x1216: Allow section register to specify date sectioned

Add to SectionRegisterContent and SectionRegisterFileReader. Record the given date as a measurement. Look up the measurement ancestrally for the section date in the release file.
sanger · Jun 26, 2024 · c13fd03 · c13fd03
1 parent b1d7635
commit c13fd03
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Showing 9 changed files with 179 additions and 31 deletions.
diff --git a/src/main/java/uk/ac/sanger/sccp/stan/request/register/SectionRegisterContent.java b/src/main/java/uk/ac/sanger/sccp/stan/request/register/SectionRegisterContent.java
@@ -4,6 +4,7 @@
 import uk.ac.sanger.sccp.stan.model.LifeStage;
 import uk.ac.sanger.sccp.utils.BasicUtils;
 
+import java.time.LocalDate;
 import java.util.Objects;
 
 /**
@@ -25,6 +26,7 @@ public class SectionRegisterContent {
     private Integer sectionNumber;
     private Integer sectionThickness;
     private String region;
+    private LocalDate dateSectioned;
 
     public SectionRegisterContent() {}
 
@@ -147,6 +149,15 @@ public void setRegion(String region) {
         this.region = region;
     }
 
+    /** The date the sample was sectioned */
+    public LocalDate getDateSectioned() {
+        return this.dateSectioned;
+    }
+
+    public void setDateSectioned(LocalDate dateSectioned) {
+        this.dateSectioned = dateSectioned;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -166,6 +177,7 @@ public boolean equals(Object o) {
                 && Objects.equals(this.sectionNumber, that.sectionNumber)
                 && Objects.equals(this.sectionThickness, that.sectionThickness)
                 && Objects.equals(this.region, that.region)
+                && Objects.equals(this.dateSectioned, that.dateSectioned)
         );
     }
 
@@ -191,6 +203,7 @@ public String toString() {
                 .add("sectionNumber", sectionNumber)
                 .add("sectionThickness", sectionThickness)
                 .add("region", region)
+                .add("dateSectioned", dateSectioned)
                 .reprStringValues()
                 .omitNullValues()
                 .toString();

diff --git a/src/main/java/uk/ac/sanger/sccp/stan/service/register/SectionRegisterServiceImp.java b/src/main/java/uk/ac/sanger/sccp/stan/service/register/SectionRegisterServiceImp.java
@@ -248,14 +248,23 @@ public Operation createOp(User user, OperationType opType, Labware lw) {
      * @return the measurements created
      */
     public Iterable<Measurement> createMeasurements(SectionRegisterLabware srl, Labware lw, Operation op,
-                                                UCMap<Sample> sampleMap) {
-        List<Measurement> measurements = srl.getContents().stream()
-                .filter(content -> content.getSectionThickness() != null)
-                .map(content -> new Measurement(
-                        null, "Thickness", content.getSectionThickness().toString(),
-                        sampleMap.get(content.getExternalIdentifier()).getId(), op.getId(),
-                        lw.getSlot(content.getAddress()).getId()))
-                .collect(toList());
+                                                    UCMap<Sample> sampleMap) {
+        List<Measurement> measurements = new ArrayList<>();
+        for (var src : srl.getContents()) {
+            if (src.getDateSectioned() == null && src.getSectionThickness() == null) {
+                continue;
+            }
+            Sample sample = sampleMap.get(src.getExternalIdentifier());
+            Slot slot = lw.getSlot(src.getAddress());
+            if (src.getSectionThickness() != null) {
+                measurements.add(new Measurement(null, "Thickness", src.getSectionThickness().toString(),
+                        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()));
+            }
+        }
         return (measurements.isEmpty() ? measurements : measurementRepo.saveAll(measurements));
     }
 

diff --git a/...in/java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReader.java b/...in/java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReader.java
@@ -6,6 +6,7 @@
 import uk.ac.sanger.sccp.stan.service.ValidationException;
 
 import java.io.IOException;
+import java.time.LocalDate;
 import java.util.List;
 import java.util.regex.Pattern;
 
@@ -34,6 +35,7 @@ enum Column implements IColumn {
         Section_external_ID,
         Section_number(Integer.class),
         Section_thickness(Integer.class),
+        Date_sectioned(LocalDate.class, Pattern.compile("date.*sectioned|section.*date", Pattern.CASE_INSENSITIVE), false),
         Section_position(Pattern.compile("(if.+)?(section\\s+)?position", Pattern.CASE_INSENSITIVE)),
         ;
 
@@ -64,7 +66,7 @@ public String toString() {
             return this.name().replace('_',' ');
         }
 
-        /** The data type (String or Integer) expected in the column. */
+        /** The data type (e.g. String or Integer) expected in the column. */
         @Override
         public Class<?> getDataType() {
             return this.dataType;

diff --git a/...java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReaderImp.java b/...java/uk/ac/sanger/sccp/stan/service/register/filereader/SectionRegisterFileReaderImp.java
@@ -9,6 +9,7 @@
 
 import java.io.IOException;
 import java.nio.file.*;
+import java.time.LocalDate;
 import java.util.*;
 
 import static java.util.stream.Collectors.toList;
@@ -39,7 +40,7 @@ public SectionRegisterRequest createRequest(Collection<String> problems, List<Ma
         String groupx = null;
         String workNumber = getUniqueString(rows.stream().map(row -> (String) row.get(Column.Work_number)),
                 () -> problems.add("Multiple work numbers specified."));
-        if(nullOrEmpty(workNumber)) {
+        if (nullOrEmpty(workNumber)) {
             problems.add("Missing work number.");
         }
 
@@ -114,6 +115,7 @@ public SectionRegisterContent createRequestContent(Collection<String> problems,
         content.setTissueType((String) row.get(Column.Tissue_type));
         content.setSpatialLocation((Integer) row.get(Column.Spatial_location));
         content.setRegion((String) row.get(Column.Section_position));
+        content.setDateSectioned((LocalDate) row.get(Column.Date_sectioned));
         return content;
     }
 

diff --git a/src/main/java/uk/ac/sanger/sccp/stan/service/releasefile/ReleaseFileService.java b/src/main/java/uk/ac/sanger/sccp/stan/service/releasefile/ReleaseFileService.java
@@ -18,6 +18,8 @@
 import uk.ac.sanger.sccp.utils.tsv.TsvColumn;
 
 import javax.persistence.EntityNotFoundException;
+import java.time.LocalDate;
+import java.time.format.DateTimeParseException;
 import java.util.*;
 import java.util.function.Consumer;
 import java.util.stream.Collectors;
@@ -514,6 +516,65 @@ public void loadSectionDate(Collection<ReleaseEntry> entries, Ancestry ancestry)
                 }
             });
         }
+
+        Map<SlotIdSampleId, LocalDate> slotSampleSectionDates = findSlotSampleDates(
+                measurementRepo.findAllBySlotIdInAndName(slotIds, "Date sectioned")
+        );
+        if (!slotSampleSectionDates.isEmpty()) {
+            for (ReleaseEntry entry : entries) {
+                if (entry.getSlot() != null && entry.getSample() != null && entry.getSectionDate() == null) {
+                    entry.setSectionDate(findEntrySectionDate(entry, slotSampleSectionDates, ancestry));
+                }
+            }
+        }
+    }
+
+    /**
+     * Loads the section date for the given entry from the given map using the given ancestry
+     * @param entry the entry to load the date for
+     * @param slotSampleSectionDates map of slot/sample ids to section date
+     * @param ancestry the ancestry for the slot/samples
+     * @return the section date for the given entry
+     */
+    public LocalDate findEntrySectionDate(ReleaseEntry entry, Map<SlotIdSampleId, LocalDate> slotSampleSectionDates,
+                                          Ancestry ancestry) {
+        SlotSample entrySs = new SlotSample(entry.getSlot(), entry.getSample());
+        for (SlotSample ss : ancestry.ancestors(entrySs)) {
+            LocalDate date = slotSampleSectionDates.get(new SlotIdSampleId(ss.slotId(), ss.sampleId()));
+            if (date != null) {
+                return date;
+            }
+        }
+        return null;
+    }
+
+    /**
+     * Builds a map from slot/sample ids to the localdate in the given measurements
+     * @param measurements the measurements to look through
+     * @return a map from slot/sample ids to the relevant date in the measurements
+     */
+    public Map<SlotIdSampleId, LocalDate> findSlotSampleDates(Collection<Measurement> measurements) {
+        if (measurements.isEmpty()) {
+            return Map.of();
+        }
+        Map<SlotIdSampleId, LocalDate> map = new HashMap<>(measurements.size());
+        for (Measurement measurement : measurements) {
+            if (measurement.getSampleId()==null || measurement.getSlotId()==null || measurement.getValue()==null) {
+                continue;
+            }
+            LocalDate value;
+            try {
+                value = LocalDate.parse(measurement.getValue());
+            } catch (DateTimeParseException e) {
+                continue;
+            }
+            SlotIdSampleId key = new SlotIdSampleId(measurement.getSlotId(), measurement.getSampleId());
+            LocalDate oldValue = map.get(key);
+            if (oldValue==null || oldValue.isBefore(value)) {
+                map.put(key, value);
+            }
+        }
+        return map;
     }
 
     /**

diff --git a/src/main/resources/schema.graphqls b/src/main/resources/schema.graphqls
@@ -336,6 +336,8 @@ input SectionRegisterContent {
     sectionThickness: Int
     """The region of this sample in this slot, if any."""
     region: String
+    """The date the sample was sectioned."""
+    dateSectioned: Date
 }
 
 """A request to register one or more sections into one piece of labware."""

diff --git a/src/test/java/uk/ac/sanger/sccp/stan/service/register/TestSectionRegisterService.java b/src/test/java/uk/ac/sanger/sccp/stan/service/register/TestSectionRegisterService.java
@@ -1,29 +1,20 @@
 package uk.ac.sanger.sccp.stan.service.register;
 
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.*;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
 import org.mockito.Mock;
 import org.mockito.MockitoAnnotations;
 import uk.ac.sanger.sccp.stan.EntityFactory;
 import uk.ac.sanger.sccp.stan.model.*;
 import uk.ac.sanger.sccp.stan.repo.*;
-import uk.ac.sanger.sccp.stan.request.register.RegisterResult;
-import uk.ac.sanger.sccp.stan.request.register.SectionRegisterContent;
-import uk.ac.sanger.sccp.stan.request.register.SectionRegisterLabware;
-import uk.ac.sanger.sccp.stan.request.register.SectionRegisterRequest;
-import uk.ac.sanger.sccp.stan.service.LabwareService;
-import uk.ac.sanger.sccp.stan.service.OperationService;
-import uk.ac.sanger.sccp.stan.service.ValidationException;
+import uk.ac.sanger.sccp.stan.request.register.*;
+import uk.ac.sanger.sccp.stan.service.*;
 import uk.ac.sanger.sccp.stan.service.work.WorkService;
 import uk.ac.sanger.sccp.utils.UCMap;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.List;
+import java.time.LocalDate;
+import java.util.*;
 import java.util.stream.IntStream;
 import java.util.stream.Stream;
 
@@ -429,8 +420,10 @@ public void testCreateMeasurements() {
                 content(A1, xns[0], 14),
                 content(A1, xns[1], 15),
                 content(B1, xns[2]),
-                content(B2, xns[3], 16)
+                content(B2, xns[3])
         );
+        contents.get(1).setDateSectioned(LocalDate.of(2024,1,13));
+        contents.get(3).setDateSectioned(LocalDate.of(2024,2,14));
 
         UCMap<Sample> sampleMap = UCMap.from((Sample sam) -> sam.getTissue().getExternalName(), samples);
         SectionRegisterLabware srl = new SectionRegisterLabware(lw.getExternalBarcode(), lt.getName(), contents);
@@ -447,7 +440,8 @@ public void testCreateMeasurements() {
         verify(mockMeasurementRepo).saveAll(List.of(
                 new Measurement(null, "Thickness", "14", samples[0].getId(), opId, slotA1.getId()),
                 new Measurement(null, "Thickness", "15", samples[1].getId(), opId, slotA1.getId()),
-                new Measurement(null, "Thickness", "16", samples[3].getId(), opId, slotB2.getId())
+                new Measurement(null, "Date sectioned", "2024-01-13", samples[1].getId(), opId, slotA1.getId()),
+                new Measurement(null, "Date sectioned", "2024-02-14", samples[3].getId(), opId, slotB2.getId())
         ));
     }
 

diff --git a/...ava/uk/ac/sanger/sccp/stan/service/register/filereader/TestSectionRegisterFileReader.java b/...ava/uk/ac/sanger/sccp/stan/service/register/filereader/TestSectionRegisterFileReader.java
@@ -129,7 +129,7 @@ void testIndexColumns() {
         Row row = mockRow("work number", "slide type", "external slide id", "xenium barcode",
                 "section address", "fixative", "embedding medium", "donor id", "life stage",
                 "species", "humfre", "tissue type", "spatial location", "replicate number",
-                "section external id", "section number", "section thickness", "if bla bla bla position", null, "");
+                "section external id", "section number", "section thickness", "date sectioned", "if bla bla bla position", null, "");
         List<String> problems = new ArrayList<>();
         var result = reader.indexColumns(problems, row);
         assertThat(problems).isEmpty();