Merge remote-tracking branch 'origin/main' into OC-923

api/.gitignore

@@ -14,4 +14,4 @@ prod.env
 coverage
 Octopus.postman_collection.json
 dist
-full-ari-import-report.txt
+ari-import-report.txt

api/jest-setup.ts

@@ -2,6 +2,5 @@
 // way serverless interprets env files.
 
 import * as dotenv from 'dotenv';
-import { expand } from 'dotenv-expand';
 
-expand(dotenv.config());
+dotenv.config();

api/package.json

@@ -13,7 +13,7 @@
         "node": "20.x"
     },
     "prisma": {
-        "seed": "ts-node -r tsconfig-paths/register prisma/seed.ts"
+        "seed": "tsx prisma/seed.ts"
     },
     "scripts": {
         "build": "swc src -d dist --copy-files -s false",
@@ -32,13 +32,13 @@
         "test:local": "STAGE=local jest --runInBand --testTimeout=60000",
         "test:watch": "npm run test:local -- --watch",
         "type": "tsc --noEmit",
-        "reindex": "ts-node scripts/reindex.ts",
-        "createOrganisationalAccounts": "ts-node -r tsconfig-paths/register scripts/createOrganisationalAccounts.ts",
-        "createTopicMappings": "ts-node -r tsconfig-paths/register scripts/createTopicMappings.ts",
-        "createTopics": "ts-node -r tsconfig-paths/register scripts/createTopics.ts",
-        "createUserMappings": "ts-node -r tsconfig-paths/register scripts/createUserMappings.ts",
-        "fullAriImport": "ts-node -r tsconfig-paths/register scripts/fullAriImport.ts",
-        "updateOrganisationalAccounts": "ts-node -r tsconfig-paths/register scripts/updateOrganisationalAccounts.ts"
+        "ariImport": "tsx scripts/ariImport.ts",
+        "createOrganisationalAccounts": "tsx scripts/createOrganisationalAccounts.ts",
+        "createTopicMappings": "tsx scripts/createTopicMappings.ts",
+        "createTopics": "tsx scripts/createTopics.ts",
+        "createUserMappings": "tsx scripts/createUserMappings.ts",
+        "reindex": "tsx scripts/reindex.ts",
+        "updateOrganisationalAccounts": "tsx scripts/updateOrganisationalAccounts.ts"
     },
     "dependencies": {
         "@middy/core": "^4.7.0",
@@ -50,11 +50,10 @@
         "@sparticuz/chromium": "^119.0.2",
         "ajv": "^8.12.0",
         "ajv-formats": "^2.1.1",
-        "axios": "^1.7.4",
         "aws-lambda": "^1.0.7",
+        "axios": "^1.7.4",
         "cheerio": "^1.0.0-rc.12",
         "dotenv": "16.4.5",
-        "dotenv-expand": "11.0.7",
         "html-to-text": "^9.0.5",
         "isomorphic-dompurify": "^2.12.0",
         "jsonwebtoken": "^9.0.2",
@@ -98,6 +97,7 @@
         "serverless-prune-plugin": "^2.1.0",
         "ts-jest": "^29.1.1",
         "ts-loader": "^9.4.4",
+        "tsx": "^4.19.2",
         "typescript": "^5.2.2"
     },
     "optionalDependencies": {

api/scripts/fullAriImport.ts → api/scripts/ariImport.ts

@@ -1,39 +1,64 @@
 import axios from 'axios';
-import * as fs from 'fs/promises';
 import * as dotenv from 'dotenv';
-import { expand } from 'dotenv-expand';
 
 // Important to do this so that environment variables are treated the same as in deployed code.
-expand(dotenv.config());
+dotenv.config();
 
 import * as ariUtils from 'integration/ariUtils';
 import * as Helpers from 'lib/helpers';
 import * as I from 'interface';
+import * as integrationService from 'integration/service';
 
-// Can take an argument to run for all departments, rather than just the ones specified in the
-// PARTICIPATING_ARI_USER_IDS environment variable.
-// npm run fullAriImport -- allDepartments=true
-const parseArguments = (): { importAllDepartments: boolean } => {
+const checkBooleanArgValue = (arg: string): void => {
+    if (arg && !(arg === 'true' || arg === 'false')) {
+        throw new Error(`"${arg}" must be "true" or "false"`);
+    }
+};
+
+/**
+ * Can take the following arguments:
+ *  - allDepartments: If "true", the script will run for all departments,
+ *    rather than just the ones specified in the PARTICIPATING_ARI_USER_IDS environment variable.
+ *    - Has no effect unless "full" is "true".
+ *    - Default: false
+ *  - dryRun: If "true", the script will not actually create or update any publications,
+ *    and instead report on what it would have done.
+ *    - Default: false
+ *  - full: If "true", the script will import all ARIs from the ARI DB, instead of stopping when it
+ *    thinks it has found all the new ones (the incremental way).
+ *    - Default: false
+ *
+ * e.g.:
+ * npm run ariImport -- allDepartments=true full=true
+ */
+const parseArguments = (): { importAllDepartments: boolean; dryRun: boolean; full: boolean } => {
     const args = Helpers.parseNpmScriptArgs();
 
     for (const arg of Object.keys(args)) {
-        if (!['allDepartments'].includes(arg)) {
+        if (!['allDepartments', 'dryRun', 'full'].includes(arg)) {
             throw new Error(`Unexpected argument: ${arg}`);
         }
     }
 
-    const allDepartmentsArg = args.allDepartments;
+    const { allDepartments: allDepartmentsArg, dryRun: dryRunArg, full: fullArg } = args;
 
-    if (allDepartmentsArg && !(allDepartmentsArg === 'true' || allDepartmentsArg === 'false')) {
-        throw new Error('allDepartments must be "true" or "false"');
+    for (const arg of [allDepartmentsArg, dryRunArg, fullArg]) {
+        checkBooleanArgValue(arg);
     }
 
     return {
-        importAllDepartments: !!allDepartmentsArg
+        importAllDepartments: !!allDepartmentsArg,
+        dryRun: !!dryRunArg,
+        full: !!fullArg
     };
 };
 
-const fullAriImport = async (allDepartments?: boolean): Promise<string> => {
+/**
+ * Full ARI ingest.
+ * Differs from incremental ingest by fetching all ARIs before processing them.
+ * It will not stop until all ARIs have been processed.
+ */
+export const fullAriIngest = async (allDepartments: boolean, dryRun: boolean): Promise<string> => {
     const startTime = performance.now();
 
     // Collect all ARIs in a variable.
@@ -87,7 +112,7 @@ const fullAriImport = async (allDepartments?: boolean): Promise<string> => {
     const unrecognisedTopics = new Set<string>();
 
     for (const ari of aris) {
-        const handleAri = await ariUtils.handleIncomingARI(ari);
+        const handleAri = await ariUtils.handleIncomingARI(ari, dryRun);
 
         if (handleAri.unrecognisedDepartment) {
             unrecognisedDepartments.add(handleAri.unrecognisedDepartment);
@@ -101,16 +126,24 @@ const fullAriImport = async (allDepartments?: boolean): Promise<string> => {
             switch (handleAri.actionTaken) {
                 case 'create':
                     createdCount++;
+
                     // Datacite test has a firewall that only 750 request per IP across a 5 minute period.
                     // https://support.datacite.org/docs/is-there-a-rate-limit-for-making-requests-against-the-datacite-apis
                     // 5 minutes = 300 seconds. 300 / 750 = 0.4 seconds per request, so we take minimum 0.5s per hit to be safe.
                     // We hit datacite twice when creating an ARI, so wait 1 second.
-                    await new Promise((resolve) => setTimeout(resolve, 1000));
+                    if (!dryRun) {
+                        await new Promise((resolve) => setTimeout(resolve, 1000));
+                    }
+
                     break;
                 case 'update':
                     updatedCount++;
+
                     // We hit datacite once when updating an ARI in place, so wait half a second.
-                    await new Promise((resolve) => setTimeout(resolve, 500));
+                    if (!dryRun) {
+                        await new Promise((resolve) => setTimeout(resolve, 500));
+                    }
+
                     break;
                 case 'none':
                     skippedCount++;
@@ -140,32 +173,35 @@ const fullAriImport = async (allDepartments?: boolean): Promise<string> => {
     }
 
     const endTime = performance.now();
+    const durationSeconds = Math.round((endTime - startTime) / 100) / 10;
 
     // Write report file.
-    const duration = ((endTime - startTime) / 1000).toFixed(1);
-    const unrecognisedDepartmentsArray = Array.from(unrecognisedDepartments).sort();
-    const unrecognisedTopicsArray = Array.from(unrecognisedTopics).sort();
-    const reportBody = `\
-Duration: ${duration} seconds.
-Publications created: ${createdCount}.
-Publications updated: ${updatedCount}.
-Publications skipped: ${skippedCount}.\
-${
-    unrecognisedDepartmentsArray.length
-        ? '\nUnrecognised departments: "' + unrecognisedDepartmentsArray.join('", "') + '".'
-        : ''
-}\
-${unrecognisedTopicsArray.length ? '\nUnrecognised topics: "' + unrecognisedTopicsArray.join('", "') + '".' : ''}
-`;
-    await fs.writeFile('full-ari-import-report.txt', reportBody);
-
-    return `Finished. Successfully handled ${aris.length - failed.length} of ${
+    await ariUtils.ingestReport('file', {
+        checkedCount: aris.length,
+        durationSeconds,
+        createdCount,
+        updatedCount,
+        unrecognisedDepartments: Array.from(unrecognisedDepartments).sort(),
+        unrecognisedTopics: Array.from(unrecognisedTopics).sort(),
+        dryRun,
+        full: true
+    });
+
+    return `${dryRun ? 'Dry run' : 'Real run'} finished. Successfully handled ${aris.length - failed.length} of ${
         aris.length
-    } ARIs in ${duration} seconds.`;
+    } ARIs in ${durationSeconds} seconds.`;
+};
+
+const ariImport = async (allDepartments: boolean, dryRun: boolean, full: boolean): Promise<string> => {
+    if (!full) {
+        return await integrationService.incrementalAriIngest(dryRun, 'file');
+    } else {
+        return await fullAriIngest(allDepartments, dryRun);
+    }
 };
 
-const { importAllDepartments } = parseArguments();
+const { importAllDepartments, dryRun, full } = parseArguments();
 
-fullAriImport(importAllDepartments)
+ariImport(importAllDepartments, dryRun, full)
     .then((message) => console.log(message))
     .catch((err) => console.log(err));

api/src/components/integration/ariUtils.ts

@@ -1,6 +1,7 @@
 import * as client from 'lib/client';
 import * as coAuthorService from 'coAuthor/service';
 import * as config from 'config';
+import * as email from 'email';
 import * as Helpers from 'lib/helpers';
 import * as I from 'interface';
 import * as publicationService from 'publication/service';
@@ -9,6 +10,7 @@ import * as topicMappingService from 'topicMapping/service';
 import * as userMappingService from 'userMapping/service';
 import * as userService from 'user/service';
 
+import * as fs from 'fs/promises';
 import { Prisma } from '@prisma/client';
 
 const parseAriTextField = (value: string): string => {
@@ -408,3 +410,88 @@ export const getParticipatingDepartmentNames = async (): Promise<string[]> => {
 
     return queryResults.flatMap((userMappings) => userMappings.map((userMapping) => userMapping.value));
 };
+
+export const ingestReport = async (
+    format: 'email' | 'file',
+    ingestDetails: {
+        checkedCount: number;
+        durationSeconds: number;
+        createdCount: number;
+        updatedCount: number;
+        unrecognisedDepartments: string[];
+        unrecognisedTopics: string[];
+        dryRun: boolean;
+        full: boolean;
+    }
+): Promise<void> => {
+    const {
+        checkedCount,
+        durationSeconds,
+        createdCount,
+        updatedCount,
+        unrecognisedDepartments,
+        unrecognisedTopics,
+        dryRun,
+        full
+    } = ingestDetails;
+    const intro = `${full ? 'Full' : 'Incremental'} ARI import ${dryRun ? 'dry ' : ''}run completed.`;
+    const timingInfo =
+        `Duration: ${durationSeconds} seconds.` +
+        (dryRun && (createdCount || updatedCount)
+            ? ` A real run would have taken a minimum of ${
+                  createdCount + updatedCount / 2
+              } additional seconds due to datacite API rate limits while creating/updating publications.`
+            : '');
+    const detailsPrefix = `The ${dryRun ? 'simulated ' : ''}results of this run are as follows.`;
+    const text = `
+${intro}
+${timingInfo}
+${detailsPrefix} 
+ARIs checked: ${checkedCount}.
+Publications created: ${createdCount}.
+Publications updated: ${updatedCount}.
+${unrecognisedDepartments.length ? 'Unrecognised departments: "' + unrecognisedDepartments.join('", "') + '".' : ''}
+${unrecognisedTopics.length ? 'Unrecognised topics: "' + unrecognisedTopics.join('", "') + '".' : ''}`;
+
+    if (format === 'file') {
+        const fileName = 'ari-import-report.txt';
+        await fs.writeFile(fileName, text);
+        console.log(`Report file written to ${fileName}.`);
+
+        return;
+    }
+
+    if (format === 'email') {
+        const cleanDepartments = unrecognisedDepartments.map((department) => Helpers.getSafeHTML(department));
+        const cleanTopics = unrecognisedTopics.map((topic) => Helpers.getSafeHTML(topic));
+        const html = `
+        <html>
+            <body>
+                <p>${intro}</p>
+                <p>${timingInfo}</p>
+                <p>${detailsPrefix}</p>
+                <ul>
+                    <li>ARIs checked: ${checkedCount}</li>
+                    <li>Publications created: ${createdCount}</li>
+                    <li>Publications updated: ${updatedCount}</li>
+                    ${
+                        cleanDepartments.length
+                            ? '<li>Unrecognised departments: <ul><li>' +
+                              cleanDepartments.join('</li><li>') +
+                              '</li></ul></li>'
+                            : ''
+                    }
+                    ${
+                        cleanTopics.length
+                            ? '<li>Unrecognised topics: <ul><li>' + cleanTopics.join('</li><li>') + '</li></ul></li>'
+                            : ''
+                    }
+                </ul>
+            </body>
+        </html>
+    `;
+        await email.ariIngestReport(html, text);
+
+        return;
+    }
+};

api/src/components/integration/controller.ts

@@ -36,7 +36,7 @@ export const incrementalAriIngest = async (
     }
 
     try {
-        const ingestResult = await integrationService.incrementalAriIngest(dryRun);
+        const ingestResult = await integrationService.incrementalAriIngest(dryRun, 'email');
 
         return response.json(
             200,