#24 Add citation style format form to the plugin's settings

Vitaliy-1 · Jul 21, 2020 · 21425c4 · 21425c4
1 parent 83e5460
commit 21425c4
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diff --git a/JatsParserPlugin.inc.php b/JatsParserPlugin.inc.php
@@ -5,7 +5,7 @@
  * Copyright (c) 2017-2018 Vitalii Bezsheiko
  * Distributed under the GNU GPL v3.
  *
- * @class JatsParserSettingsForm
+ * @class JatsParserPlugin
  * @ingroup plugins_generic_jatsParser
  *
  */
@@ -17,9 +17,10 @@
 import('plugins.generic.jatsParser.classes.components.forms.PublicationJATSUploadForm');
 import('lib.pkp.classes.file.SubmissionFileManager');
 
-use JATSParser\Body\Document as Document;
-use JATSParser\PDF\TCPDFDocument as TCPDFDocument;
+use JATSParser\Body\Document;
+use JATSParser\PDF\TCPDFDocument;
 use JATSParser\HTML\Document as HTMLDocument;
+use \PKP\components\forms\FormComponent;
 
 define("CREATE_PDF_QUERY", "download=pdf");
 
@@ -47,6 +48,7 @@ function register($category, $path, $mainContextId = null) {
 			HookRegistry::register('Publication::edit', array($this, 'editPublication'));
 			HookRegistry::register('Templates::Article::Main', array($this, 'displayFullText'));
 			HookRegistry::register('TemplateManager::display', array($this, 'themeSpecificStyles'));
+			HookRegistry::register('Form::config::before', array($this, 'addCitationsFormFields'));
 
 			return true;
 		}
@@ -488,8 +490,17 @@ public function addToSchema($hookName, $args) {
 				"nullable"
 			]
 		}';
+		$propRef = '{
+			"type": "boolean",
+			"multilingual": true,
+			"apiSummary": true,
+			"validation": [
+				"nullable"
+			]
+		}';
 		$schema->properties->{'jatsParser::fullTextFileId'} = json_decode($propId);
 		$schema->properties->{'jatsParser::fullText'} = json_decode($propText);
+		$schema->properties->{'jatsParser::references'} = json_decode($propRef);
 	}
 
 	/**
@@ -751,10 +762,55 @@ function _setSupplImgPath(SubmissionFile $submissionFile, string $htmlString): s
 	 * @brief get the list of types of files that are dependent from an original JATS XML (from which full-text was generated) and are accessible to public
 	 */
 	public static function getSupportedSupplFileTypes() {
-		return array(
+		return [
 			'image/png',
 			'image/jpeg'
-		);
+		];
+	}
+
+	public static function getSupportedCitationStyles() {
+		return [
+			[
+				'id' => 'acm-sig-proceedings',
+				'title' => 'plugins.generic.jatsParser.style.acm-sig-proceedings',
+			],
+			[
+				'id' => 'acs-nano',
+				'title' => 'plugins.generic.jatsParser.style.acs-nano',
+			],
+			[
+				'id' => 'apa',
+				'title' => 'plugins.generic.jatsParser.style.apa',
+			],
+			[
+				'id' => 'associacao-brasileira-de-normas-tecnicas',
+				'title' => 'plugins.generic.jatsParser.style.associacao-brasileira-de-normas-tecnicas',
+			],
+			[
+				'id' => 'chicago-author-date',
+				'title' => 'plugins.generic.jatsParser.style.chicago-author-date',
+			],
+			[
+				'id' => 'harvard-cite-them-right',
+				'title' => 'plugins.generic.jatsParser.style.harvard-cite-them-right',
+			],
+			[
+				'id' => 'ieee',
+				'title' => 'plugins.generic.jatsParser.style.ieee',
+			],
+			[
+				'id' => 'modern-language-association',
+				'title' => 'plugins.generic.jatsParser.style.modern-language-association',
+			],
+			[
+				'id' => 'turabian-fullnote-bibliography',
+				'title' => 'plugins.generic.jatsParser.style.turabian-fullnote-bibliography',
+			],
+			[
+				'id' => 'vancouver',
+				'title' => 'plugins.generic.jatsParser.style.vancouver',
+			],
+		];
 	}
 
 	/**
@@ -791,6 +847,10 @@ function themeSpecificStyles(string $hookname, array $args) {
 		return false;
 	}
 
+	/**
+	 * @return void
+	 * @brief iterate through all submissions and add full-text from  galleys
+	 */
 	public function importGalleys() {
 		$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
 		$request = $this->getRequest();
@@ -846,4 +906,77 @@ public function importGalleys() {
 			}
 		}
 	}
+
+	/**
+	 * @param $hookName string Form::config::before
+	 * @param $form FormComponent The form object
+	 */
+	public function addCitationsFormFields(string $hookName, FormComponent $form): void {
+		if ($form->id !== 'citations' || !empty($form->errors)) return;
+
+		$path = parse_url($form->action)['path'];
+		if (!$path) return;
+
+		$args = explode('/', $path);
+		$publicationId = 0;
+		if ($key = array_search('publications', $args)) {
+			if (array_key_exists($key+1, $args)) {
+				$publicationId = intval($args[$key+1]);
+			}
+		}
+
+		if (!$publicationId) return;
+
+		$publication = Services::get('publication')->get($publicationId);
+		if (!$publication) return;
+
+		$submissionFileIds = array_unique($publication->getData('jatsParser::fullTextFileId'));
+		if (empty($submissionFileIds)) return;
+
+		$submissionFileDao = DAORegistry::getDAO('SubmissionFileDAO');
+
+		$submissionFiles = [];
+		foreach ($submissionFileIds as $submissionFileId) {
+			$submissionFiles[] = $submissionFileDao->getLatestRevision($submissionFileId);
+		}
+
+		if (empty($submissionFiles)) return;
+
+		if (count($submissionFiles) > 1) {
+			$options = [];
+			foreach ($submissionFiles as $submissionFile) {
+				$options[] = [
+					'value' => $submissionFile->getId(),
+					'label' => $submissionFile->getLocalizedName(),
+				];
+			}
+
+			$options[] = [
+				'value' => null,
+				'label' => __('common.default'),
+			];
+
+			$form->addField(new \PKP\components\forms\FieldOptions('jatsParser::references', [
+				'label' => __('plugins.generic.jatsParser.publication.jats.references.label'),
+				'description' => __('plugins.generic.jatsParser.publication.jats.references.description'),
+				'type' => 'radio',
+				'options' => $options,
+			]));
+		} else {
+			$submissionFile = array_shift($submissionFiles);
+			$form->addField(new \PKP\components\forms\FieldOptions('jatsParser::references', [
+				'label' => __('plugins.generic.jatsParser.publication.jats.references.label'),
+				'description' => __('plugins.generic.jatsParser.publication.jats.references.description'),
+				'type' => 'checkbox',
+				'options' => [
+					[
+						'value' => $submissionFile->getId(),
+						'label' => $submissionFile->getLocalizedName(),
+					],
+				],
+
+			]));
+		}
+
+	}
 }
diff --git a/JatsParserSettingsForm.inc.php b/JatsParserSettingsForm.inc.php
@@ -2,16 +2,16 @@
 
 
 /**
-* @file plugins/generic/jatsParser/JatsParserSettingsForm.inc.php
-*
+ * @file plugins/generic/jatsParser/JatsParserSettingsForm.inc.php
+ *
  * Copyright (c) 2017-2018 Vitaliy Bezsheiko, MD, Department of Psychosomatic Medicine and Psychotherapy, Bogomolets National Medical University, Kyiv, Ukraine
-* Distributed under the GNU GPL v3.
+ * Distributed under the GNU GPL v3.
  *
  * @class JatsParserSettingsForm
  * @ingroup plugins_generic_jatsParser
-*
+ *
  * @brief Form for journal managers to modify jatsParser plugin settings
-*/
+ */
 
 import('lib.pkp.classes.form.Form');
 
@@ -48,13 +48,14 @@ function initData() {
 
 		$this->setData('references', $plugin->getSetting($contextId, 'references'));
 		$this->setData('convertToPdf', $plugin->getSetting($contextId, 'convertToPdf'));
+		$this->setData('citationStyle', $plugin->getSetting($contextId, 'citationStyle'));
 	}
 
 	/**
 	 * Assign form data to user-submitted data.
 	 */
 	function readInputData() {
-		$this->readUserVars(array('references', 'convertToPdf', 'galleysImport'));
+		$this->readUserVars(array('references', 'convertToPdf', 'citationStyle', 'customStyleInput', 'galleysImport'));
 	}
 
 	/**
@@ -63,7 +64,10 @@ function readInputData() {
 	 */
 	function fetch($request, $template = null, $display = false) {
 		$templateMgr = TemplateManager::getManager($request);
-		$templateMgr->assign('pluginName', $this->_plugin->getName());
+		$templateMgr->assign([
+			'pluginName' => $this->_plugin->getName(),
+			'citationStyles' => $this->_plugin::getSupportedCitationStyles()
+		]);
 		return parent::fetch($request, $template, $display);
 	}
 
@@ -84,6 +88,15 @@ function execute(...$functionArgs) {
 		}
 		$plugin->updateSetting($contextId, 'convertToPdf', $convertToPdf);
 
+		// Citation Style Format
+		$citationStyle = $this->getData('citationStyle');
+		if ($citationStyle == 'customStyle') {
+			$plugin->updateSetting($contextId, 'citationStyle', $this->getData('customStyleInput'));
+		} else {
+			$plugin->updateSetting($contextId, 'citationStyle', $this->getData('citationStyle'));
+		}
+
+		// Import galleys
 		if ($importGalleys = $this->getData('galleysImport')) {
 			$plugin->importGalleys();
 		}

diff --git a/classes/components/forms/PublicationJATSUploadForm.inc.php b/classes/components/forms/PublicationJATSUploadForm.inc.php
@@ -31,10 +31,10 @@ public function __construct($action, $locales, $publication, $submissionFiles, $
 		$this->successMessage = __('plugins.generic.jatsParser.publication.jats.fulltext.success');
 		$this->locales = $locales;
 
-		$options = array();
+		$options = [];
 		foreach ($locales as $value) {
 			$locale = $value['key'];
-			$lang = array();
+			$lang = [];
 			if (empty($submissionFiles)) break;
 			foreach ($submissionFiles as $submissionFile) {
 				$subName = $submissionFile->getName($locale);
@@ -64,9 +64,19 @@ public function __construct($action, $locales, $publication, $submissionFiles, $
 				'type' => 'radio',
 				'options' => $options,
 				'value' => $publication->getData('jatsParser::fullTextFileId'),
+			]))->addField(new FieldOptions('jatsParser::linksToRefs', [
+				'label' => __('plugins.generic.jatsParser.publication.jats.links.label'),
+				'type' => 'checkbox',
+				'showWhen' => 'jatsParser::references',
+				'options' => [
+					[
+						'value' => true,
+						'label' => __('common.yes')
+					]
+				],
 			]));
 		} else {
-			$this->addField(new FieldHTML("preview", array(
+			$this->addField(new FieldHTML("addProductionReadyFiles", array(
 				'description' => $msg
 			)));
 		}

diff --git a/locale/en_US/locale.xml b/locale/en_US/locale.xml
@@ -38,6 +38,7 @@
 	<message key="plugins.generic.jatsParser.galley.import">Import of JATS XML galleys</message>
 	<message key="plugins.generic.jatsParser.galley.import.description">This options allows to save JATS XML galleys as a full-text across all publications in the journal. Import is omitted if a publication already has full-text for a given galley. Import starts immediately after saving the form</message>
 	<message key="plugins.generic.jatsParser.galley.import.title">Import full-text from galleys</message>
+
 	<!-- Plugin galley settings -->
 	<message key="plugins.generic.jatsParser.galley.settings.display">Display Settings</message>
 	<message key="plugins.generic.jatsParser.galley.settings.display.description">These settings are applied to XML galleys on individual basis.</message>
@@ -48,4 +49,23 @@
 	<message key="plugins.generic.jatsParser.publication.jats.label">Generate article's fulltext from submission file in JATS XML format</message>
 	<message key="plugins.generic.jatsParser.publication.jats.description"><![CDATA[The file can be uploaded as a <a href="#workflow" id="jatsParser__linkToProduction">production ready</a> to be listed below. To see the preview, please, follow the <a id="jatsParser__linkPreview" href="{$previewPath}" target="_blank">link</a> after choosing an item from the list.]]></message>
 	<message key="plugins.generic.jatsParser.publication.jats.descriptionEmpty"><![CDATA[The list of JATS XML files is empty. Please, upload the file to the <a href="#workflow" id="jatsParser__linkToProduction">production stage</a> and it will appear below for full-text generation.]]></message>
+	<message key="plugins.generic.jatsParser.publication.jats.references.label">Retrieve references from JATS XML?</message>
+	<message key="plugins.generic.jatsParser.publication.jats.references.description">Reference list will be retrieved from JATS XML and saved as a part of the publication. If references are already included into the publication, they are going to be rewritten.</message>
+	<message key="plugins.generic.jatsParser.publication.jats.links.label">Format in-text links to references?</message>
+
+	<!-- Citation Style Formats -->
+	<message key="plugins.generic.jatsParser.style.acm-sig-proceedings">ACM</message>
+	<message key="plugins.generic.jatsParser.style.acs-nano">ACS</message>
+	<message key="plugins.generic.jatsParser.style.apa">APA</message>
+	<message key="plugins.generic.jatsParser.style.associacao-brasileira-de-normas-tecnicas">ABNT</message>
+	<message key="plugins.generic.jatsParser.style.chicago-author-date">Chicago</message>
+	<message key="plugins.generic.jatsParser.style.harvard-cite-them-right">Harvard</message>
+	<message key="plugins.generic.jatsParser.style.ieee">IEEE</message>
+	<message key="plugins.generic.jatsParser.style.modern-language-association">MLA</message>
+	<message key="plugins.generic.jatsParser.style.turabian-fullnote-bibliography">Turabian</message>
+	<message key="plugins.generic.jatsParser.style.vancouver">Vancouver</message>
+	<message key="plugins.generic.jatsParser.style.custom">Other citation style formats</message>
+	<message key="plugins.generic.jatsParser.style.description"><![CDATA[The style format for references parsed by the plugin. For other styles, visit <a target="_blank" href="https://github.com/citation-style-language/styles">CSL repository</a> to see if it's supported.]]></message>
+	<message key="plugins.generic.jatsParser.style.label">e.g.: american-medical-association</message>
+
 </locale>
diff --git a/templates/settingsForm.tpl b/templates/settingsForm.tpl
@@ -1,4 +1,4 @@
-{**
+ {**
  * plugins/generic/JATSParserPlugin/settingsForm.tpl
  *
  * Copyright (c) 2017-2018 Vitalii Bezsheiko
@@ -27,6 +27,24 @@
 		{fbvFormSection list=true}
 			{fbvElement type="checkbox" id="convertToPdf" name="convertToPdf" checked=$convertToPdf label="plugins.generic.jatsParser.settings.display.pdf"}
 		{/fbvFormSection}
+
+		{assign var='otherStyleValue' value=true}
+		{fbvFormSection list=true description="plugins.generic.jatsParser.style.description"}
+			{foreach from=$citationStyles item="citationStyleItem"}
+				{if $citationStyleItem["id"]|compare:$citationStyle}
+					{assign var='otherStyleValue' value=false}
+				{/if}
+				{fbvElement type="radio" id=$citationStyleItem["id"] name="citationStyle" value=$citationStyleItem["id"] checked=$citationStyleItem["id"]|compare:$citationStyle label=$citationStyleItem["title"]}
+			{/foreach}
+			{fbvElement type="radio" id="customStyle" name="citationStyle" value="customStyle" checked=$otherStyleValue label="plugins.generic.jatsParser.style.custom"}
+        {/fbvFormSection}
+		{fbvFormSection}
+			{if $otherStyleValue}
+                {fbvElement type="text" id="customStyleInput" name="customStyleInput" value=$citationStyle label="plugins.generic.jatsParser.style.label"}
+			{else}
+				{fbvElement type="text" id="customStyleInput" name="customStyleInput" disabled=true label="plugins.generic.jatsParser.style.label"}
+			{/if}
+		{/fbvFormSection}
 	{/fbvFormArea}
 
     {fbvFormArea id="jatsParserGalleyImport" title="plugins.generic.jatsParser.galley.import"}
@@ -39,3 +57,21 @@
 	<p><span class="formRequired">{translate key="common.requiredField"}</span></p>
 
 </form>
+<script type="text/javascript">
+    {literal}
+		$(document).ready(function() {
+			var customStyleInput = $('input[name="customStyleInput"]');
+			var inputs = $('input[name="citationStyle"]');
+			inputs.change(function () {
+				if ($(this).is(':checked')) {
+					var checkedItemId = $(this).attr('id');
+					if (checkedItemId === 'customStyle') {
+						customStyleInput.removeAttr('disabled');
+					} else {
+						customStyleInput.attr('disabled', 'disabled');
+					}
+				}
+			});
+		});
+	{/literal}
+</script>