PubMedImporter::getDefaultXsltTransformation() - Code Metrics - Inspection of "Ap5 ap6 ap1 internal format" - kitodo/kitodo-publication - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Pull Request — master (#195)

unknown

created 2021-02-10 14:24 UTC

PubMedImporter::getDefaultXsltTransformation() A

↳ Parent: PubMedImporter

Complexity

Conditions	1
Paths	1

Size

Total Lines	7
Code Lines	2

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	0	Features	0

Metric	Value
cc	1
eloc	2
c	1
b	0
f	0
nc	1
nop	0
dl	0
loc	7
rs	10

<?php
namespace EWW\Dpf\Services\ImportExternalMetadata;

/*
 * This file is part of the TYPO3 CMS project.
 *
 * It is free software; you can redistribute it and/or modify it under
 * the terms of the GNU General Public License, either version 2
 * of the License, or any later version.
 *
 * For the full copyright and license information, please read the
 * LICENSE.txt file that was distributed with this source code.
 *
 * The TYPO3 project - inspiring people to share!
 */

\Httpful\Bootstrap::init();

use \Httpful\Request;
use Symfony\Component\Serializer\Encoder\XmlEncoder;
use EWW\Dpf\Services\Transformer\DocumentTransformer;
use EWW\Dpf\Services\ProcessNumber\ProcessNumberGenerator;
use EWW\Dpf\Domain\Model\DocumentType;
use EWW\Dpf\Domain\Model\PubMedMetadata;
use EWW\Dpf\Domain\Model\ExternalMetadata;

class PubMedImporter extends AbstractImporter implements Importer
{
    /**
     * @var string
     */
    protected $apiUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";

    /**
     * @var string
     */
    protected $resource = "/esummary.fcgi?version=2.0&db=pubmed&id=";

    /**
     * @var string
     */
    protected $searchPath = "/esearch.fcgi?version=2.0&db=pubmed";

    /**
     * Returns the list of all publication types
     *
     * @return array
     */
    public static function types()
    {
        return [
            'Collected Works',
            'Congress',
            'Dataset',
            'Dictionary',
            'Journal Article'
        ];
    }

    /**
     * @param string $identifier
     * @return ExternalMetadata|null
     */
    public function findByIdentifier($identifier)
    {
        try {
            $response = Request::get($this->apiUrl . $this->resource . $identifier)->send();

            if (!$response->hasErrors() && $response->code == 200) {

                /** @var PubMedMetadata $pubMedMetadata */
                $pubMedMetadata = $this->objectManager->get(PubMedMetadata::class);

                $pubMedMetadata->setSource(get_class($this));
                $pubMedMetadata->setFeUser($this->security->getUser()->getUid());
                $pubMedMetadata->setData($response);
                $pubMedMetadata->setPublicationIdentifier($identifier);

                $xmlDataXpath = $pubMedMetadata->getDataXpath();

                $node = $xmlDataXpath->query('/eSummaryResult/ERROR');
                if ($node->length > 0) {
                    return null;
                }

                return $pubMedMetadata;

            } else {
                return null;
            }

        } catch (\Throwable $throwable) {
            $this->logger->error($throwable->getMessage());
            throw $throwable;
        }

        return null;
function fx() {
    try {
        doSomething();
        return true;
    }
    catch (\Exception $e) {
        return false;
    }

    return false;
}
    }

    /**
     * @param string $query
     * @param int $rows
     * @param int $offset
     * @param string $searchField
     * @return array|mixed
     * @throws \Throwable
     */
    public function search($query, $rows = 10, $offset = 0, $searchField = 'author')
    {
        $requestUri = $this->apiUrl . $this->searchPath . '&retmax='.$rows;

        if ($offset > 0) $requestUri .= '&retstart=' . $offset;

        if ($searchField) {
            $query .= '['.ucfirst(strtolower($searchField)).']';
        }

        $requestUri .= "&term=" . urlencode($query);
        $results = [];

        try {
            $response = Request::get($requestUri)->send();

            if (!$response->hasErrors() && $response->code == 200) {

                $dom = new \DOMDocument();
                if (is_null(@$dom->loadXML($response))) {
                    throw new \Exception("Invalid XML: " . get_class($this));
                }
                $xmlDataXpath = \EWW\Dpf\Helper\XPath::create($dom);

                $node = $xmlDataXpath->query('/eSearchResult/ERROR');
                if ($node->length > 0) {
                    return null;
                }

                $node = $xmlDataXpath->query('/eSearchResult/Count');
                if ($node->length > 0) {
                    $results['total-results'] = $node->item(0)->nodeValue;
                }

                $node = $xmlDataXpath->query('/eSearchResult/RetMax');
                if ($node->length > 0) {
                    $results['items-per-page'] = $node->item(0)->nodeValue;
                }

                $nodes = $xmlDataXpath->query('/eSearchResult/IdList/Id');
                if ($nodes->length > 0) {

                    $identifierList = [];
                    foreach ($nodes as $node) {
                        $identifierList[] = $node->nodeValue;
                    }

                    $results['items'] = $this->findByIdentifierList($identifierList);

                    return $results;
                }
            }
        } catch (\Throwable $throwable) {
            $this->logger->error($throwable->getMessage());
            throw $throwable;
        }

        return null;
    }

    /**
     * @return \EWW\Dpf\Domain\Model\TransformationFile
     */
    protected function getDefaultXsltTransformation() : ?\EWW\Dpf\Domain\Model\TransformationFile
    {
        /** @var \EWW\Dpf\Domain\Model\Client $client */
        $client = $this->clientRepository->findAll()->current();

        /** @var \EWW\Dpf\Domain\Model\TransformationFile $xsltTransformationFile */
        return $client->getPubmedTransformation()->current();
    }

    /**
     * @return string
     */
    protected function getDefaultXsltFilePath() : string
    {
        return \TYPO3\CMS\Core\Utility\GeneralUtility::getFileAbsFileName(
            'EXT:dpf/Resources/Private/Xslt/pubmed-default.xsl'
        );
    }

    /**
     * @return string
     */
    protected function getImporterName()
    {
        return 'pubmed';
    }

    /**
     * @param array $identifierList
     * @return array
     */
    protected function findByIdentifierList($identifierList)
    {
        try {
            $identifiers = implode(',', $identifierList);
            $response = Request::get($this->apiUrl . $this->resource . $identifiers)->send();

            if (!$response->hasErrors() && $response->code == 200) {

                $dom = new \DOMDocument();
                if (is_null(@$dom->loadXML($response))) {
                    throw new \Exception("Invalid XML: " . get_class($this));
                }
                $xmlDataXpath = \EWW\Dpf\Helper\XPath::create($dom);

                $node = $xmlDataXpath->query('/eSummaryResult/ERROR');
                if ($node->length > 0) {
                    return [];
                }

                $nodes = $xmlDataXpath->query('/eSummaryResult/DocumentSummarySet/DocumentSummary');
                if ($nodes->length > 0) {

                    $results = [];

                    foreach ($nodes as $nodeItem) {

                        $xml = '<eSummaryResult><DocumentSummarySet>';
                        $xml .= $dom->saveXML($nodeItem);
                        $xml .= '</DocumentSummarySet></eSummaryResult>';

                        $idNode = $xmlDataXpath->query('@uid', $nodeItem);
                        if ($idNode->length > 0) {
                            $identifier = $idNode->item(0)->nodeValue;

                            if ($identifier) {
                                $itemDom = new \DOMDocument();

                                if (is_null(@$itemDom->loadXML($xml))) {
                                    throw new \Exception("Invalid XML: " . get_class($this));
                                }

                                /** @var PubMedMetadata $pubMedMetadata */
                                $pubMedMetadata = $this->objectManager->get(PubMedMetadata::class);

                                $pubMedMetadata->setSource(get_class($this));
                                $pubMedMetadata->setFeUser($this->security->getUser()->getUid());
                                $pubMedMetadata->setData($xml);
                                $pubMedMetadata->setPublicationIdentifier($identifier);

                                $results[$identifier] = $pubMedMetadata;
                            }
                        }
                    }

                    return $results;
                }
            }
        } catch (\Throwable $throwable) {
            $this->logger->error($throwable->getMessage());
            throw $throwable;
        }

        return [];
    }
}


1			<?php
2			namespace EWW\Dpf\Services\ImportExternalMetadata;
3
4			/*
5			* This file is part of the TYPO3 CMS project.
6			*
7			* It is free software; you can redistribute it and/or modify it under
8			* the terms of the GNU General Public License, either version 2
9			* of the License, or any later version.
10			*
11			* For the full copyright and license information, please read the
12			* LICENSE.txt file that was distributed with this source code.
13			*
14			* The TYPO3 project - inspiring people to share!
15			*/
16
17			\Httpful\Bootstrap::init();
18
19			use \Httpful\Request;
20			use Symfony\Component\Serializer\Encoder\XmlEncoder;
21			use EWW\Dpf\Services\Transformer\DocumentTransformer;
22			use EWW\Dpf\Services\ProcessNumber\ProcessNumberGenerator;
23			use EWW\Dpf\Domain\Model\DocumentType;
24			use EWW\Dpf\Domain\Model\PubMedMetadata;
25			use EWW\Dpf\Domain\Model\ExternalMetadata;
26
27			class PubMedImporter extends AbstractImporter implements Importer
28			{
29			/**
30			* @var string
31			*/
32			protected $apiUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
33
34			/**
35			* @var string
36			*/
37			protected $resource = "/esummary.fcgi?version=2.0&db=pubmed&id=";
38
39			/**
40			* @var string
41			*/
42			protected $searchPath = "/esearch.fcgi?version=2.0&db=pubmed";
43
44			/**
45			* Returns the list of all publication types
46			*
47			* @return array
48			*/
49			public static function types()
50			{
51			return [
52			'Collected Works',
53			'Congress',
54			'Dataset',
55			'Dictionary',
56			'Journal Article'
57			];
58			}
59
60			/**
61			* @param string $identifier
62			* @return ExternalMetadata\|null
63			*/
64			public function findByIdentifier($identifier)
65			{
66			try {
67			$response = Request::get($this->apiUrl . $this->resource . $identifier)->send();
68
69			if (!$response->hasErrors() && $response->code == 200) {
70
71			/** @var PubMedMetadata $pubMedMetadata */
72			$pubMedMetadata = $this->objectManager->get(PubMedMetadata::class);
73
74			$pubMedMetadata->setSource(get_class($this));
75			$pubMedMetadata->setFeUser($this->security->getUser()->getUid());
76			$pubMedMetadata->setData($response);
77			$pubMedMetadata->setPublicationIdentifier($identifier);
78
79			$xmlDataXpath = $pubMedMetadata->getDataXpath();
80
81			$node = $xmlDataXpath->query('/eSummaryResult/ERROR');
82			if ($node->length > 0) {
83			return null;
84			}
85
86			return $pubMedMetadata;
87
88			} else {
89			return null;
90			}
91
92			} catch (\Throwable $throwable) {
93			$this->logger->error($throwable->getMessage());
94			throw $throwable;
95			}
96
97			return null;
			0 ignored issues – show Unused Code introduced 2020-12-15 14:55 UTC by Report Bug Copy Issue Report `return null` is not reachable. This check looks for unreachable code. It uses sophisticated control flow analysis techniques to find statements which will never be executed. Unreachable code is most often the result of `return`, `die` or `exit` statements that have been added for debug purposes. function fx() { try { doSomething(); return true; } catch (\Exception $e) { return false; } return false; } In the above example, the last `return false` will never be executed, because a return statement has already been met in every possible execution path. Loading history...
98			}
99
100			/**
101			* @param string $query
102			* @param int $rows
103			* @param int $offset
104			* @param string $searchField
105			* @return array\|mixed
106			* @throws \Throwable
107			*/
108			public function search($query, $rows = 10, $offset = 0, $searchField = 'author')
109			{
110			$requestUri = $this->apiUrl . $this->searchPath . '&retmax='.$rows;
111
112			if ($offset > 0) $requestUri .= '&retstart=' . $offset;
113
114			if ($searchField) {
115			$query .= '['.ucfirst(strtolower($searchField)).']';
116			}
117
118			$requestUri .= "&term=" . urlencode($query);
119			$results = [];
120
121			try {
122			$response = Request::get($requestUri)->send();
123
124			if (!$response->hasErrors() && $response->code == 200) {
125
126			$dom = new \DOMDocument();
127			if (is_null(@$dom->loadXML($response))) {
128			throw new \Exception("Invalid XML: " . get_class($this));
129			}
130			$xmlDataXpath = \EWW\Dpf\Helper\XPath::create($dom);
131
132			$node = $xmlDataXpath->query('/eSearchResult/ERROR');
133			if ($node->length > 0) {
134			return null;
135			}
136
137			$node = $xmlDataXpath->query('/eSearchResult/Count');
138			if ($node->length > 0) {
139			$results['total-results'] = $node->item(0)->nodeValue;
140			}
141
142			$node = $xmlDataXpath->query('/eSearchResult/RetMax');
143			if ($node->length > 0) {
144			$results['items-per-page'] = $node->item(0)->nodeValue;
145			}
146
147			$nodes = $xmlDataXpath->query('/eSearchResult/IdList/Id');
148			if ($nodes->length > 0) {
149
150			$identifierList = [];
151			foreach ($nodes as $node) {
152			$identifierList[] = $node->nodeValue;
153			}
154
155			$results['items'] = $this->findByIdentifierList($identifierList);
156
157			return $results;
158			}
159			}
160			} catch (\Throwable $throwable) {
161			$this->logger->error($throwable->getMessage());
162			throw $throwable;
163			}
164
165			return null;
166			}
167
168			/**
169			* @return \EWW\Dpf\Domain\Model\TransformationFile
170			*/
171			protected function getDefaultXsltTransformation() : ?\EWW\Dpf\Domain\Model\TransformationFile
172			{
173			/** @var \EWW\Dpf\Domain\Model\Client $client */
174			$client = $this->clientRepository->findAll()->current();
175
176			/** @var \EWW\Dpf\Domain\Model\TransformationFile $xsltTransformationFile */
177			return $client->getPubmedTransformation()->current();
178			}
179
180			/**
181			* @return string
182			*/
183			protected function getDefaultXsltFilePath() : string
184			{
185			return \TYPO3\CMS\Core\Utility\GeneralUtility::getFileAbsFileName(
186			'EXT:dpf/Resources/Private/Xslt/pubmed-default.xsl'
187			);
188			}
189
190			/**
191			* @return string
192			*/
193			protected function getImporterName()
194			{
195			return 'pubmed';
196			}
197
198			/**
199			* @param array $identifierList
200			* @return array
201			*/
202			protected function findByIdentifierList($identifierList)
203			{
204			try {
205			$identifiers = implode(',', $identifierList);
206			$response = Request::get($this->apiUrl . $this->resource . $identifiers)->send();
207
208			if (!$response->hasErrors() && $response->code == 200) {
209
210			$dom = new \DOMDocument();
211			if (is_null(@$dom->loadXML($response))) {
212			throw new \Exception("Invalid XML: " . get_class($this));
213			}
214			$xmlDataXpath = \EWW\Dpf\Helper\XPath::create($dom);
215
216			$node = $xmlDataXpath->query('/eSummaryResult/ERROR');
217			if ($node->length > 0) {
218			return [];
219			}
220
221			$nodes = $xmlDataXpath->query('/eSummaryResult/DocumentSummarySet/DocumentSummary');
222			if ($nodes->length > 0) {
223
224			$results = [];
225
226			foreach ($nodes as $nodeItem) {
227
228			$xml = '<eSummaryResult><DocumentSummarySet>';
229			$xml .= $dom->saveXML($nodeItem);
230			$xml .= '</DocumentSummarySet></eSummaryResult>';
231
232			$idNode = $xmlDataXpath->query('@uid', $nodeItem);
233			if ($idNode->length > 0) {
234			$identifier = $idNode->item(0)->nodeValue;
235
236			if ($identifier) {
237			$itemDom = new \DOMDocument();
238
239			if (is_null(@$itemDom->loadXML($xml))) {
240			throw new \Exception("Invalid XML: " . get_class($this));
241			}
242
243			/** @var PubMedMetadata $pubMedMetadata */
244			$pubMedMetadata = $this->objectManager->get(PubMedMetadata::class);
245
246			$pubMedMetadata->setSource(get_class($this));
247			$pubMedMetadata->setFeUser($this->security->getUser()->getUid());
248			$pubMedMetadata->setData($xml);
249			$pubMedMetadata->setPublicationIdentifier($identifier);
250
251			$results[$identifier] = $pubMedMetadata;
252			}
253			}
254			}
255
256			return $results;
257			}
258			}
259			} catch (\Throwable $throwable) {
260			$this->logger->error($throwable->getMessage());
261			throw $throwable;
262			}
263
264			return [];
265			}
266			}
267

kitodo / kitodo-publication

Pull Request — master (#195)

PubMedImporter::getDefaultXsltTransformation() A

Complexity

Size

Duplication

Importance

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