SCRUM-3693: roll down MaTI DB between environments

pom.xml

@@ -19,7 +19,7 @@
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 		<quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
 		<quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
-		<quarkus.platform.version>3.6.5</quarkus.platform.version>
+		<quarkus.platform.version>3.7.2</quarkus.platform.version>
 		<surefire-plugin.version>3.1.2</surefire-plugin.version>
 	</properties>
 

src/main/java/org/alliancegenome/mati/controller/AdminResource.java

@@ -2,27 +2,34 @@
 
 import jakarta.enterprise.context.RequestScoped;
 import jakarta.inject.Inject;
+import jakarta.transaction.Transactional;
 import jakarta.ws.rs.core.Response;
 import org.alliancegenome.mati.configuration.ErrorResponse;
-import org.alliancegenome.mati.entity.SubdomainEntity;
 import org.alliancegenome.mati.interfaces.AdminRESTInterface;
-import org.alliancegenome.mati.repository.SubdomainRepository;
 import org.alliancegenome.mati.repository.SubdomainSequenceRepository;
+import org.alliancegenome.mati.rolldownrepository.DBRoller;
+import org.eclipse.microprofile.config.inject.ConfigProperty;
 
+import java.util.List;
 import java.util.Map;
 
 /**
- * Controller for administrative endpoints
+ * Controller for:
+ *  getting the current values of the counters (subdomains)
+ *  and rolling down the MaTI database
  */
 @RequestScoped
 public class AdminResource implements AdminRESTInterface {
 
     @Inject
     SubdomainSequenceRepository subdomainSequenceRepository;
+
     @Inject
-    SubdomainRepository subdomainRepository;
+    DBRoller dbRoller;
+
+    private static final  String NET = System.getenv("NET");;
 
-    public Response getCounters(String auth_header) {
+    public Response getCounters() {
         Map<String,Long> counters = subdomainSequenceRepository.getSubdomainCounters();
         if (counters.isEmpty()) {
             ErrorResponse.ErrorMessage errorMessage = new ErrorResponse.ErrorMessage("admin.getCounters","No subdomains in database");
@@ -32,20 +39,34 @@ public Response getCounters(String auth_header) {
         return Response.ok().entity(counters).build();
     }
 
-    public Response setCounter(String auth_header, String subdomain, int value) {
-        SubdomainEntity subdomainEntity = subdomainRepository.findByName(subdomain);
-        if (subdomainEntity == null) {
-            ErrorResponse.ErrorMessage errorMessage = new ErrorResponse.ErrorMessage("admin.setCounter","ID subdomain " + subdomain +" not found");
-            ErrorResponse errorResponse = new ErrorResponse(errorMessage);
-            return Response.status(Response.Status.BAD_REQUEST).entity(errorResponse).build();
+    /**
+     * rolls down the status of Mati counters for the curation application
+     * @param auth_header with authorization
+     * @return a success/failure HTTP response
+     */
+    @Transactional
+    public Response rolldown_for_curation(String auth_header) {
+        if (NET.equals("alpha")) {
+            return Response.ok().build();
         }
-        boolean isDone = subdomainSequenceRepository.setSubdomainCounter(subdomainEntity, value);
-        if (isDone) {
+        List<String> subdomains = List.of("disease_annotation");
+        return rolldown(subdomains);
+    }
+
+    /**
+     * rolls down the status of Mati counters from one environment to another
+     * prod -> beta
+     * beta -> alpha
+     * @param subdomains the list of subdomains to roll down
+     * @return a success/failure HTTP response
+     */
+    private Response rolldown(List<String> subdomains) {
+        Map<String,Long> counters = subdomainSequenceRepository.getSubdomainCounters();
+        if (dbRoller.setSubdomainCounters(subdomains, counters)) {
             return Response.ok().build();
         }
         else {
-            return Response.notModified("Failure changing the value").build();
+            return Response.notModified("Failure changing the values").build();
         }
     }
-
 }

src/main/java/org/alliancegenome/mati/interfaces/AdminRESTInterface.java

@@ -13,40 +13,28 @@
 @Produces(MediaType.APPLICATION_JSON)
 @Consumes(MediaType.APPLICATION_JSON)
 @Tag(name = "Admin", description = "Administrative tasks")
-@Authenticated
 public interface AdminRESTInterface {
 
     /**
      * Gets the counters for all the subdomains
      *
-     * @param auth_header Authorization Header
      * @return an HTTP response
      */
     @Operation(summary = "Get Counter Values")
     @Path("/counters")
     @GET
-    Response getCounters(@NotNull @HeaderParam("Authorization") String auth_header);
-
+    Response getCounters();
 
     /**
-     * Sets the counters for a subdomain
-     *
+     * Rolls down the counters to another environment
+     * prod to beta, beta to alpha
      * @param auth_header Authorization Header
-     * @param subdomain the subdomain to change
-     * @param value the value to assign
      * @return an HTTP response
      */
-    @Operation(summary = "Set Counter Value")
-    @Path("/counter")
-    @PUT
-    Response setCounter(
-        @NotNull(message = "Header does not have Authorization") @HeaderParam("Authorization")
-        String auth_header,
-
-        @NotNull(message = "Header does not have subdomain") @HeaderParam("subdomain")
-        String subdomain,
-
-        @NotNull(message = "Header does not have increment value") @HeaderParam("value")
-        int value
-    );
+    @Operation(summary = "Roll down")
+    @Path("/rolldown_for_curation")
+    @POST
+    @Authenticated
+    Response rolldown_for_curation(
+            @NotNull(message = "Header does not have Authorization")  @HeaderParam("Authorization") String auth_header);
 }

src/main/java/org/alliancegenome/mati/repository/SubdomainSequenceRepository.java

@@ -1,5 +1,6 @@
 package org.alliancegenome.mati.repository;
 
+import io.quarkus.hibernate.orm.PersistenceUnit;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
 import jakarta.persistence.EntityManager;

src/main/java/org/alliancegenome/mati/rolldownrepository/DBRoller.java

@@ -0,0 +1,68 @@
+package org.alliancegenome.mati.rolldownrepository;
+
+import io.quarkus.hibernate.orm.PersistenceUnit;
+import jakarta.enterprise.context.RequestScoped;
+import jakarta.inject.Inject;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.Query;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Rolls-down the MaTI database from one environment to other
+ * prod -> beta
+ * beta -> alpha
+ */
+@RequestScoped
+public class DBRoller {
+
+    @PersistenceUnit("rolldown")
+    @Inject
+    EntityManager entityManager;
+
+    /**
+     *  Creates the SQL sentences for setting the PostgreSQL sequences values
+     * @param subdomains the list of subdomains
+     * @param counters a dictionary mapping subdomains to values (e.g. subdomain_person -> 120 )
+     * @return a list of SQL statements. For example:
+     * [ SETVAL('subdomain_name1_seq',10) ... SETVAL('subdomain_nameN_seq',N) ]
+     */
+    private List<String> prepareSETVALStatements(List<String> subdomains, Map<String,Long> counters) {
+        List<String> setVALStatements = new ArrayList<>();
+        for (String subdomain : subdomains) {
+            if (counters.containsKey(subdomain)) {
+                Long counter = counters.get(subdomain);
+                if (counter > 0) {
+                    setVALStatements.add("SETVAL('subdomain_" + subdomain + "_seq'," + counter + ")");
+                }
+            }
+        }
+        return setVALStatements;
+    }
+
+    /**
+     * Rolls down the values from one environment to other
+     * @param subdomains the list of subdomains
+     * @param counters a dictionary mapping subdomains to values (e.g. subdomain_reference -> 20 )
+     * @return a success/failure value
+     */
+    public boolean setSubdomainCounters(List<String> subdomains, Map<String,Long> counters) {
+        List<String> setStatements = prepareSETVALStatements(subdomains, counters);
+        if (!setStatements.isEmpty()) {
+            String body = String.join(",", setStatements);
+            String sql = "SELECT " + body;
+            Query query = entityManager.createNativeQuery(sql);
+            try {
+                int num_queries = query.getResultList().size();
+                if (num_queries == setStatements.size()) {
+                    return true;
+                }
+            } catch (Exception e) {
+                return false;
+            }
+        }
+        return true;
+    }
+}

src/main/resources/application.yml

@@ -10,7 +10,7 @@ okta:
   client:
     id: ""
     secret: ""
-  scopes: admin
+  scopes: ""
 
 quarkus:
   http:
@@ -20,17 +20,25 @@ quarkus:
       access-control-max-age: -1
       headers: "*"
   datasource:
+    db-kind: postgresql
     jdbc:
       driver: org.postgresql.Driver
       url: jdbc:postgresql://localhost:5432/mati
-    username: postgres
-    password: postgres
+    rolldown:
+      db-kind: postgresql
+      jdbc:
+        url: jdbc:postgresql://localhost:5432/roll
   flyway:
     migrate-at-start: true
   hibernate-orm:
     dialect: org.hibernate.dialect.PostgreSQLDialect
     database:
       generation: none
+    packages: ['org.alliancegenome.mati.entity','org.alliancegenome.mati.repository','io.quarkus.hibernate.orm.panache']
+    rolldown:
+      packages: ['org.alliancegenome.mati.rolldownrepository']
+      datasource: rolldown
+    validate-in-dev-mode: false
   swagger-ui:
     always-include: true
   smallrye-openapi.management.enabled: false
@@ -48,5 +56,8 @@ quarkus:
 
 "%test":
   quarkus.datasource.jdbc:
-      driver: org.testcontainers.jdbc.ContainerDatabaseDriver
-      url: jdbc:tc:postgresql:13:///mati
+    driver: org.testcontainers.jdbc.ContainerDatabaseDriver
+    url: jdbc:tc:postgresql:13:///mati
+  quarkus.datasource.rolldown.jdbc:
+    driver: org.testcontainers.jdbc.ContainerDatabaseDriver
+    url: jdbc:tc:postgresql:13:///roll

src/test/java/org/alliancegenome/mati/controller/AdminResourceITCase.java

@@ -10,57 +10,31 @@
 import static io.restassured.RestAssured.given;
 import static io.restassured.http.ContentType.JSON;
 
+/**
+ * Tests the /api/admin/counters endpoint
+ * It runs *after* the IdentifierResourceITcase tests
+ * that mint some identifiers
+ */
 @QuarkusIntegrationTest
 @QuarkusTestResource(PostgresResource.class)
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@Order(3)
 public class AdminResourceITCase {
-    private String authorization;
-    @BeforeAll
-    void setup() {
-        authorization = "Bearer: " + OktaHelper.fetchOktaToken();
-    }
-
-    @Test
-    public void setCounterDA() {
-        setCounterandCheckStatus("disease_annotation", 2);
-    }
-
-    @Test
-    public void setCounterPerson() {
-        setCounterandCheckStatus("person", 4);
-    }
-
-    @Test
-    public void setCounterResource() {
-        setCounterandCheckStatus("resource", 8);
-    }
 
     @Test
     public void getCounters() {
         Map<String,Integer> counters = given().
-            contentType(JSON).
-            header("Accept", "application/json").
-            header("Authorization", authorization).
-            when().
-            get("http://localhost:8081/api/admin/counters").
-            then().
-            statusCode(200)
-            .extract().body().as(Map.class);
-
-        Assertions.assertEquals(counters.get("disease_annotation"), 2);
+                contentType(JSON).
+                header("Accept", "application/json").
+                when().
+                get("http://localhost:8081/api/admin/counters").
+                then().
+                statusCode(200)
+                .extract().body().as(Map.class);
+
+        Assertions.assertEquals(counters.get("disease_annotation"), 5);
         Assertions.assertEquals(counters.get("person"), 4);
-        Assertions.assertEquals(counters.get("resource"), 8);
-    }
-
-    private void setCounterandCheckStatus(String subdomain, int value) {
-        given().
-            contentType(JSON).
-            header("Authorization", authorization).
-            header("subdomain", subdomain).
-            header("value", value).
-            when().
-            put("http://localhost:8081/api/admin/counter").
-            then().
-            statusCode(200);
+        Assertions.assertEquals(counters.get("resource"), 6);
+        Assertions.assertEquals(counters.get("reference"), 3);
     }
 }

src/test/java/org/alliancegenome/mati/controller/IdentifierResourceITCase.java

@@ -6,16 +6,18 @@
 
 import org.alliancegenome.mati.configuration.PostgresResource;
 import org.alliancegenome.mati.entity.IdentifiersRange;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.TestInstance;
+import org.junit.jupiter.api.*;
 
 import static io.restassured.RestAssured.given;
 
+/**
+ * Tests the /api/identifier (PUT, POST) endpoints
+ * for minting identifiers
+ */
 @QuarkusIntegrationTest
 @QuarkusTestResource(PostgresResource.class)
 @TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@Order(2)
 class IdentifierResourceITCase {
     private String authorization;
 

src/test/java/org/alliancegenome/mati/controller/SubdomainResourceITCase.java

@@ -9,6 +9,7 @@
 import org.alliancegenome.mati.entity.SubdomainEntity;
 import org.junit.jupiter.api.AfterEach;
 import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Order;
 import org.junit.jupiter.api.Test;
 
 import java.util.List;
@@ -18,6 +19,7 @@
 
 @QuarkusIntegrationTest
 @QuarkusTestResource(PostgresResource.class)
+@Order(1)
 class SubdomainResourceITCase {
 
     @BeforeEach

src/test/resources/junit-platform.properties

@@ -0,0 +1,2 @@
+junit.jupiter.testclass.order.default = \
+    org.junit.jupiter.api.ClassOrderer$OrderAnnotation