Add preprint information - #21

PubPeerFoundation · May 7, 2021 · 4dddeaa · 4dddeaa
1 parent 3c23131
commit 4dddeaa
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Showing 10 changed files with 1,624 additions and 22 deletions.
diff --git a/src/Models/Links.php b/src/Models/Links.php
@@ -0,0 +1,48 @@
+<?php
+
+namespace PubPeerFoundation\PublicationDataExtractor\Models;
+
+class Links extends Model
+{
+    /**
+     * Hold cherry picked list of links.
+     *
+     * @var array
+     */
+    protected $list = [];
+
+    /**
+     * Add unknown links to the current list.
+     */
+    public function add(array $links): array
+    {
+        foreach ($links as $link) {
+            if ($this->hasPreprint($link)) {
+                $this->list[] = $link;
+            }
+            if ($this->isPreprint($link)) {
+                $this->list[] = $link;
+            }
+        }
+
+        return $this->list;
+    }
+
+    private function hasPreprint(array $link): bool
+    {
+        if (! array_key_exists('has_preprint', $link)) {
+            return false;
+        }
+
+        return ! in_array(strtolower($link['has_preprint']), $this->knownIdentifierValues('has_preprint'));
+    }
+
+    private function isPreprint(array $link): bool
+    {
+        if (! array_key_exists('is_preprint_of', $link)) {
+            return false;
+        }
+
+        return ! in_array(strtolower($link['is_preprint_of']), $this->knownIdentifierValues('is_preprint_of'));
+    }
+}
diff --git a/src/Models/Tags.php b/src/Models/Tags.php
@@ -13,9 +13,6 @@ class Tags extends Model
 
     /**
      * Add unknown tags to the current list.
-     *
-     * @param  array $tags
-     * @return array
      */
     public function add(array $tags): array
     {

diff --git a/src/Resources/Extractors/Crossref.php b/src/Resources/Extractors/Crossref.php
@@ -2,10 +2,10 @@
 
 namespace PubPeerFoundation\PublicationDataExtractor\Resources\Extractors;
 
-use PubPeerFoundation\PublicationDataExtractor\Exceptions\JournalTitleNotFoundException;
 use PubPeerFoundation\PublicationDataExtractor\Exceptions\UnparseableApiException;
+use PubPeerFoundation\PublicationDataExtractor\Exceptions\JournalTitleNotFoundException;
 
-class Crossref extends Extractor implements ProvidesPublicationData, ProvidesIdentifiersData, ProvidesJournalData, ProvidesAuthorsData, ProvidesTagsData
+class Crossref extends Extractor implements ProvidesPublicationData, ProvidesIdentifiersData, ProvidesJournalData, ProvidesAuthorsData, ProvidesTagsData, ProvidesLinksData
 {
     /**
      * @throws UnparseableApiException
@@ -117,6 +117,26 @@ public function extractTagsData(): void
         }
     }
 
+    /**
+     * Extract and format data needed for the links Relationship
+     * on the Publication Model.
+     */
+    public function extractLinksData(): void
+    {
+        if (array_key_exists('relation', $this->searchTree)) {
+            foreach (get_array($this->searchTree['relation'], 'has-preprint') as $preprint) {
+                $this->resourceOutput['links'][] = [
+                    'has_preprint' => $preprint['id'],
+                ];
+            }
+            foreach (get_array($this->searchTree['relation'], 'is-preprint-of') as $preprint) {
+                $this->resourceOutput['links'][] = [
+                    'is_preprint_of' => $preprint['id'],
+                ];
+            }
+        }
+    }
+
     /**
      * @param $array
      * @return mixed

diff --git a/src/Resources/Extractors/Extractor.php b/src/Resources/Extractors/Extractor.php
@@ -2,10 +2,10 @@
 
 namespace PubPeerFoundation\PublicationDataExtractor\Resources\Extractors;
 
-use PubPeerFoundation\PublicationDataExtractor\Exceptions\JournalTitleNotFoundException;
-use PubPeerFoundation\PublicationDataExtractor\Exceptions\UnparseableApiException;
 use PubPeerFoundation\PublicationDataExtractor\Output;
 use PubPeerFoundation\PublicationDataExtractor\Schema;
+use PubPeerFoundation\PublicationDataExtractor\Exceptions\UnparseableApiException;
+use PubPeerFoundation\PublicationDataExtractor\Exceptions\JournalTitleNotFoundException;
 
 abstract class Extractor
 {
@@ -36,8 +36,7 @@ abstract class Extractor
     /**
      * Extractor constructor.
      *
-     * @param mixed  $document
-     * @param Output $output
+     * @param mixed $document
      */
     public function __construct($document, Output $output)
     {
@@ -47,8 +46,6 @@ public function __construct($document, Output $output)
 
     /**
      * Dynamically choose what methods to call on each Resource.
-     *
-     * @return array
      */
     public function extract(): array
     {

diff --git a/src/Resources/Extractors/ProvidesLinksData.php b/src/Resources/Extractors/ProvidesLinksData.php
@@ -0,0 +1,8 @@
+<?php
+
+namespace PubPeerFoundation\PublicationDataExtractor\Resources\Extractors;
+
+interface ProvidesLinksData
+{
+    public function extractLinksData(): void;
+}
diff --git a/src/Schema.php b/src/Schema.php
@@ -2,8 +2,8 @@
 
 namespace PubPeerFoundation\PublicationDataExtractor;
 
-use Volan\ValidatorResult;
 use Volan\Volan;
+use Volan\ValidatorResult;
 
 class Schema
 {
@@ -87,6 +87,15 @@ class Schema
                     '_type' => 'string',
                 ],
             ],
+            'links' => [
+                '_type' => 'nested_array',
+                'has_preprint' => [
+                    '_type' => 'string',
+                ],
+                'is_preprint_of' => [
+                    '_type' => 'string',
+                ],
+            ],
             'affiliations' => [
                 '_type' => 'nested_array',
                 'name' => [
@@ -118,7 +127,6 @@ class Schema
      * Validate the data against Schema.
      *
      * @param $data
-     * @return \Volan\ValidatorResult
      */
     public static function validate($data): ValidatorResult
     {
@@ -130,8 +138,6 @@ public static function validate($data): ValidatorResult
 
     /**
      * Get the main data types from Schema.
-     *
-     * @return array
      */
     public static function getDataTypes(): array
     {

diff --git a/src/Support/helpers.php b/src/Support/helpers.php
@@ -1,7 +1,7 @@
 <?php
 
-use PubPeerFoundation\PublicationDataExtractor\Support\DateHelper;
 use Tightenco\Collect\Support\Arr;
+use PubPeerFoundation\PublicationDataExtractor\Support\DateHelper;
 
 if (! function_exists('get_class_name')) {
     /**

diff --git a/tests/Integration/CrossrefDataExtractorTest.php b/tests/Integration/CrossrefDataExtractorTest.php
@@ -3,17 +3,17 @@
 namespace PubPeerFoundation\PublicationDataExtractor\Test\Integration;
 
 use PubPeerFoundation\PublicationDataExtractor\Output;
-use PubPeerFoundation\PublicationDataExtractor\Resources\Extractors\Crossref;
-use PubPeerFoundation\PublicationDataExtractor\Resources\Extractors\CrossrefUpdates;
 use PubPeerFoundation\PublicationDataExtractor\Test\TestCase;
 use PubPeerFoundation\PublicationDataExtractor\Test\TestHelpers;
+use PubPeerFoundation\PublicationDataExtractor\Resources\Extractors\Crossref;
+use PubPeerFoundation\PublicationDataExtractor\Resources\Extractors\CrossrefUpdates;
 
 class CrossrefDataExtractorTest extends TestCase
 {
     use TestHelpers;
 
     /** @test */
-    public function it_can_extract_publication_data_from_crossref_api()
+    public function itCanExtractPublicationDataFromCrossrefApi()
     {
         // Arrange
         $file = $this->loadJson('Crossref/valid-article');
@@ -33,7 +33,7 @@ public function it_can_extract_publication_data_from_crossref_api()
     }
 
     /** @test */
-    public function it_can_extract_identifiers_data_from_crossref_api()
+    public function itCanExtractIdentifiersDataFromCrossrefApi()
     {
         // Arrange
         $file = $this->loadJson('Crossref/valid-article');
@@ -59,7 +59,7 @@ public function it_can_extract_identifiers_data_from_crossref_api()
     }
 
     /** @test */
-    public function it_can_extract_authors_from_crossref_api()
+    public function itCanExtractAuthorsFromCrossrefApi()
     {
         // Arrange
         $file = $this->loadJson('Crossref/valid-with-orcid-article');
@@ -101,7 +101,7 @@ public function it_can_extract_authors_from_crossref_api()
     }
 
     /** @test */
-    public function it_can_extract_updates_from_crossref_api()
+    public function itCanExtractUpdatesFromCrossrefApi()
     {
         // Arrange
         $file = $this->loadJson('Crossref/valid-with-updates-article');
@@ -120,4 +120,38 @@ public function it_can_extract_updates_from_crossref_api()
             ],
         ], $extracted['updates']);
     }
+
+    /** @test */
+    public function itCanExtractHasPreprintFromCrossrefApi()
+    {
+        // Arrange
+        $file = $this->loadJson('Crossref/valid-with-has-updates-article');
+
+        // Act
+        $extracted = (new Crossref($file, new Output()))->extract();
+
+        // Assert
+        $this->assertArraySubset([
+            [
+                'has_preprint' => '10.1101/335703',
+            ],
+        ], $extracted['links']);
+    }
+
+    /** @test */
+    public function itCanExtractIsPreprintOfFromCrossrefApi()
+    {
+        // Arrange
+        $file = $this->loadJson('Crossref/valid-with-is-preprint-of');
+
+        // Act
+        $extracted = (new Crossref($file, new Output()))->extract();
+
+        // Assert
+        $this->assertArraySubset([
+            [
+                'is_preprint_of' => '10.1016/j.neuron.2019.05.022',
+            ],
+        ], $extracted['links']);
+    }
 }