Support predicate_id and mapping_justification being propagatable

cli/src/main/java/org/incenp/obofoundry/sssom/cli/SimpleCLI.java

@@ -263,6 +263,11 @@ boolean isCondensationEnabled() {
             return pr.hasMatchedOption("condensation") ? enableCondensation : defaultEnableCondensation;
         }
 
+        @Option(names = "--condense-all-slots",
+                defaultValue = "false",
+                description = "Condense all slots that can be condensed, even those for which the specification recommends against condensation. Note that `--no-condensation` takes precedence.")
+        boolean condenseAll;
+
         @Option(names = { "-f", "--output-format" },
                 paramLabel = "FMT",
                 description = "Write output in the specified format. Allowed values: ${COMPLETION-CANDIDATES}. Default is tsv.",
@@ -824,6 +829,7 @@ private SSSOMWriter getWriter(String filename, String metaFilename, Serialisatio
 
         writer.setExtraMetadataPolicy(outputOpts.getExtraMetadataPolicy());
         writer.setCondensationEnabled(outputOpts.isCondensationEnabled());
+        writer.setForceCondensation(outputOpts.condenseAll);
         writer.setSortingEnabled(outputOpts.sortMappings);
         writer.setTargetVersion(outputOpts.forceVersion);
         return writer;

core/src/main/java/org/incenp/obofoundry/sssom/JSONWriter.java

@@ -44,7 +44,6 @@
 import org.incenp.obofoundry.sssom.slots.ExtensionSlot;
 import org.incenp.obofoundry.sssom.slots.Slot;
 import org.incenp.obofoundry.sssom.slots.SlotHelper;
-import org.incenp.obofoundry.sssom.slots.SlotPropagator;
 import org.incenp.obofoundry.sssom.slots.SlotVisitorBase;
 import org.incenp.obofoundry.sssom.slots.StringSlot;
 import org.incenp.obofoundry.sssom.slots.VersionSlot;
@@ -132,7 +131,7 @@ public void setWriteCurieMapInContext(boolean enabled) {
     @Override
     protected void doWrite(MappingSet mappingSet) throws IOException {
         // Condense the set
-        Set<String> condensedSlots = new SlotPropagator(condensationPolicy).condense(mappingSet, true);
+        Set<String> condensedSlots = condenseSet(mappingSet);
 
         // Determine minimum compliant version
         mappingSet.setSssomVersion(Version.getCompliantVersion(mappingSet));

core/src/main/java/org/incenp/obofoundry/sssom/SSSOMWriter.java

@@ -47,6 +47,7 @@ public abstract class SSSOMWriter {
     protected Version targetVersion = Version.LATEST;
     protected ExtensionSlotManager extensionManager;
     protected PrefixManager prefixManager = new PrefixManager();
+    protected boolean forceCondensation = false;
     private boolean customMap = false;
     private boolean sortMappings = true;
 
@@ -85,6 +86,27 @@ public void setCondensationEnabled(boolean enabled) {
         condensationPolicy = enabled ? PropagationPolicy.NeverReplace : PropagationPolicy.Disabled;
     }
 
+    /**
+     * Enables or disables the condensation of “propagatable slots” that the SSSOM
+     * specification recommends <em>not</em> to condense.
+     * <p>
+     * The general rule about condensation is that all propagatable slots are
+     * condensable and should be condensed, but some slots are an exception in that,
+     * while they may be condensed, they generally should not be. The default
+     * behaviour of SSSOM writers is therefore not to condense such slots. Use this
+     * method to change that behaviour.
+     * <p>
+     * Note that {@link #setCondensationEnabled(boolean)} takes precedence over this
+     * method. That is, if condensation is disabled, then calling
+     * <code>setForceCondensation(true)</code> has no effect.
+     * 
+     * @param enabled If <code>true</code>, forces the writer to condense slots that
+     *                are better left non-condensed.
+     */
+    public void setForceCondensation(boolean enabled) {
+        forceCondensation = enabled;
+    }
+
     /**
      * Sets the highest version of the SSSOM specification that the written set must
      * be compliant with.
@@ -202,7 +224,7 @@ protected Set<String> getUsedPrefixes(MappingSet mappingSet, boolean includeBuil
      *         (may be empty if no slots have been condensed at all).
      */
     protected Set<String> condenseSet(MappingSet mappingSet) {
-        return new SlotPropagator(condensationPolicy, targetVersion).condense(mappingSet, true);
+        return new SlotPropagator(condensationPolicy, targetVersion, forceCondensation).condense(mappingSet, true);
     }
 
     /*

core/src/main/java/org/incenp/obofoundry/sssom/model/MappingSet.java

@@ -104,6 +104,18 @@ public class MappingSet  {
     @Propagatable
     private String objectSourceVersion;
 
+    @JsonProperty("predicate_id")
+    @EntityReference
+    @Propagatable(condensationDiscouraged=true)
+    @SlotURI("http://www.w3.org/2002/07/owl#annotatedProperty")
+    @Versionable(addedIn = Version.SSSOM_1_1)
+    private String predicateId;
+
+    @JsonProperty("predicate_label")
+    @Propagatable
+    @Versionable(addedIn = Version.SSSOM_1_1)
+    private String predicateLabel;
+
     @JsonProperty("predicate_type")
     @Propagatable
     @Versionable(addedIn = Version.SSSOM_1_1)
@@ -138,6 +150,12 @@ public class MappingSet  {
     @SlotURI("http://purl.org/dc/terms/created")
     private LocalDate mappingDate;
 
+    @JsonProperty("mapping_justification")
+    @EntityReference
+    @Propagatable(condensationDiscouraged=true)
+    @Versionable(addedIn = Version.SSSOM_1_1)
+    private String mappingJustification;
+
     @JsonProperty("publication_date")
     @SlotURI("http://purl.org/dc/terms/issued")
     private LocalDate publicationDate;
@@ -224,13 +242,16 @@ protected MappingSet(final Version sssomVersion,
             final EntityType objectType,
             final String objectSource,
             final String objectSourceVersion,
+            final String predicateId,
+            final String predicateLabel,
             final EntityType predicateType,
             final String mappingProvider,
             final List<String> cardinalityScope,
             final String mappingTool,
             final String mappingToolId,
             final String mappingToolVersion,
             final LocalDate mappingDate,
+            final String mappingJustification,
             final LocalDate publicationDate,
             final List<String> subjectMatchField,
             final List<String> objectMatchField,
@@ -263,13 +284,16 @@ protected MappingSet(final Version sssomVersion,
         this.objectType = objectType;
         this.objectSource = objectSource;
         this.objectSourceVersion = objectSourceVersion;
+        this.predicateId = predicateId;
+        this.predicateLabel = predicateLabel;
         this.predicateType = predicateType;
         this.mappingProvider = mappingProvider;
         this.cardinalityScope = cardinalityScope;
         this.mappingTool = mappingTool;
         this.mappingToolId = mappingToolId;
         this.mappingToolVersion = mappingToolVersion;
         this.mappingDate = mappingDate;
+        this.mappingJustification = mappingJustification;
         this.publicationDate = publicationDate;
         this.subjectMatchField = subjectMatchField;
         this.objectMatchField = objectMatchField;
@@ -618,6 +642,34 @@ public void setObjectSourceVersion(final String value) {
         this.objectSourceVersion = value;
     }
 
+    /**
+     * Gets the value of the <code>predicate_id</code> slot.
+     */
+    public String getPredicateId() {
+        return this.predicateId;
+    }
+
+    /**
+     * Sets the value of the <code>predicate_id</code> slot.
+     */
+    public void setPredicateId(final String value) {
+        this.predicateId = value;
+    }
+
+    /**
+     * Gets the value of the <code>predicate_label</code> slot.
+     */
+    public String getPredicateLabel() {
+        return this.predicateLabel;
+    }
+
+    /**
+     * Sets the value of the <code>predicate_label</code> slot.
+     */
+    public void setPredicateLabel(final String value) {
+        this.predicateLabel = value;
+    }
+
     /**
      * Gets the value of the <code>predicate_type</code> slot.
      */
@@ -731,6 +783,20 @@ public void setMappingDate(final LocalDate value) {
         this.mappingDate = value;
     }
 
+    /**
+     * Gets the value of the <code>mapping_justification</code> slot.
+     */
+    public String getMappingJustification() {
+        return this.mappingJustification;
+    }
+
+    /**
+     * Sets the value of the <code>mapping_justification</code> slot.
+     */
+    public void setMappingJustification(final String value) {
+        this.mappingJustification = value;
+    }
+
     /**
      * Gets the value of the <code>publication_date</code> slot.
      */
@@ -1156,6 +1222,16 @@ public String toString() {
             sb.append(this.objectSourceVersion);
             sb.append(",");
         }
+        if ( this.predicateId != null ) {
+            sb.append("predicate_id=");
+            sb.append(this.predicateId);
+            sb.append(",");
+        }
+        if ( this.predicateLabel != null ) {
+            sb.append("predicate_label=");
+            sb.append(this.predicateLabel);
+            sb.append(",");
+        }
         if ( this.predicateType != null ) {
             sb.append("predicate_type=");
             sb.append(this.predicateType);
@@ -1191,6 +1267,11 @@ public String toString() {
             sb.append(this.mappingDate);
             sb.append(",");
         }
+        if ( this.mappingJustification != null ) {
+            sb.append("mapping_justification=");
+            sb.append(this.mappingJustification);
+            sb.append(",");
+        }
         if ( this.publicationDate != null ) {
             sb.append("publication_date=");
             sb.append(this.publicationDate);
@@ -1294,13 +1375,16 @@ public boolean equals(final Object o) {
         if ( this.objectType == null ? other.objectType != null : !this.objectType.equals(other.objectType)) return false;
         if ( this.objectSource == null ? other.objectSource != null : !this.objectSource.equals(other.objectSource)) return false;
         if ( this.objectSourceVersion == null ? other.objectSourceVersion != null : !this.objectSourceVersion.equals(other.objectSourceVersion)) return false;
+        if ( this.predicateId == null ? other.predicateId != null : !this.predicateId.equals(other.predicateId)) return false;
+        if ( this.predicateLabel == null ? other.predicateLabel != null : !this.predicateLabel.equals(other.predicateLabel)) return false;
         if ( this.predicateType == null ? other.predicateType != null : !this.predicateType.equals(other.predicateType)) return false;
         if ( this.mappingProvider == null ? other.mappingProvider != null : !this.mappingProvider.equals(other.mappingProvider)) return false;
         if ( this.cardinalityScope == null ? other.cardinalityScope != null : !this.cardinalityScope.equals(other.cardinalityScope)) return false;
         if ( this.mappingTool == null ? other.mappingTool != null : !this.mappingTool.equals(other.mappingTool)) return false;
         if ( this.mappingToolId == null ? other.mappingToolId != null : !this.mappingToolId.equals(other.mappingToolId)) return false;
         if ( this.mappingToolVersion == null ? other.mappingToolVersion != null : !this.mappingToolVersion.equals(other.mappingToolVersion)) return false;
         if ( this.mappingDate == null ? other.mappingDate != null : !this.mappingDate.equals(other.mappingDate)) return false;
+        if ( this.mappingJustification == null ? other.mappingJustification != null : !this.mappingJustification.equals(other.mappingJustification)) return false;
         if ( this.publicationDate == null ? other.publicationDate != null : !this.publicationDate.equals(other.publicationDate)) return false;
         if ( this.subjectMatchField == null ? other.subjectMatchField != null : !this.subjectMatchField.equals(other.subjectMatchField)) return false;
         if ( this.objectMatchField == null ? other.objectMatchField != null : !this.objectMatchField.equals(other.objectMatchField)) return false;
@@ -1344,13 +1428,16 @@ public int hashCode() {
         result = result * PRIME + (this.objectType == null ? 43 : this.objectType.hashCode());
         result = result * PRIME + (this.objectSource == null ? 43 : this.objectSource.hashCode());
         result = result * PRIME + (this.objectSourceVersion == null ? 43 : this.objectSourceVersion.hashCode());
+        result = result * PRIME + (this.predicateId == null ? 43 : this.predicateId.hashCode());
+        result = result * PRIME + (this.predicateLabel == null ? 43 : this.predicateLabel.hashCode());
         result = result * PRIME + (this.predicateType == null ? 43 : this.predicateType.hashCode());
         result = result * PRIME + (this.mappingProvider == null ? 43 : this.mappingProvider.hashCode());
         result = result * PRIME + (this.cardinalityScope == null ? 43 : this.cardinalityScope.hashCode());
         result = result * PRIME + (this.mappingTool == null ? 43 : this.mappingTool.hashCode());
         result = result * PRIME + (this.mappingToolId == null ? 43 : this.mappingToolId.hashCode());
         result = result * PRIME + (this.mappingToolVersion == null ? 43 : this.mappingToolVersion.hashCode());
         result = result * PRIME + (this.mappingDate == null ? 43 : this.mappingDate.hashCode());
+        result = result * PRIME + (this.mappingJustification == null ? 43 : this.mappingJustification.hashCode());
         result = result * PRIME + (this.publicationDate == null ? 43 : this.publicationDate.hashCode());
         result = result * PRIME + (this.subjectMatchField == null ? 43 : this.subjectMatchField.hashCode());
         result = result * PRIME + (this.objectMatchField == null ? 43 : this.objectMatchField.hashCode());
@@ -1387,13 +1474,16 @@ public static class MappingSetBuilder {
         private EntityType objectType;
         private String objectSource;
         private String objectSourceVersion;
+        private String predicateId;
+        private String predicateLabel;
         private EntityType predicateType;
         private String mappingProvider;
         private List<String> cardinalityScope;
         private String mappingTool;
         private String mappingToolId;
         private String mappingToolVersion;
         private LocalDate mappingDate;
+        private String mappingJustification;
         private LocalDate publicationDate;
         private List<String> subjectMatchField;
         private List<String> objectMatchField;
@@ -1502,6 +1592,16 @@ public MappingSet.MappingSetBuilder objectSourceVersion(final String objectSourc
             return this;
         }
 
+        public MappingSet.MappingSetBuilder predicateId(final String predicateId) {
+            this.predicateId = predicateId;
+            return this;
+        }
+
+        public MappingSet.MappingSetBuilder predicateLabel(final String predicateLabel) {
+            this.predicateLabel = predicateLabel;
+            return this;
+        }
+
         public MappingSet.MappingSetBuilder predicateType(final EntityType predicateType) {
             this.predicateType = predicateType;
             return this;
@@ -1537,6 +1637,11 @@ public MappingSet.MappingSetBuilder mappingDate(final LocalDate mappingDate) {
             return this;
         }
 
+        public MappingSet.MappingSetBuilder mappingJustification(final String mappingJustification) {
+            this.mappingJustification = mappingJustification;
+            return this;
+        }
+
         public MappingSet.MappingSetBuilder publicationDate(final LocalDate publicationDate) {
             this.publicationDate = publicationDate;
             return this;
@@ -1626,13 +1731,16 @@ public MappingSet build() {
                 this.objectType,
                 this.objectSource,
                 this.objectSourceVersion,
+                this.predicateId,
+                this.predicateLabel,
                 this.predicateType,
                 this.mappingProvider,
                 this.cardinalityScope,
                 this.mappingTool,
                 this.mappingToolId,
                 this.mappingToolVersion,
                 this.mappingDate,
+                this.mappingJustification,
                 this.publicationDate,
                 this.subjectMatchField,
                 this.objectMatchField,
@@ -1668,13 +1776,16 @@ public String toString() {
                 + ", objectType=" + this.objectType
                 + ", objectSource=" + this.objectSource
                 + ", objectSourceVersion=" + this.objectSourceVersion
+                + ", predicateId=" + this.predicateId
+                + ", predicateLabel=" + this.predicateLabel
                 + ", predicateType=" + this.predicateType
                 + ", mappingProvider=" + this.mappingProvider
                 + ", cardinalityScope=" + this.cardinalityScope
                 + ", mappingTool=" + this.mappingTool
                 + ", mappingToolId=" + this.mappingToolId
                 + ", mappingToolVersion=" + this.mappingToolVersion
                 + ", mappingDate=" + this.mappingDate
+                + ", mappingJustification=" + this.mappingJustification
                 + ", publicationDate=" + this.publicationDate
                 + ", subjectMatchField=" + this.subjectMatchField
                 + ", objectMatchField=" + this.objectMatchField
@@ -1716,13 +1827,16 @@ public MappingSet.MappingSetBuilder toBuilder() {
             .objectType(this.objectType)
             .objectSource(this.objectSource)
             .objectSourceVersion(this.objectSourceVersion)
+            .predicateId(this.predicateId)
+            .predicateLabel(this.predicateLabel)
             .predicateType(this.predicateType)
             .mappingProvider(this.mappingProvider)
             .cardinalityScope(this.cardinalityScope)
             .mappingTool(this.mappingTool)
             .mappingToolId(this.mappingToolId)
             .mappingToolVersion(this.mappingToolVersion)
             .mappingDate(this.mappingDate)
+            .mappingJustification(this.mappingJustification)
             .publicationDate(this.publicationDate)
             .subjectMatchField(this.subjectMatchField)
             .objectMatchField(this.objectMatchField)

core/src/main/java/org/incenp/obofoundry/sssom/model/Propagatable.java

@@ -33,5 +33,5 @@
 @Retention(RUNTIME)
 @Target(FIELD)
 public @interface Propagatable {
-
+    boolean condensationDiscouraged() default false;
 }

core/src/main/java/org/incenp/obofoundry/sssom/slots/Slot.java

@@ -121,6 +121,18 @@ public boolean isPropagatable(Version inVersion) {
         return field.isAnnotationPresent(Propagatable.class) && getCompliantVersion().isCompatibleWith(inVersion);
     }
 
+    /**
+     * Indicates whether the SSSOM specification recommends against condensing this
+     * slot.
+     * 
+     * @return {@code true} if condensing the slot is discouraged by the
+     *         specification, otherwise {@code false}.
+     */
+    public boolean isCondensationDiscouraged() {
+        Propagatable annot = field.getAnnotation(Propagatable.class);
+        return annot != null ? annot.condensationDiscouraged() : false;
+    }
+
     /**
      * Indicates whether the slot is expected to contain a URI.
      *