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feat:2117 rewritting the api endpoint returning a dataset as xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,289 @@ | ||
| <?php | ||
|
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| declare(strict_types=1); | ||
|
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| namespace GigaDB\services; | ||
|
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| use yii\base\Component; | ||
|
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| class DatasetToXmlService | ||
| { | ||
| public function convertToXml( | ||
| \Dataset $model, | ||
| ?\Image $image = null, | ||
| bool $isAll = false, | ||
| bool $isDatasetOnly = false, | ||
| bool $isOnlySample = false, | ||
| bool $isOnlyFile = false | ||
| ): string | ||
| { | ||
| $xml = new \SimpleXMLElement("<?xml version=\"1.0\" encoding=\"UTF-8\"?><gigadb_entry></gigadb_entry>"); | ||
|
|
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| if ($isAll || $isDatasetOnly) { | ||
| $xml = $this->buildDataset($xml, $model, $image); | ||
| } | ||
|
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| if ($isDatasetOnly) { | ||
| if (!$xml->asXML()) { | ||
| return 'XML is invalid'; | ||
| } | ||
|
|
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| return $xml->asXML(); | ||
| } | ||
|
|
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| if ($isAll || $isOnlySample) { | ||
| $xml = $this->buildSamples($xml, $model); | ||
| } | ||
|
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| if ($isAll) { | ||
| $xml->addChild('experiments'); | ||
| } | ||
|
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| if ($isAll || $isOnlyFile) { | ||
| $xml = $this->buildFiles($xml, $model); | ||
| } | ||
|
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| if (!$xml->asXML()) { | ||
| return 'XML is invalid'; | ||
| } | ||
|
|
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| return $xml->asXML(); | ||
| } | ||
|
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| private function buildSamples(\SimpleXMLElement $xml, \Dataset $model): \SimpleXMLElement | ||
| { | ||
| $samplesElement = $xml->addChild('samples'); | ||
| $samples = $model->samples; | ||
|
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| foreach ($samples as $sample) { | ||
| $sampleElement = $samplesElement->addChild('sample'); | ||
| $sampleElement->addAttribute('submission_date', $sample->submission_date); | ||
| $sampleElement->addAttribute('id', (string) $sample->id); | ||
|
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| $sampleElement->addChild('name', $sample->name); | ||
| $species = $sample->species; | ||
|
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| $speciesElement = $sampleElement->addChild('species'); | ||
| $speciesElement->addChild('tax_id', (string) $species->tax_id); | ||
| $speciesElement->addChild('common_name', $species->common_name); | ||
| $speciesElement->addChild('genbank_name', $species->genbank_name); | ||
| $speciesElement->addChild('scientific_name', $species->scientific_name); | ||
| $speciesElement->addChild('eol_link', $species->eol_link); | ||
|
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| $sampleElement->addChild('sampling_protocol', $sample->sampling_protocol); | ||
| $sampleElement->addChild('consent_doc', $sample->consent_document); | ||
|
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| $contactAuthor = $sampleElement->addChild('contact_author'); | ||
| $contactAuthor->addChild('name', $sample->contact_author_name); | ||
| $contactAuthor->addChild('email', $sample->contact_author_email); | ||
|
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| $relsamples = $sample->sampleRels; | ||
| $relatedSamplesElement = $sampleElement->addChild('related_samples'); | ||
| foreach ($relsamples as $relsample) { | ||
| $relSample = $relatedSamplesElement->addChild('related_sample', $sample->name); | ||
| $relSample->addAttribute('relationship_type', $relsample->relationship->name); | ||
| } | ||
|
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| $samplesAttrElement = $sampleElement->addChild('sample_attributes'); | ||
| $sa_attributes = $sample->sampleAttributes; | ||
| foreach ($sa_attributes as $sa_attribute) { | ||
| $saattribute = $sa_attribute->attribute; | ||
| $attr = $samplesAttrElement->addChild('attribute'); | ||
| $attr->addChild('key', $saattribute->attribute_name); | ||
| $attr->addChild('value', $sa_attribute->value); | ||
| $unit = $attr->addChild('unit', $sample_unit->name ?: NULL); | ||
| $unit->addAttribute('id', (string) $sa_attribute->unit_id); | ||
| $sample_unit = $sa_attribute->unit; | ||
| } | ||
| } | ||
|
|
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| return $xml; | ||
| } | ||
|
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| private function buildFiles(\SimpleXMLElement $xml, \Dataset $model): \SimpleXMLElement | ||
| { | ||
| $files = $model->files; | ||
| $filesElement = $xml->addChild('files'); | ||
|
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| foreach ($files as $file) { | ||
| $fileElement = $filesElement->addChild('file'); | ||
| $fileElement->addAttribute('id', (string) $file->id); | ||
| $fileElement->addAttribute('index4blast', (string) $file->index4blast); | ||
| $fileElement->addAttribute('download_count', (string) $file->download_count); | ||
| $fileElement->addChild('name', $file->name); | ||
| $fileElement->addChild('location', $file->location); | ||
| $fdescription = preg_replace('/[<>]/', '', $file->description); | ||
| $fileElement->addChild('description', $fdescription); | ||
| $fileElement->addChild('extension', $file->extension); | ||
| $size = $fileElement->addChild('size', (string) $file->size); | ||
| $size->addAttribute('units', 'bytes'); | ||
| $fileElement->addChild('release_date', $file->date_stamp); | ||
| $file_type = $file->type; | ||
| $type = $fileElement->addChild('type', $file_type->name); | ||
| $type->addAttribute('id', (string) $file_type->id); | ||
| $format = $fileElement->addChild('format', $file->format->name); | ||
| $format->addAttribute('id', (string) $file->format_id); | ||
|
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| $linkedSamples = $fileElement->addChild('linked_samples'); | ||
| $filesamples = $file->fileSamples; | ||
| foreach ($filesamples as $filesample) { | ||
| $fi_sample = $filesample->sample; | ||
|
|
||
| if (!$fi_sample) { | ||
| continue; | ||
| } | ||
| $linkedSample = $linkedSamples->addChild('linked_sample', $fi_sample->name); | ||
| $linkedSample->addAttribute('sample_id', (string) $filesample->sample_id); | ||
| } | ||
|
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| $fileAttributes = $fileElement->addChild('file_attributes'); | ||
| $fileattributes = $file->fileAttributes; | ||
|
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| foreach ($fileattributes as $fileattribute) { | ||
| $attr = $fileAttributes->addChild('attribute'); | ||
| $file_att = $fileattribute->attribute; | ||
| $file_unit = $fileattribute->unit; | ||
| $attr->addChild('key', $file_att->attribute_name); | ||
| $attr->addChild('value', $fileattribute->value); | ||
| $unit = $attr->addChild('unit', $file_unit ? $file_unit->name: NULL); | ||
| $unit->addAttribute('id', $file_unit ? $file_unit->id: ''); | ||
| } | ||
|
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| $fileElement->addChild('related_file'); | ||
| } | ||
|
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| return $xml; | ||
| } | ||
|
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| private function buildDataset(\SimpleXMLElement $xml, \Dataset $model, ?\Image $image = null): \SimpleXMLElement | ||
| { | ||
| $datasetElement = $xml->addChild('dataset'); | ||
| $datasetElement->addAttribute('id', (string) $model->id); | ||
| $datasetElement->addAttribute('doi', $model->identifier); | ||
|
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| $submitterElement = $datasetElement->addChild('submitter'); | ||
| $submitterElement->addChild('first_name', $submitter_first_name); | ||
| $submitterElement->addChild('last_name', $submitter_last_name); | ||
| $submitterElement->addChild('affiliation', $submitter_affiliation); | ||
| $submitterElement->addChild('username', $submitter_username); | ||
| $submitterElement->addChild('email', $submitter_email); | ||
|
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| $title = strip_tags($model->title); | ||
| $datasetElement->addChild('title', $title); | ||
| $model->description = htmlspecialchars(str_replace('<br>', '<br />', $model->description), ENT_XML1, 'UTF-8'); | ||
| $datasetElement->addChild('description', $model->description); | ||
|
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| $authorsElement = $datasetElement->addChild('authors'); | ||
| $authors = $model->authors; | ||
| usort($authors, function ($a, $b) { | ||
| return $a['id'] - $b['id']; | ||
| }); | ||
| foreach ($authors as $author) { | ||
| $authorElement = $authorsElement->addChild('author'); | ||
| $authorElement->addChild('firstname', $author->first_name); | ||
| $authorElement->addChild('middlename', $author->middle_name); | ||
| $authorElement->addChild('surname', $author->surname); | ||
| $authorElement->addChild('orcid', $author->orcid); | ||
| } | ||
|
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| $dataTypeElement = $datasetElement->addChild('data_types'); | ||
| $dataset_types = $model->datasetTypes; | ||
| foreach ($dataset_types as $dataset_type) { | ||
| $type = $dataTypeElement->addChild('dataset_type'); | ||
| $type->addChild('type_name', $dataset_type->name); | ||
| $type->addChild('type_id', (string) $dataset_type->id); | ||
| } | ||
|
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| $imageElement = $datasetElement->addChild('image'); | ||
| $imageElement->addChild('image_filename', $image->location); | ||
| $imageElement->addChild('tag', $image->tag); | ||
| $imageElement->addChild('license', $image->license); | ||
| $imageElement->addChild('source', $image->source); | ||
| $imageElement->addChild('credit', $image->photographer); | ||
|
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| $size = $datasetElement->addChild('dataset_size', (string) $model->dataset_size); | ||
| $size->addAttribute('units', 'bytes'); | ||
| $datasetElement->addChild('ftp_site', $model->ftp_site); | ||
|
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| $publication = $datasetElement->addChild('publication'); | ||
| $publication->addAttribute('date', $model->publication_date); | ||
| $publisher = $publication->addChild('publisher'); | ||
| $publisher->addAttribute('name', 'GigaScience database'); | ||
| $publication->addChild('modification_date', $model->modification_date); | ||
| $fairUse = $publication->addChild('fair_use'); | ||
| $fairUse->addAttribute('date', $this->fairnuse ?: ''); | ||
|
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| $links = $datasetElement->addChild('links'); | ||
|
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| $externalLinks = $links->addChild('external_links'); | ||
| $external_links = $model->externalLinks; | ||
| foreach ($external_links as $external_link) { | ||
| $subLink = $externalLinks->addChild('external_link', $external_link->url); | ||
| $subLink->addAttribute('type', $external_link->externalLinkType->name); | ||
| } | ||
|
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| $projectLinks = $links->addChild('project_links'); | ||
| $project_links = $model->projects; | ||
| foreach ($project_links as $project) { | ||
| $projectLink = $projectLinks->addChild('project_link'); | ||
| $projectLink->addChild('project_name', $project->name); | ||
| $projectLink->addChild('project_url', $project->url); | ||
| } | ||
|
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| $internalLinks = $links->addChild('internal_links'); | ||
| $internal_links = $model->relations; | ||
| foreach ($internal_links as $relation) { | ||
| $internalLink = $internalLinks->addChild('related_DOI'); | ||
| $internalLink->addAttribute('relationship', $relation->relationship->name); | ||
| } | ||
|
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| $manuscriptLinks = $links->addChild('manuscript_links'); | ||
| $manuscripts = $model->manuscripts; | ||
| foreach ($manuscripts as $manuscript) { | ||
| $manuscriptLink = $internalLinks->addChild('manuscript_link'); | ||
| $manuscriptLink->addChild('manuscript_DOI', $manuscript->identifier); | ||
| $manuscriptLink->addChild('manuscript_pmid', (string) $manuscript->pmid); | ||
| } | ||
|
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| $alternativeIdentifierLinks = $links->addChild('alternative_identifiers'); | ||
| $alternative_identifiers = $model->links; | ||
| foreach ($alternative_identifiers as $link) { | ||
| $linkname = explode(':', $link->link); | ||
| $name = $linkname[0]; | ||
| $modelurl = \Prefix::model()->find('lower(prefix) = :p', array(':p' => strtolower($name))); | ||
| $value = $modelurl ? sprintf('%s%s',$modelurl->url, $linkname[1]) : $linkname[1]; | ||
| $alternativeIdentifer = $alternativeIdentifierLinks->addChild('alternative_identifier', $value); | ||
| $alternativeIdentifer->addAttribute('is_primary', (string) $link->is_primary); | ||
| $alternativeIdentifer->addAttribute('prefix', $name); | ||
| } | ||
|
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| $fundingLinks = $links->addChild('funding_links'); | ||
| $dataset_funders = $model->datasetFunders; | ||
| foreach ($dataset_funders as $dataset_funder) { | ||
| $grant = $fundingLinks->addChild('grant'); | ||
| $funder = $dataset_funder->funder; | ||
| $grant->addChild('funder_name', $funder->primary_name_display); | ||
| $grant->addChild('fundref_url', $funder->uri); | ||
| $grant->addChild('award', $dataset_funder->grant_award); | ||
| $grant->addChild('comment', $dataset_funder->comments); | ||
| } | ||
|
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| $attribute = $datasetElement->addChild('ds_attributes'); | ||
| $dataset_attributes = $model->datasetAttributes; | ||
| foreach ($dataset_attributes as $dataset_attribute) { | ||
| if (!$dataset_attribute->value) { | ||
| continue; | ||
| } | ||
|
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| $attribute->addChild('attribute'); | ||
| $attr = $dataset_attribute->attribute; | ||
| $unit = $dataset_attribute->units; | ||
| $attribute->addChild('key', $attr ? $attr->attribute_name : NULL); | ||
| $attribute->addChild('value', $dataset_attribute->value); | ||
| $unitEl = $attribute->addChild('unit'); | ||
| $unitEl->addAttribute('id', $unit ? $unit->id : ''); | ||
| } | ||
|
|
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| return $xml; | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| <?php | ||
| header('Content-Type: text/xml'); | ||
|
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| echo $xml; |
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