Feat 2117 rewritting the api endpoint returning dataset as xml

CHANGELOG.md

@@ -4,6 +4,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ## Unreleased
 
+- Feat #2117: Rewritting the api endpoint returning a dataset as xml
+- Fix #1975: Remove empty line at the beginning of the xml result
 - Feat #456: Improve DataCite metadata by migrating to Datacite version 4.6
 - Fix #1727: Sort files and samples by id in descending order when querying
 

gigadb/app/services/DatasetToXmlService.php

@@ -0,0 +1,289 @@
+<?php
+
+declare(strict_types=1);
+
+namespace GigaDB\services;
+
+use yii\base\Component;
+
+class DatasetToXmlService
+{
+    public function convertToXml(
+        \Dataset $model,
+        ?\Image $image = null,
+        bool $isAll = false,
+        bool $isDatasetOnly = false,
+        bool $isOnlySample = false,
+        bool $isOnlyFile = false
+    ): string
+    {
+        $xml = new \SimpleXMLElement("<?xml version=\"1.0\" encoding=\"UTF-8\"?><gigadb_entry></gigadb_entry>");
+
+        if ($isAll || $isDatasetOnly) {
+            $xml = $this->buildDataset($xml, $model, $image);
+        }
+
+        if ($isDatasetOnly) {
+            if (!$xml->asXML()) {
+                return 'XML is invalid';
+            }
+
+            return $xml->asXML();
+        }
+
+        if ($isAll || $isOnlySample) {
+            $xml = $this->buildSamples($xml, $model);
+        }
+
+        if ($isAll) {
+            $xml->addChild('experiments');
+        }
+
+        if ($isAll || $isOnlyFile) {
+            $xml = $this->buildFiles($xml, $model);
+        }
+
+        if (!$xml->asXML()) {
+            return 'XML is invalid';
+        }
+
+        return $xml->asXML();
+    }
+
+    private function buildSamples(\SimpleXMLElement $xml, \Dataset $model): \SimpleXMLElement
+    {
+        $samplesElement = $xml->addChild('samples');
+        $samples = $model->samples;
+
+        foreach ($samples as $sample) {
+            $sampleElement = $samplesElement->addChild('sample');
+            $sampleElement->addAttribute('submission_date', $sample->submission_date);
+            $sampleElement->addAttribute('id', (string) $sample->id);
+
+            $sampleElement->addChild('name', $sample->name);
+            $species = $sample->species;
+
+            $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);
+
+            $sampleElement->addChild('sampling_protocol', $sample->sampling_protocol);
+            $sampleElement->addChild('consent_doc', $sample->consent_document);
+
+            $contactAuthor = $sampleElement->addChild('contact_author');
+            $contactAuthor->addChild('name', $sample->contact_author_name);
+            $contactAuthor->addChild('email', $sample->contact_author_email);
+
+            $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);
+            }
+
+            $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;
+            }
+        }
+
+        return $xml;
+    }
+
+    private function buildFiles(\SimpleXMLElement $xml, \Dataset $model): \SimpleXMLElement
+    {
+        $files = $model->files;
+        $filesElement = $xml->addChild('files');
+
+        foreach ($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);
+
+            $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);
+            }
+
+            $fileAttributes = $fileElement->addChild('file_attributes');
+            $fileattributes = $file->fileAttributes;
+
+            foreach ($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: '');
+            }
+
+            $fileElement->addChild('related_file');
+        }
+
+        return $xml;
+    }
+
+    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);
+
+        $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);
+
+        $title = strip_tags($model->title);
+        $datasetElement->addChild('title', $title);
+        $model->description = htmlspecialchars(str_replace('<br>', '<br />', $model->description), ENT_XML1, 'UTF-8');
+        $datasetElement->addChild('description', $model->description);
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $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);
+
+        $size = $datasetElement->addChild('dataset_size', (string) $model->dataset_size);
+        $size->addAttribute('units', 'bytes');
+        $datasetElement->addChild('ftp_site', $model->ftp_site);
+
+        $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 ?: '');
+
+        $links = $datasetElement->addChild('links');
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $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);
+        }
+
+        $attribute = $datasetElement->addChild('ds_attributes');
+        $dataset_attributes = $model->datasetAttributes;
+        foreach ($dataset_attributes as $dataset_attribute) {
+            if (!$dataset_attribute->value) {
+                continue;
+            }
+
+            $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 : '');
+        }
+
+        return $xml;
+    }
+}

ops/configuration/yii-conf/web.dev.CI.php.dist

@@ -16,6 +16,9 @@ return [
             ]
     ],
     'components' => [
+        'datasetToXml' => [
+            'class' => 'GigaDB\services\DatasetToXmlService'
+        ],
         'mailer' => [
             'class' => 'yii\swiftmailer\Mailer',
             'useFileTransport' => true,

protected/controllers/ApiController.php

@@ -2,9 +2,6 @@
 
 class ApiController extends Controller
 {
-    // Members
-
-
     const RESULTS = ['file', 'sample', 'dataset'];
 
 	/**
@@ -81,18 +78,27 @@ public function actionDataset()
             $this->_sendResponse(400, 'An error occurred, please check your parameters');
         }
 
+        // needed in order to remove the empty line
+        ob_start();
+        $image = $model->image;
+        ob_get_clean();
+
+
+        /** @var \GigaDB\services\DatasetToXmlService $datasetXml */
+        $datasetXml = \Yii::$app->datasetToXml;
+
          switch ($result) {
                 case "dataset":
-                    $this->renderPartial('singledatasetonly',array('model'=> $model));
+                    $this->renderPartial('datasetAsXml', array('xml'=> $datasetXml->convertToXml($model, $image, false, true)));
                     break;
                 case "sample":
-                    $this->renderPartial('singlesample',array('model'=> $model));
+                    $this->renderPartial('datasetAsXml', array('xml'=> $datasetXml->convertToXml($model, null, false, false, true, false)));
                     break;
                 case "file":
-                    $this->renderPartial('singlefile',array('model'=> $model));
+                    $this->renderPartial('datasetAsXml', array('xml'=> $datasetXml->convertToXml($model, null, false, false, false, true)));
                     break;
                 case "all":
-                    $this->renderPartial('singledataset',array('model'=> $model));
+                    $this->renderPartial('datasetAsXml', array('xml'=> $datasetXml->convertToXml($model, $image, true)));
                     break;
                 default:
                     $this->_sendResponse(500, 'A problem occurred');