Merge pull request #480 from sanger/strip

x1206 Label printing for strip-tube labels

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

@@ -11,6 +11,9 @@
 import java.util.function.Function;
 
 import static java.util.stream.Collectors.toMap;
+import static java.util.stream.Collectors.toSet;
+import static uk.ac.sanger.sccp.utils.BasicUtils.inMap;
+import static uk.ac.sanger.sccp.utils.BasicUtils.stream;
 
 public interface WorkRepo extends CrudRepository<Work, Integer> {
     Optional<Work> findByWorkNumber(String workNumber);
@@ -146,6 +149,32 @@ default Map<Integer, String> findWorkNumbersForReleaseIds(Collection<Integer> re
     @Query(value="select * from work_sample ws join work on (ws.work_id=work.id) where ws.sample_id=(?1) and ws.slot_id = (?2)", nativeQuery = true)
     Set<Work> findWorkForSampleIdAndSlotId(Integer sampleId, Integer slotId);
 
+    @Query(value="select slot_id, sample_id, work_id from work_sample ws where ws.slot_id in (?1)", nativeQuery = true)
+    List<Object[]> slotSampleWorkIdsForSlotIds(Collection<Integer> slotIds);
+
+    /**
+     * Loads works linked to the given slot ids.
+     * @param slotIds slot ids to look for works
+     * @return a map from slot/sample ids to the set of linked works
+     */
+    default Map<SlotIdSampleId, Set<Work>> slotSampleWorksForSlotIds(Collection<Integer> slotIds) {
+        List<Object[]> rows = slotIds.isEmpty() ? List.of() : slotSampleWorkIdsForSlotIds(slotIds);
+        if (rows.isEmpty()) {
+            return Map.of();
+        }
+        Set<Integer> workIds = rows.stream()
+                .map(arr -> (Integer) arr[2])
+                .collect(toSet());
+        Map<Integer, Work> workMap = stream(findAllById(workIds))
+                .collect(inMap(Work::getId));
+        Map<SlotIdSampleId, Set<Work>> map = new HashMap<>();
+        for (Object[] row: rows) {
+            SlotIdSampleId key = new SlotIdSampleId((Integer) row[0], (Integer) row[1]);
+            map.computeIfAbsent(key, k -> new HashSet<>()).add(workMap.get((Integer) row[2]));
+        }
+        return map;
+    }
+
     default Set<Work> getSetByWorkNumberIn(Collection<String> workNumbers) throws EntityNotFoundException {
         return RepoUtils.getSetByField(this::findAllByWorkNumberIn, workNumbers, Work::getWorkNumber,
                 "Unknown work number{s}: ", String::toUpperCase);

src/main/java/uk/ac/sanger/sccp/stan/service/label/LabwareLabelData.java

@@ -4,6 +4,8 @@
 
 import java.util.*;
 
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullToEmpty;
+
 /**
  * A collection of information that may be printed onto a labware label.
  * @author dr6
@@ -13,16 +15,22 @@ public class LabwareLabelData {
     private final String externalBarcode;
     private final String medium;
     private final String date;
-
     private final List<LabelContent> contents;
+    private final Map<String, String> extraFields;
 
     public LabwareLabelData(String barcode, String externalBarcode, String medium, String date,
-                            List<LabelContent> contents) {
+                            List<LabelContent> contents, Map<String, String> extraFields) {
         this.barcode = barcode;
         this.externalBarcode = externalBarcode;
         this.medium = medium;
         this.date = date;
-        this.contents = List.copyOf(contents);
+        this.contents = nullToEmpty(contents);
+        this.extraFields = nullToEmpty(extraFields);
+    }
+
+    public LabwareLabelData(String barcode, String externalBarcode, String medium, String date,
+                            List<LabelContent> contents) {
+        this(barcode, externalBarcode, medium, date, contents, null);
     }
 
     public String getBarcode() {
@@ -45,6 +53,10 @@ public List<LabelContent> getContents() {
         return this.contents;
     }
 
+    public Map<String, String> getExtraFields() {
+        return this.extraFields;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -54,7 +66,9 @@ public boolean equals(Object o) {
                 && Objects.equals(this.externalBarcode, that.externalBarcode)
                 && Objects.equals(this.medium, that.medium)
                 && Objects.equals(this.date, that.date)
-                && Objects.equals(this.contents, that.contents));
+                && Objects.equals(this.contents, that.contents)
+                && Objects.equals(this.extraFields, that.extraFields)
+        );
     }
 
     @Override
@@ -70,6 +84,7 @@ public String toString() {
                 .add("medium", medium)
                 .add("date", date)
                 .add("contents", contents)
+                .add("extraFields", extraFields)
                 .omitNullValues()
                 .reprStringValues()
                 .toString();
@@ -81,6 +96,7 @@ public Map<String, String> getFields() {
         fields.put("medium", getMedium());
         fields.put("date", getDate());
         fields.put("external", getExternalBarcode());
+        fields.putAll(getExtraFields());
         int index = 0;
         for (LabelContent content : contents) {
             addField(fields, "donor", index, content.donorName());

src/main/java/uk/ac/sanger/sccp/stan/service/label/LabwareLabelDataService.java

@@ -14,6 +14,7 @@
 
 import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toSet;
+import static uk.ac.sanger.sccp.utils.BasicUtils.reverseIter;
 
 /**
  * Service for creating LabwareLabelData from labware.
@@ -96,6 +97,53 @@ public LabwareLabelData toLabelData(Labware labware, List<LabelContent> content,
         return new LabwareLabelData(labware.getBarcode(), labware.getExternalBarcode(), medium, dateString, content);
     }
 
+    /**
+     * Label data for labware that has a label per slot
+     * @param lw the labware being labelled
+     * @param workNumbers the work number linked to each slot/sample combination
+     * @param lp the lp number linked to the labware, if any
+     * @return label data for the labware
+     */
+    public List<LabwareLabelData> getSplitLabelData(Labware lw, Map<SlotIdSampleId, String> workNumbers, String lp) {
+        List<LabwareLabelData> datas = new ArrayList<>(lw.getSlots().size());
+        // Iterate the slots in reverse order
+        for (Slot slot : reverseIter(lw.getSlots())) {
+            if (!slot.getSamples().isEmpty()) {
+                Sample sample = slot.getSamples().getFirst();
+                String workNumber = workNumbers.get(new SlotIdSampleId(slot, sample));
+                Tissue tissue = sample.getTissue();
+                LabelContent lc = new LabelContent(tissue.getDonor().getDonorName(), tissue.getExternalName(),
+                        null, sample.getBioState().toString());
+                Map<String, String> extra = filteredMap("lp", lp, "work", workNumber,
+                        "address", slot.getAddress().toString());
+                datas.add(new LabwareLabelData(lw.getBarcode(), lw.getExternalBarcode(), null, null,
+                        List.of(lc), extra));
+            }
+        }
+        return datas;
+    }
+
+    /**
+     * Returns a map containing the given keys and values, omitted null keys and null values
+     * @param data alternating keys and values
+     * @return a map containing the data, excluding null keys and values
+     * @param <B> type of data array given (base type of K and V)
+     * @param <K> key type
+     * @param <V> value type
+     */
+    @SuppressWarnings("unchecked")
+    static <B, K extends B, V extends B> Map<K,V> filteredMap(B... data) {
+        Map<K,V> map = new HashMap<>(data.length/2);
+        for (int i = 0; i < data.length; i+=2) {
+            K key = (K) data[i];
+            V value = (V) data[i+1];
+            if (key!=null && value!=null) {
+                map.put(key, value);
+            }
+        }
+        return map;
+    }
+
     /**
      * Label data where we list the tissue for each row.
      * @param labware the labware the label describes

src/main/java/uk/ac/sanger/sccp/stan/service/label/print/LabelPrintService.java

@@ -1,20 +1,24 @@
 package uk.ac.sanger.sccp.stan.service.label.print;
 
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import uk.ac.sanger.sccp.stan.model.*;
 import uk.ac.sanger.sccp.stan.repo.*;
+import uk.ac.sanger.sccp.stan.service.LabwareNoteService;
 import uk.ac.sanger.sccp.stan.service.LabwareService;
 import uk.ac.sanger.sccp.stan.service.label.*;
+import uk.ac.sanger.sccp.stan.service.work.WorkService;
+import uk.ac.sanger.sccp.utils.UCMap;
 
 import javax.persistence.EntityNotFoundException;
 import java.io.IOException;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 import java.util.function.Function;
 
-import static java.util.stream.Collectors.toList;
-import static java.util.stream.Collectors.toSet;
+import static java.util.stream.Collectors.*;
+import static uk.ac.sanger.sccp.utils.BasicUtils.nullOrEmpty;
+import static uk.ac.sanger.sccp.utils.UCMap.toUCMap;
 
 /**
  * Service to perform and record labware label printing
@@ -29,18 +33,22 @@ public class LabelPrintService {
     private final LabwarePrintRepo labwarePrintRepo;
     private final LabelTypeRepo labelTypeRepo;
     private final LabwareService labwareService;
+    private final LabwareNoteService noteService;
+    private final WorkService workService;
 
     @Autowired
     public LabelPrintService(LabwareLabelDataService labwareLabelDataService, PrintClientFactory printClientFactory,
                              LabwareRepo labwareRepo, PrinterRepo printerRepo, LabwarePrintRepo labwarePrintRepo,
-                             LabelTypeRepo labelTypeRepo, LabwareService labwareService) {
+                             LabelTypeRepo labelTypeRepo, LabwareService labwareService, LabwareNoteService noteService, WorkService workService) {
         this.labwareLabelDataService = labwareLabelDataService;
         this.printClientFactory = printClientFactory;
         this.labwareRepo = labwareRepo;
         this.printerRepo = printerRepo;
         this.labwarePrintRepo = labwarePrintRepo;
         this.labelTypeRepo = labelTypeRepo;
         this.labwareService = labwareService;
+        this.noteService = noteService;
+        this.workService = workService;
     }
 
     public void printLabwareBarcodes(User user, String printerName, List<String> barcodes) throws IOException {
@@ -66,20 +74,46 @@ public void printLabware(User user, String printerName, List<Labware> labware) t
             throw new IllegalArgumentException("Cannot perform a print request incorporating multiple different label types.");
         }
         LabelType labelType = labelTypes.iterator().next();
-        final Function<Labware, LabwareLabelData> labelFunction;
-        if (labelType.getName().equalsIgnoreCase("adh")) {
-            labelFunction = labwareLabelDataService::getRowBasedLabelData;
+        List<LabwareLabelData> labelData;
+        if (labelType.getName().equalsIgnoreCase("strip")) {
+            // NB if we try and label empty strip tubes from planned actions, it won't work
+            labelData = stripLabwareLabelData(labware);
         } else {
-            labelFunction = labwareLabelDataService::getLabelData;
+            final Function<Labware, LabwareLabelData> labelFunction;
+            if (labelType.getName().equalsIgnoreCase("adh")) {
+                labelFunction = labwareLabelDataService::getRowBasedLabelData;
+            } else {
+                labelFunction = labwareLabelDataService::getLabelData;
+            }
+            labelData = labware.stream()
+                    .map(labelFunction)
+                    .toList();
         }
-        List<LabwareLabelData> labelData = labware.stream()
-                .map(labelFunction)
-                .collect(toList());
         LabelPrintRequest request = new LabelPrintRequest(labelType, labelData);
         print(printer, request);
         recordPrint(printer, user, labware);
     }
 
+    /**
+     * Loads the strip label data for the given labware.
+     * Strip tube labware has multiple labels for each item of labware.
+     * @param labware the labware being labelled
+     * @return the label data for all the labware
+     */
+    @NotNull
+    List<LabwareLabelData> stripLabwareLabelData(List<Labware> labware) {
+        UCMap<String> lpNumbers = noteService.findNoteValuesForLabware(labware, "lp number").entrySet().stream()
+                .filter(e -> !nullOrEmpty(e.getValue()))
+                .collect(toUCMap(Map.Entry::getKey, e -> e.getValue().iterator().next()));
+        Map<SlotIdSampleId, Set<Work>> slotWorks = workService.loadWorksForSlotsIn(labware);
+        Map<SlotIdSampleId, String> slotWorkNumbers = slotWorks.entrySet().stream()
+                .filter(e -> !nullOrEmpty(e.getValue()))
+                .collect(toMap(Map.Entry::getKey, e -> e.getValue().iterator().next().getWorkNumber()));
+        return labware.stream()
+                .flatMap(lw -> labwareLabelDataService.getSplitLabelData(lw, slotWorkNumbers, lpNumbers.get(lw.getBarcode())).stream())
+                .toList();
+    }
+
     public void print(Printer printer, LabelPrintRequest request) throws IOException {
         PrintClient<? super LabelPrintRequest> printClient = printClientFactory.getClient(printer.getService());
         printClient.print(printer.getName(), request);

src/main/java/uk/ac/sanger/sccp/stan/service/work/WorkService.java

@@ -6,8 +6,7 @@
 import uk.ac.sanger.sccp.stan.request.WorkWithComment;
 import uk.ac.sanger.sccp.utils.UCMap;
 
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
 import java.util.stream.Stream;
 
 /**
@@ -222,6 +221,13 @@ Work createWork(User user, String prefix, String workTypeName, String workReques
      */
     List<Work> getWorksCreatedBy(User user);
 
+    /**
+     * Loads works linked to the slots in the given labware
+     * @param labware labware
+     * @return map of slot/sample ids to works
+     */
+    Map<SlotIdSampleId, Set<Work>> loadWorksForSlotsIn(Collection<Labware> labware);
+
     /**
      * struct-like container for a work and an operation
      */

src/main/java/uk/ac/sanger/sccp/stan/service/work/WorkServiceImp.java

@@ -507,6 +507,17 @@ public List<Work> getWorksCreatedBy(User user) {
                 .collect(toList());
     }
 
+    @Override
+    public Map<SlotIdSampleId, Set<Work>> loadWorksForSlotsIn(Collection<Labware> labware) {
+        return loadWorksForSlots(labware.stream()
+                .flatMap(lw -> lw.getSlots().stream()));
+    }
+
+    public Map<SlotIdSampleId, Set<Work>> loadWorksForSlots(Stream<Slot> slots) {
+        List<Integer> slotIds = slots.map(Slot::getId).toList();
+        return workRepo.slotSampleWorksForSlotIds(slotIds);
+    }
+
     public void fillInComments(Collection<WorkWithComment> wcs, Map<Integer, WorkEvent> workEvents) {
         for (WorkWithComment wc : wcs) {
             Work work = wc.getWork();

src/main/resources/sprint.properties

@@ -3,6 +3,7 @@ sprint.host = http://sprint.psd.sanger.ac.uk/graphql
 sprint.template_dir = sprint
 
 sprint.templates = {\
+  'strip' : 'strip.json',\
   'adh' : 'adh.json',\
   'slide@3' : 'slide3.json',\
   'slide@6' : 'slide6.json',\

src/main/resources/sprint/strip.json

@@ -0,0 +1,61 @@
+{
+  "labelSize": {
+    "width": 39,
+    "height": 8,
+    "displacement": 8
+  },
+  "barcodeFields": [
+    {
+      "x": 8,
+      "y": 1,
+      "value": "#barcode#",
+      "barcodeType": "datamatrix",
+      "cellWidth": 0.25
+    },
+    {
+      "x": 32,
+      "y": 1,
+      "value": "#barcode#",
+      "barcodeType": "datamatrix",
+      "cellWidth": 0.25
+    }
+  ],
+  "textFields": [
+    {
+      "x": 20,
+      "y": 2,
+      "value": "#work#",
+      "fontSize": 1.7
+    },
+    {
+      "x": 27,
+      "y": 2,
+      "value": "#lp#",
+      "fontSize": 1.7
+    },
+    {
+      "x": 12,
+      "y": 4,
+      "value": "#address#",
+      "fontSize": 1.8
+    },
+    {
+      "x": 20,
+      "y": 4,
+      "value": "#state[0]#",
+      "fontSize": 1.8
+    },
+    {
+      "x": 20,
+      "y": 6,
+      "value": "#tissue[0]#",
+      "fontSize": 1.5
+    },
+    {
+      "x": 8,
+      "y": 7,
+      "value": "#barcode#",
+      "fontSize": 1.5
+    }
+  ]
+}