x1508 Support multiple slot addresses per section in section reg

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

@@ -5,8 +5,11 @@
 import uk.ac.sanger.sccp.utils.BasicUtils;
 
 import java.time.LocalDate;
+import java.util.List;
 import java.util.Objects;
 
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullToEmpty;
+
 /**
  * One section in one labware of a section registration request.
  * @author dr6
@@ -15,7 +18,7 @@ public class SectionRegisterContent {
     private String donorIdentifier;
     private LifeStage lifeStage;
     private String species;
-    private Address address;
+    private List<Address> addresses = List.of();
     private String hmdmc;
     private String externalIdentifier;
     private String tissueType;
@@ -38,12 +41,12 @@ public SectionRegisterContent(String donorIdentifier, LifeStage lifeStage, Strin
         this.species = species;
     }
 
-    public Address getAddress() {
-        return this.address;
+    public List<Address> getAddresses() {
+        return this.addresses;
     }
 
-    public void setAddress(Address address) {
-        this.address = address;
+    public void setAddresses(List<Address> addresses) {
+        this.addresses = nullToEmpty(addresses);
     }
 
     public String getSpecies() {
@@ -183,7 +186,7 @@ public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         SectionRegisterContent that = (SectionRegisterContent) o;
-        return (Objects.equals(this.address, that.address)
+        return (Objects.equals(this.addresses, that.addresses)
                 && Objects.equals(this.species, that.species)
                 && Objects.equals(this.hmdmc, that.hmdmc)
                 && Objects.equals(this.donorIdentifier, that.donorIdentifier)
@@ -205,13 +208,13 @@ public boolean equals(Object o) {
 
     @Override
     public int hashCode() {
-        return Objects.hash(address, externalIdentifier);
+        return Objects.hash(addresses, externalIdentifier);
     }
 
     @Override
     public String toString() {
         return BasicUtils.describe("SectionRegisterContent")
-                .add("address", address)
+                .add("addresses", addresses)
                 .add("species", species)
                 .add("hmdmc", hmdmc)
                 .add("donorIdentifier", donorIdentifier)

src/main/java/uk/ac/sanger/sccp/stan/service/register/SectionRegisterServiceImp.java

@@ -9,6 +9,7 @@
 import uk.ac.sanger.sccp.utils.UCMap;
 
 import java.util.*;
+import java.util.stream.Stream;
 
 import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toMap;
@@ -194,10 +195,10 @@ public Labware createLabware(SectionRegisterLabware srl, UCMap<LabwareType> labw
         }
         Labware lw = lwService.create(lt, prebarcode, externalBarcode);
         for (var content : srl.getContents()) {
-            Slot slot = lw.getSlot(content.getAddress());
             Sample sample = sampleMap.get(content.getExternalIdentifier());
-            slot.getSamples().add(sample);
-            slotRepo.save(slot);
+            List<Slot> slots = lwSlots(lw, content.getAddresses()).toList();
+            slots.forEach(slot -> slot.addSample(sample));
+            slotRepo.saveAll(slots);
         }
         return lw;
     }
@@ -271,14 +272,18 @@ public Iterable<Measurement> createMeasurements(SectionRegisterLabware srl, Labw
                 continue;
             }
             Sample sample = sampleMap.get(src.getExternalIdentifier());
-            Slot slot = lw.getSlot(src.getAddress());
+            List<Slot> slots = lwSlots(lw, src.getAddresses()).toList();
             if (src.getSectionThickness() != null) {
-                measurements.add(new Measurement(null, "Thickness", src.getSectionThickness(),
-                        sample.getId(), op.getId(), slot.getId()));
+                for (Slot slot : slots) {
+                    measurements.add(new Measurement(null, "Thickness", src.getSectionThickness(),
+                            sample.getId(), op.getId(), slot.getId()));
+                }
             }
             if (src.getDateSectioned() != null) {
-                measurements.add(new Measurement(null, "Date sectioned", src.getDateSectioned().toString(),
-                        sample.getId(), op.getId(), slot.getId()));
+                for (Slot slot : slots) {
+                    measurements.add(new Measurement(null, "Date sectioned", src.getDateSectioned().toString(),
+                            sample.getId(), op.getId(), slot.getId()));
+                }
             }
         }
         return (measurements.isEmpty() ? measurements : measurementRepo.saveAll(measurements));
@@ -297,13 +302,20 @@ public Iterable<SamplePosition> createSamplePositions(SectionRegisterLabware srl
                                                           UCMap<Sample> sampleMap, UCMap<SlotRegion> regionMap) {
         List<SamplePosition> samps = srl.getContents().stream()
                 .filter(src -> !nullOrEmpty(src.getRegion()))
-                .map(src -> new SamplePosition(lw.getSlot(src.getAddress()).getId(),
-                        sampleMap.get(src.getExternalIdentifier()).getId(),
-                        regionMap.get(src.getRegion()), opId))
-                .collect(toList());
+                .flatMap(src -> newSamplePositions(src, lw, opId, sampleMap, regionMap))
+                .toList();
         return (samps.isEmpty() ? samps : samplePositionRepo.saveAll(samps));
     }
 
+    /** Makes new (unsaved) sample position objects for a given source */
+    Stream<SamplePosition> newSamplePositions(final SectionRegisterContent src, final Labware lw, final Integer opId,
+                                              final UCMap<Sample> sampleMap, final UCMap<SlotRegion> regionMap) {
+        final Integer sampleId = sampleMap.get(src.getExternalIdentifier()).getId();
+        final SlotRegion region = regionMap.get(src.getRegion());
+        return lwSlots(lw, src.getAddresses())
+                .map(slot -> new SamplePosition(slot.getId(), sampleId, region, opId));
+    }
+
     /**
      * Links the indicated bio risks to the new samples
      * @param srl relevant part of the request
@@ -317,4 +329,14 @@ public void linkBioRisks(SectionRegisterLabware srl, Integer opId, UCMap<Sample>
                 .collect(toMap(src -> sampleMap.get(src.getExternalIdentifier()).getId(), src -> bioRiskMap.get(src.getBioRiskCode())));
         bioRiskService.recordSampleBioRisks(sampleBioRisks, opId);
     }
+
+    /**
+     * Streams the slots with the given addresses from the given labware
+     * @param lw the labware to get slots from
+     * @param addresses the addresses of the slots
+     * @return a stream of slots
+     */
+    static Stream<Slot> lwSlots(Labware lw, Collection<Address> addresses) {
+        return addresses.stream().map(lw::getSlot);
+    }
 }

src/main/java/uk/ac/sanger/sccp/stan/service/register/SectionRegisterValidation.java

@@ -198,15 +198,23 @@ public UCMap<LabwareType> validateLabwareTypes() {
                 continue;
             }
             for (var content : lw.getContents()) {
-                Address address = content.getAddress();
-                if (address==null) {
+                if (nullOrEmpty(content.getAddresses())) {
                     addProblem("Missing slot address.");
-                } else if (lt.indexOf(address) < 0) {
-                    addProblem("Invalid address %s in labware type %s.", address, lt.getName());
+                    continue;
+                }
+                Set<Address> seen = new HashSet<>(content.getAddresses().size());
+                for (Address address : content.getAddresses()) {
+                    if (address == null) {
+                        addProblem("Missing slot address.");
+                    } else if (!seen.add(address)) {
+                        addProblem("Slot address %s given multiple times for the same section.", address);
+                    } else if (lt.indexOf(address) < 0) {
+                        addProblem("Invalid address %s in labware type %s.", address, lt.getName());
+                    }
                 }
             }
         }
-        // Allow duplicate addresses
+        // Allow duplicate addresses across different sections but not in the same section
         return lwTypeMap;
     }
 
@@ -510,8 +518,9 @@ public UCMap<SlotRegion> validateRegions() {
 
         for (var srl : request.getLabware()) {
             Stream<Map.Entry<Address, String>> regionStream = srl.getContents().stream()
-                    .filter(src -> !nullOrEmpty(src.getRegion()) && src.getAddress()!=null)
-                    .map(src -> Map.entry(src.getAddress(), src.getRegion()));
+                    .filter(src -> !nullOrEmpty(src.getRegion()) && !nullOrEmpty(src.getAddresses()))
+                    .flatMap(src -> src.getAddresses().stream()
+                            .map(ad -> Map.entry(ad, src.getRegion())));
             problems.addAll(slotRegionService.validateSlotRegions(slotRegions, regionStream));
         }
 
@@ -520,8 +529,10 @@ public UCMap<SlotRegion> validateRegions() {
 
     public boolean anyMissingRegions(SectionRegisterLabware srl) {
         return slotRegionService.anyMissingRegions(srl.getContents().stream()
-                .filter(src -> src.getAddress()!=null)
-                .map(src -> simpleEntry(src.getAddress(), src.getRegion())));
+                .filter(src -> !nullOrEmpty(src.getAddresses()))
+                .flatMap(src -> src.getAddresses().stream()
+                        .filter(Objects::nonNull)
+                        .map(ad -> simpleEntry(ad, src.getRegion()))));
     }
 
     private Stream<SectionRegisterContent> contentStream() {
@@ -551,9 +562,9 @@ public void throwError() throws ValidationException {
     }
 
     private <E> UCMap<E> loadAllFromSectionsToStringMap(SectionRegisterRequest request,
-                                                              Function<SectionRegisterContent, String> requestFunction,
-                                                              Function<? super E, String> entityFunction,
-                                                              Function<? super Set<String>, ? extends Collection<E>> lookupFunction) {
+                                                        Function<SectionRegisterContent, String> requestFunction,
+                                                        Function<? super E, String> entityFunction,
+                                                        Function<? super Set<String>, ? extends Collection<E>> lookupFunction) {
         Set<String> strings = request.getLabware().stream()
                 .flatMap(lw -> lw.getContents().stream().map(requestFunction))
                 .filter(s -> s!=null && !s.isEmpty())

src/main/java/uk/ac/sanger/sccp/stan/service/register/filereader/BaseRegisterFileReader.java

@@ -151,15 +151,28 @@ public LifeStage valueToLifeStage(Collection<String> problems, String lifeStageS
         return null;
     }
 
-    public Address valueToAddress(Collection<String> problems, String addressString) {
-        if (!nullOrEmpty(addressString)) {
-            try {
-                return Address.valueOf(addressString);
-            } catch (IllegalArgumentException e) {
-                problems.add(e.getMessage());
-            }
+    /** Converts a string to a list of slot addresses */
+    public List<Address> valueToAddresses(Collection<String> problems, String addressString) {
+        if (nullOrEmpty(addressString)) {
+            return List.of();
         }
-        return null;
+        try {
+            return Arrays.stream(addressString.replace(',', ' ').split("\\s+"))
+                    .filter(s -> !s.isEmpty())
+                    .map(Address::valueOf)
+                    .toList();
+        } catch (IllegalArgumentException ignored) {
+            // try again without removing commas
+        }
+        try {
+            return Arrays.stream(addressString.split("\\s+"))
+                    .filter(s -> !s.isEmpty())
+                    .map(Address::valueOf)
+                    .toList();
+        } catch (IllegalArgumentException e) {
+            problems.add("Invalid addresses: "+repr(addressString));
+        }
+        return List.of();
     }
 
     /**

src/main/java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReader.java

@@ -24,7 +24,7 @@ enum Column implements IColumn {
         External_slide_ID(Pattern.compile("(external )?(slide (barcode|id|identifier)|barcode.*slide)", Pattern.CASE_INSENSITIVE|Pattern.DOTALL)),
         Prebarcode(String.class, Pattern.compile("(xenium( slide)?\\s*|pre)barcode", Pattern.CASE_INSENSITIVE), false),
         Lot(String.class, Pattern.compile("(xenium )?(slide )?lot\\b.*", Pattern.CASE_INSENSITIVE|Pattern.DOTALL), false),
-        Section_address,
+        Section_address(Pattern.compile("(section|slot)\\s*address(es)?\\b.*", Pattern.CASE_INSENSITIVE|Pattern.DOTALL)),
         Fixative,
         Embedding_medium,
         Donor_ID,
@@ -41,6 +41,7 @@ enum Column implements IColumn {
         Section_thickness(String.class),
         Date_sectioned(LocalDate.class, Pattern.compile("date.*sectioned|section.*date", Pattern.CASE_INSENSITIVE|Pattern.DOTALL), false),
         Section_position(Pattern.compile("(if.+)?(section\\s+)?position|position.*slot.*", Pattern.CASE_INSENSITIVE|Pattern.DOTALL)),
+        Comment(Void.class, Pattern.compile("(information|comment).*", Pattern.CASE_INSENSITIVE|Pattern.DOTALL), false),
         ;
 
         private final Pattern pattern;

src/main/java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReaderImp.java

@@ -104,7 +104,7 @@ public SectionRegisterLabware createRequestLabware(Collection<String> problems,
      */
     public SectionRegisterContent createRequestContent(Collection<String> problems, Map<Column, Object> row) {
         SectionRegisterContent content = new SectionRegisterContent();
-        content.setAddress(valueToAddress(problems, (String) row.get(Column.Section_address)));
+        content.setAddresses(valueToAddresses(problems, (String) row.get(Column.Section_address)));
         content.setExternalIdentifier((String) row.get(Column.Section_external_ID));
         content.setFixative((String) row.get(Column.Fixative));
         content.setHmdmc((String) row.get(Column.HuMFre));

src/main/resources/schema.graphqls

@@ -377,8 +377,8 @@ input BlockRegisterRequest {
 
 """Information about a section of tissue (already taken from some a block tracked elsewhere) to register."""
 input SectionRegisterContent {
-    """The address of the slot in the labware where this section should be created."""
-    address: Address!
+    """The addresses of the slots in the labware where this section should be created."""
+    addresses: [Address!]!
     """The species from which this section originates."""
     species: String!
     """The cellular classification of the section."""

src/test/java/uk/ac/sanger/sccp/stan/service/register/TestSectionRegisterService.java

@@ -295,8 +295,8 @@ public void testCreateLabware(boolean prebarcode) {
 
         verify(mockLwService).create(lt, prebarcode ? xb : null, xb);
 
-        verify(mockSlotRepo, times(2)).save(lw.getSlot(A1));
-        verify(mockSlotRepo).save(lw.getSlot(B2));
+        verify(mockSlotRepo, times(2)).saveAll(List.of(lw.getSlot(A1)));
+        verify(mockSlotRepo).saveAll(List.of(lw.getSlot(B2)));
 
         assertEquals(lw, result);
         assertThat(lw.getSlot(A1).getSamples()).containsExactlyInAnyOrder(sample1, sample2);
@@ -310,15 +310,15 @@ private SectionRegisterContent content(Address address, String extName) {
 
     private SectionRegisterContent content(Address address, String extName, String regionName) {
         SectionRegisterContent src = new SectionRegisterContent();
-        src.setAddress(address);
+        src.setAddresses(address==null ? List.of() : List.of(address));
         src.setExternalIdentifier(extName);
         src.setRegion(regionName);
         return src;
     }
 
     private SectionRegisterContent content(Address address, String extName, Integer thickness) {
         SectionRegisterContent content = new SectionRegisterContent();
-        content.setAddress(address);
+        content.setAddresses(address==null ? List.of() : List.of(address));
         content.setExternalIdentifier(extName);
         content.setSectionThickness(thickness==null ? null : thickness.toString());
         return content;

src/test/java/uk/ac/sanger/sccp/stan/service/register/TestSectionRegisterValidation.java

@@ -852,7 +852,7 @@ private static SectionRegisterContent content(String extName, Integer section, I
 
     private static SectionRegisterContent content(Address address, String regionName) {
         SectionRegisterContent src = new SectionRegisterContent();
-        src.setAddress(address);
+        src.setAddresses(address==null ? List.of() : List.of(address));
         src.setRegion(regionName);
         return src;
     }
@@ -966,7 +966,7 @@ private static SectionRegisterRequest labwareTypeRequest(Collection<?> data) {
                 assert current != null;
                 Address ad = (Address) obj;
                 SectionRegisterContent content = new SectionRegisterContent();
-                content.setAddress(ad);
+                content.setAddresses(ad==null ? List.of() : List.of(ad));
                 current.getContents().add(content);
             }
         }