Merge branch '7.x-1.0-dev' into '7.x-1.x'

Version 1.0

See merge request !1

classes/RDPWikidataCommons.php

@@ -9,11 +9,25 @@ abstract class RDPWikidataCommons {
 
   const MODULE_NAME = 'rdp_wikidata';
 
+  private static $module_path = '';
+
+  /**
+   * Return file system path to rdp_wikidata module
+   *
+   * @return string file system path
+   */
+  public static function module_path() {
+    if (empty(self::$module_path)) {
+      self::$module_path = drupal_get_path('module', self::MODULE_NAME);
+    }
+    return self::$module_path;
+  }
+
   /**
    * Trigger autoloading for composer-installed dependencies.
    */
   public static function autoload() {
-    include_once(drupal_get_path('module', self::MODULE_NAME)
+    include_once(self::module_path()
       . '/vendor/autoload.php');
   }
 
@@ -24,12 +38,13 @@ abstract class RDPWikidataCommons {
    * @return string
    */
   public static function path_resources($type = '') {
-    $path = base_path() . drupal_get_path('module', 'rdp_wikidata')
+    $path = base_path() . self::module_path()
       . '/resources/';
 
     if ($type == 'icon') {
       $path .= 'wikidata_logo.svg';
-    }elseif ($type == 'icon_scholia'){
+    }
+    elseif ($type == 'icon_scholia') {
       $path .= 'scholia_logo.png';
     }
 
@@ -79,4 +94,63 @@ abstract class RDPWikidataCommons {
       ],
     ];
   }
+
+  /**
+   * Returns internal ID of the Subject defined by the External-ID module. @return int
+   *
+   * @see \ExternalIDSubject
+   *
+   */
+  public static function rdp_external_id_wikidata_id_type() {
+    return "Wikidata ID";
+  }
+
+  /**
+   * Check if a Wikidata ID exists for a \Publication based on PubMed-ID and/or DOI
+   *
+   * @param int $publication_id
+   *
+   * @return bool|string
+   */
+  public static function publication_fetch_wikidata_id($publication_id) {
+
+    $type = RDPWikidataCommons::rdp_external_id_wikidata_id_type();
+    $subject = PublicationExternalIdentifier::EX_ID_SUBJECT;
+    $exid = ExternalIDRepository::findByTypeSubjectId($type, $subject, $publication_id);
+    /**
+     * @var \ExternalID $exid
+     */
+    if ($exid) {
+      $wikidata_id = $exid->getValue();
+    }
+    else {
+      /**
+       * Try to find Wikidata ID for the publication by DOI, then PMID.
+       */
+      $publication = PublicationRepository::findById($publication_id);
+      $client = new WikidataClient();
+      $wikidata_id = $client->findByDoi($publication->getDOI());
+      if (!$wikidata_id) {
+        $wikidata_id = $client->findByPMID($publication->getPMID());
+      }
+      if ($wikidata_id) {
+        /**
+         * Store \ExternalIdentifier for future use.
+         */
+        $exid = new ExternalID();
+        $exid->setSubject(ExternalIDSubjectRepository::findBySubject(PublicationExternalIdentifier::EX_ID_SUBJECT)
+          ->getId());
+        $exid->setSubjectId($publication_id);
+        $exid->setType(ExternalIDTypeRepository::findByLabel(RDPWikidataCommons::rdp_external_id_wikidata_id_type())
+          ->getId());
+        $exid->setValue($wikidata_id);
+        $exid->save();
+        $pub_exid = new PublicationExternalIdentifier();
+        $pub_exid->setExternalId($exid->getId());
+        $pub_exid->setDescription("Wikidata ID");
+        $pub_exid->save();
+      }
+    }
+    return $wikidata_id;
+  }
 }
\ No newline at end of file

rdp_wikidata.info

 name = RDP Wikidata
 package = Research Data Platform
 description = Integration of Wikidata linking into Research Data Platform
-version = 0.1
+version = 1.0
 core = 7.x
 
+; Literature module 1.2 introduces rdp_external_id module dependency
+dependencies[] = sfb_literature (>=1.2)
+
 files[] = classes/RDPWikidataCommons.php
 files[] = classes/WikidataClient.php
\ No newline at end of file

rdp_wikidata.module

@@ -3,24 +3,35 @@
  * @file Integration of Wikidata linking into Research Data Platform
  */
 
+define('RDP_WIKIDATA_URL_REPORTS_PUBLICATION_OVERVIEW', 'admin/reports/rdp_wikidata_publications');
+
 /**
- * Implements @see \hook_rdp_publication_display_table_alter()
+ * Implements @see \hook_menu()
  */
-function rdp_wikidata_rdp_publication_display_table_alter(
-  $publication_id,
-  $rows
-) {
+function rdp_wikidata_menu() {
+  $items = [];
+
+  $items[RDP_WIKIDATA_URL_REPORTS_PUBLICATION_OVERVIEW] = [
+    'title' => 'RDP Wikidata Publications Overview',
+    'description' => 'Overview of all publications and assigned Wikidata IDs. (Loading the report may 
+       take a while initially depending on the number of registered publications)',
+    'page callback' => 'rdp_wikidata_reports_publications_overview',
+    'access arguments' => ['administer site configuration'],
+    'type' => MENU_NORMAL_ITEM,
+  ];
+
+  return $items;
+}
 
-  $publication = PublicationRepository::findById($publication_id);
+/**
+ * Implements @see \hook_rdp_publication_display_table_alter()
+ */
+function rdp_wikidata_rdp_publication_display_table_alter($publication_id, $rows) {
 
   /**
-   * Try to find Wikidata ID for the publication by DOI, then PMID.
+   * Fetch and/or register the Wikidata ID of the current publication
    */
-  $client = new WikidataClient();
-  $wikidata_id = $client->findByDoi($publication->getDOI());
-  if (!$wikidata_id) {
-    $wikidata_id = $client->findByPMID($publication->getPMID());
-  }
+  $wikidata_id = RDPWikidataCommons::publication_fetch_wikidata_id($publication_id);
 
   /**
    * Display Wikidata link if ID was found.
@@ -35,16 +46,6 @@ function rdp_wikidata_rdp_publication_display_table_alter(
       WikidataClient::idToUrl($wikidata_id), $l_parameters);
     $rows['title']['value'] .= ' ' . $link;
 
-    /**
-     * Add a designated Wikidata ID row at the bottom of the table.
-     */
-    $link = l(RDPWikidataCommons::icon_wikidata_inline() . ' ' . $wikidata_id,
-      WikidataClient::idToUrl($wikidata_id), $l_parameters);
-    $rows['wikidata'] = [
-      'title' => t("Wikidata Identifier"),
-      'value' => $link,
-    ];
-
     /**
      * Add a designated Scholia-link row at the bottom of the table.
      */
@@ -58,4 +59,45 @@ function rdp_wikidata_rdp_publication_display_table_alter(
     ];
   }
   return $rows;
+}
+
+/**
+ * Page callback: list all registered publications and indicate whether a Wikidata ID could be matched or not
+ *
+ * @return string HTML markup
+ */
+function rdp_wikidata_reports_publications_overview() {
+  $publications = PublicationRepository::findAll();
+
+  $rows = [];
+  $count_wikidata = 0;
+  $count_total = count($publications);
+  foreach ($publications as $publication) {
+    $wikidata_id = RDPWikidataCommons::publication_fetch_wikidata_id($publication->id);
+
+    $link = '';
+    $l_parameters = ['attributes' => ['target' => '_blank']];
+    if ($wikidata_id) {
+      $link = l($wikidata_id, WikidataClient::idToUrl($wikidata_id), $l_parameters);
+      $count_wikidata++;
+    }
+    $rows[] = [l($publication->title, Publication::url_by_id($publication->id)), $publication->publication_year, $link];
+  }
+  $header = ['Publication', 'Year', 'Wikidata ID'];
+
+  /**
+   * Print basic statistical info
+   */
+  $coverage = round($count_wikidata / $count_total * 100, 2);
+  $display = "<div><p>Total number of <strong>$count_total</strong> publications registered, 
+        <strong>$count_wikidata</strong> of which could be automatically identified 
+        as Wikidata items. (<strong>$coverage%</strong>)</p></div>";
+
+  try {
+    $display .= theme('table', ['header' => $header, 'rows' => $rows]);
+  } catch (Exception $exception) {
+    // do nothing
+  }
+
+  return $display;
 }
\ No newline at end of file

readme.md

+# Research Data Platform Wikidata Integration Module
+
+## What it does
+
+Queries the public collaborative knowledge base 
+[Wikidata](https://wikidata.org) for items describing scholarly articles 
+that are registered in an instance of the 
+[Research Data Platform](https://gitlab.gwdg.de/research-data-platform)
+
+* Checks for each publication item registered through the "Literature" 
+module of the Research Data Platform whether a Wikidata ID can be 
+assigned based on PubMed ID or DOI
+* If Wikidata ID can be assigned, it is stored as an "External ID" object
+* If Wikidata ID is available, it is added to the literature module's 
+publication display page using the Drupal hook 
+`hook_rdp_publication_display_table_alter`
+
+## Requirements
+
+Since this is a Drupal module, a working base instance 
+of [Drupal](https://drupal.org/) 7.x including all subsequent depencies is required. 
+For third party library installation, [Composer](https://getcomposer.org/) 
+must be installed.
+
+This Drupal module requires the following custom Drupal modules 
+installed and enabled to work:
+* [RDP Commons](https://gitlab.gwdg.de/research-data-platform/sfb-commons)
+* [RDP Literature](https://gitlab.gwdg.de/research-data-platform/sfb-literature)
+* RDP External ID (part of RDP Literature module distribution 
+since version `7.x-1.2`)
+
+## Installation
+
+1. Make sure all the dependencies are installed/copied to the Drupal modules 
+directory.
+2. Run `composer install` in RDP_Wikidata module folder
+3. Go to the Drupal modules administration page of your Drupal instance 
+(`$BASE_PATH/admin/modules`) to install and enable the module.
+
+## Libraries
+
+* [PHP Wikidata API client](https://github.com/freearhey/wikidata)
+ by Aleksandr Statciuk, MIT license
\ No newline at end of file