Add "linked from" section

dataload/linker/src/main/java/LinkerPass2.java

@@ -149,13 +149,14 @@ private static void writeEntityArray(JsonReader jsonReader, JsonWriter jsonWrite
             jsonWriter.beginObject();
             jsonReader.beginObject();
 
-            Set<String> stringsInEntity = new HashSet<String>();
+            Set<String> relatedFromStringsInEntity = new HashSet<String>();
+            Set<String> allOtherStringsInEntity = new HashSet<String>();
             String entityIri = null;
 
             while(jsonReader.peek() != JsonToken.END_OBJECT) {
 
                 String name = jsonReader.nextName();
-                stringsInEntity.add(ExtractIriFromPropertyName.extract(name));
+                allOtherStringsInEntity.add(ExtractIriFromPropertyName.extract(name));
                 jsonWriter.name(name);
 
                 if(name.equals("iri")) {
@@ -165,8 +166,10 @@ private static void writeEntityArray(JsonReader jsonReader, JsonWriter jsonWrite
                     processCurieObject(jsonReader, jsonWriter, pass1Result, entityIri);
                 } else if (name.equalsIgnoreCase("shortForm")) {
                     processShortFormObject(jsonReader, jsonWriter, pass1Result, entityIri);
+                } else if (name.equalsIgnoreCase("relatedFrom")) {
+                    CopyJsonGatheringStrings.copyJsonGatheringStrings(jsonReader, jsonWriter, relatedFromStringsInEntity);
                 } else {
-                    CopyJsonGatheringStrings.copyJsonGatheringStrings(jsonReader, jsonWriter, stringsInEntity);
+                    CopyJsonGatheringStrings.copyJsonGatheringStrings(jsonReader, jsonWriter, allOtherStringsInEntity);
                 }
             }
 
@@ -197,7 +200,24 @@ private static void writeEntityArray(JsonReader jsonReader, JsonWriter jsonWrite
             }
 
             jsonWriter.name("linkedEntities");
-            var linksToIris = writeLinkedEntitiesFromGatheredStrings(jsonWriter, stringsInEntity, ontologyId, entityIri, leveldb, pass1Result);
+            jsonWriter.beginObject();
+
+            /*
+             * "relatedFrom" is a special field because it contains INCOMING properties
+             * rather than outgoing. We therefore don't want to include any of the IRIs
+             * referenced in "relatedFrom" in the "linksTo" array because they are not
+             * actually linked to (rather the opposite). But we still need them in "linkedEntities"
+             * so we can display them in the UI. 
+             */
+
+            var linksToIris = writeLinkedEntitiesFromGatheredStrings(jsonWriter, allOtherStringsInEntity, ontologyId, entityIri, leveldb, pass1Result);
+
+            relatedFromStringsInEntity.removeAll(allOtherStringsInEntity);
+            if(relatedFromStringsInEntity.size() > 0) {
+                writeLinkedEntitiesFromGatheredStrings(jsonWriter, relatedFromStringsInEntity, ontologyId, entityIri, leveldb, pass1Result);
+            }
+
+            jsonWriter.endObject(); // linkedEntities
 
             jsonWriter.name("linksTo");
             jsonWriter.beginArray();
@@ -248,8 +268,6 @@ private static Set<String> writeLinkedEntitiesFromGatheredStrings(JsonWriter jso
 
         Set<String> linksToIris = new HashSet<>();
 
-        jsonWriter.beginObject();
-
         for(String str : strings) {
 
             if(str.trim().length() == 0) {
@@ -371,8 +389,6 @@ private static Set<String> writeLinkedEntitiesFromGatheredStrings(JsonWriter jso
 
         }
 
-        jsonWriter.endObject(); // linkedEntities
-
         return linksToIris;
     }
 

frontend/.env

@@ -1,9 +1,9 @@
 
 PUBLIC_URL=/
 
-REACT_APP_APIURL=http://localhost:8080/
-#OLS_DEV_BACKEND_PROXY_URL=http://www.ebi.ac.uk/ols4/
-OLS_DEV_BACKEND_PROXY_URL=http://localhost:8080/
+REACT_APP_APIURL=http://localhost:3000/
+OLS_DEV_BACKEND_PROXY_URL=http://www.ebi.ac.uk/ols4/
+#OLS_DEV_BACKEND_PROXY_URL=http://localhost:8080/
 
 REACT_APP_EBI_LICENSING=https://www.ebi.ac.uk/licencing
 REACT_APP_SPOT_HOME=https://www.ebi.ac.uk/spot

frontend/src/model/Entity.ts

@@ -3,10 +3,10 @@ import { LinkedEntity } from "./LinkedEntities";
 import Reified from "./Reified";
 import Thing from "./Thing";
 
-export default abstract class Entity extends Thing {
-  abstract getParents(): Reified<any>[];
-  abstract getSuperEntities(): Reified<any>[];
-  abstract getEquivalents(): Reified<any>[];
+export default class Entity extends Thing {
+  getParents(): Reified<any>[] { return [] }
+  getSuperEntities(): Reified<any>[] { return [] }
+  getEquivalents(): Reified<any>[] { return [] }
 
   isCanonical(): boolean {
     return this.properties["isDefiningOntology"] === true;

frontend/src/pages/ontologies/entities/EntityPage.tsx

@@ -51,6 +51,7 @@ import addLinksToText from "./entityPageSections/addLinksToText";
 import { Helmet } from 'react-helmet'
 import { Typography } from "@mui/material";
 import SimilarEntitiesSection from "./entityPageSections/SimilarEntitiesSection";
+import LinkedFromSection from "./entityPageSections/LinkedFromSection";
 
 export default function EntityPage({
   entityType,
@@ -499,6 +500,10 @@ export default function EntityPage({
                       classInstances={classInstances}
                       linkedEntities={linkedEntities}
                     />
+                    <LinkedFromSection
+                      entity={entity}
+                      linkedEntities={linkedEntities}
+                    />
                   </div>
                 </details>
                 <details open className="p-2">

frontend/src/pages/ontologies/entities/entityPageSections/LinkedFromSection.tsx

@@ -0,0 +1,76 @@
+
+import { Fragment, useEffect, useState } from "react";
+import { randomString } from "../../../../app/util";
+import EntityLink from "../../../../components/EntityLink";
+import Class from "../../../../model/Class";
+import Entity from "../../../../model/Entity";
+import LinkedEntities from "../../../../model/LinkedEntities";
+import Property from "../../../../model/Property";
+import { Link, useSearchParams } from "react-router-dom";
+import { getPaginated, Page } from "../../../../app/api";
+
+export default function LinkedFromSection({entity, linkedEntities}:{entity:Entity, linkedEntities:LinkedEntities}) {
+
+    let [linkedfrom, setLinkedFrom] = useState<Page<any>|null>(null);
+
+    const [searchParams] = useSearchParams();
+    let lang = searchParams.get("lang") || "en";
+
+    useEffect(() => {
+        setLinkedFrom(null)
+        const fetchLinkedFromEntities = async () => {
+            let page = await getPaginated<any>(`api/v2/entities`, { linksTo: entity.getIri(), size: '5' })
+            setLinkedFrom(page)
+        };
+        fetchLinkedFromEntities();
+
+    }, [entity?.getOntologyId(), entity?.getIri()])
+
+    if(!entity) {
+        return <Fragment/>
+    }
+
+    return <div>
+        <div className="font-bold">Linked from</div>
+        { !linkedfrom && <i>Loading...</i> }
+        { linkedfrom && linkedfrom.numElements === 0 && <Fragment/> }
+        { linkedfrom && linkedfrom.numElements > 0 && <Fragment> <ul className="list-disc list-inside">
+            {linkedfrom.elements.map(
+                (elem) => {
+                    return new Entity(elem)
+                }
+            ).map((otherEntity:Entity) => {
+                return (
+                <li key={entity.getId()}>
+                <Link
+                    className="link-default"
+                    to={`/ontologies/${otherEntity.getOntologyId()}/${
+                        otherEntity.getTypePlural()
+                    }/${encodeURIComponent(encodeURIComponent(otherEntity.getIri()))}?lang=${lang}`}
+                >
+                    {otherEntity.getName()}
+                    <span
+                    className="link-ontology px-2 py-0.5 rounded-md text-sm text-white uppercase ml-1"
+                    title={otherEntity.getOntologyId().toUpperCase()}
+                    >
+                    {otherEntity.getOntologyId()}
+                    </span>
+                </Link>
+                </li>
+                )
+            })}
+        </ul>
+
+        {linkedfrom.totalElements > 5 && (
+            <Link
+              className="link-default italic"
+              to={`/search?linksTo=${encodeURIComponent(entity.getIri())}&lang=${lang}`}
+            >
+                + {linkedfrom.totalElements - 5}
+            </Link>
+        )}
+        </Fragment>
+        }
+    </div>
+
+}

frontend/src/pages/ontologies/entities/entityPageSections/SimilarEntitiesSection.tsx

@@ -30,7 +30,7 @@ export default function SimilarEntitiesSection({entity}:{entity:Entity}) {
             fetchSimilarEntities();
         }
 
-    }, [entity?.getIri()])
+    }, [entity?.getOntologyId(), entity?.getIri()])
 
     if(!entity || (entity.getType() !== 'class' && entity.getType() !== 'property')) {
         return <Fragment/>