Examples with QuadStore nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore used on opensource projects

Example 1 with QuadStore

use of nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore in project timbuctoo by HuygensING.

the class RootQuery method rebuildSchema.

public synchronized GraphQLSchema rebuildSchema() {
    final TypeDefinitionRegistry staticQuery = schemaParser.parse(this.staticQuery);
    if (archetypes != null && !archetypes.isEmpty()) {
        staticQuery.merge(schemaParser.parse(archetypes + "extend type DataSetMetadata {\n" + "  archetypes: Archetypes! @passThrough\n" + "}\n" + "\n"));
    }
    TypeDefinitionRegistry registry = new TypeDefinitionRegistry();
    registry.merge(staticQuery);
    final RuntimeWiring.Builder wiring = RuntimeWiring.newRuntimeWiring();
    wiring.type("Query", builder -> builder.dataFetcher("promotedDataSets", env -> dataSetRepository.getPromotedDataSets().stream().map(DataSetWithDatabase::new).collect(Collectors.toList())).dataFetcher("allDataSets", env -> dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new).filter(x -> {
        if (x.isPublished()) {
            return true;
        } else {
            ContextData contextData = env.getContext();
            UserPermissionCheck userPermissionCheck = contextData.getUserPermissionCheck();
            return userPermissionCheck.getPermissions(x.getDataSet().getMetadata()).contains(Permission.READ);
        }
    }).collect(Collectors.toList())).dataFetcher("dataSetMetadata", env -> {
        final String dataSetId = env.getArgument("dataSetId");
        ContextData context = env.getContext();
        final User user = context.getUser().orElse(null);
        Tuple<String, String> splitCombinedId = DataSetMetaData.splitCombinedId(dataSetId);
        return dataSetRepository.getDataSet(user, splitCombinedId.getLeft(), splitCombinedId.getRight()).map(DataSetWithDatabase::new);
    }).dataFetcher("dataSetMetadataList", env -> {
        Stream<DataSetWithDatabase> dataSets = dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new);
        if (env.getArgument("promotedOnly")) {
            dataSets = dataSets.filter(DataSetWithDatabase::isPromoted);
        }
        if (env.getArgument("publishedOnly")) {
            dataSets = dataSets.filter(DataSetWithDatabase::isPublished);
        }
        return dataSets.filter(x -> {
            ContextData contextData = env.getContext();
            UserPermissionCheck userPermissionCheck = contextData.getUserPermissionCheck();
            return userPermissionCheck.getPermissions(x.getDataSet().getMetadata()).contains(Permission.READ);
        }).collect(Collectors.toList());
    }).dataFetcher("aboutMe", env -> ((RootData) env.getRoot()).getCurrentUser().orElse(null)).dataFetcher("availableExportMimetypes", env -> supportedFormats.getSupportedMimeTypes().stream().map(MimeTypeDescription::create).collect(Collectors.toList())));
    wiring.type("DataSetMetadata", builder -> builder.dataFetcher("currentImportStatus", env -> {
        DataSetMetaData input = env.getSource();
        Optional<User> currentUser = ((RootData) env.getRoot()).getCurrentUser();
        if (!currentUser.isPresent()) {
            throw new RuntimeException("User is not provided");
        }
        return dataSetRepository.getDataSet(currentUser.get(), input.getOwnerId(), input.getDataSetId()).map(dataSet -> dataSet.getImportManager().getImportStatus());
    }).dataFetcher("dataSetImportStatus", env -> {
        Optional<User> currentUser = ((RootData) env.getRoot()).getCurrentUser();
        if (!currentUser.isPresent()) {
            throw new RuntimeException("User is not provided");
        }
        DataSetMetaData input = env.getSource();
        return dataSetRepository.getDataSet(currentUser.get(), input.getOwnerId(), input.getDataSetId()).map(dataSet -> dataSet.getImportManager().getDataSetImportStatus());
    }).dataFetcher("collectionList", env -> getCollections(env.getSource(), ((ContextData) env.getContext()).getUser())).dataFetcher("collection", env -> {
        String collectionId = (String) env.getArguments().get("collectionId");
        if (collectionId != null && collectionId.endsWith("List")) {
            collectionId = collectionId.substring(0, collectionId.length() - "List".length());
        }
        DataSetMetaData input = env.getSource();
        ContextData context = env.getContext();
        final User user = context.getUser().orElse(null);
        final DataSet dataSet = dataSetRepository.getDataSet(user, input.getOwnerId(), input.getDataSetId()).get();
        final TypeNameStore typeNameStore = dataSet.getTypeNameStore();
        String collectionUri = typeNameStore.makeUri(collectionId);
        if (dataSet.getSchemaStore().getStableTypes() == null || dataSet.getSchemaStore().getStableTypes().get(collectionUri) == null) {
            return null;
        } else {
            return getCollection(dataSet, typeNameStore, dataSet.getSchemaStore().getStableTypes().get(collectionUri));
        }
    }).dataFetcher("dataSetId", env -> ((DataSetMetaData) env.getSource()).getCombinedId()).dataFetcher("dataSetName", env -> ((DataSetMetaData) env.getSource()).getDataSetId()).dataFetcher("ownerId", env -> ((DataSetMetaData) env.getSource()).getOwnerId()));
    wiring.type("CurrentImportStatus", builder -> builder.dataFetcher("elapsedTime", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((ImportStatus) env.getSource()).getElapsedTime(timeUnit);
    }));
    wiring.type("DataSetImportStatus", builder -> builder.dataFetcher("lastImportDuration", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((DataSetImportStatus) env.getSource()).getLastImportDuration(timeUnit);
    }));
    wiring.type("EntryImportStatus", builder -> builder.dataFetcher("elapsedTime", env -> {
        final String timeUnit = env.getArgument("unit");
        return ((EntryImportStatus) env.getSource()).getElapsedTime(timeUnit);
    }));
    wiring.type("CollectionMetadata", builder -> builder.dataFetcher("indexConfig", env -> {
        SubjectReference source = env.getSource();
        final QuadStore qs = source.getDataSet().getQuadStore();
        try (Stream<CursorQuad> quads = qs.getQuads(source.getSubjectUri(), TIM_HASINDEXERCONFIG, Direction.OUT, "")) {
            final Map result = quads.findFirst().map(q -> {
                try {
                    return objectMapper.readValue(q.getObject(), Map.class);
                } catch (IOException e) {
                    LOG.error("Value not a Map", e);
                    return new HashMap<>();
                }
            }).orElse(new HashMap());
            if (!result.containsKey("facet") || !(result.get("facet") instanceof List)) {
                result.put("facet", new ArrayList<>());
            }
            if (!result.containsKey("fullText") || !(result.get("fullText") instanceof List)) {
                result.put("fullText", new ArrayList<>());
            }
            return result;
        }
    }).dataFetcher("viewConfig", new ViewConfigFetcher(objectMapper)));
    wiring.type("AboutMe", builder -> builder.dataFetcher("dataSets", env -> (Iterable) () -> dataSetRepository.getDataSetsWithWriteAccess(env.getSource()).stream().map(DataSetWithDatabase::new).iterator()).dataFetcher("dataSetMetadataList", env -> (Iterable) () -> {
        Stream<DataSetWithDatabase> dataSets = dataSetRepository.getDataSets().stream().map(DataSetWithDatabase::new);
        if (env.getArgument("ownOnly")) {
            String userId = ((ContextData) env.getContext()).getUser().map(u -> "u" + u.getPersistentId()).orElse(null);
            dataSets = dataSets.filter(d -> d.getOwnerId().equals(userId));
        }
        Permission permission = Permission.valueOf(env.getArgument("permission"));
        if (permission != Permission.READ) {
            // Read is implied
            UserPermissionCheck check = ((ContextData) env.getContext()).getUserPermissionCheck();
            dataSets = dataSets.filter(d -> check.getPermissions(d).contains(permission));
        }
        return dataSets.iterator();
    }).dataFetcher("id", env -> ((User) env.getSource()).getPersistentId()).dataFetcher("name", env -> ((User) env.getSource()).getDisplayName()).dataFetcher("personalInfo", env -> "http://example.com").dataFetcher("canCreateDataSet", env -> true));
    wiring.type("Mutation", builder -> builder.dataFetcher("setViewConfig", new ViewConfigMutation(dataSetRepository)).dataFetcher("setSummaryProperties", new SummaryPropsMutation(dataSetRepository)).dataFetcher("setIndexConfig", new IndexConfigMutation(dataSetRepository)).dataFetcher("createDataSet", new CreateDataSetMutation(dataSetRepository)).dataFetcher("deleteDataSet", new DeleteDataSetMutation(dataSetRepository)).dataFetcher("publish", new MakePublicMutation(dataSetRepository)).dataFetcher("extendSchema", new ExtendSchemaMutation(dataSetRepository)).dataFetcher("setDataSetMetadata", new DataSetMetadataMutation(dataSetRepository)).dataFetcher("setCollectionMetadata", new CollectionMetadataMutation(dataSetRepository)));
    wiring.wiringFactory(wiringFactory);
    StringBuilder root = new StringBuilder("type DataSets {\n sillyWorkaroundWhenNoDataSetsAreVisible: Boolean\n");
    boolean[] dataSetAvailable = new boolean[] { false };
    dataSetRepository.getDataSets().forEach(dataSet -> {
        final DataSetMetaData dataSetMetaData = dataSet.getMetadata();
        final String name = dataSetMetaData.getCombinedId();
        Map<String, Type> types = dataSet.getSchemaStore().getStableTypes();
        Map<String, List<ExplicitField>> customSchema = dataSet.getCustomSchema();
        final Map<String, Type> customTypes = new HashMap<>();
        for (Map.Entry<String, List<ExplicitField>> entry : customSchema.entrySet()) {
            ExplicitType explicitType = new ExplicitType(entry.getKey(), entry.getValue());
            customTypes.put(entry.getKey(), explicitType.convertToType());
        }
        Map<String, Type> mergedTypes;
        MergeSchemas mergeSchemas = new MergeSchemas();
        mergedTypes = mergeSchemas.mergeSchema(types, customTypes);
        types = mergedTypes;
        if (types != null) {
            dataSetAvailable[0] = true;
            root.append("  ").append(name).append(":").append(name).append(" @dataSet(userId:\"").append(dataSetMetaData.getOwnerId()).append("\", dataSetId:\"").append(dataSetMetaData.getDataSetId()).append("\")\n");
            wiring.type(name, c -> c.dataFetcher("metadata", env -> new DataSetWithDatabase(dataSet)));
            final String schema = typeGenerator.makeGraphQlTypes(name, types, dataSet.getTypeNameStore());
            staticQuery.merge(schemaParser.parse(schema));
        }
    });
    root.append("}\n\nextend type Query {\n  #The actual dataSets\n  dataSets: DataSets @passThrough\n}\n\n");
    if (dataSetAvailable[0]) {
        staticQuery.merge(schemaParser.parse(root.toString()));
    }
    SchemaGenerator schemaGenerator = new SchemaGenerator();
    return schemaGenerator.makeExecutableSchema(staticQuery, wiring.build());
}

Example 2 with QuadStore

use of nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore in project timbuctoo by HuygensING.

the class SummaryPropDataRetriever method createSummaryProperty.

public Optional<TypedValue> createSummaryProperty(SubjectReference source, DataSet dataSet) {
    QuadStore quadStore = dataSet.getQuadStore();
    final Optional<TypedValue> localConfiguredSummaryProp = getQuad(quadStore, source.getSubjectUri(), RdfConstants.RDF_TYPE).flatMap(collection -> getQuad(quadStore, collection.getObject(), summaryPropConfigPredicate)).flatMap(userConfigured -> {
        try {
            SummaryProp summaryProp = OBJECT_MAPPER.readValue(userConfigured.getObject(), SummaryProp.class);
            return getQuad(summaryProp.getPath(), source.getSubjectUri(), quadStore).map(quad -> createTypedValue(quad, dataSet));
        } catch (IOException e) {
            LOG.error("Cannot parse SummaryProp: '{}'", userConfigured.getObject());
        }
        return Optional.empty();
    });
    if (localConfiguredSummaryProp.isPresent()) {
        return localConfiguredSummaryProp;
    } else {
        // fallback to default summary props
        for (SummaryProp prop : defaultProperties) {
            Optional<CursorQuad> quad = getQuad(prop.getPath(), source.getSubjectUri(), quadStore);
            if (quad.isPresent()) {
                return Optional.of(createTypedValue(quad.get(), dataSet));
            }
        }
        return Optional.empty();
    }
}

Example 3 with QuadStore

use of nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore in project timbuctoo by HuygensING.

the class JsonProvenanceToRdfPatch method collectReplacements.

public static Map<String, List<CursorQuad>> collectReplacements(JsonNode activity, QuadStore quadStore) {
    Map<String, List<CursorQuad>> toReplace = new HashMap<>();
    for (JsonNode revision : activity.get(PROV_GENERATES)) {
        final JsonNode replacements = revision.get(TIM_REPLACEMENTS);
        if (replacements != null) {
            String entity = revision.get(PROV_SPECIALIZATION_OF).get(0).get("@id").asText();
            List<CursorQuad> quads = new ArrayList<>();
            toReplace.put(revision.get("@id").asText(), quads);
            for (JsonNode replacement : replacements) {
                if (replacement.has(TIM_PREDICATE)) {
                    final String predicate = replacement.get(TIM_PREDICATE).get(0).get("@value").asText();
                    try (Stream<CursorQuad> source = quadStore.getQuads(entity, predicate, Direction.OUT, "")) {
                        source.forEach(quads::add);
                    }
                }
            }
        }
    }
    return toReplace;
}

Example 4 with QuadStore

use of nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore in project timbuctoo by HuygensING.

the class ViewConfigFetcher method get.

@Override
public Object get(DataFetchingEnvironment env) {
    SubjectReference source = env.getSource();
    final DataSet dataSet = source.getDataSet();
    final QuadStore qs = dataSet.getQuadStore();
    final Map<String, Type> schema = dataSet.getSchemaStore().getStableTypes();
    final TypeNameStore typeNameStore = dataSet.getTypeNameStore();
    try (Stream<CursorQuad> quads = qs.getQuads(source.getSubjectUri(), HAS_VIEW_CONFIG, Direction.OUT, "")) {
        return quads.findFirst().flatMap(q -> {
            try {
                return Optional.ofNullable(objectMapper.readValue(q.getObject(), List.class));
            } catch (IOException e) {
                LOG.error("view config is not a valid JSON object", e);
                return Optional.empty();
            }
        }).orElseGet(() -> makeDefaultViewConfig(source.getSubjectUri(), schema, typeNameStore));
    }
}

Example 5 with QuadStore

use of nl.knaw.huygens.timbuctoo.v5.datastores.quadstore.QuadStore in project timbuctoo by HuygensING.

the class SummaryPropDataRetrieverTest method createSummaryPropertyIgnoresValueTypesIfThePathIsLongerThanOne.

@Test
public void createSummaryPropertyIgnoresValueTypesIfThePathIsLongerThanOne() {
    List<SummaryProp> defaultProperties = Lists.newArrayList(summaryPropertyWithPath("http://example.org/path", "http://example.org/path2"));
    SummaryPropDataRetriever instance = new SummaryPropDataRetriever("http://example.org/userConfigured", defaultProperties);
    QuadStore quadStore = mock(QuadStore.class);
    CursorQuad foundQuad1 = quadWithObject("http://example.org/objectFound1", Optional.of(RdfConstants.STRING));
    CursorQuad foundQuad2 = quadWithObject("http://example.org/objectFound2", Optional.empty());
    given(quadStore.getQuads("http://example.org/source", "http://example.org/path", Direction.OUT, "")).willReturn(Stream.of(foundQuad1, foundQuad2));
    CursorQuad quadThatShouldNotBeFound = quadWithObject("http://example.org/objectThatShouldNotBeRetrieved", Optional.empty());
    given(quadStore.getQuads("http://example.org/objectFound1", "http://example.org/path2", Direction.OUT, "")).willReturn(Stream.of(quadThatShouldNotBeFound));
    CursorQuad quadWithObjectUriOfPath2 = quadWithObject("http://example.org/objectOfPath2", Optional.empty());
    given(quadStore.getQuads("http://example.org/objectFound2", "http://example.org/path2", Direction.OUT, "")).willReturn(Stream.of(quadWithObjectUriOfPath2));
    Optional<TypedValue> summaryProperty = instance.createSummaryProperty(subjectWithUri("http://example.org/source"), dataSetWithQuadStore(quadStore));
    assertThat(summaryProperty, is(present()));
    assertThat(summaryProperty.get(), hasProperty("value", is("http://example.org/objectOfPath2")));
    verify(quadStore).getQuads("http://example.org/source", "http://example.org/path", Direction.OUT, "");
    verify(quadStore).getQuads("http://example.org/objectFound2", "http://example.org/path2", Direction.OUT, "");
}