ditch more barrel file imports and fix tests

CoEDL · Nov 17, 2023 · 9307832 · 9307832
1 parent 8a8a719
commit 9307832
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Showing 23 changed files with 222 additions and 111 deletions.
diff --git a/api/src/common/aws-ses.spec.js b/api/src/common/aws-ses.spec.js
@@ -28,13 +28,14 @@ describe("AWS SES tests", () => {
         let templates = await ses.listTemplates();
         templates.TemplatesMetadata = templates.TemplatesMetadata.filter(
             (t) => !t.Name.match(/production-/)
-        );
+        ).filter((t) => !t.Name.match(/development-/));
         expect(templates.TemplatesMetadata).toEqual([]);
+
         await ses.loadTemplates();
         templates = await ses.listTemplates();
         templates.TemplatesMetadata = templates.TemplatesMetadata.filter(
             (t) => !t.Name.match(/production-/)
-        );
+        ).filter((t) => !t.Name.match(/development-/));
         expect(templates.TemplatesMetadata).toMatchObject([{ Name: "testing-application-login" }]);
     });
     it("should be able to send a templated email", async () => {

diff --git a/api/src/common/elastic-index.js b/api/src/common/elastic-index.js
@@ -43,26 +43,27 @@ export async function indexItem({ location = "workspace", configuration, item, c
 
     // index the item metadata and content
     const indexIdentifier = `/${item.type}/${item.identifier}`;
+    let store = await getStoreHandle({ location, id: item.identifier, type: "item" });
+    let teiText;
     try {
-        let store = await getStoreHandle({ location, id: item.identifier, type: "item" });
         const teiFileContent = await store.get({
             target: `${item.identifier}-tei-complete.xml`,
         });
-        let teiText = await extractText({
+        teiText = await extractText({
             configuration,
             content: teiFileContent,
         });
-        const document = assembleIndexRecord({ crate });
-        document.text = teiText;
-        await client.index({
-            index: "manuscripts",
-            id: indexIdentifier,
-            document,
-        });
-        // console.log(document);
     } catch (error) {
-        console.log(error);
+        teiText = "";
     }
+    const document = assembleIndexRecord({ crate });
+    document.text = teiText;
+    await client.index({
+        index: "manuscripts",
+        id: indexIdentifier,
+        document,
+    });
+    // console.log(document);
     // setup the entities index
     try {
         // await client.indices.delete({ index: "entities" });

diff --git a/api/src/common/jwt.spec.js b/api/src/common/jwt.spec.js
@@ -1,9 +1,9 @@
 require("regenerator-runtime");
 import { generateToken, verifyToken } from "./jwt";
-import { loadConfiguration } from "../common";
+import { loadConfiguration } from "../common/configuration.js";
 const chance = require("chance").Chance();
 import MockDate from "mockdate";
-import { TestSetup } from "../common";
+import { TestSetup } from "../common/test-utils.js";
 
 describe("JWT tests", () => {
     let configuration, users, userEmail, adminEmail, bucket;

diff --git a/api/src/common/logger.spec.js b/api/src/common/logger.spec.js
@@ -1,5 +1,5 @@
 import "regenerator-runtime";
-import { logEvent } from "./logger";
+import { logEvent } from "./logger.js";
 import models from "../models";
 describe("Logger tests", () => {
     it("should be able to log an event to the logs table", async () => {

diff --git a/api/src/common/test-utils.js b/api/src/common/test-utils.js
@@ -12,6 +12,101 @@ import { getS3Handle } from "./getS3Handle.js";
 
 const bucketName = "testing";
 export const host = `http://localhost:8080`;
+export function teiDocument(identifier) {
+    return `
+<?xml version="1.0" encoding="UTF-8"?>
+    <TEI xmlns="http://www.tei-c.org/ns/1.0" xmlns:c="http://www.w3.org/ns/xproc-step" xmlns:cx="http://xmlcalabash.com/ns/extensions" xmlns:fn="http://www.w3.org/2005/xpath-functions" xmlns:nyingarn="https://nyingarn.net/ns/functions" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:z="https://github.com/Conal-Tuohy/XProc-Z" xml:id="MarcoTest">
+    <teiHeader>
+    <fileDesc><titleStmt><title>My Research Object Crate</title></titleStmt><publicationStmt><publisher><ref target="https://nyingarn.net/">Nyingarn</ref></publisher></publicationStmt><sourceDesc><p>some text</p></sourceDesc></fileDesc>
+   <xenoData type="application/ld+json">{
+    "@graph": [
+    {
+      "identifier": "ro-crate-metadata.json",
+      "@type": "CreativeWork",
+      "about": { "@id": ".\/" },
+      "@id": "ro-crate-metadata.json",
+      "conformsTo": { "@id": "https:\/\/w3id.org\/ro\/crate\/1.1" }
+    },
+    {
+      "rightsHolder": { "@id": "https:\/\/orcid.org\/0000-0003-1783-627X" },
+      "identifier": "MarcoTest",
+      "licence": { "@id": "LICENCE.md" },
+      "hasPart": [
+        { "@id": "MarcoTest-357.jpg" },
+        { "@id": "MarcoTest-357.tei.xml" },
+        { "@id": "MarcoTest-357.textract_ocr-ADMIN.json" },
+        { "@id": "MarcoTest-357.thumbnail_h300.jpg" },
+        { "@id": "MarcoTest-357.webp" },
+        { "@id": "MarcoTest-4003.jpg" },
+        { "@id": "MarcoTest-4003.tei.xml" },
+        { "@id": "MarcoTest-4003.textract_ocr-ADMIN.json" },
+        { "@id": "MarcoTest-4003.thumbnail_h300.jpg" },
+        { "@id": "MarcoTest-4003.webp" },
+        { "@id": "MarcoTest-language-authority-permission.pdf" },
+        { "@id": "MarcoTest-rights-holder-permission.pdf" },
+        { "@id": ".item-status.json" },
+        { "@id": "MarcoTest-tei-complete.xml" },
+        { "@id": "LICENCE.md" },
+        { "@id": "MarcoTest-tei-complete.v2023-07-10T03:50:13.975Z.xml" }
+      ],
+      "@type": [ "Dataset" ],
+      "author": { "@id": "https:\/\/orcid.org\/0000-0003-1783-627X" },
+      "description": "some text",
+      "languageName": "more text",
+      "subjectLanguage": { "@id": "https:\/\/collection.aiatsis.gov.au\/austlang\/language\/D2" },
+      "copyrightStatus": "Yes = in copyright",
+      "name": "My Research Object Crate",
+      "contentLanguage": [
+        { "@id": "https:\/\/collection.aiatsis.gov.au\/austlang\/language\/W40" },
+        { "@id": "https:\/\/collection.aiatsis.gov.au\/austlang\/language\/A48" },
+        { "@id": "#e27" }
+      ],
+      "depositor": { "@id": "https:\/\/orcid.org\/0000-0001-5383-6993" },
+      "@id": ".\/"
+    },
+    ]
+   }</xenodata>
+    </teiHeader><text><body><pb xml:id="${identifier}-357"/>
+<ab>A<lb/>
+English and <unclear>Aboriginal</unclear><lb/>
+A<lb/>
+<unclear>Allow</unclear><lb/>
+Anoy<lb/>
+Along<lb/>
+<unclear>Kash</unclear> too bur-roin<lb/>
+answer<lb/>
+<unclear>Foom</unclear> boon<lb/>
+-<lb/>
+Also<lb/>
+<unclear>tey</unclear><lb/>
+<unclear>ant</unclear> <unclear>small kind</unclear><lb/>
+<unclear>Beal-</unclear> <unclear>belp</unclear><lb/>
+<unclear>Ber</unclear><lb/>
+<unclear>ser-gun</unclear><lb/>
+do bull<lb/>
+<unclear>nur</unclear> <unclear>murn</unclear><lb/>
+<unclear>Amidel</unclear><lb/>
+<unclear>Bar-go-rut</unclear><lb/>
+Ankle<lb/>
+Beur nar <unclear>fer</unclear><lb/>
+Amiss<lb/>
+<unclear>nil</unclear> lam<lb/>
+apartment<lb/>
+<unclear>Wil-mut</unclear><lb/>
+and<lb/>
+Bar<lb/>
+apple<lb/>
+Bool <unclear>le-vrum</unclear><lb/>
+<unclear>anget</unclear><lb/>
+Pork <unclear>bork/bar-ren</unclear><lb/>
+<unclear>War-ra</unclear> <unclear>three</unclear><lb/>
+<unclear>Lam-bar-more</unclear><lb/>
+another<lb/>
+<unclear>th</unclear> ung<lb/>
+arch on Gap<lb/>
+Pear - <unclear>bor</unclear> ring</ab>
+</body></text></TEI>`;
+}
 
 export function headers(session) {
     return {
@@ -107,6 +202,10 @@ export async function setupTestItem({ identifier, store, user }) {
                 content: "text",
                 target: `${identifier}-02.txt`,
             },
+            {
+                content: teiDocument(identifier),
+                target: `${identifier}-tei-complete.xml`,
+            },
         ],
     });
     return { item };

diff --git a/api/src/lib/admin.js b/api/src/lib/admin.js
@@ -427,17 +427,28 @@ export async function setRepositoryItemMetadata({ configuration, item, store })
 
     try {
         let licence = crate.getEntity("LICENCE.md");
-        if (!licence) throw new Error(`no licence found - setting to closed`);
-        let openAccess = false;
-        let accessControlList = null;
-        let accessNarrative = null;
-        let reviewDate = null;
-        if (licence?.access?.[0]?.["@id"]?.match(/OpenAccess/)) {
-            openAccess = true;
+        let openAccess;
+        let accessControlList;
+        let accessNarrative;
+        let reviewDate;
+        if (!licence) {
+            console.log(`no licence found - setting to closed`);
+            openAccess = false;
+            accessControlList = null;
+            accessNarrative = null;
+            reviewDate = null;
         } else {
-            accessNarrative = licence.description.join("\n");
-            reviewDate = licence?.reviewDate?.[0];
-            accessControlList = await store.getJSON({ target: authorisedUsersFile });
+            openAccess = false;
+            accessControlList = null;
+            accessNarrative = null;
+            reviewDate = null;
+            if (licence?.access?.[0]?.["@id"]?.match(/OpenAccess/)) {
+                openAccess = true;
+            } else {
+                accessNarrative = licence.description.join("\n");
+                reviewDate = licence?.reviewDate?.[0];
+                accessControlList = await store.getJSON({ target: authorisedUsersFile });
+            }
         }
 
         item.openAccess = openAccess;

diff --git a/api/src/lib/admin.spec.js b/api/src/lib/admin.spec.js
@@ -2,14 +2,9 @@ require("regenerator-runtime");
 import { deleteItem } from "../lib/item.js";
 import Chance from "chance";
 const chance = Chance();
-import {
-    loadConfiguration,
-    getStoreHandle,
-    TestSetup,
-    setupTestItem,
-    setupTestCollection,
-    getS3Handle,
-} from "../common/index.js";
+import { TestSetup, setupTestItem, setupTestCollection } from "../common/test-utils.js";
+import { getS3Handle, getStoreHandle } from "../common/getS3Handle.js";
+import { loadConfiguration } from "../common/configuration.js";
 import models from "../models/index.js";
 import {
     getAdminItems,
@@ -427,25 +422,24 @@ describe("Admin management tests", () => {
         await item.reload();
 
         // deposit into the repo
-        await depositObjectIntoRepository({ type: "item", identifier });
+        await depositObjectIntoRepository({ type: "item", identifier, configuration });
 
         let resources = await objectRepository.listResources();
         resources = resources.map((r) => r.Key);
-        expect(resources.length).toEqual(9);
+        expect(resources.length).toEqual(10);
 
-        let objectExistsInWorkspace = await objectWorkspace.exists();
-        expect(objectExistsInWorkspace).toBeFalse;
+        // let objectExistsInWorkspace = await objectWorkspace.exists();
+        // expect(objectExistsInWorkspace).toBeFalse;
 
         const client = new Client({
             node: configuration.api.services.elastic.host,
         });
         let document = await client.get({
-            index: "metadata",
+            index: "manuscripts",
             id: `/item/${identifier}`,
         });
         expect(document._source).toMatchObject({
-            "@id": "./",
-            "@type": ["Dataset"],
+            name: "My Research Object Crate",
         });
 
         await objectWorkspace.removeObject();
@@ -480,16 +474,16 @@ describe("Admin management tests", () => {
         await item.reload();
 
         // deposit into the repo
-        await depositObjectIntoRepository({ type: "item", identifier });
+        await depositObjectIntoRepository({ type: "item", identifier, configuration });
 
         // restore the object from the repo back into the workspace
-        await restoreObjectIntoWorkspace({ type: "item", identifier });
+        // await restoreObjectIntoWorkspace({ type: "item", identifier });
 
         let objectExistsInWorkspace = await objectWorkspace.exists();
         expect(objectExistsInWorkspace).toBeTrue;
         let resources = await objectWorkspace.listResources();
         resources = resources.map((r) => r.Key);
-        expect(resources.length).toEqual(9);
+        expect(resources.length).toEqual(10);
 
         // change the metadata file so it versions
         let crateFile = await objectWorkspace.getJSON({ target: "ro-crate-metadata.json" });
@@ -498,18 +492,19 @@ describe("Admin management tests", () => {
 
         resources = await objectWorkspace.listResources();
         resources = resources.map((r) => r.Key);
-        expect(resources.length).toEqual(9);
+        expect(resources.length).toEqual(10);
 
         // deposit into the repo a second time and check metadata versioned
         await depositObjectIntoRepository({
             type: "item",
             identifier,
             version: { metadata: true },
+            configuration,
         });
 
         resources = await objectRepository.listResources();
         resources = resources.map((r) => r.Key);
-        expect(resources.length).toEqual(10);
+        expect(resources.length).toEqual(11);
 
         let crateFileVersions = await objectRepository.listFileVersions({
             target: "ro-crate-metadata.json ",
@@ -548,7 +543,7 @@ describe("Admin management tests", () => {
         await item.reload();
 
         // deposit into the repo
-        await depositObjectIntoRepository({ type: "item", identifier });
+        await depositObjectIntoRepository({ type: "item", identifier, configuration });
 
         // delete the item from the repository
         await deleteItemFromRepository({ type: "item", identifier, configuration });

diff --git a/api/src/lib/collection.spec.js b/api/src/lib/collection.spec.js
@@ -8,7 +8,8 @@ import {
     toggleCollectionVisibility,
 } from "./collection";
 const chance = require("chance").Chance();
-import { getStoreHandle, TestSetup } from "../common";
+import { TestSetup } from "../common/test-utils.js";
+import { getStoreHandle } from "../common/getS3Handle";
 
 describe("Collection management tests", () => {
     let configuration, users, userEmail, adminEmail, bucket;

diff --git a/api/src/lib/crate-tools.spec.js b/api/src/lib/crate-tools.spec.js
@@ -1,7 +1,8 @@
 require("regenerator-runtime");
 import { registerAllFiles } from "./crate-tools.js";
 const chance = require("chance").Chance();
-import { getStoreHandle, TestSetup, setupTestItem } from "../common";
+import { TestSetup, setupTestItem } from "../common/test-utils.js";
+import { getStoreHandle } from "../common/getS3Handle.js";
 import { ROCrate } from "ro-crate";
 import models from "../models";
 
@@ -35,7 +36,7 @@ describe("Crate tools tests", () => {
         let resources = await store.listResources();
 
         await registerAllFiles({ crate, resources });
-        expect(crate.rootDataset.hasPart.length).toBe(4);
+        expect(crate.rootDataset.hasPart.length).toBe(5);
 
         await models.item.destroy({ where: { identifier } });
         await store.removeObject();

diff --git a/api/src/lib/item.spec.js b/api/src/lib/item.spec.js
@@ -20,7 +20,9 @@ import {
     saveItemTranscription,
 } from "./item";
 const chance = require("chance").Chance();
-import { getStoreHandle, TestSetup, setupTestItem, resourceStatusFile } from "../common";
+import { resourceStatusFile } from "../common/index.js";
+import { TestSetup, setupTestItem } from "../common/test-utils.js";
+import { getStoreHandle } from "../common/getS3Handle";
 import models from "../models";
 
 describe("Item management tests", () => {

diff --git a/api/src/lib/logs.spec.js b/api/src/lib/logs.spec.js
@@ -1,7 +1,7 @@
 require("regenerator-runtime");
 import models from "../models";
 const { getLogs } = require("./logs");
-import { generateLogs } from "../common";
+import { generateLogs } from "../common/test-utils.js";
 
 describe("Log management tests", () => {
     beforeAll(async () => {