x1263 add priority field to flag

src/main/java/uk/ac/sanger/sccp/stan/GraphQLDataFetchers.java

@@ -13,6 +13,8 @@
 import uk.ac.sanger.sccp.stan.repo.*;
 import uk.ac.sanger.sccp.stan.request.*;
 import uk.ac.sanger.sccp.stan.request.LabwareRoi.RoiResult;
+import uk.ac.sanger.sccp.stan.request.history.History;
+import uk.ac.sanger.sccp.stan.request.history.HistoryGraph;
 import uk.ac.sanger.sccp.stan.service.*;
 import uk.ac.sanger.sccp.stan.service.extract.ExtractResultQueryService;
 import uk.ac.sanger.sccp.stan.service.flag.FlagLookupService;
@@ -214,10 +216,10 @@ public DataFetcher<LabwareFlagged> findLabwareFlagged() {
                 throw new IllegalArgumentException("No barcode supplied.");
             }
             Labware lw = labwareRepo.getByBarcode(barcode);
-            if (requestsField(dfe, "flagged")) {
+            if (requestsField(dfe, "flagged") || requestsField(dfe, "flagPriority")) {
                 return flagLookupService.getLabwareFlagged(lw);
             }
-            return new LabwareFlagged(lw, false);
+            return new LabwareFlagged(lw, null);
         };
     }
 

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

@@ -11,6 +11,10 @@
  */
 @Entity
 public class LabwareFlag {
+    public enum Priority implements Comparable<Priority> {
+        note, flag
+    }
+
     @Id
     @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Integer id;
@@ -23,12 +27,17 @@ public class LabwareFlag {
     private User user;
     private Integer operationId;
 
-    public LabwareFlag(Integer id, Labware labware, String description, User user, Integer operationId) {
+    @Column(columnDefinition = "enum('note', 'flag')")
+    @Enumerated(EnumType.STRING)
+    private Priority priority = Priority.flag;
+
+    public LabwareFlag(Integer id, Labware labware, String description, User user, Integer operationId, Priority priority) {
         this.id = id;
         this.labware = labware;
         this.description = description;
         this.user = user;
         this.operationId = operationId;
+        this.priority = priority;
     }
 
     public LabwareFlag() {}
@@ -77,6 +86,14 @@ public void setOperationId(Integer operationId) {
         this.operationId = operationId;
     }
 
+    public Priority getPriority() {
+        return this.priority;
+    }
+
+    public void setPriority(Priority priority) {
+        this.priority = priority;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
@@ -86,7 +103,9 @@ public boolean equals(Object o) {
                 && Objects.equals(this.labware, that.labware)
                 && Objects.equals(this.description, that.description)
                 && Objects.equals(this.user, that.user)
-                && Objects.equals(this.operationId, that.operationId));
+                && Objects.equals(this.operationId, that.operationId)
+                && this.priority==that.priority
+        );
     }
 
     @Override
@@ -102,6 +121,7 @@ public String toString() {
                 .addRepr("description", description)
                 .add("user", user==null ? null : user.getUsername())
                 .add("operationId", operationId)
+                .add("priority", priority)
                 .toString();
     }
 }

src/main/java/uk/ac/sanger/sccp/stan/request/FlagDetail.java

@@ -1,5 +1,7 @@
 package uk.ac.sanger.sccp.stan.request;
 
+import uk.ac.sanger.sccp.stan.model.LabwareFlag.Priority;
+
 import java.util.List;
 import java.util.Objects;
 
@@ -17,10 +19,12 @@ public class FlagDetail {
     public static class FlagSummary {
         private String barcode;
         private String description;
+        private Priority priority;
 
-        public FlagSummary(String barcode, String description) {
+        public FlagSummary(String barcode, String description, Priority priority) {
             this.barcode = barcode;
             this.description = description;
+            this.priority = priority;
         }
 
         /**
@@ -45,13 +49,23 @@ public void setDescription(String description) {
             this.description = description;
         }
 
+        public Priority getPriority() {
+            return this.priority;
+        }
+
+        public void setPriority(Priority priority) {
+            this.priority = priority;
+        }
+
         @Override
         public boolean equals(Object o) {
             if (this == o) return true;
             if (o == null || getClass() != o.getClass()) return false;
             FlagSummary that = (FlagSummary) o;
             return (Objects.equals(this.barcode, that.barcode)
-                    && Objects.equals(this.description, that.description));
+                    && Objects.equals(this.description, that.description)
+                    && this.priority == that.priority
+            );
         }
 
         @Override
@@ -61,7 +75,7 @@ public int hashCode() {
 
         @Override
         public String toString() {
-            return String.format("[%s: %s]", barcode, repr(description));
+            return String.format("[%s: %s: %s]", priority, barcode, repr(description));
         }
     }
 

src/main/java/uk/ac/sanger/sccp/stan/request/FlagLabwareRequest.java

@@ -1,5 +1,6 @@
 package uk.ac.sanger.sccp.stan.request;
 
+import uk.ac.sanger.sccp.stan.model.LabwareFlag.Priority;
 import uk.ac.sanger.sccp.utils.BasicUtils;
 
 import java.util.Objects;
@@ -12,11 +13,13 @@ public class FlagLabwareRequest {
     private String barcode;
     private String description;
     private String workNumber;
+    private Priority priority;
 
-    public FlagLabwareRequest(String barcode, String description, String workNumber) {
+    public FlagLabwareRequest(String barcode, String description, String workNumber, Priority priority) {
         this.barcode = barcode;
         this.description = description;
         this.workNumber = workNumber;
+        this.priority = priority;
     }
 
     // required for framework
@@ -53,14 +56,24 @@ public void setWorkNumber(String workNumber) {
         this.workNumber = workNumber;
     }
 
+    public Priority getPriority() {
+        return this.priority;
+    }
+
+    public void setPriority(Priority priority) {
+        this.priority = priority;
+    }
+
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         FlagLabwareRequest that = (FlagLabwareRequest) o;
         return (Objects.equals(this.barcode, that.barcode)
                 && Objects.equals(this.description, that.description)
-                && Objects.equals(this.workNumber, that.workNumber));
+                && Objects.equals(this.workNumber, that.workNumber)
+                && this.priority == that.priority
+        );
     }
 
     @Override
@@ -74,6 +87,7 @@ public String toString() {
                 .add("barcode", barcode)
                 .add("description", description)
                 .addIfNotNull("workNumber", workNumber)
+                .add("priority", priority)
                 .reprStringValues()
                 .toString();
     }

src/main/java/uk/ac/sanger/sccp/stan/request/LabwareFlagged.java

@@ -2,6 +2,7 @@
 
 import org.jetbrains.annotations.NotNull;
 import uk.ac.sanger.sccp.stan.model.*;
+import uk.ac.sanger.sccp.stan.model.LabwareFlag.Priority;
 
 import java.time.LocalDateTime;
 import java.util.List;
@@ -15,11 +16,11 @@
 public class LabwareFlagged {
     @NotNull
     private final Labware labware;
-    private final boolean flagged;
+    private final Priority flagPriority;
 
-    public LabwareFlagged(Labware labware, boolean flagged) {
+    public LabwareFlagged(Labware labware, Priority priority) {
         this.labware = requireNonNull(labware, "labware is null");
-        this.flagged = flagged;
+        this.flagPriority = priority;
     }
 
     /**
@@ -108,15 +109,20 @@ public Labware getLabware() {
      * Is there a labware flag applicable to this labware?
      */
     public boolean isFlagged() {
-        return this.flagged;
+        return this.flagPriority != null;
+    }
+
+    /** The highest priority of flag on the labware, if any */
+    public Priority getFlagPriority() {
+        return this.flagPriority;
     }
 
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         LabwareFlagged that = (LabwareFlagged) o;
-        return (this.flagged == that.flagged
+        return (this.flagPriority == that.flagPriority
                 && this.labware.equals(that.labware));
     }
 
@@ -127,6 +133,6 @@ public int hashCode() {
 
     @Override
     public String toString() {
-        return String.format("LabwareFlagged(%s, %s)", labware.getBarcode(), flagged);
+        return String.format("LabwareFlagged(%s, %s)", labware.getBarcode(), flagPriority);
     }
 }

src/main/java/uk/ac/sanger/sccp/stan/request/history/FlagBarcodes.java

@@ -0,0 +1,47 @@
+package uk.ac.sanger.sccp.stan.request.history;
+
+import uk.ac.sanger.sccp.stan.model.LabwareFlag.Priority;
+
+import java.util.List;
+import java.util.Objects;
+
+/**
+ * A flagged labware barcode and its flag priority
+ * @author dr6
+ */
+public class FlagBarcodes {
+    private final Priority priority;
+    private final List<String> barcodes;
+
+    public FlagBarcodes(Priority priority, List<String> barcodes) {
+        this.priority = priority;
+        this.barcodes = barcodes;
+    }
+
+    public Priority getPriority() {
+        return this.priority;
+    }
+
+    public List<String> getBarcodes() {
+        return this.barcodes;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        FlagBarcodes that = (FlagBarcodes) o;
+        return (this.priority == that.priority
+                && Objects.equals(this.barcodes, that.barcodes));
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(priority, barcodes);
+    }
+
+    @Override
+    public String toString() {
+        return String.format("(%s: %s)", priority, barcodes);
+    }
+}

src/main/java/uk/ac/sanger/sccp/stan/request/History.java → src/main/java/uk/ac/sanger/sccp/stan/request/history/History.java

@@ -1,13 +1,10 @@
-package uk.ac.sanger.sccp.stan.request;
+package uk.ac.sanger.sccp.stan.request.history;
 
-import uk.ac.sanger.sccp.stan.model.Labware;
-import uk.ac.sanger.sccp.stan.model.Sample;
-import uk.ac.sanger.sccp.utils.BasicUtils;
+import uk.ac.sanger.sccp.stan.model.*;
 
-import java.util.List;
-import java.util.Objects;
+import java.util.*;
 
-import static uk.ac.sanger.sccp.utils.BasicUtils.nullToEmpty;
+import static uk.ac.sanger.sccp.utils.BasicUtils.*;
 
 /**
  * @author dr6
@@ -16,21 +13,22 @@ public class History {
     private List<HistoryEntry> entries;
     private List<Sample> samples;
     private List<Labware> labware;
-    private List<String> flaggedBarcodes;
+    private Map<LabwareFlag.Priority, List<String>> flagPriorityBarcodes;
 
-    public History(List<HistoryEntry> entries, List<Sample> samples, List<Labware> labware, List<String> flaggedBarcodes) {
+    public History(List<HistoryEntry> entries, List<Sample> samples, List<Labware> labware,
+                   Map<LabwareFlag.Priority, List<String>> flagPriorityBarcodes) {
         setEntries(entries);
         setSamples(samples);
         setLabware(labware);
-        setFlaggedBarcodes(flaggedBarcodes);
+        setFlagPriorityBarcodes(flagPriorityBarcodes);
     }
 
     public History(List<HistoryEntry> entries, List<Sample> samples, List<Labware> labware) {
         this(entries, samples, labware, null);
     }
 
     public History() {
-        this(null, null, null);
+        this(null, null, null, null);
     }
 
     public List<HistoryEntry> getEntries() {
@@ -57,12 +55,25 @@ public void setLabware(List<Labware> labware) {
         this.labware = nullToEmpty(labware);
     }
 
-    public List<String> getFlaggedBarcodes() {
-        return this.flaggedBarcodes;
+    public Map<LabwareFlag.Priority, List<String>> getFlagPriorityBarcodes() {
+        return this.flagPriorityBarcodes;
     }
 
-    public void setFlaggedBarcodes(List<String> flaggedBarcodes) {
-        this.flaggedBarcodes = nullToEmpty(flaggedBarcodes);
+    public void setFlagPriorityBarcodes(Map<LabwareFlag.Priority, List<String>> flagPriorityBarcodes) {
+        this.flagPriorityBarcodes = nullToEmpty(flagPriorityBarcodes);
+    }
+
+    /**
+     * Gets flagged barcodes as a list pairing up a priority with a list of barcodes
+     * @return a list of {@code FlagBarcodes} objects
+     */
+    public List<FlagBarcodes> getFlagBarcodes() {
+        if (nullOrEmpty(flagPriorityBarcodes)) {
+            return List.of();
+        }
+        return flagPriorityBarcodes.entrySet().stream()
+                .map(e -> new FlagBarcodes(e.getKey(), e.getValue()))
+                .toList();
     }
 
     @Override
@@ -73,7 +84,7 @@ public boolean equals(Object o) {
         return (Objects.equals(this.entries, that.entries)
                 && Objects.equals(this.samples, that.samples)
                 && Objects.equals(this.labware, that.labware)
-                && Objects.equals(this.flaggedBarcodes, that.flaggedBarcodes));
+                && Objects.equals(this.flagPriorityBarcodes, that.flagPriorityBarcodes));
     }
 
     @Override
@@ -83,11 +94,11 @@ public int hashCode() {
 
     @Override
     public String toString() {
-        return BasicUtils.describe("History")
+        return describe("History")
                 .add("entries", entries)
                 .add("samples", samples)
                 .add("labware", labware)
-                .add("flaggedBarcodes", flaggedBarcodes)
+                .add("flagPriorityBarcodes", flagPriorityBarcodes)
                 .toString();
     }
 }