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- add ui for editor for publishing dois

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- composer updates
- unit test with test credentials
This commit is contained in:
Arno Kaimbacher 2021-05-18 13:17:29 +02:00
parent 367dd328ef
commit b5abcef327
14 changed files with 422 additions and 102 deletions
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181
app/Http/Controllers/Publish/EditorController.php
View file

@ -1,4 +1,5 @@
<?php
namespace App\Http\Controllers\Publish;
use App\Exceptions\GeneralException;
@ -28,11 +29,40 @@ use Illuminate\Support\Facades\View;
use \Exception;
use Illuminate\Support\Facades\Config;
use App\Models\DatasetIdentifier;
use App\Models\Oai\OaiModelError;
use App\Exceptions\OaiModelException;
use App\Interfaces\DoiInterface;
class EditorController extends Controller
{
public function __construct()
/**
* Holds xml representation of document information to be processed.
*
* @var \DomDocument Defaults to null.
*/
protected $xml = null;
/**
* Holds the stylesheet for the transformation.
*
* @var \DomDocument Defaults to null.
*/
protected $xslt = null;
/**
* Holds the xslt processor.
*
* @var \XSLTProcessor Defaults to null.
*/
protected $proc = null;
public function __construct(DoiInterface $DoiClient)
{
$this->doiClient = $DoiClient;
//$this->middleware('auth');
$this->xml = new \DomDocument();
$this->proc = new \XSLTProcessor();
}
/**
@ -48,11 +78,12 @@ class EditorController extends Controller
$builder = Dataset::query();
//"select * from [documents] where [server_state] in (?) or ([server_state] = ? and [editor_id] = ?)"
$datasets = $builder
->where('server_state', 'released')
// ->whereIn('server_state', ['released'])
->orWhere(function ($query) use ($user_id) {
$query->whereIn('server_state', ['editor_accepted', 'rejected_reviewer', 'reviewed'])
->where('editor_id', $user_id);
$query->whereIn('server_state', ['editor_accepted', 'rejected_reviewer', 'reviewed', 'published'])
->where('editor_id', $user_id)->doesntHave('identifier', 'and');
})
->orderBy('server_date_modified', 'desc')
->get();
@ -105,8 +136,10 @@ class EditorController extends Controller
$dataset->load('licenses', 'authors', 'contributors', 'titles', 'abstracts', 'files', 'coverage', 'subjects', 'references');
$titleTypes = ['Main' => 'Main', 'Sub' => 'Sub', 'Alternative' => 'Alternative', 'Translated' => 'Translated', 'Other' => 'Other'];
$descriptionTypes = ['Abstract' => 'Abstract', 'Methods' => 'Methods', 'Series_information' => 'Series_information',
'Technical_info' => 'Technical_info', 'Translated' => 'Translated', 'Other' => 'Other'];
$descriptionTypes = [
'Abstract' => 'Abstract', 'Methods' => 'Methods', 'Series_information' => 'Series_information',
'Technical_info' => 'Technical_info', 'Translated' => 'Translated', 'Other' => 'Other'
];
$languages = DB::table('languages')
->where('active', true)
->pluck('part1', 'part1');
@ -126,7 +159,7 @@ class EditorController extends Controller
$languages = DB::table('languages')
->where('active', true)
->pluck('part1', 'part1');
$contributorTypes = Config::get('enums.contributor_types');
$nameTypes = Config::get('enums.name_types');
@ -142,8 +175,10 @@ class EditorController extends Controller
$referenceTypes = ["rdr-id", "doi", "handle", "isbn", "issn", "url", "urn"];
$referenceTypes = array_combine($referenceTypes, $referenceTypes);
$relationTypes = ["IsSupplementTo", "IsSupplementedBy", "IsContinuedBy", "Continues",
"IsNewVersionOf", "IsPartOf", "HasPart", "Compiles", "IsVariantFormOf"];
$relationTypes = [
"IsSupplementTo", "IsSupplementedBy", "IsContinuedBy", "Continues",
"IsNewVersionOf", "IsPartOf", "HasPart", "Compiles", "IsVariantFormOf"
];
$relationTypes = array_combine($relationTypes, $relationTypes);
return View::make(
@ -415,7 +450,8 @@ class EditorController extends Controller
$formCoverage
);
} elseif (isset($data['coverage']) && $this->containsOnlyNull($data['coverage'])
&& !is_null($dataset->coverage)) {
&& !is_null($dataset->coverage)
) {
$dataset->coverage()->delete();
}
@ -592,4 +628,131 @@ class EditorController extends Controller
}
throw new GeneralException(trans('exceptions.publish.publish.update_error'));
}
/**
* Display the specified dataset for publishing.
*
* @param int $id
* @return \Illuminate\View\View
*/
public function doi($id): \Illuminate\Contracts\View\View
{
$dataset = Dataset::query()
->with([
'titles',
'persons' => function ($query) {
$query->wherePivot('role', 'author');
},
])->findOrFail($id);
return View::make('workflow.editor.doi', [
'dataset' => $dataset,
]);
}
/**
* Store a newly created resource in storage.
*
* @param \Illuminate\Http\Request $request
* @return \Illuminate\Http\Response
*/
public function doiStore(Request $request, $publish_id)
{
$dataId = $publish_id; //$request->input('publish_id');
// Setup stylesheet
$this->loadStyleSheet(public_path() . '/prefixes/doi_datacite.xslt');
// set timestamp
$date = new \DateTime();
$unixTimestamp = $date->getTimestamp();
$this->proc->setParameter('', 'unixTimestamp', $unixTimestamp);
$prefix = "";
$base_domain = "";
$datacite_environment = config('tethys.datacite_environment');
if ($datacite_environment == "debug") {
$prefix = config('tethys.datacite_test_prefix');
$base_domain = config('tethys.test_base_domain');
} elseif ($datacite_environment == "production") {
$prefix = config('tethys.datacite_prefix');
$base_domain = config('tethys.base_domain');
}
// $prefix = config('tethys.datacite_prefix');
$this->proc->setParameter('', 'prefix', $prefix);
$repIdentifier = "tethys";
$this->proc->setParameter('', 'repIdentifier', $repIdentifier);
$this->xml->appendChild($this->xml->createElement('Datasets'));
$dataset = Dataset::where('publish_id', '=', $dataId)->firstOrFail();
if (is_null($dataset)) {
throw new OaiModelException('Dataset is not available for registering DOI!', OaiModelError::NORECORDSMATCH);
}
$dataset->fetchValues();
$xmlModel = new \App\Library\Xml\XmlModel();
$xmlModel->setModel($dataset);
$xmlModel->excludeEmptyFields();
$cache = ($dataset->xmlCache) ? $dataset->xmlCache : new \App\Models\XmlCache();
$xmlModel->setXmlCache($cache);
$domNode = $xmlModel->getDomDocument()->getElementsByTagName('Rdr_Dataset')->item(0);
$node = $this->xml->importNode($domNode, true);
$this->addSpecInformation($node, 'data-type:' . $dataset->type);
$this->xml->documentElement->appendChild($node);
$xmlMeta = $this->proc->transformToXML($this->xml);
// Log::alert($xmlMeta);
//create doiValue and correspunfing landingpage of tehtys
$doiValue = $prefix . '/tethys.' . $dataset->publish_id;
// $appUrl = config('app.url');
$landingPageUrl = $base_domain . "/dataset/" . $dataset->publish_id;
$response = $this->doiClient->registerDoi($doiValue, $xmlMeta, $landingPageUrl);
// if operation successful, store dataste identifier
if ($response->getStatusCode() == 201) {
$doi = new DatasetIdentifier();
$doi['value'] = $doiValue; //$landingPageUrl;
$doi['dataset_id'] = $dataset->id;
$doi['type'] = "doi";
$doi['status'] = "findable";
if ($doi->save()) {
// update server_date_modified for triggering nex xml cache (doi interface)
$time = new \Illuminate\Support\Carbon();
$dataset->server_date_modified = $time;
$dataset->save();
return redirect()
->route('publish.workflow.editor.index')
->with('flash_message', 'You have successfully created a DOI for the dataset!');
}
} else {
$message = 'unexpected DataCite MDS response code ' . $response->getStatusCode();
// $this->log($message, 'err');
throw new GeneralException($message);
}
}
/**
* Load an xslt stylesheet.
*
* @return void
*/
private function loadStyleSheet($stylesheet)
{
$this->xslt = new \DomDocument;
$this->xslt->load($stylesheet);
$this->proc->importStyleSheet($this->xslt);
if (isset($_SERVER['HTTP_HOST'])) {
$this->proc->setParameter('', 'host', $_SERVER['HTTP_HOST']);
}
//$this->proc->setParameter('', 'server', $this->getRequest()->getBaseUrl());
}
private function addSpecInformation(\DOMNode $document, $information)
{
$setSpecAttribute = $this->xml->createAttribute('Value');
$setSpecAttributeValue = $this->xml->createTextNode($information);
$setSpecAttribute->appendChild($setSpecAttributeValue);
$setSpecElement = $this->xml->createElement('SetSpec');
//$setSpecElement =new \DOMElement("SetSpec");
$setSpecElement->appendChild($setSpecAttribute);
$document->appendChild($setSpecElement);
}
}

6
app/Library/Xml/DatasetExtension.php
View file

@ -7,6 +7,7 @@ use App\Models\License;
use App\Models\Person;
use App\Models\File;
use App\Models\Coverage;
use App\Models\DatasetIdentifier;
use App\Models\Subject;
use App\Models\DatasetReference;
@ -70,6 +71,11 @@ trait DatasetExtension
'relation' => 'references',
'fetch' => 'eager'
),
'Identifier' => array(
'model' => DatasetIdentifier::class,
'relation' => 'identifier',
'fetch' => 'eager'
),
'Subject' => array(
'model' => Subject::class,
'relation' => 'subjects',

9
app/Models/Dataset.php
View file

@ -13,6 +13,7 @@ use App\Models\Project;
use App\Models\Title;
use App\Models\User;
use App\Models\XmlCache;
use App\Models\DatasetIdentifier;
use Carbon\Carbon;
// use App\Models\GeolocationBox;
use Illuminate\Database\Eloquent\Model;
@ -96,6 +97,14 @@ class Dataset extends Model
return $this->belongsTo(Project::class, 'project_id', 'id');
}
/**
* Get the doi indentifier that owns the dataset.
*/
public function identifier()
{
return $this->hasOne(DatasetIdentifier::class, 'dataset_id', 'id');
}
/**
* Get the account that the dataset belongs to
*/

2
app/Models/DatasetIdentifier.php
View file

@ -14,6 +14,6 @@ class DatasetIdentifier extends Model
*/
public function dataset()
{
return $this->belongsTo(Dataset::class, 'document_id', 'id');
return $this->belongsTo(Dataset::class, 'dataset_id', 'id');
}
}

7
app/Providers/DoiServiceProvider.php
View file

@ -7,7 +7,8 @@
namespace App\Providers;
use App\Tethys\Utils\DoiService;
use App\Tethys\Utils\DoiClient;
use App\Interfaces\DoiInterface;
use Illuminate\Support\ServiceProvider;
class DoiServiceProvider extends ServiceProvider
@ -33,12 +34,12 @@ class DoiServiceProvider extends ServiceProvider
{
//
$this->app->singleton('App\Interfaces\DoiInterface', function ($app) {
return new DoiService();
return new DoiClient();
});
}
public function provides()
{
return [DoiService::class];
return [DoiClient::class];
}
}

15
app/Tethys/Utils/DoiClient.php
View file

@ -10,20 +10,24 @@ class DoiClient implements DoiInterface
private $username;
private $password;
private $serviceUrl;
private $prefix;
private $base_domain;
public function __construct()
{
$datacite_environment = "production"; //config('tethys.datacite_environment');
$datacite_environment = config('tethys.datacite_environment');
if ($datacite_environment == "debug") {
$this->username = config('tethys.datacite_test_username');
$this->password = config('tethys.datacite_test_password');
$this->serviceUrl = config('tethys.test_datacite_service_url');
$this->prefix = config('tethys.datacite_prefix');
$this->serviceUrl = config('tethys.datacite_test_service_url');
$this->prefix = config('tethys.datacite_test_prefix');
$this->base_domain = config('tethys.test_base_domain');
} elseif ($datacite_environment == "production") {
$this->username = config('tethys.datacite_username');
$this->password = config('tethys.datacite_password');
$this->serviceUrl = config('tethys.datacite_service_url');
$this->prefix = config('tethys.datacite_prefix');
$this->base_domain = config('tethys.base_domain');
}
if (is_null($this->username) || is_null($this->password) || is_null($this->serviceUrl)) {
$message = 'missing configuration settings to properly initialize DOI client';
@ -45,6 +49,7 @@ class DoiClient implements DoiInterface
{
// Schritt 1: Metadaten als XML registrieren
// state draft
$response = null;
$url = $this->serviceUrl . '/metadata/' . $doiValue;
try {
@ -79,7 +84,7 @@ class DoiClient implements DoiInterface
}
// Schritt 2: Register the DOI name
// DOI und URL der Frontdoor des zugehörigen Dokuments übergeben
// DOI und URL der Frontdoor des zugehörigen Dokuments übergeben: state findable
$url = $this->serviceUrl . '/doi/' . $doiValue;
try {
$client = new Client(
@ -199,7 +204,7 @@ class DoiClient implements DoiInterface
public function updateMetadataForDoi($doiValue, $newMeta)
{
$response = null;
$url = $this->serviceUrl . '/metadata/' . $doiValue;
$url = $this->serviceUrl . '/metadata/' . $doiValue;
try {
$client = new Client([
'auth' => [$this->username, $this->password],