Fixes for local R environment

commons/src/main/java/com/odysseusinc/arachne/execution_engine_common/api/v1/dto/EngineStatus.java

@@ -2,6 +2,7 @@
 
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.DockerEnvironmentDTO;
+import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.LocalEnvironmentDTO;
 import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.TarballEnvironmentDTO;
 import lombok.AllArgsConstructor;
 import lombok.Getter;
@@ -36,5 +37,6 @@ public class EngineStatus {
     public static class Environments {
         private List<TarballEnvironmentDTO> tarball;
         private List<DockerEnvironmentDTO> docker;
+        private List<LocalEnvironmentDTO> local;
     }
 }

commons/src/main/java/com/odysseusinc/arachne/execution_engine_common/descriptor/dto/LocalEnvironmentDTO.java

@@ -0,0 +1,14 @@
+package com.odysseusinc.arachne.execution_engine_common.descriptor.dto;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+
+@Getter
+@Setter
+@NoArgsConstructor
+@JsonIgnoreProperties(ignoreUnknown = true)
+public class LocalEnvironmentDTO {
+    // TODO add data describing the local environment
+}

engine/src/main/java/com/odysseusinc/arachne/executionengine/execution/AnalysisService.java

@@ -36,11 +36,13 @@
 import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.ExecutionOutcome;
 import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.Stage;
 import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.DockerEnvironmentDTO;
+import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.LocalEnvironmentDTO;
 import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.TarballEnvironmentDTO;
 import com.odysseusinc.arachne.executionengine.aspect.FileDescriptorCount;
 import com.odysseusinc.arachne.executionengine.auth.AuthEffects;
 import com.odysseusinc.arachne.executionengine.auth.CredentialsProvider;
 import com.odysseusinc.arachne.executionengine.execution.r.DockerEnvironmentService;
+import com.odysseusinc.arachne.executionengine.execution.r.LocalEnvironmentService;
 import com.odysseusinc.arachne.executionengine.model.descriptor.converter.DescriptorConverter;
 import com.odysseusinc.arachne.executionengine.service.CdmMetadataService;
 import com.odysseusinc.arachne.executionengine.service.impl.DescriptorServiceImpl;
@@ -99,6 +101,8 @@ public class AnalysisService {
     private DockerEnvironmentService dockerDescriptorService;
     @Autowired
     private DescriptorServiceImpl tarballDescriptorService;
+    @Autowired
+    private LocalEnvironmentService localEnvironmentService;
 
 
     @Value("${submission.update.interval}")
@@ -197,16 +201,15 @@ private void attachMetadata(AnalysisSyncRequestDTO analysis, File analysisDir) {
     public EngineStatus getStatus(List<Long> idsMaybe) {
         Map<Long, ExecutionOutcome> statuses = Optional.ofNullable(idsMaybe).map(ids ->
                 ids.stream().flatMap(id ->
-                        Optional.ofNullable(overseers.get(id)).map(overseer ->
-                                Stream.of(Pair.of(id, getStatus(overseer)))
-                        ).orElseGet(Stream::of)
+                        Stream.ofNullable(overseers.get(id)).map(overseer -> Pair.of(id, getStatus(overseer)))
                 ).collect(Collectors.toMap(Pair::getKey, Pair::getValue))
         ).orElseGet(Collections::emptyMap);
 
         List<TarballEnvironmentDTO> tarballs = tarballDescriptorService.getDescriptors().stream().map(DescriptorConverter::toDto).collect(Collectors.toList());
         List<DockerEnvironmentDTO> dockers = dockerDescriptorService.getEnvironments();
+        List<LocalEnvironmentDTO> locals = localEnvironmentService.getEnvironments();
 
-        return new EngineStatus(Instant.now(), statuses, new Environments(tarballs, dockers));
+        return new EngineStatus(Instant.now(), statuses, new Environments(tarballs, dockers, locals));
     }
 
     private static ExecutionOutcome getStatus(Overseer overseer) {

engine/src/main/java/com/odysseusinc/arachne/executionengine/execution/r/LocalEnvironmentService.java

@@ -0,0 +1,20 @@
+package com.odysseusinc.arachne.executionengine.execution.r;
+
+import com.odysseusinc.arachne.execution_engine_common.descriptor.dto.LocalEnvironmentDTO;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.stereotype.Service;
+
+import java.util.List;
+
+@Slf4j
+@Service
+public class LocalEnvironmentService  {
+    @Value("${runtime.local:false}")
+    private boolean useLocalREnv;
+
+    public List<LocalEnvironmentDTO> getEnvironments() {
+        return useLocalREnv ? List.of(new LocalEnvironmentDTO()) : List.of();
+    }
+
+}

engine/src/main/java/com/odysseusinc/arachne/executionengine/execution/r/LocalRService.java

@@ -0,0 +1,43 @@
+package com.odysseusinc.arachne.executionengine.execution.r;
+
+import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.AnalysisSyncRequestDTO;
+import com.odysseusinc.arachne.executionengine.execution.Overseer;
+import lombok.extern.slf4j.Slf4j;
+import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
+import org.springframework.stereotype.Service;
+
+import java.io.File;
+import java.io.IOException;
+import java.time.Instant;
+import java.util.Map;
+import java.util.function.BiConsumer;
+
+@Service
+@Slf4j
+@ConditionalOnProperty(name = "runtime.local")
+public class LocalRService extends RService {
+
+    @Override
+    protected Overseer analyze(AnalysisSyncRequestDTO analysis, File file, Integer updateInterval, Map<String, String> envp, BiConsumer<String, String> callback) {
+        Long id = analysis.getId();
+        String executableFileName = analysis.getExecutableFileName();
+
+        try {
+            Instant started = Instant.now();
+            log.info("Execution [{}] using local R environment (runtime.local=true)", id);
+            ProcessBuilder pb = new ProcessBuilder(EXECUTION_COMMAND, executableFileName).directory(file).redirectErrorStream(true);
+            pb.environment().putAll(envp);
+            log.info("Execution [{}] start local R process: {}", id, String.join(" ", new String[]{EXECUTION_COMMAND, executableFileName}));
+            Process process = pb.start();
+
+            return new TarballROverseer(
+                    id, process, runtimeTimeOutSec, callback, updateInterval, started, "local", killTimeoutSec
+            );
+
+        } catch (IOException ex) {
+            log.error("Execution [{}] error building runtime command", id, ex);
+            throw new RuntimeException(ex.getMessage(), ex);
+        }
+    }
+
+}

engine/src/main/java/com/odysseusinc/arachne/executionengine/execution/r/RExecutionService.java

@@ -5,8 +5,10 @@
 import com.odysseusinc.arachne.executionengine.execution.ExecutionService;
 import com.odysseusinc.arachne.executionengine.execution.Overseer;
 import com.odysseusinc.arachne.executionengine.service.DescriptorService;
+import jakarta.annotation.PostConstruct;
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 import org.springframework.util.CollectionUtils;
 
@@ -22,6 +24,11 @@ public class RExecutionService implements ExecutionService {
     private DescriptorService descriptorService;
     @Autowired
     private DockerService dockerService;
+    @Autowired(required = false)
+    private LocalRService localService;
+
+    @Value("${runtime.local:false}")
+    private boolean useLocalREnv;
 
     public String getExtension() {
         return "r";
@@ -34,7 +41,10 @@ public Overseer analyze(AnalysisSyncRequestDTO analysis, File dir, BiConsumer<St
     }
 
     private RService calcEnv(Long id, String image, String descriptorId) {
-        if (image != null) {
+        if (useLocalREnv) {
+            log.info("Analysis [{}] will be executed in LOCAL R environment (forced by runtime.local=true)", id);
+            return localService;
+        } else if (image != null) {
             log.info("Analysis [{}] requested image [{}], force DOCKER runtime", id, image);
             return dockerService;
         } else if (descriptorId != null) {
@@ -49,4 +59,11 @@ private RService calcEnv(Long id, String image, String descriptorId) {
         }
     }
 
-}
+    @PostConstruct
+    public void init() {
+        if (useLocalREnv) {
+            log.info("Runtime service running in LOCAL environment mode");
+        }
+    }
+
+}

engine/src/main/java/com/odysseusinc/arachne/executionengine/execution/r/TarballRService.java

@@ -32,14 +32,11 @@
 import com.odysseusinc.arachne.executionengine.model.descriptor.r.RDependency;
 import com.odysseusinc.arachne.executionengine.model.descriptor.r.RExecutionRuntime;
 import com.odysseusinc.arachne.executionengine.service.DescriptorService;
-import com.odysseusinc.datasourcemanager.krblogin.RuntimeServiceMode;
-import jakarta.annotation.PostConstruct;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.ResourceLoader;
 import org.springframework.stereotype.Service;
 
@@ -76,18 +73,6 @@ public class TarballRService extends RService {
     @Autowired
     private RIsolatedRuntimeProperties rIsolatedRuntimeProps;
 
-    @Value("${runtime.local:false}")
-    private boolean useLocalREnv;
-
-    @PostConstruct
-    public void init() {
-        if (RuntimeServiceMode.ISOLATED.equals(getRuntimeServiceMode())) {
-            log.info("Runtime service running in ISOLATED environment mode");
-        } else {
-            log.info("Runtime service running in SINGLE mode");
-        }
-    }
-
     @Override
     protected Overseer analyze(AnalysisSyncRequestDTO analysis, File file, Integer updateInterval, Map<String, String> envp, BiConsumer<String, String> callback) {
         DescriptorBundle descriptorBundle = descriptorService.getDescriptorBundle(
@@ -215,21 +200,9 @@ private String[] buildRuntimeCommand(File runFile, File workingDir, String fileN
             throw new FileNotFoundException("file '"
                     + fileName + "' is not exists in directory '" + workingDir.getAbsolutePath() + "'");
         }
-        String[] command;
-        if (RuntimeServiceMode.ISOLATED.equals(getRuntimeServiceMode())) {
-            command = ArrayUtils.addAll(rIsolatedRuntimeProps.getRunCmd(),
-                    runFile.getAbsolutePath(), workingDir.getAbsolutePath(), fileName, bundlePath);
-        } else {
-            command = new String[]{EXECUTION_COMMAND, fileName};
-        }
-        return command;
-    }
-
-    private RuntimeServiceMode getRuntimeServiceMode() {
-        return useLocalREnv ? RuntimeServiceMode.SINGLE : RuntimeServiceMode.ISOLATED;
+        return ArrayUtils.addAll(rIsolatedRuntimeProps.getRunCmd(), runFile.getAbsolutePath(), workingDir.getAbsolutePath(), fileName, bundlePath);
     }
 
-
     @SuppressWarnings("SameParameterValue")
     private static File extractToTempFile(ResourceLoader loader, String resourceName, String prefix, String suffix) throws IOException {
         File runFile = Files.createTempFile(prefix, suffix).toFile();