Get rid of Symbols synchronization on Usages, Builders feaures (#190)

* Indexing is broken in case of turned on Foreign keys #184

* Indexing is broken in case of turned on Foreign keys #184

* fix tests

Author: lehvolk

build.gradle.kts

@@ -5,14 +5,14 @@ val semVer: String? by project
 val includeDokka: String? by project
 
 group = "org.jacodb"
-version = semVer ?: "1.3-SNAPSHOT"
+version = semVer ?: "1.4-SNAPSHOT"
 
 plugins {
     kotlin("jvm") version Versions.kotlin
     kotlin("plugin.allopen") version Versions.kotlin
     kotlin("plugin.serialization") version Versions.kotlin apply false
-    with(Plugins.Dokka) { id(id) version (version) }
-    with(Plugins.Licenser) { id(id) version (version) }
+    id(Plugins.Dokka)
+    id(Plugins.Licenser)
     `java-library`
     `java-test-fixtures`
     `maven-publish`
@@ -96,6 +96,13 @@ allprojects {
             setup(jacocoTestReport)
         }
 
+        jar {
+            manifest {
+                attributes["Implementation-Title"] = project.name
+                attributes["Implementation-Version"] = archiveVersion
+            }
+        }
+
         val lifecycleTest by creating(Test::class) {
             useJUnitPlatform {
                 includeTags(Tests.lifecycleTag)

buildSrc/src/main/kotlin/Dependencies.kt

@@ -1,12 +1,15 @@
 @file:Suppress("PublicApiImplicitType", "MemberVisibilityCanBePrivate", "unused", "ConstPropertyName")
 
+import org.gradle.plugin.use.PluginDependenciesSpec
+
+
 object Versions {
     const val asm = "9.5"
     const val dokka = "1.7.20"
     const val gradle_download = "5.3.0"
     const val gradle_versions = "0.47.0"
-    const val guava = "31.1-jre"
     const val hikaricp = "5.0.1"
+    const val guava = "31.1-jre"
     const val javax_activation = "1.1"
     const val javax_mail = "1.4.7"
     const val javax_servlet_api = "2.5"
@@ -27,7 +30,6 @@ object Versions {
     const val kotlinx_serialization = "1.4.1"
     const val licenser = "0.6.1"
     const val mockito = "4.8.0"
-    const val postgresql = "42.5.1"
     const val shadow = "8.1.1"
     const val slf4j = "1.7.36"
     const val soot_utbot_fork = "4.4.0-FORK-2"
@@ -157,13 +159,6 @@ object Libs {
         version = Versions.kotlinx_cli
     )
 
-    // https://github.com/pgjdbc/pgjdbc
-    val postgresql = dep(
-        group = "org.postgresql",
-        name = "postgresql",
-        version = Versions.postgresql
-    )
-
     // https://github.com/brettwooldridge/HikariCP
     val hikaricp = dep(
         group = "com.zaxxer",
@@ -283,39 +278,46 @@ object Libs {
 }
 
 object Plugins {
+
+    abstract class ProjectPlugin(val version: String, val id: String)
+
     // https://github.com/Kotlin/dokka
-    object Dokka {
-        const val version = Versions.dokka
-        const val id = "org.jetbrains.dokka"
-    }
+    object Dokka: ProjectPlugin(
+        version = Versions.dokka,
+        id = "org.jetbrains.dokka"
+    )
 
     // https://github.com/michel-kraemer/gradle-download-task
-    object GradleDownload {
-        const val version = Versions.gradle_download
-        const val id = "de.undercouch.download"
-    }
+    object GradleDownload: ProjectPlugin(
+        version = Versions.gradle_download,
+        id = "de.undercouch.download"
+    )
 
     // https://github.com/ben-manes/gradle-versions-plugin
-    object GradleVersions {
-        const val version = Versions.gradle_versions
-        const val id = "com.github.ben-manes.versions"
-    }
+    object GradleVersions: ProjectPlugin(
+        version = Versions.gradle_versions,
+        id = "com.github.ben-manes.versions"
+    )
 
     // https://github.com/Kotlin/kotlinx-benchmark
-    object KotlinxBenchmark {
-        const val version = Versions.kotlinx_benchmark
-        const val id = "org.jetbrains.kotlinx.benchmark"
-    }
+    object KotlinxBenchmark : ProjectPlugin(
+        version = Versions.kotlinx_benchmark,
+        id = "org.jetbrains.kotlinx.benchmark"
+    )
 
     // https://github.com/CadixDev/licenser
-    object Licenser {
-        const val version = Versions.licenser
-        const val id = "org.cadixdev.licenser"
-    }
+    object Licenser : ProjectPlugin(
+        version = Versions.licenser,
+        id = "org.cadixdev.licenser"
+    )
 
     // https://github.com/johnrengelman/shadow
-    object Shadow {
-        const val version = Versions.shadow
-        const val id = "com.github.johnrengelman.shadow"
-    }
+    object Shadow : ProjectPlugin(
+        version = Versions.shadow,
+        id = "com.github.johnrengelman.shadow"
+    )
 }
+
+fun PluginDependenciesSpec.id(plugin: Plugins.ProjectPlugin) {
+    id(plugin.id).version(plugin.version)
+}

jacodb-api/src/main/kotlin/org/jacodb/api/Api.kt

@@ -158,8 +158,6 @@ interface JcDatabasePersistence : Closeable {
     fun findClassSources(cp: JcClasspath, fullName: String): List<ClassSource>
 
     fun createIndexes() {}
-
-    fun getScript(name: String): String
 }
 
 interface RegisteredLocation {

jacodb-benchmarks/build.gradle.kts

@@ -3,8 +3,8 @@ import kotlinx.benchmark.gradle.JvmBenchmarkTarget
 
 plugins {
     `java-test-fixtures`
-    with(Plugins.GradleDownload) { id(id) version (version) }
-    with(Plugins.KotlinxBenchmark) { id(id) version (version) }
+    id(Plugins.GradleDownload)
+    id(Plugins.KotlinxBenchmark)
 }
 
 dependencies {

jacodb-benchmarks/src/test/kotlin/org/jacodb/testing/performance/TakeMemoryDump.kt

@@ -29,9 +29,9 @@ fun main() {
     runBlocking {
         val db = jacodb {
             loadByteCode(allClasspath)
-            persistent(
-                "d:\\work\\jacodb\\jacodb-classpath.db",
-            )
+//            persistent(
+//                "d:\\work\\jacodb\\jacodb-classpath.db",
+//            )
             installFeatures(InMemoryHierarchy, Usages, Builders)
         }.also {
             println("AWAITING db took ${System.currentTimeMillis() - start}ms")

jacodb-core/build.gradle.kts

@@ -1,9 +1,6 @@
 import org.jooq.codegen.GenerationTool
+import org.jooq.meta.jaxb.*
 import org.jooq.meta.jaxb.Configuration
-import org.jooq.meta.jaxb.Database
-import org.jooq.meta.jaxb.Generate
-import org.jooq.meta.jaxb.Generator
-import org.jooq.meta.jaxb.Jdbc
 import org.jooq.meta.jaxb.Target
 import java.nio.file.Paths
 
@@ -18,7 +15,7 @@ buildscript {
         classpath(Libs.jooq_kotlin)
         // classpath(Libs.postgresql)
         // classpath(Libs.hikaricp)
-        // classpath(Libs.sqlite)
+         classpath(Libs.sqlite)
     }
 }
 
@@ -38,15 +35,13 @@ dependencies {
     implementation(Libs.kotlinx_serialization_cbor)
     implementation(Libs.jdot)
     implementation(Libs.guava)
-    implementation(Libs.postgresql)
-    implementation(Libs.hikaricp)
     implementation(Libs.sqlite)
 
     testImplementation(Libs.javax_activation)
     testImplementation(Libs.javax_mail)
     testImplementation(Libs.joda_time)
     testImplementation(Libs.slf4j_simple)
-    // testImplementation(files("src/test/resources/samples"))
+    testImplementation(Libs.hikaricp)
 
     testFixturesImplementation(project(":jacodb-api"))
     testFixturesImplementation(kotlin("reflect"))
@@ -58,10 +53,10 @@ dependencies {
     testFixturesImplementation(Libs.kotlinx_coroutines_core)
 }
 
-tasks.register("generateSqlScheme") {
-    val databaseLocation = project.properties["database_location"]
-    if (databaseLocation != null) {
-        val url = "jdbc:sqlite:file:$databaseLocation"
+tasks {
+    register("generateSqlScheme") {
+        val location = "src/main/resources/sqlite/empty.db"
+        val url = "jdbc:sqlite:file:$location"
         val driver = "org.sqlite.JDBC"
         GenerationTool.generate(
             Configuration()
@@ -86,12 +81,18 @@ tasks.register("generateSqlScheme") {
                 )
         )
     }
-}
 
-tasks.register<JavaExec>("generateDocSvgs") {
-    dependsOn("testClasses")
-    mainClass.set("org.utbot.jcdb.impl.cfg.IRSvgGeneratorKt")
-    classpath = sourceSets.test.get().runtimeClasspath
-    val svgDocs = Paths.get(rootDir.absolutePath, "docs", "svg").toFile()
-    args = listOf(svgDocs.absolutePath)
+    register<JavaExec>("generateDocSvgs") {
+        dependsOn("testClasses")
+        mainClass.set("org.utbot.jcdb.impl.cfg.IRSvgGeneratorKt")
+        classpath = sourceSets.test.get().runtimeClasspath
+        val svgDocs = Paths.get(rootDir.absolutePath, "docs", "svg").toFile()
+        args = listOf(svgDocs.absolutePath)
+    }
+
+    processResources {
+        filesMatching("**/*.properties") {
+            expand("version" to project.version)
+        }
+    }
 }

jacodb-core/src/main/jooq/org/jacodb/impl/storage/jooq/DefaultSchema.kt

@@ -20,24 +20,10 @@
 package org.jacodb.impl.storage.jooq
 
 
-import kotlin.collections.List
-
+import org.jacodb.impl.storage.jooq.tables.*
 import org.jooq.Catalog
 import org.jooq.Table
 import org.jooq.impl.SchemaImpl
-import org.jacodb.impl.storage.jooq.tables.Annotations
-import org.jacodb.impl.storage.jooq.tables.Annotationvalues
-import org.jacodb.impl.storage.jooq.tables.Builders
-import org.jacodb.impl.storage.jooq.tables.Bytecodelocations
-import org.jacodb.impl.storage.jooq.tables.Calls
-import org.jacodb.impl.storage.jooq.tables.Classes
-import org.jacodb.impl.storage.jooq.tables.Classhierarchies
-import org.jacodb.impl.storage.jooq.tables.Classinnerclasses
-import org.jacodb.impl.storage.jooq.tables.Fields
-import org.jacodb.impl.storage.jooq.tables.Methodparameters
-import org.jacodb.impl.storage.jooq.tables.Methods
-import org.jacodb.impl.storage.jooq.tables.Outerclasses
-import org.jacodb.impl.storage.jooq.tables.Symbols
 
 
 /**
@@ -63,6 +49,11 @@ open class DefaultSchema : SchemaImpl("", DefaultCatalog.DEFAULT_CATALOG) {
      */
     val ANNOTATIONVALUES get() = Annotationvalues.ANNOTATIONVALUES
 
+    /**
+     * The table <code>ApplicationMetadata</code>.
+     */
+    val APPLICATIONMETADATA get() = Applicationmetadata.APPLICATIONMETADATA
+
     /**
      * The table <code>Builders</code>.
      */
@@ -113,6 +104,11 @@ open class DefaultSchema : SchemaImpl("", DefaultCatalog.DEFAULT_CATALOG) {
      */
     val OUTERCLASSES get() = Outerclasses.OUTERCLASSES
 
+    /**
+     * The table <code>Refactorings</code>.
+     */
+    val REFACTORINGS get() = Refactorings.REFACTORINGS
+
     /**
      * The table <code>Symbols</code>.
      */
@@ -123,6 +119,7 @@ open class DefaultSchema : SchemaImpl("", DefaultCatalog.DEFAULT_CATALOG) {
     override fun getTables(): List<Table<*>> = listOf(
         Annotations.ANNOTATIONS,
         Annotationvalues.ANNOTATIONVALUES,
+        Applicationmetadata.APPLICATIONMETADATA,
         Builders.BUILDERS,
         Bytecodelocations.BYTECODELOCATIONS,
         Calls.CALLS,
@@ -133,6 +130,7 @@ open class DefaultSchema : SchemaImpl("", DefaultCatalog.DEFAULT_CATALOG) {
         Methodparameters.METHODPARAMETERS,
         Methods.METHODS,
         Outerclasses.OUTERCLASSES,
+        Refactorings.REFACTORINGS,
         Symbols.SYMBOLS
     )
 }

jacodb-core/src/main/jooq/org/jacodb/impl/storage/jooq/indexes/Indexes.kt

@@ -20,19 +20,36 @@
 package org.jacodb.impl.storage.jooq.indexes
 
 
+import org.jacodb.impl.storage.jooq.tables.*
 import org.jooq.Index
 import org.jooq.impl.DSL
 import org.jooq.impl.Internal
-import org.jacodb.impl.storage.jooq.tables.Builders
-import org.jacodb.impl.storage.jooq.tables.Calls
-
 
 
 // -------------------------------------------------------------------------
 // INDEX definitions
 // -------------------------------------------------------------------------
 
-val BUILDERSJOIN: Index = Internal.createIndex(DSL.name("BuildersJoin"), Builders.BUILDERS, arrayOf(Builders.BUILDERS.BUILDER_CLASS_SYMBOL_ID), false)
-val BUILDERSSEARCH: Index = Internal.createIndex(DSL.name("BuildersSearch"), Builders.BUILDERS, arrayOf(Builders.BUILDERS.LOCATION_ID, Builders.BUILDERS.CLASS_SYMBOL_ID, Builders.BUILDERS.PRIORITY), false)
+val ANNOTATIONS_CLASSID: Index = Internal.createIndex(DSL.name("Annotations_classId"), Annotations.ANNOTATIONS, arrayOf(Annotations.ANNOTATIONS.CLASS_ID), false)
+val ANNOTATIONS_FIELDID: Index = Internal.createIndex(DSL.name("Annotations_fieldId"), Annotations.ANNOTATIONS, arrayOf(Annotations.ANNOTATIONS.FIELD_ID), false)
+val ANNOTATIONS_METHODID: Index = Internal.createIndex(DSL.name("Annotations_methodId"), Annotations.ANNOTATIONS, arrayOf(Annotations.ANNOTATIONS.METHOD_ID), false)
+val ANNOTATIONS_PARAMSID: Index = Internal.createIndex(DSL.name("Annotations_paramsId"), Annotations.ANNOTATIONS, arrayOf(Annotations.ANNOTATIONS.PARAM_ID), false)
+val BUILDERSJOIN: Index = Internal.createIndex(DSL.name("BuildersJoin"), Builders.BUILDERS, arrayOf(Builders.BUILDERS.BUILDER_CLASS_NAME), false)
+val BUILDERSSEARCH: Index = Internal.createIndex(DSL.name("BuildersSearch"), Builders.BUILDERS, arrayOf(Builders.BUILDERS.LOCATION_ID, Builders.BUILDERS.CLASS_NAME, Builders.BUILDERS.PRIORITY), false)
 val BUILDERSSORTING: Index = Internal.createIndex(DSL.name("BuildersSorting"), Builders.BUILDERS, arrayOf(Builders.BUILDERS.PRIORITY), false)
-val CALLSSEARCH: Index = Internal.createIndex(DSL.name("CallsSearch"), Calls.CALLS, arrayOf(Calls.CALLS.OPCODE, Calls.CALLS.LOCATION_ID, Calls.CALLS.CALLEE_CLASS_SYMBOL_ID, Calls.CALLS.CALLEE_NAME_SYMBOL_ID, Calls.CALLS.CALLEE_DESC_HASH), false)
+val BYTECODELOCATIONS_HASH: Index = Internal.createIndex(DSL.name("Bytecodelocations_hash"), Bytecodelocations.BYTECODELOCATIONS, arrayOf(Bytecodelocations.BYTECODELOCATIONS.UNIQUEID), true)
+val CALLSSEARCH: Index = Internal.createIndex(DSL.name("CallsSearch"), Calls.CALLS, arrayOf(Calls.CALLS.OPCODE, Calls.CALLS.LOCATION_ID, Calls.CALLS.CALLEE_CLASS_NAME, Calls.CALLS.CALLEE_NAME, Calls.CALLS.CALLEE_DESC_HASH), false)
+val `CLASS HIERARCHIES`: Index = Internal.createIndex(DSL.name("Class Hierarchies"), Classhierarchies.CLASSHIERARCHIES, arrayOf(Classhierarchies.CLASSHIERARCHIES.SUPER_ID), false)
+val CLASSES_LOCATION: Index = Internal.createIndex(DSL.name("Classes_location"), Classes.CLASSES, arrayOf(Classes.CLASSES.LOCATION_ID), false)
+val CLASSES_NAME: Index = Internal.createIndex(DSL.name("Classes_name"), Classes.CLASSES, arrayOf(Classes.CLASSES.NAME), false)
+val CLASSES_OUTERMETHODID: Index = Internal.createIndex(DSL.name("Classes_outerMethodId"), Classes.CLASSES, arrayOf(Classes.CLASSES.OUTER_METHOD), false)
+val CLASSHIERARCHIES_CLASSID: Index = Internal.createIndex(DSL.name("ClassHierarchies_classId"), Classhierarchies.CLASSHIERARCHIES, arrayOf(Classhierarchies.CLASSHIERARCHIES.CLASS_ID), false)
+val CLASSHIERARCHIES_SUPERID: Index = Internal.createIndex(DSL.name("ClassHierarchies_superId"), Classhierarchies.CLASSHIERARCHIES, arrayOf(Classhierarchies.CLASSHIERARCHIES.SUPER_ID), false)
+val CLASSINNERCLASSES_CLASSID: Index = Internal.createIndex(DSL.name("ClassInnerClasses_classId"), Classinnerclasses.CLASSINNERCLASSES, arrayOf(Classinnerclasses.CLASSINNERCLASSES.CLASS_ID), false)
+val CLASSINNERCLASSES_INNERCLASSID: Index = Internal.createIndex(DSL.name("ClassInnerClasses_innerClassId"), Classinnerclasses.CLASSINNERCLASSES, arrayOf(Classinnerclasses.CLASSINNERCLASSES.INNER_CLASS_ID), false)
+val FIELDS_CLASS_ID_NAME: Index = Internal.createIndex(DSL.name("Fields_class_id_name"), Fields.FIELDS, arrayOf(Fields.FIELDS.CLASS_ID, Fields.FIELDS.NAME), true)
+val FIELDS_CLASSID: Index = Internal.createIndex(DSL.name("Fields_classId"), Fields.FIELDS, arrayOf(Fields.FIELDS.CLASS_ID), false)
+val METHODPARAMETERS_METHODID: Index = Internal.createIndex(DSL.name("MethodParameters_methodId"), Methodparameters.METHODPARAMETERS, arrayOf(Methodparameters.METHODPARAMETERS.METHOD_ID), false)
+val METHODS_CLASS_ID_NAME_DESC: Index = Internal.createIndex(DSL.name("Methods_class_id_name_desc"), Methods.METHODS, arrayOf(Methods.METHODS.CLASS_ID, Methods.METHODS.NAME, Methods.METHODS.DESC), true)
+val METHODS_CLASSID: Index = Internal.createIndex(DSL.name("Methods_classId"), Methods.METHODS, arrayOf(Methods.METHODS.CLASS_ID), false)
+val SYMBOLS_NAME: Index = Internal.createIndex(DSL.name("Symbols_name"), Symbols.SYMBOLS, arrayOf(Symbols.SYMBOLS.NAME), true)