From 4b9d49e3acff618ead44a53199b2c3c4a16d613c Mon Sep 17 00:00:00 2001 From: Elizabeth Paige Harper Date: Mon, 5 Aug 2024 13:09:34 -0400 Subject: [PATCH 1/4] reconciler endpoint ref #259 --- docker-compose.yml | 1 + docs/env-vars.adoc | 5 + docs/vdi-api.html | 9 +- .../component/db/app/AppDatabaseRegistry.kt | 11 +- .../main/kotlin/vdi/component/env/EnvKey.kt | 10 ++ lib/reconciler/build.gradle.kts | 38 ++++++ .../kotlin/vdi/lib}/reconciler/AppDBTarget.kt | 2 +- .../vdi/lib}/reconciler/CacheDBTarget.kt | 2 +- .../kotlin/vdi/lib/reconciler/Reconciler.kt | 111 ++++++++++++++++++ .../vdi/lib/reconciler/ReconcilerConfig.kt | 31 +++++ .../vdi/lib}/reconciler/ReconcilerInstance.kt | 15 ++- .../vdi/lib}/reconciler/ReconcilerTarget.kt | 2 +- .../lib}/reconciler/ReconcilerTargetType.kt | 2 +- .../reconciler/UnsupportedTypeException.kt | 2 +- .../vdi/lib}/reconciler/ReconcilerTest.kt | 18 +-- .../src/main/kotlin/vdi/bootstrap/Main.kt | 2 +- service/daemon/reconciler/build.gradle.kts | 10 +- ...lerConfig.kt => ReconcilerDaemonConfig.kt} | 20 +--- .../vdi/daemon/reconciler/ReconcilerImpl.kt | 89 +++----------- .../kotlin/vdi/daemon/reconciler/index.kt | 4 +- service/rest-service/api.raml | 13 +- service/rest-service/build.gradle.kts | 1 + .../generated/model/DatasetPostMetaImpl.java | 2 +- .../service/vdi/generated/model/Error.java | 12 +- .../vdi/generated/resources/Admin.java | 24 ++++ .../vdi/generated/resources/VdiDatasets.java | 8 ++ .../generated/support/ResponseDelegate.java | 8 +- .../vdi/server/controllers/AdminRPC.kt | 11 ++ .../rest-service/src/main/resources/api.html | 9 +- settings.gradle.kts | 1 + 30 files changed, 333 insertions(+), 140 deletions(-) create mode 100644 lib/reconciler/build.gradle.kts rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/AppDBTarget.kt (98%) rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/CacheDBTarget.kt (97%) create mode 100644 lib/reconciler/src/main/kotlin/vdi/lib/reconciler/Reconciler.kt create mode 100644 lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerConfig.kt rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/ReconcilerInstance.kt (97%) rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/ReconcilerTarget.kt (96%) rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/ReconcilerTargetType.kt (66%) rename {service/daemon/reconciler/src/main/kotlin/vdi/daemon => lib/reconciler/src/main/kotlin/vdi/lib}/reconciler/UnsupportedTypeException.kt (72%) rename {service/daemon/reconciler/src/test/kotlin/vdi/daemon => lib/reconciler/src/test/kotlin/vdi/lib}/reconciler/ReconcilerTest.kt (98%) rename service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/{ReconcilerConfig.kt => ReconcilerDaemonConfig.kt} (56%) diff --git a/docker-compose.yml b/docker-compose.yml index 44eb7e31..dca42d53 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -205,6 +205,7 @@ services: RECONCILER_FULL_ENABLED: ${RECONCILER_FULL_ENABLED} RECONCILER_FULL_RUN_INTERVAL: ${RECONCILER_FULL_RUN_INTERVAL} RECONCILER_SLIM_RUN_INTERVAL: ${RECONCILER_SLIM_RUN_INTERVAL} + RECONCILER_DELETES_ENABLED: ${RECONCILER_DELETES_ENABLED} # # Wildcard Plugin Variables diff --git a/docs/env-vars.adoc b/docs/env-vars.adoc index d0107746..e62b6028 100644 --- a/docs/env-vars.adoc +++ b/docs/env-vars.adoc @@ -268,6 +268,11 @@ VDI system | RECONCILER_SLIM_RUN_INTERVAL | Duration | Interval at which the slim reconciliation process will run. + +| +| RECONCILER_DELETES_ENABLED +| boolean +| Whether the reconciler should perform delete operations. |=== diff --git a/docs/vdi-api.html b/docs/vdi-api.html index a93fca38..c57a4df6 100644 --- a/docs/vdi-api.html +++ b/docs/vdi-api.html @@ -1222,7 +1222,7 @@ bindFilters(); }); -

VEuPathDB Dataset Installer v2.0.0

link

Resources

get /vdi-datasets

List Datasets  

Returns a list of datasets available to the requesting user, optionally filtered by query parameters.

Results are sorted by creation date in reverse order. This means the most recently created datasets will be first and the oldest dataset will be last in the list.

Parameters chevron_right expand_more

ParameterTypeDescription
Query
project_id Project IDstring

ID of the VEuPathDB project that results should be filtered to.

This means only datasets that are relevant to the project ID given will be returned.

Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, PlasmoDB, the status block in the response objects will only include installation status details for PlasmoDB and not any other sites that the dataset may have been installed into.

Inherits: string

ownership Dataset Ownership Filterstring

Ownership status filter.

Enum of:

  • any
  • owned
  • shared

If set to any the results are not filtered.

If set to owned, the results will be filtered to only results that are owned by the requesting user.

If set to shared, the results will be filtered to only results that are shared with the requesting user.

Default value: "any"

curl -X GET \
+		
VEuPathDB Dataset Installer v2.1.0
link 
Resources
get /vdi-datasets
List Datasets  
Returns a list of datasets available to the requesting user, optionally filtered by query parameters.
Results are sorted by creation date in reverse order. This means the most recently created datasets will be first and the oldest dataset will be last in the list.
Parameters chevron_right expand_more
ParameterTypeDescription
Query
project_id Project IDstring
ID of the VEuPathDB project that results should be filtered to.
This means only datasets that are relevant to the project ID given will be returned.
Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, PlasmoDB, the status block in the response objects will only include installation status details for PlasmoDB and not any other sites that the dataset may have been installed into.
Inherits: string
ownership Dataset Ownership Filterstring
Ownership status filter.
Enum of:
  • any
  • owned
  • shared
If set to any the results are not filtered.
If set to owned, the results will be filtered to only results that are owned by the requesting user.
If set to shared, the results will be filtered to only results that are shared with the requesting user.
Default value: "any"
curl -X GET \
   undefined/vdi-datasets?ProjectID=<value>&ownership=<value>
200 OK chevron_right expand_more
Success.
This response means that all checks passed and zero or more dataset records were found for the requesting user.
application/json
application/json
ParameterTypeDescription
[] Dataset List Itemobject
Short entry with basic details about a dataset.
Inherits: object
[].datasetId* Dataset IDstring
Unique VDI Dataset identifier string.
Pattern: ^[a-zA-Z0-9_-]{14}$
Min. length: 14
Max. length: 14
Inherits: lib.VDI-ID
[].owner* Owner Detailsobject
Details about the owner of a VDI dataset.
Inherits: lib.DatasetOwner
[].owner.userId* Owner User IDinteger
VEuPathDB user ID of the owner of the dataset.
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: lib.User-ID
[].owner.firstName Owner First Namestring
[].owner.lastName Owner Last Namestring
[].owner.email Owner Emailstring
[].owner.organization Owner Organizationstring
[].datasetType* Dataset Typeobject
Information about a specific dataset type.
Inherits: lib.DatasetTypeInfo
[].datasetType.name* Type Namestring
[].datasetType.displayName Type Display Namestring
Display name for the type. This field is ignored in requests and will always be present in responses.
[].datasetType.version* Type Versionstring
[].visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public
Inherits: lib.DatasetVisibility
[].name* Dataset Namestring
User provided name for the dataset.
[].summary Dataset Summarystring
User provided summary of the dataset.
[].description Dataset Descriptionstring
User provided description of the dataset.
[].sourceUrl Source URLstring
URL of the dataset data source, if the dataset was uploaded via URL.
[].origin* Dataset Originstring
String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.
[].projectIds* Project IDsarray
Project IDs for projects the dataset record was submitted to.
[].projectIds[] Project IDstring
Name or ID of a target VEuPathDB project.
Valid project IDs are:
  • AmoebaDB
  • ClinEpiDB
  • CryptoDB
  • FungiDB
  • GiardiaDB
  • HostDB
  • MicrobiomeDB
  • MicrosporidiaDB
  • PiroplasmaDB
  • PlasmoDB
  • ToxoDB
  • TrichDB
  • TriTrypDB
  • VectorBase
  • VEuPathDB
Inherits: lib.ProjectID
[].status* Status Infoobject
Information about the import and install status of a dataset.
Inherits: lib.DatasetStatusInfo
[].status.import*string
Import status of the dataset.
ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed
Inherits: lib.DatasetImportStatus
[].status.installarray
[].status.install[] Dataset Install Status Entryobject
Entry in a list of install statuses for a dataset.
Inherits: lib.DatasetInstallStatusEntry
[].status.install[].projectId*string
Name or ID of a target VEuPathDB project.
Valid project IDs are:
  • AmoebaDB
  • ClinEpiDB
  • CryptoDB
  • FungiDB
  • GiardiaDB
  • HostDB
  • MicrobiomeDB
  • MicrosporidiaDB
  • PiroplasmaDB
  • PlasmoDB
  • ToxoDB
  • TrichDB
  • TriTrypDB
  • VectorBase
  • VEuPathDB
Inherits: lib.ProjectID
[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency
Inherits: lib.DatasetInstallStatus
[].status.install[].metaMessagestring
[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency
Inherits: lib.DatasetInstallStatus
[].status.install[].dataMessagestring
[].shares* Shared Witharray
[].shares[]object
Inherits: object
[].shares[].userId*integer
Unique user identifier
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: lib.User-ID
[].shares[].firstName*string
[].shares[].lastName*string
[].shares[].organization*string
[].shares[].accepted*boolean
[].fileCount* File Countinteger
Number of files uploaded for this dataset.
[].fileSizeTotal* File Size Totalinteger
Sum of the sizes of all the files uploaded for this dataset.
Format: int64
[].created* Creation Timestampdatetime
Timestamp of the creation of this dataset.
Response Body
[
   {
     "datasetId": "zaZqAAGLGJhBgg",
@@ -1306,11 +1306,16 @@
       ]
     }
   }
+}
424 Failed Dependency chevron_right expand_more
Failed Dependency.
Returned when the dataset data source was a URL and the VDI service encountered a non-success HTTP status code from the target URL. This could be, for example, a 403 error from an expired AWS S3 URL, or a 404 for a file that no longer exists on the remote server.
Failed Dependency Error FailedDependencyError
application/json
Discriminator: status
Discriminator value: failed-dependency
Inherits: lib.Error
ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • failed-dependency
  • server-error
Inherits: lib.ErrorType
message*string
dependency*string
Response Body
{
+  "status": "failed-dependency",
+  "dependency": "google.com",
+  "message": "unexpected status code 403 from google.com"
 }
500 Internal Server Error chevron_right expand_more
Internal Server Error.
This status is returned when an unhandled or unexpected issue arises when attempting to process the request.
Internal Server Error ServerError
application/json
Discriminator: status
Discriminator value: server-error
Inherits: lib.Error
ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • failed-dependency
  • server-error
Inherits: lib.ErrorType
message*string
requestId*string
Response Body
{
   "status": "server-error",
   "message": "Dataset store is unreachable",
   "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
-}
post /admin/proxy-upload
  
Upload a dataset on behalf of another user.
Headers chevron_right expand_more
ParameterTypeDescription
User-ID* VEuPathDB User IDinteger
ID of the target user on whose behalf a dataset is being uploaded
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: integer
curl -X POST \
+}

post /admin/reconciler

Execute Reconciler  

Triggers a full reconciliation run if one is not already in progress.

curl -X POST \
+  undefined/admin/reconciler

204 No Content chevron_right expand_more

Success

409 Conflict chevron_right expand_more

Reconciler already running.

post /admin/proxy-upload

 

Upload a dataset on behalf of another user.

Headers chevron_right expand_more

ParameterTypeDescription
User-ID* VEuPathDB User IDinteger

ID of the target user on whose behalf a dataset is being uploaded

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X POST \
   -H "User-ID: <value>" \
   -H "Content-type: multipart/form-data"
   -d @file \
diff --git a/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDatabaseRegistry.kt b/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDatabaseRegistry.kt
index ae09769f..42fb595f 100644
--- a/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDatabaseRegistry.kt
+++ b/lib/app-db/src/main/kotlin/vdi/component/db/app/AppDatabaseRegistry.kt
@@ -27,13 +27,14 @@ object AppDatabaseRegistry {
 
   operator fun get(key: String): AppDBRegistryEntry? = dataSources[key]
 
-  operator fun iterator() =
+  operator fun iterator() = asSequence().iterator()
+
+  fun size() = dataSources.size
+
+  fun asSequence() =
     dataSources.entries
       .asSequence()
       .map { (key, value) -> key to value }
-      .iterator()
-
-  fun size() = dataSources.size
 
   fun require(key: String): AppDBRegistryEntry =
     get(key) ?: throw IllegalStateException("required AppDB connection $key was not registered with AppDatabases")
@@ -80,7 +81,7 @@ object AppDatabaseRegistry {
       TNS: {}
       Pool Size: {}
       Port: {}
-      DBNamme: {}
+      DBName: {}
       User/Schema: {}""",
       env.name,
       env.name,
diff --git a/lib/env/src/main/kotlin/vdi/component/env/EnvKey.kt b/lib/env/src/main/kotlin/vdi/component/env/EnvKey.kt
index 3c24c1d2..f49de5d5 100644
--- a/lib/env/src/main/kotlin/vdi/component/env/EnvKey.kt
+++ b/lib/env/src/main/kotlin/vdi/component/env/EnvKey.kt
@@ -656,6 +656,16 @@ object EnvKey {
      * Required: no
      */
     const val SlimRunInterval = "RECONCILER_SLIM_RUN_INTERVAL"
+
+    /**
+     * Whether the reconciler should perform delete operations.  If set to
+     * `false`, the reconciler will only log when a delete would have taken
+     * place.
+     *
+     * Type: Boolean
+     * Required: no
+     */
+    const val DeletesEnabled = "RECONCILER_DELETES_ENABLED"
   }
 
   object ReconciliationTriggerHandler {
diff --git a/lib/reconciler/build.gradle.kts b/lib/reconciler/build.gradle.kts
new file mode 100644
index 00000000..d19d345a
--- /dev/null
+++ b/lib/reconciler/build.gradle.kts
@@ -0,0 +1,38 @@
+plugins {
+  kotlin("jvm")
+}
+
+dependencies {
+  implementation(platform(project(":platform")))
+
+
+  implementation(project(":lib:app-db"))
+  implementation(project(":lib:cache-db"))
+  implementation(project(":lib:env"))
+  implementation(project(":lib:plugin-client"))
+  implementation(project(":lib:kafka"))
+  implementation(project(":lib:metrics"))
+  implementation(project(":lib:module-core"))
+  implementation(project(":lib:plugin-mapping"))
+  implementation(project(":lib:s3"))
+
+  implementation("org.veupathdb.vdi:vdi-component-common")
+
+  implementation("org.veupathdb.lib.s3:s34k-minio")
+
+  implementation("org.apache.logging.log4j:log4j-api-kotlin")
+
+  implementation("org.jetbrains.kotlinx:kotlinx-coroutines-core")
+
+  testImplementation(kotlin("test"))
+  testImplementation("org.junit.jupiter:junit-jupiter-api:5.9.2")
+  testImplementation("org.mockito:mockito-core:5.2.0")
+  testRuntimeOnly("org.junit.jupiter:junit-jupiter-engine:5.9.2")
+  testRuntimeOnly("org.apache.logging.log4j:log4j-slf4j-impl")
+}
+
+tasks.test {
+  useJUnitPlatform()
+
+  testLogging.showStandardStreams = true
+}
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/AppDBTarget.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/AppDBTarget.kt
similarity index 98%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/AppDBTarget.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/AppDBTarget.kt
index 045f6ee8..f03988df 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/AppDBTarget.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/AppDBTarget.kt
@@ -1,4 +1,4 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 import org.veupathdb.vdi.lib.common.model.VDIReconcilerTargetRecord
 import org.veupathdb.vdi.lib.common.util.CloseableIterator
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/CacheDBTarget.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/CacheDBTarget.kt
similarity index 97%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/CacheDBTarget.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/CacheDBTarget.kt
index 4e818e2b..3ed389a3 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/CacheDBTarget.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/CacheDBTarget.kt
@@ -1,4 +1,4 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 import org.veupathdb.vdi.lib.common.model.VDIReconcilerTargetRecord
 import org.veupathdb.vdi.lib.common.util.CloseableIterator
diff --git a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/Reconciler.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/Reconciler.kt
new file mode 100644
index 00000000..d519f179
--- /dev/null
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/Reconciler.kt
@@ -0,0 +1,111 @@
+package vdi.lib.reconciler
+
+import kotlinx.coroutines.coroutineScope
+import kotlinx.coroutines.launch
+import kotlinx.coroutines.runBlocking
+import kotlinx.coroutines.sync.Mutex
+import kotlinx.coroutines.sync.withLock
+import org.apache.logging.log4j.kotlin.CoroutineThreadContext
+import org.apache.logging.log4j.kotlin.ThreadContextData
+import org.apache.logging.log4j.kotlin.logger
+import org.veupathdb.lib.s3.s34k.S3Api
+import vdi.component.db.app.AppDatabaseRegistry
+import vdi.component.kafka.router.KafkaRouter
+import vdi.component.kafka.router.KafkaRouterFactory
+import vdi.component.metrics.Metrics
+import vdi.component.modules.AbortCB
+import vdi.component.s3.DatasetManager
+
+object Reconciler {
+  private val logger = logger().delegate
+
+  private val config = ReconcilerConfig()
+
+  private val active = Mutex()
+
+  private var initialized = false
+
+  private lateinit var datasetManager: DatasetManager
+
+  private lateinit var kafkaRouter: KafkaRouter
+
+  fun initialize(abortCB: AbortCB) {
+    // We lock while initializing to avoid double init.
+    if (active.isLocked)
+      return
+
+    // If we've already successfully initialized, nothing to do.
+    if (initialized)
+      return
+
+    // Initialize
+    runBlocking {
+      active.withLock {
+        try {
+          val s3 = S3Api.newClient(config.s3Config)
+          val bucket = s3.buckets[config.s3Bucket]
+            ?: throw IllegalStateException("S3 bucket ${config.s3Bucket} does not exist!")
+
+          datasetManager = DatasetManager(bucket)
+        } catch (e: Throwable) {
+          logger.error("failed to init dataset manager", e)
+          abortCB(e.message)
+        }
+
+        try {
+          kafkaRouter = KafkaRouterFactory(config.kafkaRouterConfig).newKafkaRouter()
+        } catch (e: Throwable) {
+          logger.error("failed to init kafka router", e)
+          abortCB(e.message)
+        }
+      }
+    }
+  }
+
+  suspend fun runFull(): Boolean {
+    if (active.isLocked)
+      return false
+
+    val targets = AppDatabaseRegistry.asSequence()
+      .map { (project, _) -> AppDBTarget(project, project) }
+      .toMutableList()
+    targets.add(CacheDBTarget())
+
+    val timer = Metrics.Reconciler.Full.reconcilerTimes.startTimer()
+
+    logger.info("running full reconciler for ${targets.size} targets")
+
+    coroutineScope {
+      targets.forEach {
+        launch(CoroutineThreadContext(ThreadContextData(mapOf("workerID" to workerName(false, it))))) {
+          ReconcilerInstance(it, datasetManager, kafkaRouter, false, config.deletesEnabled).reconcile()
+        }
+      }
+    }
+
+    timer.observeDuration()
+
+    return true
+  }
+
+  suspend fun runSlim(): Boolean {
+    if (active.isLocked)
+      return false
+
+    val timer = Metrics.Reconciler.Slim.executionTime.startTimer()
+
+    val target = CacheDBTarget()
+
+    coroutineScope {
+      launch(CoroutineThreadContext(ThreadContextData(mapOf("workerID" to workerName(true, target))))) {
+        ReconcilerInstance(target, datasetManager, kafkaRouter, true, false).reconcile()
+      }
+    }
+
+    timer.observeDuration()
+
+    return true
+  }
+
+  private fun workerName(slim: Boolean, tgt: ReconcilerTarget) = if (slim) "slim-${tgt.name}" else "full-${tgt.name}"
+}
\ No newline at end of file
diff --git a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerConfig.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerConfig.kt
new file mode 100644
index 00000000..6d1b4913
--- /dev/null
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerConfig.kt
@@ -0,0 +1,31 @@
+package vdi.lib.reconciler
+
+import org.veupathdb.lib.s3.s34k.S3Config
+import org.veupathdb.lib.s3.s34k.fields.BucketName
+import org.veupathdb.vdi.lib.common.env.Environment
+import org.veupathdb.vdi.lib.common.env.optBool
+import org.veupathdb.vdi.lib.common.env.require
+import vdi.component.env.EnvKey
+import vdi.component.kafka.router.KafkaRouterConfig
+import vdi.component.s3.util.S3Config
+
+internal data class ReconcilerConfig(
+  val kafkaRouterConfig: KafkaRouterConfig,
+  val s3Config:          S3Config,
+  val s3Bucket:          BucketName,
+  val deletesEnabled:    Boolean,
+) {
+  constructor() : this(System.getenv())
+
+  constructor(env: Environment) : this(
+    kafkaRouterConfig = KafkaRouterConfig(env, "reconciler"),
+    s3Config          = S3Config(env),
+    s3Bucket          = BucketName(env.require(EnvKey.S3.BucketName)),
+    deletesEnabled    = env.optBool(EnvKey.Reconciler.DeletesEnabled) ?: DefaultDeletesEnabled,
+  )
+
+  companion object {
+    const val DefaultDeletesEnabled = true
+  }
+}
+
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerInstance.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
similarity index 97%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerInstance.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
index 16b31afe..1ab99620 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerInstance.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
@@ -1,4 +1,4 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 import org.apache.logging.log4j.kotlin.logger
 import org.veupathdb.vdi.lib.common.field.DatasetID
@@ -27,7 +27,7 @@ internal class ReconcilerInstance(
   private val datasetManager: DatasetManager,
   private val kafkaRouter: KafkaRouter,
   private val slim: Boolean,
-  private val deleteDryMode: Boolean = false
+  private val deletesEnabled: Boolean
 ) {
   private val log = logger().delegate
 
@@ -35,7 +35,7 @@ internal class ReconcilerInstance(
 
   val name = targetDB.name
 
-  suspend fun reconcile() {
+  internal suspend fun reconcile() {
     try {
       tryReconcile()
 
@@ -136,7 +136,9 @@ internal class ReconcilerInstance(
           // database
           if (!nextTargetDataset!!.isUninstalled)
             // then fire a sync event
-            sendSyncEvent(nextTargetDataset!!.ownerID, nextTargetDataset!!.datasetID, SyncReason.NeedsUninstall(targetDB))
+            sendSyncEvent(nextTargetDataset!!.ownerID, nextTargetDataset!!.datasetID,
+              SyncReason.NeedsUninstall(targetDB)
+            )
         } else {
           // The dataset does not have a delete flag present in MinIO
 
@@ -200,7 +202,7 @@ internal class ReconcilerInstance(
 
     try {
       Metrics.Reconciler.Full.reconcilerDatasetDeleted.labels(targetDB.name).inc()
-      if (!deleteDryMode) {
+      if (deletesEnabled) {
         log.info("trying to delete dataset {}/{}", record.ownerID, record.datasetID)
         targetDB.deleteDataset(record)
       } else {
@@ -279,7 +281,8 @@ internal class ReconcilerInstance(
   }
 
   private interface SyncReason {
-    class OutOfSync(val meta: Boolean, val shares: Boolean, val install: Boolean, val target: ReconcilerTarget) : SyncReason {
+    class OutOfSync(val meta: Boolean, val shares: Boolean, val install: Boolean, val target: ReconcilerTarget) :
+      SyncReason {
       override fun toString() =
         "out of sync:" +
           (if (meta) " meta" else "") +
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTarget.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTarget.kt
similarity index 96%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTarget.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTarget.kt
index 33c578df..573d72db 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTarget.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTarget.kt
@@ -1,4 +1,4 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 import org.veupathdb.vdi.lib.common.model.VDIReconcilerTargetRecord
 import org.veupathdb.vdi.lib.common.util.CloseableIterator
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTargetType.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTargetType.kt
similarity index 66%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTargetType.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTargetType.kt
index e014f239..5fdb2c78 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerTargetType.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerTargetType.kt
@@ -1,3 +1,3 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 internal enum class ReconcilerTargetType { Cache, Install }
\ No newline at end of file
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/UnsupportedTypeException.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/UnsupportedTypeException.kt
similarity index 72%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/UnsupportedTypeException.kt
rename to lib/reconciler/src/main/kotlin/vdi/lib/reconciler/UnsupportedTypeException.kt
index 77c06b7f..116f8ca7 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/UnsupportedTypeException.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/UnsupportedTypeException.kt
@@ -1,3 +1,3 @@
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 internal class UnsupportedTypeException(message: String) : Exception(message)
\ No newline at end of file
diff --git a/service/daemon/reconciler/src/test/kotlin/vdi/daemon/reconciler/ReconcilerTest.kt b/lib/reconciler/src/test/kotlin/vdi/lib/reconciler/ReconcilerTest.kt
similarity index 98%
rename from service/daemon/reconciler/src/test/kotlin/vdi/daemon/reconciler/ReconcilerTest.kt
rename to lib/reconciler/src/test/kotlin/vdi/lib/reconciler/ReconcilerTest.kt
index 0d936666..869fccdc 100644
--- a/service/daemon/reconciler/src/test/kotlin/vdi/daemon/reconciler/ReconcilerTest.kt
+++ b/lib/reconciler/src/test/kotlin/vdi/lib/reconciler/ReconcilerTest.kt
@@ -1,6 +1,6 @@
 @file:Suppress("NOTHING_TO_INLINE")
 
-package vdi.daemon.reconciler
+package vdi.lib.reconciler
 
 import kotlinx.coroutines.runBlocking
 import org.junit.jupiter.api.DisplayName
@@ -31,7 +31,7 @@ class ReconcilerTest {
         val datasetManager = mock()
         val kafkaRouter = mock()
 
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, true)
 
         `when`(cacheDb.streamSortedSyncControlRecords()).thenReturn(
             closeableIterator(
@@ -64,7 +64,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, false)
 
         `when`(cacheDb.streamSortedSyncControlRecords())
             .thenReturn(closeableIterator(listOf(makeTargetRecord(111, "12345678123456781234567812345678")).iterator()))
@@ -86,7 +86,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, false)
 
         `when`(cacheDb.streamSortedSyncControlRecords())
             .thenReturn(closeableIterator(listOf(makeTargetRecord(111, "12345678123456781234567812345678")).iterator()))
@@ -104,7 +104,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, false)
 
         `when`(cacheDb.streamSortedSyncControlRecords()).thenReturn(
             closeableIterator(emptyList().iterator())
@@ -127,7 +127,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, true)
 
         `when`(cacheDb.streamSortedSyncControlRecords()).thenReturn(
             closeableIterator(listOf(
@@ -160,7 +160,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, true)
 
         `when`(cacheDb.type).thenReturn(ReconcilerTargetType.Cache)
 
@@ -194,7 +194,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, false)
 
         `when`(cacheDb.type).thenReturn(ReconcilerTargetType.Cache)
 
@@ -226,7 +226,7 @@ class ReconcilerTest {
         `when`(cacheDb.name).thenReturn("CacheDB")
         val datasetManager = mock()
         val kafkaRouter = mock()
-        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false)
+        val recon = ReconcilerInstance(cacheDb, datasetManager, kafkaRouter, false, false)
 
         `when`(cacheDb.type).thenReturn(ReconcilerTargetType.Cache)
 
diff --git a/service/bootstrap/src/main/kotlin/vdi/bootstrap/Main.kt b/service/bootstrap/src/main/kotlin/vdi/bootstrap/Main.kt
index a414ad96..dcc2e592 100644
--- a/service/bootstrap/src/main/kotlin/vdi/bootstrap/Main.kt
+++ b/service/bootstrap/src/main/kotlin/vdi/bootstrap/Main.kt
@@ -35,7 +35,7 @@ object Main {
       ShareTriggerHandler(::fatality),
       SoftDeleteTriggerHandler(::fatality),
       UpdateMetaTriggerHandler(::fatality),
-      Reconciler(::fatality),
+      Reconciler(abortCB = ::fatality),
       ReconciliationEventHandler(::fatality),
     )
 
diff --git a/service/daemon/reconciler/build.gradle.kts b/service/daemon/reconciler/build.gradle.kts
index 32fc83d9..514a8cb8 100644
--- a/service/daemon/reconciler/build.gradle.kts
+++ b/service/daemon/reconciler/build.gradle.kts
@@ -7,17 +7,9 @@ dependencies {
 
   implementation("org.veupathdb.vdi:vdi-component-common")
 
-  implementation(project(":lib:app-db"))
-  implementation(project(":lib:cache-db"))
   implementation(project(":lib:env"))
-  implementation(project(":lib:plugin-client"))
-  implementation(project(":lib:kafka"))
-  implementation(project(":lib:metrics"))
   implementation(project(":lib:module-core"))
-  implementation(project(":lib:plugin-mapping"))
-  implementation(project(":lib:s3"))
-
-  implementation("org.veupathdb.lib.s3:s34k-minio")
+  implementation(project(":lib:reconciler"))
 
   implementation("org.apache.logging.log4j:log4j-api-kotlin")
 
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerConfig.kt b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerDaemonConfig.kt
similarity index 56%
rename from service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerConfig.kt
rename to service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerDaemonConfig.kt
index 4b635e67..337ce2d4 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerConfig.kt
+++ b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerDaemonConfig.kt
@@ -1,32 +1,21 @@
 package vdi.daemon.reconciler
 
-import org.veupathdb.lib.s3.s34k.S3Config
-import org.veupathdb.lib.s3.s34k.fields.BucketName
-import org.veupathdb.vdi.lib.common.env.Environment
 import org.veupathdb.vdi.lib.common.env.optBool
 import org.veupathdb.vdi.lib.common.env.optDuration
-import org.veupathdb.vdi.lib.common.env.require
 import vdi.component.env.EnvKey
-import vdi.component.kafka.router.KafkaRouterConfig
-import vdi.component.s3.util.S3Config
+import vdi.component.env.Environment
 import kotlin.time.Duration
 import kotlin.time.Duration.Companion.hours
 import kotlin.time.Duration.Companion.minutes
 
-data class ReconcilerConfig(
-  val kafkaRouterConfig: KafkaRouterConfig,
-  val s3Config:          S3Config,
-  val s3Bucket:          BucketName,
+data class ReconcilerDaemonConfig(
   val reconcilerEnabled: Boolean,
-  val fullRunInterval:   Duration,
-  val slimRunInterval:   Duration,
+  val fullRunInterval: Duration,
+  val slimRunInterval: Duration,
 ) {
   constructor() : this(System.getenv())
 
   constructor(env: Environment) : this(
-    kafkaRouterConfig = KafkaRouterConfig(env, "reconciler"),
-    s3Config          = S3Config(env),
-    s3Bucket          = BucketName(env.require(EnvKey.S3.BucketName)),
     reconcilerEnabled = env.optBool(EnvKey.Reconciler.Enabled) ?: DefaultEnabledValue,
     fullRunInterval   = env.optDuration(EnvKey.Reconciler.FullRunInterval) ?: DefaultFullRunInterval,
     slimRunInterval   = env.optDuration(EnvKey.Reconciler.SlimRunInterval) ?: DefaultSlimRunInterval,
@@ -38,4 +27,3 @@ data class ReconcilerConfig(
     inline val DefaultSlimRunInterval get() = 5.minutes
   }
 }
-
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
index cd6689ec..fb282b57 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
+++ b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
@@ -1,56 +1,38 @@
 package vdi.daemon.reconciler
 
 import kotlinx.coroutines.coroutineScope
-import kotlinx.coroutines.launch
-import kotlinx.coroutines.runBlocking
-import org.apache.logging.log4j.kotlin.CoroutineThreadContext
-import org.apache.logging.log4j.kotlin.ThreadContextData
+import kotlinx.coroutines.delay
 import org.apache.logging.log4j.kotlin.logger
-import vdi.component.db.app.AppDatabaseRegistry
-import vdi.component.kafka.router.KafkaRouter
-import vdi.component.kafka.router.KafkaRouterFactory
-import vdi.component.metrics.Metrics
 import vdi.component.modules.AbortCB
 import vdi.component.modules.AbstractJobExecutor
-import vdi.component.s3.DatasetManager
+import vdi.lib.reconciler.Reconciler as Recon
 import kotlin.time.Duration.Companion.milliseconds
 
-internal class ReconcilerImpl(private val config: ReconcilerConfig, abortCB: AbortCB)
+internal class ReconcilerImpl(private val config: ReconcilerDaemonConfig, abortCB: AbortCB)
   : Reconciler
   , AbstractJobExecutor("reconciler", abortCB)
 {
-  private val log = logger().delegate
-
-  private var datasetManager: DatasetManager
-
-  private var kafkaRouter: KafkaRouter
-
-  private val targets: List
+  private val logger = logger().delegate
 
   private var lastSlimRun = 0L
 
   private var lastFullRun = 0L
 
-  private val cacheDBTarget: ReconcilerTarget
-
   init {
-    runBlocking {
-      datasetManager = requireDatasetManager(config.s3Config, config.s3Bucket)
-      kafkaRouter = requireKafkaRouter()
-    }
-
-    targets = ArrayList(AppDatabaseRegistry.size() + 1)
-
-    AppDatabaseRegistry.iterator().asSequence()
-      .map { (project, _) -> AppDBTarget(project, project) }
-      .forEach { targets.add(it) }
-
-    cacheDBTarget = CacheDBTarget()
-
-    targets.add(cacheDBTarget)
+    Recon.initialize(abortCB)
   }
 
   override suspend fun runJob() {
+    // If the reconciler thread is disabled, just log a reminder every once in a
+    // while.
+    if (!config.reconcilerEnabled) {
+      coroutineScope {
+        logger.info("reconciler disabled by config")
+        delay(config.fullRunInterval)
+      }
+      return
+    }
+
     val now = System.currentTimeMillis()
 
     when {
@@ -58,52 +40,15 @@ internal class ReconcilerImpl(private val config: ReconcilerConfig, abortCB: Abo
       // full reconciler run interval
       (now - lastFullRun).milliseconds >= config.fullRunInterval -> {
         lastFullRun = now
-        runFull()
+        Recon.runFull()
       }
 
       // delta between last slim run and now is greater than or equal to the
       // slim reconciler run interval
       (now - lastSlimRun).milliseconds >= config.slimRunInterval -> {
         lastSlimRun = now
-        runSlim()
+        Recon.runSlim()
       }
     }
   }
-
-  private suspend fun runSlim() {
-    log.info("scheduling slim reconciler")
-
-    val timer = Metrics.Reconciler.Slim.executionTime.startTimer()
-
-    coroutineScope {
-      launch(CoroutineThreadContext(ThreadContextData(mapOf("workerID" to workerName(true, cacheDBTarget))))) {
-        ReconcilerInstance(cacheDBTarget, datasetManager, kafkaRouter, true).reconcile()
-      }
-    }
-
-    timer.observeDuration()
-  }
-
-  private suspend fun runFull() {
-    log.info("scheduling reconciler for {} targets", targets.size)
-
-    val timer = Metrics.Reconciler.Full.reconcilerTimes.startTimer()
-
-    // Schedule the reconciler for each target database.
-    coroutineScope {
-      targets.forEach {
-        launch(CoroutineThreadContext(ThreadContextData(mapOf("workerID" to workerName(false, it))))) {
-          ReconcilerInstance(it, datasetManager, kafkaRouter, false).reconcile()
-        }
-      }
-    }
-
-    timer.observeDuration()
-  }
-
-  private fun workerName(slim: Boolean, tgt: ReconcilerTarget) = if (slim) "slim-${tgt.name}" else "full-${tgt.name}"
-
-  private suspend fun requireKafkaRouter() = safeExec("failed to create KafkaRouter instance") {
-    KafkaRouterFactory(config.kafkaRouterConfig).newKafkaRouter()
-  }
 }
\ No newline at end of file
diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/index.kt b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/index.kt
index 09898338..825c6806 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/index.kt
+++ b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/index.kt
@@ -1,4 +1,6 @@
 package vdi.daemon.reconciler
 
-fun Reconciler(abortCB: (String?) -> Nothing, config: ReconcilerConfig = ReconcilerConfig()): Reconciler =
+import vdi.component.modules.AbortCB
+
+fun Reconciler(config: ReconcilerDaemonConfig = ReconcilerDaemonConfig(), abortCB: AbortCB): Reconciler =
   ReconcilerImpl(config, abortCB)
\ No newline at end of file
diff --git a/service/rest-service/api.raml b/service/rest-service/api.raml
index f0201856..a97ad7ce 100644
--- a/service/rest-service/api.raml
+++ b/service/rest-service/api.raml
@@ -244,6 +244,18 @@ uses:
 /admin:
   displayName: Admin RPC
 
+  /reconciler:
+    displayName: Reconciler
+    post:
+      displayName: Execute Reconciler
+      description: |
+        Triggers a full reconciliation run if one is not already in progress.
+      responses:
+        204:
+          description: Success
+        409:
+          description: Reconciler already running.
+
   /proxy-upload:
     displayName: Proxy Upload
     post:
@@ -329,7 +341,6 @@ uses:
       displayName: List
       description: |
         Lists datasets that failed to import.
-      headers:
       queryParameters:
         user:
           type: lib.User-ID
diff --git a/service/rest-service/build.gradle.kts b/service/rest-service/build.gradle.kts
index 334b8ef0..b9efa32a 100644
--- a/service/rest-service/build.gradle.kts
+++ b/service/rest-service/build.gradle.kts
@@ -55,6 +55,7 @@ dependencies {
   implementation(project(":lib:install-cleanup"))
   implementation(project(":lib:plugin-mapping"))
   implementation(project(":lib:pruner"))
+  implementation(project(":lib:reconciler"))
   implementation(project(":lib:s3"))
   implementation(project(":lib:metrics"))
 
diff --git a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/DatasetPostMetaImpl.java b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/DatasetPostMetaImpl.java
index d4a76447..38784dc1 100644
--- a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/DatasetPostMetaImpl.java
+++ b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/DatasetPostMetaImpl.java
@@ -47,8 +47,8 @@ public class DatasetPostMetaImpl implements DatasetPostMeta {
   @JsonProperty("dependencies")
   private List dependencies;
 
-  @JsonProperty("createdOn")
 
+  @JsonProperty("createdOn")
   private OffsetDateTime createdOn;
 
   @JsonProperty("datasetType")
diff --git a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/Error.java b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/Error.java
index 4ef1bc1b..5038e851 100644
--- a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/Error.java
+++ b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/Error.java
@@ -11,15 +11,15 @@
     property = "status"
 )
 @JsonSubTypes({
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ConflictError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.MethodNotAllowedError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.FailedDependencyError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ServerError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.BadRequestError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.UnauthorizedError.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.NotFoundError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ServerError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.FailedDependencyError.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ForbiddenError.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.UnprocessableEntityError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.UnauthorizedError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.BadRequestError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ConflictError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.MethodNotAllowedError.class),
     @JsonSubTypes.Type(java.lang.String.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.Error.class)
 })
diff --git a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/Admin.java b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/Admin.java
index 3f2f22c9..e11d61ec 100644
--- a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/Admin.java
+++ b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/Admin.java
@@ -25,6 +25,10 @@
 
 @Path("/admin")
 public interface Admin {
+  @POST
+  @Path("/reconciler")
+  PostAdminReconcilerResponse postAdminReconciler();
+
   @POST
   @Path("/proxy-upload")
   @Produces("application/json")
@@ -79,6 +83,26 @@ GetAdminListAllDatasetsResponse getAdminListAllDatasets(
       @QueryParam("project_id") String projectId,
       @QueryParam("include_deleted") @DefaultValue("false") Boolean includeDeleted);
 
+  class PostAdminReconcilerResponse extends ResponseDelegate {
+    private PostAdminReconcilerResponse(Response response, Object entity) {
+      super(response, entity);
+    }
+
+    private PostAdminReconcilerResponse(Response response) {
+      super(response);
+    }
+
+    public static PostAdminReconcilerResponse respond204() {
+      Response.ResponseBuilder responseBuilder = Response.status(204);
+      return new PostAdminReconcilerResponse(responseBuilder.build());
+    }
+
+    public static PostAdminReconcilerResponse respond409() {
+      Response.ResponseBuilder responseBuilder = Response.status(409);
+      return new PostAdminReconcilerResponse(responseBuilder.build());
+    }
+  }
+
   class PostAdminProxyUploadResponse extends ResponseDelegate {
     private PostAdminProxyUploadResponse(Response response, Object entity) {
       super(response, entity);
diff --git a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/VdiDatasets.java b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/VdiDatasets.java
index 8acca442..dfef8fd4 100644
--- a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/VdiDatasets.java
+++ b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/VdiDatasets.java
@@ -14,6 +14,7 @@
 import org.veupathdb.service.vdi.generated.model.DatasetListEntry;
 import org.veupathdb.service.vdi.generated.model.DatasetPostRequest;
 import org.veupathdb.service.vdi.generated.model.DatasetPostResponse;
+import org.veupathdb.service.vdi.generated.model.FailedDependencyError;
 import org.veupathdb.service.vdi.generated.model.ServerError;
 import org.veupathdb.service.vdi.generated.model.UnauthorizedError;
 import org.veupathdb.service.vdi.generated.model.UnprocessableEntityError;
@@ -102,6 +103,13 @@ public static PostVdiDatasetsResponse respond422WithApplicationJson(
       return new PostVdiDatasetsResponse(responseBuilder.build(), entity);
     }
 
+    public static PostVdiDatasetsResponse respond424WithApplicationJson(
+        FailedDependencyError entity) {
+      Response.ResponseBuilder responseBuilder = Response.status(424).header("Content-Type", "application/json");
+      responseBuilder.entity(entity);
+      return new PostVdiDatasetsResponse(responseBuilder.build(), entity);
+    }
+
     public static PostVdiDatasetsResponse respond500WithApplicationJson(ServerError entity) {
       Response.ResponseBuilder responseBuilder = Response.status(500).header("Content-Type", "application/json");
       responseBuilder.entity(entity);
diff --git a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/support/ResponseDelegate.java b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/support/ResponseDelegate.java
index 0ece4085..6c7e8cf5 100644
--- a/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/support/ResponseDelegate.java
+++ b/service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/support/ResponseDelegate.java
@@ -144,15 +144,15 @@ public MultivaluedMap getMetadata() {
     return this.delegate.getMetadata();
   }
 
-  @Override
-  public Object getEntity() {
-    return this.entity;}
-
   @Override
   public MultivaluedMap getStringHeaders() {
     return this.delegate.getStringHeaders();
   }
 
+  @Override
+  public Object getEntity() {
+    return this.entity;}
+
   @Override
   public String getHeaderString(String p0) {
     return this.delegate.getHeaderString(p0);
diff --git a/service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/server/controllers/AdminRPC.kt b/service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/server/controllers/AdminRPC.kt
index 7cd0cda6..838c51b4 100644
--- a/service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/server/controllers/AdminRPC.kt
+++ b/service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/server/controllers/AdminRPC.kt
@@ -26,6 +26,7 @@ import vdi.component.install_cleanup.InstallCleaner
 import vdi.component.install_cleanup.ReinstallTarget
 import vdi.component.pruner.Pruner
 import vdi.component.reinstaller.DatasetReinstaller
+import vdi.lib.reconciler.Reconciler
 
 // Broken Import Query Constants
 private const val biQueryLimitMinimum = 0
@@ -45,6 +46,16 @@ class AdminRPC : Admin {
       .respond200WithApplicationJson(listBrokenDatasets(expanded ?: true))
   }
 
+  override fun postAdminReconciler(): Admin.PostAdminReconcilerResponse {
+    return runBlocking {
+      if (Reconciler.runFull()) {
+        Admin.PostAdminReconcilerResponse.respond204()
+      } else {
+        Admin.PostAdminReconcilerResponse.respond409()
+      }
+    }
+  }
+
   override fun postAdminFixBrokenInstalls(
     skipRun: Boolean,
     entity: InstallCleanupRequest?
diff --git a/service/rest-service/src/main/resources/api.html b/service/rest-service/src/main/resources/api.html
index a93fca38..c57a4df6 100644
--- a/service/rest-service/src/main/resources/api.html
+++ b/service/rest-service/src/main/resources/api.html
@@ -1222,7 +1222,7 @@
 	bindFilters();
 
 });
-		
VEuPathDB Dataset Installer v2.0.0
link 
Resources
get /vdi-datasets
List Datasets  
Returns a list of datasets available to the requesting user, optionally filtered by query parameters.
Results are sorted by creation date in reverse order. This means the most recently created datasets will be first and the oldest dataset will be last in the list.
Parameters chevron_right expand_more
ParameterTypeDescription
Query
project_id Project IDstring
ID of the VEuPathDB project that results should be filtered to.
This means only datasets that are relevant to the project ID given will be returned.
Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, PlasmoDB, the status block in the response objects will only include installation status details for PlasmoDB and not any other sites that the dataset may have been installed into.
Inherits: string
ownership Dataset Ownership Filterstring
Ownership status filter.
Enum of:
  • any
  • owned
  • shared
If set to any the results are not filtered.
If set to owned, the results will be filtered to only results that are owned by the requesting user.
If set to shared, the results will be filtered to only results that are shared with the requesting user.
Default value: "any"
curl -X GET \
+		
VEuPathDB Dataset Installer v2.1.0
link 
Resources
get /vdi-datasets
List Datasets  
Returns a list of datasets available to the requesting user, optionally filtered by query parameters.
Results are sorted by creation date in reverse order. This means the most recently created datasets will be first and the oldest dataset will be last in the list.
Parameters chevron_right expand_more
ParameterTypeDescription
Query
project_id Project IDstring
ID of the VEuPathDB project that results should be filtered to.
This means only datasets that are relevant to the project ID given will be returned.
Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, PlasmoDB, the status block in the response objects will only include installation status details for PlasmoDB and not any other sites that the dataset may have been installed into.
Inherits: string
ownership Dataset Ownership Filterstring
Ownership status filter.
Enum of:
  • any
  • owned
  • shared
If set to any the results are not filtered.
If set to owned, the results will be filtered to only results that are owned by the requesting user.
If set to shared, the results will be filtered to only results that are shared with the requesting user.
Default value: "any"
curl -X GET \
   undefined/vdi-datasets?ProjectID=<value>&ownership=<value>
200 OK chevron_right expand_more
Success.
This response means that all checks passed and zero or more dataset records were found for the requesting user.
application/json
application/json
ParameterTypeDescription
[] Dataset List Itemobject
Short entry with basic details about a dataset.
Inherits: object
[].datasetId* Dataset IDstring
Unique VDI Dataset identifier string.
Pattern: ^[a-zA-Z0-9_-]{14}$
Min. length: 14
Max. length: 14
Inherits: lib.VDI-ID
[].owner* Owner Detailsobject
Details about the owner of a VDI dataset.
Inherits: lib.DatasetOwner
[].owner.userId* Owner User IDinteger
VEuPathDB user ID of the owner of the dataset.
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: lib.User-ID
[].owner.firstName Owner First Namestring
[].owner.lastName Owner Last Namestring
[].owner.email Owner Emailstring
[].owner.organization Owner Organizationstring
[].datasetType* Dataset Typeobject
Information about a specific dataset type.
Inherits: lib.DatasetTypeInfo
[].datasetType.name* Type Namestring
[].datasetType.displayName Type Display Namestring
Display name for the type. This field is ignored in requests and will always be present in responses.
[].datasetType.version* Type Versionstring
[].visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public
Inherits: lib.DatasetVisibility
[].name* Dataset Namestring
User provided name for the dataset.
[].summary Dataset Summarystring
User provided summary of the dataset.
[].description Dataset Descriptionstring
User provided description of the dataset.
[].sourceUrl Source URLstring
URL of the dataset data source, if the dataset was uploaded via URL.
[].origin* Dataset Originstring
String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.
[].projectIds* Project IDsarray
Project IDs for projects the dataset record was submitted to.
[].projectIds[] Project IDstring
Name or ID of a target VEuPathDB project.
Valid project IDs are:
  • AmoebaDB
  • ClinEpiDB
  • CryptoDB
  • FungiDB
  • GiardiaDB
  • HostDB
  • MicrobiomeDB
  • MicrosporidiaDB
  • PiroplasmaDB
  • PlasmoDB
  • ToxoDB
  • TrichDB
  • TriTrypDB
  • VectorBase
  • VEuPathDB
Inherits: lib.ProjectID
[].status* Status Infoobject
Information about the import and install status of a dataset.
Inherits: lib.DatasetStatusInfo
[].status.import*string
Import status of the dataset.
ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed
Inherits: lib.DatasetImportStatus
[].status.installarray
[].status.install[] Dataset Install Status Entryobject
Entry in a list of install statuses for a dataset.
Inherits: lib.DatasetInstallStatusEntry
[].status.install[].projectId*string
Name or ID of a target VEuPathDB project.
Valid project IDs are:
  • AmoebaDB
  • ClinEpiDB
  • CryptoDB
  • FungiDB
  • GiardiaDB
  • HostDB
  • MicrobiomeDB
  • MicrosporidiaDB
  • PiroplasmaDB
  • PlasmoDB
  • ToxoDB
  • TrichDB
  • TriTrypDB
  • VectorBase
  • VEuPathDB
Inherits: lib.ProjectID
[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency
Inherits: lib.DatasetInstallStatus
[].status.install[].metaMessagestring
[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency
Inherits: lib.DatasetInstallStatus
[].status.install[].dataMessagestring
[].shares* Shared Witharray
[].shares[]object
Inherits: object
[].shares[].userId*integer
Unique user identifier
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: lib.User-ID
[].shares[].firstName*string
[].shares[].lastName*string
[].shares[].organization*string
[].shares[].accepted*boolean
[].fileCount* File Countinteger
Number of files uploaded for this dataset.
[].fileSizeTotal* File Size Totalinteger
Sum of the sizes of all the files uploaded for this dataset.
Format: int64
[].created* Creation Timestampdatetime
Timestamp of the creation of this dataset.
Response Body
[
   {
     "datasetId": "zaZqAAGLGJhBgg",
@@ -1306,11 +1306,16 @@
       ]
     }
   }
+}
424 Failed Dependency chevron_right expand_more
Failed Dependency.
Returned when the dataset data source was a URL and the VDI service encountered a non-success HTTP status code from the target URL. This could be, for example, a 403 error from an expired AWS S3 URL, or a 404 for a file that no longer exists on the remote server.
Failed Dependency Error FailedDependencyError
application/json
Discriminator: status
Discriminator value: failed-dependency
Inherits: lib.Error
ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • failed-dependency
  • server-error
Inherits: lib.ErrorType
message*string
dependency*string
Response Body
{
+  "status": "failed-dependency",
+  "dependency": "google.com",
+  "message": "unexpected status code 403 from google.com"
 }
500 Internal Server Error chevron_right expand_more
Internal Server Error.
This status is returned when an unhandled or unexpected issue arises when attempting to process the request.
Internal Server Error ServerError
application/json
Discriminator: status
Discriminator value: server-error
Inherits: lib.Error
ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • failed-dependency
  • server-error
Inherits: lib.ErrorType
message*string
requestId*string
Response Body
{
   "status": "server-error",
   "message": "Dataset store is unreachable",
   "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
-}
post /admin/proxy-upload
  
Upload a dataset on behalf of another user.
Headers chevron_right expand_more
ParameterTypeDescription
User-ID* VEuPathDB User IDinteger
ID of the target user on whose behalf a dataset is being uploaded
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: integer
curl -X POST \
+}
post /admin/reconciler
Execute Reconciler  
Triggers a full reconciliation run if one is not already in progress.
curl -X POST \
+  undefined/admin/reconciler
204 No Content chevron_right expand_more
Success
409 Conflict chevron_right expand_more
Reconciler already running.
post /admin/proxy-upload
  
Upload a dataset on behalf of another user.
Headers chevron_right expand_more
ParameterTypeDescription
User-ID* VEuPathDB User IDinteger
ID of the target user on whose behalf a dataset is being uploaded
Min. value: 1
Max. value: 9223372036854776000
Format: int64
Inherits: integer
curl -X POST \
   -H "User-ID: <value>" \
   -H "Content-type: multipart/form-data"
   -d @file \
diff --git a/settings.gradle.kts b/settings.gradle.kts
index 357e5883..08319936 100644
--- a/settings.gradle.kts
+++ b/settings.gradle.kts
@@ -53,6 +53,7 @@ include(":lib:metrics")
 include(":lib:module-core")
 include(":lib:pruner")
 include(":lib:rabbit")
+include(":lib:reconciler")
 include(":lib:s3")
 include(":lib:test-utils")
 

From 5230a47a1458620457640bc15ce3d10869a4761d Mon Sep 17 00:00:00 2001
From: Elizabeth Paige Harper 
Date: Mon, 5 Aug 2024 13:28:46 -0400
Subject: [PATCH 2/4] fix reconciler check to allow slim reconciler to run
 always

---
 .../vdi/daemon/reconciler/ReconcilerImpl.kt   | 20 +++++++------------
 1 file changed, 7 insertions(+), 13 deletions(-)

diff --git a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
index fb282b57..7650a583 100644
--- a/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
+++ b/service/daemon/reconciler/src/main/kotlin/vdi/daemon/reconciler/ReconcilerImpl.kt
@@ -1,7 +1,5 @@
 package vdi.daemon.reconciler
 
-import kotlinx.coroutines.coroutineScope
-import kotlinx.coroutines.delay
 import org.apache.logging.log4j.kotlin.logger
 import vdi.component.modules.AbortCB
 import vdi.component.modules.AbstractJobExecutor
@@ -23,16 +21,6 @@ internal class ReconcilerImpl(private val config: ReconcilerDaemonConfig, abortC
   }
 
   override suspend fun runJob() {
-    // If the reconciler thread is disabled, just log a reminder every once in a
-    // while.
-    if (!config.reconcilerEnabled) {
-      coroutineScope {
-        logger.info("reconciler disabled by config")
-        delay(config.fullRunInterval)
-      }
-      return
-    }
-
     val now = System.currentTimeMillis()
 
     when {
@@ -40,7 +28,13 @@ internal class ReconcilerImpl(private val config: ReconcilerDaemonConfig, abortC
       // full reconciler run interval
       (now - lastFullRun).milliseconds >= config.fullRunInterval -> {
         lastFullRun = now
-        Recon.runFull()
+
+        // If the reconciler thread is disabled, just log a reminder.
+        if (!config.reconcilerEnabled) {
+          logger.info("reconciler disabled by config")
+        } else {
+          Recon.runFull()
+        }
       }
 
       // delta between last slim run and now is greater than or equal to the

From fc640187e0ba081b47569b4f7d1d7b2f8ff074ae Mon Sep 17 00:00:00 2001
From: Elizabeth Paige Harper 
Date: Mon, 5 Aug 2024 13:31:30 -0400
Subject: [PATCH 3/4] undo autoformatting change

---
 .../src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt  | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
index 1ab99620..69247155 100644
--- a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
@@ -136,9 +136,7 @@ internal class ReconcilerInstance(
           // database
           if (!nextTargetDataset!!.isUninstalled)
             // then fire a sync event
-            sendSyncEvent(nextTargetDataset!!.ownerID, nextTargetDataset!!.datasetID,
-              SyncReason.NeedsUninstall(targetDB)
-            )
+            sendSyncEvent(nextTargetDataset!!.ownerID, nextTargetDataset!!.datasetID, SyncReason.NeedsUninstall(targetDB))
         } else {
           // The dataset does not have a delete flag present in MinIO
 

From 67aee950d52475e762da8e3eb361c62ea5c91860 Mon Sep 17 00:00:00 2001
From: Elizabeth Paige Harper 
Date: Mon, 5 Aug 2024 13:32:01 -0400
Subject: [PATCH 4/4] undo autoformatting change

---
 .../src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt   | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
index 69247155..17f00362 100644
--- a/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
+++ b/lib/reconciler/src/main/kotlin/vdi/lib/reconciler/ReconcilerInstance.kt
@@ -279,8 +279,7 @@ internal class ReconcilerInstance(
   }
 
   private interface SyncReason {
-    class OutOfSync(val meta: Boolean, val shares: Boolean, val install: Boolean, val target: ReconcilerTarget) :
-      SyncReason {
+    class OutOfSync(val meta: Boolean, val shares: Boolean, val install: Boolean, val target: ReconcilerTarget) : SyncReason {
       override fun toString() =
         "out of sync:" +
           (if (meta) " meta" else "") +