Repository: BlueBrain/nexus (scala)

Issue:
Allow incremental import
**Motivation**
When importing an import file (and probably a set of import files), we want to be able to skip part of the import by providing an offset which will allow to skip any entry with a lower offset

**Acceptance criteria**
1. Offsets with a lower offset are skipped

**Implementation notes**
The idea is to filter by offset in ch.epfl.bluebrain.nexus.ship.Main#eventStream

Pull request description:
Closes #4772

Patch:
diff --git a/delta/sourcing-psql/src/main/scala/ch/epfl/bluebrain/nexus/delta/sourcing/Transactors.scala b/delta/sourcing-psql/src/main/scala/ch/epfl/bluebrain/nexus/delta/sourcing/Transactors.scala
index 4efa8a459f..110a08df7f 100644
--- a/delta/sourcing-psql/src/main/scala/ch/epfl/bluebrain/nexus/delta/sourcing/Transactors.scala
+++ b/delta/sourcing-psql/src/main/scala/ch/epfl/bluebrain/nexus/delta/sourcing/Transactors.scala
@@ -69,7 +69,7 @@ object Transactors {
   /**
     * For testing purposes, drop the current tables and then executes the different available scripts
     */
-  private[sourcing] def dropAndCreateDDLs: IO[List[String]] = ddls.map(dropScript :: _)
+  def dropAndCreateDDLs: IO[List[String]] = ddls.map(dropScript :: _)
 
   /** Type of a cache that contains the hashed names of the projectRefs for which a partition was already created. */
   type PartitionsCache = LocalCache[String, Unit]
diff --git a/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/Main.scala b/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/Main.scala
index 66e1cbdc9d..cb776417f8 100644
--- a/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/Main.scala
+++ b/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/Main.scala
@@ -41,8 +41,8 @@ object Main
   override def main: Opts[IO[ExitCode]] =
     (run orElse showConfig)
       .map {
-        case Run(file, config, _) => new RunShip().run(file, config)
-        case ShowConfig(config)   => showConfig(config)
+        case Run(file, config, offset) => new RunShip().run(file, config, offset)
+        case ShowConfig(config)        => showConfig(config)
       }
       .map(_.as(ExitCode.Success))
 
diff --git a/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/RunShip.scala b/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/RunShip.scala
index c38f78a7b4..9f8faefca6 100644
--- a/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/RunShip.scala
+++ b/ship/src/main/scala/ch/epfl/bluebrain/nexus/ship/RunShip.scala
@@ -9,6 +9,7 @@ import ch.epfl.bluebrain.nexus.delta.sdk.projects.FetchContext
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.model.ApiMappings
 import ch.epfl.bluebrain.nexus.delta.sdk.quotas.Quotas
 import ch.epfl.bluebrain.nexus.delta.sourcing.Transactors
+import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
 import ch.epfl.bluebrain.nexus.ship.config.ShipConfig
 import ch.epfl.bluebrain.nexus.ship.model.InputEvent
 import ch.epfl.bluebrain.nexus.ship.organizations.OrganizationProvider
@@ -25,7 +26,7 @@ class RunShip {
 
   private val logger = Logger[RunShip]
 
-  def run(file: Path, config: Option[Path]): IO[ImportReport] = {
+  def run(file: Path, config: Option[Path], fromOffset: Offset = Offset.start): IO[ImportReport] = {
     val clock                         = Clock[IO]
     val uuidF                         = UUIDF.random
     // Resources may have been created with different configurations so we adopt the lenient one for the import
@@ -42,7 +43,7 @@ class RunShip {
                   for {
                     // Provision organizations
                     _                           <- orgProvider.create(config.organizations.values)
-                    events                       = eventStream(file)
+                    events                       = eventStream(file, fromOffset)
                     fetchActiveOrg               = FetchActiveOrganization(xas)
                     // Wiring
                     eventClock                  <- EventClock.init()
@@ -83,11 +84,17 @@ class RunShip {
     } yield report
   }
 
-  private def eventStream(file: Path): Stream[IO, InputEvent] =
-    Files[IO].readUtf8Lines(file).zipWithIndex.evalMap { case (line, index) =>
-      IO.fromEither(decode[InputEvent](line)).onError { err =>
-        logger.error(err)(s"Error parsing to event at line $index")
+  private def eventStream(file: Path, fromOffset: Offset): Stream[IO, InputEvent] =
+    Files[IO]
+      .readUtf8Lines(file)
+      .zipWithIndex
+      .evalMap { case (line, index) =>
+        IO.fromEither(decode[InputEvent](line)).onError { err =>
+          logger.error(err)(s"Error parsing to event at line $index")
+        }
+      }
+      .filter { event =>
+        event.ordering.value >= fromOffset.value
       }
-    }
 
 }


Test patch:
diff --git a/delta/sourcing-psql/src/test/scala/ch/epfl/bluebrain/nexus/delta/sourcing/postgres/Doobie.scala b/delta/sourcing-psql/src/test/scala/ch/epfl/bluebrain/nexus/delta/sourcing/postgres/Doobie.scala
index d910e7924b..a87e5cb068 100644
--- a/delta/sourcing-psql/src/test/scala/ch/epfl/bluebrain/nexus/delta/sourcing/postgres/Doobie.scala
+++ b/delta/sourcing-psql/src/test/scala/ch/epfl/bluebrain/nexus/delta/sourcing/postgres/Doobie.scala
@@ -17,7 +17,7 @@ object Doobie {
   val PostgresUser     = "postgres"
   val PostgresPassword = "postgres"
 
-  private def transactors(
+  def transactors(
       postgres: Resource[IO, PostgresContainer],
       user: String,
       pass: String
diff --git a/ship/src/test/resources/import/two-projects.json b/ship/src/test/resources/import/two-projects.json
new file mode 100644
index 0000000000..87c04ac9d7
--- /dev/null
+++ b/ship/src/test/resources/import/two-projects.json
@@ -0,0 +1,2 @@
+{"ordering":1,"type":"project","org":"public","project":"sscx","id":"projects/public/sscx","rev":1,"value":{"rev": 1, "base": "https://bbp.epfl.ch/neurosciencegraph/data/", "uuid": "c7d70522-4305-480a-b190-75d757ed9a49", "@type": "ProjectCreated", "label": "sscx", "vocab": "https://bbp.epfl.ch/nexus/v1/resources/public/sscx/_/", "instant": "2020-01-22T16:03:33.105Z", "subject": {"@type": "User", "realm": "bbp", "subject": "bob"}, "apiMappings": {"prov": "http://www.w3.org/ns/prov#", "context": "https://incf.github.io/neuroshapes/contexts/", "schemaorg": "http://schema.org/", "datashapes": "https://neuroshapes.org/dash/", "ontologies": "https://neuroshapes.org/dash/ontology", "taxonomies": "https://neuroshapes.org/dash/taxonomy", "commonshapes": "https://neuroshapes.org/commons/", "provdatashapes": "https://provshapes.org/datashapes/", "provcommonshapes": "https://provshapes.org/commons/"}, "description": "This project contains somatosensorycortex dissemination publication data.", "organizationUuid": "d098a020-508b-4131-a28d-75f73b7f5f0e", "organizationLabel": "public"},"instant":"2020-01-22T17:03:33.105+01:00"}
+{"ordering":2,"type":"project","org":"public","project":"other","id":"projects/public/other","rev":1,"value":{"rev": 1, "base": "https://bbp.epfl.ch/neurosciencegraph/data/", "uuid": "c7d70522-4305-480a-b190-75d757ed9a49", "@type": "ProjectCreated", "label": "other", "vocab": "https://bbp.epfl.ch/nexus/v1/resources/public/other/_/", "instant": "2020-01-22T16:03:33.105Z", "subject": {"@type": "User", "realm": "bbp", "subject": "bob"}, "apiMappings": {"prov": "http://www.w3.org/ns/prov#", "context": "https://incf.github.io/neuroshapes/contexts/", "schemaorg": "http://schema.org/", "datashapes": "https://neuroshapes.org/dash/", "ontologies": "https://neuroshapes.org/dash/ontology", "taxonomies": "https://neuroshapes.org/dash/taxonomy", "commonshapes": "https://neuroshapes.org/commons/", "provdatashapes": "https://provshapes.org/datashapes/", "provcommonshapes": "https://provshapes.org/commons/"}, "description": "This is a second project.", "organizationUuid": "d098a020-508b-4131-a28d-75f73b7f5f0e", "organizationLabel": "public"},"instant":"2020-01-22T17:03:33.105+01:00"}
\ No newline at end of file
diff --git a/ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/MainSuite.scala b/ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/RunShipSuite.scala
similarity index 51%
rename from ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/MainSuite.scala
rename to ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/RunShipSuite.scala
index f2dcc8279e..08593cc71f 100644
--- a/ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/MainSuite.scala
+++ b/ship/src/test/scala/ch/epfl/bluebrain/nexus/ship/RunShipSuite.scala
@@ -6,22 +6,32 @@ import ch.epfl.bluebrain.nexus.delta.kernel.utils.ClasspathResourceLoader
 import ch.epfl.bluebrain.nexus.delta.sdk.projects.Projects
 import ch.epfl.bluebrain.nexus.delta.sdk.resolvers.Resolvers
 import ch.epfl.bluebrain.nexus.delta.sdk.resources.Resources
+import ch.epfl.bluebrain.nexus.delta.sourcing.Transactors
 import ch.epfl.bluebrain.nexus.delta.sourcing.model.EntityType
 import ch.epfl.bluebrain.nexus.delta.sourcing.offset.Offset
-import ch.epfl.bluebrain.nexus.delta.sourcing.postgres.Doobie.{PostgresPassword, PostgresUser}
+import ch.epfl.bluebrain.nexus.delta.sourcing.postgres.Doobie.{PostgresPassword, PostgresUser, transactors}
 import ch.epfl.bluebrain.nexus.ship.ImportReport.Count
+import ch.epfl.bluebrain.nexus.ship.RunShipSuite.clearDB
 import ch.epfl.bluebrain.nexus.testkit.config.SystemPropertyOverride
 import ch.epfl.bluebrain.nexus.testkit.mu.NexusSuite
 import ch.epfl.bluebrain.nexus.testkit.postgres.PostgresContainer
+import doobie.implicits._
 import fs2.io.file.Path
-import munit.{AnyFixture, CatsEffectSuite}
 import munit.catseffect.IOFixture
+import munit.{AnyFixture, CatsEffectSuite}
 
 import java.time.Instant
 
-class MainSuite extends NexusSuite with MainSuite.Fixture {
+class RunShipSuite extends NexusSuite with RunShipSuite.Fixture {
 
   override def munitFixtures: Seq[AnyFixture[_]] = List(mainFixture)
+  private lazy val xas                           = mainFixture()
+
+  override def beforeEach(context: BeforeEach): Unit = {
+    super.beforeEach(context)
+    clearDB(xas).accepted
+    ()
+  }
 
   test("Run import") {
     val expected = ImportReport(
@@ -35,18 +45,41 @@ class MainSuite extends NexusSuite with MainSuite.Fixture {
       )
     )
     for {
-      importFile <- ClasspathResourceLoader().absolutePath("import/import.json").map(Path(_))
+      importFile <- asPath("import/import.json")
       _          <- new RunShip().run(importFile, None).assertEquals(expected)
     } yield ()
   }
 
+  test("Test the increment") {
+    for {
+      importFileWithTwoProjects <- asPath("import/two-projects.json")
+      startFrom                  = Offset.at(2)
+      _                         <- new RunShip().run(importFileWithTwoProjects, None, startFrom).map { report =>
+                                     assert(report.offset == Offset.at(2L))
+                                     assert(thereIsOneProjectEventIn(report))
+                                   }
+    } yield ()
+  }
+
   test("Show config") {
     Main.showConfig(None)
   }
 
+  private def asPath(path: String): IO[Path] = {
+    ClasspathResourceLoader().absolutePath(path).map(Path(_))
+  }
+
+  private def thereIsOneProjectEventIn(report: ImportReport) =
+    report.progress == Map(Projects.entityType -> Count(1L, 0L))
+
 }
 
-object MainSuite {
+object RunShipSuite {
+
+  def clearDB(xas: Transactors) =
+    sql"""
+         | DELETE FROM scoped_events; DELETE FROM scoped_states;
+         |""".stripMargin.update.run.void.transact(xas.write)
 
   trait Fixture { self: CatsEffectSuite =>
 
@@ -58,15 +91,15 @@ object MainSuite {
         "ship.organizations.values.public" -> "The public organization"
       )
 
-    private def resource(): Resource[IO, Unit] =
-      PostgresContainer
-        .resource(PostgresUser, PostgresPassword)
-        .flatMap { postgres =>
-          SystemPropertyOverride(initConfig(postgres))
-        }
-        .void
+    private val resource: Resource[IO, Transactors] = transactors(
+      PostgresContainer.resource(PostgresUser, PostgresPassword).flatTap { pg =>
+        SystemPropertyOverride(initConfig(pg)).void
+      },
+      PostgresUser,
+      PostgresPassword
+    )
 
-    val mainFixture: IOFixture[Unit] = ResourceSuiteLocalFixture("main", resource())
+    val mainFixture: IOFixture[Transactors] = ResourceSuiteLocalFixture("main", resource)
   }
 
 }