From b6a1ef18c2f701d4332c766dda84a7ca768511dd Mon Sep 17 00:00:00 2001
From: Bruce Herr II <bherr@indiana.edu>
Date: Wed, 27 Sep 2023 20:06:15 -0400
Subject: [PATCH] Added support for graph digital objects

---
 src/enrichment/enrich-graph.js       | 80 ++++++++++++++++++++++++++++
 src/enrichment/enrich.js             |  5 ++
 src/normalization/normalize-graph.js | 33 ++++++++++++
 src/normalization/normalize.js       |  5 ++
 4 files changed, 123 insertions(+)
 create mode 100644 src/enrichment/enrich-graph.js
 create mode 100644 src/normalization/normalize-graph.js

diff --git a/src/enrichment/enrich-graph.js b/src/enrichment/enrich-graph.js
new file mode 100644
index 0000000..0584b70
--- /dev/null
+++ b/src/enrichment/enrich-graph.js
@@ -0,0 +1,80 @@
+import { existsSync, readFileSync } from 'fs';
+import { load } from 'js-yaml';
+import { resolve } from 'path';
+import { error, info } from '../utils/logging.js';
+import { convert, merge } from '../utils/robot.js';
+import { cleanTemporaryFiles, convertNormalizedDataToOwl, convertNormalizedMetadataToRdf, logOutput } from './utils.js';
+
+export function enrichGraphMetadata(context) {
+  const { selectedDigitalObject: obj } = context;
+  const normalizedPath = resolve(obj.path, 'normalized/normalized-metadata.yaml');
+  const enrichedPath = resolve(obj.path, 'enriched/enriched-metadata.ttl');
+  convertNormalizedMetadataToRdf(context, normalizedPath, enrichedPath, 'basic');
+}
+
+export function enrichGraphData(context) {
+  try {
+    const { selectedDigitalObject: obj } = context;
+
+    const normalizedPath = resolve(obj.path, 'normalized/normalized.yaml');
+    const baseGraphPath = resolve(obj.path, 'enriched/base-input.ttl');
+    convertNormalizedDataToOwl(context, normalizedPath, baseGraphPath, 'basic');
+    logOutput(baseGraphPath);
+
+    info(`Reading data: ${normalizedPath}`);
+    const digitalObjects = load(readFileSync(normalizedPath))['data'];
+
+    info('Validating digital objects in the graph...');
+    validateGraph(context, digitalObjects);
+
+    const toMerge = [baseGraphPath];
+    for (const inputRdfFile of digitalObjects) {
+      const inputRdf = resolve(obj.path, 'raw', inputRdfFile);
+      const extension = inputRdfFile.split('.').slice(-1)[0];
+      if (extension === 'ttl') {
+        toMerge.push(inputRdf);
+      } else {
+        const outputTtl = resolve(obj.path, 'enriched', inputRdfFile + '.ttl');
+        convert(inputRdf, outputTtl, 'ttl');
+        toMerge.push(outputTtl);
+      }
+    }
+
+    const enrichedMergePath = resolve(obj.path, 'enriched/enriched-merge.owl');
+    merge(toMerge, enrichedMergePath);
+    logOutput(enrichedMergePath);
+
+    const enrichedPath = resolve(obj.path, 'enriched/enriched.ttl');
+    info(`Creating graph: ${enrichedPath}`);
+    convert(enrichedMergePath, enrichedPath, 'ttl');
+
+    info('Optimizing graph...')
+    const redundantPath = resolve(obj.path, 'enriched/redundant.ttl');
+    runCompleteClosure(enrichedPath, redundantPath);
+    logOutput(redundantPath);
+
+  } catch (e) {
+    error(e);
+  } finally {
+    // Clean up
+    info('Cleaning up temporary files.');
+    cleanTemporaryFiles(context);
+    info('Done.');
+  }
+}
+
+function validateGraph(context, data) {
+  const { path } = context.selectedDigitalObject;
+  let isValid = true;
+  if (!context.skipValidation) {
+    for (const collectedObj of data) {
+      if (!existsSync(resolve(path, 'raw', collectedObj))) {
+        error(`${collectedObj} does not exist or is invalid`);
+        isValid = false;
+      }
+    }
+  }
+  if (!isValid) {
+    throw new Error(`Cannot enrich ${obj.doString} until all referenced datatable items are found.`);
+  }
+}
diff --git a/src/enrichment/enrich.js b/src/enrichment/enrich.js
index 6e3dde2..8fab4d3 100644
--- a/src/enrichment/enrich.js
+++ b/src/enrichment/enrich.js
@@ -5,6 +5,7 @@ import { enrich2dFtuData, enrich2dFtuMetadata } from './enrich-2d-ftu.js';
 import { enrichAsctbData, enrichAsctbMetadata } from './enrich-asct-b.js';
 import { enrichBasicData, enrichBasicMetadata } from './enrich-basic.js';
 import { enrichCollectionData, enrichCollectionMetadata } from './enrich-collection.js';
+import { enrichGraphData, enrichGraphMetadata } from './enrich-graph.js';
 import { enrichRefOrganData, enrichRefOrganMetadata } from './enrich-ref-organ.js';
 
 export function enrich(context) {
@@ -29,6 +30,10 @@ export function enrich(context) {
       enrichCollectionMetadata(context);
       enrichCollectionData(context);
       break;
+    case 'graph':
+      enrichGraphMetadata(context);
+      enrichGraphData(context);
+      break;
     default:
       warning(`"${obj.type}" digital object type is using basic processing.`);
       enrichBasicMetadata(context);
diff --git a/src/normalization/normalize-graph.js b/src/normalization/normalize-graph.js
new file mode 100644
index 0000000..0fde4f3
--- /dev/null
+++ b/src/normalization/normalize-graph.js
@@ -0,0 +1,33 @@
+import { existsSync } from 'fs';
+import { resolve } from 'path';
+import { error } from '../utils/logging.js';
+import { normalizeMetadata, readMetadata, writeNormalizedData, writeNormalizedMetadata } from './utils.js';
+
+export function normalizeGraphMetadata(context) {
+  const rawMetadata = readMetadata(context);
+  const normalizedMetadata = normalizeMetadata(context, rawMetadata);
+  writeNormalizedMetadata(context, normalizedMetadata);
+}
+
+export function normalizeGraphData(context) {
+  const metadata = readMetadata(context);
+  const data = metadata.datatable;
+  checkGraphItems(context, data);
+  writeNormalizedData(context, data);
+}
+
+function checkGraphItems(context, data) {
+  const { path } = context.selectedDigitalObject;
+  let isValid = true;
+  if (!context.skipValidation) {
+    for (const collectedObj of data) {
+      if (!existsSync(resolve(path, 'raw', collectedObj))) {
+        error(`${collectedObj} does not exist or is invalid`);
+        isValid = false;
+      }
+    }
+  }
+  if (!isValid) {
+    throw new Error(`Cannot normalize ${obj.doString} until all referenced datatable items are found.`);
+  }
+}
diff --git a/src/normalization/normalize.js b/src/normalization/normalize.js
index c3c7bbf..be49051 100644
--- a/src/normalization/normalize.js
+++ b/src/normalization/normalize.js
@@ -6,6 +6,7 @@ import { normalize2dFtuData, normalize2dFtuMetadata } from './normalize-2d-ftu.j
 import { normalizeAsctbData, normalizeAsctbMetadata } from './normalize-asct-b.js';
 import { normalizeBasicData, normalizeBasicMetadata } from './normalize-basic.js';
 import { normalizeCollectionData, normalizeCollectionMetadata } from './normalize-collection.js';
+import { normalizeGraphData, normalizeGraphMetadata } from './normalize-graph.js';
 import { normalizeRefOrganData, normalizeRefOrganMetadata } from './normalize-ref-organ.js';
 
 export async function normalize(context) {
@@ -30,6 +31,10 @@ export async function normalize(context) {
       normalizeCollectionMetadata(context);
       normalizeCollectionData(context);
       break;
+    case 'graph':
+      normalizeGraphMetadata(context);
+      normalizeGraphData(context);
+      break;
     default:
       warning(`"${obj.type}" digital object type is using basic processing.`);
       normalizeBasicMetadata(context);