CoEDL
diff --git a/‎api/package-lock.json
+963-947 b/‎api/package-lock.json
+963-947
diff --git a/‎api/package.json
+9-8 b/‎api/package.json
+9-8
diff --git a/‎api/src/common/elastic-index.js
+42-59 b/‎api/src/common/elastic-index.js
+42-59
diff --git a/‎api/src/lib/admin.js
+23-9 b/‎api/src/lib/admin.js
+23-9
diff --git a/‎api/src/routes/admin.js
+1 b/‎api/src/routes/admin.js
+1
@@ -15,11 +15,11 @@
     },
     "devDependencies": {
         "@babel/cli": "^7.22.15",
-        "@babel/core": "^7.22.17",
-        "@babel/node": "^7.22.15",
+        "@babel/core": "^7.22.20",
+        "@babel/node": "^7.22.19",
         "@babel/plugin-proposal-optional-chaining": "^7.21.0",
         "@babel/plugin-syntax-import-assertions": "^7.22.5",
-        "@babel/preset-env": "^7.22.15",
+        "@babel/preset-env": "^7.22.20",
         "babel-jest": "^29.7.0",
         "babel-loader": "^9.1.3",
         "chance": "^1.1.11",
@@ -29,20 +29,20 @@
         "nodemon": "^3.0.1"
     },
     "dependencies": {
-        "@aws-sdk/client-ses": "^3.410.0",
+        "@aws-sdk/client-ses": "^3.414.0",
         "@coedl/nocfl-js": "^2.0.0",
         "@describo/data-packs": "^0.10.0",
         "@elastic/elasticsearch": "^8.9.0",
         "@fastify/compress": "^6.4.0",
-        "@fastify/cors": "^8.3.0",
+        "@fastify/cors": "^8.4.0",
         "@fastify/one-line-logger": "^1.2.0",
-        "@fastify/sensible": "^5.2.0",
+        "@fastify/sensible": "^5.3.0",
         "@paradisec-platform/fastify-tus-s3-plugin": "^1.0.0",
         "cross-fetch": "^4.0.0",
         "date-fns": "^2.30.0",
         "elastic-builder": "^2.22.0",
-        "fastify": "^4.23.0",
-        "fastify-socket.io": "^4.0.0",
+        "fastify": "^4.23.2",
+        "fastify-socket.io": "^5.0.0",
         "foo-foo-mq": "^8.0.1",
         "form-data": "^4.0.0",
         "fs-extra": "^11.1.1",
@@ -60,6 +60,7 @@
         "saxon-js": "^2.5.0",
         "sequelize": "^6.33.0",
         "sequelize-cli": "^6.6.1",
+        "socket.io": "^4.7.2",
         "uuid": "^9.0.1",
         "validator": "^13.11.0",
         "winston": "^3.10.0"
 
@@ -1,6 +1,6 @@
 import { getStoreHandle } from "./index.js";
 import lodashPkg from "lodash";
-const { isArray, isString, isPlainObject, flattenDeep } = lodashPkg;
+const { isArray, isString, isPlainObject, flattenDeep, compact } = lodashPkg;
 import fsExtraPkg from "fs-extra";
 const { createReadStream } = fsExtraPkg;
 import { Client } from "@elastic/elasticsearch";
@@ -10,16 +10,9 @@ import { ROCrate } from "ro-crate";
 import FormData from "form-data";
 import fetch from "cross-fetch";
 
-const typesToExcludeFromIndex = ["File", "GeoShape", "GeoCoordinates", "Language"];
-
-export async function indexItem({ configuration, item, crate }) {
-    // let configuration = await loadConfiguration();
-    // console.log(configuration);
-    // console.log(item);
-    // console.log(crate);
-
-    // get the complete tei file and run it through the webservice to extract the text
+const typesToExcludeFromIndex = ["File", "GeoShape", "GeoCoordinates"];
 
+export async function indexItem({ location = "workspace", configuration, item, crate }) {
     crate = new ROCrate(crate, { array: true, link: true });
     // let document = crate.getTree({ valueObject: false });
 
@@ -29,18 +22,29 @@ export async function indexItem({ configuration, item, crate }) {
 
     // setup the metadata index
     try {
-        // await client.indices.delete({ index: "metadata" });
-        await client.indices.get({ index: "metadata" });
+        // await client.indices.delete({ index: "manuscripts" });
+        await client.indices.get({ index: "manuscripts" });
     } catch (error) {
         await client.indices.create({
-            index: "metadata",
+            index: "manuscripts",
+            mappings: {
+                properties: {
+                    location: {
+                        type: "geo_shape",
+                    },
+                    // languageSuggest: {
+                    //     type: "completion",
+                    // },
+                },
+            },
             settings: { "index.mapping.ignore_malformed": true },
         });
     }
 
+    // index the item metadata and content
     const indexIdentifier = `/${item.type}/${item.identifier}`;
     try {
-        let store = await getStoreHandle({ id: item.identifier, type: "item" });
+        let store = await getStoreHandle({ location, id: item.identifier, type: "item" });
         const teiFileContent = await store.get({
             target: `${item.identifier}-tei-complete.xml`,
         });
@@ -51,10 +55,11 @@ export async function indexItem({ configuration, item, crate }) {
         const document = assembleIndexRecord({ crate });
         document.text = teiText;
         await client.index({
-            index: "metadata",
+            index: "manuscripts",
             id: indexIdentifier,
             document,
         });
+        // console.log(document);
     } catch (error) {
         console.log(error);
     }
@@ -83,7 +88,7 @@ export async function deleteItemFromIndex({ item, configuration }) {
 
     const indexIdentifier = `/${item.type}/${item.identifier}`;
     await client.delete({
-        index: "metadata",
+        index: "manuscripts",
         id: indexIdentifier,
     });
 }
@@ -112,7 +117,7 @@ export function assembleIndexRecord({ crate }) {
         access: crate.rootDataset?.licence?.[0].name?.[0] ?? "Restricted",
         location: geography,
     };
-    // console.log(record);
+    // record.languageSuggest = [...record.subjectLanguage, ...record.contentLanguage];
     return record;
 }
 
@@ -133,49 +138,27 @@ export function extractGeography({ crate }) {
             '{"type":"Feature","geometry":{"type":"Polygon","coordinates":[[[58.07810783386231,29.095852076791065],[58.07810783386231,-19.12303093039881],[11.671857833862305,-19.12303093039881],[11.671857833862305,29.095852076791065]]]}}',
         ],
     });
-    const geography = entities.map((entity) => {
-        if (entity?.geojson?.length) {
-            let geojson = JSON.parse(entity.geojson[0]);
-
-            let coordinates = geojson?.geometry?.coordinates.map((e) => {
-                if (isString(e)) return parseFloat(e);
-                if (isArray(e)) {
-                    return [
-                        e.map((c) => {
-                            return parseFloat(c);
-                        }),
-                    ];
-                }
-            });
-            // console.log(JSON.stringify(coordinates, null, 2));
-            return coordinates;
+    let coordinates = flattenDeep(entities.map((e) => JSON.parse(e.geojson).geometry)).map(
+        (feature) => {
+            feature.coordinates = parseValuesAsFloat(feature.coordinates);
+            if (feature.type.match(/polygon/i)) {
+                feature.coordinates[0].push(feature.coordinates[0][0]);
+            }
+            return feature;
         }
-    });
-
-    // console.log(JSON.stringify(geography, null, 2));
-
-    return geography;
-
-    // const feature = {
-    //     type: "Feature",
-    //     properties: { name: "Yorta Yorta" },
-    //     geometry: { type: "Point", coordinates: [145.26357989848, -36.093929709321] },
-    // };
-
-    // const feature = {
-    //     type: "Feature",
-    //     geometry: {
-    //         type: "Polygon",
-    //         coordinates: [
-    //             [
-    //                 [144.56249892711642, -27.126287638023676],
-    //                 [144.56249892711642, -29.486150057382325],
-    //                 [138.27831923961642, -29.486150057382325],
-    //                 [138.27831923961642, -27.126287638023676],
-    //             ],
-    //         ],
-    //     },
-    // };
+    );
+    // console.log("2", JSON.stringify(coordinates, null, 2));
+    coordinates = compact(coordinates);
+    return coordinates;
+
+    function parseValuesAsFloat(arr) {
+        return arr.map((v) => {
+            if (isArray(v)) {
+                return parseValuesAsFloat(v);
+            }
+            return parseFloat(v);
+        });
+    }
 }
 
 // TODO this method does not have tests
 
@@ -190,7 +190,7 @@ export async function publishObject({ user, type, identifier, configuration }) {
 
     // try indexing the content and fail early if the metadata is bad
     try {
-        await indexItem({ item: { identifier, type }, crate: crate.toJSON() });
+        await indexItem({ configuration, item: { identifier, type }, crate: crate.toJSON() });
     } catch (error) {
         throw new Error(
             `Metadata is invalid and can't be indexed. It needs to be fixed in order to publish the object.`
@@ -274,6 +274,7 @@ export async function objectRequiresMoreWork({ type, identifier }) {
 }
 
 export async function depositObjectIntoRepository({
+    configuration,
     type,
     identifier,
     version = { metadata: false, images: false, documents: false },
@@ -334,7 +335,11 @@ export async function depositObjectIntoRepository({
         msg: `Copying ${type} resources to the repository`,
         date: new Date(),
     });
-    await objectRepository.copy({ batch: resources });
+    try {
+        await objectRepository.copy({ batch: resources });
+    } catch (error) {
+        console.error(error);
+    }
 
     // delete the files from the workspace entry
     io.emit(`deposit-${type}`, {
@@ -351,7 +356,11 @@ export async function depositObjectIntoRepository({
     item = item[0];
 
     // setup the metadata in the db
-    await setRepositoryItemMetadata({ item, store: objectRepository });
+    try {
+        await setRepositoryItemMetadata({ configuration, item, store: objectRepository });
+    } catch (error) {
+        console.error(error);
+    }
 }
 
 export async function restoreObjectIntoWorkspace({ type, identifier, io = { emit: () => {} } }) {
@@ -386,11 +395,11 @@ export async function restoreObjectIntoWorkspace({ type, identifier, io = { emit
     let resources = await objectRepository.listResources();
     resources = resources
         .filter((resource) => !resource.Key.match(/nocfl.*/))
-        // .filter((resource) => {
-        //     return !resource.Key.match(
-        //         /.*\.v\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d:[0-5]\d\.\d+([+-][0-2]\d:[0-5]\d|Z).*/
-        //     );
-        // })
+        .filter((resource) => {
+            return !resource.Key.match(
+                /.*\.v\d{4}-[01]\d-[0-3]\dT[0-2]\d:[0-5]\d:[0-5]\d\.\d+([+-][0-2]\d:[0-5]\d|Z).*/
+            );
+        })
         .map((resource) => {
             return {
                 target: resource.Key,
@@ -440,7 +449,12 @@ export async function setRepositoryItemMetadata({ configuration, item, store })
         await item.save();
 
         // index the item data in the repository
-        await indexItem({ configuration, item: { identifier, type }, crate: crate.toJSON() });
+        await indexItem({
+            location: "repository",
+            configuration,
+            item: { identifier, type },
+            crate: crate.toJSON(),
+        });
     } catch (error) {
         console.log(error);
         log.error(`There was an issue depositing '${type}:${identifier}: ${error.message}`);
 
@@ -176,6 +176,7 @@ async function putDepositObjectHandler(req, res) {
         date: new Date(),
     });
     await depositObjectIntoRepository({
+        configuration: req.session.configuration,
         type,
         identifier,
         version,