wip

.github/workflows/api-docs.yml

@@ -1,7 +1,7 @@
 on:
   push:
     branches:
-    - main
+    - production
     paths:
     - 'docs/vdi-api.html'
 

lib/env/src/main/kotlin/vdi/component/env/EnvKey.kt

@@ -3,7 +3,11 @@ package vdi.component.env
 import org.veupathdb.vdi.lib.common.env.EnvKey
 
 object EnvKey {
-  inline val Admin get() = EnvKey.Admin
+  object Admin {
+    inline val SecretKey get() = EnvKey.Admin.SecretKey
+
+    const val EnablePurgeEndpoint = "ENABLE_USER_DATASET_PURGE_ENDPOINT"
+  }
 
   inline val AppDB get() = EnvKey.AppDB
 

service/rest-service/api.raml

@@ -623,6 +623,41 @@ uses:
             application/json:
               type: lib.AllDatasetsListResponse
 
+  /system-purge:
+    displayName: System Purge
+    get:
+      displayName: Generate Purge Token
+      description: |
+        Generates a temporary system purge token which will be required by a
+        `POST` request to this endpoint to execute the system purge.
+        
+        Having this process be 2 steps is to help avoid accidental calls to the
+        endpoint resulting in an unwanted system wipe.
+        
+        Any scripts wrapping or automating system purges should include a prompt
+        confirming the user actually intends to perform this action.
+      responses:
+        200:
+          body:
+            text/plain:
+              type: string
+              example: ccdc1583ae814b4da99f689ad88f0394303c2ec49a264dc28fa5262bcd7f9091
+    post:
+      displayName: Execute Purge
+      description: |
+        Executes a full system purge, uninstalling all datasets known to VDI.
+        
+        This endpoint does not perform the uninstallation synchronously, instead
+        it marks all datasets
+      body:
+        text/plain:
+          type: string
+          example: ccdc1583ae814b4da99f689ad88f0394303c2ec49a264dc28fa5262bcd7f9091
+      responses:
+        204:
+          description: Success
+
+
 /vdi-datasets/community:
   displayName: Community Datasets
   get:
@@ -662,7 +697,6 @@ uses:
               message: Dataset store is unreachable
               requestId: b296c3d9-4032-41b1-906e-c97ccfc447e3
 
-
 /vdi-datasets/{vd-id}:
   displayName: Dataset by ID
 
@@ -976,7 +1010,6 @@ uses:
             application/json:
               type: lib.ServerError
 
-
 /vdi-datasets/{vd-id}/shares/{recipient-user-id}:
   displayName: Dataset Sharing
 

service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/model/Error.java

@@ -11,14 +11,14 @@
     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(java.lang.String.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.UnprocessableEntityError.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.UnauthorizedError.class),
-    @JsonSubTypes.Type(java.lang.String.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.UnprocessableEntityError.class),
-    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.NotFoundError.class),
+    @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.MethodNotAllowedError.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.ForbiddenError.class),
     @JsonSubTypes.Type(org.veupathdb.service.vdi.generated.model.Error.class)
 })

service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/resources/Admin.java

@@ -79,6 +79,16 @@ GetAdminListAllDatasetsResponse getAdminListAllDatasets(
       @QueryParam("project_id") String projectId,
       @QueryParam("include_deleted") @DefaultValue("false") Boolean includeDeleted);
 
+  @GET
+  @Path("/system-purge")
+  @Produces("text/plain")
+  GetAdminSystemPurgeResponse getAdminSystemPurge();
+
+  @POST
+  @Path("/system-purge")
+  @Consumes("text/plain")
+  PostAdminSystemPurgeResponse postAdminSystemPurge(String entity);
+
   class PostAdminProxyUploadResponse extends ResponseDelegate {
     private PostAdminProxyUploadResponse(Response response, Object entity) {
       super(response, entity);
@@ -297,4 +307,35 @@ public static GetAdminListAllDatasetsResponse respond200WithApplicationJson(
       return new GetAdminListAllDatasetsResponse(responseBuilder.build(), entity);
     }
   }
+
+  class GetAdminSystemPurgeResponse extends ResponseDelegate {
+    private GetAdminSystemPurgeResponse(Response response, Object entity) {
+      super(response, entity);
+    }
+
+    private GetAdminSystemPurgeResponse(Response response) {
+      super(response);
+    }
+
+    public static GetAdminSystemPurgeResponse respond200WithTextPlain(String entity) {
+      Response.ResponseBuilder responseBuilder = Response.status(200).header("Content-Type", "text/plain");
+      responseBuilder.entity(entity);
+      return new GetAdminSystemPurgeResponse(responseBuilder.build(), entity);
+    }
+  }
+
+  class PostAdminSystemPurgeResponse extends ResponseDelegate {
+    private PostAdminSystemPurgeResponse(Response response, Object entity) {
+      super(response, entity);
+    }
+
+    private PostAdminSystemPurgeResponse(Response response) {
+      super(response);
+    }
+
+    public static PostAdminSystemPurgeResponse respond204() {
+      Response.ResponseBuilder responseBuilder = Response.status(204);
+      return new PostAdminSystemPurgeResponse(responseBuilder.build());
+    }
+  }
 }

service/rest-service/src/main/java/org/veupathdb/service/vdi/generated/support/ResponseDelegate.java

@@ -65,12 +65,12 @@ public int getStatus() {
   }
 
   @Override
-  public Response.StatusType getStatusInfo() {
-    return this.delegate.getStatusInfo();
+  public <T> T readEntity(Class<T> p0, Annotation[] p1) {
+    return this.delegate.readEntity(p0,p1);
   }
 
   @Override
-  public <T> T readEntity(Class<T> p0, Annotation[] p1) {
+  public <T> T readEntity(GenericType<T> p0, Annotation[] p1) {
     return this.delegate.readEntity(p0,p1);
   }
 
@@ -80,13 +80,13 @@ public <T> T readEntity(GenericType<T> p0) {
   }
 
   @Override
-  public <T> T readEntity(GenericType<T> p0, Annotation[] p1) {
-    return this.delegate.readEntity(p0,p1);
+  public <T> T readEntity(Class<T> p0) {
+    return this.delegate.readEntity(p0);
   }
 
   @Override
-  public <T> T readEntity(Class<T> p0) {
-    return this.delegate.readEntity(p0);
+  public Response.StatusType getStatusInfo() {
+    return this.delegate.getStatusInfo();
   }
 
   @Override

service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/admin/common.kt

@@ -0,0 +1,5 @@
+package org.veupathdb.service.vdi.service.admin
+
+import org.slf4j.LoggerFactory
+
+internal val Logger = LoggerFactory.getLogger("AdminRPC")

service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/admin/get-dataset-details.kt

@@ -2,8 +2,10 @@ package org.veupathdb.service.vdi.service.admin
 
 import jakarta.ws.rs.NotFoundException
 import org.veupathdb.vdi.lib.common.field.DatasetID
+import vdi.component.db.cache.CacheDB
 import vdi.component.db.cache.model.AdminDatasetDetailsRecord
 
 internal fun getDatasetDetails(datasetID: DatasetID): AdminDatasetDetailsRecord {
-    return vdi.component.db.cache.CacheDB().selectAdminDatasetDetails(datasetID = datasetID) ?: throw NotFoundException("No such dataset $datasetID")
+  return CacheDB().selectAdminDatasetDetails(datasetID = datasetID)
+    ?: throw NotFoundException("No such dataset $datasetID")
 }

service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/admin/system-purge.kt

@@ -0,0 +1,12 @@
+package org.veupathdb.service.vdi.service.admin
+
+import vdi.component.db.cache.CacheDB
+
+
+internal fun purgeUserDatasets() {
+  Logger.warn("BEGINNING USER DATASET PURGE")
+
+  val cacheDB = CacheDB()
+
+
+}

service/rest-service/src/main/kotlin/org/veupathdb/service/vdi/service/datasets/delete-dataset-by-id.kt

@@ -5,10 +5,11 @@ import jakarta.ws.rs.NotFoundException
 import org.veupathdb.service.vdi.s3.DatasetStore
 import org.veupathdb.vdi.lib.common.field.DatasetID
 import org.veupathdb.vdi.lib.common.field.UserID
+import vdi.component.db.cache.CacheDB
 import vdi.component.db.cache.withTransaction
 
 internal fun adminDeleteDataset(datasetID: DatasetID) {
-  val ds = vdi.component.db.cache.CacheDB().selectDataset(datasetID) ?: throw NotFoundException()
+  val ds = CacheDB().selectDataset(datasetID) ?: throw NotFoundException()
   deleteUserDataset(ds.ownerID, datasetID)
 }
 
@@ -27,7 +28,7 @@ internal fun adminDeleteDataset(datasetID: DatasetID) {
  */
 internal fun userDeleteDataset(userID: UserID, datasetID: DatasetID) {
   // Verify that the target dataset exists.
-  val ds = vdi.component.db.cache.CacheDB().selectDataset(datasetID) ?: throw NotFoundException()
+  val ds = CacheDB().selectDataset(datasetID) ?: throw NotFoundException()
 
   // Verify the dataset is owned by the requesting user.
   if (ds.ownerID != userID)
@@ -37,7 +38,7 @@ internal fun userDeleteDataset(userID: UserID, datasetID: DatasetID) {
 }
 
 private fun deleteUserDataset(userID: UserID, datasetID: DatasetID) {
-  vdi.component.db.cache.CacheDB().withTransaction {
+  CacheDB().withTransaction {
     // Update the deleted flag in the local pg.
     it.updateDatasetDeleted(datasetID, true)