New GraphQL version

HuygensING · Feb 1, 2023 · e600e77 · e600e77
1 parent 8ae355c
commit e600e77
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Showing 24 changed files with 252 additions and 284 deletions.
diff --git a/timbuctoo-instancev4/pom.xml b/timbuctoo-instancev4/pom.xml
@@ -265,7 +265,7 @@
     <dependency>
       <groupId>com.graphql-java</groupId>
       <artifactId>graphql-java</artifactId>
-      <version>11.0</version>
+      <version>20.0</version>
     </dependency>
 
     <dependency>

diff --git a/...main/java/nl/knaw/huygens/timbuctoo/v5/datastores/implementations/bdb/BdbSchemaStore.java b/...main/java/nl/knaw/huygens/timbuctoo/v5/datastores/implementations/bdb/BdbSchemaStore.java
@@ -11,7 +11,6 @@
 import nl.knaw.huygens.timbuctoo.v5.dataset.ImportStatus;
 import nl.knaw.huygens.timbuctoo.v5.dataset.OptimizedPatchListener;
 import nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.dto.ChangeType;
-import nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.dto.CursorQuad;
 import nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.dto.Direction;
 import nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.dto.QuadGraphs;
 import nl.knaw.huygens.timbuctoo.v5.datastores.schemastore.SchemaStore;

diff --git a/...o-instancev4/src/main/java/nl/knaw/huygens/timbuctoo/v5/dropwizard/endpoints/GraphQl.java b/...o-instancev4/src/main/java/nl/knaw/huygens/timbuctoo/v5/dropwizard/endpoints/GraphQl.java
@@ -3,17 +3,14 @@
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import com.sleepycat.je.DatabaseException;
 import graphql.ExecutionResult;
 import graphql.GraphQL;
 import graphql.GraphQLException;
 import graphql.schema.GraphQLSchema;
 import nl.knaw.huygens.timbuctoo.util.UriHelper;
 import nl.knaw.huygens.timbuctoo.v5.dataset.DataSetRepository;
-import nl.knaw.huygens.timbuctoo.v5.dataset.exceptions.RdfProcessingFailedException;
 import nl.knaw.huygens.timbuctoo.v5.dropwizard.contenttypes.SerializerWriter;
 import nl.knaw.huygens.timbuctoo.v5.dropwizard.contenttypes.SerializerWriterRegistry;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.RootData;
 import nl.knaw.huygens.timbuctoo.v5.graphql.security.PermissionBasedFieldVisibility;
 import nl.knaw.huygens.timbuctoo.v5.graphql.security.UserPermissionCheck;
 import nl.knaw.huygens.timbuctoo.v5.graphql.serializable.SerializerExecutionStrategy;
@@ -44,7 +41,6 @@
 import static graphql.ExecutionInput.newExecutionInput;
 import static nl.knaw.huygens.timbuctoo.util.JsonBuilder.jsn;
 import static nl.knaw.huygens.timbuctoo.util.JsonBuilder.jsnO;
-import static nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.ContextData.contextData;
 
 @Path("/v5/graphql")
 public class GraphQl {
@@ -58,8 +54,7 @@ public class GraphQl {
 
   public GraphQl(Supplier<GraphQLSchema> graphqlGetter, SerializerWriterRegistry serializerWriterRegistry,
                  UserValidator userValidator, UriHelper uriHelper, PermissionFetcher permissionFetcher,
-                 DataSetRepository dataSetRepository)
-    throws DatabaseException, RdfProcessingFailedException {
+                 DataSetRepository dataSetRepository) {
     this.graphqlGetter = graphqlGetter;
     this.serializerWriterRegistry = serializerWriterRegistry;
     this.userValidator = userValidator;
@@ -85,7 +80,7 @@ public Response postJson(JsonNode body, @QueryParam("query") String query,
     } else {
       queryFromBody = null;
     }
-    Map variables = null;
+    Map<String, Object> variables = null;
     if (body.has("variables")) {
       try {
         variables = objectMapper.treeToValue(body.get("variables"), HashMap.class);
@@ -119,14 +114,13 @@ public Response get(@QueryParam("query") String query, @HeaderParam("accept") St
     return executeGraphql(null, acceptHeader, acceptParam, query, null, null, authHeader);
   }
 
-
   public Response executeGraphql(String query, String acceptHeader, String acceptParam, String queryFromBody,
-                                 Map variables, String operationName, String authHeader) {
+                                 Map<String, Object> variables, String operationName, String authHeader) {
     final SerializerWriter serializerWriter;
     if (acceptParam != null && !acceptParam.isEmpty()) {
       acceptHeader = acceptParam; //Accept param overrules header because it's more under the user's control
     }
-    if (unSpecifiedAcceptHeader(acceptHeader)) {
+    if (acceptHeader == null || acceptHeader.isEmpty() || "*/*".equals(acceptHeader)) {
       acceptHeader = MediaType.APPLICATION_JSON;
     }
     if (MediaType.APPLICATION_JSON.equals(acceptHeader)) {
@@ -166,14 +160,11 @@ public Response executeGraphql(String query, String acceptHeader, String acceptP
       user = Optional.empty();
     }
 
-    UserPermissionCheck userPermissionCheck = new UserPermissionCheck(
-      user,
-      permissionFetcher
-    );
-
-    final GraphQLSchema transform = graphqlGetter
-      .get()
-      .transform(b -> b.fieldVisibility(new PermissionBasedFieldVisibility(userPermissionCheck,dataSetRepository)));
+    final UserPermissionCheck userPermissionCheck = new UserPermissionCheck(user, permissionFetcher);
+    final GraphQLSchema schema = graphqlGetter.get();
+    final GraphQLSchema transform = schema.transform(sb ->
+        sb.codeRegistry(schema.getCodeRegistry().transform(crb ->
+            crb.fieldVisibility(new PermissionBasedFieldVisibility(userPermissionCheck, dataSetRepository)))));
     final GraphQL.Builder builder = GraphQL.newGraphQL(transform);
 
     if (serializerWriter != null) {
@@ -185,8 +176,8 @@ public Response executeGraphql(String query, String acceptHeader, String acceptP
     try {
       final ExecutionResult result = graphQl
         .execute(newExecutionInput()
-          .root(new RootData(user))
-          .context(contextData(userPermissionCheck, user))
+          .root(new Object())
+          .graphQLContext(Map.of("userPermissionCheck", userPermissionCheck, "user", user))
           .query(queryFromBody)
           .operationName(operationName)
           .variables(variables == null ? Collections.emptyMap() : variables)
@@ -219,10 +210,4 @@ public Response executeGraphql(String query, String acceptHeader, String acceptP
       // throw e;
     }
   }
-
-
-  public boolean unSpecifiedAcceptHeader(@HeaderParam("accept") String acceptHeader) {
-    return acceptHeader == null || acceptHeader.isEmpty() || "*/*".equals(acceptHeader);
-  }
-
 }
diff --git a/...too-instancev4/src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/DirectiveRetriever.java b/...too-instancev4/src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/DirectiveRetriever.java
@@ -9,25 +9,23 @@
 public class DirectiveRetriever {
   public static Optional<String> getDirectiveArgument(GraphQLObjectType parentType, String directiveName,
                                                       String argumentName) {
-    //    if (parentType.getDefinition().getDirectives(directiveName).isEmpty()) {
-    //      return Optional.empty();
-    //    }
+    if (parentType.getDefinition().getDirectives(directiveName).isEmpty()) {
+      return Optional.empty();
+    }
 
-    //    return Optional.of(parentType.getDefinition().getDirectives(directiveName).get(0))
-    return Optional.ofNullable(parentType.getDefinition().getDirective(directiveName))
+    return Optional.of(parentType.getDefinition().getDirectives(directiveName).get(0))
       .map(d -> d.getArgument(argumentName))
       .map(v -> (StringValue) v.getValue())
       .map(StringValue::getValue);
   }
 
   public static Optional<String> getDirectiveArgument(GraphQLFieldDefinition field, String directiveName,
                                                       String argumentName) {
-    //    if (field.getDefinition().getDirectives(directiveName).isEmpty()) {
-    //      return Optional.empty();
-    //    }
-    //
-    //    return Optional.of(field.getDefinition().getDirectives(directiveName).get(0))
-    return Optional.ofNullable(field.getDefinition().getDirective(directiveName))
+    if (field.getDefinition().getDirectives(directiveName).isEmpty()) {
+      return Optional.empty();
+    }
+
+    return Optional.of(field.getDefinition().getDirectives(directiveName).get(0))
       .map(d -> d.getArgument(argumentName))
       .map(v -> (StringValue) v.getValue())
       .map(StringValue::getValue);

diff --git a/.../main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/DataMetaDataListFetcher.java b/.../main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/DataMetaDataListFetcher.java
@@ -3,16 +3,15 @@
 import graphql.schema.DataFetcher;
 import graphql.schema.DataFetchingEnvironment;
 import nl.knaw.huygens.timbuctoo.v5.dataset.DataSetRepository;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.ContextData;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.DataSetWithDatabase;
 import nl.knaw.huygens.timbuctoo.v5.graphql.security.UserPermissionCheck;
 import nl.knaw.huygens.timbuctoo.v5.graphql.security.UserPermissionCheck.OldGraphQlPermission;
-import nl.knaw.huygens.timbuctoo.v5.security.dto.Permission;
+import nl.knaw.huygens.timbuctoo.v5.security.dto.User;
 
+import java.util.Optional;
 import java.util.stream.Stream;
 
 public class DataMetaDataListFetcher implements DataFetcher {
-
   private final DataSetRepository dataSetRepository;
 
   public DataMetaDataListFetcher(DataSetRepository dataSetRepository) {
@@ -22,20 +21,19 @@ public DataMetaDataListFetcher(DataSetRepository dataSetRepository) {
   @Override
   public Object get(DataFetchingEnvironment env) {
     return (Iterable) () -> {
-      Stream<DataSetWithDatabase> dataSets = dataSetRepository.getDataSets()
-                                                              .stream()
-                                                              .map(dataSet -> new DataSetWithDatabase(dataSet,
-                                                                ((ContextData) env.getContext())
-                                                                  .getUserPermissionCheck()));
+      Stream<DataSetWithDatabase> dataSets = dataSetRepository
+          .getDataSets()
+          .stream()
+          .map(dataSet -> new DataSetWithDatabase(dataSet, env.getGraphQlContext().get("userPermissionCheck")));
       if (env.getArgument("ownOnly")) {
-        String userId =
-          ((ContextData) env.getContext()).getUser().map(u -> "u" + u.getPersistentId()).orElse(null);
+        Optional<User> user = env.getGraphQlContext().get("user");
+        String userId = user.map(u -> "u" + u.getPersistentId()).orElse(null);
         dataSets = dataSets.filter(d -> d.getOwnerId().equals(userId));
       }
       // translate
       OldGraphQlPermission permission = OldGraphQlPermission.valueOf(env.getArgument("permission"));
-      dataSets = dataSets.filter(d -> ((ContextData) env.getContext()).getUserPermissionCheck()
-                                                                      .hasOldGraphQlPermission(d, permission));
+      UserPermissionCheck userPermissionCheck = env.getGraphQlContext().get("userPermissionCheck");
+      dataSets = dataSets.filter(d -> userPermissionCheck.hasOldGraphQlPermission(d, permission));
 
       return dataSets.iterator();
     };

diff --git a/...in/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/DataSetImportStatusFetcher.java b/...in/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/DataSetImportStatusFetcher.java
@@ -7,7 +7,6 @@
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet;
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSetMetaData;
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.LogEntry;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.ContextData;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.LogEntryImportStatus;
 import nl.knaw.huygens.timbuctoo.v5.graphql.mutations.MutationHelpers;
 import nl.knaw.huygens.timbuctoo.v5.security.dto.Permission;
@@ -29,11 +28,10 @@ public DataSetImportStatusFetcher(DataSetRepository dataSetRepository) {
 
   @Override
   public List<LogEntryImportStatus> get(DataFetchingEnvironment env) {
-    User currentUser = env.<ContextData>getContext().getUser()
-                                                    .orElseThrow(() -> new RuntimeException("You are not logged in"));
+    Optional<User> user = env.getGraphQlContext().get("user");
+    User currentUser = user.orElseThrow(() -> new RuntimeException("You are not logged in"));
 
     DataSetMetaData dataSetMetaData = env.getSource();
-
     MutationHelpers.checkPermission(env, dataSetMetaData, Permission.READ_IMPORT_STATUS);
 
     DataSetMetaData input = env.getSource();
@@ -43,16 +41,16 @@ public List<LogEntryImportStatus> get(DataFetchingEnvironment env) {
       input.getDataSetId()
     );
 
-    return dataSetOpt.map(dataSet -> dataSet.getImportManager().getLogList())
-                     .map(logList -> {
-                       final int[] num = new int[]{0};
-                       return logList.getEntries().stream().map(logEntry -> {
-                         Iterable<LogEntry> unprocessedEntries = logList::getUnprocessed;
-                         boolean unprocessed = stream(unprocessedEntries.spliterator(), false)
-                           .anyMatch(unprocessedEntry -> unprocessedEntry.equals(logEntry));
-                         return new LogEntryImportStatus(logEntry, num[0]++, unprocessed);
-                       }).collect(toList());
-                     }).orElse(Lists.newArrayList());
+    return dataSetOpt
+      .map(dataSet -> dataSet.getImportManager().getLogList())
+      .map(logList -> {
+        final int[] num = new int[]{0};
+        return logList.getEntries().stream().map(logEntry -> {
+          Iterable<LogEntry> unprocessedEntries = logList::getUnprocessed;
+          boolean unprocessed = stream(unprocessedEntries.spliterator(), false)
+              .anyMatch(unprocessedEntry -> unprocessedEntry.equals(logEntry));
+          return new LogEntryImportStatus(logEntry, num[0]++, unprocessed);
+        }).collect(toList());
+      }).orElse(Lists.newArrayList());
   }
-
 }
diff --git a/.../src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/ImportStatusFetcher.java b/.../src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/ImportStatusFetcher.java
@@ -6,7 +6,6 @@
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet;
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSetMetaData;
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.LogEntry;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.ContextData;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.LogEntryImportStatus;
 import nl.knaw.huygens.timbuctoo.v5.graphql.mutations.MutationHelpers;
 import nl.knaw.huygens.timbuctoo.v5.security.dto.Permission;
@@ -26,11 +25,10 @@ public ImportStatusFetcher(DataSetRepository dataSetRepository) {
 
   @Override
   public LogEntryImportStatus get(DataFetchingEnvironment env) {
-    User currentUser = env.<ContextData>getContext().getUser()
-                                                    .orElseThrow(() -> new RuntimeException("You are not logged in"));
+    Optional<User> user = env.getGraphQlContext().get("user");
+    User currentUser = user.orElseThrow(() -> new RuntimeException("You are not logged in"));
 
     DataSetMetaData dataSetMetaData = env.getSource();
-
     MutationHelpers.checkPermission(env, dataSetMetaData, Permission.READ_IMPORT_STATUS);
 
     Optional<DataSet> dataSetOpt = dataSetRepository.getDataSet(
@@ -39,19 +37,19 @@ public LogEntryImportStatus get(DataFetchingEnvironment env) {
       dataSetMetaData.getDataSetId()
     );
 
-    return dataSetOpt.map(dataSet -> dataSet.getImportManager().getLogList())
-                     .map(logList -> {
-                       int id = Integer.parseInt(env.getArgument("id"));
-                       List<LogEntry> entries = logList.getEntries();
-                       if (entries.size() > id) {
-                         LogEntry logEntry = logList.getEntries().get(id);
-                         Iterable<LogEntry> unprocessedEntries = logList::getUnprocessed;
-                         boolean unprocessed = stream(unprocessedEntries.spliterator(), false)
-                           .anyMatch(unprocessedEntry -> unprocessedEntry.equals(logEntry));
-                         return new LogEntryImportStatus(logEntry, id, unprocessed);
-                       }
-                       return null;
-                     }).orElseThrow(() -> new RuntimeException("No import status with id: " + env.getArgument("id")));
-
+    return dataSetOpt
+      .map(dataSet -> dataSet.getImportManager().getLogList())
+      .map(logList -> {
+        int id = Integer.parseInt(env.getArgument("id"));
+        List<LogEntry> entries = logList.getEntries();
+        if (entries.size() > id) {
+          LogEntry logEntry = logList.getEntries().get(id);
+          Iterable<LogEntry> unprocessedEntries = logList::getUnprocessed;
+          boolean unprocessed = stream(unprocessedEntries.spliterator(), false)
+            .anyMatch(unprocessedEntry -> unprocessedEntry.equals(logEntry));
+          return new LogEntryImportStatus(logEntry, id, unprocessed);
+        }
+        return null;
+      }).orElseThrow(() -> new RuntimeException("No import status with id: " + env.getArgument("id")));
   }
 }
diff --git a/.../src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/OtherDataSetFetcher.java b/.../src/main/java/nl/knaw/huygens/timbuctoo/v5/graphql/datafetchers/OtherDataSetFetcher.java
@@ -8,10 +8,10 @@
 import nl.knaw.huygens.timbuctoo.v5.dataset.dto.DataSet;
 import nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.dto.CursorQuad;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.berkeleydb.dto.LazyTypeSubjectReference;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.ContextData;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.DataSetWithDatabase;
 import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.SubjectGraphReference;
-import nl.knaw.huygens.timbuctoo.v5.graphql.datafetchers.dto.SubjectReference;
+import nl.knaw.huygens.timbuctoo.v5.graphql.security.UserPermissionCheck;
+import nl.knaw.huygens.timbuctoo.v5.security.dto.User;
 
 import java.util.HashSet;
 import java.util.List;
@@ -24,7 +24,6 @@
 import static nl.knaw.huygens.timbuctoo.util.Tuple.tuple;
 
 public class OtherDataSetFetcher implements DataFetcher<List<Map>> {
-
   private final DataSetRepository repo;
 
   public OtherDataSetFetcher(DataSetRepository repo) {
@@ -34,15 +33,16 @@ public OtherDataSetFetcher(DataSetRepository repo) {
   @Override
   public List<Map> get(DataFetchingEnvironment env) {
     if (env.getSource() instanceof SubjectGraphReference) {
-      final Set<String> dataSetIds = new HashSet<>();
       SubjectGraphReference source = env.getSource();
-      ContextData contextData = env.getContext();
-      Stream<DataSet> dataSets = contextData.getUser()
+      Optional<User> optUser = env.getGraphQlContext().get("user");
+      UserPermissionCheck userPermissionCheck = env.getGraphQlContext().get("userPermissionCheck");
+
+      Stream<DataSet> dataSets = optUser
         .map(user -> repo.getDataSetsWithReadAccess(user).stream())
         .orElseGet(() -> repo.getDataSets().stream().filter(d -> d.getMetadata().isPublished()));
 
       if (env.containsArgument("dataSetIds")) {
-        dataSetIds.addAll(env.getArgument("dataSetIds"));
+        final Set<String> dataSetIds = new HashSet<>(env.getArgument("dataSetIds"));
         dataSets = dataSets.filter(d -> dataSetIds.contains(d.getMetadata().getCombinedId()));
       }
       final String ownId = source.getDataSet().getMetadata().getCombinedId();
@@ -55,13 +55,11 @@ public List<Map> get(DataFetchingEnvironment env) {
         })
         .filter(i -> i.getRight().isPresent())
         .map(i -> ImmutableMap.of(
-          "metadata", new DataSetWithDatabase(i.getLeft(), env.<ContextData>getContext().getUserPermissionCheck()),
+          "metadata", new DataSetWithDatabase(i.getLeft(), userPermissionCheck),
           "entity", new LazyTypeSubjectReference(i.getRight().get().getSubject(), source.getGraph(), i.getLeft())
         ))
         .collect(toList());
-
     }
     return Lists.newArrayList();
   }
-
 }