ALS-7014: Implement handling of signed URLs from HPDS (#202)

hms-dbmi · Sep 6, 2024 · e24ff0b · e24ff0b
1 parent 755015a
commit e24ff0b
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Showing 15 changed files with 159 additions and 20 deletions.
diff --git a/pic-sure-api-data/pom.xml b/pic-sure-api-data/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-api</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-api-data</artifactId>
 	<name>pic-sure-api-data</name>

diff --git a/pic-sure-api-war/pom.xml b/pic-sure-api-war/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-api</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-api-war</artifactId>
 	<name>PIC-SURE API war</name>

diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java
@@ -154,20 +154,37 @@ public QueryStatus queryStatus(
     @POST
     @Path("/query/{queryId}/result")
     @Operation(
-        summary = "Returns result for given query",
-        responses = {@ApiResponse(
-            responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class))
-        )}
+            summary = "Returns result for given query",
+            responses = {@ApiResponse(
+                    responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class))
+            )}
     )
     @Produces(MediaType.APPLICATION_OCTET_STREAM)
     public Response queryResult(
-        @Parameter(
-            description = "The UUID of the query to fetch the status of. The UUID is "
-                + "returned by the /query endpoint as the \"picsureResultId\" in the response object"
-        ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers
+            @Parameter(
+                    description = "The UUID of the query to fetch the status of. The UUID is "
+                            + "returned by the /query endpoint as the \"picsureResultId\" in the response object"
+            ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers
     ) {
         return queryService.queryResult(queryId, credentialsQueryRequest, headers);
     }
+    @POST
+    @Path("/query/{queryId}/signed-url")
+    @Operation(
+            summary = "Returns a signed url for given query",
+            responses = {@ApiResponse(
+                    responseCode = "200", description = "Query result", content = @Content(schema = @Schema(implementation = Response.class))
+            )}
+    )
+    @Produces(MediaType.APPLICATION_JSON)
+    public Response queryResultSignedUrl(
+            @Parameter(
+                    description = "The UUID of the query to fetch the status of. The UUID is "
+                            + "returned by the /query endpoint as the \"picsureResultId\" in the response object"
+            ) @PathParam("queryId") UUID queryId, @Parameter QueryRequest credentialsQueryRequest, @Context HttpHeaders headers
+    ) {
+        return queryService.queryResultSignedUrl(queryId, credentialsQueryRequest, headers);
+    }
 
     @POST
     @Path("/query/sync")

diff --git a/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java b/pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java
@@ -149,15 +149,55 @@ public Response queryResult(UUID queryId, QueryRequest credentialsQueryRequest,
         }
 
         logger.info(
-            "path=/query/{queryId}/result, resourceId={}, requestSource={}, queryRequest={}", queryId,
-            Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest)
+                "path=/query/{queryId}/result, resourceId={}, requestSource={}, queryRequest={}", queryId,
+                Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest)
         );
 
 
         credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
         return resourceWebClient.queryResult(resource.getResourceRSPath(), query.getResourceResultId(), credentialsQueryRequest);
     }
 
+    /**
+     * Returns a signed URL from HPDS that is a reference to the query result
+     *
+     * @param queryId - id of target resource
+     * @param credentialsQueryRequest - contains resource specific credentials object
+     * @return Response containing a signed URL
+     */
+    @Transactional
+    public Response queryResultSignedUrl(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
+        if (queryId == null) {
+            throw new ProtocolException(ProtocolException.MISSING_QUERY_ID);
+        }
+        Query query = queryRepo.getById(queryId);
+        if (query == null) {
+            throw new ProtocolException(ProtocolException.QUERY_NOT_FOUND + queryId.toString());
+        }
+        Resource resource = query.getResource();
+        if (resource == null) {
+            throw new ApplicationException(ApplicationException.MISSING_RESOURCE);
+        }
+        if (resource.getResourceRSPath() == null) {
+            throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
+        }
+        if (credentialsQueryRequest == null) {
+            throw new ProtocolException(ProtocolException.MISSING_DATA);
+        }
+        if (credentialsQueryRequest.getResourceCredentials() == null) {
+            credentialsQueryRequest.setResourceCredentials(new HashMap<>());
+        }
+
+        logger.info(
+                "path=/query/{queryId}/signed-url, resourceId={}, requestSource={}, queryRequest={}", queryId,
+                Utilities.getRequestSourceFromHeader(headers), Utilities.convertQueryRequestToString(mapper, credentialsQueryRequest)
+        );
+
+
+        credentialsQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
+        return resourceWebClient.queryResultSignedUrl(resource.getResourceRSPath(), query.getResourceResultId(), credentialsQueryRequest);
+    }
+
     /**
      * Streams the result for a query by looking up the target resource from the database and calling the target resource for a result.
      *

diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-resources</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-aggregate-data-sharing-resource</artifactId>
 	<name>pic-sure-aggregate-data-sharing-resource</name>

diff --git a/pic-sure-resources/pic-sure-ga4gh-dos/pom.xml b/pic-sure-resources/pic-sure-ga4gh-dos/pom.xml
@@ -6,7 +6,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-resources</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-ga4gh-dos</artifactId>
 	<name>pic-sure-ga4gh-dos</name>

diff --git a/pic-sure-resources/pic-sure-passthrough-resource/pom.xml b/pic-sure-resources/pic-sure-passthrough-resource/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-resources</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-passthrough-resource</artifactId>
 	<name>pic-sure-passthrough-resource</name>

diff --git a/pic-sure-resources/pic-sure-resource-api/pom.xml b/pic-sure-resources/pic-sure-resource-api/pom.xml
@@ -5,7 +5,7 @@
   <parent>
     <groupId>edu.harvard.hms.dbmi.avillach</groupId>
     <artifactId>pic-sure-resources</artifactId>
-    <version>2.1.0-SNAPSHOT</version>
+    <version>2.2.0-SNAPSHOT</version>
   </parent>
   <artifactId>pic-sure-resource-api</artifactId>
   <name>pic-sure-resource-api</name>

diff --git a/...c-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java b/...c-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponse.java
@@ -0,0 +1,33 @@
+package edu.harvard.dbmi.avillach.domain;
+
+import com.fasterxml.jackson.annotation.JsonCreator;
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.Objects;
+
+public class SignedUrlResponse {
+
+    private final String signedUrl;
+
+    @JsonCreator
+    public SignedUrlResponse(@JsonProperty("signedUrl") String signedUrl) {
+        this.signedUrl = signedUrl;
+    }
+
+    public String getSignedUrl() {
+        return signedUrl;
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        SignedUrlResponse that = (SignedUrlResponse) o;
+        return Objects.equals(signedUrl, that.signedUrl);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(signedUrl);
+    }
+}
diff --git a/...-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ResourceWebClient.java b/...-sure-resource-api/src/main/java/edu/harvard/dbmi/avillach/service/ResourceWebClient.java
@@ -211,6 +211,37 @@ public Response queryResult(String rsURL, String queryId, QueryRequest queryRequ
             throw new ResourceInterfaceException("Error getting results", e);
         }
     }
+
+    public Response queryResultSignedUrl(String rsURL, String queryId, QueryRequest queryRequest){
+        logger.debug("Calling ResourceWebClient querySignedUrl()");
+        try {
+            if (queryRequest == null){
+                throw new ProtocolException(ProtocolException.MISSING_DATA);
+            }
+            if (queryRequest.getResourceCredentials() == null){
+                throw new NotAuthorizedException("Missing credentials");
+            }
+            if (rsURL == null){
+                throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
+            }
+            if (queryId == null){
+                throw new ProtocolException(ProtocolException.MISSING_QUERY_ID);
+            }
+            String pathName = "/query/" + queryId + "/signed-url";
+            String body = json.writeValueAsString(queryRequest);
+            HttpResponse resourcesResponse = retrievePostResponse(composeURL(rsURL, pathName), createHeaders(queryRequest.getResourceCredentials()), body);
+            if (resourcesResponse.getStatusLine().getStatusCode() != 200) {
+                logger.error("ResourceRS did not return a 200");
+                throwResponseError(resourcesResponse, rsURL);
+            }
+            return Response.ok(resourcesResponse.getEntity().getContent()).build();
+        } catch (JsonProcessingException e){
+            logger.error("Unable to encode resource credentials");
+            throw new NotAuthorizedException("Unable to encode resource credentials", e);
+        } catch (IOException e){
+            throw new ResourceInterfaceException("Error getting results", e);
+        }
+    }
 
 
     public Response queryFormat(String rsURL, QueryRequest queryRequest){

diff --git a/...re-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java b/...re-resource-api/src/test/java/edu/harvard/dbmi/avillach/domain/SignedUrlResponseTest.java
@@ -0,0 +1,18 @@
+package edu.harvard.dbmi.avillach.domain;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+public class SignedUrlResponseTest {
+
+    @Test
+    public void testJacksonSerialization() throws JsonProcessingException {
+        SignedUrlResponse signedUrlResponse = new SignedUrlResponse("http://google.com/");
+        ObjectMapper objectMapper = new ObjectMapper();
+        String serialized = objectMapper.writeValueAsString(signedUrlResponse);
+        SignedUrlResponse deserialized = objectMapper.readValue(serialized, SignedUrlResponse.class);
+        assertEquals(signedUrlResponse.getSignedUrl(), deserialized.getSignedUrl());
+    }
+}
diff --git a/pic-sure-resources/pic-sure-visualization-resource/pom.xml b/pic-sure-resources/pic-sure-visualization-resource/pom.xml
@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<artifactId>pic-sure-resources</artifactId>
-		<version>2.1.0-SNAPSHOT</version>
+		<version>2.2.0-SNAPSHOT</version>
 	</parent>
 	<artifactId>pic-sure-visualization-resource</artifactId>
 	<name>PIC-SURE Visualization Resource</name>

diff --git a/pic-sure-resources/pom.xml b/pic-sure-resources/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>pic-sure-api</artifactId>
     <groupId>edu.harvard.hms.dbmi.avillach</groupId>
-    <version>2.1.0-SNAPSHOT</version>
+    <version>2.2.0-SNAPSHOT</version>
   </parent>
   <artifactId>pic-sure-resources</artifactId>
   <packaging>pom</packaging>

diff --git a/pic-sure-util/pom.xml b/pic-sure-util/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>pic-sure-api</artifactId>
         <groupId>edu.harvard.hms.dbmi.avillach</groupId>
-        <version>2.1.0-SNAPSHOT</version>
+        <version>2.2.0-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>pic-sure-util</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>edu.harvard.hms.dbmi.avillach</groupId>
   <artifactId>pic-sure-api</artifactId>
-  <version>2.1.0-SNAPSHOT</version>
+  <version>2.2.0-SNAPSHOT</version>
   <packaging>pom</packaging>
   <name>pic-sure-api</name>
   <modules>