From c078412dacb14709acfbebf1e4ebf612b2fc5014 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Tue, 21 Nov 2023 18:50:58 +0100 Subject: [PATCH 01/42] change Bioschema to Bioschemas --- .../BioschemasController.php} | 131 ++++++++++++++---- .../DataCatalogController.php | 6 +- .../{Bioschema => Bioschemas}/BioSample.php | 2 +- .../BioSchemas.php} | 4 +- .../{Bioschema => Bioschemas}/Project.php | 2 +- .../{Bioschema => Bioschemas}/Sample.php | 2 +- .../{Bioschema => Bioschemas}/Study.php | 2 +- docs/introduction/data/ontologies.md | 2 +- docs/introduction/data/schemas.md | 2 +- resources/js/Pages/Public/Project/Dataset.vue | 2 +- resources/js/Pages/Public/Project/Show.vue | 2 +- resources/js/Pages/Public/Project/Study.vue | 2 +- resources/js/Pages/Welcome.vue | 2 +- routes/api.php | 12 +- 14 files changed, 127 insertions(+), 46 deletions(-) rename app/Http/Controllers/API/Schemas/{Bioschema/BiochemaController.php => Bioschemas/BioschemasController.php} (82%) rename app/Http/Controllers/API/Schemas/{Bioschema => Bioschemas}/DataCatalogController.php (97%) rename app/Models/{Bioschema => Bioschemas}/BioSample.php (99%) rename app/Models/{Bioschema/BioSchema.php => Bioschemas/BioSchemas.php} (84%) rename app/Models/{Bioschema => Bioschemas}/Project.php (99%) rename app/Models/{Bioschema => Bioschemas}/Sample.php (99%) rename app/Models/{Bioschema => Bioschemas}/Study.php (99%) diff --git a/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php similarity index 82% rename from app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php rename to app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php index 405c2013..a7ade54e 100644 --- a/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php @@ -1,9 +1,9 @@ name($name); + $definedTerm->alternateName($alternateName); + $definedTerm->identifier($identifier); + $definedTerm->url($url); + $definedTerm->inDefinedTermSet($inDefinedTermSet); + + return $definedTerm; + } + + /** + * Get Defined Term set for ontology service. + * + * + * @param string $name + * @param string $url + * @return object $definedTermSet + */ + public function getDefinedTermSet($name, $url) + { + $definedTermSet = Schema::DefinedTermSet(); + $definedTermSet->name($name); + $definedTermSet->url($url); + + return $definedTermSet; + } + /** * Get Property value from ontologies. * @@ -233,24 +273,24 @@ public function getMolecules($sample) $inchiKey = $molecule->inchi_key; $pubchemLink = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'.$inchiKey.'/property/IUPACName/JSON'; $json = json_decode(Http::get($pubchemLink)->body(), true); - // $cid = $json['PropertyTable']['Properties'][0]['CID']; - // $iupacName = $json['PropertyTable']['Properties'][0]['IUPACName']; - - // $moleculeSchema = Schema::MolecularEntity(); - // $moleculeSchema['@id'] = $inchiKey; - // $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); - // $moleculeSchema['identifier'] = $inchiKey; - // $moleculeSchema->name($molecule->cas); - // $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); - // $moleculeSchema->inChI('InChI='.$molecule->standard_inchi); - // $moleculeSchema->inChIKey($inchiKey); - // $moleculeSchema->iupacName($iupacName); - // $moleculeSchema->molecularFormula($molecule->molecular_formula); - // $moleculeSchema->molecularWeight($molecule->molecular_weight); - // $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]); - // $moleculeSchema->hasRepresentation($molecule->MOL); - // $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%'); - // array_push($molecules, $moleculeSchema); + $cid = $json['PropertyTable']['Properties'][0]['CID']; + $iupacName = $json['PropertyTable']['Properties'][0]['IUPACName']; + + $moleculeSchema = Schema::MolecularEntity(); + $moleculeSchema['@id'] = $inchiKey; + $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); + $moleculeSchema['identifier'] = $inchiKey; + $moleculeSchema->name($molecule->cas); + $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); + $moleculeSchema->inChI($molecule->standard_inchi); + $moleculeSchema->inChIKey($inchiKey); + $moleculeSchema->iupacName($iupacName); + $moleculeSchema->molecularFormula($molecule->molecular_formula); + $moleculeSchema->molecularWeight($molecule->molecular_weight); + $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]); + $moleculeSchema->hasRepresentation($molecule->MOL); + $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%'); + array_push($molecules, $moleculeSchema); } return $molecules; @@ -268,16 +308,55 @@ public function getMolecules($sample) public function getSample($study) { $sample = $study->sample; - $sampleSchema = BioSchema::ChemicalSubstance(); + $molecules = $this->getMolecules($sample); + //$solvents = $this->getSolvents($study); + + $sampleSchema = BioSchemas::ChemicalSubstance(); $sampleSchema['@id'] = $study->doi; $sampleSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); $sampleSchema->name($study->project->name.'.'.$sample->name); $sampleSchema->description($sample->description); $sampleSchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]); - $sampleSchema->hasBioChemEntityPart($this->getMolecules($sample)); + //$parts = array_merge($molecules, $solvents); + //$sampleSchema->hasBioChemEntityPart($parts); + $sampleSchema->hasBioChemEntityPart($molecules); return $sampleSchema; } + // /** + // * Implement Bioschemas' ChemicalSubstance on sample's solvent found in study's datasets. + // * + // * @link https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE + // * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + // * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + // * + // * @param App\Models\Study $study + // * @return object $sampleSchema + // */ + // public function getSolvents($study) + // { + // $chebi = $this->getDefinedTermSet('Chemical Entities of Biological Interest', 'https://www.ebi.ac.uk/chebi/init.do'); + // $nmrSolvent = $this->getDefinedTerm('NMR solvent', null, 'CHEBI:197449', 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:197449', $chebi); + + // $solvents = []; + // foreach ($study->datasets as $dataset) { + // $solvent = $this->getNMRiumInfo($dataset)[0][0]; + // array_push($solvents, $solvent); + // } + // $solvents = array_unique($solvents); + + // $solventSchemas = []; + // foreach ($solvents as $solvent) { + // $solventSchema = BioSchemas::ChemicalSubstance(); + // $solventSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); + // $solventSchema->name($solvent); + // $solventSchema->chemicalRole($nmrSolvent); + // array_push($solventSchemas, $solventSchema); + // }; + + // return $solventSchemas; + // } + /** * Get NMRium info from a dataset. @@ -493,7 +572,7 @@ public function dataset($dataset) public function studyLite($study) { $prefix = $study->project->name.':'; - $studySchema = BioSchema::Study(); + $studySchema = BioSchemas::Study(); $studySchema['@id'] = $study->doi; $studySchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); $studySchema->name($prefix.$study->name); @@ -534,7 +613,7 @@ public function study($study) */ public function projectLite($project) { - $projectSchema = BioSchema::Study(); + $projectSchema = BioSchemas::Study(); $projectSchema['@id'] = $project->doi; $projectSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); $projectSchema->name($project->name); @@ -560,3 +639,5 @@ public function project($project) return $projectSchema; } } + + diff --git a/app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php similarity index 97% rename from app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php rename to app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php index 01522e6a..39059287 100644 --- a/app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php @@ -1,19 +1,19 @@ { this.schema = response.data; }); diff --git a/resources/js/Pages/Public/Project/Show.vue b/resources/js/Pages/Public/Project/Show.vue index 4734692c..68d7c94d 100644 --- a/resources/js/Pages/Public/Project/Show.vue +++ b/resources/js/Pages/Public/Project/Show.vue @@ -176,7 +176,7 @@ export default { computed: {}, mounted() { axios - .get(route("bioschema.id", this.project.data.identifier)) + .get(route("bioschemas.id", this.project.data.identifier)) .then((response) => { this.schema = response.data; }); diff --git a/resources/js/Pages/Public/Project/Study.vue b/resources/js/Pages/Public/Project/Study.vue index bb50946c..8fd11ad9 100644 --- a/resources/js/Pages/Public/Project/Study.vue +++ b/resources/js/Pages/Public/Project/Study.vue @@ -485,7 +485,7 @@ export default { } axios - .get(route("bioschema.id", this.study.data.identifier)) + .get(route("bioschemas.id", this.study.data.identifier)) .then((response) => { this.schema = response.data; }); diff --git a/resources/js/Pages/Welcome.vue b/resources/js/Pages/Welcome.vue index 265ec93f..36e3e987 100644 --- a/resources/js/Pages/Welcome.vue +++ b/resources/js/Pages/Welcome.vue @@ -1013,7 +1013,7 @@ export default { }, mounted() { - axios.get(route("bioschema.datacatalog")).then((response) => { + axios.get(route("bioschemas.datacatalog")).then((response) => { this.schema = response.data; }); }, diff --git a/routes/api.php b/routes/api.php index 700caef4..76367c22 100644 --- a/routes/api.php +++ b/routes/api.php @@ -5,8 +5,8 @@ use App\Http\Controllers\API\Auth\UserController; use App\Http\Controllers\API\FileSystemController; use App\Http\Controllers\API\ProjectController; -use App\Http\Controllers\API\Schemas\Bioschema\BiochemaController; -use App\Http\Controllers\API\Schemas\Bioschema\DataCatalogController; +use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasController; +use App\Http\Controllers\API\Schemas\Bioschemas\DataCatalogController; use App\Http\Controllers\API\Schemas\Datacite\DataCiteController; use App\Http\Controllers\API\SearchController; use Illuminate\Support\Facades\Route; @@ -40,10 +40,10 @@ ->name('public.projects'); Route::prefix('schemas')->group(function () { - Route::prefix('bioschema')->group(function () { - Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschema.datacatalog'); - Route::get('/{username}/{project}/{study?}/{dataset?}', [BiochemaController::class, 'modelSchemaByName'])->name('bioschema.model'); - Route::get('/{id}', [BiochemaController::class, 'modelSchemaByID'])->name('bioschema.id'); + Route::prefix('bioschemas')->group(function () { + Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschemas.datacatalog'); + Route::get('/{username}/{project}/{study?}/{dataset?}', [BioschemasController::class, 'modelSchemaByName'])->name('bioschemas.model'); + Route::get('/{id}', [BioschemasController::class, 'modelSchemaByID'])->name('bioschemas.id'); }); Route::prefix('datacite')->group(function () { From b3a3a9a859d0e433f5055819f22a7695fcb8d988 Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Tue, 28 Nov 2023 16:53:53 +0100 Subject: [PATCH 02/42] fix: app env check updates --- app/Providers/AppServiceProvider.php | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/Providers/AppServiceProvider.php b/app/Providers/AppServiceProvider.php index a630baed..8f258d27 100644 --- a/app/Providers/AppServiceProvider.php +++ b/app/Providers/AppServiceProvider.php @@ -14,7 +14,7 @@ class AppServiceProvider extends ServiceProvider */ public function register() { - if (App::environment() == 'local') { + if (App::environment('local')) { $this->app->register(\Laravel\Telescope\TelescopeServiceProvider::class); $this->app->register(TelescopeServiceProvider::class); } @@ -27,7 +27,7 @@ public function register() */ public function boot() { - if (App::environment() == 'production') { + if (App::environment('production')) { \URL::forceScheme('https'); } } From 63daccf2549eb09b3e3a2a7aeb26549855291bfa Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Wed, 29 Nov 2023 16:48:41 +0100 Subject: [PATCH 03/42] fix: remove abstract Bioschemas models --- app/Models/Bioschemas/BioSample.php | 119 ------------- app/Models/Bioschemas/BioSchemas.php | 10 -- app/Models/Bioschemas/Project.php | 253 --------------------------- app/Models/Bioschemas/Sample.php | 95 ---------- 4 files changed, 477 deletions(-) delete mode 100644 app/Models/Bioschemas/BioSample.php delete mode 100644 app/Models/Bioschemas/Project.php delete mode 100644 app/Models/Bioschemas/Sample.php diff --git a/app/Models/Bioschemas/BioSample.php b/app/Models/Bioschemas/BioSample.php deleted file mode 100644 index b5d0af3f..00000000 --- a/app/Models/Bioschemas/BioSample.php +++ /dev/null @@ -1,119 +0,0 @@ -setProperty('additionalProperty', $additionalProperty); - } - - /** - * Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. - * Inverse property: isPartOfBioChemEntity - * - * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[] $hasPart - * @return static - * - * @link http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_bibex - */ - public function hasBioChemEntityPart($hasBioChemEntityPart) - { - return $this->setProperty('hasBioChemEntityPart', $hasBioChemEntityPart); - } - - /** - * An alias for the item. - * - * @param string|string[] $alternateName - * @return static - * - * @see https://schema.org/name - */ - public function alternateName($alternateName) - { - return $this->setProperty('alternateName', $alternateName); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The identifier property represents any kind of identifier for any kind of - * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides - * dedicated properties for representing many of these, either as textual - * strings or as URL (URI) links. See [background - * notes](/docs/datamodel.html#identifierBg) for more details. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier - * @return static - * - * @see https://schema.org/identifier - */ - public function identifier($identifier) - { - return $this->setProperty('identifier', $identifier); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } -} diff --git a/app/Models/Bioschemas/BioSchemas.php b/app/Models/Bioschemas/BioSchemas.php index e9898222..5167ee28 100644 --- a/app/Models/Bioschemas/BioSchemas.php +++ b/app/Models/Bioschemas/BioSchemas.php @@ -13,14 +13,4 @@ public static function study(): Study { return new Study(); } - - public static function sample(): Sample - { - return new Sample(); - } - - public static function bioSample(): BioSample - { - return new BioSample(); - } } diff --git a/app/Models/Bioschemas/Project.php b/app/Models/Bioschemas/Project.php deleted file mode 100644 index e46862e8..00000000 --- a/app/Models/Bioschemas/Project.php +++ /dev/null @@ -1,253 +0,0 @@ -setProperty('author', $author); - } - - /** - * Date of first broadcast/publication. - * - * @param \DateTimeInterface|\DateTimeInterface[] $datePublished - * @return static - * - * @see https://schema.org/datePublished - */ - public function datePublished($datePublished) - { - return $this->setProperty('datePublished', $datePublished); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The identifier property represents any kind of identifier for any kind of - * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides - * dedicated properties for representing many of these, either as textual - * strings or as URL (URI) links. See [background - * notes](/docs/datamodel.html#identifierBg) for more details. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier - * @return static - * - * @see https://schema.org/identifier - */ - public function identifier($identifier) - { - return $this->setProperty('identifier', $identifier); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } - - /** - * Define the domain of the study. For example, the domain could be astrophysics, - * functional genomics or earth science. Those domains can also have an ontology - * reference. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyDomain - * @return static - */ - public function projectDomain($projectDomain) - { - return $this->setProperty('projectDomain', $projectDomain); - } - - /** - * A subject of the study, i.e. one of the medical conditions, therapies, devices, - * drugs, etc. investigated by the study. - * - * @param \Spatie\SchemaOrg\Contracts\BioChemEntityContract|\Spatie\SchemaOrg\Contracts\MedicalEntityContract[] $studySubject - - * @return static - */ - public function projectSubject($projectSubject) - { - return $this->setProperty('projectSubject', $projectSubject); - } - - /** - * The subject matter of the content. - * - * @param \Spatie\SchemaOrg\Contracts\ThingContract|\Spatie\SchemaOrg\Contracts\ThingContract[] $about - * @return static - * - * @see https://schema.org/about - * @link https://github.com/schemaorg/schemaorg/issues/1670 - */ - public function about($about) - { - return $this->setProperty('about', $about); - } - - /** - * A property-value pair representing an additional characteristics of the - * entitity, e.g. a product feature or another characteristic for which there - * is no matching property in schema.org. Note: Publishers should be aware that - * applications designed to use specific schema.org properties (e.g. http://schema.org/width, - * http://schema.org/color, http://schema.org/gtin13, …) will typically expect - * such data to be provided using those properties, rather than using the generic - * property/value mechanism. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty - * @return static - * - * @see https://schema.org/additionalProperty - */ - public function additionalProperty($additionalProperty) - { - return $this->setProperty('additionalProperty', $additionalProperty); - } - - /** - * A citation or reference to another creative work, such as another - * publication, web page, scholarly article, etc. - * - * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[]|string|string[] $citation - * @return static - * - * @see https://schema.org/citation - */ - public function citation($citation) - { - return $this->setProperty('citation', $citation); - } - - /** - * The creator/author of this CreativeWork. This is the same as the Author - * property for CreativeWork. - * - * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $creator - * @return static - * - * @see https://schema.org/creator - */ - public function creator($creator) - { - return $this->setProperty('creator', $creator); - } - - /** - * The date on which the CreativeWork was created or the item was added to a - * DataFeed. - * - * @param \DateTimeInterface|\DateTimeInterface[] $dateCreated - * @return static - * - * @see https://schema.org/dateCreated - */ - public function dateCreated($dateCreated) - { - return $this->setProperty('dateCreated', $dateCreated); - } - - /** - * The end date and time of the item (in ISO 8601 date format). - * - * @param \DateTimeInterface|\DateTimeInterface[] $endDate - * @return static - * - * @see https://schema.org/endDate - */ - public function endDate($endDate) - { - return $this->setProperty('endDate', $endDate); - } - - /** - * The start date and time of the item (in ISO 8601 date format). - * - * @param \DateTimeInterface|\DateTimeInterface[] $startDate - * @return static - * - * @see https://schema.org/startDate - */ - public function startDate($startDate) - { - return $this->setProperty('startDate', $startDate); - } - - /** - * Keywords or tags used to describe some item. Multiple textual entries in - * a keywords list are typically delimited by commas, or by repeating the - * property. - * - * @param \Spatie\SchemaOrg\Contracts\DefinedTermContract|\Spatie\SchemaOrg\Contracts\DefinedTermContract[]|string|string[] $keywords - * @return static - * - * @see https://schema.org/keywords - */ - public function keywords($keywords) - { - return $this->setProperty('keywords', $keywords); - } - - /** - * TA process performed as part of an experiment or wider study, i.e. intentionally - * designed. These processes can have ontology URL attached to. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyProcess - * @return static - */ - public function studyProcess($studyProcess) - { - return $this->setProperty('studyProcess', $studyProcess); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } -} diff --git a/app/Models/Bioschemas/Sample.php b/app/Models/Bioschemas/Sample.php deleted file mode 100644 index 1de11d8b..00000000 --- a/app/Models/Bioschemas/Sample.php +++ /dev/null @@ -1,95 +0,0 @@ -setProperty('identifier', $identifier); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } - - /** - * A property-value pair representing an additional characteristics of the - * entitity, e.g. a product feature or another characteristic for which there - * is no matching property in schema.org. Note: Publishers should be aware that - * applications designed to use specific schema.org properties (e.g. http://schema.org/width, - * http://schema.org/color, http://schema.org/gtin13, …) will typically expect - * such data to be provided using those properties, rather than using the generic - * property/value mechanism. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty - * @return static - * - * @see https://schema.org/additionalProperty - */ - public function additionalProperty($additionalProperty) - { - return $this->setProperty('additionalProperty', $additionalProperty); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } -} From 385a0ecc9180fb1142cfd98e832d4567904d003d Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Thu, 30 Nov 2023 10:59:04 +0100 Subject: [PATCH 04/42] fix: add L5 Swagger package and fix imort error in existing files. --- app/Events/ProjectInvite.php | 1 + app/Events/StudyInvite.php | 1 + .../Schemas/DataCite/DataCiteController.php | 4 +- app/Http/Controllers/Controller.php | 7 + composer.json | 2 + composer.lock | 2029 ++++--- config/app.php | 1 + config/l5-swagger.php | 300 + public/vendor/telescope/mix-manifest.json | 6 +- resources/views/vendor/l5-swagger/.gitkeep | 0 .../views/vendor/l5-swagger/index.blade.php | 78 + storage/api-docs/api-docs.json | 54 + yarn.lock | 5209 ++++++++--------- 13 files changed, 4264 insertions(+), 3428 deletions(-) create mode 100644 config/l5-swagger.php create mode 100644 resources/views/vendor/l5-swagger/.gitkeep create mode 100644 resources/views/vendor/l5-swagger/index.blade.php create mode 100644 storage/api-docs/api-docs.json diff --git a/app/Events/ProjectInvite.php b/app/Events/ProjectInvite.php index f1b43a3e..3a1f5d64 100644 --- a/app/Events/ProjectInvite.php +++ b/app/Events/ProjectInvite.php @@ -4,6 +4,7 @@ use Illuminate\Broadcasting\PrivateChannel; use Illuminate\Foundation\Events\Dispatchable; +use Illuminate\Contracts\Broadcasting\ShouldBroadcastNow; class ProjectInvite implements ShouldBroadcastNow { diff --git a/app/Events/StudyInvite.php b/app/Events/StudyInvite.php index 1b28c366..4f9e650b 100644 --- a/app/Events/StudyInvite.php +++ b/app/Events/StudyInvite.php @@ -4,6 +4,7 @@ use Illuminate\Broadcasting\PrivateChannel; use Illuminate\Foundation\Events\Dispatchable; +use Illuminate\Contracts\Broadcasting\ShouldBroadcastNow; class StudyInvite implements ShouldBroadcastNow { diff --git a/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php b/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php index 8e8bf2d9..33afc379 100644 --- a/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php +++ b/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php @@ -1,6 +1,6 @@ =8.40.0 || ^7.0", + "php": "^7.2 || ^8.0", + "swagger-api/swagger-ui": "^3.0 || >=4.1.3", + "symfony/yaml": "^5.0 || ^6.0", + "zircote/swagger-php": "^3.2.0 || ^4.0.0" + }, + "require-dev": { + "mockery/mockery": "1.*", + "orchestra/testbench": "^8.0 || 7.* || ^6.15 || 5.*", + "php-coveralls/php-coveralls": "^2.0", + "phpunit/phpunit": "^10.0 || ^9.5" + }, + "type": "library", + "extra": { + "laravel": { + "providers": [ + "L5Swagger\\L5SwaggerServiceProvider" + ], + "aliases": { + "L5Swagger": "L5Swagger\\L5SwaggerFacade" + } + } + }, + "autoload": { + "files": [ + "src/helpers.php" + ], + "psr-4": { + "L5Swagger\\": "src" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "authors": [ + { + "name": "Darius Matulionis", + "email": "darius@matulionis.lt" + } + ], + "description": "OpenApi or Swagger integration to Laravel", + "keywords": [ + "api", + "documentation", + "laravel", + "openapi", + "specification", + "swagger", + "ui" + ], + "support": { + "issues": "https://github.com/DarkaOnLine/L5-Swagger/issues", + "source": "https://github.com/DarkaOnLine/L5-Swagger/tree/8.5.1" + }, + "funding": [ + { + "url": "https://github.com/DarkaOnLine", + "type": "github" + } + ], + "time": "2023-06-05T04:21:50+00:00" + }, { "name": "dasprid/enum", - "version": "1.0.4", + "version": "1.0.5", "source": { "type": "git", "url": "https://github.com/DASPRiD/Enum.git", - "reference": "8e6b6ea76eabbf19ea2bf5b67b98e1860474012f" + "reference": "6faf451159fb8ba4126b925ed2d78acfce0dc016" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/DASPRiD/Enum/zipball/8e6b6ea76eabbf19ea2bf5b67b98e1860474012f", - "reference": "8e6b6ea76eabbf19ea2bf5b67b98e1860474012f", + "url": "https://api.github.com/repos/DASPRiD/Enum/zipball/6faf451159fb8ba4126b925ed2d78acfce0dc016", + "reference": "6faf451159fb8ba4126b925ed2d78acfce0dc016", "shasum": "" }, "require": { @@ -376,9 +455,9 @@ ], "support": { "issues": "https://github.com/DASPRiD/Enum/issues", - "source": "https://github.com/DASPRiD/Enum/tree/1.0.4" + "source": "https://github.com/DASPRiD/Enum/tree/1.0.5" }, - "time": "2023-03-01T18:44:03+00:00" + "time": "2023-08-25T16:18:39+00:00" }, { "name": "dflydev/dot-access-data", @@ -455,6 +534,82 @@ }, "time": "2022-10-27T11:44:00+00:00" }, + { + "name": "doctrine/annotations", + "version": "2.0.1", + "source": { + "type": "git", + "url": "https://github.com/doctrine/annotations.git", + "reference": "e157ef3f3124bbf6fe7ce0ffd109e8a8ef284e7f" + }, + "dist": { + "type": "zip", + "url": "https://api.github.com/repos/doctrine/annotations/zipball/e157ef3f3124bbf6fe7ce0ffd109e8a8ef284e7f", + "reference": "e157ef3f3124bbf6fe7ce0ffd109e8a8ef284e7f", + "shasum": "" + }, + "require": { + "doctrine/lexer": "^2 || ^3", + "ext-tokenizer": "*", + "php": "^7.2 || ^8.0", + "psr/cache": "^1 || ^2 || ^3" + }, + "require-dev": { + "doctrine/cache": "^2.0", + "doctrine/coding-standard": "^10", + "phpstan/phpstan": "^1.8.0", + "phpunit/phpunit": "^7.5 || ^8.5 || ^9.5", + "symfony/cache": "^5.4 || ^6", + "vimeo/psalm": "^4.10" + }, + "suggest": { + "php": "PHP 8.0 or higher comes with attributes, a native replacement for annotations" + }, + "type": "library", + "autoload": { + "psr-4": { + "Doctrine\\Common\\Annotations\\": "lib/Doctrine/Common/Annotations" + } + }, + "notification-url": "https://packagist.org/downloads/", + "license": [ + "MIT" + ], + "authors": [ + { + "name": "Guilherme Blanco", + "email": "guilhermeblanco@gmail.com" + }, + { + "name": "Roman Borschel", + "email": "roman@code-factory.org" + }, + { + "name": "Benjamin Eberlei", + "email": "kontakt@beberlei.de" + }, + { + "name": "Jonathan Wage", + "email": "jonwage@gmail.com" + }, + { + "name": "Johannes Schmitt", + "email": "schmittjoh@gmail.com" + } + ], + "description": "Docblock Annotations Parser", + "homepage": "https://www.doctrine-project.org/projects/annotations.html", + "keywords": [ + "annotations", + "docblock", + "parser" + ], + "support": { + "issues": "https://github.com/doctrine/annotations/issues", + "source": "https://github.com/doctrine/annotations/tree/2.0.1" + }, + "time": "2023-02-02T22:02:53+00:00" + }, { "name": "doctrine/cache", "version": "2.2.0", @@ -550,16 +705,16 @@ }, { "name": "doctrine/dbal", - 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"source": "https://github.com/sebastianbergmann/lines-of-code/tree/2.0.0" + "security": "https://github.com/sebastianbergmann/lines-of-code/security/policy", + "source": "https://github.com/sebastianbergmann/lines-of-code/tree/2.0.1" }, "funding": [ { @@ -11454,7 +11923,7 @@ "type": "github" } ], - "time": "2023-02-03T07:08:02+00:00" + "time": "2023-08-31T09:25:50+00:00" }, { "name": "sebastian/object-enumerator", @@ -11804,35 +12273,35 @@ }, { "name": "spatie/flare-client-php", - "version": "1.4.2", + "version": "1.4.3", "source": { "type": "git", "url": "https://github.com/spatie/flare-client-php.git", - "reference": "5f2c6a7a0d2c1d90c12559dc7828fd942911a544" + "reference": "5db2fdd743c3ede33f2a5367d89ec1a7c9c1d1ec" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/spatie/flare-client-php/zipball/5f2c6a7a0d2c1d90c12559dc7828fd942911a544", - "reference": "5f2c6a7a0d2c1d90c12559dc7828fd942911a544", + "url": "https://api.github.com/repos/spatie/flare-client-php/zipball/5db2fdd743c3ede33f2a5367d89ec1a7c9c1d1ec", + "reference": "5db2fdd743c3ede33f2a5367d89ec1a7c9c1d1ec", "shasum": "" }, "require": { - 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"source": "https://github.com/spatie/flare-client-php/tree/1.4.2" + "source": "https://github.com/spatie/flare-client-php/tree/1.4.3" }, "funding": [ { @@ -11870,20 +12339,20 @@ "type": "github" } ], - "time": "2023-07-28T08:07:24+00:00" + "time": "2023-10-17T15:54:07+00:00" }, { "name": "spatie/ignition", - "version": "1.10.1", + "version": "1.11.3", "source": { "type": "git", "url": "https://github.com/spatie/ignition.git", - "reference": "d92b9a081e99261179b63a858c7a4b01541e7dd1" + "reference": "3d886de644ff7a5b42e4d27c1e1f67c8b5f00044" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/spatie/ignition/zipball/d92b9a081e99261179b63a858c7a4b01541e7dd1", - "reference": "d92b9a081e99261179b63a858c7a4b01541e7dd1", + "url": "https://api.github.com/repos/spatie/ignition/zipball/3d886de644ff7a5b42e4d27c1e1f67c8b5f00044", + "reference": "3d886de644ff7a5b42e4d27c1e1f67c8b5f00044", "shasum": "" }, "require": { @@ -11892,19 +12361,19 @@ "php": "^8.0", "spatie/backtrace": "^1.5.3", "spatie/flare-client-php": "^1.4.0", - "symfony/console": "^5.4|^6.0", - "symfony/var-dumper": "^5.4|^6.0" + "symfony/console": "^5.4|^6.0|^7.0", + "symfony/var-dumper": "^5.4|^6.0|^7.0" }, "require-dev": { - "illuminate/cache": "^9.52", + "illuminate/cache": "^9.52|^10.0|^11.0", "mockery/mockery": "^1.4", - "pestphp/pest": "^1.20", + "pestphp/pest": "^1.20|^2.0", "phpstan/extension-installer": "^1.1", "phpstan/phpstan-deprecation-rules": "^1.0", "phpstan/phpstan-phpunit": "^1.0", "psr/simple-cache-implementation": "*", - "symfony/cache": "^6.0", - "symfony/process": "^5.4|^6.0", + "symfony/cache": "^5.4|^6.0|^7.0", + "symfony/process": "^5.4|^6.0|^7.0", "vlucas/phpdotenv": "^5.5" }, "suggest": { @@ -11953,20 +12422,20 @@ "type": "github" } ], - "time": "2023-08-21T15:06:37+00:00" + "time": "2023-10-18T14:09:40+00:00" }, { "name": "spatie/laravel-ignition", - "version": "2.2.0", + "version": "2.3.1", "source": { "type": "git", "url": "https://github.com/spatie/laravel-ignition.git", - "reference": "dd15fbe82ef5392798941efae93c49395a87d943" + "reference": "bf21cd15aa47fa4ec5d73bbc932005c70261efc8" }, "dist": { "type": "zip", - 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"symfony/console": "<5.4" - }, - "require-dev": { - "symfony/console": "^5.4|^6.0" - }, - "bin": [ - "Resources/bin/yaml-lint" - ], - "type": "library", - "autoload": { - "psr-4": { - "Symfony\\Component\\Yaml\\": "" - }, - "exclude-from-classmap": [ - "/Tests/" - ] - }, - "notification-url": "https://packagist.org/downloads/", - "license": [ - "MIT" - ], - "authors": [ - { - "name": "Fabien Potencier", - "email": "fabien@symfony.com" - }, - { - "name": "Symfony Community", - "homepage": "https://symfony.com/contributors" - } - ], - "description": "Loads and dumps YAML files", - "homepage": "https://symfony.com", - "support": { - "source": "https://github.com/symfony/yaml/tree/v6.3.3" - }, - "funding": [ - { - "url": "https://symfony.com/sponsor", - "type": "custom" - }, - { - "url": "https://github.com/fabpot", - "type": "github" - }, - { - "url": "https://tidelift.com/funding/github/packagist/symfony/symfony", - "type": "tidelift" - } - ], - "time": "2023-07-31T07:08:24+00:00" + "time": "2023-10-09T12:55:26+00:00" }, { "name": "theseer/tokenizer", - "version": "1.2.1", + "version": "1.2.2", "source": { "type": "git", "url": "https://github.com/theseer/tokenizer.git", - "reference": "34a41e998c2183e22995f158c581e7b5e755ab9e" + "reference": "b2ad5003ca10d4ee50a12da31de12a5774ba6b96" }, "dist": { "type": "zip", - "url": "https://api.github.com/repos/theseer/tokenizer/zipball/34a41e998c2183e22995f158c581e7b5e755ab9e", - "reference": "34a41e998c2183e22995f158c581e7b5e755ab9e", + "url": "https://api.github.com/repos/theseer/tokenizer/zipball/b2ad5003ca10d4ee50a12da31de12a5774ba6b96", + "reference": "b2ad5003ca10d4ee50a12da31de12a5774ba6b96", "shasum": "" }, "require": { @@ -12159,7 +12556,7 @@ "description": "A small library for converting tokenized PHP source code into XML and potentially other formats", "support": { "issues": "https://github.com/theseer/tokenizer/issues", - "source": "https://github.com/theseer/tokenizer/tree/1.2.1" + "source": "https://github.com/theseer/tokenizer/tree/1.2.2" }, "funding": [ { @@ -12167,7 +12564,7 @@ "type": "github" } ], - "time": "2021-07-28T10:34:58+00:00" + "time": "2023-11-20T00:12:19+00:00" } ], "aliases": [], diff --git a/config/app.php b/config/app.php index 8868768e..f55d671d 100644 --- a/config/app.php +++ b/config/app.php @@ -185,6 +185,7 @@ App\Providers\DOIServiceProvider::class, Lab404\Impersonate\ImpersonateServiceProvider::class, + L5Swagger\L5SwaggerServiceProvider::class, ], /* diff --git a/config/l5-swagger.php b/config/l5-swagger.php new file mode 100644 index 00000000..40717f66 --- /dev/null +++ b/config/l5-swagger.php @@ -0,0 +1,300 @@ + 'default', + 'documentations' => [ + 'default' => [ + 'api' => [ + 'title' => 'L5 Swagger UI', + ], + + 'routes' => [ + /* + * Route for accessing api documentation interface + */ + 'api' => 'api/documentation', + ], + 'paths' => [ + /* + * Edit to include full URL in ui for assets + */ + 'use_absolute_path' => env('L5_SWAGGER_USE_ABSOLUTE_PATH', true), + + /* + * File name of the generated json documentation file + */ + 'docs_json' => 'api-docs.json', + + /* + * File name of the generated YAML documentation file + */ + 'docs_yaml' => 'api-docs.yaml', + + /* + * Set this to `json` or `yaml` to determine which documentation file to use in UI + */ + 'format_to_use_for_docs' => env('L5_FORMAT_TO_USE_FOR_DOCS', 'json'), + + /* + * Absolute paths to directory containing the swagger annotations are stored. + */ + 'annotations' => [ + base_path('app'), + ], + + ], + ], + ], + 'defaults' => [ + 'routes' => [ + /* + * Route for accessing parsed swagger annotations. + */ + 'docs' => 'docs', + + /* + * Route for Oauth2 authentication callback. + */ + 'oauth2_callback' => 'api/oauth2-callback', + + /* + * Middleware allows to prevent unexpected access to API documentation + */ + 'middleware' => [ + 'api' => [], + 'asset' => [], + 'docs' => [], + 'oauth2_callback' => [], + ], + + /* + * Route Group options + */ + 'group_options' => [], + ], + + 'paths' => [ + /* + * Absolute path to location where parsed annotations will be stored + */ + 'docs' => storage_path('api-docs'), + + /* + * Absolute path to directory where to export views + */ + 'views' => base_path('resources/views/vendor/l5-swagger'), + + /* + * Edit to set the api's base path + */ + 'base' => env('L5_SWAGGER_BASE_PATH', null), + + /* + * Edit to set path where swagger ui assets should be stored + */ + 'swagger_ui_assets_path' => env('L5_SWAGGER_UI_ASSETS_PATH', 'vendor/swagger-api/swagger-ui/dist/'), + + /* + * Absolute path to directories that should be exclude from scanning + * @deprecated Please use `scanOptions.exclude` + * `scanOptions.exclude` overwrites this + */ + 'excludes' => [], + ], + + 'scanOptions' => [ + /** + * analyser: defaults to \OpenApi\StaticAnalyser . + * + * @see \OpenApi\scan + */ + 'analyser' => null, + + /** + * analysis: defaults to a new \OpenApi\Analysis . + * + * @see \OpenApi\scan + */ + 'analysis' => null, + + /** + * Custom query path processors classes. + * + * @link https://github.com/zircote/swagger-php/tree/master/Examples/schema-query-parameter-processor + * @see \OpenApi\scan + */ + 'processors' => [ + // new \App\SwaggerProcessors\SchemaQueryParameter(), + ], + + /** + * pattern: string $pattern File pattern(s) to scan (default: *.php) . + * + * @see \OpenApi\scan + */ + 'pattern' => null, + + /* + * Absolute path to directories that should be excluded from scanning + * @note This option overwrites `paths.excludes` + * @see \OpenApi\scan + */ + 'exclude' => [], + + /* + * Allows to generate specs either for OpenAPI 3.0.0 or OpenAPI 3.1.0. + * By default the spec will be in version 3.0.0 + */ + 'open_api_spec_version' => env('L5_SWAGGER_OPEN_API_SPEC_VERSION', \L5Swagger\Generator::OPEN_API_DEFAULT_SPEC_VERSION), + ], + + /* + * API security definitions. Will be generated into documentation file. + */ + 'securityDefinitions' => [ + 'securitySchemes' => [ + /* + * Examples of Security schemes + */ + /* + 'api_key_security_example' => [ // Unique name of security + 'type' => 'apiKey', // The type of the security scheme. Valid values are "basic", "apiKey" or "oauth2". + 'description' => 'A short description for security scheme', + 'name' => 'api_key', // The name of the header or query parameter to be used. + 'in' => 'header', // The location of the API key. Valid values are "query" or "header". + ], + 'oauth2_security_example' => [ // Unique name of security + 'type' => 'oauth2', // The type of the security scheme. Valid values are "basic", "apiKey" or "oauth2". + 'description' => 'A short description for oauth2 security scheme.', + 'flow' => 'implicit', // The flow used by the OAuth2 security scheme. Valid values are "implicit", "password", "application" or "accessCode". + 'authorizationUrl' => 'http://example.com/auth', // The authorization URL to be used for (implicit/accessCode) + //'tokenUrl' => 'http://example.com/auth' // The authorization URL to be used for (password/application/accessCode) + 'scopes' => [ + 'read:projects' => 'read your projects', + 'write:projects' => 'modify projects in your account', + ] + ], + */ + + /* Open API 3.0 support + 'passport' => [ // Unique name of security + 'type' => 'oauth2', // The type of the security scheme. Valid values are "basic", "apiKey" or "oauth2". + 'description' => 'Laravel passport oauth2 security.', + 'in' => 'header', + 'scheme' => 'https', + 'flows' => [ + "password" => [ + "authorizationUrl" => config('app.url') . '/oauth/authorize', + "tokenUrl" => config('app.url') . '/oauth/token', + "refreshUrl" => config('app.url') . '/token/refresh', + "scopes" => [] + ], + ], + ], + 'sanctum' => [ // Unique name of security + 'type' => 'apiKey', // Valid values are "basic", "apiKey" or "oauth2". + 'description' => 'Enter token in format (Bearer )', + 'name' => 'Authorization', // The name of the header or query parameter to be used. + 'in' => 'header', // The location of the API key. Valid values are "query" or "header". + ], + */ + ], + 'security' => [ + /* + * Examples of Securities + */ + [ + /* + 'oauth2_security_example' => [ + 'read', + 'write' + ], + + 'passport' => [] + */ + ], + ], + ], + + /* + * Set this to `true` in development mode so that docs would be regenerated on each request + * Set this to `false` to disable swagger generation on production + */ + 'generate_always' => env('L5_SWAGGER_GENERATE_ALWAYS', false), + + /* + * Set this to `true` to generate a copy of documentation in yaml format + */ + 'generate_yaml_copy' => env('L5_SWAGGER_GENERATE_YAML_COPY', false), + + /* + * Edit to trust the proxy's ip address - needed for AWS Load Balancer + * string[] + */ + 'proxy' => false, + + /* + * Configs plugin allows to fetch external configs instead of passing them to SwaggerUIBundle. + * See more at: https://github.com/swagger-api/swagger-ui#configs-plugin + */ + 'additional_config_url' => null, + + /* + * Apply a sort to the operation list of each API. It can be 'alpha' (sort by paths alphanumerically), + * 'method' (sort by HTTP method). + * Default is the order returned by the server unchanged. + */ + 'operations_sort' => env('L5_SWAGGER_OPERATIONS_SORT', null), + + /* + * Pass the validatorUrl parameter to SwaggerUi init on the JS side. + * A null value here disables validation. + */ + 'validator_url' => null, + + /* + * Swagger UI configuration parameters + */ + 'ui' => [ + 'display' => [ + /* + * Controls the default expansion setting for the operations and tags. It can be : + * 'list' (expands only the tags), + * 'full' (expands the tags and operations), + * 'none' (expands nothing). + */ + 'doc_expansion' => env('L5_SWAGGER_UI_DOC_EXPANSION', 'none'), + + /** + * If set, enables filtering. The top bar will show an edit box that + * you can use to filter the tagged operations that are shown. Can be + * Boolean to enable or disable, or a string, in which case filtering + * will be enabled using that string as the filter expression. Filtering + * is case-sensitive matching the filter expression anywhere inside + * the tag. + */ + 'filter' => env('L5_SWAGGER_UI_FILTERS', true), // true | false + ], + + 'authorization' => [ + /* + * If set to true, it persists authorization data, and it would not be lost on browser close/refresh + */ + 'persist_authorization' => env('L5_SWAGGER_UI_PERSIST_AUTHORIZATION', false), + + 'oauth2' => [ + /* + * If set to true, adds PKCE to AuthorizationCodeGrant flow + */ + 'use_pkce_with_authorization_code_grant' => false, + ], + ], + ], + /* + * Constants which can be used in annotations + */ + 'constants' => [ + 'L5_SWAGGER_CONST_HOST' => env('L5_SWAGGER_CONST_HOST', 'http://my-default-host.com'), + ], + ], +]; diff --git a/public/vendor/telescope/mix-manifest.json b/public/vendor/telescope/mix-manifest.json index fce358c4..c2c33326 100644 --- a/public/vendor/telescope/mix-manifest.json +++ b/public/vendor/telescope/mix-manifest.json @@ -1,5 +1,5 @@ { - "/app.js": "/app.js?id=32e4311235d3e2c0508cd4267558b319", - "/app-dark.css": "/app-dark.css?id=a9022d8e130bf3ec3a93350be9bf858e", - "/app.css": "/app.css?id=b89676ee10846bfd767c6836074db724" + "/app.js": "/app.js?id=140ed4bc5b10bc99492b97668c59272d", + "/app-dark.css": "/app-dark.css?id=b11fa9a28e9d3aeb8c92986f319b3c44", + "/app.css": "/app.css?id=b3ccfbe68f24cff776f83faa8dead721" } diff --git a/resources/views/vendor/l5-swagger/.gitkeep b/resources/views/vendor/l5-swagger/.gitkeep new file mode 100644 index 00000000..e69de29b diff --git a/resources/views/vendor/l5-swagger/index.blade.php b/resources/views/vendor/l5-swagger/index.blade.php new file mode 100644 index 00000000..da60adac --- /dev/null +++ b/resources/views/vendor/l5-swagger/index.blade.php @@ -0,0 +1,78 @@ + + + + + {{config('l5-swagger.documentations.'.$documentation.'.api.title')}} + + + + + + + +
+ + + + + + diff --git a/storage/api-docs/api-docs.json b/storage/api-docs/api-docs.json new file mode 100644 index 00000000..4657f0c8 --- /dev/null +++ b/storage/api-docs/api-docs.json @@ -0,0 +1,54 @@ +{ + "openapi": "3.0.0", + "info": { + "title": "nmrXiv", + "version": "1.0" + }, + "paths": { + "/api/v1/search": { + "post": { + "tags": [ + "search" + ], + "summary": "Get compound details by Compound name, SMILES, InChi & InChiKey.", + "description": "Get compound details by Compound name, SMILES, InChi & InChiKey.", + "operationId": "search", + "requestBody": { + "description": "Pass search query and type such as InChiKey, InChi, SMILES & text", + "required": true, + "content": { + "application/json": { + "schema": { + "required": [ + "query", + "type" + ], + "properties": { + "query": { + "type": "string", + "format": "query", + "example": "AAAAWQOPBUPWEV-UHFFFAOYSA-N" + }, + "type": { + "type": "string", + "format": "type", + "example": "InChiKey" + } + }, + "type": "object" + } 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"sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==" + "resolved" "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz" + "version" "4.0.2" + +"yallist@^4.0.0": + "integrity" "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" + "resolved" "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz" + "version" "4.0.0" + +"yaml@^1.10.2": + "integrity" "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==" + "resolved" "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz" + "version" "1.10.2" + +"yocto-queue@^0.1.0": + "integrity" "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==" + "resolved" "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz" + "version" "0.1.0" From f81b02552ad771411845068a233ae040b5f5cf3c Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Thu, 30 Nov 2023 11:35:34 +0100 Subject: [PATCH 05/42] fix: Exception missing import fix --- app/Http/Controllers/ApplicationController.php | 1 + 1 file changed, 1 insertion(+) diff --git a/app/Http/Controllers/ApplicationController.php b/app/Http/Controllers/ApplicationController.php index 53f76077..701b2f44 100644 --- a/app/Http/Controllers/ApplicationController.php +++ b/app/Http/Controllers/ApplicationController.php @@ -8,6 +8,7 @@ use Illuminate\Http\Request; use Illuminate\Support\Facades\Gate; use Inertia\Inertia; +use Illuminate\Auth\Access\AuthorizationException; class ApplicationController extends Controller { From f7ce84f9b2818478799755146024a6f0b57d6416 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Thu, 30 Nov 2023 15:35:28 +0100 Subject: [PATCH 06/42] fix: add swagger doc for auths and public projects --- .../Controllers/API/Auth/LoginController.php | 43 +++++ .../API/Auth/RegisterController.php | 58 +++++- .../Controllers/API/ProjectController.php | 59 ++++++ app/Http/Controllers/Controller.php | 1 - config/l5-swagger.php | 2 +- storage/api-docs/api-docs.json | 179 ++++++++++++++++++ 6 files changed, 333 insertions(+), 9 deletions(-) diff --git a/app/Http/Controllers/API/Auth/LoginController.php b/app/Http/Controllers/API/Auth/LoginController.php index 07a917c9..2943fd8f 100644 --- a/app/Http/Controllers/API/Auth/LoginController.php +++ b/app/Http/Controllers/API/Auth/LoginController.php @@ -10,6 +10,36 @@ class LoginController extends Controller { + /** + * @OA\Post( + * path="/api/v1/auth/login", + * summary="Sign in", + * description="Login by email and password", + * operationId="authLogin", + * tags={"auth"}, + * + * @OA\RequestBody( + * required=true, + * description="Pass user credentials", + * + * @OA\JsonContent( + * required={"email","password"}, + * + * @OA\Property(property="email", type="string", format="email", example="nisha.sharma@email.com"), + * @OA\Property(property="password", type="string", format="password", example="secret1234"), + * ), + * ), + * + * @OA\Response( + * response=200, + * description="Successful Operation", + * ), + * @OA\Response( + * response=401, + * description="Wrong Credentials Response", + * ), + * ) + */ public function login(Request $request): JsonResponse { if (! Auth::attempt($request->only('email', 'password'))) { @@ -28,6 +58,19 @@ public function login(Request $request): JsonResponse ]); } + /** + * @OA\Get( + * path="/api/v1/auth/logout", + * summary="Sign out", + * tags={"auth"}, + * security={{"sanctum":{}}}, + * + * @OA\Response( + * response=200, + * description="successful operation" + * ), + * ) + */ public function logout(Request $request): JsonResponse { $request->user()->currentAccessToken()->delete(); diff --git a/app/Http/Controllers/API/Auth/RegisterController.php b/app/Http/Controllers/API/Auth/RegisterController.php index dd1a28a9..901e15f4 100644 --- a/app/Http/Controllers/API/Auth/RegisterController.php +++ b/app/Http/Controllers/API/Auth/RegisterController.php @@ -6,33 +6,77 @@ use App\Models\User; use Illuminate\Http\JsonResponse; use Illuminate\Http\Request; +use Illuminate\Support\Facades\Auth; use Illuminate\Support\Facades\Hash; class RegisterController extends Controller { + /** + * @OA\Post( + * path="/api/v1/auth/register", + * summary="Register", + * description="Register by providing details.", + * operationId="authRegister", + * tags={"auth"}, + * + * @OA\RequestBody( + * required=true, + * description="Pass registration details.", + * + * @OA\JsonContent( + * required={"first_name","last_name","email","password","username"}, + * + * @OA\Property(property="first_name", type="string", format="first_name", example="Nisha"), + * @OA\Property(property="last_name", type="string", format="last_name", example="Sharma"), + * @OA\Property(property="email", type="string", format="email", example="nisha.sharma@email.com"), + * @OA\Property(property="username", type="string", format="username", example="nis123"), + * @OA\Property(property="orcid_id", type="string", format="orcid_id", example="0009-0006-4755-1039"), + * @OA\Property(property="password", type="string", format="password", example="secret1234"), + * + * ), + * ), + * + * @OA\Response( + * response=201, + * description="Successful Operation" + * ), + * @OA\Response( + * response=422, + * description="Unprocessable Content" + * ) + * ) + */ public function register(Request $request): JsonResponse { $validatedData = $request->validate([ - 'name' => 'required|string|max:255', + 'first_name' => 'required|string|max:255', + 'last_name' => 'required|string|max:255', 'email' => 'required|string|email|max:255|unique:users', 'password' => 'required|string|min:8', - 'orcid_id' => string, - 'affiliation' => string, + 'username' => 'required|string', ]); $user = User::create([ - 'name' => $validatedData['name'], + 'name' => $validatedData['first_name'].' '.$validatedData['last_name'], + 'first_name' => $validatedData['first_name'], + 'last_name' => $validatedData['last_name'], 'email' => $validatedData['email'], - 'orcid_id' => $validatedData['orcid_id'], - 'affiliation' => $validatedData['affiliation'], + 'username' => $validatedData['username'], + 'orcid_id' => $request['orcid_id'], + 'affiliation' => $request['affiliation'], 'password' => Hash::make($validatedData['password']), ]); + $user->sendEmailVerificationNotification(); + $token = $user->createToken('auth_token')->plainTextToken; return response()->json([ + 'success' => true, + 'message' => 'User creation successful. Kindly confirm your email address by clicking the link sent to your inbox.', 'access_token' => $token, 'token_type' => 'Bearer', - ]); + ], + 201); } } diff --git a/app/Http/Controllers/API/ProjectController.php b/app/Http/Controllers/API/ProjectController.php index 7d26c9d0..67d65ba4 100644 --- a/app/Http/Controllers/API/ProjectController.php +++ b/app/Http/Controllers/API/ProjectController.php @@ -9,6 +9,24 @@ class ProjectController extends Controller { + /** + * @OA\Get( + * path="/api/v1/projects", + * summary="Fetch all public projects", + * description="Fetch details for all publicly available projects on nmrXiv.", + * operationId="publicProjects", + * tags={"public"}, + * + * @OA\Response( + * response=200, + * description="Successful Operation" + * ), + * @OA\Response( + * response=500, + * description="Internal Server Error" + * ) + * ) + */ public function all(Request $request) { $sort = $request->get('sort'); @@ -21,4 +39,45 @@ public function all(Request $request) return ProjectResource::collection(Project::where('is_public', true)->paginate(15)); } + + /** + * @OA\Get( + * path="/api/v1/project/?id={id}", + * summary="Fetch nmrXiv public project based on identifier", + * description="Fetch details of nmrXiv public project based on identifier.", + * operationId="publicProject", + * tags={"public"}, + * + * @OA\Parameter( + * name="id", + * in="query", + * description="Public project identifier e.g. P12", + * required=true, + * + * @OA\Schema( + * type="string", + * ) + * ), + * + * @OA\Response( + * response=200, + * description="Successful Operation" + * ), + * @OA\Response( + * response=500, + * description="Internal Server Error" + * ) + * ) + */ + public function id(Request $request) + { + $id = $request->query('id'); + + if ($id) { + return $project = Project::where([ + ['is_public', true], + ['identifier', str_replace('P', '', $id)], + ])->get(); + } + } } diff --git a/app/Http/Controllers/Controller.php b/app/Http/Controllers/Controller.php index 438c97f8..4d564870 100644 --- a/app/Http/Controllers/Controller.php +++ b/app/Http/Controllers/Controller.php @@ -13,7 +13,6 @@ * title="nmrXiv" * ) */ - class Controller extends BaseController { use AuthorizesRequests, DispatchesJobs, ValidatesRequests; diff --git a/config/l5-swagger.php b/config/l5-swagger.php index 40717f66..00c1b17b 100644 --- a/config/l5-swagger.php +++ b/config/l5-swagger.php @@ -5,7 +5,7 @@ 'documentations' => [ 'default' => [ 'api' => [ - 'title' => 'L5 Swagger UI', + 'title' => 'nmrXiv - Swagger UI', ], 'routes' => [ diff --git a/storage/api-docs/api-docs.json b/storage/api-docs/api-docs.json index 4657f0c8..9a5a104c 100644 --- a/storage/api-docs/api-docs.json +++ b/storage/api-docs/api-docs.json @@ -5,6 +5,185 @@ "version": "1.0" }, "paths": { + "/api/v1/auth/login": { + "post": { + "tags": [ + "auth" + ], + "summary": "Sign in", + "description": "Login by email and password", + "operationId": "authLogin", + "requestBody": { + "description": "Pass user credentials", + "required": true, + "content": { + "application/json": { + "schema": { + "required": [ + "email", + "password" + ], + "properties": { + "email": { + "type": "string", + "format": "email", + "example": "nisha.sharma@email.com" + }, + "password": { + "type": "string", + "format": "password", + "example": "secret1234" + } + }, + "type": "object" + } + } + } + }, + "responses": { + "200": { + "description": "Successful Operation" + }, + "401": { + "description": "Wrong Credentials Response" + } + } + } + }, + "/api/v1/auth/logout": { + "get": { + "tags": [ + "auth" + ], + "summary": "Sign out", + "operationId": "84358406c526dc97519e0eab688b4efe", + "responses": { + "200": { + "description": "successful operation" + } + }, + "security": [ + { + "sanctum": [] + } + ] + } + }, + "/api/v1/auth/register": { + "post": { + "tags": [ + "auth" + ], + "summary": "Register", + "description": "Register by providing details.", + "operationId": "authRegister", + "requestBody": { + "description": "Pass registration details.", + "required": true, + "content": { + "application/json": { + "schema": { + "required": [ + "first_name", + "last_name", + "email", + "password", + "username" + ], + "properties": { + "first_name": { + "type": "string", + "format": "first_name", + "example": "Nisha" + }, + "last_name": { + "type": "string", + "format": "last_name", + "example": "Sharma" + }, + "email": { + "type": "string", + "format": "email", + "example": "nisha.sharma@email.com" + }, + "username": { + "type": "string", + "format": "username", + "example": "nis123" + }, + "orcid_id": { + "type": "string", + "format": "orcid_id", + "example": "0009-0006-4755-1039" + }, + "password": { + "type": "string", + "format": "password", + "example": "secret1234" + } + }, + "type": "object" + } + } + } + }, + "responses": { + "201": { + "description": "Successful Operation" + }, + "422": { + "description": "Unprocessable Content" + } + } + } + }, + "/api/v1/projects": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch all public projects", + "description": "Fetch details for all publicly available projects on nmrXiv.", + "operationId": "publicProjects", + "responses": { + "200": { + "description": "Successful Operation" + }, + "500": { + "description": "Internal Server Error" + } + } + } + }, + "/api/v1/project/?id={id}": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch nmrXiv public project based on identifier", + "description": "Fetch details of nmrXiv public project based on identifier.", + "operationId": "publicProject", + "parameters": [ + { + "name": "id", + "in": "query", + "description": "Public project identifier e.g. P12", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "Successful Operation" + }, + "500": { + "description": "Internal Server Error" + } + } + } + }, "/api/v1/search": { "post": { "tags": [ From 17181389d2f930ba1e5d109ff22a862445d1135c Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Fri, 1 Dec 2023 12:46:39 +0100 Subject: [PATCH 07/42] fix: formatting, UX/UI updates and zipping bug fix --- .../Controllers/ApplicationController.php | 2 +- app/Jobs/ArchiveStudy.php | 8 +- resources/js/App/Onboarding.vue | 4 +- resources/js/Pages/Publish.vue | 10 +- resources/js/Pages/Upload.vue | 91 ++++++++++++------- resources/js/Shared/FileSystemBrowser.vue | 9 ++ resources/js/Shared/Primer.vue | 8 +- 7 files changed, 92 insertions(+), 40 deletions(-) diff --git a/app/Http/Controllers/ApplicationController.php b/app/Http/Controllers/ApplicationController.php index 701b2f44..d967ce8d 100644 --- a/app/Http/Controllers/ApplicationController.php +++ b/app/Http/Controllers/ApplicationController.php @@ -5,10 +5,10 @@ use App\Http\Resources\DatasetResource; use App\Http\Resources\ProjectResource; use App\Http\Resources\StudyResource; +use Illuminate\Auth\Access\AuthorizationException; use Illuminate\Http\Request; use Illuminate\Support\Facades\Gate; use Inertia\Inertia; -use Illuminate\Auth\Access\AuthorizationException; class ApplicationController extends Controller { diff --git a/app/Jobs/ArchiveStudy.php b/app/Jobs/ArchiveStudy.php index 6d497aef..04bdd546 100644 --- a/app/Jobs/ArchiveStudy.php +++ b/app/Jobs/ArchiveStudy.php @@ -62,12 +62,13 @@ public function handle(): void $bucket = config('filesystems.disks.'.env('FILESYSTEM_DRIVER').'.bucket'); $s3keys = []; $environment = env('APP_ENV', 'local'); + $relative_URL = $fsObject->relative_url; if ($fsObject->type == 'file') { if (Storage::has($path)) { array_push($s3keys, substr($fsObject->path, 1)); } } else { - + $relative_URL = $relative_URL.'/'; $command = [ 'Bucket' => $bucket, ]; @@ -102,12 +103,13 @@ public function handle(): void foreach ($s3keys as $key) { $s3path = 's3://'.$bucket.'/'.$key; if ($streamRead = fopen($s3path, 'r')) { - $sPath = explode($fsObject->relative_url, $key)[1]; + $sPath = explode($relative_URL, $key)[1]; if ($sPath != '') { - $sPath = $fsObject->key.'/'.explode($fsObject->relative_url, $key)[1]; + $sPath = $fsObject->key.'/'.explode($relative_URL, $key)[1]; } else { $sPath = $fsObject->key; } + $sPath = preg_replace('#/+#', '/', $sPath); $zip->addFileFromStream($sPath, $streamRead); } else { exit('Could not open stream for reading'); diff --git a/resources/js/App/Onboarding.vue b/resources/js/App/Onboarding.vue index e5acc755..69ef0c41 100644 --- a/resources/js/App/Onboarding.vue +++ b/resources/js/App/Onboarding.vue @@ -321,14 +321,14 @@ Get started -
+
diff --git a/resources/js/Pages/Publish.vue b/resources/js/Pages/Publish.vue index 0e9961c7..8e01c2d3 100644 --- a/resources/js/Pages/Publish.vue +++ b/resources/js/Pages/Publish.vue @@ -5,6 +5,12 @@
+ Step 3 / 3 - + + Publish data +
@@ -12,14 +18,14 @@ class="text-sm text-gray-700 uppercase font-bold tracking-widest" > ←

- DRAFT: {{ draft.name }} + {{ draft.name }}

diff --git a/resources/js/Pages/Upload.vue b/resources/js/Pages/Upload.vue index bfcb1038..62d6c7b6 100644 --- a/resources/js/Pages/Upload.vue +++ b/resources/js/Pages/Upload.vue @@ -65,30 +65,59 @@
-

- + Step + {{ currentStep.id }} + + / 3 - + + + Introduction + + File Upload + + + Auto Processing, Assignments and + Validation + + +

- ← - - -

- {{ currentDraft.name }} -

- - - Submit data to nmrXiv -

+ ← + + +

+ {{ currentDraft.name }} +

+ + + + Submit data to nmrXiv + + +
@@ -138,7 +167,7 @@ - +
@@ -431,7 +460,7 @@ class="mt-2" />
-
+
@@ -1561,7 +1590,7 @@
-
+
to "{{ $page.props.selectedFolder }}" folder +
+ Need help? Check out our + submission guides + +
-
+
@@ -10,6 +10,12 @@ Basic Concepts

+ Submission to nmrXiv is divided into 3 steps
+ 1) File upload
+ 2) Auto - Processing, Assignments and Validation +
+ 3) Publish

+ In nmrXiv, data is organised as projects. Consider a project is equivalent to your publication with the From 265d3bcb8ede27039e3c8ea07db385b9aa47e7f9 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Fri, 1 Dec 2023 15:33:34 +0100 Subject: [PATCH 08/42] feat: add public api for Dataset and Samples --- .../Controllers/API/DatasetController.php | 89 +++++++++++++++ .../Controllers/API/ProjectController.php | 14 ++- app/Http/Controllers/API/StudyController.php | 89 +++++++++++++++ routes/api.php | 20 ++++ storage/api-docs/api-docs.json | 103 ++++++++++++++++++ 5 files changed, 311 insertions(+), 4 deletions(-) create mode 100644 app/Http/Controllers/API/DatasetController.php create mode 100644 app/Http/Controllers/API/StudyController.php diff --git a/app/Http/Controllers/API/DatasetController.php b/app/Http/Controllers/API/DatasetController.php new file mode 100644 index 00000000..6d375e66 --- /dev/null +++ b/app/Http/Controllers/API/DatasetController.php @@ -0,0 +1,89 @@ +get('sort'); + + if ($sort == 'latest') { + return DatasetResource::collection(Dataset::where('is_public', true)->orderByDesc('updated_at')->paginate(15)); + } elseif ($sort == 'trending') { + return DatasetResource::collection(Dataset::where('is_public', true)->paginate(15)); + } + + return DatasetResource::collection(Dataset::where('is_public', true)->paginate(15)); + } + + /** + * @OA\Get( + * path="/api/v1/dataset/?id={id}", + * summary="Fetch nmrXiv public datasets based on identifier", + * description="Fetch details of nmrXiv public dataset based on identifier.", + * operationId="publicDataset", + * tags={"public"}, + * + * @OA\Parameter( + * name="id", + * in="query", + * description="Public dataset identifier e.g. D12", + * required=true, + * + * @OA\Schema( + * type="string", + * ) + * ), + * + * @OA\Response( + * response=200, + * description="Successful Operation" + * ), + * @OA\Response( + * response=400, + * description="Bad Request" + * ), + * @OA\Response( + * response=500, + * description="Internal Server Error" + * ) + * ) + */ + public function id(Request $request) + { + $id = $request->query('id'); + + if ($id) { + return $Dataset = DatasetResource::collection(Dataset::where([['is_public', true], ['identifier', str_replace('D', '', $id)]])->get()); + } else { + return response()->json([ + 'message' => 'Input missing.', + ], + 400); + } + } +} diff --git a/app/Http/Controllers/API/ProjectController.php b/app/Http/Controllers/API/ProjectController.php index 67d65ba4..79832a2b 100644 --- a/app/Http/Controllers/API/ProjectController.php +++ b/app/Http/Controllers/API/ProjectController.php @@ -64,6 +64,10 @@ public function all(Request $request) * description="Successful Operation" * ), * @OA\Response( + * response=400, + * description="Bad Request" + * ), + * @OA\Response( * response=500, * description="Internal Server Error" * ) @@ -74,10 +78,12 @@ public function id(Request $request) $id = $request->query('id'); if ($id) { - return $project = Project::where([ - ['is_public', true], - ['identifier', str_replace('P', '', $id)], - ])->get(); + return $project = ProjectResource::collection(Project::where([['is_public', true], ['identifier', str_replace('P', '', $id)]])->get()); + } else { + return response()->json([ + 'message' => 'Input missing.', + ], + 400); } } } diff --git a/app/Http/Controllers/API/StudyController.php b/app/Http/Controllers/API/StudyController.php new file mode 100644 index 00000000..a5430a62 --- /dev/null +++ b/app/Http/Controllers/API/StudyController.php @@ -0,0 +1,89 @@ +get('sort'); + + if ($sort == 'latest') { + return StudyResource::collection(Study::where('is_public', true)->orderByDesc('updated_at')->paginate(15)); + } elseif ($sort == 'trending') { + return StudyResource::collection(Study::where('is_public', true)->paginate(15)); + } + + return StudyResource::collection(Study::where('is_public', true)->paginate(15)); + } + + /** + * @OA\Get( + * path="/api/v1/sample/?id={id}", + * summary="Fetch nmrXiv public samples based on identifier", + * description="Fetch details of nmrXiv public sample based on identifier.", + * operationId="publicSample", + * tags={"public"}, + * + * @OA\Parameter( + * name="id", + * in="query", + * description="Public sample identifier e.g. S12", + * required=true, + * + * @OA\Schema( + * type="string", + * ) + * ), + * + * @OA\Response( + * response=200, + * description="Successful Operation" + * ), + * @OA\Response( + * response=400, + * description="Bad Request" + * ), + * @OA\Response( + * response=500, + * description="Internal Server Error" + * ) + * ) + */ + public function id(Request $request) + { + $id = $request->query('id'); + + if ($id) { + return $study = StudyResource::collection(Study::where([['is_public', true], ['identifier', str_replace('S', '', $id)]])->get()); + } else { + return response()->json([ + 'message' => 'Input missing.', + ], + 400); + } + } +} diff --git a/routes/api.php b/routes/api.php index 76367c22..34c914b5 100644 --- a/routes/api.php +++ b/routes/api.php @@ -3,12 +3,14 @@ use App\Http\Controllers\API\Auth\LoginController; use App\Http\Controllers\API\Auth\RegisterController; use App\Http\Controllers\API\Auth\UserController; +use App\Http\Controllers\API\DatasetController; use App\Http\Controllers\API\FileSystemController; use App\Http\Controllers\API\ProjectController; use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasController; use App\Http\Controllers\API\Schemas\Bioschemas\DataCatalogController; use App\Http\Controllers\API\Schemas\Datacite\DataCiteController; use App\Http\Controllers\API\SearchController; +use App\Http\Controllers\API\StudyController; use Illuminate\Support\Facades\Route; /* @@ -36,9 +38,27 @@ Route::get('/children/{file}', [FileSystemController::class, 'children']); }); + //Public Projects Route::get('projects', [ProjectController::class, 'all']) ->name('public.projects'); + Route::get('project', [ProjectController::class, 'id']) + ->name('public.project'); + + //Public Samples + Route::get('samples', [StudyController::class, 'all']) + ->name('public.samples'); + + Route::get('sample', [StudyController::class, 'id']) + ->name('public.sample'); + + //Public Datasets + Route::get('datasets', [DatasetController::class, 'all']) + ->name('public.datasets'); + + Route::get('dataset', [DatasetController::class, 'id']) + ->name('public.dataset'); + Route::prefix('schemas')->group(function () { Route::prefix('bioschemas')->group(function () { Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschemas.datacatalog'); diff --git a/storage/api-docs/api-docs.json b/storage/api-docs/api-docs.json index 9a5a104c..270e87c8 100644 --- a/storage/api-docs/api-docs.json +++ b/storage/api-docs/api-docs.json @@ -137,6 +137,56 @@ } } }, + "/api/v1/datasets": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch all public datasets", + "description": "Fetch details for all publicly available datasets on nmrXiv.", + "operationId": "publicDatasets", + "responses": { + "200": { + "description": "Successful Operation" + }, + "500": { + "description": "Internal Server Error" + } + } + } + }, + "/api/v1/dataset/?id={id}": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch nmrXiv public datasets based on identifier", + "description": "Fetch details of nmrXiv public dataset based on identifier.", + "operationId": "publicDataset", + "parameters": [ + { + "name": "id", + "in": "query", + "description": "Public dataset identifier e.g. D12", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "Successful Operation" + }, + "400": { + "description": "Bad Request" + }, + "500": { + "description": "Internal Server Error" + } + } + } + }, "/api/v1/projects": { "get": { "tags": [ @@ -178,6 +228,9 @@ "200": { "description": "Successful Operation" }, + "400": { + "description": "Bad Request" + }, "500": { "description": "Internal Server Error" } @@ -228,6 +281,56 @@ } } } + }, + "/api/v1/samples": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch all public samples", + "description": "Fetch details for all publicly available samples on nmrXiv.", + "operationId": "publicSamples", + "responses": { + "200": { + "description": "Successful Operation" + }, + "500": { + "description": "Internal Server Error" + } + } + } + }, + "/api/v1/sample/?id={id}": { + "get": { + "tags": [ + "public" + ], + "summary": "Fetch nmrXiv public samples based on identifier", + "description": "Fetch details of nmrXiv public sample based on identifier.", + "operationId": "publicSample", + "parameters": [ + { + "name": "id", + "in": "query", + "description": "Public sample identifier e.g. S12", + "required": true, + "schema": { + "type": "string" + } + } + ], + "responses": { + "200": { + "description": "Successful Operation" + }, + "400": { + "description": "Bad Request" + }, + "500": { + "description": "Internal Server Error" + } + } + } } } } \ No newline at end of file From 58a3960c9c569b0c371b2c30e6da896a1138b35b Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Sun, 3 Dec 2023 23:29:51 +0100 Subject: [PATCH 09/42] fix: many datacite fixes Fixes #560 --- .../Controllers/API/Schemas/DataCite/DataCiteController.php | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php b/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php index 8e8bf2d9..33afc379 100644 --- a/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php +++ b/app/Http/Controllers/API/Schemas/DataCite/DataCiteController.php @@ -1,6 +1,6 @@ Date: Sun, 3 Dec 2023 23:30:50 +0100 Subject: [PATCH 10/42] many datacite fixes --- app/Models/HasDOI.php | 144 ++++++++++++++++++++++-------------------- routes/api.php | 2 +- 2 files changed, 78 insertions(+), 68 deletions(-) diff --git a/app/Models/HasDOI.php b/app/Models/HasDOI.php index be580ff7..1d77e8d8 100644 --- a/app/Models/HasDOI.php +++ b/app/Models/HasDOI.php @@ -19,34 +19,40 @@ public function generateDOI($doiService) $suffix = null; $url = 'https://www.nmrxiv.org/'; $publicationYear = Carbon::now()->year; - $citations = []; - $citationDois = []; - $license = $this->license; + + $license = License::where([['id', $this->license_id]])->firstOrFail(); + $dates = [ + [ + 'date' => $this->release_date, + 'dateType' => 'Available', + ], + [ + 'date' => $this->created_at, + 'dateType' => 'Submitted', + ], + [ + 'date' => $this->updated_at, + 'dateType' => 'Updated', + ], + ]; if ($this instanceof Project) { + $title = $this->name; $users = $this->allUsers(); $authors = $this->authors ? $this->authors : []; $suffix = 'P'.$identifier; $url = $url.'P'.$identifier; $resourceType = 'Project'; - $citations = $this->citation ? $this->citation : []; - - if (! $citations == []) { - foreach ($citations as $citation) { - $citationDoi = $citation->doi ? $citation->doi : null; - array_push($citationDois, [ - 'doi' => $citationDoi, - ]); - } - } + $citations = $this->citations ? $this->citations : []; + } elseif ($this instanceof Study) { + $title = $this->name; $users = $this->allUsers(); - $citations = []; if ($this->project) { $authors = $this->project->authors ? $this->project->authors : []; $projectIdentifier = $this->getIdentifier($this->project, 'identifier'); $suffix = 'P'.$projectIdentifier.'.'.'S'.$identifier; - $citations = $this->project->citation ? $this->project->citation : []; + $citations = $this->project->citations ? $this->project->citations : []; } else { $suffix = 'S'.$identifier; } @@ -54,87 +60,89 @@ public function generateDOI($doiService) $url = $url.'S'.$identifier; $resourceType = 'Study'; - if (! $citations == []) { - foreach ($citations as $citation) { - $citationDoi = $citation->doi ? $citation->doi : null; - array_push($citationDois, [ - 'doi' => $citationDoi, - ]); - } - } } elseif ($this instanceof Dataset) { + $studyName = $this->study->name; + $title = $studyName.'['.$this->name.']'; $users = $this->study->allUsers(); $studyIdentifier = $this->getIdentifier($this->study, 'identifier'); - $citations = []; if ($this->project) { $authors = $this->project->authors ? $this->project->authors : []; $projectIdentifier = $this->getIdentifier($this->project, 'identifier'); $suffix = 'P'.$projectIdentifier.'.'.'S'.$studyIdentifier.'.'.'D'.$identifier; - $citations = $this->project->citation ? $this->project->citation : []; + $citations = $this->project->citations ? $this->project->citations : []; } else { $suffix = 'S'.$studyIdentifier.'.'.'D'.$identifier; } $url = $url.'D'.$identifier; $resourceType = 'Dataset'; - - if (! $citations == []) { - foreach ($citations as $citation) { - $citationDoi = $citation->doi ? $citation->doi : null; - array_push($citationDois, [ - 'doi' => $citationDoi, - ]); - } - } } $creators = []; - foreach ($authors as $user) { - array_push($creators, [ - 'name' => $user->family_name.', '.$user->given_name, + foreach ($authors as $author) { + $creator = [ + 'name' => $author->family_name.', '.$author->given_name, 'nameType' => 'Personal', - 'givenName' => $user->given_name, - 'familyName' => $user->family_name, - 'nameIdentifiers' => $user->orcid_id ? $user->orcid_id : null, - 'nameIdentifierScheme' => 'ORCID', - 'schemeURI' => 'https://orcid.org', - 'affiliation' => $user->affiliation ? $user->affiliation : null, - ]); + 'givenName' => $author->given_name, + 'familyName' => $author->family_name, + 'nameIdentifiers' => [ + [ + 'nameIdentifier' => $author->orcid_id ? $author->orcid_id : null, + 'nameIdentifierScheme' => 'ORCID', + 'schemeUri' => 'https://orcid.org', + ], + ], + 'affiliations' => [ + [ + 'affiliation' => $author->affiliation ? $author->affiliation : null, + ], + ], + ]; + array_push($creators, $creator); } $contributors = []; foreach ($users as $user) { - array_push($contributors, [ + $contributor = [ 'contributorType' => 'Other', 'name' => $user->last_name.', '.$user->first_name, 'nameType' => 'Personal', 'givenName' => $user->first_name, 'familyName' => $user->last_name, - ]); + 'nameIdentifiers' => [ + [ + 'nameIdentifier' => $user->orcid_id ? $user->orcid_id : null, + 'nameIdentifierScheme' => 'ORCID', + 'schemeUri' => 'https://orcid.org', + ], + ], + 'affiliations' => [ + [ + 'affiliation' => $user->affiliation ? $user->affiliation : null, + ], + ], + ]; + array_push($contributors, $contributor); } - $citations = [ - 'relatedIdentifier' => $this->citationDois, - 'relatedIdentifierType' => 'DOI', - 'relationType' => 'IsSupplementTo', - ]; + $relatedIdentifiers = []; + foreach ($citations as $citation) { + $relatedIdentifier = [ + 'relatedIdentifier' => $citation->doi ? $citation->doi : null, + 'relatedIdentifierType' => 'DOI', + 'relationType' => 'IsSupplementTo', + ]; + array_push($relatedIdentifiers, $relatedIdentifier); + } - if (! $license == null) { - $rights = [ - 'rights' => $license, - 'rightsURI' => $license->url, + $rights = [ + [ + 'rights' => $license->title, + 'rightsUri' => $license->url, 'rightsIdentifier' => $license->spdx_id, 'rightsIdentifierScheme' => 'SPDX', - 'schemeURI' => 'https://spdx.org/licenses/', - ]; - } else { - $rights = [ - 'rights' => null, - 'rightsURI' => null, - 'rightsIdentifier' => null, - 'rightsIdentifierScheme' => 'SPDX', - 'schemeURI' => 'https://spdx.org/licenses/', - ]; - } + 'schemeUri' => 'https://spdx.org/licenses/', + ], + ]; $description = [ 'description' => $this->description, @@ -145,17 +153,19 @@ public function generateDOI($doiService) 'creators' => count($creators) > 0 ? $creators : $contributors, 'titles' => [ [ - 'title' => $this->name, + 'title' => $title, ], ], 'publisher' => 'nmrXiv', 'contributors' => $contributors, 'publicationYear' => $publicationYear, + 'dates' => $dates, 'language' => 'en', 'resourceType' => $this->resourceType, 'resourceTypeGeneral' => 'Dataset', 'rights' => $rights, 'description' => $description, + 'relatedIdentifiers' => $relatedIdentifiers, 'url' => $url, 'isActive' => true, 'event' => 'publish', diff --git a/routes/api.php b/routes/api.php index 700caef4..e5194d7e 100644 --- a/routes/api.php +++ b/routes/api.php @@ -7,7 +7,7 @@ use App\Http\Controllers\API\ProjectController; use App\Http\Controllers\API\Schemas\Bioschema\BiochemaController; use App\Http\Controllers\API\Schemas\Bioschema\DataCatalogController; -use App\Http\Controllers\API\Schemas\Datacite\DataCiteController; +use App\Http\Controllers\API\Schemas\DataCite\DataCiteController; use App\Http\Controllers\API\SearchController; use Illuminate\Support\Facades\Route; From c4a67a8ae350e458c7356ddcdb45d9a492f242e5 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 10:34:40 +0100 Subject: [PATCH 11/42] Declare $title before assignment --- app/Models/HasDOI.php | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/app/Models/HasDOI.php b/app/Models/HasDOI.php index 1d77e8d8..d20e4649 100644 --- a/app/Models/HasDOI.php +++ b/app/Models/HasDOI.php @@ -14,12 +14,12 @@ public function generateDOI($doiService) $identifier = $this->getIdentifier($this, 'identifier'); if ($this->doi == null) { + $title = null; $authors = []; $users = []; $suffix = null; $url = 'https://www.nmrxiv.org/'; $publicationYear = Carbon::now()->year; - $license = License::where([['id', $this->license_id]])->firstOrFail(); $dates = [ [ @@ -36,6 +36,11 @@ public function generateDOI($doiService) ], ]; + $description = [ + 'description' => $this->description, + 'descriptionType' => 'Other', + ]; + if ($this instanceof Project) { $title = $this->name; $users = $this->allUsers(); @@ -144,11 +149,6 @@ public function generateDOI($doiService) ], ]; - $description = [ - 'description' => $this->description, - 'descriptionType' => 'Other', - ]; - $attributes = [ 'creators' => count($creators) > 0 ? $creators : $contributors, 'titles' => [ From 88fa48d68628890fae150dc10d902df2eac706b5 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 4 Dec 2023 11:04:55 +0100 Subject: [PATCH 12/42] review changes for .env.example --- .env.example | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/.env.example b/.env.example index 5f9e13d2..6620f622 100644 --- a/.env.example +++ b/.env.example @@ -14,6 +14,9 @@ EUROPEMC_WS_API=https://www.ebi.ac.uk/europepmc/webservices/rest/search ORCID_ID_SEARCH_API=https://pub.orcid.org/v2.1/search ORCID_ID_EMPLOYMENT_API=https://pub.orcid.org/v3.0/{orcid_id}/employments ORCID_ID_PERSON_API=https://pub.orcid.org/v3.0/{orcid_id}/person +CM_API=https://api.naturalproducts.net/latest/ +CROSSREF_API=https://api.crossref.org/works/ + LOG_CHANNEL=stack LOG_LEVEL=debug @@ -94,3 +97,9 @@ NMRXIV_PROVIDER=NFDI4Chem NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/ MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613 +#DATACITE Properties +DOI_HOST=datacite +DATACITE_USERNAME= +DATACITE_SECRET= +DATACITE_PREFIX= +DATACITE_ENDPOINT= \ No newline at end of file From f2d3718641a594d6562d0bb84bfa3a4ac90c986a Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 4 Dec 2023 11:22:43 +0100 Subject: [PATCH 13/42] update return commands --- app/Http/Controllers/API/Auth/RegisterController.php | 1 - app/Http/Controllers/API/DatasetController.php | 2 +- app/Http/Controllers/API/ProjectController.php | 2 +- app/Http/Controllers/API/StudyController.php | 2 +- 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/app/Http/Controllers/API/Auth/RegisterController.php b/app/Http/Controllers/API/Auth/RegisterController.php index 901e15f4..03f3258e 100644 --- a/app/Http/Controllers/API/Auth/RegisterController.php +++ b/app/Http/Controllers/API/Auth/RegisterController.php @@ -6,7 +6,6 @@ use App\Models\User; use Illuminate\Http\JsonResponse; use Illuminate\Http\Request; -use Illuminate\Support\Facades\Auth; use Illuminate\Support\Facades\Hash; class RegisterController extends Controller diff --git a/app/Http/Controllers/API/DatasetController.php b/app/Http/Controllers/API/DatasetController.php index 6d375e66..532548fa 100644 --- a/app/Http/Controllers/API/DatasetController.php +++ b/app/Http/Controllers/API/DatasetController.php @@ -78,7 +78,7 @@ public function id(Request $request) $id = $request->query('id'); if ($id) { - return $Dataset = DatasetResource::collection(Dataset::where([['is_public', true], ['identifier', str_replace('D', '', $id)]])->get()); + return DatasetResource::collection(Dataset::where([['is_public', true], ['identifier', str_replace('D', '', $id)]])->get()); } else { return response()->json([ 'message' => 'Input missing.', diff --git a/app/Http/Controllers/API/ProjectController.php b/app/Http/Controllers/API/ProjectController.php index 79832a2b..4920fa38 100644 --- a/app/Http/Controllers/API/ProjectController.php +++ b/app/Http/Controllers/API/ProjectController.php @@ -78,7 +78,7 @@ public function id(Request $request) $id = $request->query('id'); if ($id) { - return $project = ProjectResource::collection(Project::where([['is_public', true], ['identifier', str_replace('P', '', $id)]])->get()); + return ProjectResource::collection(Project::where([['is_public', true], ['identifier', str_replace('P', '', $id)]])->get()); } else { return response()->json([ 'message' => 'Input missing.', diff --git a/app/Http/Controllers/API/StudyController.php b/app/Http/Controllers/API/StudyController.php index a5430a62..a9b7030f 100644 --- a/app/Http/Controllers/API/StudyController.php +++ b/app/Http/Controllers/API/StudyController.php @@ -78,7 +78,7 @@ public function id(Request $request) $id = $request->query('id'); if ($id) { - return $study = StudyResource::collection(Study::where([['is_public', true], ['identifier', str_replace('S', '', $id)]])->get()); + return StudyResource::collection(Study::where([['is_public', true], ['identifier', str_replace('S', '', $id)]])->get()); } else { return response()->json([ 'message' => 'Input missing.', From 5c08136a5b1fb7cbfa41385b5ceb6ed58f25aa96 Mon Sep 17 00:00:00 2001 From: NishaSharma14 Date: Mon, 4 Dec 2023 15:31:13 +0100 Subject: [PATCH 14/42] fix: register api 422 error in swagger --- .../API/Auth/RegisterController.php | 45 +++++++++++-------- .../Controllers/API/ProjectController.php | 2 +- app/Http/Controllers/Controller.php | 7 +++ 3 files changed, 35 insertions(+), 19 deletions(-) diff --git a/app/Http/Controllers/API/Auth/RegisterController.php b/app/Http/Controllers/API/Auth/RegisterController.php index 03f3258e..f846b15a 100644 --- a/app/Http/Controllers/API/Auth/RegisterController.php +++ b/app/Http/Controllers/API/Auth/RegisterController.php @@ -4,25 +4,24 @@ use App\Http\Controllers\Controller; use App\Models\User; -use Illuminate\Http\JsonResponse; use Illuminate\Http\Request; use Illuminate\Support\Facades\Hash; class RegisterController extends Controller { /** - * @OA\Post( - * path="/api/v1/auth/register", - * summary="Register", - * description="Register by providing details.", - * operationId="authRegister", - * tags={"auth"}, + * Register * - * @OA\RequestBody( - * required=true, - * description="Pass registration details.", + * @OA\Post ( + * path="/api/v1/auth/register", + * tags={"auth"}, * - * @OA\JsonContent( + * @OA\RequestBody( + * + * @OA\MediaType( + * mediaType="application/json", + * + * @OA\Schema( * required={"first_name","last_name","email","password","username"}, * * @OA\Property(property="first_name", type="string", format="first_name", example="Nisha"), @@ -31,21 +30,31 @@ class RegisterController extends Controller * @OA\Property(property="username", type="string", format="username", example="nis123"), * @OA\Property(property="orcid_id", type="string", format="orcid_id", example="0009-0006-4755-1039"), * @OA\Property(property="password", type="string", format="password", example="secret1234"), + + * ) + * ) + * ), * - * ), - * ), + * @OA\Response( + * response=201, + * description="Success", + * + * @OA\JsonContent( + * + * @OA\Property(property="success", type="boolean", example=true), + * @OA\Property(property="message", type="string", example="User creation successful. Kindly confirm your email address by clicking the link sent to your inbox"), + * @OA\Property(property="access_token", type="string", example="randomtokenasfhajskfhajf398rureuuhfdshk"), + * @OA\Property(property="token_type", type="string", example="bearer"), + * ) + * ), * - * @OA\Response( - * response=201, - * description="Successful Operation" - * ), * @OA\Response( * response=422, * description="Unprocessable Content" * ) * ) */ - public function register(Request $request): JsonResponse + public function register(Request $request) { $validatedData = $request->validate([ 'first_name' => 'required|string|max:255', diff --git a/app/Http/Controllers/API/ProjectController.php b/app/Http/Controllers/API/ProjectController.php index 4920fa38..dc60318e 100644 --- a/app/Http/Controllers/API/ProjectController.php +++ b/app/Http/Controllers/API/ProjectController.php @@ -78,7 +78,7 @@ public function id(Request $request) $id = $request->query('id'); if ($id) { - return ProjectResource::collection(Project::where([['is_public', true], ['identifier', str_replace('P', '', $id)]])->get()); + return ProjectResource::collection(Project::where([['is_public', true], ['identifier', str_replace('P', '', $id)]])->get()); } else { return response()->json([ 'message' => 'Input missing.', diff --git a/app/Http/Controllers/Controller.php b/app/Http/Controllers/Controller.php index 4d564870..b5dfa22a 100644 --- a/app/Http/Controllers/Controller.php +++ b/app/Http/Controllers/Controller.php @@ -12,6 +12,13 @@ * version="1.0", * title="nmrXiv" * ) + * + * @OA\SecurityScheme( + * type="apiKey", + * in="header", + * securityScheme="token", + * name="Authorization" + * ) */ class Controller extends BaseController { From c80eefc936c95bf5a6c128e534e67e13ac7bcf08 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 15:52:26 +0100 Subject: [PATCH 15/42] replace bioschema by bioschemas --- .env.ci.test | 2 +- .env.example | 2 +- .../Bioschema/DataCatalogController.php | 177 ------------------ .../BioschemasController.php} | 162 +++++++++++----- .../Bioschemas/DataCatalogController.php | 120 ++++++++++++ app/Models/Bioschema/BioSchema.php | 26 --- app/Models/Bioschemas/Bioschemas.php | 16 ++ .../{Bioschema => Bioschemas}/Study.php | 2 +- docs/introduction/data/ontologies.md | 2 +- resources/js/Pages/Public/Project/Dataset.vue | 2 +- resources/js/Pages/Public/Project/Show.vue | 2 +- resources/js/Pages/Public/Project/Study.vue | 2 +- resources/js/Pages/Welcome.vue | 2 +- routes/api.php | 12 +- 14 files changed, 265 insertions(+), 264 deletions(-) delete mode 100644 app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php rename app/Http/Controllers/API/Schemas/{Bioschema/BiochemaController.php => Bioschemas/BioschemasController.php} (85%) create mode 100644 app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php delete mode 100644 app/Models/Bioschema/BioSchema.php create mode 100644 app/Models/Bioschemas/Bioschemas.php rename app/Models/{Bioschema => Bioschemas}/Study.php (99%) diff --git a/.env.ci.test b/.env.ci.test index d6782e03..b1b07db3 100644 --- a/.env.ci.test +++ b/.env.ci.test @@ -83,7 +83,7 @@ TWITTER_REDIRECT_URL=http://localhost:80/auth/login/twitter/callback TELESCOPE_ENABLED=false -#Bioschema Properties. +#Bioschemas Properties. NMRXIV_PROVIDER=NFDI4Chem NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/ MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613 diff --git a/.env.example b/.env.example index 65e05d8e..5d84b607 100644 --- a/.env.example +++ b/.env.example @@ -92,7 +92,7 @@ ORCID_ENVIRONMENT=sandbox TELESCOPE_ENABLED=false -#Bioschema Properties. +#Bioschemas Properties. NMRXIV_PROVIDER=NFDI4Chem NMRXIV_PROVIDER_URL=https://www.nfdi4chem.de/ MEASUREMENT_TECHNIQUE=http://purl.obolibrary.org/obo/CHMO_0000613 diff --git a/app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php deleted file mode 100644 index 01522e6a..00000000 --- a/app/Http/Controllers/API/Schemas/Bioschema/DataCatalogController.php +++ /dev/null @@ -1,177 +0,0 @@ -prepareKeywords(); - $contributors = $this->prepareContributors(); - - $nmrXivProvider = Schema::Organization(); - $nmrXivProvider->name(env('NMRXIV_PROVIDER')); - $nmrXivProvider->url(env('NMRXIV_PROVIDER_URL')); - - $dataCatalog = Schema::DataCatalog(); - $dataCatalog['@id'] = url(env('APP_URL')); - $dataCatalog['dct:conformsTo'] = $confromsTo; - $dataCatalog->description(env('APP_DESCRIPTION')); - $dataCatalog->keywords($keywords); - $dataCatalog->name(env('APP_NAME')); - $dataCatalog->provider($nmrXivProvider); - $dataCatalog->url(env('APP_URL')); - $dataCatalog->identifier(env('APP_URL')); - $dataCatalog->license('https://mit-license.org/'); - $dataCatalog->contributor($contributors); - $dataCatalog->isAccessibleForFree(true); - - $dataCatalog->measurementTechnique(env('MEASUREMENT_TECHNIQUE')); - - return $dataCatalog; - } - - /** - * Get Defined Term for ontology term. - * - * - * @param string $name - * @param array $alternameName - * @param string $identifier - * @param string $url - * @param object $inDefinedTermSet - * @return object $definedTerm - */ - public function getDefinedTerm($name, $alternateName, $identifier, $url, $inDefinedTermSet) - { - $definedTerm = Schema::DefinedTerm(); - $definedTerm->name($name); - $definedTerm->alternateName($alternateName); - $definedTerm->identifier($identifier); - $definedTerm->url($url); - $definedTerm->inDefinedTermSet($inDefinedTermSet); - - return $definedTerm; - } - - /** - * Get Defined Term set for ontology service. - * - * - * @param string $name - * @param string $url - * @return object $definedTermSet - */ - public function getDefinedTermSet($name, $url) - { - $definedTermSet = Schema::DefinedTermSet(); - $definedTermSet->name($name); - $definedTermSet->url($url); - - return $definedTermSet; - } - - /** - * Prepare Keywords. - * - * @param null - * @return array $keywords - */ - public function prepareKeywords() - { - //Prepare Defined Term Set - $chmo = $this->getDefinedTermSet('Chemical Methods Ontology', 'http://purl.obolibrary.org/obo/chmo.owl'); - $nmrcv = $this->getDefinedTermSet('nuclear magnetic resonance CV', 'http://nmrml.org/cv/'); - - //Prepare Defined Term - $nmr = $this->getDefinedTerm('nuclear magnetic resonance spectroscopy', ['NMR', 'NMR spectroscopy', 'nuclear magnetic resonance (NMR) spectroscopy'], 'CHMO:0000591', 'http://purl.obolibrary.org/obo/CHMO_0000591', $chmo); - $pulsedNMR = $this->getDefinedTerm('pulsed nuclear magnetic resonance spectroscopy', ['NMR', 'nuclear magnetic resonance spectroscopy', 'NMR spectroscopy'], 'CHMO:0000613', 'https://ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000613', $chmo); - $oneDNMR = $this->getDefinedTerm('one-dimensional nuclear magnetic resonance spectroscopy', ['1D NMR spectroscopy', '1-D NMR', 'one-dimensional nuclear magnetic resonance spectroscopy', '1D NMR', '1D nuclear magnetic resonance spectroscopy'], 'CHMO:0000592', 'http://purl.obolibrary.org/obo/CHMO_0000592', $chmo); - $twoDNMR = $this->getDefinedTerm('two-dimensional nuclear magnetic resonance spectroscopy', ['2-D NMR', '2D NMR', 'two-dimensional nuclear magnetic resonance spectroscopy', '2D NMR spectroscopy', 'two-dimensional NMR', '2D nuclear magnetic resonance'], 'CHMO:0000598', 'http://purl.obolibrary.org/obo/CHMO_0000598', $chmo); - $cosy = $this->getDefinedTerm('correlation spectroscopy spectrum', ['COSY spectra', 'COSY spectrum', 'COSY NMR spectrum', 'COSY NMR spectra'], 'CHMO:0002450', 'http://purl.obolibrary.org/obo/CHMO_0002450', $chmo); - $hsqc = $this->getDefinedTerm('heteronuclear single quantum coherence', ['HSQC'], 'CHMO:0000604', 'http://purl.obolibrary.org/obo/CHMO_0000604', $chmo); - $hmbc = $this->getDefinedTerm('heteronuclear multiple bond coherence', ['HMBC NMR', 'HMBC'], 'CHMO:0000601', 'http://purl.obolibrary.org/obo/CHMO_0000601', $chmo); - $noesy = $this->getDefinedTerm('two-dimensional nuclear Overhauser enhancement spectrum', ['2D NOESY-NMR spectrum', '2D NOESY-NMR spectra', '2D NOESY spectra', '2D NOESY spectrum'], 'CHMO:0001171', 'http://purl.obolibrary.org/obo/CHMO_0001171', $chmo); - $brukerNMR = $this->getDefinedTerm('Bruker', [], 'NMR:1400256', 'http://nmrML.org/nmrCV#NMR:1400256', $nmrcv); - $joel = $this->getDefinedTerm('JEOL', [], 'NMR:1400258', 'http://nmrML.org/nmrCV#NMR:1400258', $nmrcv); - $nmreData = $this->getDefinedTerm('NMReDATA', [], 'format:3906', 'http://edamontology.org/format_3906', $nmrcv); - - $keywords = [$nmr, $pulsedNMR, $oneDNMR, $twoDNMR, $cosy, $hsqc, $hmbc, $noesy, $brukerNMR, $joel, $nmreData]; - - return $keywords; - } - - /** - * Get Person from given and family names. - * - * - * @param string $givenName - * @param string $familyName - * @return object $Person - */ - public function getPerson($id, $givenName, $familyName) - { - $contributor = Schema::Person(); - $contributor->identifier($id); - $contributor->givenName($givenName); - $contributor->familyName($familyName); - - return $contributor; - } - - /** - * Prepare Contributors. - * - * @param null - * @return array $contributors - */ - public function prepareContributors() - { - $Annett = $this->getPerson('0000-0002-2542-0867', 'Annett', 'Schröter'); - $Christian = $this->getPerson(null, 'Christian', 'Popp'); - $Christoph = $this->getPerson('0000-0001-6966-0814', 'Christoph', 'Steinbeck'); - $Darina = $this->getPerson(null, 'Darina', 'Storozhuk'); - $David = $this->getPerson('0000-0001-7499-1693', 'David', 'Rauh'); - $Guido = $this->getPerson('0000-0003-1022-4326', 'Guido', 'Pauli'); - $Hamed = $this->getPerson(null, 'Hamed', 'Musallam'); - $Johannes = $this->getPerson('0000-0003-2060-842X', 'Johannes', 'Liermann'); - $Julien = $this->getPerson('0000-0002-3416-2572', 'Julien', 'Wist'); - $Kohulan = $this->getPerson('0000-0003-1066-7792', 'Kohulan', 'Rajan'); - $Luc = $this->getPerson('0000-0002-4943-2643', 'Luc', 'Patiny'); - $Markus = $this->getPerson(null, 'Markus', 'Lange'); - $Nazar = $this->getPerson('0000-0002-5870-8496', 'Nazar', 'Stefaniuk'); - $Nils = $this->getPerson('0000-0002-0990-9582', 'Nils', 'Schlörer'); - $Nisha = $this->getPerson('0009-0006-4755-1039', 'Nisha', 'Sharma'); - $Noura = $this->getPerson('0009-0001-5998-5030', 'Noura', 'Rayya'); - $Pascal = $this->getPerson(null, 'Pascal', 'Scherreiks'); - $Stefan = $this->getPerson('0000-0002-5990-4157', 'Stefan', 'Kuhn'); - $Steffen = $this->getPerson('0000-0002-7899-7192', 'Steffen', 'Neumann'); - $Tillmann = $this->getPerson('0000-0003-4480-8661', 'Tillmann', 'Fischer'); - $Venkata = $this->getPerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala'); - - $contributors = [$Annett, $Christian, $Christoph, $Darina, $Guido, $Hamed, $Johannes, $Julien, $Kohulan, $Luc, $Markus, $Nazar, $Nils, $Nisha, $Noura, $Pascal, $Stefan, $Steffen, $Tillmann, $Venkata]; - - return $contributors; - } -} diff --git a/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php similarity index 85% rename from app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php rename to app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php index 405c2013..f5e08568 100644 --- a/app/Http/Controllers/API/Schemas/Bioschema/BiochemaController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php @@ -1,9 +1,9 @@ is_public) { $projectSchema = $this->project($project); if ($studyName) { - // send study back with project info added to it\ $study = Study::where([['slug', $studyName], ['owner_id', $user->id], ['project_id', $project->id]])->firstOrFail(); if ($study) { if ($study->is_public) { $studySchema = $this->study($study); if ($datasetName) { $dataset = Dataset::where([['slug', $datasetName], ['owner_id', $user->id], ['project_id', $project->id], ['study_id', $study->id]])->firstOrFail(); - // send dataset with project and study details if ($dataset) { if ($dataset->is_public) { $datasetSchema = $this->dataset($dataset); @@ -114,9 +112,50 @@ public function modelSchemaByID(Request $request, $identifier) } } + /** + * Get Defined Term for ontology term. + * + * + * @param string $name + * @param array $alternameName + * @param string $identifier + * @param string $url + * @param object $inDefinedTermSet + * @return object $definedTerm + */ + public function getDefinedTerm($name, $alternateName, $identifier, $url, $inDefinedTermSet) + { + $definedTerm = Schema::DefinedTerm(); + $definedTerm->name($name); + $definedTerm->alternateName($alternateName); + $definedTerm->identifier($identifier); + $definedTerm->url($url); + $definedTerm->inDefinedTermSet($inDefinedTermSet); + + return $definedTerm; + } + + /** + * Get Defined Term set for ontology service. + * + * + * @param string $name + * @param string $url + * @return object $definedTermSet + */ + public function getDefinedTermSet($name, $url) + { + $definedTermSet = Schema::DefinedTermSet(); + $definedTermSet->name($name); + $definedTermSet->url($url); + + return $definedTermSet; + } + /** * Get Property value from ontologies. * + * @param string $name * @param string $ontologyID * @param string $value * @param string $unitUrl @@ -223,7 +262,7 @@ public function getCitations($model) * * @link https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE * - * @param App\Models\BioSample $sample + * @param App\Models\Sample $sample * @return array $molecules */ public function getMolecules($sample) @@ -233,24 +272,24 @@ public function getMolecules($sample) $inchiKey = $molecule->inchi_key; $pubchemLink = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'.$inchiKey.'/property/IUPACName/JSON'; $json = json_decode(Http::get($pubchemLink)->body(), true); - // $cid = $json['PropertyTable']['Properties'][0]['CID']; - // $iupacName = $json['PropertyTable']['Properties'][0]['IUPACName']; - - // $moleculeSchema = Schema::MolecularEntity(); - // $moleculeSchema['@id'] = $inchiKey; - // $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); - // $moleculeSchema['identifier'] = $inchiKey; - // $moleculeSchema->name($molecule->cas); - // $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); - // $moleculeSchema->inChI('InChI='.$molecule->standard_inchi); - // $moleculeSchema->inChIKey($inchiKey); - // $moleculeSchema->iupacName($iupacName); - // $moleculeSchema->molecularFormula($molecule->molecular_formula); - // $moleculeSchema->molecularWeight($molecule->molecular_weight); - // $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]); - // $moleculeSchema->hasRepresentation($molecule->MOL); - // $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%'); - // array_push($molecules, $moleculeSchema); + $cid = $json['PropertyTable']['Properties'][0]['CID']; + $iupacName = $json['PropertyTable']['Properties'][0]['IUPACName']; + + $moleculeSchema = Schema::MolecularEntity(); + $moleculeSchema['@id'] = $inchiKey; + $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); + $moleculeSchema['identifier'] = $inchiKey; + $moleculeSchema->name($molecule->cas); + $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); + $moleculeSchema->inChI($molecule->standard_inchi); + $moleculeSchema->inChIKey($inchiKey); + $moleculeSchema->iupacName($iupacName); + $moleculeSchema->molecularFormula($molecule->molecular_formula); + $moleculeSchema->molecularWeight($molecule->molecular_weight); + $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]); + $moleculeSchema->hasRepresentation($molecule->MOL); + $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%'); + array_push($molecules, $moleculeSchema); } return $molecules; @@ -268,7 +307,9 @@ public function getMolecules($sample) public function getSample($study) { $sample = $study->sample; - $sampleSchema = BioSchema::ChemicalSubstance(); + $molecules = $this->getMolecules($sample); + + $sampleSchema = Bioschemas::ChemicalSubstance(); $sampleSchema['@id'] = $study->doi; $sampleSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); $sampleSchema->name($study->project->name.'.'.$sample->name); @@ -283,7 +324,6 @@ public function getSample($study) * Get NMRium info from a dataset. * * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT * * @param App\Models\Dataset $dataset * @return array $nmriumInfo @@ -355,12 +395,10 @@ public function getNMRiumInfo($dataset) /** * Get Dataset download details info from a dataset. * - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE - * @link https://schema.org/distribution * @link https://schema.org/DataDownload * * @param App\Models\Dataset $dataset - * return object $distribution + * @return object $distribution */ public function getDistribution($dataset) { @@ -373,6 +411,8 @@ public function getDistribution($dataset) $distribution->name($dataset->project->name); $distribution->encodingFormat('zip'); $distribution->contentURL($contentURL); + + return $distribution; } /** @@ -393,13 +433,12 @@ public function DataCatalogLite() } /** - * Implement Bioschemas' study with only few properties, including the sample and molecules, - * to be included in the project schema. + * * @link https://bioschemas.org/profiles/Study/0.3-DRAFT * * @param App\Models\Project $project - * @return object $projectSchema + * @return array $schemas */ public function prepareStudies($project) { @@ -413,6 +452,12 @@ public function prepareStudies($project) return $schemas; } + /** + * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * + * @param App\Models\Study $study + * @return array $schemas + */ public function prepareDatasets($study) { $schemas = []; @@ -424,6 +469,11 @@ public function prepareDatasets($study) return $schemas; } + /** + * @link https://schema.org/organization + * + * @return object $publisher + */ public function preparePublisher() { $publisher = Schema::Organization(); @@ -434,14 +484,11 @@ public function preparePublisher() } /** - * Implement Bioschemas' Dataset, along with the project and study it belongs to. + * Implement Bioschemas' Dataset. * * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT * * @param App\Models\Dataset $dataset - * @param App\Models\Study $study - * @param App\Models\Project $project * @return object $datasetSchema */ public function datasetLite($dataset) @@ -469,7 +516,15 @@ public function datasetLite($dataset) return $datasetSchema; } } - + /** + * Implement Bioschemas' Dataset, along with the project and study it belongs to. + * + * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * + * @param App\Models\Dataset $dataset + * @return object $datasetSchema + */ public function dataset($dataset) { $datasetSchema = $this->datasetLite($dataset); @@ -482,8 +537,7 @@ public function dataset($dataset) } /** - * Implement Bioschemas' Study, including the sample and molecules, along - * with the project it belongs to and, briefly, the datasets it contains. + * Implement Bioschemas' Study. * * @link https://bioschemas.org/profiles/Study/0.3-DRAFT * @@ -493,7 +547,7 @@ public function dataset($dataset) public function studyLite($study) { $prefix = $study->project->name.':'; - $studySchema = BioSchema::Study(); + $studySchema = Bioschemas::Study(); $studySchema['@id'] = $study->doi; $studySchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); $studySchema->name($prefix.$study->name); @@ -510,7 +564,16 @@ public function studyLite($study) return $studySchema; } - + + /** + * Implement Bioschemas' Study, including the sample and molecules, along + * with the project it belongs to and, briefly, the datasets it contains. + * + * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * + * @param App\Models\Study $study + * @return object $studySchema + */ public function study($study) { $studySchema = $this->studyLite($study); @@ -521,20 +584,16 @@ public function study($study) } /** - * Implement Bioschemas' project along with brief details about - * the studies and datasets it contains. + * Implement Bioschemas' project. * * @link https://bioschemas.org/profiles/Study/0.3-DRAFT - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE - * @link https://bioschemas.org/profiles/Sample/0.2-RELEASE-2018_11_10 - * @link https://bioschemas.org/types/MolecularEntity/0.3-RELEASE-2019_09_02 * * @param App\Models\Project $project * @return object $projectSchema */ public function projectLite($project) { - $projectSchema = BioSchema::Study(); + $projectSchema = Bioschemas::Study(); $projectSchema['@id'] = $project->doi; $projectSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); $projectSchema->name($project->name); @@ -552,6 +611,15 @@ public function projectLite($project) return $projectSchema; } + /** + * Implement Bioschemas' project along with brief details about + * the studies and datasets it contains. + * + * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * + * @param App\Models\Project $project + * @return object $projectSchema + */ public function project($project) { $projectSchema = $this->projectLite($project); diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php new file mode 100644 index 00000000..8fb99d58 --- /dev/null +++ b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php @@ -0,0 +1,120 @@ +prepareKeywords(); + $contributors = $this->prepareContributors(); + + $nmrXivProvider = Schema::Organization(); + $nmrXivProvider->name(env('NMRXIV_PROVIDER')); + $nmrXivProvider->url(env('NMRXIV_PROVIDER_URL')); + + $dataCatalog = Schema::DataCatalog(); + $dataCatalog['@id'] = url(env('APP_URL')); + $dataCatalog['dct:conformsTo'] = $confromsTo; + $dataCatalog->description(env('APP_DESCRIPTION')); + $dataCatalog->keywords($keywords); + $dataCatalog->name(env('APP_NAME')); + $dataCatalog->provider($nmrXivProvider); + $dataCatalog->url(env('APP_URL')); + $dataCatalog->identifier(env('APP_URL')); + $dataCatalog->license('https://mit-license.org/'); + $dataCatalog->contributor($contributors); + $dataCatalog->isAccessibleForFree(true); + + $dataCatalog->measurementTechnique(env('MEASUREMENT_TECHNIQUE')); + + return $dataCatalog; + } + + /** + * Prepare Keywords. + * + * @param null + * @return array $keywords + */ + public function prepareKeywords() + { + //Prepare Defined Term Set + $chmo = BioschemasHelper::prepareDefinedTermSet('Chemical Methods Ontology', 'http://purl.obolibrary.org/obo/chmo.owl'); + $nmrcv = BioschemasHelper::prepareDefinedTermSet('nuclear magnetic resonance CV', 'http://nmrml.org/cv/'); + + //Prepare Defined Term + $nmr = BioschemasHelper::prepareDefinedTerm('nuclear magnetic resonance spectroscopy', ['NMR', 'NMR spectroscopy', 'nuclear magnetic resonance (NMR) spectroscopy'], 'CHMO:0000591', 'http://purl.obolibrary.org/obo/CHMO_0000591', $chmo); + $pulsedNMR = BioschemasHelper::prepareDefinedTerm('pulsed nuclear magnetic resonance spectroscopy', ['NMR', 'nuclear magnetic resonance spectroscopy', 'NMR spectroscopy'], 'CHMO:0000613', 'https://ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000613', $chmo); + $oneDNMR = BioschemasHelper::prepareDefinedTerm('one-dimensional nuclear magnetic resonance spectroscopy', ['1D NMR spectroscopy', '1-D NMR', 'one-dimensional nuclear magnetic resonance spectroscopy', '1D NMR', '1D nuclear magnetic resonance spectroscopy'], 'CHMO:0000592', 'http://purl.obolibrary.org/obo/CHMO_0000592', $chmo); + $twoDNMR = BioschemasHelper::prepareDefinedTerm('two-dimensional nuclear magnetic resonance spectroscopy', ['2-D NMR', '2D NMR', 'two-dimensional nuclear magnetic resonance spectroscopy', '2D NMR spectroscopy', 'two-dimensional NMR', '2D nuclear magnetic resonance'], 'CHMO:0000598', 'http://purl.obolibrary.org/obo/CHMO_0000598', $chmo); + $cosy = BioschemasHelper::prepareDefinedTerm('correlation spectroscopy spectrum', ['COSY spectra', 'COSY spectrum', 'COSY NMR spectrum', 'COSY NMR spectra'], 'CHMO:0002450', 'http://purl.obolibrary.org/obo/CHMO_0002450', $chmo); + $hsqc = BioschemasHelper::prepareDefinedTerm('heteronuclear single quantum coherence', ['HSQC'], 'CHMO:0000604', 'http://purl.obolibrary.org/obo/CHMO_0000604', $chmo); + $hmbc = BioschemasHelper::prepareDefinedTerm('heteronuclear multiple bond coherence', ['HMBC NMR', 'HMBC'], 'CHMO:0000601', 'http://purl.obolibrary.org/obo/CHMO_0000601', $chmo); + $noesy = BioschemasHelper::prepareDefinedTerm('two-dimensional nuclear Overhauser enhancement spectrum', ['2D NOESY-NMR spectrum', '2D NOESY-NMR spectra', '2D NOESY spectra', '2D NOESY spectrum'], 'CHMO:0001171', 'http://purl.obolibrary.org/obo/CHMO_0001171', $chmo); + $brukerNMR = BioschemasHelper::prepareDefinedTerm('Bruker', [], 'NMR:1400256', 'http://nmrML.org/nmrCV#NMR:1400256', $nmrcv); + $joel = BioschemasHelper::prepareDefinedTerm('JEOL', [], 'NMR:1400258', 'http://nmrML.org/nmrCV#NMR:1400258', $nmrcv); + $nmreData = BioschemasHelper::prepareDefinedTerm('NMReDATA', [], 'format:3906', 'http://edamontology.org/format_3906', $nmrcv); + + $keywords = [$nmr, $pulsedNMR, $oneDNMR, $twoDNMR, $cosy, $hsqc, $hmbc, $noesy, $brukerNMR, $joel, $nmreData]; + + return $keywords; + } + + /** + * Prepare Contributors. + * + * @param null + * @return array $contributors + */ + public function prepareContributors() + { + $Annett = BioschemasHelper::preparePerson('0000-0002-2542-0867', 'Annett', 'Schröter'); + $Christian = BioschemasHelper::preparePerson(null, 'Christian', 'Popp'); + $Christoph = BioschemasHelper::preparePerson('0000-0001-6966-0814', 'Christoph', 'Steinbeck'); + $Darina = BioschemasHelper::preparePerson(null, 'Darina', 'Storozhuk'); + $David = BioschemasHelper::preparePerson('0000-0001-7499-1693', 'David', 'Rauh'); + $Guido = BioschemasHelper::preparePerson('0000-0003-1022-4326', 'Guido', 'Pauli'); + $Hamed = BioschemasHelper::preparePerson(null, 'Hamed', 'Musallam'); + $Johannes = BioschemasHelper::preparePerson('0000-0003-2060-842X', 'Johannes', 'Liermann'); + $Julien = BioschemasHelper::preparePerson('0000-0002-3416-2572', 'Julien', 'Wist'); + $Kohulan = BioschemasHelper::preparePerson('0000-0003-1066-7792', 'Kohulan', 'Rajan'); + $Luc = BioschemasHelper::preparePerson('0000-0002-4943-2643', 'Luc', 'Patiny'); + $Markus = BioschemasHelper::preparePerson(null, 'Markus', 'Lange'); + $Nazar = BioschemasHelper::preparePerson('0000-0002-5870-8496', 'Nazar', 'Stefaniuk'); + $Nils = BioschemasHelper::preparePerson('0000-0002-0990-9582', 'Nils', 'Schlörer'); + $Nisha = BioschemasHelper::preparePerson('0009-0006-4755-1039', 'Nisha', 'Sharma'); + $Noura = BioschemasHelper::preparePerson('0009-0001-5998-5030', 'Noura', 'Rayya'); + $Pascal = BioschemasHelper::preparePerson(null, 'Pascal', 'Scherreiks'); + $Stefan = BioschemasHelper::preparePerson('0000-0002-5990-4157', 'Stefan', 'Kuhn'); + $Steffen = BioschemasHelper::preparePerson('0000-0002-7899-7192', 'Steffen', 'Neumann'); + $Tillmann = BioschemasHelper::preparePerson('0000-0003-4480-8661', 'Tillmann', 'Fischer'); + $Venkata = BioschemasHelper::preparePerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala'); + + $contributors = [$Annett, $Christian, $Christoph, $Darina, $Guido, $Hamed, $Johannes, $Julien, $Kohulan, $Luc, $Markus, $Nazar, $Nils, $Nisha, $Noura, $Pascal, $Stefan, $Steffen, $Tillmann, $Venkata]; + + return $contributors; + } +} diff --git a/app/Models/Bioschema/BioSchema.php b/app/Models/Bioschema/BioSchema.php deleted file mode 100644 index 7ea6084f..00000000 --- a/app/Models/Bioschema/BioSchema.php +++ /dev/null @@ -1,26 +0,0 @@ - { this.schema = response.data; }); diff --git a/resources/js/Pages/Public/Project/Show.vue b/resources/js/Pages/Public/Project/Show.vue index 4734692c..68d7c94d 100644 --- a/resources/js/Pages/Public/Project/Show.vue +++ b/resources/js/Pages/Public/Project/Show.vue @@ -176,7 +176,7 @@ export default { computed: {}, mounted() { axios - .get(route("bioschema.id", this.project.data.identifier)) + .get(route("bioschemas.id", this.project.data.identifier)) .then((response) => { this.schema = response.data; }); diff --git a/resources/js/Pages/Public/Project/Study.vue b/resources/js/Pages/Public/Project/Study.vue index bb50946c..8fd11ad9 100644 --- a/resources/js/Pages/Public/Project/Study.vue +++ b/resources/js/Pages/Public/Project/Study.vue @@ -485,7 +485,7 @@ export default { } axios - .get(route("bioschema.id", this.study.data.identifier)) + .get(route("bioschemas.id", this.study.data.identifier)) .then((response) => { this.schema = response.data; }); diff --git a/resources/js/Pages/Welcome.vue b/resources/js/Pages/Welcome.vue index 265ec93f..36e3e987 100644 --- a/resources/js/Pages/Welcome.vue +++ b/resources/js/Pages/Welcome.vue @@ -1013,7 +1013,7 @@ export default { }, mounted() { - axios.get(route("bioschema.datacatalog")).then((response) => { + axios.get(route("bioschemas.datacatalog")).then((response) => { this.schema = response.data; }); }, diff --git a/routes/api.php b/routes/api.php index e5194d7e..e52eccde 100644 --- a/routes/api.php +++ b/routes/api.php @@ -5,8 +5,8 @@ use App\Http\Controllers\API\Auth\UserController; use App\Http\Controllers\API\FileSystemController; use App\Http\Controllers\API\ProjectController; -use App\Http\Controllers\API\Schemas\Bioschema\BiochemaController; -use App\Http\Controllers\API\Schemas\Bioschema\DataCatalogController; +use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasController; +use App\Http\Controllers\API\Schemas\Bioschemas\DataCatalogController; use App\Http\Controllers\API\Schemas\DataCite\DataCiteController; use App\Http\Controllers\API\SearchController; use Illuminate\Support\Facades\Route; @@ -40,10 +40,10 @@ ->name('public.projects'); Route::prefix('schemas')->group(function () { - Route::prefix('bioschema')->group(function () { - Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschema.datacatalog'); - Route::get('/{username}/{project}/{study?}/{dataset?}', [BiochemaController::class, 'modelSchemaByName'])->name('bioschema.model'); - Route::get('/{id}', [BiochemaController::class, 'modelSchemaByID'])->name('bioschema.id'); + Route::prefix('bioschemas')->group(function () { + Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschemas.datacatalog'); + Route::get('/{username}/{project}/{study?}/{dataset?}', [BiochemaController::class, 'modelSchemaByName'])->name('bioschemas.model'); + Route::get('/{id}', [BiochemaController::class, 'modelSchemaByID'])->name('bioschemas.id'); }); Route::prefix('datacite')->group(function () { From 4da3dc3ad9da1b7d0bc4535b72a90dc5e51aa24d Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 15:52:50 +0100 Subject: [PATCH 16/42] delete abstract models --- app/Models/Bioschema/BioSample.php | 119 -------------- app/Models/Bioschema/Project.php | 253 ----------------------------- app/Models/Bioschema/Sample.php | 95 ----------- 3 files changed, 467 deletions(-) delete mode 100644 app/Models/Bioschema/BioSample.php delete mode 100644 app/Models/Bioschema/Project.php delete mode 100644 app/Models/Bioschema/Sample.php diff --git a/app/Models/Bioschema/BioSample.php b/app/Models/Bioschema/BioSample.php deleted file mode 100644 index 7d1e72e6..00000000 --- a/app/Models/Bioschema/BioSample.php +++ /dev/null @@ -1,119 +0,0 @@ -setProperty('additionalProperty', $additionalProperty); - } - - /** - * Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part. - * Inverse property: isPartOfBioChemEntity - * - * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[] $hasPart - * @return static - * - * @link http://www.w3.org/wiki/WebSchemas/SchemaDotOrgSources#source_bibex - */ - public function hasBioChemEntityPart($hasBioChemEntityPart) - { - return $this->setProperty('hasBioChemEntityPart', $hasBioChemEntityPart); - } - - /** - * An alias for the item. - * - * @param string|string[] $alternateName - * @return static - * - * @see https://schema.org/name - */ - public function alternateName($alternateName) - { - return $this->setProperty('alternateName', $alternateName); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The identifier property represents any kind of identifier for any kind of - * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides - * dedicated properties for representing many of these, either as textual - * strings or as URL (URI) links. See [background - * notes](/docs/datamodel.html#identifierBg) for more details. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier - * @return static - * - * @see https://schema.org/identifier - */ - public function identifier($identifier) - { - return $this->setProperty('identifier', $identifier); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } -} diff --git a/app/Models/Bioschema/Project.php b/app/Models/Bioschema/Project.php deleted file mode 100644 index a0b5631f..00000000 --- a/app/Models/Bioschema/Project.php +++ /dev/null @@ -1,253 +0,0 @@ -setProperty('author', $author); - } - - /** - * Date of first broadcast/publication. - * - * @param \DateTimeInterface|\DateTimeInterface[] $datePublished - * @return static - * - * @see https://schema.org/datePublished - */ - public function datePublished($datePublished) - { - return $this->setProperty('datePublished', $datePublished); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The identifier property represents any kind of identifier for any kind of - * [[Thing]], such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides - * dedicated properties for representing many of these, either as textual - * strings or as URL (URI) links. See [background - * notes](/docs/datamodel.html#identifierBg) for more details. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $identifier - * @return static - * - * @see https://schema.org/identifier - */ - public function identifier($identifier) - { - return $this->setProperty('identifier', $identifier); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } - - /** - * Define the domain of the study. For example, the domain could be astrophysics, - * functional genomics or earth science. Those domains can also have an ontology - * reference. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyDomain - * @return static - */ - public function projectDomain($projectDomain) - { - return $this->setProperty('projectDomain', $projectDomain); - } - - /** - * A subject of the study, i.e. one of the medical conditions, therapies, devices, - * drugs, etc. investigated by the study. - * - * @param \Spatie\SchemaOrg\Contracts\BioChemEntityContract|\Spatie\SchemaOrg\Contracts\MedicalEntityContract[] $studySubject - - * @return static - */ - public function projectSubject($projectSubject) - { - return $this->setProperty('projectSubject', $projectSubject); - } - - /** - * The subject matter of the content. - * - * @param \Spatie\SchemaOrg\Contracts\ThingContract|\Spatie\SchemaOrg\Contracts\ThingContract[] $about - * @return static - * - * @see https://schema.org/about - * @link https://github.com/schemaorg/schemaorg/issues/1670 - */ - public function about($about) - { - return $this->setProperty('about', $about); - } - - /** - * A property-value pair representing an additional characteristics of the - * entitity, e.g. a product feature or another characteristic for which there - * is no matching property in schema.org. Note: Publishers should be aware that - * applications designed to use specific schema.org properties (e.g. http://schema.org/width, - * http://schema.org/color, http://schema.org/gtin13, …) will typically expect - * such data to be provided using those properties, rather than using the generic - * property/value mechanism. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty - * @return static - * - * @see https://schema.org/additionalProperty - */ - public function additionalProperty($additionalProperty) - { - return $this->setProperty('additionalProperty', $additionalProperty); - } - - /** - * A citation or reference to another creative work, such as another - * publication, web page, scholarly article, etc. - * - * @param \Spatie\SchemaOrg\Contracts\CreativeWorkContract|\Spatie\SchemaOrg\Contracts\CreativeWorkContract[]|string|string[] $citation - * @return static - * - * @see https://schema.org/citation - */ - public function citation($citation) - { - return $this->setProperty('citation', $citation); - } - - /** - * The creator/author of this CreativeWork. This is the same as the Author - * property for CreativeWork. - * - * @param \Spatie\SchemaOrg\Contracts\OrganizationContract|\Spatie\SchemaOrg\Contracts\OrganizationContract[]|\Spatie\SchemaOrg\Contracts\PersonContract|\Spatie\SchemaOrg\Contracts\PersonContract[] $creator - * @return static - * - * @see https://schema.org/creator - */ - public function creator($creator) - { - return $this->setProperty('creator', $creator); - } - - /** - * The date on which the CreativeWork was created or the item was added to a - * DataFeed. - * - * @param \DateTimeInterface|\DateTimeInterface[] $dateCreated - * @return static - * - * @see https://schema.org/dateCreated - */ - public function dateCreated($dateCreated) - { - return $this->setProperty('dateCreated', $dateCreated); - } - - /** - * The end date and time of the item (in ISO 8601 date format). - * - * @param \DateTimeInterface|\DateTimeInterface[] $endDate - * @return static - * - * @see https://schema.org/endDate - */ - public function endDate($endDate) - { - return $this->setProperty('endDate', $endDate); - } - - /** - * The start date and time of the item (in ISO 8601 date format). - * - * @param \DateTimeInterface|\DateTimeInterface[] $startDate - * @return static - * - * @see https://schema.org/startDate - */ - public function startDate($startDate) - { - return $this->setProperty('startDate', $startDate); - } - - /** - * Keywords or tags used to describe some item. Multiple textual entries in - * a keywords list are typically delimited by commas, or by repeating the - * property. - * - * @param \Spatie\SchemaOrg\Contracts\DefinedTermContract|\Spatie\SchemaOrg\Contracts\DefinedTermContract[]|string|string[] $keywords - * @return static - * - * @see https://schema.org/keywords - */ - public function keywords($keywords) - { - return $this->setProperty('keywords', $keywords); - } - - /** - * TA process performed as part of an experiment or wider study, i.e. intentionally - * designed. These processes can have ontology URL attached to. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[]|string|string[] $studyProcess - * @return static - */ - public function studyProcess($studyProcess) - { - return $this->setProperty('studyProcess', $studyProcess); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } -} diff --git a/app/Models/Bioschema/Sample.php b/app/Models/Bioschema/Sample.php deleted file mode 100644 index 36837024..00000000 --- a/app/Models/Bioschema/Sample.php +++ /dev/null @@ -1,95 +0,0 @@ -setProperty('identifier', $identifier); - } - - /** - * URL of the item. - * - * @param string|string[] $url - * @return static - * - * @see https://schema.org/url - */ - public function url($url) - { - return $this->setProperty('url', $url); - } - - /** - * A property-value pair representing an additional characteristics of the - * entitity, e.g. a product feature or another characteristic for which there - * is no matching property in schema.org. Note: Publishers should be aware that - * applications designed to use specific schema.org properties (e.g. http://schema.org/width, - * http://schema.org/color, http://schema.org/gtin13, …) will typically expect - * such data to be provided using those properties, rather than using the generic - * property/value mechanism. - * - * @param \Spatie\SchemaOrg\Contracts\PropertyValueContract|\Spatie\SchemaOrg\Contracts\PropertyValueContract[] $additionalProperty - * @return static - * - * @see https://schema.org/additionalProperty - */ - public function additionalProperty($additionalProperty) - { - return $this->setProperty('additionalProperty', $additionalProperty); - } - - /** - * A description of the item. - * - * @param string|string[] $description - * @return static - * - * @see https://schema.org/description - */ - public function description($description) - { - return $this->setProperty('description', $description); - } - - /** - * The name of the item. - * - * @param string|string[] $name - * @return static - * - * @see https://schema.org/name - */ - public function name($name) - { - return $this->setProperty('name', $name); - } -} From ed3e18c5697c2365106dfb6cbb706bb72cf77510 Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Mon, 4 Dec 2023 16:27:50 +0100 Subject: [PATCH 17/42] fix: updating delete projects names to enable name reusing --- app/Actions/Project/DeleteProject.php | 1 + 1 file changed, 1 insertion(+) diff --git a/app/Actions/Project/DeleteProject.php b/app/Actions/Project/DeleteProject.php index 31e4997b..ac8a9670 100644 --- a/app/Actions/Project/DeleteProject.php +++ b/app/Actions/Project/DeleteProject.php @@ -37,6 +37,7 @@ public function delete($project) if ($draft) { $draft->update(['is_deleted' => true]); } + $project->name = $project->name.'- deleted'; $project->deleted_on = Carbon::now(); $project->is_deleted = true; $project->sendNotification('deletion', $this->prepareSendList($project)); From 5650ad2037fa774c26933606a97e00bef60768f4 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 17:23:06 +0100 Subject: [PATCH 18/42] refactor: use BioschemasHelper --- .../Bioschemas/BioschemasController.php | 275 ++---------------- .../Schemas/Bioschemas/BioschemasHelper.php | 269 +++++++++++++++++ .../Bioschemas/DataCatalogController.php | 59 ++-- app/Models/Bioschemas/Bioschemas.php | 2 +- routes/api.php | 4 +- 5 files changed, 330 insertions(+), 279 deletions(-) create mode 100644 app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php index f5e08568..d3eff5a9 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php @@ -14,6 +14,8 @@ use Illuminate\Http\Request; use Illuminate\Support\Facades\Http; use Spatie\SchemaOrg\Schema; +use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasHelper; + /** * Implement Bioschemas profiles types on nmrXiv project, study, and dataset @@ -112,151 +114,6 @@ public function modelSchemaByID(Request $request, $identifier) } } - /** - * Get Defined Term for ontology term. - * - * - * @param string $name - * @param array $alternameName - * @param string $identifier - * @param string $url - * @param object $inDefinedTermSet - * @return object $definedTerm - */ - public function getDefinedTerm($name, $alternateName, $identifier, $url, $inDefinedTermSet) - { - $definedTerm = Schema::DefinedTerm(); - $definedTerm->name($name); - $definedTerm->alternateName($alternateName); - $definedTerm->identifier($identifier); - $definedTerm->url($url); - $definedTerm->inDefinedTermSet($inDefinedTermSet); - - return $definedTerm; - } - - /** - * Get Defined Term set for ontology service. - * - * - * @param string $name - * @param string $url - * @return object $definedTermSet - */ - public function getDefinedTermSet($name, $url) - { - $definedTermSet = Schema::DefinedTermSet(); - $definedTermSet->name($name); - $definedTermSet->url($url); - - return $definedTermSet; - } - - /** - * Get Property value from ontologies. - * - * @param string $name - * @param string $ontologyID - * @param string $value - * @param string $unitUrl - * @return object $propertyValue - */ - public function getPropertyValue($name, $ontologyID, $value, $unitUrl) - { - $propertyValue = Schema::PropertyValue(); - $propertyValue->name($name); - $propertyValue->propertyID($ontologyID); - $propertyValue->value($value); - $propertyValue->unitCode($unitUrl); - - return $propertyValue; - } - - /** - * Create a list of all the schemas an object conforms to based on their urls. - * - * @link https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#conformsTo - * - * @param array $urls - * @return array $confromsToList - */ - public function conformsTo($urls) - { - $confromsToList = []; - foreach ($urls as &$url) { - $creativeWork = Schema::CreativeWork(); - $creativeWork['@id'] = $url; - $confromsTo = $creativeWork; - array_push($confromsToList, $confromsTo); - } - - return $confromsToList; - } - - /** - * Get the tags (keywords) of a model. - * - * @param object $model - * @return object $tags - */ - public function getTags($model) - { - $tags = []; - foreach ($model->tags as &$tag) { - $tag = $tag->name; - array_push($tags, $tag); - } - - return $tags; - } - - /** - * Implement Schemas' Person on a model's authors. - * - * @link https://schema.org/Person. - * - * @param object $model - * @return array $authors - */ - public function getAuthors($model) - { - $authors = []; - foreach ($model->authors as &$author) { - $authorSchema = Schema::Person(); - $authorSchema->givenName($author->given_name); - $authorSchema->familyName($author->family_name); - $authorSchema->identifier($author->orcid_id); - $authorSchema->email($author->email_id); - $authorSchema->affiliation($author->affiliation); - array_push($authors, $authorSchema); - } - - return $authors; - } - - /** - * Implement Schema' CreativeWork on a model's citations. - * - * @link https://schema.org/CreativeWork - * - * @param object $model - * @return array $citations - */ - public function getCitations($model) - { - $citations = []; - foreach ($model->citations as &$citation) { - $citationSchema = Schema::CreativeWork(); - $citationSchema->abstract($citation->abstract); - $citationSchema->author($citation->authors); - $citationSchema->headline($citation->title); - $citationSchema->identifier($citation->doi); - array_push($citations, $citationSchema); - } - - return $citations; - } - /** * Implement Bioschemas' MolecularEntity on molecules found in a sample. * @@ -277,7 +134,7 @@ public function getMolecules($sample) $moleculeSchema = Schema::MolecularEntity(); $moleculeSchema['@id'] = $inchiKey; - $moleculeSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); + $moleculeSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); $moleculeSchema['identifier'] = $inchiKey; $moleculeSchema->name($molecule->cas); $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); @@ -311,7 +168,7 @@ public function getSample($study) $sampleSchema = Bioschemas::ChemicalSubstance(); $sampleSchema['@id'] = $study->doi; - $sampleSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); + $sampleSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); $sampleSchema->name($study->project->name.'.'.$sample->name); $sampleSchema->description($sample->description); $sampleSchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]); @@ -328,27 +185,9 @@ public function getSample($study) * @param App\Models\Dataset $dataset * @return array $nmriumInfo */ - public function getNMRiumInfo($dataset) + public function prepareNMRiumInfo($dataset) { - $info = null; - $nmrium = $dataset->nmrium; - if (! $nmrium) { - $study = $dataset->study; - if ($study->nmrium) { - $NMRiumInfo = json_decode($study->nmrium->nmrium_info); - foreach ($NMRiumInfo->data->spectra as $spectra) { - $fileSource = $spectra->sourceSelector->files[0]; - $fileName = pathinfo($fileSource); - if ($fileName['basename'] == $dataset->fsObject->name) { - $info = $spectra->info; - } - } - } - } else { - $NMRiumInfo = json_decode($nmrium->nmrium_info); - $spectra = $NMRiumInfo->data->spectra[0]; - $info = $spectra->info; - } + $info = BioschemasHelper::getNMRiumInfo($dataset); if ($info) { $solvent = $info->solvent; $nucleus = $info->nucleus; @@ -367,19 +206,19 @@ public function getNMRiumInfo($dataset) $numberOfPoints = $info->numberOfPoints; $relaxationTime = $info->relaxationTime; - $solventProperty = $this->getPropertyValue('NMR solvent', 'NMR:1000330', $solvent, null); - $nucleusProperty = $this->getPropertyValue('acquisition nucleus', 'NMR:1400083', $nucleus, null); - $dimensionProperty = $this->getPropertyValue('NMR spectrum by dimensionality', 'NMR:1000117', $dimension, null); - $probeNameProperty = $this->getPropertyValue('NMR probe', 'OBI:0000516', $probeName, null); - $experimentProperty = $this->getPropertyValue('pulsed nuclear magnetic resonance spectroscopy', 'CHMO:0000613', $experiment, null); - $temperatureProperty = $this->getPropertyValue('Temperature', 'NCIT:C25206', $temperature, 'https://ontobee.org/ontology/UO?iri=http://purl.obolibrary.org/obo/UO_0000012'); - $baseFrequencyProperty = $this->getPropertyValue('irradiation frequency', 'NMR:1400026', $baseFrequency, 'http://purl.obolibrary.org/obo/UO_0000325'); - $fieldStrengthProperty = $this->getPropertyValue('magnetic field strength', 'MR:1400253', $fieldStrength, 'http://purl.obolibrary.org/obo/UO_0000228'); - $numberOfScansProperty = $this->getPropertyValue('number of scans', 'NMR:1400087', $numberOfScans, 'scans'); - $pulseSequenceProperty = $this->getPropertyValue('nuclear magnetic resonance pulse sequence', 'CHMO:0001841', $pulseSequence, null); - $spectralWidthProperty = $this->getPropertyValue('Spectral Width', 'NCIT:C156496', $spectralWidth, null); //todo: add unit - $numberOfPointsProperty = $this->getPropertyValue('number of data points', 'NMR:1000176', $numberOfPoints, 'points'); - $relaxationTimeProperty = $this->getPropertyValue('relaxation time measurement', 'FIX:0000202', $relaxationTime, 'http://purl.obolibrary.org/obo/UO_0000010'); + $solventProperty = BioschemasHelper::preparePropertyValue('NMR solvent', 'NMR:1000330', $solvent, null); + $nucleusProperty = BioschemasHelper::preparePropertyValue('acquisition nucleus', 'NMR:1400083', $nucleus, null); + $dimensionProperty = BioschemasHelper::preparePropertyValue('NMR spectrum by dimensionality', 'NMR:1000117', $dimension, null); + $probeNameProperty = BioschemasHelper::preparePropertyValue('NMR probe', 'OBI:0000516', $probeName, null); + $experimentProperty = BioschemasHelper::preparePropertyValue('pulsed nuclear magnetic resonance spectroscopy', 'CHMO:0000613', $experiment, null); + $temperatureProperty = BioschemasHelper::preparePropertyValue('Temperature', 'NCIT:C25206', $temperature, 'https://ontobee.org/ontology/UO?iri=http://purl.obolibrary.org/obo/UO_0000012'); + $baseFrequencyProperty = BioschemasHelper::preparePropertyValue('irradiation frequency', 'NMR:1400026', $baseFrequency, 'http://purl.obolibrary.org/obo/UO_0000325'); + $fieldStrengthProperty = BioschemasHelper::preparePropertyValue('magnetic field strength', 'MR:1400253', $fieldStrength, 'http://purl.obolibrary.org/obo/UO_0000228'); + $numberOfScansProperty = BioschemasHelper::preparePropertyValue('number of scans', 'NMR:1400087', $numberOfScans, 'scans'); + $pulseSequenceProperty = BioschemasHelper::preparePropertyValue('nuclear magnetic resonance pulse sequence', 'CHMO:0001841', $pulseSequence, null); + $spectralWidthProperty = BioschemasHelper::preparePropertyValue('Spectral Width', 'NCIT:C156496', $spectralWidth, null); //todo: add unit + $numberOfPointsProperty = BioschemasHelper::preparePropertyValue('number of data points', 'NMR:1000176', $numberOfPoints, 'points'); + $relaxationTimeProperty = BioschemasHelper::preparePropertyValue('relaxation time measurement', 'FIX:0000202', $relaxationTime, 'http://purl.obolibrary.org/obo/UO_0000010'); $keywords = [$solvent, $dimension.'D', $experiment]; foreach ($nucleus as $e) { @@ -392,46 +231,6 @@ public function getNMRiumInfo($dataset) } } - /** - * Get Dataset download details info from a dataset. - * - * @link https://schema.org/DataDownload - * - * @param App\Models\Dataset $dataset - * @return object $distribution - */ - public function getDistribution($dataset) - { - $url = env('APP_URL'); - $user = $dataset->owner; - $slug = $dataset->project->slug; - $contentURL = $url.'/'.$user.'/datasets/'.$slug; - - $distribution = Schema::DataDownload(); - $distribution->name($dataset->project->name); - $distribution->encodingFormat('zip'); - $distribution->contentURL($contentURL); - - return $distribution; - } - - /** - * Implement Bioschemas' DataCatalog with only few properties to be - * included in the dataset schema. - * - * @link https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01 - * - * @return object $dataCatalogSchema - */ - public function DataCatalogLite() - { - $dataCatalogSchema = Schema::DataCatalog(); - $dataCatalogSchema->name(env('APP_NAME')); - $dataCatalogSchema->url(env('APP_URL')); - - return $dataCatalogSchema; - } - /** * @@ -469,19 +268,7 @@ public function prepareDatasets($study) return $schemas; } - /** - * @link https://schema.org/organization - * - * @return object $publisher - */ - public function preparePublisher() - { - $publisher = Schema::Organization(); - $publisher->name(env('APP_NAME')); - $publisher->url(env('APP_URL')); - - return $publisher; - } + /** * Implement Bioschemas' Dataset. @@ -493,12 +280,12 @@ public function preparePublisher() */ public function datasetLite($dataset) { - $nmriumInfo = $this->getNMRiumInfo($dataset); + $nmriumInfo = $this->prepareNMRiumInfo($dataset); if ($nmriumInfo) { $prefix = $dataset->study->project->name.':'.$dataset->study->name.'.'; $datasetSchema = Schema::Dataset(); $datasetSchema['@id'] = $dataset->doi; - $datasetSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Dataset/1.0-RELEASE', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay']); + $datasetSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Dataset/1.0-RELEASE', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay']); $datasetSchema->name($prefix.$nmriumInfo[2]); $datasetSchema->description($dataset->description); $datasetSchema->keywords($nmriumInfo[0]); @@ -507,8 +294,8 @@ public function datasetLite($dataset) $datasetSchema->dateCreated($dataset->created_at); $datasetSchema->dateModified($dataset->updated_at); $datasetSchema->datePublished($dataset->release_date); - $datasetSchema->distribution($this->getDistribution($dataset)); - $datasetSchema->includedInDataCatalog($this->DataCatalogLite()); + $datasetSchema->distribution(BioschemasHelper::prepareDataDownload($dataset)); + $datasetSchema->includedInDataCatalog(BioschemasHelper::prepareDataCatalogLite()); $datasetSchema->measurementTechnique(env('MEASUREMENT_TECHNIQUE')); $datasetSchema->variableMeasured($nmriumInfo[1]); $datasetSchema->isAccessibleForFree(true); @@ -549,10 +336,10 @@ public function studyLite($study) $prefix = $study->project->name.':'; $studySchema = Bioschemas::Study(); $studySchema['@id'] = $study->doi; - $studySchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); + $studySchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); $studySchema->name($prefix.$study->name); $studySchema->description($study->description); - $studySchema->keywords($this->getTags($study)); + $studySchema->keywords(BioschemasHelper::getTags($study)); $studySchema->license($study->license->url); $studySchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]); $studySchema->dateCreated($study->created_at); @@ -595,18 +382,18 @@ public function projectLite($project) { $projectSchema = Bioschemas::Study(); $projectSchema['@id'] = $project->doi; - $projectSchema['dct:conformsTo'] = $this->conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); + $projectSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); $projectSchema->name($project->name); $projectSchema->description($project->description); - $projectSchema->keywords($this->getTags($project)); + $projectSchema->keywords(BioschemasHelper::getTags($project)); $projectSchema->license($project->license->url); - $projectSchema->publisher($this->preparePublisher()); + $projectSchema->publisher(BioschemasHelper::preparePublisher()); $projectSchema->url(env('APP_URL').'/'.explode(':', $project->identifier ? $project->identifier : ':')[1]); $projectSchema->dateCreated($project->created_at); $projectSchema->dateModified($project->updated_at); $projectSchema->datePublished($project->release_date); - $projectSchema->author($this->getAuthors($project)); - $projectSchema->citation($this->getCitations($project)); + $projectSchema->author(BioschemasHelper::prepareAuthors($project)); + $projectSchema->citation(BioschemasHelper::prepareCitations($project)); return $projectSchema; } diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php new file mode 100644 index 00000000..340774d3 --- /dev/null +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php @@ -0,0 +1,269 @@ +name($name); + $propertyValueSchema->propertyID($id); + $propertyValueSchema->value($value); + $propertyValueSchema->unitCode($unitUrl); + + return $propertyValueSchema; + } + + + /** + * Use Schema.org DefinedTerm type to represent terms from controlled vocabularies. + * + * @link https://schema.org/DefinedTerm + * + * @param string $name + * @param array $alternameName + * @param string $identifier + * @param string $url + * @param object $inDefinedTermSet + * @return object $definedTermSchema + */ + public static function prepareDefinedTerm($name, $alternateName, $identifier, $url, $inDefinedTermSet) + { + $definedTermSchema = Schema::DefinedTerm(); + $definedTermSchema->name($name); + $definedTermSchema->alternateName($alternateName); + $definedTermSchema->identifier($identifier); + $definedTermSchema->url($url); + $definedTermSchema->inDefinedTermSet($inDefinedTermSet); + + return $definedTermSchema; + } + + /** + * Use Schema.org DefinedTermSet type to represent controlled vocabularies. + * + * @link https://schema.org/DefinedTermSet + * + * @param string $name + * @param string $url + * @return object $definedTermSetSchema + */ + public static function prepareDefinedTermSet($name, $url) + { + $definedTermSetSchema = Schema::DefinedTermSet(); + $definedTermSetSchema->name($name); + $definedTermSetSchema->url($url); + + return $definedTermSetSchema; + } + + /** + * Use Schema.org Person type to represent a person. + * + * @link https://schema.org/Person + * + * @param string $id + * @param string $givenName + * @param string $familyName + * @param string $email + * @param string $affiliation + * + * @return object $personSchema + */ + public static function preparePerson($id, $givenName, $familyName, $email, $affiliation) + { + $personSchema = Schema::Person(); + $personSchema->identifier($id); + $personSchema->givenName($givenName); + $personSchema->familyName($familyName); + $personSchema->email($email); + $personSchema->affiliation($affiliation); + + return $personSchema; + } + + /** + * Use Schema.org Person type to represent the authors of a model. + * + * @link https://schema.org/Person. + * + * @param object $model + * @return array $authorsSchemas + */ + public static function prepareAuthors($model) + { + $helper = new self(); + $authorsSchemas = []; + foreach ($model->authors as &$author) { + $authorSchema = $helper->preparePerson($author->orcid_id, $author->given_name, $author->family_name, $author->email_id, $author->affiliation); + array_push($authorsSchemas, $authorSchema); + } + return $authorsSchemas; + } + + + /** + * Use Schema.org CreativeWork type to represent a model's citations. + * + * @link https://schema.org/CreativeWork + * + * @param object $model + * @return array $citationsSchemas + */ + public static function prepareCitations($model) + { + $citationsSchemas = []; + foreach ($model->citations as &$citation) { + $citationSchema = Schema::CreativeWork(); + $citationSchema->abstract($citation->abstract); + $citationSchema->author($citation->authors); + $citationSchema->headline($citation->title); + $citationSchema->identifier($citation->doi); + array_push($citationsSchemas, $citationSchema); + } + return $citationsSchemas; + } + + /** + * Use Schema.org DataDownload type to represent Dataset download details. + * + * @link https://schema.org/DataDownload + * + * @param App\Models\Dataset $dataset + * @return object $DataDownloadSchema + */ + public static function prepareDataDownload($dataset) + { + $url = env('APP_URL'); + $user = $dataset->owner; + $slug = $dataset->project->slug; + $contentURL = $url.'/'.$user.'/datasets/'.$slug; + + $DataDownloadSchema = Schema::DataDownload(); + $DataDownloadSchema->name($dataset->project->name); + $DataDownloadSchema->encodingFormat('zip'); + $DataDownloadSchema->contentURL($contentURL); + + return $DataDownloadSchema; + } + + /** + * Use Schema.org Organization type to represent nmrXiv as a publisher. + * + * @link https://schema.org/Organization + * + * @return object $publisherSchema + */ + public static function preparePublisher() + { + $publisherSchema = Schema::Organization(); + $publisherSchema->name(env('APP_NAME')); + $publisherSchema->url(env('APP_URL')); + + return $publisherSchema; + } + + + /** + * Use Schema.org DataCatalog type with only few properties to represent nmrXiv as the repository to be + * included in the dataset schema. + * + * @link https://schema.org/DataCatalog + * + * @return object $dataCatalogSchema + */ + public static function prepareDataCatalogLite() + { + $dataCatalogSchema = Schema::DataCatalog(); + $dataCatalogSchema->name(env('APP_NAME')); + $dataCatalogSchema->url(env('APP_URL')); + + return $dataCatalogSchema; + } + + /** + * Get NMRium info from a dataset. + * + * @param App\Models\Dataset $dataset + * @return object $info + */ + public static function getNMRiumInfo($dataset) + { + $info = null; + $nmrium = $dataset->nmrium; + if (! $nmrium) { + $study = $dataset->study; + if ($study->nmrium) { + $NMRiumInfo = json_decode($study->nmrium->nmrium_info); + foreach ($NMRiumInfo->data->spectra as $spectra) { + $fileSource = $spectra->sourceSelector->files[0]; + $fileName = pathinfo($fileSource); + if ($fileName['basename'] == $dataset->fsObject->name) { + $info = $spectra->info; + } + } + } + } else { + $NMRiumInfo = json_decode($nmrium->nmrium_info); + $spectra = $NMRiumInfo->data->spectra[0]; + $info = $spectra->info; + } + return $info; + } + + + + + /** + * Use Schema.org CreativeWork type to represent Schema.org and ISA types that an object conforms to. + * + * @link https://schema.org/CreativeWork + * + * @param array $urls + * @return array $confromsToList + */ + public static function conformsTo($urls) + { + $confromsToList = []; + foreach ($urls as &$url) { + $creativeWorkSchema = Schema::CreativeWork(); + $creativeWorkSchema['@id'] = $url; + array_push($confromsToList, $creativeWorkSchema); + } + return $confromsToList; + } + + /** + * Get the tags names (keywords) of a model. + * + * @param object $model + * @return object $tags + */ + public static function getTags($model) + { + $tags = []; + foreach ($model->tags as &$tag) { + $tag = $tag->name; + array_push($tags, $tag); + } + + return $tags; + } +} + diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php index 8fb99d58..96358883 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php @@ -6,28 +6,22 @@ use Illuminate\Http\Request; use Spatie\SchemaOrg\Schema; use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasHelper; - + /** - * Implement Bioschemas Data Catalog type on nmrXiv as a repository to enable exporting - * its metadata with a json endpoint. + * Use Schema.org DataCatalog type to represent nmrXiv as a repository. */ class DataCatalogController extends Controller { /** - * Implement Bioschemas Data Catalog type on nmrXiv as a repository. + * Use Schema.org DataCatalog type to represent nmrXiv as a repository. * - * @link https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01 + * @link https://schema.org/DataCatalog * * @param Illuminate\Http\Request $request * @return object $dataCatalog */ public function dataCatalogSchema(Request $request) { - $creativeWork = Schema::CreativeWork(); - $creativeWork['@id'] = 'https://schema.org/DataCatalog"'; - - $confromsTo = $creativeWork; - $keywords = $this->prepareKeywords(); $contributors = $this->prepareContributors(); @@ -37,7 +31,7 @@ public function dataCatalogSchema(Request $request) $dataCatalog = Schema::DataCatalog(); $dataCatalog['@id'] = url(env('APP_URL')); - $dataCatalog['dct:conformsTo'] = $confromsTo; + $dataCatalog['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://schema.org/DataCatalog']); $dataCatalog->description(env('APP_DESCRIPTION')); $dataCatalog->keywords($keywords); $dataCatalog->name(env('APP_NAME')); @@ -91,27 +85,28 @@ public function prepareKeywords() */ public function prepareContributors() { - $Annett = BioschemasHelper::preparePerson('0000-0002-2542-0867', 'Annett', 'Schröter'); - $Christian = BioschemasHelper::preparePerson(null, 'Christian', 'Popp'); - $Christoph = BioschemasHelper::preparePerson('0000-0001-6966-0814', 'Christoph', 'Steinbeck'); - $Darina = BioschemasHelper::preparePerson(null, 'Darina', 'Storozhuk'); - $David = BioschemasHelper::preparePerson('0000-0001-7499-1693', 'David', 'Rauh'); - $Guido = BioschemasHelper::preparePerson('0000-0003-1022-4326', 'Guido', 'Pauli'); - $Hamed = BioschemasHelper::preparePerson(null, 'Hamed', 'Musallam'); - $Johannes = BioschemasHelper::preparePerson('0000-0003-2060-842X', 'Johannes', 'Liermann'); - $Julien = BioschemasHelper::preparePerson('0000-0002-3416-2572', 'Julien', 'Wist'); - $Kohulan = BioschemasHelper::preparePerson('0000-0003-1066-7792', 'Kohulan', 'Rajan'); - $Luc = BioschemasHelper::preparePerson('0000-0002-4943-2643', 'Luc', 'Patiny'); - $Markus = BioschemasHelper::preparePerson(null, 'Markus', 'Lange'); - $Nazar = BioschemasHelper::preparePerson('0000-0002-5870-8496', 'Nazar', 'Stefaniuk'); - $Nils = BioschemasHelper::preparePerson('0000-0002-0990-9582', 'Nils', 'Schlörer'); - $Nisha = BioschemasHelper::preparePerson('0009-0006-4755-1039', 'Nisha', 'Sharma'); - $Noura = BioschemasHelper::preparePerson('0009-0001-5998-5030', 'Noura', 'Rayya'); - $Pascal = BioschemasHelper::preparePerson(null, 'Pascal', 'Scherreiks'); - $Stefan = BioschemasHelper::preparePerson('0000-0002-5990-4157', 'Stefan', 'Kuhn'); - $Steffen = BioschemasHelper::preparePerson('0000-0002-7899-7192', 'Steffen', 'Neumann'); - $Tillmann = BioschemasHelper::preparePerson('0000-0003-4480-8661', 'Tillmann', 'Fischer'); - $Venkata = BioschemasHelper::preparePerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala'); + + $Annett = BioschemasHelper::preparePerson('0000-0002-2542-0867', 'Annett', 'Schröter', 'annett.schroeter@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $Christian = BioschemasHelper::preparePerson(null, 'Christian', 'Popp', null, null); + $Christoph = BioschemasHelper::preparePerson('0000-0001-6966-0814', 'Christoph', 'Steinbeck', 'christoph.steinbeck@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $Darina = BioschemasHelper::preparePerson(null, 'Darina', 'Storozhuk', 'darina.storozhuk@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $David = BioschemasHelper::preparePerson('0000-0001-7499-1693', 'David', 'Rauh', null, null); + $Guido = BioschemasHelper::preparePerson('0000-0003-1022-4326', 'Guido', 'Pauli', null, 'University of Illinois'); + $Hamed = BioschemasHelper::preparePerson(null, 'Hamed', 'Musallam', 'hamed.musallam@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $Johannes = BioschemasHelper::preparePerson('0000-0003-2060-842X', 'Johannes', 'Liermann', null, null); + $Julien = BioschemasHelper::preparePerson('0000-0002-3416-2572', 'Julien', 'Wist', null, null); + $Kohulan = BioschemasHelper::preparePerson('0000-0003-1066-7792', 'Kohulan', 'Rajan', null, null); + $Luc = BioschemasHelper::preparePerson('0000-0002-4943-2643', 'Luc', 'Patiny', null, null); + $Markus = BioschemasHelper::preparePerson(null, 'Markus', 'Lange', null, null); + $Nazar = BioschemasHelper::preparePerson('0000-0002-5870-8496', 'Nazar', 'Stefaniuk', null, null); + $Nils = BioschemasHelper::preparePerson('0000-0002-0990-9582', 'Nils', 'Schlörer', null, null); + $Nisha = BioschemasHelper::preparePerson('0009-0006-4755-1039', 'Nisha', 'Sharma', null, null); + $Noura = BioschemasHelper::preparePerson('0009-0001-5998-5030', 'Noura', 'Rayya', null, null); + $Pascal = BioschemasHelper::preparePerson(null, 'Pascal', 'Scherreiks', null, null); + $Stefan = BioschemasHelper::preparePerson('0000-0002-5990-4157', 'Stefan', 'Kuhn', null, null); + $Steffen = BioschemasHelper::preparePerson('0000-0002-7899-7192', 'Steffen', 'Neumann', null, null); + $Tillmann = BioschemasHelper::preparePerson('0000-0003-4480-8661', 'Tillmann', 'Fischer', null, null); + $Venkata = BioschemasHelper::preparePerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala', null, null); $contributors = [$Annett, $Christian, $Christoph, $Darina, $Guido, $Hamed, $Johannes, $Julien, $Kohulan, $Luc, $Markus, $Nazar, $Nils, $Nisha, $Noura, $Pascal, $Stefan, $Steffen, $Tillmann, $Venkata]; diff --git a/app/Models/Bioschemas/Bioschemas.php b/app/Models/Bioschemas/Bioschemas.php index 46fc3328..519e78eb 100644 --- a/app/Models/Bioschemas/Bioschemas.php +++ b/app/Models/Bioschemas/Bioschemas.php @@ -7,7 +7,7 @@ /** * Factory class for all Schema.org types. */ -class Bioschema extends Schema +class Bioschemas extends Schema { public static function study(): Study { diff --git a/routes/api.php b/routes/api.php index e52eccde..60b1e734 100644 --- a/routes/api.php +++ b/routes/api.php @@ -42,8 +42,8 @@ Route::prefix('schemas')->group(function () { Route::prefix('bioschemas')->group(function () { Route::get('/', [DataCatalogController::class, 'dataCatalogSchema'])->name('bioschemas.datacatalog'); - Route::get('/{username}/{project}/{study?}/{dataset?}', [BiochemaController::class, 'modelSchemaByName'])->name('bioschemas.model'); - Route::get('/{id}', [BiochemaController::class, 'modelSchemaByID'])->name('bioschemas.id'); + Route::get('/{username}/{project}/{study?}/{dataset?}', [BioschemasController::class, 'modelSchemaByName'])->name('bioschemas.model'); + Route::get('/{id}', [BioschemasController::class, 'modelSchemaByID'])->name('bioschemas.id'); }); Route::prefix('datacite')->group(function () { From de5b810bf4c6a8373a910353f442a516f1b0a510 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 17:40:04 +0100 Subject: [PATCH 19/42] update contributors details --- .../Bioschemas/DataCatalogController.php | 62 +++++++++---------- 1 file changed, 30 insertions(+), 32 deletions(-) diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php index 96358883..d384a86b 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php @@ -18,7 +18,7 @@ class DataCatalogController extends Controller * @link https://schema.org/DataCatalog * * @param Illuminate\Http\Request $request - * @return object $dataCatalog + * @return object $dataCatalogSchema */ public function dataCatalogSchema(Request $request) { @@ -29,37 +29,36 @@ public function dataCatalogSchema(Request $request) $nmrXivProvider->name(env('NMRXIV_PROVIDER')); $nmrXivProvider->url(env('NMRXIV_PROVIDER_URL')); - $dataCatalog = Schema::DataCatalog(); - $dataCatalog['@id'] = url(env('APP_URL')); - $dataCatalog['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://schema.org/DataCatalog']); - $dataCatalog->description(env('APP_DESCRIPTION')); - $dataCatalog->keywords($keywords); - $dataCatalog->name(env('APP_NAME')); - $dataCatalog->provider($nmrXivProvider); - $dataCatalog->url(env('APP_URL')); - $dataCatalog->identifier(env('APP_URL')); - $dataCatalog->license('https://mit-license.org/'); - $dataCatalog->contributor($contributors); - $dataCatalog->isAccessibleForFree(true); + $dataCatalogSchema = Schema::DataCatalog(); + $dataCatalogSchema['@id'] = url(env('APP_URL')); + $dataCatalogSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://schema.org/DataCatalog']); + $dataCatalogSchema->description(env('APP_DESCRIPTION')); + $dataCatalogSchema->keywords($keywords); + $dataCatalogSchema->name(env('APP_NAME')); + $dataCatalogSchema->provider($nmrXivProvider); + $dataCatalogSchema->url(env('APP_URL')); + $dataCatalogSchema->identifier(env('APP_URL')); + $dataCatalogSchema->license('https://mit-license.org/'); + $dataCatalogSchema->contributor($contributors); + $dataCatalogSchema->isAccessibleForFree(true); - $dataCatalog->measurementTechnique(env('MEASUREMENT_TECHNIQUE')); + $dataCatalogSchema->measurementTechnique(env('MEASUREMENT_TECHNIQUE')); - return $dataCatalog; + return $dataCatalogSchema; } /** - * Prepare Keywords. + * Prepare keywords associated with nmrXiv. * - * @param null * @return array $keywords */ public function prepareKeywords() { - //Prepare Defined Term Set + //Prepare Defined Term Sets $chmo = BioschemasHelper::prepareDefinedTermSet('Chemical Methods Ontology', 'http://purl.obolibrary.org/obo/chmo.owl'); $nmrcv = BioschemasHelper::prepareDefinedTermSet('nuclear magnetic resonance CV', 'http://nmrml.org/cv/'); - //Prepare Defined Term + //Prepare Defined Terms $nmr = BioschemasHelper::prepareDefinedTerm('nuclear magnetic resonance spectroscopy', ['NMR', 'NMR spectroscopy', 'nuclear magnetic resonance (NMR) spectroscopy'], 'CHMO:0000591', 'http://purl.obolibrary.org/obo/CHMO_0000591', $chmo); $pulsedNMR = BioschemasHelper::prepareDefinedTerm('pulsed nuclear magnetic resonance spectroscopy', ['NMR', 'nuclear magnetic resonance spectroscopy', 'NMR spectroscopy'], 'CHMO:0000613', 'https://ontobee.org/ontology/CHMO?iri=http://purl.obolibrary.org/obo/CHMO_0000613', $chmo); $oneDNMR = BioschemasHelper::prepareDefinedTerm('one-dimensional nuclear magnetic resonance spectroscopy', ['1D NMR spectroscopy', '1-D NMR', 'one-dimensional nuclear magnetic resonance spectroscopy', '1D NMR', '1D nuclear magnetic resonance spectroscopy'], 'CHMO:0000592', 'http://purl.obolibrary.org/obo/CHMO_0000592', $chmo); @@ -78,9 +77,8 @@ public function prepareKeywords() } /** - * Prepare Contributors. + * Prepare contributors to nmrXiv. * - * @param null * @return array $contributors */ public function prepareContributors() @@ -93,20 +91,20 @@ public function prepareContributors() $David = BioschemasHelper::preparePerson('0000-0001-7499-1693', 'David', 'Rauh', null, null); $Guido = BioschemasHelper::preparePerson('0000-0003-1022-4326', 'Guido', 'Pauli', null, 'University of Illinois'); $Hamed = BioschemasHelper::preparePerson(null, 'Hamed', 'Musallam', 'hamed.musallam@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); - $Johannes = BioschemasHelper::preparePerson('0000-0003-2060-842X', 'Johannes', 'Liermann', null, null); - $Julien = BioschemasHelper::preparePerson('0000-0002-3416-2572', 'Julien', 'Wist', null, null); - $Kohulan = BioschemasHelper::preparePerson('0000-0003-1066-7792', 'Kohulan', 'Rajan', null, null); - $Luc = BioschemasHelper::preparePerson('0000-0002-4943-2643', 'Luc', 'Patiny', null, null); + $Johannes = BioschemasHelper::preparePerson('0000-0003-2060-842X', 'Johannes', 'Liermann', 'liermann@uni-mainz.de', 'Johannes Gutenberg-Universität Mainz'); + $Julien = BioschemasHelper::preparePerson('0000-0002-3416-2572', 'Julien', 'Wist', null, 'Murdoch University: Murdoch, WA, AU'); + $Kohulan = BioschemasHelper::preparePerson('0000-0003-1066-7792', 'Kohulan', 'Rajan', 'kohulan.rajan@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $Luc = BioschemasHelper::preparePerson('0000-0002-4943-2643', 'Luc', 'Patiny', null, 'École Polytechnique Fédérale de Lausanne: Lausanne, VD, CH'); $Markus = BioschemasHelper::preparePerson(null, 'Markus', 'Lange', null, null); $Nazar = BioschemasHelper::preparePerson('0000-0002-5870-8496', 'Nazar', 'Stefaniuk', null, null); - $Nils = BioschemasHelper::preparePerson('0000-0002-0990-9582', 'Nils', 'Schlörer', null, null); - $Nisha = BioschemasHelper::preparePerson('0009-0006-4755-1039', 'Nisha', 'Sharma', null, null); - $Noura = BioschemasHelper::preparePerson('0009-0001-5998-5030', 'Noura', 'Rayya', null, null); + $Nils = BioschemasHelper::preparePerson('0000-0002-0990-9582', 'Nils', 'Schlörer', null, 'Friedrich-Schiller-Universität Jena'); + $Nisha = BioschemasHelper::preparePerson('0009-0006-4755-1039', 'Nisha', 'Sharma', 'nisha.sharma@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); + $Noura = BioschemasHelper::preparePerson('0009-0001-5998-5030', 'Noura', 'Rayya', 'noura.rayya@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); $Pascal = BioschemasHelper::preparePerson(null, 'Pascal', 'Scherreiks', null, null); - $Stefan = BioschemasHelper::preparePerson('0000-0002-5990-4157', 'Stefan', 'Kuhn', null, null); - $Steffen = BioschemasHelper::preparePerson('0000-0002-7899-7192', 'Steffen', 'Neumann', null, null); - $Tillmann = BioschemasHelper::preparePerson('0000-0003-4480-8661', 'Tillmann', 'Fischer', null, null); - $Venkata = BioschemasHelper::preparePerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala', null, null); + $Stefan = BioschemasHelper::preparePerson('0000-0002-5990-4157', 'Stefan', 'Kuhn', null, 'University of Tartu, Tartu'); + $Steffen = BioschemasHelper::preparePerson('0000-0002-7899-7192', 'Steffen', 'Neumann', null, 'Leibniz-Institut für Pflanzenbiochemie, Halle'); + $Tillmann = BioschemasHelper::preparePerson('0000-0003-4480-8661', 'Tillmann', 'Fischer', null, 'Leibniz-Institut für Pflanzenbiochemie, Halle'); + $Venkata = BioschemasHelper::preparePerson('0000-0002-2564-3243', 'Venkata Chandrasekhar', 'Nainala', 'chandu.nainala@uni-jena.de', 'Friedrich-Schiller-Universität Jena'); $contributors = [$Annett, $Christian, $Christoph, $Darina, $Guido, $Hamed, $Johannes, $Julien, $Kohulan, $Luc, $Markus, $Nazar, $Nils, $Nisha, $Noura, $Pascal, $Stefan, $Steffen, $Tillmann, $Venkata]; From af4f77fc01de01ffcee4fc9979839780297d3839 Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 21:28:19 +0100 Subject: [PATCH 20/42] update code documentation --- .../Bioschemas/BioschemasController.php | 132 +++++++++--------- .../Schemas/Bioschemas/BioschemasHelper.php | 32 ++--- .../Bioschemas/DataCatalogController.php | 5 +- 3 files changed, 81 insertions(+), 88 deletions(-) diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php index d3eff5a9..ad85e33e 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasController.php @@ -14,21 +14,18 @@ use Illuminate\Http\Request; use Illuminate\Support\Facades\Http; use Spatie\SchemaOrg\Schema; -use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasHelper; - /** - * Implement Bioschemas profiles types on nmrXiv project, study, and dataset - * to enable exporting their metadata with a json endpoint, including the - * samples and molecules. + * Implement Bioschemas types on nmrXiv project, study, and dataset, including the + * samples and molecules details. */ class BioschemasController extends Controller { /** * Implement Bioschemas upon request by model's name to generate a project, study, or dataset schema. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * @link https://bioschemas.org/types/Study/0.3-DRAFT + * @link https://schema.org/Dataset * * @param Illuminate\Http\Request $request * @param App\Models\User $username @@ -79,10 +76,10 @@ public function modelSchemaByName(Request $request, $username, $projectName, $st } /** - * Implement Bioschemas upon request by model id to generate a project, study, or dataset schema. + * Implement Bioschemas upon request by model's id to generate a project, study, or dataset schema. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * @link https://bioschemas.org/types/Study/0.3-DRAFT + * @link https://schema.org/Dataset * * @param Illuminate\Http\Request $request * @param string $identifier @@ -99,32 +96,35 @@ public function modelSchemaByID(Request $request, $identifier) $projectSchema = $this->project($model); return $projectSchema; + } elseif ($namespace == 'Study') { $studySchema = $this->study($model); return $studySchema; - } elseif ($namespace == 'Dataset') { + } elseif ($namespace == 'Dataset') { $datasetSchema = $this->dataset($model); return $datasetSchema; } + } else { throw new AuthorizationException; } } /** - * Implement Bioschemas' MolecularEntity on molecules found in a sample. + * Use Bioschemas MolecularEntity type to represent molecules found in a sample. * - * @link https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE + * @link https://bioschemas.org/types/MolecularEntity/0.3-RELEASE-2019_09_02 * * @param App\Models\Sample $sample - * @return array $molecules + * @return array $moleculesSchemas */ - public function getMolecules($sample) + public function prepareMoleculesSchemas($sample) { - $molecules = []; + $moleculesSchemas = []; + foreach ($sample->molecules as &$molecule) { $inchiKey = $molecule->inchi_key; $pubchemLink = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/'.$inchiKey.'/property/IUPACName/JSON'; @@ -134,7 +134,7 @@ public function getMolecules($sample) $moleculeSchema = Schema::MolecularEntity(); $moleculeSchema['@id'] = $inchiKey; - $moleculeSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE']); + $moleculeSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/MolecularEntity/0.3-RELEASE-2019_09_02']); $moleculeSchema['identifier'] = $inchiKey; $moleculeSchema->name($molecule->cas); $moleculeSchema->url('https://pubchem.ncbi.nlm.nih.gov/compound/'.$cid); @@ -146,17 +146,17 @@ public function getMolecules($sample) $moleculeSchema->smiles([$molecule->SMILES, $molecule->absolute_smiles, $molecule->canonical_smiles]); $moleculeSchema->hasRepresentation($molecule->MOL); $moleculeSchema->description('Percentage composition: '.$molecule->pivot->percentage_composition.'%'); - array_push($molecules, $moleculeSchema); + array_push($moleculesSchemas, $moleculeSchema); } - return $molecules; + return $moleculesSchemas; } /** - * Implement Bioschemas' ChemicalSubstance on samples found in studies. + * Use Bioschemas ChemicalSubstance type to represent samples found in studies. * - * @link https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/ChemicalSubstance/0.3-RELEASE-2019_09_02 + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Study $study * @return object $sampleSchema @@ -164,26 +164,24 @@ public function getMolecules($sample) public function getSample($study) { $sample = $study->sample; - $molecules = $this->getMolecules($sample); + $molecules = $this->prepareMoleculesSchemas($sample); - $sampleSchema = Bioschemas::ChemicalSubstance(); + $sampleSchema = Schema::ChemicalSubstance(); $sampleSchema['@id'] = $study->doi; - $sampleSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/ChemicalSubstance/0.4-RELEASE']); + $sampleSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/ChemicalSubstance/0.3-RELEASE-2019_09_02']); $sampleSchema->name($study->project->name.'.'.$sample->name); $sampleSchema->description($sample->description); $sampleSchema->url(env('APP_URL').'/'.explode(':', $study->identifier ? $study->identifier : ':')[1]); - $sampleSchema->hasBioChemEntityPart($this->getMolecules($sample)); + $sampleSchema->hasBioChemEntityPart($this->prepareMoleculesSchemas($sample)); return $sampleSchema; } /** - * Get NMRium info from a dataset. - * - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * Represent NMRium info as PropertyValue schemas. * * @param App\Models\Dataset $dataset - * @return array $nmriumInfo + * @return array $array */ public function prepareNMRiumInfo($dataset) { @@ -221,59 +219,61 @@ public function prepareNMRiumInfo($dataset) $relaxationTimeProperty = BioschemasHelper::preparePropertyValue('relaxation time measurement', 'FIX:0000202', $relaxationTime, 'http://purl.obolibrary.org/obo/UO_0000010'); $keywords = [$solvent, $dimension.'D', $experiment]; - foreach ($nucleus as $e) { - array_push($keywords, $e); + foreach ($nucleus as $keyword) { + array_push($keywords, $keyword); } $variables = [$solventProperty, $nucleusProperty, $dimensionProperty, $probeNameProperty, $experimentProperty, $temperatureProperty, $baseFrequencyProperty, $fieldStrengthProperty, $numberOfScansProperty, $pulseSequenceProperty, $spectralWidthProperty, $numberOfPointsProperty, $relaxationTimeProperty, ]; - return [$keywords, $variables, $experiment]; + $array = [$keywords, $variables, $experiment]; + + return $array; } } /** - + * Use Bioschemas Study type to represent studies found in a project with their datasets. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Project $project - * @return array $schemas + * @return array $studiesSchemas */ public function prepareStudies($project) { - $schemas = []; + $studiesSchemas = []; foreach ($project->studies as $study) { $studySchema = $this->studyLite($study); $studySchema->hasPart($this->prepareDatasets($study)); - array_push($schemas, $studySchema); + array_push($studiesSchemas, $studySchema); } - return $schemas; + return $studiesSchemas; } /** - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * Use Schema.org Dataset type to represent datasets found in a study. + * + * @link https://schema.org/Dataset * * @param App\Models\Study $study - * @return array $schemas + * @return array $datasetsSchemas */ public function prepareDatasets($study) { - $schemas = []; + $datasetsSchemas = []; foreach ($study->datasets as $dataset) { $datasetSchema = $this->datasetLite($dataset); - array_push($schemas, $datasetSchema); + array_push($datasetsSchemas, $datasetSchema); } - return $schemas; + return $datasetsSchemas; } - - /** - * Implement Bioschemas' Dataset. + * Use Schema.org Dataset type to represent an nmrXiv dataset without its relations. * - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE + * @link https://schema.org/Dataset * * @param App\Models\Dataset $dataset * @return object $datasetSchema @@ -285,7 +285,7 @@ public function datasetLite($dataset) $prefix = $dataset->study->project->name.':'.$dataset->study->name.'.'; $datasetSchema = Schema::Dataset(); $datasetSchema['@id'] = $dataset->doi; - $datasetSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Dataset/1.0-RELEASE', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay']); + $datasetSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://schema.org/Dataset', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay']); $datasetSchema->name($prefix.$nmriumInfo[2]); $datasetSchema->description($dataset->description); $datasetSchema->keywords($nmriumInfo[0]); @@ -303,20 +303,22 @@ public function datasetLite($dataset) return $datasetSchema; } } + /** - * Implement Bioschemas' Dataset, along with the project and study it belongs to. + * Use Schema.org Dataset type to represent an nmrXiv dataset with its relations. * - * @link https://bioschemas.org/profiles/Dataset/1.0-RELEASE - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://schema.org/Dataset + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Dataset $dataset * @return object $datasetSchema */ public function dataset($dataset) { - $datasetSchema = $this->datasetLite($dataset); $projectSchema = $this->projectLite($dataset->project); $studySchema = $this->studyLite($dataset->study); + $datasetSchema = $this->datasetLite($dataset); + $studySchema->isPartOf($projectSchema); $datasetSchema->isPartOf($studySchema); @@ -324,9 +326,9 @@ public function dataset($dataset) } /** - * Implement Bioschemas' Study. + * Use Bioschemas Study type to represent an nmrXiv study without its relations. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Study $study * @return object $studySchema @@ -336,7 +338,7 @@ public function studyLite($study) $prefix = $study->project->name.':'; $studySchema = Bioschemas::Study(); $studySchema['@id'] = $study->doi; - $studySchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); + $studySchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#study']); $studySchema->name($prefix.$study->name); $studySchema->description($study->description); $studySchema->keywords(BioschemasHelper::getTags($study)); @@ -351,12 +353,11 @@ public function studyLite($study) return $studySchema; } - + /** - * Implement Bioschemas' Study, including the sample and molecules, along - * with the project it belongs to and, briefly, the datasets it contains. + * Use Bioschemas Study type to represent an nmrXiv study with its relations. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Study $study * @return object $studySchema @@ -371,9 +372,9 @@ public function study($study) } /** - * Implement Bioschemas' project. + * Use Bioschemas Study type to represent an nmrXiv project without its relations. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Project $project * @return object $projectSchema @@ -382,7 +383,7 @@ public function projectLite($project) { $projectSchema = Bioschemas::Study(); $projectSchema['@id'] = $project->doi; - $projectSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/profiles/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); + $projectSchema['dct:conformsTo'] = BioschemasHelper::conformsTo(['https://bioschemas.org/types/Study/0.3-DRAFT', 'https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation']); $projectSchema->name($project->name); $projectSchema->description($project->description); $projectSchema->keywords(BioschemasHelper::getTags($project)); @@ -399,10 +400,9 @@ public function projectLite($project) } /** - * Implement Bioschemas' project along with brief details about - * the studies and datasets it contains. + * Use Bioschemas Study type to represent an nmrXiv project with its relations. * - * @link https://bioschemas.org/profiles/Study/0.3-DRAFT + * @link https://bioschemas.org/types/Study/0.3-DRAFT * * @param App\Models\Project $project * @return object $projectSchema diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php index 340774d3..e16cf2fa 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/BioschemasHelper.php @@ -4,15 +4,13 @@ use Spatie\SchemaOrg\Schema; - - class BioschemasHelper { /** * Use Schema.org PropertyValue type to represent terms from controlled vocabularies. * * @link https://schema.org/PropertyValue - * + * * @param string $name * @param string $id * @param string $value @@ -30,12 +28,11 @@ public static function preparePropertyValue($name, $id, $value, $unitUrl) return $propertyValueSchema; } - /** * Use Schema.org DefinedTerm type to represent terms from controlled vocabularies. * * @link https://schema.org/DefinedTerm - * + * * @param string $name * @param array $alternameName * @param string $identifier @@ -53,7 +50,7 @@ public static function prepareDefinedTerm($name, $alternateName, $identifier, $u $definedTermSchema->inDefinedTermSet($inDefinedTermSet); return $definedTermSchema; - } + } /** * Use Schema.org DefinedTermSet type to represent controlled vocabularies. @@ -77,13 +74,12 @@ public static function prepareDefinedTermSet($name, $url) * Use Schema.org Person type to represent a person. * * @link https://schema.org/Person - * + * * @param string $id * @param string $givenName * @param string $familyName * @param string $email * @param string $affiliation - * * @return object $personSchema */ public static function preparePerson($id, $givenName, $familyName, $email, $affiliation) @@ -97,8 +93,8 @@ public static function preparePerson($id, $givenName, $familyName, $email, $affi return $personSchema; } - - /** + + /** * Use Schema.org Person type to represent the authors of a model. * * @link https://schema.org/Person. @@ -107,17 +103,17 @@ public static function preparePerson($id, $givenName, $familyName, $email, $affi * @return array $authorsSchemas */ public static function prepareAuthors($model) - { + { $helper = new self(); $authorsSchemas = []; foreach ($model->authors as &$author) { $authorSchema = $helper->preparePerson($author->orcid_id, $author->given_name, $author->family_name, $author->email_id, $author->affiliation); array_push($authorsSchemas, $authorSchema); } + return $authorsSchemas; } - /** * Use Schema.org CreativeWork type to represent a model's citations. * @@ -137,6 +133,7 @@ public static function prepareCitations($model) $citationSchema->identifier($citation->doi); array_push($citationsSchemas, $citationSchema); } + return $citationsSchemas; } @@ -165,7 +162,7 @@ public static function prepareDataDownload($dataset) /** * Use Schema.org Organization type to represent nmrXiv as a publisher. - * + * * @link https://schema.org/Organization * * @return object $publisherSchema @@ -179,7 +176,6 @@ public static function preparePublisher() return $publisherSchema; } - /** * Use Schema.org DataCatalog type with only few properties to represent nmrXiv as the repository to be * included in the dataset schema. @@ -199,7 +195,7 @@ public static function prepareDataCatalogLite() /** * Get NMRium info from a dataset. - * + * * @param App\Models\Dataset $dataset * @return object $info */ @@ -224,12 +220,10 @@ public static function getNMRiumInfo($dataset) $spectra = $NMRiumInfo->data->spectra[0]; $info = $spectra->info; } + return $info; } - - - /** * Use Schema.org CreativeWork type to represent Schema.org and ISA types that an object conforms to. * @@ -246,6 +240,7 @@ public static function conformsTo($urls) $creativeWorkSchema['@id'] = $url; array_push($confromsToList, $creativeWorkSchema); } + return $confromsToList; } @@ -266,4 +261,3 @@ public static function getTags($model) return $tags; } } - diff --git a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php index d384a86b..ddb80805 100644 --- a/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php +++ b/app/Http/Controllers/API/Schemas/Bioschemas/DataCatalogController.php @@ -5,10 +5,9 @@ use App\Http\Controllers\Controller; use Illuminate\Http\Request; use Spatie\SchemaOrg\Schema; -use App\Http\Controllers\API\Schemas\Bioschemas\BioschemasHelper; - + /** - * Use Schema.org DataCatalog type to represent nmrXiv as a repository. + * Use Schema.org DataCatalog type to represent nmrXiv as a repository. */ class DataCatalogController extends Controller { From 68c26798a54f881fd3d656fac99ce4814aa37ecf Mon Sep 17 00:00:00 2001 From: NRayya <82588017+NRayya@users.noreply.github.com> Date: Mon, 4 Dec 2023 23:19:35 +0100 Subject: [PATCH 21/42] docs: revisit and review data schemas Fixes #943 --- docs/introduction/data/schemas.md | 53 +++++++++++++++++-------------- 1 file changed, 29 insertions(+), 24 deletions(-) diff --git a/docs/introduction/data/schemas.md b/docs/introduction/data/schemas.md index 51b5f829..a29f3534 100644 --- a/docs/introduction/data/schemas.md +++ b/docs/introduction/data/schemas.md @@ -1,50 +1,55 @@ # Data Schemas -Data schemas enable structuring the data in a well-designed form by providing precise definitions of entities with relations among them. Additionally, they enable data indexing and feasible metadata export making those schema a valuable asset to improve data findability on the web, and to enhance machine-readability and data analysis, especially when considering that many of the available schemas support ontologies usage by accepting/requesting values to be provided as ontology terms and providing links and identifiers to the terms. +Data schemas play a crucial role in organizing information effectively by offering precise definitions of entities and their relationships. These structured forms not only facilitate data indexing but also enable seamless metadata export. As valuable assets, these schemas significantly contribute to enhancing data findability on the web. Moreover, they play a pivotal role in improving machine-readability and facilitating data analysis. A noteworthy aspect is that many of these schemas support the utilization of ontologies. They achieve this by either accepting or requesting values to be provided as ontology terms and by providing links and identifiers to these terms, further enhancing the depth and richness of the structured data. ## nmrXiv Data Model -nmrXiv uses the ISA [(Investigation, Study, Assay)](https://isa-tools.org/format/specification.html) approach to capture the experimental metadata in a structured format, though it has opted for a different terminology than the one used by ISA: -- Investigation ⇛ Project -- Study ⇛ Study -- Assay ⇛ Experiment +nmrXiv initially adopted the ISA [(Investigation, Study, Assay)](https://isa-tools.org/format/specification.html) approach for structuring experimental metadata, as outlined by the ISA specifications. However, nmrXiv has chosen a distinct terminology to align with its specific requirements: -For more details about the objects and relations among them, please check the [Data Model folder](/submission-guides/data-model/project.html) +- ISA Investigation ⇛ nmrXiv Project +- ISA Study ⇛ nmrXiv Study +- ISA Assay ⇛ nmrXiv Dataset + +For a comprehensive understanding of the objects and their relationships, you can refer to the [Data Model folder](/submission-guides/data-model/project.html). + +As each study corresponds to one sample and each dataset corresponds to one spectrum, nmrXiv frontend tends to display these later, more chemistry-friendly terms to enhance user experience. + +In a recent development, nmrXiv has extended its data model to accommodate the submission of individual samples independently, eliminating the requirement to include them in projects. This enhancement aims to streamline the submission process, reducing complexity and offering users greater flexibility when submitting single samples to the platform. ## Data Schemas in nmrXiv -nmrXiv focus on obtaining DOIs for the different entities and describing the data with ontology terms led to prioritizing a list of schemas. Some have been already implemented, and others will be coming soon. Here you can find a list of those schemas: +nmrXiv's emphasis on obtaining Digital Object Identifiers (DOIs) for various entities, coupled with a commitment to describe the data using ontology terms, has prompted the prioritization of a list of schemas. While some schemas have already been implemented, others are in the pipeline and will be introduced soon. Below is a list of these schemas: -### Bioschemas (Repository, Project, Studay, Dataset, Sample) +### Bioschemas (Repository, Project, Studay, Dataset, Sample, Molecule) [Bioschemas](https://bioschemas.org/) aims to improve the Findability of life sciences resources (such as datasets) on the Web by using [Schema.org](https://schema.org/) markup in the websites, so that they are indexable by search engines and other services. Bioschemas is making two main contributions: - Proposing new [types and properties](https://bioschemas.org/types) to [Schema.org](https://schema.org/) to allow for the description of life science resources. - Defining usage [profiles](https://bioschemas.org/profiles) over the [Schema.org](https://schema.org/) types that identify the essential properties to use in describing a resource.[1] -nmrXiv uses Bioschemas profiles to describe both data structuring components (such as datasets) and experiment-related components (such as samples and molecules). Missing profiles will be contributed to Bioschemas and discussion about NMR-specific schemas is going on. Here is a list of the used profiles/types: +nmrXiv uses Bioschemas types to describe both data structuring components (such as datasets) and experiment-related components (such as samples and molecules). Here is a list of the used types: + +#### [DataCatalog](https://schema.org/DataCatalog) +The DataCatalog type can be used to describe repositories, and thus, it is used to describe nmrXiv repository.[DataCatalog API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-31c24120-14f0-41c4-b511-292fd310db79) -#### [DataCatalog](https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01) -DataCatalog profile can be used as a guide to describe repositories, and thus, it is used to describe nmrXiv repository.[DataCatalog API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-31c24120-14f0-41c4-b511-292fd310db79) -#### [Project](https://github.com/NFDI4Chem/nmrxiv/blob/main/app/Models/Bioschema/Project.php) -[Project type](https://schema.org/Project) already exists in [Schema.org](https://schema.org/), but it refers to enterprises rather than a scientific investigation. However, as the project metadata is somehow similar to the study metadata (id, name, URL, etc.), nmrXiv initially defines a new project type similarly to the [study](https://bioschemas.org/types/Study/0.3-DRAFT) provided by [Bioschemas](https://bioschemas.org/). Further enhancements will be applied upon discussion with field experts, and possible submission to [Bioschemas](https://bioschemas.org/) will take place. Project properties allow linking with the included studies and their inner data. [Project API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-d7481762-e431-4975-b786-9cfd7f007d56). +#### [Study](https://bioschemas.org/types/Study/0.3-DRAFT) +While the [Schema.org](https://schema.org/) already encompasses a [Project type](https://schema.org/Project), it primarily pertains to enterprises rather than scientific investigations. Given the similarity in metadata structure between project and study in nmrXiv (e.g., id, name, URL), nmrXiv leverages the [study draft](https://bioschemas.org/types/Study/0.3-DRAFT) offered by Bioschemas to represent projects. This enables seamless linking to included studies and their respective datasets. [Project API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-d7481762-e431-4975-b786-9cfd7f007d56). -#### [Study](https://bioschemas.org/profiles/Study/0.2-DRAFT) -Study profile is currently still a draft in Bioschemas. It is used in nmrXiv to describe the study, and its properties are used to link the study to the corresponding sample and the contained datasets, while being a part of a project. [Study API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-910d6c75-2a1d-42ff-9f0d-b669bbfa6db5). +Moreover, nmrXiv adopts the [study draft](https://bioschemas.org/types/Study/0.3-DRAFT) to describe the study. The properties of this draft can establish connections between the study, its parent project, its associated sample, and the contained datasets. Importantly, this study entity is an integral part of a broader project. [Study API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-910d6c75-2a1d-42ff-9f0d-b669bbfa6db5). -#### [Sample](https://bioschemas.org/profiles/Sample/0.2-RELEASE-2018_11_10) -Sample profile is used in nmrXiv to describe NMR samples. It is attached to the study as a value of "about" property indicating that the study is about this sample. Furthermore, the molecules existing in the Sample are added to it as a value of the property "additionalProperty". There is no API endpoint for the Sample as it can be found in the Study. +#### [ChemicalSubstance](https://bioschemas.org/types/ChemicalSubstance/0.3-RELEASE-2019_09_02) +The ChemicalSubstance type is used in nmrXiv to characterize NMR samples. It is associated with the study through the "about" property, indicating that the study pertains to this specific sample. Additionally, the molecules present in the sample are incorporated into it as values of the "hasBioChemEntityPart" property. While there is no dedicated API endpoint for the Sample, it can be accessed within the Study. -#### [MolecularEntity](https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE) -MolecularEntity can be used for any constitutionally or isotopically distinct atom, molecule, ion, etc., identifiable as a separately distinguishable entity. At the moment, it is used in nmrXiv only to describe the molecules in a sample, but further usages such as describing the nucleus or the solvent are possible too. There is no API endpoint for the MolecularEntity as it can be found in the Study ⇛ Sample. +#### [MolecularEntity](https://bioschemas.org/types/MolecularEntity/0.3-RELEASE-2019_09_02) +The MolecularEntity erves to characterize any constitutionally or isotopically distinct atom, molecule, ion, etc., identifiable as a separately distinguishable entity. Currently, its application in nmrXiv is focused on describing the molecules present in a sample. However, it holds potential for broader applications, such as detailing the nucleus or the solvent. While there is no dedicated API endpoint for the MolecularEntity, it is accessible within the Study ⇛ Sample structure. -#### [Dataset](https://bioschemas.org/profiles/Dataset/1.0-RELEASE) -Dataset schema is used in nmrXiv to describe the datasets there. Each dataset is linked to the parent project and study through the property "isPartOf". [Dataset API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-0408e3df-3c8f-4899-b440-eda6d8f71193). +#### [Dataset](https://schema.org/Dataset) +The Dataset schema is used in nmrXiv to describe the datasets there. Each dataset is linked to its parent project and study through the "isPartOf" property. [Dataset API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-0408e3df-3c8f-4899-b440-eda6d8f71193). ### ISA (Sample, Assay, Ontology) [ISA is a metadata framework](https://isa-tools.org/) to manage a diverse set of life science, environmental, and biomedical experiments that employ one or a combination of technologies, built around the **I**nvestigation (the project context), **S**tudy (a unit of research), and **A**ssay (analytical measurement) data model and serializations (tabular, JSON and RDF).[2] -nmrXiv will comply with ISA Schema specifications to capture NMR metadata (Assay, Sample, and Ontology) to provide a detailed description of the experimental metadata for both synthetic and biological experiments (i.e., sample characteristics, technology and measurement types, sample-to-data relationships). ISA enables interoperability with other platforms and services while keeping the information in a simplistic and open-text format that is FAIR compliant. nmrXiv back-end will be designed to support ISA for newly entered data. However, ISA still comes with few limitations from the data management (repository) perspective, configurable templates on the go and redundant data being some of them. nmrXiv will contribute to extending the existing ISA models with NMR domain-specific requirements to ensure total flexibility for the end user to define their own templates while still being complaint with ISA Specifications and the minimum information standards. +nmrXiv will comply with ISA Schema specifications to capture NMR metadata (Assay, Sample, and Ontology) to provide a detailed description of the experimental metadata for both synthetic and biological experiments (i.e., sample characteristics, technology and measurement types, sample-to-data relationships). ISA enables interoperability with other platforms and services while keeping the information in a simplistic and open-text format that is FAIR-compliant. nmrXiv back-end will be designed to support ISA for newly entered data. However, ISA still comes with few limitations from the data management (repository) perspective, configurable templates on the go and redundant data being some of them. nmrXiv will contribute to extending the existing ISA models with NMR domain-specific requirements to ensure total flexibility for the end user to define their own templates while still being complaint with ISA Specifications and the minimum information standards. ![ISA Specifications](/img/nmrXiv-isa.png) @@ -96,5 +101,5 @@ Complying with the DataCite schema enables the creation of new [Digital Object I Complying with [OpenAIRE Guidelines for Data Archive Managers](https://guidelines.openaire.eu/en/latest/) ensures compatibility with the OpenAIRE infrastructure, which facilitates interoperability with other repositories already adhering to those guidelines, enhancing data exposure and visibility. OpenAIRE has already adopted the DataCite Metadata Schema, yet with some minor adjustments, such as accepting other persistent identifier schemes rather than the DOI and some changes in the obligations of properties. # References -1- [https://bioschemas.org/](https://bioschemas.org/) -2- [https://isa-tools.org/](https://isa-tools.org/) \ No newline at end of file +1. [https://bioschemas.org/](https://bioschemas.org/) +2. [https://isa-tools.org/](https://isa-tools.org/) \ No newline at end of file From 4fb0d5fb0dbd6726bdc9054368f12553423c68df Mon Sep 17 00:00:00 2001 From: Venkata Chandra Sekhar Nainala Date: Tue, 5 Dec 2023 10:21:37 +0100 Subject: [PATCH 22/42] fix: refactored upload view, updated controllers and various bug fixes --- app/Http/Controllers/DraftController.php | 8 +- resources/css/app.css | 13 + resources/js/Pages/Publish.vue | 931 ++--- resources/js/Pages/Upload.vue | 4382 +++++++++------------- resources/js/Shared/StudyInfo.vue | 11 +- resources/js/Shared/Validation.vue | 44 +- 6 files changed, 2334 insertions(+), 3055 deletions(-) diff --git a/app/Http/Controllers/DraftController.php b/app/Http/Controllers/DraftController.php index 49f142ba..eab96a57 100644 --- a/app/Http/Controllers/DraftController.php +++ b/app/Http/Controllers/DraftController.php @@ -165,7 +165,7 @@ public function complete(Request $request, Draft $draft) $validation->process(); return response()->json([ - 'project' => Project::with(['studies.datasets', 'owner', 'citations', 'authors'])->where('draft_id', $draft->id)->first(), + 'project' => Project::with(['studies.datasets', 'owner', 'citations', 'authors', 'tags'])->where('draft_id', $draft->id)->first(), 'validation' => $validation, ]); } @@ -215,7 +215,7 @@ public function process(Request $request, Draft $draft) $team_id = $user->current_team_id; } - return DB::transaction(function () use ($draft, $user, $user_id, $team, $team_id, $request, $project) { + return DB::transaction(function () use ($draft, $user, $user_id, $team, $team_id, $project) { $nmrXivValidation = null; if (! $project) { $project = Project::create([ @@ -243,12 +243,12 @@ public function process(Request $request, Draft $draft) ); } - $project->syncTagsWithType($request->get('tags_array'), 'Project'); + // $project->syncTagsWithType($request->get('tags_array'), 'Project'); $project->save(); } else { $project->name = $draft->name; $project->description = $draft->description; - $project->syncTagsWithType($request->get('tags_array'), 'Project'); + // $project->syncTagsWithType($request->get('tags_array'), 'Project'); $project->save(); } diff --git a/resources/css/app.css b/resources/css/app.css index 16dca16a..d2b7e128 100644 --- a/resources/css/app.css +++ b/resources/css/app.css @@ -51,6 +51,19 @@ visibility: visible; } +.shake { + animation: shake 0.5s; + animation-iteration-count: infinite; +} + +@keyframes shake { + 0% { transform: translateX(0) } + 25% { transform: translateX(5px) } + 50% { transform: translateX(-5px) } + 75% { transform: translateX(5px) } + 100% { transform: translateX(0) } +} + .vue-tags-input { max-width: 100% !important; } diff --git a/resources/js/Pages/Publish.vue b/resources/js/Pages/Publish.vue index 8e01c2d3..0198b09b 100644 --- a/resources/js/Pages/Publish.vue +++ b/resources/js/Pages/Publish.vue @@ -19,7 +19,11 @@ > ← @@ -37,490 +41,456 @@

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