Removed RDF config variables.

clowder-framework · Feb 3, 2020 · 8eb7234 · 8eb7234
1 parent 7ea32ff
commit 8eb7234
Show file tree

Hide file tree

Showing 6 changed files with 171 additions and 266 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## 1.8.1 - 2020-01-29
 
+### Removed
+- Removed unused RDF libraries. This was probably used by the rdf/xml functionality that was removed a while back but 
+the dependencies were never removed.
+- Removed Jena validation of JSON-LD metadata. It was creating a blank graph and clients couldn't upload metadata when 
+Clowder runs in a location that doesn't not have access to https://clowderframework.org/contexts/metadata.jsonld. 
+
 ### Added
 - Scripts to migrate files on disk AWS S3.
   [CATS-1034](https://opensource.ncsa.illinois.edu/jira/browse/CATS-1034)

diff --git a/app/api/Datasets.scala b/app/api/Datasets.scala
@@ -622,66 +622,51 @@ class  Datasets @Inject()(
         datasets.get(id) match {
           case Some(x) => {
             val json = request.body
-            // parse request for JSON-LD model
-            var model: RDFModel = null
-            json.validate[RDFModel] match {
-              case e: JsError => {
-                Logger.error("Errors: " + JsError.toFlatForm(e))
-                BadRequest(JsError.toFlatJson(e))
-              }
-              case s: JsSuccess[RDFModel] => {
-                model = s.get
-
-                //parse request for agent/creator info
-                //creator can be UserAgent or ExtractorAgent
-                var creator: models.Agent = null
-                json.validate[Agent] match {
-                  case s: JsSuccess[Agent] => {
-                    creator = s.get
-
-                    // check if the context is a URL to external endpoint
-                    val contextURL: Option[URL] = (json \ "@context").asOpt[String].map(new URL(_))
-
-                    // check if context is a JSON-LD document
-                    val contextID: Option[UUID] = (json \ "@context").asOpt[JsObject]
-                      .map(contextService.addContext(new JsString("context name"), _))
-
-                    // when the new metadata is added
-                    val createdAt = new Date()
-
-                    //parse the rest of the request to create a new models.Metadata object
-                    val attachedTo = ResourceRef(ResourceRef.dataset, id)
-                    val content = (json \ "content")
-                    val version = None
-                    val metadata = models.Metadata(UUID.generate, attachedTo, contextID, contextURL, createdAt, creator,
-                      content, version)
-
-                    //add metadata to mongo
-                    val metadataId = metadataService.addMetadata(metadata)
-                    val mdMap = metadata.getExtractionSummary
-
-                    //send RabbitMQ message
-                    current.plugin[RabbitmqPlugin].foreach { p =>
-                      p.metadataAddedToResource(metadataId, metadata.attachedTo, mdMap, Utils.baseUrl(request), request.apiKey, request.user)
-                    }
-
-                    events.addObjectEvent(request.user, id, x.name,EventType.ADD_METADATA_DATASET.toString)
+            //parse request for agent/creator info
+            json.validate[Agent] match {
+              case s: JsSuccess[Agent] => {
+                val creator = s.get
+
+                // check if the context is a URL to external endpoint
+                val contextURL: Option[URL] = (json \ "@context").asOpt[String].map(new URL(_))
+
+                // check if context is a JSON-LD document
+                val contextID: Option[UUID] = (json \ "@context").asOpt[JsObject]
+                  .map(contextService.addContext(new JsString("context name"), _))
+
+                // when the new metadata is added
+                val createdAt = new Date()
+
+                //parse the rest of the request to create a new models.Metadata object
+                val attachedTo = ResourceRef(ResourceRef.dataset, id)
+                val content = (json \ "content")
+                val version = None
+                val metadata = models.Metadata(UUID.generate, attachedTo, contextID, contextURL, createdAt, creator,
+                  content, version)
+
+                //add metadata to mongo
+                val metadataId = metadataService.addMetadata(metadata)
+                val mdMap = metadata.getExtractionSummary
+
+                //send RabbitMQ message
+                current.plugin[RabbitmqPlugin].foreach { p =>
+                  p.metadataAddedToResource(metadataId, metadata.attachedTo, mdMap, Utils.baseUrl(request), request.apiKey, request.user)
+                }
 
-                    datasets.index(id)
-                    Ok(toJson("Metadata successfully added to db"))
+                events.addObjectEvent(request.user, id, x.name, EventType.ADD_METADATA_DATASET.toString)
 
-                  }
-                  case e: JsError => {
-                    Logger.error("Error getting creator");
-                    BadRequest(toJson(s"Creator data is missing or incorrect."))
-                  }
-                }
+                datasets.index(id)
+                Ok(toJson("Metadata successfully added to db"))
+              }
+              case e: JsError => {
+                Logger.error("Error getting creator");
+                BadRequest(toJson(s"Creator data is missing or incorrect."))
               }
             }
           }
           case None => Logger.error(s"Error getting dataset $id"); NotFound
         }
-      }
+     }
 
 
   def getMetadataDefinitions(id: UUID, currentSpace: Option[String]) = PermissionAction(Permission.AddMetadata, Some(ResourceRef(ResourceRef.dataset, id))) { implicit request =>

diff --git a/app/api/Files.scala b/app/api/Files.scala
@@ -309,66 +309,53 @@ class Files @Inject()(
     files.get(id) match {
       case Some(x) => {
         val json = request.body
+        //parse request for agent/creator info
+        //creator can be UserAgent or ExtractorAgent
+        var creator: models.Agent = null
+        json.validate[Agent] match {
+          case s: JsSuccess[Agent] => {
+            creator = s.get
+            //if creator is found, continue processing
+            val context: JsValue = (json \ "@context")
+
+            // check if the context is a URL to external endpoint
+            val contextURL: Option[URL] = context.asOpt[String].map(new URL(_))
+
+            // check if context is a JSON-LD document
+            val contextID: Option[UUID] =
+              if (context.isInstanceOf[JsObject]) {
+                context.asOpt[JsObject].map(contextService.addContext(new JsString("context name"), _))
+              } else if (context.isInstanceOf[JsArray]) {
+                context.asOpt[JsArray].map(contextService.addContext(new JsString("context name"), _))
+              } else None
+
+            // when the new metadata is added
+            val createdAt = Parsers.parseDate((json \ "created_at")).fold(new Date())(_.toDate)
+
+            //parse the rest of the request to create a new models.Metadata object
+            val attachedTo = ResourceRef(ResourceRef.file, id)
+            val content = (json \ "content")
+            val version = None
+            val metadata = models.Metadata(UUID.generate, attachedTo, contextID, contextURL, createdAt, creator,
+              content, version)
+
+            //add metadata to mongo
+            val metadataId = metadataService.addMetadata(metadata)
+            val mdMap = metadata.getExtractionSummary
+
+            //send RabbitMQ message
+            current.plugin[RabbitmqPlugin].foreach { p =>
+              p.metadataAddedToResource(metadataId, metadata.attachedTo, mdMap, Utils.baseUrl(request), request.apiKey, request.user)
+            }
 
-        // parse request for JSON-LD model
-        var model: RDFModel = null
-        json.validate[RDFModel] match {
-          case e: JsError => {
-            Logger.error("Errors: " + JsError.toFlatForm(e) + "\n\t" + json.toString())
-            BadRequest(JsError.toFlatJson(e))
-          }
-          case s: JsSuccess[RDFModel] => {
-            model = s.get
-
-            //parse request for agent/creator info
-            //creator can be UserAgent or ExtractorAgent
-            var creator: models.Agent = null
-            json.validate[Agent] match {
-              case s: JsSuccess[Agent] => {
-                creator = s.get
-                //if creator is found, continue processing
-                val context: JsValue = (json \ "@context")
-
-                // check if the context is a URL to external endpoint
-                val contextURL: Option[URL] = context.asOpt[String].map(new URL(_))
-
-                // check if context is a JSON-LD document
-                val contextID: Option[UUID] =
-                  if (context.isInstanceOf[JsObject]) {
-                    context.asOpt[JsObject].map(contextService.addContext(new JsString("context name"), _))
-                  } else if (context.isInstanceOf[JsArray]) {
-                    context.asOpt[JsArray].map(contextService.addContext(new JsString("context name"), _))
-                  } else None
-
-                // when the new metadata is added
-                val createdAt = Parsers.parseDate((json \ "created_at")).fold(new Date())(_.toDate)
-
-                //parse the rest of the request to create a new models.Metadata object
-                val attachedTo = ResourceRef(ResourceRef.file, id)
-                val content = (json \ "content")
-                val version = None
-                val metadata = models.Metadata(UUID.generate, attachedTo, contextID, contextURL, createdAt, creator,
-                  content, version)
-
-                //add metadata to mongo
-                val metadataId = metadataService.addMetadata(metadata)
-                val mdMap = metadata.getExtractionSummary
-
-                //send RabbitMQ message
-                current.plugin[RabbitmqPlugin].foreach { p =>
-                  p.metadataAddedToResource(metadataId, metadata.attachedTo, mdMap, Utils.baseUrl(request), request.apiKey, request.user)
-                }
-
-                events.addObjectEvent(request.user, id, x.filename, EventType.ADD_METADATA_FILE.toString)
+            events.addObjectEvent(request.user, id, x.filename, EventType.ADD_METADATA_FILE.toString)
 
-                files.index(id)
-                Ok(toJson("Metadata successfully added to db"))
-              }
-              case e: JsError => {
-                Logger.error("Error getting creator")
-                BadRequest(toJson(s"Creator data is missing or incorrect."))
-              }
-            }
+            files.index(id)
+            Ok(toJson("Metadata successfully added to db"))
+          }
+          case e: JsError => {
+            Logger.error("Error getting creator")
+            BadRequest(toJson(s"Creator data is missing or incorrect."))
           }
         }
       }
@@ -382,17 +369,6 @@ class Files @Inject()(
     try {
       val fileList: JsValue = (json \ "files")
       val metadata: JsValue = (json \ "metadata")
-
-      // parse request for JSON-LD model
-      var model: RDFModel = null
-      metadata.validate[RDFModel] match {
-        case e: JsError => {
-          Logger.error("Errors: " + JsError.toFlatForm(e) + "\n\t" + metadata.toString())
-          BadRequest(JsError.toFlatJson(e))
-        }
-        case s: JsSuccess[RDFModel] => {
-          model = s.get
-
           //parse request for agent/creator info
           //creator can be UserAgent or ExtractorAgent
           var creator: models.Agent = null
@@ -444,8 +420,6 @@ class Files @Inject()(
               Logger.error("Error getting creator")
               BadRequest(toJson(s"Creator data is missing or incorrect."))
             }
-          }
-        }
       }
     } catch {
       case e: ClassCastException => {