From ba7250155afb052c1e5f236bf9adfd245049faab Mon Sep 17 00:00:00 2001
From: GaziYucel <84437883+GaziYucel@users.noreply.github.com>
Date: Fri, 24 Oct 2025 12:02:45 +0200
Subject: [PATCH 1/3] arxiv, handle fixes, enums/dropdowns type and source
 type, openalex type <> type_crossref, edit enable metadata lookup after
 submission, enable / disable citationsMetadataLookup for journal, reprocess
 all citations

---
 .../CitationManager.stories.js                |   2 +-
 .../CitationManager/CitationManager.vue       |  25 +++-
 .../CitationManagerCellCitation.vue           |   6 +-
 .../CitationManager/citationManagerStore.js   | 115 +++++++++---------
 .../useCitationManagerActions.js              |   4 +-
 .../useCitationManagerFormAddRawCitation.js   |   2 +
 .../useCitationManagerFormEnableLookup.js     |  95 ---------------
 .../workflowConfigAuthorOJS.js                |   6 +-
 .../workflowConfigEditorialOJS.js             |   6 +-
 9 files changed, 90 insertions(+), 171 deletions(-)
 delete mode 100644 src/managers/CitationManager/useCitationManagerFormEnableLookup.js

diff --git a/src/managers/CitationManager/CitationManager.stories.js b/src/managers/CitationManager/CitationManager.stories.js
index 60a5a9179..52409f63d 100644
--- a/src/managers/CitationManager/CitationManager.stories.js
+++ b/src/managers/CitationManager/CitationManager.stories.js
@@ -18,7 +18,6 @@ export const Base = {
 	args: {
 		submission: getSubmissionMock(),
 		publication: getPublicationMock({
-			citationsMetadataLookup: true,
 			citations: [
 				{
 					_href:
@@ -180,6 +179,7 @@ export const Base = {
 				},
 			],
 		}),
+		citationsMetadataLookup: true,
 		canEdit: true,
 		componentForms: {
 			citationStructuredEditForm: {
diff --git a/src/managers/CitationManager/CitationManager.vue b/src/managers/CitationManager/CitationManager.vue
index 1ca8e54ec..5e2a64d47 100644
--- a/src/managers/CitationManager/CitationManager.vue
+++ b/src/managers/CitationManager/CitationManager.vue
@@ -1,6 +1,18 @@
 <template>
 	<div>
-		<CitationManagerMetadataLookup />
+		<div v-if="citationStore.citationsMetadataLookup">
+			<span class="font-semibold">
+				{{ t('submission.citations.structured') }}
+			</span>
+			<br />
+			<p class="text-lg-normal leading-6">
+				{{
+					t(
+						'submission.citations.structured.citationsMetadataLookup.description',
+					)
+				}}
+			</p>
+		</div>
 		<div class="pt-3">
 			<CitationManagerAddRawCitations />
 		</div>
@@ -11,10 +23,17 @@
 			<PkpButton
 				:is-disabled="!citationStore.canEditPublication"
 				:is-link="true"
-				@click="citationStore.citationDeleteAllCitations"
+				@click="citationStore.deleteAllCitations"
 			>
 				{{ t('submission.citations.structured.deleteAllLink') }}
 			</PkpButton>
+			<PkpButton
+				:is-disabled="!citationStore.canEditPublication"
+				:is-link="true"
+				@click="citationStore.reprocessAllCitations"
+			>
+				{{ t('submission.citations.structured.reprocessAllCitations') }}
+			</PkpButton>
 		</div>
 		<PkpTable :aria-label="t('submission.citations.structured')">
 			<template #label>
@@ -84,7 +103,6 @@ import CitationManagerCellActions from '@/managers/CitationManager/CitationManag
 import CitationManagerSearchField from '@/managers/CitationManager/CitationManagerSearchField.vue';
 import CitationManagerStatusProcessed from '@/managers/CitationManager/CitationManagerStatusProcessed.vue';
 import CitationManagerAddRawCitations from '@/managers/CitationManager/CitationManagerAddRawCitations.vue';
-import CitationManagerMetadataLookup from '@/managers/CitationManager/CitationManagerMetadataLookup.vue';
 import {useCitationManagerStore} from './citationManagerStore.js';
 
 const {t} = useLocalize();
@@ -100,6 +118,7 @@ const Components = {
 const props = defineProps({
 	submission: {type: Object, required: true},
 	publication: {type: Object, required: true},
+	citationsMetadataLookup: {type: Boolean, required: true},
 	canEdit: {type: Boolean, required: true},
 	componentForms: {type: Object, required: true},
 });
diff --git a/src/managers/CitationManager/CitationManagerCellCitation.vue b/src/managers/CitationManager/CitationManagerCellCitation.vue
index 90bfe2512..495cf4e13 100644
--- a/src/managers/CitationManager/CitationManagerCellCitation.vue
+++ b/src/managers/CitationManager/CitationManagerCellCitation.vue
@@ -7,7 +7,7 @@
 				<a
 					v-if="citation.doi"
 					:is-link="true"
-					:href="citationStore.doiPrefix + '/' + citation.doi"
+					:href="citationStore.doiUrlPrefix + citation.doi"
 					target="_blank"
 				>
 					{{ citation.doi }}
@@ -23,7 +23,7 @@
 				<a
 					v-if="citation.arxiv"
 					:is-link="true"
-					:href="citation.arxiv"
+					:href="citationStore.arxivUrlPrefix + citation.arxiv"
 					target="_blank"
 				>
 					{{ citation.arxiv }}
@@ -31,7 +31,7 @@
 				<a
 					v-if="citation.handle"
 					:is-link="true"
-					:href="citation.handle"
+					:href="citationStore.handleUrlPrefix + citation.handle"
 					target="_blank"
 				>
 					{{ citation.handle }}
diff --git a/src/managers/CitationManager/citationManagerStore.js b/src/managers/CitationManager/citationManagerStore.js
index 869f4c848..e7bcc6437 100644
--- a/src/managers/CitationManager/citationManagerStore.js
+++ b/src/managers/CitationManager/citationManagerStore.js
@@ -9,7 +9,6 @@ import {useFetch} from '@/composables/useFetch';
 import {useCitationManagerConfig} from './useCitationManagerConfig';
 import {useCitationManagerActions} from './useCitationManagerActions';
 import {useCitationManagerFormAddRawCitation} from './useCitationManagerFormAddRawCitation';
-import {useCitationManagerFormEnableLookup} from './useCitationManagerFormEnableLookup';
 
 export const useCitationManagerStore = defineComponentStore(
 	'citationManager',
@@ -37,6 +36,7 @@ export const useCitationManagerStore = defineComponentStore(
 		const {
 			submission,
 			publication,
+			citationsMetadataLookup,
 			canEdit: canEditPublication,
 		} = toRefs(props);
 		const citations = computed(() => publication.value.citations ?? []);
@@ -44,43 +44,18 @@ export const useCitationManagerStore = defineComponentStore(
 		/**
 		 * constants
 		 */
-		const doiPrefix = 'https://doi.org';
+		const arxivUrlPrefix = 'https://arxiv.org/abs/';
+		const doiUrlPrefix = 'https://doi.org/';
+		const handleUrlPrefix = 'https://hdl.handle.net/';
 		const apiPathCitations = 'citations';
 		const apiPathSubmissions = `submissions/${submission.value.id}/publications/${publication.value.id}/citations`;
 
-		/**
-		 * citations metadata lookup
-		 */
-
-		const citationsMetadataLookup = computed(
-			() => publication.value.citationsMetadataLookup,
-		);
-
-		const {form: formEnableLookup} = useCitationManagerFormEnableLookup({
-			citationsMetadataLookup,
-			onCitationMetadataLookupChange: async (newValue) => {
-				console.log('onCitationMetadataLookUPChange');
-				await citationsMetadataLookupChanged(newValue);
-			},
-		});
-
-		async function citationsMetadataLookupChanged(newValue) {
-			const {apiUrl} = useUrl(apiPathSubmissions);
-			const {fetch} = useFetch(`${apiUrl.value}/metadataLookup`, {
-				method: 'PUT',
-				body: {
-					citationsMetadataLookup: newValue,
-				},
-			});
-			await fetch();
-			dataUpdateCallback();
-		}
-
 		/**
 		 * add new raw citations
 		 */
 		const {form: formAddRawCitations} = useCitationManagerFormAddRawCitation({
 			apiPathSubmissions,
+			canEditPublication,
 			onSuccess: () => {
 				dataUpdateCallback();
 			},
@@ -115,7 +90,7 @@ export const useCitationManagerStore = defineComponentStore(
 		/**
 		 * delete all citations
 		 */
-		function citationDeleteAllCitations() {
+		function deleteAllCitations() {
 			openDialog({
 				title: t('submission.citations.structured.deleteAllDialog.title'),
 				message: t('submission.citations.structured.deleteAllDialog.confirm'),
@@ -146,6 +121,45 @@ export const useCitationManagerStore = defineComponentStore(
 			});
 		}
 
+		/**
+		 * reprocess all citations
+		 */
+		function reprocessAllCitations() {
+			console.log('publication store', publication);
+			openDialog({
+				title: t('submission.citations.structured.reprocessAllCitations.title'),
+				message: t(
+					'submission.citations.structured.reprocessAllCitations.confirm',
+				),
+				modalStyle: 'negative',
+				actions: [
+					{
+						label: t('common.ok'),
+						isWarnable: true,
+						callback: async (close) => {
+							const {apiUrl} = useUrl(apiPathSubmissions);
+							const {fetch} = useFetch(
+								`${apiUrl.value}/reprocessCitationsByPublicationId`,
+								{
+									method: 'POST',
+								},
+							);
+							await fetch();
+							dataUpdateCallback();
+							close();
+						},
+					},
+					{
+						label: t('common.cancel'),
+						isSecondary: true,
+						callback: (close) => {
+							close();
+						},
+					},
+				],
+			});
+		}
+
 		/**
 		 * Toggle all / toggle status
 		 */
@@ -187,35 +201,16 @@ export const useCitationManagerStore = defineComponentStore(
 		const citationsFiltered = computed(() => {
 			const data = citations.value || [];
 			return searchPhrase.value
-				? filterArrayByPhrase(data, searchPhrase.value)
+				? data.filter((item) =>
+						JSON.stringify(item)
+							.toLowerCase()
+							.includes(searchPhrase.value.toString().toLowerCase()),
+					)
 				: data;
 		});
 		function setSearchPhrase(value) {
 			searchPhrase.value = value;
 		}
-		function containsSearchPhrase(obj, phrase) {
-			function deepSearch(value) {
-				if (value === null || value === undefined) return false;
-				if (typeof value === 'string') {
-					return value
-						.toLowerCase()
-						.includes(String(phrase ?? '').toLowerCase());
-				}
-				if (Array.isArray(value)) {
-					return value.some(deepSearch);
-				}
-				if (typeof value === 'object') {
-					return Object.values(value).some(deepSearch);
-				}
-				return false;
-			}
-			return deepSearch(obj);
-		}
-		function filterArrayByPhrase(data, phrase) {
-			return (Array.isArray(data) ? data : []).filter((item) =>
-				containsSearchPhrase(item, phrase),
-			);
-		}
 
 		/**
 		 * Actions
@@ -225,6 +220,7 @@ export const useCitationManagerStore = defineComponentStore(
 			return {
 				submission: props.submission,
 				publication: props.publication,
+				citationsMetadataLookup: props.citationsMetadataLookup,
 				componentForms: props.componentForms,
 				...additionalArgs,
 			};
@@ -257,20 +253,20 @@ export const useCitationManagerStore = defineComponentStore(
 			publication,
 			canEditPublication,
 
-			doiPrefix,
+			arxivUrlPrefix,
+			doiUrlPrefix,
+			handleUrlPrefix,
 			apiPathCitations,
 			apiPathSubmissions,
 
-			formEnableLookup,
 			citationsMetadataLookup,
-			citationsMetadataLookupChanged,
 
 			formAddRawCitations,
 
 			totalCitations,
 			processedCitations,
 
-			citationDeleteAllCitations,
+			deleteAllCitations,
 
 			allIdsExpanded,
 			expandedIds,
@@ -284,6 +280,7 @@ export const useCitationManagerStore = defineComponentStore(
 
 			citationEditCitation,
 			citationDeleteCitation,
+			reprocessAllCitations,
 			citationReprocessCitation,
 		};
 
diff --git a/src/managers/CitationManager/useCitationManagerActions.js b/src/managers/CitationManager/useCitationManagerActions.js
index fef12d7bf..53cd553b9 100644
--- a/src/managers/CitationManager/useCitationManagerActions.js
+++ b/src/managers/CitationManager/useCitationManagerActions.js
@@ -16,14 +16,14 @@ export function useCitationManagerActions() {
 	const {t} = useLocalize();
 
 	function citationEditCitation(
-		{publication, componentForms, citation},
+		{publication, citationsMetadataLookup, componentForms, citation},
 		finishedCallback,
 	) {
 		if (!citation.authors) {
 			citation.authors = [];
 		}
 		let formName = 'citationRawEditForm';
-		if (publication.citationsMetadataLookup) {
+		if (citationsMetadataLookup) {
 			formName = 'citationStructuredEditForm';
 		}
 
diff --git a/src/managers/CitationManager/useCitationManagerFormAddRawCitation.js b/src/managers/CitationManager/useCitationManagerFormAddRawCitation.js
index 8558ae500..e6515834a 100644
--- a/src/managers/CitationManager/useCitationManagerFormAddRawCitation.js
+++ b/src/managers/CitationManager/useCitationManagerFormAddRawCitation.js
@@ -4,6 +4,7 @@ import {useLocalize} from '@/composables/useLocalize';
 
 export function useCitationManagerFormAddRawCitation({
 	apiPathSubmissions,
+	canEditPublication,
 	onSuccess,
 }) {
 	const {t} = useLocalize();
@@ -21,6 +22,7 @@ export function useCitationManagerFormAddRawCitation({
 			setValue('rawCitations', '');
 			onSuccess();
 		},
+		canSubmit: canEditPublication.value,
 	});
 
 	addPage('default', {
diff --git a/src/managers/CitationManager/useCitationManagerFormEnableLookup.js b/src/managers/CitationManager/useCitationManagerFormEnableLookup.js
deleted file mode 100644
index 569af47a4..000000000
--- a/src/managers/CitationManager/useCitationManagerFormEnableLookup.js
+++ /dev/null
@@ -1,95 +0,0 @@
-import {useForm} from '@/composables/useForm';
-import {useLocalize} from '@/composables/useLocalize';
-import {watch} from 'vue';
-import {useModal} from '@/composables/useModal';
-
-export function useCitationManagerFormEnableLookup({
-	citationsMetadataLookup,
-	onCitationMetadataLookupChange,
-} = {}) {
-	const {t} = useLocalize();
-
-	const {
-		form,
-		setValue,
-		initEmptyForm,
-		addFieldOptions,
-		addPage,
-		addGroup,
-		getField,
-	} = useForm({});
-
-	initEmptyForm('enableLookup', {
-		action: 'emit',
-		spacingVariant: 'fullWidth',
-	});
-
-	addPage('default', {
-		submitButton: null,
-	});
-
-	addGroup('default');
-
-	addFieldOptions('metadataLookup', 'checkbox', {
-		label: t('submission.citations.structured'),
-		description: t(
-			'submission.citations.structured.citationsMetadataLookup.description',
-		),
-		value: citationsMetadataLookup.value,
-		options: [
-			{
-				label: t(
-					'submission.citations.structured.enableCitationsMetadataLookup',
-				),
-				value: true,
-			},
-		],
-	});
-
-	watch(citationsMetadataLookup, (newValue) => {
-		setValue('metadataLookup', newValue);
-	});
-
-	watch(
-		() => getField('metadataLookup')?.value,
-		(newValue) => {
-			// skip when the value is being rollback in cancel
-			if (newValue === citationsMetadataLookup.value) {
-				return;
-			}
-
-			const {openDialog} = useModal();
-			openDialog({
-				title: citationsMetadataLookup.value
-					? t('submission.citations.structured.disableModal.title')
-					: t('submission.citations.structured.enableModal.title'),
-				message: citationsMetadataLookup.value
-					? t('submission.citations.structured.disableModal.confirm')
-					: t('submission.citations.structured.enableModal.confirm'),
-				actions: [
-					{
-						label: t('common.ok'),
-						isPrimary: true,
-						callback: async (close) => {
-							await onCitationMetadataLookupChange(
-								!citationsMetadataLookup.value,
-							);
-							close();
-						},
-					},
-					{
-						label: t('common.cancel'),
-						isWarnable: true,
-						callback: (close) => {
-							setValue('metadataLookup', citationsMetadataLookup.value);
-							close();
-						},
-					},
-				],
-				close: () => {},
-			});
-		},
-	);
-
-	return {form};
-}
diff --git a/src/pages/workflow/composables/useWorkflowConfig/workflowConfigAuthorOJS.js b/src/pages/workflow/composables/useWorkflowConfig/workflowConfigAuthorOJS.js
index 05d2c6049..dc003151d 100644
--- a/src/pages/workflow/composables/useWorkflowConfig/workflowConfigAuthorOJS.js
+++ b/src/pages/workflow/composables/useWorkflowConfig/workflowConfigAuthorOJS.js
@@ -396,16 +396,14 @@ export const PublicationConfig = {
 			pageInitConfig,
 			permissions,
 		}) => {
-			selectedPublication.citationsMetadataLookup =
-				selectedPublication.citationsMetadataLookup ??
-				pageInitConfig.contextCitationsMetadataLookup ??
-				false;
 			return [
 				{
 					component: 'CitationManager',
 					props: {
 						submission: submission,
 						publication: selectedPublication,
+						citationsMetadataLookup:
+							pageInitConfig.contextCitationsMetadataLookup ?? false,
 						canEdit: permissions.canEditPublication,
 						componentForms: pageInitConfig.componentForms,
 					},
diff --git a/src/pages/workflow/composables/useWorkflowConfig/workflowConfigEditorialOJS.js b/src/pages/workflow/composables/useWorkflowConfig/workflowConfigEditorialOJS.js
index 52a677856..29f716d10 100644
--- a/src/pages/workflow/composables/useWorkflowConfig/workflowConfigEditorialOJS.js
+++ b/src/pages/workflow/composables/useWorkflowConfig/workflowConfigEditorialOJS.js
@@ -942,16 +942,14 @@ export const PublicationConfig = {
 			pageInitConfig,
 			permissions,
 		}) => {
-			selectedPublication.citationsMetadataLookup =
-				selectedPublication.citationsMetadataLookup ??
-				pageInitConfig.contextCitationsMetadataLookup ??
-				false;
 			return [
 				{
 					component: 'CitationManager',
 					props: {
 						submission: submission,
 						publication: selectedPublication,
+						citationsMetadataLookup:
+							pageInitConfig.contextCitationsMetadataLookup ?? false,
 						canEdit: permissions.canEditPublication,
 						componentForms: pageInitConfig.componentForms,
 					},

From fa57ce32a62a3b846ff2138e307342db06098f64 Mon Sep 17 00:00:00 2001
From: GaziYucel <84437883+GaziYucel@users.noreply.github.com>
Date: Mon, 27 Oct 2025 10:26:12 +0100
Subject: [PATCH 2/3] fixes review 2025-10-27

---
 src/managers/CitationManager/citationManagerStore.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/managers/CitationManager/citationManagerStore.js b/src/managers/CitationManager/citationManagerStore.js
index e7bcc6437..617dc2985 100644
--- a/src/managers/CitationManager/citationManagerStore.js
+++ b/src/managers/CitationManager/citationManagerStore.js
@@ -125,7 +125,6 @@ export const useCitationManagerStore = defineComponentStore(
 		 * reprocess all citations
 		 */
 		function reprocessAllCitations() {
-			console.log('publication store', publication);
 			openDialog({
 				title: t('submission.citations.structured.reprocessAllCitations.title'),
 				message: t(

From 35d89125df113e639acdd54c158630101732858c Mon Sep 17 00:00:00 2001
From: GaziYucel <84437883+GaziYucel@users.noreply.github.com>
Date: Tue, 4 Nov 2025 15:47:34 +0100
Subject: [PATCH 3/3] review fixes 20251104

---
 .../CitationManager/CitationManager.vue       | 10 ++++----
 .../CitationManager/citationManagerStore.js   | 23 ++++++++++++++-----
 2 files changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/managers/CitationManager/CitationManager.vue b/src/managers/CitationManager/CitationManager.vue
index 5e2a64d47..ac6e0e31e 100644
--- a/src/managers/CitationManager/CitationManager.vue
+++ b/src/managers/CitationManager/CitationManager.vue
@@ -1,10 +1,9 @@
 <template>
 	<div>
-		<div v-if="citationStore.citationsMetadataLookup">
-			<span class="font-semibold">
+		<div v-if="citationStore.citationsMetadataLookup" class="pb-3">
+			<h3 class="text-xl-bold">
 				{{ t('submission.citations.structured') }}
-			</span>
-			<br />
+			</h3>
 			<p class="text-lg-normal leading-6">
 				{{
 					t(
@@ -13,7 +12,7 @@
 				}}
 			</p>
 		</div>
-		<div class="pt-3">
+		<div>
 			<CitationManagerAddRawCitations />
 		</div>
 		<CitationManagerStatusProcessed
@@ -28,6 +27,7 @@
 				{{ t('submission.citations.structured.deleteAllLink') }}
 			</PkpButton>
 			<PkpButton
+				v-show="citationStore.citationsMetadataLookup"
 				:is-disabled="!citationStore.canEditPublication"
 				:is-link="true"
 				@click="citationStore.reprocessAllCitations"
diff --git a/src/managers/CitationManager/citationManagerStore.js b/src/managers/CitationManager/citationManagerStore.js
index 617dc2985..618e117be 100644
--- a/src/managers/CitationManager/citationManagerStore.js
+++ b/src/managers/CitationManager/citationManagerStore.js
@@ -199,12 +199,23 @@ export const useCitationManagerStore = defineComponentStore(
 		const searchPhrase = ref('');
 		const citationsFiltered = computed(() => {
 			const data = citations.value || [];
-			return searchPhrase.value
-				? data.filter((item) =>
-						JSON.stringify(item)
-							.toLowerCase()
-							.includes(searchPhrase.value.toString().toLowerCase()),
-					)
+			const searchWords = searchPhrase.value
+				? searchPhrase.value.toLowerCase().split(' ')
+				: [];
+
+			return searchWords.length > 0
+				? data.filter((citation) => {
+						// remove all keys from object and search in values only
+						let values = Object.values(citation).map((value) => {
+							if (Array.isArray(value)) {
+								return value.map((innerObj) => Object.values(innerObj));
+							}
+							return value;
+						});
+						return searchWords.every((word) => {
+							return JSON.stringify(values).toLowerCase().includes(word);
+						});
+					})
 				: data;
 		});
 		function setSearchPhrase(value) {