Merge pull request #813 from molgenis/feat/#809-vanilla-rserve

feat: reimplement rserve route
molgenis · Feb 18, 2025 · 0e9fae1 · 0e9fae1
2 parents 2c9ea51 + 7661e4d
commit 0e9fae1
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Showing 24 changed files with 1,359 additions and 172 deletions.
diff --git a/armadillo/src/main/java/org/molgenis/armadillo/metadata/ProfileConfig.java b/armadillo/src/main/java/org/molgenis/armadillo/metadata/ProfileConfig.java
@@ -78,6 +78,7 @@ public EnvironmentConfigProps toEnvironmentConfigProps() {
     props.setName(getName());
     props.setHost(getHost());
     props.setPort(getPort());
+    props.setImage(getImage());
     return props;
   }
 }
diff --git a/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java b/armadillo/src/main/java/org/molgenis/armadillo/profile/DockerService.java
@@ -95,7 +95,7 @@ public Map<String, ContainerInfo> getAllProfileStatuses() {
    */
   String asContainerName(String profileName) {
     if (!inContainer) {
-      LOG.warn("NO ".repeat(100) + " " + profileName);
+      LOG.warn("Profile not running in docker container: " + profileName);
       return profileName;
     }
 
@@ -104,7 +104,7 @@ String asContainerName(String profileName) {
       return profileName;
     }
 
-    LOG.warn("YES ".repeat(100) + " " + profileName);
+    LOG.warn("Profile running in docker container: " + profileName);
     return containerPrefix + profileName + "-1";
   }
 
@@ -148,12 +148,13 @@ public void startProfile(String profileName) {
     startContainer(containerName);
   }
 
-  private void installImage(ProfileConfig profileConfig) {
+  void installImage(ProfileConfig profileConfig) {
     if (profileConfig.getImage() == null) {
       throw new MissingImageException(profileConfig.getImage());
     }
 
-    int imageExposed = 8085;
+    // if rock is in the image name, it's rock
+    int imageExposed = profileConfig.getImage().contains("rock") ? 8085 : 6311;
     ExposedPort exposed = ExposedPort.tcp(imageExposed);
     Ports portBindings = new Ports();
     portBindings.bind(exposed, Ports.Binding.bindPort(profileConfig.getPort()));

diff --git a/armadillo/src/test/java/org/molgenis/armadillo/controller/ArmadilloUtilsTest.java b/armadillo/src/test/java/org/molgenis/armadillo/controller/ArmadilloUtilsTest.java
@@ -5,14 +5,13 @@
 import static org.molgenis.armadillo.controller.ArmadilloUtils.createRawResponse;
 
 import java.nio.charset.Charset;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 import org.molgenis.r.RServerResult;
 import org.molgenis.r.exceptions.RExecutionException;
-import org.molgenis.r.rock.RockResult;
+import org.molgenis.r.rserve.RserveResult;
 import org.rosuda.REngine.REXPRaw;
 
 @ExtendWith(MockitoExtension.class)
@@ -27,18 +26,11 @@ void testSerializeCommand() {
     assertEquals("try(base::serialize({meanDS(D$age}, NULL))", serializedCommand);
   }
 
-  @Disabled
   @Test
   void testCreateRawResponse() {
     byte[] bytes = {0x01, 0x02, 0x03};
     REXPRaw rexpDouble = new REXPRaw(bytes);
-    // rexpDouble renders to String "org.rosuda.REngine.REXPRaw@3a3f96ab[3]"
-    byte[] actual = createRawResponse(new RockResult(rexpDouble));
-    StringBuilder sb = new StringBuilder();
-    for (byte b : actual) {
-      sb.append((char) b);
-    }
-    String str = sb.toString();
+    byte[] actual = createRawResponse(new RserveResult(rexpDouble));
     assertArrayEquals(bytes, actual);
   }
 

diff --git a/armadillo/src/test/java/org/molgenis/armadillo/controller/DataControllerTest.java b/armadillo/src/test/java/org/molgenis/armadillo/controller/DataControllerTest.java
@@ -24,7 +24,6 @@
 import java.security.Principal;
 import java.util.*;
 import java.util.concurrent.CompletableFuture;
-import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.junit.jupiter.params.ParameterizedTest;
@@ -45,6 +44,7 @@
 import org.molgenis.armadillo.storage.ArmadilloStorageService;
 import org.molgenis.r.model.RPackage;
 import org.molgenis.r.rock.RockResult;
+import org.molgenis.r.rserve.RserveResult;
 import org.obiba.datashield.core.DSEnvironment;
 import org.obiba.datashield.core.DSMethod;
 import org.obiba.datashield.core.impl.DefaultDSMethod;
@@ -288,7 +288,6 @@ void getAggregateMethods() throws Exception {
             Map.of("sessionId", sessionId, "roles", List.of("ROLE_USER"))));
   }
 
-  @Disabled
   @Test
   @WithMockUser
   void testGetLastResultNoResult() throws Exception {
@@ -297,13 +296,12 @@ void testGetLastResultNoResult() throws Exception {
     mockMvc.perform(asyncDispatch(result)).andExpect(status().isNotFound());
   }
 
-  @Disabled
   @Test
   @WithMockUser
   void testGetLastResult() throws Exception {
     byte[] bytes = {0x0, 0x1, 0x2};
     when(commands.getLastExecution())
-        .thenReturn(Optional.of(completedFuture(new RockResult(new REXPRaw(bytes)))));
+        .thenReturn(Optional.of(completedFuture(new RserveResult(new REXPRaw(bytes)))));
 
     MvcResult result =
         mockMvc.perform(get("/lastresult").accept(APPLICATION_OCTET_STREAM)).andReturn();

diff --git a/armadillo/src/test/java/org/molgenis/armadillo/metadata/ProfileConfigTest.java b/armadillo/src/test/java/org/molgenis/armadillo/metadata/ProfileConfigTest.java
@@ -0,0 +1,47 @@
+package org.molgenis.armadillo.metadata;
+
+import static org.junit.jupiter.api.Assertions.assertDoesNotThrow;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.molgenis.armadillo.metadata.ProfileConfig.create;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import org.junit.jupiter.api.Test;
+import org.molgenis.r.config.EnvironmentConfigProps;
+
+public class ProfileConfigTest {
+
+  @Test
+  public void testToEnvironmentConfigProps() {
+    String name = "myName";
+    String img = "myImage";
+    String host = "localhost";
+    int port = 6311;
+    ProfileConfig config =
+        create(name, img, host, port, new HashSet<>(), new HashSet<>(), new HashMap<>());
+    EnvironmentConfigProps actual = config.toEnvironmentConfigProps();
+    assertEquals(img, actual.getImage());
+  }
+
+  @Test
+  public void testToEnvironmentConfigPropsDoesNotThrowErrorWhenImageNull() {
+    ProfileConfig config =
+        create(
+            "myName", null, "localhost", 6311, new HashSet<>(), new HashSet<>(), new HashMap<>());
+    assertDoesNotThrow(config::toEnvironmentConfigProps);
+  }
+
+  @Test
+  public void testCreateEmptyHost() {
+    ProfileConfig config =
+        create("myName", null, null, 6311, new HashSet<>(), new HashSet<>(), new HashMap<>());
+    assertEquals("localhost", config.getHost());
+  }
+
+  @Test
+  public void testCreateEmptyOptions() {
+    ProfileConfig config =
+        create("myName", null, null, 6311, new HashSet<>(), new HashSet<>(), null);
+    assertEquals("java.util.ImmutableCollections$MapN", config.getOptions().getClass().getName());
+  }
+}
diff --git a/...s/armadillo/config/DockerServiceTest.java → .../armadillo/profile/DockerServiceTest.java b/...s/armadillo/config/DockerServiceTest.java → .../armadillo/profile/DockerServiceTest.java
@@ -1,9 +1,8 @@
-package org.molgenis.armadillo.config;
+package org.molgenis.armadillo.profile;
 
 import static java.util.Collections.emptyMap;
 import static java.util.Collections.emptySet;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.verify;
 import static org.mockito.Mockito.when;
@@ -29,8 +28,6 @@
 import org.molgenis.armadillo.metadata.ProfileConfig;
 import org.molgenis.armadillo.metadata.ProfileService;
 import org.molgenis.armadillo.metadata.ProfileStatus;
-import org.molgenis.armadillo.profile.ContainerInfo;
-import org.molgenis.armadillo.profile.DockerService;
 
 @ExtendWith(MockitoExtension.class)
 class DockerServiceTest {
@@ -125,6 +122,23 @@ void testStartProfileNoImage() {
     assertThrows(MissingImageException.class, () -> dockerService.startProfile("default"));
   }
 
+  @Test
+  void testInstallImageNull() {
+    ProfileConfig profileConfig = mock(ProfileConfig.class);
+    when(profileConfig.getImage()).thenReturn(null);
+    assertThrows(MissingImageException.class, () -> dockerService.installImage(profileConfig));
+  }
+
+  @Test
+  void testInstallImage() {
+    ProfileConfig profileConfig = mock(ProfileConfig.class);
+    String image = "datashield/rock-something-something:latest";
+    when(profileConfig.getImage()).thenReturn(image);
+    when(profileConfig.getPort()).thenReturn(6311);
+    assertDoesNotThrow(() -> dockerService.installImage(profileConfig));
+    verify(dockerClient).createContainerCmd(image);
+  }
+
   @SuppressWarnings("ConstantConditions")
   @Test
   void testStartProfile() {

diff --git a/docker/ci/application.yml b/docker/ci/application.yml
@@ -40,13 +40,17 @@ armadillo:
         datashield:
           # the seed can only be 9 digits
           seed: 342325352
-    - name: rock
-      image: datashield/rock-base:latest
-      host: rock
-      port: 8085
+    - name: xenon-vanilla
+      image: datashield/armadillo-rserver_caravan-xenon:latest
+      host: xenon-vanilla
+      port: 6012
       package-whitelist:
         - dsBase
         - resourcer
+        - dsMediation
+        - dsMTLBase
+        - dsSurvival
+        - dsOmics
       function-blacklist: [ ]
       options:
         datashield:

diff --git a/docker/ci/docker-compose.yml b/docker/ci/docker-compose.yml
@@ -27,5 +27,3 @@ services:
   xenon:
     hostname: xenon
     image: datashield/rock-dolomite-xenon:latest
-    environment:
-      DEBUG: "TRUE"
diff --git a/r/src/main/java/org/molgenis/r/RServerConnectionFactory.java b/r/src/main/java/org/molgenis/r/RServerConnectionFactory.java
@@ -2,8 +2,10 @@
 
 import java.io.IOException;
 import java.net.*;
+import java.util.Objects;
 import org.molgenis.r.config.EnvironmentConfigProps;
 import org.molgenis.r.rock.RockConnectionFactory;
+import org.molgenis.r.rserve.RserveConnectionFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -46,24 +48,45 @@ RockStatusCode doHead(String uri) {
     }
   }
 
+  String getMessageFromStatus(RockStatusCode statusCode, String url) {
+    if (statusCode == RockStatusCode.SERVER_DOWN) {
+      return ("Container for '" + url + "'  is down");
+    } else if (statusCode == RockStatusCode.SERVER_NOT_READY) {
+      return ("Container for '" + url + "' is not ready");
+    } else if (statusCode == RockStatusCode.OK) {
+      return ("Container for '" + url + "' is running");
+    } else if (statusCode == RockStatusCode.UNEXPECTED_RESPONSE_CODE) {
+      return ("Unexpected response code on " + url);
+    } else if (statusCode == RockStatusCode.UNEXPECTED_RESPONSE) {
+      return ("Unexpected response on " + url);
+    } else if (statusCode == RockStatusCode.UNEXPECTED_URL) {
+      return ("MalformedURLException on " + url);
+    } else {
+      return "";
+    }
+  }
+
+  Boolean isWarningStatus(RockStatusCode rockStatusCode) {
+    return rockStatusCode == RockStatusCode.SERVER_DOWN
+        || rockStatusCode == RockStatusCode.SERVER_NOT_READY
+        || rockStatusCode == RockStatusCode.UNEXPECTED_URL;
+  }
+
   @Override
   public RServerConnection tryCreateConnection() {
-    String url = "http://" + environment.getHost() + ":" + environment.getPort();
-    RockStatusCode rockStatus = doHead(url);
-    if (rockStatus == RockStatusCode.SERVER_DOWN) {
-      logger.warn("Container for '" + url + "'  is down");
-    } else if (rockStatus == RockStatusCode.SERVER_NOT_READY) {
-      logger.warn("Container for '" + url + "' is not ready");
-    } else if (rockStatus == RockStatusCode.OK) {
-      logger.info("Container for '" + url + "' is running");
-    } else if (rockStatus == RockStatusCode.UNEXPECTED_RESPONSE_CODE) {
-      logger.info("Unexpected response code on " + url);
-    } else if (rockStatus == RockStatusCode.UNEXPECTED_RESPONSE) {
-      logger.info("Unexpected response on " + url);
-    } else if (rockStatus == RockStatusCode.UNEXPECTED_URL) {
-      logger.warn("MalformedURLException on " + url);
+    if (environment.getImage().contains("rock")) {
+      String url = "http://" + environment.getHost() + ":" + environment.getPort();
+      RockStatusCode rockStatus = doHead(url);
+      String statusMessage = getMessageFromStatus(rockStatus, url);
+      if (isWarningStatus(rockStatus)) {
+        logger.warn(statusMessage);
+      } else if (!Objects.equals(statusMessage, "")) {
+        logger.info(statusMessage);
+      }
+      return new RockConnectionFactory(environment).tryCreateConnection();
+    } else {
+      return new RserveConnectionFactory(environment).tryCreateConnection();
     }
-    return new RockConnectionFactory(environment).tryCreateConnection();
   }
 }
 
@@ -80,8 +103,4 @@ enum RockStatusCode {
   RockStatusCode(int code) {
     this.code = code;
   }
-
-  public int getCode() {
-    return this.code;
-  }
 }
diff --git a/r/src/main/java/org/molgenis/r/config/EnvironmentConfigProps.java b/r/src/main/java/org/molgenis/r/config/EnvironmentConfigProps.java
@@ -6,6 +6,7 @@
 public class EnvironmentConfigProps {
   @NotEmpty private String name;
   @NotEmpty private String host = "localhost";
+  private String image = "";
   @Positive private int port = 6311;
 
   public String getHost() {
@@ -31,4 +32,12 @@ public String getName() {
   public void setName(String name) {
     this.name = name;
   }
+
+  public String getImage() {
+    return image;
+  }
+
+  public void setImage(String image) {
+    this.image = image;
+  }
 }