Merge branch 'develop'

stellio-hub · Feb 28, 2023 · 205687a · 205687a
2 parents 921973c + 95f2456
commit 205687a
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diff --git a/.editorconfig b/.editorconfig
@@ -2,4 +2,5 @@
 indent_size=4
 insert_final_newline=true
 max_line_length=120
-disabled_rules=no-wildcard-imports,experimental:multiline-if-else
+ktlint_standard_no-wildcard-imports=false
+ktlint_standard_multiline-if-else=false
diff --git a/.env b/.env
@@ -11,3 +11,6 @@ STELLIO_AUTHENTICATION_ENABLED=false
 ENVIRONMENT=docker
 
 APPLICATION_ENTITY_SERVICE_URL=http://search-service:8083
+
+# Used as a base URL by subscription service when serving contexts for notifications
+APPLICATION_STELLIO_URL=http://localhost:8080
diff --git a/.github/workflows/cla.yml b/.github/workflows/cla.yml
@@ -12,7 +12,7 @@ jobs:
       - name: "CLA Assistant"
         if: (github.event.comment.body == 'recheck' || github.event.comment.body == 'I have read the CLA Document and I hereby sign the CLA') || github.event_name == 'pull_request_target'
         # Beta Release
-        uses: cla-assistant/github-action@v2.2.1
+        uses: cla-assistant/github-action@v2.3.0
         env: 
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           # the below token should have repo scope and must be manually added by you in the repository's secret

diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
@@ -0,0 +1,76 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "develop" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "develop" ]
+  schedule:
+    - cron: '34 6 * * 3'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
diff --git a/.sdkmanrc b/.sdkmanrc
@@ -0,0 +1,3 @@
+# Enable auto-env through the sdkman_auto_env config
+# Add key=value pairs of SDKs to use below
+java=17.0.6-tem
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -19,21 +19,22 @@ plugins {
     java
     // only apply the plugin in the subprojects requiring it because it expects a Spring Boot app
     // and the shared lib is obviously not one
-    id("org.springframework.boot") version "3.0.2" apply false
+    id("org.springframework.boot") version "3.0.3" apply false
     id("io.spring.dependency-management") version "1.1.0" apply false
-    id("org.graalvm.buildtools.native") version "0.9.19"
+    id("org.graalvm.buildtools.native") version "0.9.20"
     kotlin("jvm") version "1.8.10" apply false
     kotlin("plugin.spring") version "1.8.10" apply false
-    id("org.jlleitschuh.gradle.ktlint") version "11.1.0"
+    id("org.jlleitschuh.gradle.ktlint") version "11.2.0"
     id("com.google.cloud.tools.jib") version "3.3.1" apply false
     id("io.gitlab.arturbosch.detekt") version "1.22.0" apply false
-    id("org.sonarqube") version "3.5.0.2730"
+    id("org.sonarqube") version "4.0.0.2929"
     jacoco
 }
 
 subprojects {
     repositories {
         mavenCentral()
+        maven { url = uri("https://jitpack.io") }
     }
 
     apply(plugin = "io.spring.dependency-management")
@@ -92,7 +93,7 @@ subprojects {
     tasks.withType<KotlinCompile> {
         kotlinOptions {
             freeCompilerArgs = listOf("-Xjsr305=strict", "-opt-in=kotlin.RequiresOptIn")
-            jvmTarget = "17"
+            jvmTarget = "${JavaVersion.VERSION_17}"
         }
     }
     tasks.withType<Test> {
@@ -104,7 +105,7 @@ subprojects {
     }
 
     ktlint {
-        disabledRules.set(setOf("experimental:multiline-if-else", "no-wildcard-imports"))
+        disabledRules.set(setOf("multiline-if-else", "no-wildcard-imports"))
         reporters {
             reporter(ReporterType.CHECKSTYLE)
             reporter(ReporterType.PLAIN)
@@ -174,7 +175,7 @@ subprojects {
 
 allprojects {
     group = "com.egm.stellio"
-    version = "2.1.0"
+    version = "2.2.0"
 
     repositories {
         mavenCentral()

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -75,6 +75,7 @@ services:
       - SPRING_R2DBC_PASSWORD=${POSTGRES_PASS}
       - APPLICATION_AUTHENTICATION_ENABLED=${STELLIO_AUTHENTICATION_ENABLED}
       - APPLICATION_ENTITY_SERVICE-URL=${APPLICATION_ENTITY_SERVICE_URL}
+      - APPLICATION_STELLIO_URL=${APPLICATION_STELLIO_URL}
     ports:
       - "8084:8084"
     depends_on:

diff --git a/search-service/build.gradle.kts b/search-service/build.gradle.kts
@@ -19,7 +19,8 @@ dependencies {
     implementation("org.flywaydb:flyway-core")
     // implementation (and not runtime) because we are using the native jsonb encoding provided by PG
     implementation("org.postgresql:r2dbc-postgresql")
-    implementation("com.savvasdalkitsis:json-merge:0.0.6")
+    implementation("com.github.stellio-hub:json-merge:0.1.0")
+    implementation("org.json:json:20230227")
     implementation(project(":shared"))
 
     detektPlugins("io.gitlab.arturbosch.detekt:detekt-formatting:1.22.0")

diff --git a/search-service/config/detekt/baseline.xml b/search-service/config/detekt/baseline.xml
@@ -9,25 +9,21 @@
     <ID>Filename:db.migration.V0_29__JsonLd_migration.kt:1</ID>
     <ID>LongMethod:AttributeInstanceService.kt$AttributeInstanceService$@Transactional suspend fun create(attributeInstance: AttributeInstance): Either&lt;APIException, Unit&gt;</ID>
     <ID>LongMethod:EntityAccessControlHandler.kt$EntityAccessControlHandler$@PostMapping("/{subjectId}/attrs", consumes = [MediaType.APPLICATION_JSON_VALUE, JSON_LD_CONTENT_TYPE]) suspend fun addRightsOnEntities( @RequestHeader httpHeaders: HttpHeaders, @PathVariable subjectId: String, @RequestBody requestBody: Mono&lt;String&gt; ): ResponseEntity&lt;*&gt;</ID>
-    <ID>LongMethod:EntityEventServiceTests.kt$EntityEventServiceTests$@Test fun `it should publish ATTRIBUTE_APPEND and ATTRIBUTE_REPLACE events if attributes were appended and replaced`()</ID>
-    <ID>LongMethod:EntityEventServiceTests.kt$EntityEventServiceTests$@Test fun `it should publish ATTRIBUTE_REPLACE events if a multi-attribute is replaced`()</ID>
-    <ID>LongMethod:EntityEventServiceTests.kt$EntityEventServiceTests$@Test fun `it should publish ATTRIBUTE_REPLACE events if two attributes are replaced`()</ID>
     <ID>LongMethod:ParameterizedTests.kt$ParameterizedTests.Companion$@JvmStatic fun rawResultsProvider(): Stream&lt;Arguments&gt;</ID>
     <ID>LongMethod:QueryServiceTests.kt$QueryServiceTests$@Test fun `it should query temporal entities as requested by query params`()</ID>
-    <ID>LongMethod:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$@Transactional suspend fun appendEntityAttributes( entityUri: URI, ngsiLdAttributes: List&lt;NgsiLdAttribute&gt;, jsonLdAttributes: Map&lt;String, Any&gt;, disallowOverwrite: Boolean, sub: Sub? ): Either&lt;APIException, UpdateResult&gt;</ID>
-    <ID>LongMethod:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$@Transactional suspend fun partialUpdateEntityAttribute( entityId: URI, expandedPayload: Map&lt;String, List&lt;Map&lt;String, List&lt;Any&gt;&gt;&gt;&gt;, sub: Sub? ): Either&lt;APIException, UpdateResult&gt;</ID>
     <ID>LongMethod:V0_29__JsonLd_migration.kt$V0_29__JsonLd_migration$override fun migrate(context: Context)</ID>
-    <ID>LongParameterList:AttributeInstance.kt$AttributeInstance.Companion$( temporalEntityAttribute: UUID, instanceId: URI? = null, timeProperty: TemporalProperty, time: ZonedDateTime, value: String? = null, measuredValue: Double? = null, geoValue: WKTCoordinates? = null, payload: ExpandedAttributePayloadEntry, sub: String? = null )</ID>
-    <ID>LongParameterList:EntityEventService.kt$EntityEventService$( sub: String?, entityId: URI, attributeName: String, datasetId: URI? = null, deleteAll: Boolean, contexts: List&lt;String&gt; )</ID>
+    <ID>LongParameterList:AttributeInstance.kt$AttributeInstance.Companion$( temporalEntityAttribute: UUID, instanceId: URI? = null, timeProperty: TemporalProperty, time: ZonedDateTime, value: String? = null, measuredValue: Double? = null, geoValue: WKTCoordinates? = null, payload: ExpandedAttributeInstance, sub: String? = null )</ID>
+    <ID>LongParameterList:EntityEventService.kt$EntityEventService$( sub: String?, entityId: URI, attributeName: ExpandedTerm, datasetId: URI? = null, deleteAll: Boolean, contexts: List&lt;String&gt; )</ID>
     <ID>LongParameterList:EntityEventService.kt$EntityEventService$( sub: String?, entityId: URI, jsonLdAttributes: Map&lt;String, Any&gt;, updateResult: UpdateResult, overwrite: Boolean, contexts: List&lt;String&gt; )</ID>
-    <ID>LongParameterList:EntityHandler.kt$EntityHandler$( private val applicationProperties: ApplicationProperties, private val entityPayloadService: EntityPayloadService, private val temporalEntityAttributeService: TemporalEntityAttributeService, private val queryService: QueryService, private val authorizationService: AuthorizationService, private val entityAccessRightsService: EntityAccessRightsService, private val entityEventService: EntityEventService )</ID>
     <ID>LongParameterList:EntityPayloadService.kt$EntityPayloadService$( entityId: URI, types: List&lt;ExpandedTerm&gt;, createdAt: ZonedDateTime, entityPayload: String, contexts: List&lt;String&gt;, specificAccessPolicy: SpecificAccessPolicy? = null )</ID>
-    <ID>LongParameterList:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$( entityId: URI, ngsiLdAttribute: NgsiLdAttribute, attributeMetadata: AttributeMetadata, createdAt: ZonedDateTime, attributePayload: ExpandedAttributePayloadEntry, sub: Sub? )</ID>
-    <ID>LongParameterList:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$( temporalEntityAttribute: TemporalEntityAttribute, ngsiLdAttribute: NgsiLdAttribute, attributeMetadata: AttributeMetadata, createdAt: ZonedDateTime, attributePayload: ExpandedAttributePayloadEntry, sub: Sub? )</ID>
-    <ID>LongParameterList:V0_29__JsonLd_migration.kt$V0_29__JsonLd_migration$( entityId: URI, attributeName: ExpandedTerm, datasetId: URI?, attributePayload: ExpandedAttributePayloadEntry, ngsiLdAttributeInstance: NgsiLdAttributeInstance, defaultCreatedAt: ZonedDateTime )</ID>
+    <ID>LongParameterList:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$( entityId: URI, ngsiLdAttribute: NgsiLdAttribute, attributeMetadata: AttributeMetadata, createdAt: ZonedDateTime, attributePayload: ExpandedAttributeInstance, sub: Sub? )</ID>
+    <ID>LongParameterList:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$( entityUri: URI, ngsiLdAttributes: List&lt;NgsiLdAttribute&gt;, jsonLdAttributes: Map&lt;String, Any&gt;, disallowOverwrite: Boolean, createdAt: ZonedDateTime, sub: Sub? )</ID>
+    <ID>LongParameterList:TemporalEntityAttributeService.kt$TemporalEntityAttributeService$( temporalEntityAttribute: TemporalEntityAttribute, ngsiLdAttribute: NgsiLdAttribute, attributeMetadata: AttributeMetadata, createdAt: ZonedDateTime, attributePayload: ExpandedAttributeInstance, sub: Sub? )</ID>
+    <ID>LongParameterList:V0_29__JsonLd_migration.kt$V0_29__JsonLd_migration$( entityId: URI, attributeName: ExpandedTerm, datasetId: URI?, attributePayload: ExpandedAttributeInstance, ngsiLdAttributeInstance: NgsiLdAttributeInstance, defaultCreatedAt: ZonedDateTime )</ID>
     <ID>NestedBlockDepth:V0_29__JsonLd_migration.kt$V0_29__JsonLd_migration$override fun migrate(context: Context)</ID>
     <ID>SwallowedException:QueryUtils.kt$e: IllegalArgumentException</ID>
     <ID>ThrowsCount:QueryUtils.kt$fun buildTemporalQuery(params: MultiValueMap&lt;String, String&gt;, inQueryEntities: Boolean = false): TemporalQuery</ID>
+    <ID>TooManyFunctions:EntityPayloadService.kt$EntityPayloadService</ID>
     <ID>TooManyFunctions:TemporalEntityAttributeService.kt$TemporalEntityAttributeService</ID>
     <ID>UtilityClassWithPublicConstructor:ParameterizedTests.kt$ParameterizedTests</ID>
     <ID>UtilityClassWithPublicConstructor:QueryParameterizedTests.kt$QueryParameterizedTests</ID>

diff --git a/search-service/docker-compose.yml b/search-service/docker-compose.yml
@@ -1,7 +1,7 @@
-version: '3.5'
+version: '3.9'
 services:
   kafka:
-    image: confluentinc/cp-kafka:7.2.0
+    image: confluentinc/cp-kafka:7.3.1
     container_name: stellio-kafka
     hostname: stellio-kafka
     ports:
@@ -22,19 +22,24 @@ services:
       - ../config/kafka/update_run.sh:/tmp/update_run.sh
     command: "bash -c 'if [ ! -f /tmp/update_run.sh ]; then echo \"ERROR: Did you forget the update_run.sh file that came with this docker-compose.yml file?\" && exit 1 ; else /tmp/update_run.sh && /etc/confluent/docker/run ; fi'"
   postgres:
-    image: stellio/postgis:14-3.3-timescale
+    image: stellio/stellio-timescale-postgis:14-2.9.1-3.3
+    container_name: stellio-postgres
     environment:
-      - DATADIR=/var/lib/postgresql/data
-      - POSTGRES_TEMPLATE_EXTENSIONS=true
       - POSTGRES_USER=${POSTGRES_USER}
       - POSTGRES_PASS=${POSTGRES_PASS}
       - POSTGRES_DBNAME=stellio_search
-      - POSTGRES_MULTIPLE_EXTENSIONS=postgis,hstore,postgis_topology,postgis_raster,pgrouting,timescaledb,pgcrypto
+      - POSTGRES_MULTIPLE_EXTENSIONS=postgis,timescaledb,pgcrypto
       - ACCEPT_TIMESCALE_TUNING=TRUE
     ports:
       - "5432:5432"
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready -h localhost -U stellio"]
+      interval: 10s
+      timeout: 5s
+      retries: 20
+      start_period: 10s
     volumes:
-      - stellio-search-postgres-storage:/var/lib/postgresql/data
+      - stellio-search-postgres-storage:/var/lib/postgresql
 
 volumes:
   stellio-search-postgres-storage:
diff --git a/search-service/src/main/kotlin/com/egm/stellio/search/authorization/AuthorizationService.kt b/search-service/src/main/kotlin/com/egm/stellio/search/authorization/AuthorizationService.kt
@@ -16,13 +16,15 @@ interface AuthorizationService {
     suspend fun userCanReadEntity(entityId: URI, sub: Option<Sub>): Either<APIException, Unit>
     suspend fun userCanUpdateEntity(entityId: URI, sub: Option<Sub>): Either<APIException, Unit>
     suspend fun userCanAdminEntity(entityId: URI, sub: Option<Sub>): Either<APIException, Unit>
-    suspend fun createAdminLink(entityId: URI, sub: Option<Sub>): Either<APIException, Unit>
-    suspend fun createAdminLinks(entitiesId: List<URI>, sub: Option<Sub>): Either<APIException, Unit>
+
+    suspend fun createAdminRight(entityId: URI, sub: Option<Sub>): Either<APIException, Unit>
+    suspend fun createAdminRights(entitiesId: List<URI>, sub: Option<Sub>): Either<APIException, Unit>
+    suspend fun removeRightsOnEntity(entityId: URI): Either<APIException, Unit>
 
     suspend fun getAuthorizedEntities(
         queryParams: QueryParams,
         context: String,
-        sub: Option<Sub>,
+        sub: Option<Sub>
     ): Either<APIException, Pair<Int, List<JsonLdEntity>>>
 
     suspend fun getGroupsMemberships(

diff --git a/...vice/src/main/kotlin/com/egm/stellio/search/authorization/DisabledAuthorizationService.kt b/...vice/src/main/kotlin/com/egm/stellio/search/authorization/DisabledAuthorizationService.kt
@@ -29,14 +29,16 @@ class DisabledAuthorizationService : AuthorizationService {
     override suspend fun userCanAdminEntity(entityId: URI, sub: Option<Sub>): Either<APIException, Unit> =
         Unit.right()
 
-    override suspend fun createAdminLink(entityId: URI, sub: Option<Sub>): Either<APIException, Unit> =
+    override suspend fun createAdminRight(entityId: URI, sub: Option<Sub>): Either<APIException, Unit> =
         Unit.right()
 
-    override suspend fun createAdminLinks(
+    override suspend fun createAdminRights(
         entitiesId: List<URI>,
         sub: Option<Sub>
     ): Either<APIException, Unit> = Unit.right()
 
+    override suspend fun removeRightsOnEntity(entityId: URI): Either<APIException, Unit> = Unit.right()
+
     override suspend fun getAuthorizedEntities(
         queryParams: QueryParams,
         context: String,

diff --git a/...rvice/src/main/kotlin/com/egm/stellio/search/authorization/EnabledAuthorizationService.kt b/...rvice/src/main/kotlin/com/egm/stellio/search/authorization/EnabledAuthorizationService.kt
@@ -82,14 +82,17 @@ class EnabledAuthorizationService(
             rights
         )
 
-    override suspend fun createAdminLink(entityId: URI, sub: Option<Sub>): Either<APIException, Unit> =
-        createAdminLinks(listOf(entityId), sub)
+    override suspend fun createAdminRight(entityId: URI, sub: Option<Sub>): Either<APIException, Unit> =
+        createAdminRights(listOf(entityId), sub)
 
-    override suspend fun createAdminLinks(entitiesId: List<URI>, sub: Option<Sub>): Either<APIException, Unit> =
+    override suspend fun createAdminRights(entitiesId: List<URI>, sub: Option<Sub>): Either<APIException, Unit> =
         entitiesId.parTraverseEither {
             entityAccessRightsService.setAdminRoleOnEntity((sub as Some).value, it)
         }.map { it.first() }
 
+    override suspend fun removeRightsOnEntity(entityId: URI): Either<APIException, Unit> =
+        entityAccessRightsService.removeRolesOnEntity(entityId)
+
     override suspend fun getAuthorizedEntities(
         queryParams: QueryParams,
         context: String,
@@ -130,7 +133,7 @@ class EnabledAuthorizationService(
         val count = entityAccessRightsService.getSubjectAccessRightsCount(
             sub,
             accessRights,
-            queryParams.types,
+            queryParams.types
         ).bind()
 
         Pair(count, entitiesAccessControlWithSubjectRights)

diff --git a/search-service/src/main/kotlin/com/egm/stellio/search/authorization/EntityAccessRights.kt b/search-service/src/main/kotlin/com/egm/stellio/search/authorization/EntityAccessRights.kt
@@ -37,7 +37,7 @@ data class EntityAccessRights(
     ) {
         val datasetId: URI = (DATASET_ID_PREFIX + uri.extractSub()).toUri()
 
-        fun serializeProperties(): ExpandedAttributePayload =
+        fun serializeProperties(): ExpandedAttributeInstances =
             buildExpandedRelationship(uri)
                 .addSubAttribute(NGSILD_DATASET_ID_PROPERTY, buildNonReifiedProperty(datasetId.toString()))
                 .addSubAttribute(AUTH_PROP_SUBJECT_INFO, buildExpandedSubjectInfo(subjectInfo))
@@ -100,7 +100,7 @@ data class EntityAccessRights(
  *   }
  * ]
  */
-private fun buildExpandedSubjectInfo(value: Map<String, String>): ExpandedAttributePayload =
+private fun buildExpandedSubjectInfo(value: Map<String, String>): ExpandedAttributeInstances =
     listOf(
         mapOf(
             JSONLD_TYPE to listOf(NGSILD_PROPERTY_TYPE.uri),

diff --git a/...service/src/main/kotlin/com/egm/stellio/search/authorization/EntityAccessRightsService.kt b/...service/src/main/kotlin/com/egm/stellio/search/authorization/EntityAccessRightsService.kt
@@ -203,6 +203,18 @@ class EntityAccessRightsService(
                 else it
             }
             .allToMappedList { rowToEntityAccessControl(it, isStellioAdmin) }
+            .groupBy { it.id }
+            // a user may have multiple rights on a given entity (e.g., through groups memberships)
+            // retain the one with the "higher" right
+            .mapValues {
+                val ear = it.value.first()
+                EntityAccessRights(
+                    ear.id,
+                    ear.types,
+                    it.value.maxOf { it.right },
+                    ear.specificAccessPolicy
+                )
+            }.values.toList()
     }
 
     suspend fun getSubjectAccessRightsCount(