Fix undefined prefixes

Recast/README.md

@@ -0,0 +1,180 @@
+# Recast
+[![Contribution Guidelines][2]](./CONTRIBUTING.md)
+[![LICENSE][3]](./LICENSE)
+
+## Introduction
+
+Microservice that remaps Drupal URIs to add Fedora to Fedora links based on associated Drupal URIs in RDF.
+
+## Installation
+
+Recast requires a functioning LDP server to provide RDF (like a [Fedora](http://fedorarepository.org/) repository).
+You will also need a working [Gemini](../Gemini) system to use for looking up the URI mappings.
+
+- Clone this repository.
+- Install `composer`.  [Install instructions here.][4]
+- `$ cd /path/to/Recast` and run `$ composer install`
+- Then either
+  - For production, configure your web server appropriately (e.g. add a VirtualHost for Recast in Apache) OR
+  - For development, run the PHP built-in webserver `$ php -S localhost:8888 -t src` from Recast root.
+
+## Configuration
+
+Make a copy of the [config file](cfg/config.example.yaml) and name it `config.yaml` in the `cfg` directory.
+
+You will need to set the `fedora_base_url` entry to point to your Fedora installation.
+
+You will also need to set up the `drupal_base_url` entry to point to your Drupal 8 installation.
+
+You will also need to set up the `gemini_base_url` entry to point to you Gemini instance.
+
+You can also configure namespace prefixes, logging level and file and JWT security.
+
+## Usage
+
+Recast sets up a single endpoint, `/recast/{action}`, which accepts GET requests. The action can be one of:
+
+* add - add Fedora URIs along with the provided Drupal URIs
+* replace - replace Drupal URIs with the mapped Fedora URIs
+
+By default the `add` action is assumed if no `action` is provided.
+
+The Recast service looks to the `Apix-Ldp-Resource` header for the resource to map.
+
+The Recast service will provide RDF in the format directed by the `Accept` header sent, or `text/turtle` if 
+the `Accept` header is not provided or the system is unable to provide the requested format.
+
+If requests are successful, they return the response from the Fedora server.  If the Drupal entity cannot be requested,
+the error response from Drupal is returned.  If there is an exception thrown during execution, a 500 response is returned
+with the exception's message.
+
+
+### GET
+
+This retrieves a representation of the specified Fedora entity with Drupal URIs remapped.
+
+For example, a Drupal node that is a member of a collection would have a properties like:
+```
+<> <http://pcdm.org/models#memberOf> <some Drupal node>
+```
+
+Here is the RDF returned from the Fedora repository
+```
+> curl -H"Authorization: Bearer islandora" -H"Accept: text/turtle" http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b
+
+@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix fedora:  <http://fedora.info/definitions/v4/repository#> .
+@prefix ldp:  <http://www.w3.org/ns/ldp#> .
+@prefix dcterms:  <http://purl.org/dc/terms/> .
+
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b>
+        rdf:type                    fedora:Container ;
+        rdf:type                    fedora:Resource ;
+        rdf:type                    <http://pcdm.org/models#Object> ;
+        fedora:lastModifiedBy       "bypassAdmin" ;
+        <http://schema.org/dateModified>  "2019-03-22T19:23:29+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        <http://schema.org/author>  <http://localhost:8000/user/1?_format=jsonld> ;
+        <http://schema.org/sameAs>  "http://localhost:8000/node/2?_format=jsonld" ;
+        <http://schema.org/dateCreated>  "2019-03-22T19:23:11+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        dcterms:extent              "1 item" ;
+        fedora:createdBy            "bypassAdmin" ;
+        fedora:lastModified         "2019-03-22T19:23:30.273Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        fedora:created              "2019-03-22T19:23:30.273Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+        <http://pcdm.org/models#memberOf>  <http://localhost:8000/node/1?_format=jsonld> ;
+        dcterms:title               "A basic image"@en ;
+        rdf:type                    ldp:RDFSource ;
+        rdf:type                    ldp:Container .
+```
+
+In this case the `memberOf` triple is
+
+```
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b> <http://pcdm.org/models#memberOf>  <http://localhost:8000/node/1?_format=jsonld> ;
+```
+
+#### Add (default behaviour)
+
+Passed through the Recast service (http://localhost:8000/recast in our example) we get:
+
+```
+> curl -H"Authorization: Bearer islandora" -H"Accept: text/turtle" -H"Apix-Ldp-Resource: http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b" http://localhost:8000/recast/
+
+@prefix fedora: <http://fedora.info/definitions/v4/repository#> .
+@prefix pcdm: <http://pcdm.org/models#> .
+@prefix ldp: <http://www.w3.org/ns/ldp#> .
+@prefix schema: <http://schema.org/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dc: <http://purl.org/dc/terms/> .
+
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b>
+  a fedora:Container, fedora:Resource, pcdm:Object, ldp:RDFSource, ldp:Container ;
+  fedora:lastModifiedBy "bypassAdmin" ;
+  schema:dateModified "2019-03-22T19:23:29+00:00"^^xsd:dateTime ;
+  schema:author <http://localhost:8000/user/1?_format=jsonld> ;
+  schema:sameAs "http://localhost:8000/node/2?_format=jsonld" ;
+  schema:dateCreated "2019-03-22T19:23:11+00:00"^^xsd:dateTime ;
+  dc:extent "1 item" ;
+  fedora:createdBy "bypassAdmin" ;
+  fedora:lastModified "2019-03-22T19:23:30.273Z"^^xsd:dateTime ;
+  fedora:created "2019-03-22T19:23:30.273Z"^^xsd:dateTime ;
+  pcdm:memberOf <http://localhost:8000/node/1?_format=jsonld>, <http://localhost:8080/fcrepo/rest/c5/57/56/e8/c55756e8-8aac-4460-9699-e7c6efe0a89a> ;
+  dc:title "A basic image"@en .
+```
+
+You'll notice that in this case the `pcdm:memberOf` has two objects. The original Drupal URI and the Fedora URI that maps to it.
+
+```
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b> pcdm:memberOf <http://localhost:8000/node/1?_format=jsonld>, <http://localhost:8080/fcrepo/rest/c5/57/56/e8/c55756e8-8aac-4460-9699-e7c6efe0a89a> ;
+```
+
+You can also explicitly specify the **add** action by using the Recast URI `http://localhost:8000/recast/add`
+
+#### Replace
+
+If you provide the **replace** action, the original Drupal URI will be removed for any URI that can be mapped. 
+
+```
+> curl -H"Authorization: Bearer islandora" -H"Accept: text/turtle" -H"Apix-Ldp-Resource: http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b" http://localhost:8000/recast/replace
+
+@prefix fedora: <http://fedora.info/definitions/v4/repository#> .
+@prefix pcdm: <http://pcdm.org/models#> .
+@prefix ldp: <http://www.w3.org/ns/ldp#> .
+@prefix schema: <http://schema.org/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix dc: <http://purl.org/dc/terms/> .
+
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b>
+  a fedora:Container, fedora:Resource, pcdm:Object, ldp:RDFSource, ldp:Container ;
+  fedora:lastModifiedBy "bypassAdmin" ;
+  schema:dateModified "2019-03-22T19:23:29+00:00"^^xsd:dateTime ;
+  schema:author <http://localhost:8000/user/1?_format=jsonld> ;
+  schema:sameAs "http://localhost:8000/node/2?_format=jsonld" ;
+  schema:dateCreated "2019-03-22T19:23:11+00:00"^^xsd:dateTime ;
+  dc:extent "1 item" ;
+  fedora:createdBy "bypassAdmin" ;
+  fedora:lastModified "2019-03-22T19:23:30.273Z"^^xsd:dateTime ;
+  fedora:created "2019-03-22T19:23:30.273Z"^^xsd:dateTime ;
+  pcdm:memberOf <http://localhost:8080/fcrepo/rest/c5/57/56/e8/c55756e8-8aac-4460-9699-e7c6efe0a89a> ;
+  dc:title "A basic image"@en .
+```
+
+In this example the `pcdm:memberOf` triple only contains the Fedora URI
+
+```
+<http://localhost:8080/fcrepo/rest/82/67/81/b2/826781b2-327d-47b2-9de0-18f85ccfa29b> pcdm:memberOf <http://localhost:8080/fcrepo/rest/c5/57/56/e8/c55756e8-8aac-4460-9699-e7c6efe0a89a>
+```
+
+However:
+
+1. `schema:author <http://localhost:8000/user/1?_format=jsonld> ;` is not changed because we have no mapping for this URI.
+1. `schema:sameAs "http://localhost:8000/node/2?_format=jsonld" ;` is not changed because it is a string and not a URI.
+
+## Maintainers
+
+Current maintainers:
+
+* [Jared Whiklo](https://github.com/whikloj)
+
+[2]: http://img.shields.io/badge/CONTRIBUTING-Guidelines-blue.svg
+[3]: https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square
+[4]: https://getcomposer.org/download/

Recast/cfg/config.example.yaml

@@ -22,4 +22,17 @@ syn:
   # Path to the syn config file for authentication.
   # example can be found here:
   # https://github.com/Islandora-CLAW/Syn/blob/master/conf/syn-settings.example.xml
-  config: ../syn-settings.xml
+  config: ../syn-settings.xml
+
+# Add namespace prefixes used by Fedora for recast service
+# Must be inside an array to maintain the internal associative array.
+namespaces:
+-
+  acl: "http://www.w3.org/ns/auth/acl#"
+  fedora: "http://fedora.info/definitions/v4/repository#"
+  ldp: "http://www.w3.org/ns/ldp#"
+  memento: "http://mementoweb.org/ns#"
+  pcdm: "http://pcdm.org/models#"
+  pcdmuse: "http://pcdm.org/use#"
+  webac: "http://fedora.info/definitions/v4/webac#"
+  vcard: "http://www.w3.org/2006/vcard/ns#"

Recast/src/Controller/RecastController.php

@@ -126,23 +126,26 @@ public function recast(Request $request, Application $app, $operation)
                     if (is_array($reverse_uri)) {
                         $reverse_uri = reset($reverse_uri);
                     }
+                    // Don't rewrite the current URI (in-case of sameAs)
+                    if ($reverse_uri !== $fedora_uri) {
                         $predicate = $this->findPredicateForObject($graph, $uri);
                         $this->log->debug('Found a reverse URI', [
-                          'original_uri' => $uri,
-                          'reverse_uri' => $reverse_uri,
+                            'original_uri' => $uri,
+                            'reverse_uri' => $reverse_uri,
                         ]);
-                    if (!is_null($predicate)) {
-                                      $graph->addResource(
-                                          $fedora_uri,
-                                          $predicate,
-                                          $reverse_uri
-                                      );
-                        if (strtolower($operation) == 'replace') {
-                                                          $graph->deleteResource(
-                                                              $fedora_uri,
-                                                              $predicate,
-                                                              $uri
-                                                          );
+                        if (!is_null($predicate)) {
+                            $graph->addResource(
+                                $fedora_uri,
+                                $predicate,
+                                $reverse_uri
+                            );
+                            if (strtolower($operation) == 'replace') {
+                                $graph->deleteResource(
+                                    $fedora_uri,
+                                    $predicate,
+                                    $uri
+                                );
+                            }
                         }
                     }
                 }
@@ -170,6 +173,20 @@ public function recast(Request $request, Application $app, $operation)
             $output_type = 'text/turtle';
         }
 
+        // Add in user configured prefixes/uris for rdf mapping.
+        if (isset($app['crayfish.namespaces'])) {
+            // To get the prefixes we nest the associative array inside an array
+            $namespaces = $app['crayfish.namespaces'][0];
+            if (is_array($namespaces) && count($namespaces) > 0) {
+                foreach ($namespaces as $prefix => $uri) {
+                    if (\EasyRdf_Namespace::prefixOfUri($uri) == '') {
+                        $this->log->debug("Adding $prefix -> $uri");
+                        \EasyRdf_Namespace::set($prefix, $uri);
+                    }
+                }
+            }
+        }
+
         $new_body = $graph->serialise($format);
 
         if ($format == 'jsonld') {

Recast/tests/RecastControllerTests.php

@@ -25,6 +25,13 @@ class RecastControllerTest extends TestCase
 
     private $logger_prophecy;
 
+    private $namespaces = array(
+        array(
+            "fedora" => "http://fedora.info/definitions/v4/repository#",
+            "pcdm" => "http://pcdm.org/models#",
+        ),
+    );
+
   /**
    * {@inheritdoc}
    */
@@ -136,15 +143,66 @@ public function testInvalidType()
         $this->assertEquals(400, $response->getStatusCode(), "Invalid status code");
     }
 
+    /**
+     * @covers ::recast
+     */
+    public function testPrefixes()
+    {
+        $resource_id = 'http://localhost:8080/fcrepo/rest/object1';
+
+        $this->gemini_prophecy->findByUri('http://localhost:8000/user/1?_format=jsonld', Argument::any())
+            ->willReturn(null);
+        $this->gemini_prophecy->findByUri('http://localhost:8000/node/1?_format=jsonld', Argument::any())
+            ->willReturn('http://localhost:8080/fcrepo/rest/collection99');
+
+        $mock_silex_app = new Application();
+        $mock_silex_app['crayfish.drupal_base_url'] = 'http://localhost:8000';
+        $mock_silex_app['crayfish.namespaces'] = $this->namespaces;
+
+        $mock_fedora_response = $this->getMockFedoraStream(
+            realpath(__DIR__ . '/resources/drupal_image.ttl'),
+            'text/turtle'
+        );
+
+        $controller = new RecastController(
+            $this->gemini_prophecy->reveal(),
+            $this->logger_prophecy->reveal()
+        );
+
+        $request = Request::create(
+            "/add",
+            "GET"
+        );
+        $request->headers->set('Authorization', 'some_token');
+        $request->headers->set('Apix-Ldp-Resource', $resource_id);
+        $request->headers->set('Accept', 'text/turtle');
+        $request->attributes->set('fedora_resource', $mock_fedora_response);
+
+        $response = $controller->recast($request, $mock_silex_app, 'add');
+        $body = $response->getContent();
+        $this->assertContains('fedora:', $body, "Did not find fedora: prefix");
+        $this->assertNotContains('ldp:', $body, "Found ldp: prefix");
+        $this->assertContains('pcdm:', $body, "Did not find pcdm: prefix");
+        $this->assertContains('<http://www.w3.org/ns/ldp#RDFSource>', $body, "Did not find full LDP uri");
+    }
+
   /**
    * Generate a mock response containing mock Fedora body stream.
    *
+   * @param string $input_resource
+   *    The path to the file containing the stream contents.
+   * @param string $content_type
+   *    The content type of the input_resource.
+   *
    * @return object
    *   The returned stream object.
    */
-    protected function getMockFedoraStream()
+    protected function getMockFedoraStream($input_resource = null, $content_type = 'application/ld+json')
     {
-        $input_resource = realpath(__DIR__ . '/resources/drupal_image.json');
+        if (is_null($input_resource)) {
+            // Provide a default.
+            $input_resource = realpath(__DIR__ . '/resources/drupal_image.json');
+        }
 
         $prophecy = $this->prophesize(StreamInterface::class);
         $prophecy->isReadable()->willReturn(true);
@@ -156,7 +214,7 @@ protected function getMockFedoraStream()
         $prophecy = $this->prophesize(ResponseInterface::class);
         $prophecy->getStatusCode()->willReturn(200);
         $prophecy->getBody()->willReturn($mock_stream);
-        $prophecy->getHeader('Content-type')->willReturn('application/ld+json');
+        $prophecy->getHeader('Content-type')->willReturn($content_type);
         $mock_fedora_response = $prophecy->reveal();
         return $mock_fedora_response;
     }

Recast/tests/resources/drupal_image.ttl

@@ -0,0 +1,22 @@
+@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix fedora:  <http://fedora.info/definitions/v4/repository#> .
+@prefix ldp:  <http://www.w3.org/ns/ldp#> .
+@prefix dcterms:  <http://purl.org/dc/terms/> .
+
+<http://localhost:8080/fcrepo/rest/object34>
+    rdf:type fedora:Container ;
+    rdf:type fedora:Resource ;
+    rdf:type <http://pcdm.org/models#Object> ;
+    fedora:lastModifiedBy "bypassAdmin" ;
+    <http://schema.org/dateModified> "2019-03-22T19:23:29+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    <http://schema.org/author> <http://localhost:8000/user/1?_format=jsonld> ;
+    <http://schema.org/sameAs> "http://localhost:8000/node/2?_format=jsonld" ;
+    <http://schema.org/dateCreated> "2019-03-22T19:23:11+00:00"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    dcterms:extent "1 item" ;
+    fedora:createdBy "bypassAdmin" ;
+    fedora:lastModified "2019-03-22T19:23:30.273Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    fedora:created "2019-03-22T19:23:30.273Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> ;
+    <http://pcdm.org/models#memberOf> <http://localhost:8000/node/1?_format=jsonld> ;
+    dcterms:title "A basic image"@en ;
+    rdf:type ldp:RDFSource ;
+    rdf:type ldp:Container .