasefile.Ancestoriser.SlotSample;
+import uk.ac.sanger.sccp.utils.BasicUtils;
 
 import java.time.LocalDateTime;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.IntStream;
 
 import static java.util.stream.Collectors.*;
 import static uk.ac.sanger.sccp.utils.BasicUtils.inMap;
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullOrEmpty;
 
 /**
  * @author dr6
@@ -160,10 +163,10 @@ public String describeBio(Collection<Sample> samples) {
             return null;
         }
         String desc = samples.iterator().next().getBioState().getName();
-        List<Integer> sections = samples.stream()
+        List<String> sections = samples.stream()
                 .map(Sample::getSection)
-                .filter(Objects::nonNull)
-                .sorted()
+                .filter(s -> !nullOrEmpty(s))
+                .sorted(BasicUtils.numberStringComparator())
                 .distinct()
                 .toList();
         if (!sections.isEmpty()) {
@@ -177,19 +180,23 @@ public String describeBio(Collection<Sample> samples) {
      * @param sections a monotonic sequence of ints
      * @return a string describing the given sections
      */
-    public String summariseSections(List<Integer> sections) {
+    public String summariseSections(List<String> sections) {
         if (sections.isEmpty()) {
             return null;
         }
         if (sections.size()==1) {
-            return sections.getFirst().toString();
+            return sections.getFirst();
         }
         if (sections.size()==2) {
-            return sections.getFirst().toString()+","+sections.getLast().toString();
-        }
-        if (sections.getLast()==sections.getFirst()+sections.size()-1) {
-            return sections.getFirst()+"-"+sections.getLast();
+            return sections.getFirst()+","+sections.getLast();
         }
+        try {
+            int firstNum = Integer.parseInt(sections.getFirst());
+            if (IntStream.range(1, sections.size())
+                    .allMatch(i -> Integer.toString(i+firstNum).equals(sections.get(i)))) {
+                return firstNum+"-"+sections.getLast();
+            }
+        } catch (NumberFormatException ignored) {}
         return sections.stream()
                 .map(Object::toString)
                 .collect(joining(","));