Merge pull request #60 from UtrechtUniversity/feature/labs

Feature/labs

.env.example

@@ -53,4 +53,6 @@ MIX_PUSHER_APP_CLUSTER="${PUSHER_APP_CLUSTER}"
 
 CKAN_API_URL=
 CKAN_API_TOKEN=
-CKAN_ROOT_URL=
+CKAN_ROOT_URL=
+
+FAST_API_TOKEN=

CHANGELOG.md

@@ -13,6 +13,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add vocabulary display names to database, seeding, vocabulary api and exports
 - Add new tag field to datapublication schema to work with matched vocabulary terms
 - Add child uri to enriched keywords for displaying connections in frontend 
+- Add new lab data management to msl_api;
+  - Setup facility/equipment and origanization models as setup in FAST
+  - Create update function to synch data from fast to msl_api
+  - Populate facility organization data using ROR identifier as set in FAST
+  - Add function to ass keywords to facilities based on vocabularies and facility description/title
+  - Add option to serialise facility data to RDF/turtle for data exange with EPOS  
 
 ## [1.5.1] - 2024-02-28
 

app/Exports/epos/RegistryExport.php

@@ -0,0 +1,257 @@
+<?php
+namespace App\Exports\epos;
+
+use App\Models\Keyword;
+use App\Models\Vocabulary;
+use EasyRdf\Graph;
+use App\Models\LaboratoryOrganization;
+use EasyRdf\Resource;
+use EasyRdf;
+use EasyRdf\RdfNamespace;
+use App\Models\LaboratoryContactPerson;
+use App\Models\Laboratory;
+use EasyRdf\Literal;
+use App\Models\LaboratoryEquipment;
+
+class RegistryExport
+{
+    public $organizations;
+
+    public function __construct($organizations) {
+        $this->organizations = $organizations;
+    }
+
+    public function export($type = 'turtle')
+    {        
+        $graph = new Graph();
+
+        // Set namespaces
+        RdfNamespace::delete('dc');
+        RdfNamespace::delete('dcterms');
+        RdfNamespace::set('dct', 'http://purl.org/dc/terms/');
+        RdfNamespace::set('epos', 'https://www.epos-eu.org/epos-dcat-ap#');       
+        RdfNamespace::set('locn', 'http://www.w3.org/ns/locn#');
+        RdfNamespace::set('gsp', 'http://www.opengis.net/ont/geosparql#');
+        RdfNamespace::set('skos', 'http://www.w3.org/2004/02/skos/core#');
+
+        foreach ($this->organizations as $organization) {
+            // Add organization to graph
+            $organizationGraph = $graph->resource($organization->external_identifier, 'schema:Organization');
+            $schemaIdentifier = $graph->newBnode('schema:PropertyValue');
+            $schemaIdentifier->set('schema:propertyID', "ROR");
+            $schemaIdentifier->set('schema:value', $organization->external_identifier);
+            $organizationGraph->set('schema:identifier', $schemaIdentifier);
+            $organizationGraph->set('schema:legalName', $organization->name);
+            // add address information
+            $organizationAddress = $graph->newBnode('schema:PostalAddress');
+            $organizationAddress->set('schema:addressCountry', $organization->ror_country_code);
+            $organizationGraph->set('schema:address', $organizationAddress);
+
+            $organizationGraph->set('schema:url', Literal::create($organization->ror_website , null, 'xsd:anyURI'));                                    
+
+            // Get laboratories belonging to organization
+            foreach ($organization->laboratories as $laboratory) {
+                /*
+                 * Skip if no location data is present
+                 */
+
+                if((strlen($laboratory->latitude) == 0) || (strlen($laboratory->longitude) == 0)) {
+                    continue;
+                }
+
+
+                // Add contactpoint of laboratory to graph
+                $contactPerson = $laboratory->laboratoryContactPerson;
+
+                $contactPointGraph = $graph->resource($this->generateContactPersonURI($contactPerson), 'schema:ContactPoint');
+                $contactPointGraph->set('schema:email', $contactPerson->email);
+                $contactPointGraph->set('schema:availableLanguage', 'en');
+                $contactPointGraph->set('schema:contactType', 'Contact');
+
+                // Add Laboratory to graph
+                $facilityGraph = $graph->resource($this->generateFacilityURI($laboratory), 'epos:Facility');
+                $facilityGraph->set('dct:identifier', $facilityGraph->getUri());
+                $facilityGraph->set('dct:title', $laboratory->name);
+                $facilityGraph->set('dct:description', $this->formatNewlines($laboratory->description));
+                $facilityGraph->set('dct:type', ['type' => 'uri', 'value' => '<epos:Laboratory>']);                
+                $facilityGraph->set('dcat:theme', ['type' => 'uri', 'value' => $this->getEPOSlabType($laboratory)]);
+                $facilityGraph->set('dcat:contactPoint', ['type' => 'uri', 'value' => $contactPointGraph->getUri()]);
+                if((strlen($laboratory->latitude) > 0) && (strlen($laboratory->longitude) > 0)) {
+                    $facilityLocation = $graph->newBNode('dct:Location');
+                    $facilityLocation->add("locn:geometry", Literal::create($this->generateGeonometryString($laboratory), null, 'gsp:wktLiteral'));
+                    $facilityGraph->set('dct:spatial', $facilityLocation);
+                }
+
+                // Add keywords
+                $facilityGraph->set('dcat:keyword', $laboratory->fast_domain_name);
+                $facilityKeywords = $laboratory->laboratoryKeywords->pluck('value')->toArray();
+                $facilityKeywords = array_unique($facilityKeywords);
+
+                foreach ($facilityKeywords as $facilityKeyword) {                    
+                    $facilityGraph->add('dcat:keyword', $facilityKeyword);
+                }
+
+                // optional
+                if(strlen($laboratory->website) > 0) {
+                    $facilityGraph->add(
+                        'foaf:page', Literal::create($laboratory->website, null, 'xsd:anyURI')
+                    );
+                }
+
+                // Add facility to organization owns
+                if ($organizationGraph->hasProperty('schema:owns')) {
+                    $organizationGraph->add('schema:owns', $facilityGraph);
+                } else {
+                    $organizationGraph->set('schema:owns', $facilityGraph);
+                }
+
+                // Add equipment belonging to lab
+                foreach ($laboratory->laboratoryEquipment as $equipment) {
+                    $equipmentGraph = $graph->resource($this->generateEquipmentURI($equipment), 'epos:Equipment');
+                    $equipmentGraph->set('schema:identifier', $this->generateEquipmentURI($equipment));
+                    $equipmentGraph->set('schema:name', $equipment->group_name);
+                    $equipmentGraph->set('schema:description', $this->formatNewlines($equipment->description));
+
+                    $equipmentGraph->set('dct:type', ['type' => 'uri', 'value' => $this->getEquipmentType($equipment)]);
+
+                    $equipmentGraph->set('dct:isPartOf', ['type' => 'uri', 'value' => $facilityGraph->getUri()]);
+                    $equipmentGraph->add('dcat:keyword', $equipment->category_name);
+                    $equipmentGraph->add('dcat:keyword', $equipment->type_name);
+
+                    $equipmentLocation = $graph->newBNode('dct:Location');
+                    $equipmentLocation->add("locn:geometry", Literal::create($this->generateGeonometryString($laboratory), null, 'gsp:wktLiteral'));
+                    $equipmentGraph->set('dct:spatial', $equipmentLocation);
+
+                }
+
+            }
+
+        }
+
+
+
+        // concepts
+
+        // lab concepts
+
+        $facilityTypeConcept = $graph->resource('epos:Facility_Type', 'skos:ConceptScheme');
+        $facilityTypeConcept->set('dct:description', 'Facility type');        
+        $facilityTypeConcept->set('dct:title', 'Facility type');
+
+        $laboratoryConcept = $graph->resource('epos:Laboratory', 'skos:Concept');
+        $laboratoryConcept->set('skos:definition', 'Laboratory');
+        $laboratoryConcept->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Facility_Type>']);
+        $laboratoryConcept->set('skos:prefLabel', 'Laboratory');
+
+
+        // equipment concepts
+
+        $equipmentConcept = $graph->resource('epos:Equipment_Type', 'skos:ConceptScheme');
+        $equipmentConcept->set('dct:description', 'Equipment type');
+        $equipmentConcept->set('dct:title', 'Equipment type');
+
+        $equipmentDefinition = $graph->resource('epos:Atomic_Force_Microscopy_definition', 'skos:Concept');
+        $equipmentDefinition->set('skos:definition', 'Atomic Force Microscopy');
+        $equipmentDefinition->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Equipment_Type>']);
+        $equipmentDefinition->set('skos:prefLabel', 'Atomic Force Microscopy');
+
+        $equipmentDefinition = $graph->resource('epos:Electron_Microscopy_definition', 'skos:Concept');
+        $equipmentDefinition->set('skos:definition', 'Electron Microscopy');
+        $equipmentDefinition->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Equipment_Type>']);
+        $equipmentDefinition->set('skos:prefLabel', 'Electron Microscopy');
+
+        $equipmentDefinition = $graph->resource('epos:Electron_Probe_Micro_Analyzer_definition', 'skos:Concept');
+        $equipmentDefinition->set('skos:definition', 'Electron Probe Micro Analyzer');
+        $equipmentDefinition->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Equipment_Type>']);
+        $equipmentDefinition->set('skos:prefLabel', 'Electron Probe Micro Analyzer');
+
+        $equipmentDefinition = $graph->resource('epos:Mass_Spectrometer_definition', 'skos:Concept');
+        $equipmentDefinition->set('skos:definition', 'Mass Spectrometer');
+        $equipmentDefinition->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Equipment_Type>']);
+        $equipmentDefinition->set('skos:prefLabel', 'Mass Spectrometer');
+
+        $equipmentDefinition = $graph->resource('epos:X-Ray_Tomography_definition', 'skos:Concept');
+        $equipmentDefinition->set('skos:definition', 'X-Ray Tomography');
+        $equipmentDefinition->set('skos:inScheme', ['type' => 'uri', 'value' => '<epos:Equipment_Type>']);
+        $equipmentDefinition->set('skos:prefLabel', 'X-Ray Tomography');
+
+
+
+        return $graph->serialise($type);        
+    }
+
+    private function generateContactPersonURI(LaboratoryContactPerson $contactPerson) {
+        // Return orcid if available otherwise generate custom uri
+        if(strlen($contactPerson->orcid) > 5) {
+            return 'http://orcid.org/' . $contactPerson->orcid . '/contactperson';
+        } else {
+            return 'https:/epos-msl/contactperson/' . $contactPerson->fast_id;
+        }        
+    }
+
+    private function generateFacilityURI(Laboratory $laboratory) {
+        return 'https:/epos-msl/facility/' . $laboratory->fast_id;
+    }
+
+    private function generateEquipmentURI(LaboratoryEquipment $equipment) {
+        return 'https:/epos-msl/equipment/' . $equipment->fast_id;
+    }
+
+    private function generateGeonometryString(Laboratory $laboratory) {        
+        return "POINT(" . str_replace(',', '.', $laboratory->longitude) . " " . str_replace(',', '.', $laboratory->latitude) . ")";
+    }
+
+    private function getEPOSlabType(Laboratory $laboratory) {
+        $fastLaboratoryDomain = $laboratory->fast_domain_name;
+
+        switch ($fastLaboratoryDomain) {
+            case 'Analogue modelling of geological processes':
+                return '<category:AnalogueModelling_conc>';
+
+            case 'Geochemistry':
+                return '<category:Geochemistry_conc>';
+
+            case 'Microscopy and tomography':
+                return '<category:MicroscopyAndTomography_conc>';
+
+            case 'Paleomagnetism':
+                return '<category:Paleomagnetism_conc>';
+
+            case 'Rock and melt physics':
+                return '<category:RockPhysics_conc>';
+
+            default:
+                return '';
+        }
+    }
+
+    private function getEquipmentType(LaboratoryEquipment $laboratoryEquipment) {
+        $equipmentType = $laboratoryEquipment->type_name;
+
+        switch ($equipmentType) {
+            case 'Atomic Force Microscopy':
+                return '<epos:Atomic_Force_Microscopy_definition>';
+
+            case 'Electron Microscopy':
+                return '<epos:Electron_Microscopy_definition>';
+
+            case 'Electron Probe Micro Analyzer':
+                return '<epos:Electron_Probe_Micro_Analyzer_definition>';
+
+            case 'Mass Spectrometer':
+                return '<epos:Mass_Spectrometer_definition>';
+
+            case 'X-Ray Tomography':
+                return '<epos:X-Ray_Tomography_definition>';
+
+            default:
+                return '';
+        }
+    }
+
+    private function formatNewlines($text) {
+        return preg_replace('/\R/', '', nl2br($text, false));
+        return str_replace(PHP_EOL, '', nl2br($text, false));
+    }
+}
+

app/Fast/Fast.php

@@ -0,0 +1,47 @@
+<?php
+namespace App\fast;
+
+use Illuminate\Support\Facades\App;
+
+class Fast
+{
+
+    protected $client;
+
+    public function __construct()
+    {
+        if (App::environment('local')) {
+            $this->client = new \GuzzleHttp\Client(['verify' => false, 'http_errors' => false]);
+        } else {
+            $this->client = new \GuzzleHttp\Client(['http_errors' => false]);
+        }
+    }
+
+
+    public function facilityRequest($facilityId)
+    {        
+        $result =  new \stdClass();               
+
+        try {
+            $response = $this->client->request('GET', "https://fast.geo.uu.nl/api/facility/$facilityId", [
+                'headers' => [
+                    'Authorization' => config('fast.fast_api_token'),
+                ],
+            ]);
+        } catch (\Exception $e) {
+            dd($e->getMessage());
+        }
+
+        $result->response_code = $response->getStatusCode();
+        $result->response_body = [];
+
+        if($result->response_code == 200) {
+            $result->response_body = json_decode($response->getBody(), true);
+        }
+
+        return $result;
+    }
+
+
+}
+

app/Http/Controllers/LabController.php

@@ -0,0 +1,69 @@
+<?php
+
+namespace App\Http\Controllers;
+
+use Illuminate\Http\Request;
+use App\Models\LaboratoryUpdateGroupFast;
+use App\Jobs\ProcessLaboratoryUpdateGroupFast;
+use App\Exports\epos\RegistryExport;
+use App\Models\Laboratory;
+use App\Models\LaboratoryOrganization;
+use App\Models\LaboratoryOrganizationUpdateGroupRor;
+use App\Jobs\ProcessLaboratoryOrganizationUpdateGroupRor;
+use App\Jobs\ProcessLaboratoryKeywordUpdateGroup;
+
+class LabController extends Controller
+{
+    /**
+     * Create a new controller instance.
+     *
+     * @return void
+     */
+    public function __construct()
+    {
+        $this->middleware('auth');
+    }
+
+    public function importLabData()
+    {           
+        return view('import-labdata');
+    }
+
+    public function updateFastData(Request $request)
+    {
+        $laboratoryUpdateGroup = LaboratoryUpdateGroupFast::create();        
+        ProcessLaboratoryUpdateGroupFast::dispatch($laboratoryUpdateGroup);
+
+        $request->session()->flash('status', 'Updating using Fast started');        
+        return redirect()->route('importers');        
+    }
+
+    public function updateLaboratoryOrganizationsByROR(Request $request)
+    {
+        $laboratoryOrganizationUpdateGroupRor = LaboratoryOrganizationUpdateGroupRor::create();
+        ProcessLaboratoryOrganizationUpdateGroupRor::dispatch($laboratoryOrganizationUpdateGroupRor);
+
+        $request->session()->flash('status', 'Updating organizations using ROR api');
+        return redirect()->route('importers'); 
+    }
+
+    public function updateLaboratoryKeywords(Request $request)
+    {
+        ProcessLaboratoryKeywordUpdateGroup::dispatch();
+
+        $request->session()->flash('status', 'Updating laboratory keywords using vocabularies');
+        return redirect()->route('importers');
+    }
+
+    public function registryTurtle(Request $request)
+    {
+        $organizations = LaboratoryOrganization::where('ror_country_code', '<>', '')->get();               
+        $exporter = new RegistryExport($organizations);         
+
+        return response()->streamDownload(function () use($exporter, $request) {
+            echo $exporter->export();
+        }, 'msl-labs.ttl');       
+    }
+
+
+}