Merge pull request #112 from OHDSI/issue-73-environment-parameters

#73 Add support for additional ENV parameters to be stored with analysis and sent to execution engine

datanode/pom.xml

@@ -80,7 +80,7 @@
         <dependency>
             <groupId>com.odysseusinc.arachne</groupId>
             <artifactId>execution-engine-commons</artifactId>
-            <version>2.3</version>
+            <version>2.6.0</version>
         </dependency>
         <dependency>
             <artifactId>arachne-sys-settings</artifactId>

datanode/src/main/java/com/odysseusinc/arachne/datanode/controller/analysis/AnalysisController.java

@@ -92,7 +92,7 @@ public UploadDTO uploadFiles(Principal principal, @RequestPart("file") List<Mult
     }
 
     @Async
-    @PostMapping(path = "/execute/{id}")
+    @PostMapping(path = "/execute/{id}", consumes = MediaType.APPLICATION_JSON_VALUE)
     public CompletableFuture<?> execute(Principal principal, String id, @Valid @RequestBody AnalysisRequestDTO request) {
         User user = userService.getUser(principal);
         return analysisService.run(user, request, id);

datanode/src/main/java/com/odysseusinc/arachne/datanode/converter/GsonConverter.java

@@ -0,0 +1,43 @@
+/*
+ * Copyright 2024 Odysseus Data Services, Inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.odysseusinc.arachne.datanode.converter;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
+import lombok.extern.slf4j.Slf4j;
+
+import javax.persistence.AttributeConverter;
+import java.lang.reflect.Type;
+
+@Slf4j
+public abstract class GsonConverter<T> implements AttributeConverter<T, String> {
+    private static final Gson GSON = new Gson();
+
+    private final Type type;
+
+    public GsonConverter(TypeToken<T> type) {
+        this.type = type.getType();
+    }
+
+    @Override
+    public String convertToDatabaseColumn(T value) {
+        return GSON.toJson(value, type);
+    }
+
+    @Override
+    public T convertToEntityAttribute(String field) {
+        return GSON.fromJson(field, type);
+    }
+}

datanode/src/main/java/com/odysseusinc/arachne/datanode/converter/StringMapConverter.java

@@ -0,0 +1,25 @@
+/*
+ * Copyright 2024 Odysseus Data Services, Inc.
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package com.odysseusinc.arachne.datanode.converter;
+
+import com.google.gson.reflect.TypeToken;
+
+import java.util.Map;
+
+public class StringMapConverter extends GsonConverter<Map<String, String>> {
+    public StringMapConverter() {
+        super(new TypeToken<Map<String, String>>(){});
+    }
+}

datanode/src/main/java/com/odysseusinc/arachne/datanode/dto/analysis/AnalysisRequestDTO.java

@@ -20,6 +20,7 @@
 
 import javax.validation.constraints.NotBlank;
 import javax.validation.constraints.NotNull;
+import java.util.Map;
 
 @Getter
 @Setter
@@ -42,4 +43,6 @@ public class AnalysisRequestDTO {
     private String environmentId;
 
     private String dockerImage;
+
+    private Map<String, String> parameters;
 }

datanode/src/main/java/com/odysseusinc/arachne/datanode/model/analysis/Analysis.java

@@ -14,6 +14,8 @@
  */
 package com.odysseusinc.arachne.datanode.model.analysis;
 
+import com.odysseusinc.arachne.datanode.converter.GsonConverter;
+import com.odysseusinc.arachne.datanode.converter.StringMapConverter;
 import com.odysseusinc.arachne.datanode.environment.EnvironmentDescriptor;
 import com.odysseusinc.arachne.datanode.model.datasource.DataSource;
 import com.odysseusinc.arachne.execution_engine_common.api.v1.dto.AnalysisResultStatusDTO;
@@ -24,6 +26,7 @@
 import javax.persistence.AttributeOverrides;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
+import javax.persistence.Convert;
 import javax.persistence.Embedded;
 import javax.persistence.Entity;
 import javax.persistence.EnumType;
@@ -39,6 +42,7 @@
 import javax.validation.constraints.NotNull;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 
 @Getter
 @Setter
@@ -117,5 +121,9 @@ public class Analysis {
     @JoinColumn(name = "actual_environment_id")
     private EnvironmentDescriptor actualEnvironment;
 
+    @Column(name = "parameters")
+    @Convert(converter = StringMapConverter.class)
+    private Map<String, String> parameters;
+
 
 }

datanode/src/main/java/com/odysseusinc/arachne/datanode/service/AnalysisService.java

@@ -287,6 +287,7 @@ public AnalysisDTO get(Long id) {
 		dto.setTitle(analysis.getTitle());
 		dto.setStudy(analysis.getStudyTitle());
 		dto.setExecutableFileName(analysis.getExecutableFileName());
+		dto.setParameters(analysis.getParameters());
         dto.setFiles(UploadService.scan(sourcedir, UploadService.toRelativePath(sourcedir)));
 		String environmentId = Optional.ofNullable(analysis.getActualEnvironment()).map(EnvironmentDescriptor::getDescriptorId).orElseGet(() ->
 				Optional.ofNullable(analysis.getEnvironment()).map(EnvironmentDescriptor::getDescriptorId).orElse(null)
@@ -337,6 +338,7 @@ private Analysis save(com.odysseusinc.arachne.datanode.dto.analysis.AnalysisRequ
 		Analysis analysis = new Analysis();
 
 		analysis.setExecutableFileName(dto.getExecutableFileName());
+		analysis.setParameters(dto.getParameters());
 		analysis.setSourceFolder(sourceFolder);
 		// This is not used but we need to have something because not null in DB
 		analysis.setAnalysisFolder(AnalysisUtils.createUniqueDir(filesStorePath).getAbsolutePath());
@@ -391,6 +393,7 @@ private AnalysisRequestDTO toDto(Analysis analysis) {
 		dto.setDataSource(dataSourceService.toUnsecuredDto(analysis.getDataSource()));
 		dto.setId(analysis.getId());
 		dto.setExecutableFileName(analysis.getExecutableFileName());
+		dto.setParameters(analysis.getParameters());;
 		dto.setRequestedDescriptorId(Optional.ofNullable(analysis.getEnvironment()).map(EnvironmentDescriptor::getDescriptorId).orElse(null));
 		dto.setDockerImage(analysis.getDockerImage());
 		dto.setUpdateStatusCallback(analysis.getUpdateStatusCallback());

datanode/src/main/resources/db/migration/V20241019000000__analysis-env.sql

@@ -0,0 +1 @@
+ALTER TABLE analyses ADD COLUMN parameters VARCHAR;