Change Absolute File URLs To Forwarded URL

Author: Lucas0T

README.md

@@ -79,8 +79,6 @@ For the latest build see: https://github.com/medizininformatik-initiative/torch/
 | TORCH_CONCEPT_TREE_FILE                             | ontology/mapping_tree.json          | The file for the concept tree mapping.                                                               |
 | TORCH_DSE_MAPPING_TREE_FILE                         | ontology/dse_mapping_tree.json      | The file for DSE concept tree mapping.                                                               |
 | TORCH_USE_CQL                                       | true                                | Flag indicating if CQL should be used.                                                               |
-| TORCH_BASE_URL                                      | –                                   | The server name before the proxy from which torch is accessed                                        |
-| TORCH_OUTPUT_FILE_SERVER_URL                        | –                                   | The URL to access Result location TORCH_RESULTS_DIR  served by a proxy/fileserver                    |
 | LOG_LEVEL<br/>_DE_MEDIZININFORMATIKINITIATIVE_TORCH | info                                | Log level for torch core functionality.                                                              |
 | LOG_LEVEL<br/>_CA_UHN_FHIR                          | error                               | Log level for HAPI FHIR library.                                                                     |
 | SPRING_PROFILES_ACTIVE                              | active                              | The active Spring profile.                                                                           |
@@ -217,6 +215,9 @@ This can be used to track the progress of your data extraction.
 
 If a server is set up for the files e.g. NGINX, the files can be fetched by a Request on the URL set in
 TORCH_OUTPUT_FILE_SERVER_URL in [enviroment variables](#environment-variables).
+**Torch assumes that the files are served from the baseurl that is next to the fhir api**
+E.g.: if localhost:8080/test/fhir is the url from which torch gets called (before forwarding), then
+the file url would start with **http://localhost:8080/test/**
 
 ```sh
 curl -s "http://localhost:8080/da4a1c56-f5d9-468c-b57a-b8186ea4fea8/f33634bd-d51b-463c-a956-93409d96935f.ndjson"

src/main/java/de/medizininformatikinitiative/torch/config/AppConfig.java

@@ -58,6 +58,7 @@
 import org.springframework.web.reactive.function.client.ExchangeFilterFunctions;
 import org.springframework.web.reactive.function.client.ExchangeStrategies;
 import org.springframework.web.reactive.function.client.WebClient;
+import org.springframework.web.server.adapter.ForwardedHeaderTransformer;
 import reactor.netty.http.client.HttpClient;
 import reactor.netty.resources.ConnectionProvider;
 
@@ -92,6 +93,11 @@ public AppConfig(TorchProperties torchProperties) {
         this.torchProperties = torchProperties;
     }
 
+    @Bean
+    public ForwardedHeaderTransformer forwardedHeaderTransformer() {
+        return new ForwardedHeaderTransformer();
+    }
+
 
     @Bean
     public String searchParametersFile(@Value("${torch.search_parameters_file}") String searchParametersFile) {
@@ -370,7 +376,7 @@ public StructureDefinitionHandler cdsStructureDefinitionHandler(ResourceReader r
 
     @Bean
     public ResultFileManager resultFileManager(FhirContext fhirContext) {
-        return new ResultFileManager(torchProperties.results().dir(), torchProperties.results().persistence(), fhirContext, torchProperties.base().url(), torchProperties.output().file().server().url());
+        return new ResultFileManager(torchProperties.results().dir(), torchProperties.results().persistence(), fhirContext);
     }
 
     @Bean

src/main/java/de/medizininformatikinitiative/torch/config/TorchProperties.java

@@ -4,8 +4,6 @@
 
 @ConfigurationProperties(prefix = "torch")
 public record TorchProperties(
-        Base base,
-        Output output,
         Profile profile,
         Mapping mapping,
         Fhir fhir,
@@ -19,24 +17,9 @@ public record TorchProperties(
         String dseMappingTreeFile,
         boolean useCql
 ) {
-
-    public record Base(String url) {
-
-    }
-
     public record Max(int connections) {
     }
 
-    public record Output(File file) {
-        public record File(Server server) {
-            public record Server(String url) {
-
-            }
-        }
-
-    }
-
-
     public record Profile(String dir) {
     }
 

src/main/java/de/medizininformatikinitiative/torch/rest/FhirController.java

@@ -20,10 +20,12 @@
 import org.springframework.web.reactive.function.server.RouterFunction;
 import org.springframework.web.reactive.function.server.ServerRequest;
 import org.springframework.web.reactive.function.server.ServerResponse;
+import org.springframework.web.util.UriComponentsBuilder;
 import reactor.core.publisher.Mono;
 import reactor.core.scheduler.Schedulers;
 
 import java.io.IOException;
+import java.net.URI;
 import java.time.Instant;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
@@ -47,6 +49,7 @@ public class FhirController {
     private static final Logger logger = LoggerFactory.getLogger(FhirController.class);
 
     private static final MediaType MEDIA_TYPE_FHIR_JSON = MediaType.valueOf("application/fhir+json");
+    public static final String FHIR_STATUS = "/fhir/__status/";
 
     private final ObjectMapper objectMapper;
     private final FhirContext fhirContext;
@@ -82,7 +85,7 @@ private record DecodedContent(byte[] crtdl, List<String> patientIds) {
 
     @Autowired
     public FhirController(ObjectMapper objectMapper, FhirContext fhirContext, ResultFileManager resultFileManager,
-            CrtdlProcessingService crtdlProcessingService, CrtdlValidatorService validatorService) {
+                          CrtdlProcessingService crtdlProcessingService, CrtdlValidatorService validatorService) {
         this.objectMapper = objectMapper;
         this.fhirContext = fhirContext;
         this.resultFileManager = resultFileManager;
@@ -119,7 +122,7 @@ private static DecodedContent decodeCrtdlContent(Parameters parameters) {
     public RouterFunction<ServerResponse> queryRouter() {
         logger.info("Init FhirController Router");
         return route(POST("/fhir/$extract-data").and(accept(MEDIA_TYPE_FHIR_JSON)), this::handleExtractData)
-                .andRoute(GET("/fhir/__status/{jobId}"), this::checkStatus).andRoute(GET("/fhir/__status/"), this::getGlobalStatus);
+                .andRoute(GET("/fhir/__status/{jobId}"), this::checkStatus).andRoute(GET(FHIR_STATUS), this::getGlobalStatus);
     }
 
     private record DecodedCRTDLContent(Crtdl crtdl, List<String> patientIds) {
@@ -183,7 +186,7 @@ public Mono<ServerResponse> handleExtractData(ServerRequest request) {
                             .subscribeOn(Schedulers.boundedElastic()).subscribe(); // final fire-and-forget
 
                     return accepted()
-                            .header("Content-Location", request.uriBuilder().replacePath("/fhir/__status/" + jobId).build().toString())
+                            .header("Content-Location", request.uriBuilder().replacePath(FHIR_STATUS + jobId).build().toString())
                             .build();
                 })
                 .onErrorResume(IllegalArgumentException.class, e -> {
@@ -228,7 +231,30 @@ private Crtdl parseCrtdlContent(byte[] content) throws IOException {
         return objectMapper.readValue(content, Crtdl.class);
     }
 
+    public String stripToBasePath(URI originalUri, String basePath) {
+
+        String fullPath = originalUri.getPath();
+
+        int index = fullPath.indexOf(basePath);
+        if (index == -1) {
+            return originalUri.toString(); // fallback: no change
+        }
+
+        String newPath = fullPath.substring(0, index);
+
+        return UriComponentsBuilder
+                .fromUri(originalUri)
+                .replacePath(newPath)
+                .replaceQuery(null)
+                .fragment(null)
+                .build()
+                .toUriString();
+    }
+
+
     public Mono<ServerResponse> checkStatus(ServerRequest request) {
+        String truncatedUrl = stripToBasePath(request.uri(), FHIR_STATUS);
+        logger.info("Base url: {}", truncatedUrl);
         var jobId = request.pathVariable("jobId");
         HttpStatus status = resultFileManager.getStatus(jobId);
 
@@ -242,7 +268,7 @@ public Mono<ServerResponse> checkStatus(ServerRequest request) {
             case HttpStatus.OK -> {
                 // Capture the full request URL and transaction time
                 String transactionTime = DateTimeFormatter.ISO_INSTANT.format(Instant.now());
-                return Mono.fromCallable(() -> resultFileManager.loadBundleFromFileSystem(jobId, transactionTime))
+                return Mono.fromCallable(() -> resultFileManager.loadBundleFromFileSystem(truncatedUrl, jobId, transactionTime))
                         .flatMap(bundleMap -> {
                             if (bundleMap == null) {
                                 return ServerResponse.notFound().build();

src/main/java/de/medizininformatikinitiative/torch/util/ResultFileManager.java

@@ -4,17 +4,14 @@
 import ca.uhn.fhir.context.FhirContext;
 import de.medizininformatikinitiative.torch.management.OperationOutcomeCreator;
 import de.medizininformatikinitiative.torch.model.consent.PatientBatchWithConsent;
-import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.OperationOutcome;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.HttpStatus;
-import reactor.core.publisher.Flux;
 import reactor.core.publisher.Mono;
 import reactor.core.scheduler.Schedulers;
 
 import java.io.BufferedWriter;
-import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.charset.StandardCharsets;
@@ -23,7 +20,13 @@
 import java.nio.file.Paths;
 import java.nio.file.StandardOpenOption;
 import java.time.Duration;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
+import java.util.Set;
+import java.util.UUID;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.stream.Stream;
 
@@ -38,18 +41,14 @@ public class ResultFileManager {
 
     private final Path resultsDirPath;
     private final FhirContext fhirContext;
-    private final String hostname;
-    private final String fileServerName;
     public final ConcurrentHashMap<String, HttpStatus> jobStatusMap = new ConcurrentHashMap<>();
 
-    public ResultFileManager(String resultsDir, String duration, FhirContext fhirContext, String hostname, String fileServerName) {
+    public ResultFileManager(String resultsDir, String duration, FhirContext fhirContext) {
         this.resultsDirPath = Paths.get(resultsDir).toAbsolutePath();
         this.fhirContext = fhirContext;
 
 
         Duration duration1 = Duration.parse(duration);
-        this.hostname = hostname;
-        this.fileServerName = fileServerName;
 
 
         logger.debug("Duration of persistence {}", duration1);
@@ -213,7 +212,15 @@ public String loadErrorFromFileSystem(String jobId) {
         }
     }
 
-    public Map<String, Object> loadBundleFromFileSystem(String jobId, String transactionTime) {
+    /**
+     * Generates the server response for a successful operation.
+     *
+     * @param url             of the calling request.
+     * @param jobId           id to be handled
+     * @param transactionTime time of the transaction
+     * @return Map Containing the server response with file locations
+     */
+    public Map<String, Object> loadBundleFromFileSystem(String url, String jobId, String transactionTime) {
         Map<String, Object> response = new HashMap<>();
         try {
             Path jobDir = getJobDirectory(jobId);
@@ -224,10 +231,9 @@ public Map<String, Object> loadBundleFromFileSystem(String jobId, String transac
 
                 Files.list(jobDir).forEach(file -> {
                     String fileName = file.getFileName().toString();
-                    String url = fileServerName + "/" + jobId + "/" + fileName;
 
                     Map<String, String> fileEntry = new HashMap<>();
-                    fileEntry.put("url", url);
+                    fileEntry.put("url", url + "/" + jobId + "/" + fileName);
 
                     if (fileName.endsWith(".ndjson")) {
                         fileEntry.put("type", "NDJSON Bundle");
@@ -244,7 +250,7 @@ public Map<String, Object> loadBundleFromFileSystem(String jobId, String transac
                 logger.debug("OutputFiles size {}", outputFiles.size());
 
                 response.put("transactionTime", transactionTime);
-                response.put("request", hostname + "/fhir/$extract-data");
+                response.put("request", url + "/fhir/$extract-data");
                 response.put("requiresAccessToken", false);
                 response.put("output", outputFiles);
                 response.put("deleted", deletedFiles);

src/test/java/de/medizininformatikinitiative/torch/config/TestConfig.java

@@ -52,6 +52,7 @@
 import org.springframework.http.client.reactive.ReactorClientHttpConnector;
 import org.springframework.web.reactive.function.client.ExchangeStrategies;
 import org.springframework.web.reactive.function.client.WebClient;
+import org.springframework.web.server.adapter.ForwardedHeaderTransformer;
 import reactor.netty.http.client.HttpClient;
 import reactor.netty.resources.ConnectionProvider;
 
@@ -89,6 +90,10 @@ public TestConfig(TorchProperties torchProperties) {
         this.torchProperties = torchProperties;
     }
 
+    @Bean
+    public ForwardedHeaderTransformer forwardedHeaderTransformer() {
+        return new ForwardedHeaderTransformer();
+    }
 
     @Bean
     public CascadingDelete cascadingDelete() {
@@ -304,7 +309,7 @@ public StructureDefinitionHandler cdsStructureDefinitionHandler(ResourceReader r
 
     @Bean
     public ResultFileManager resultFileManager(FhirContext fhirContext) {
-        return new ResultFileManager(torchProperties.results().dir(), torchProperties.results().persistence(), fhirContext, torchProperties.base().url(), torchProperties.output().file().server().url());
+        return new ResultFileManager(torchProperties.results().dir(), torchProperties.results().persistence(), fhirContext);
     }
 
     @Bean