Release 0006

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/DataSharingStatus.java

@@ -0,0 +1,5 @@
+package edu.harvard.dbmi.avillach.data.entity;
+
+public enum DataSharingStatus {
+    Unknown, Pending, Error, Complete, NotShared
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/entity/Site.java

@@ -0,0 +1,53 @@
+package edu.harvard.dbmi.avillach.data.entity;
+
+import io.swagger.v3.oas.annotations.media.Schema;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.Table;
+import javax.persistence.UniqueConstraint;
+
+@Schema(description = "A site that contains a PIC-SURE installation that we can send data to")
+@Table(uniqueConstraints = {
+    @UniqueConstraint(name = "unique_code", columnNames = { "code" }),
+    @UniqueConstraint(name = "unique_email", columnNames = { "domain" })
+})
+@Entity(name = "site")
+public class Site extends BaseEntity {
+
+    @Schema(description = "The site code. Ex: BCH")
+    @Column(length = 15)
+    private String code;
+
+    @Schema(description = "The site name. Ex: Boston Children's")
+    @Column(length = 255)
+    private String name;
+
+    @Schema(description = "The email domain of users for this site. Ex: childrens.harvard.edu")
+    @Column(length = 255)
+    private String domain;
+
+    public String getCode() {
+        return code;
+    }
+
+    public void setCode(String code) {
+        this.code = code;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getDomain() {
+        return domain;
+    }
+
+    public void setDomain(String domain) {
+        this.domain = domain;
+    }
+}

pic-sure-api-data/src/main/java/edu/harvard/dbmi/avillach/data/repository/SiteRepository.java

@@ -0,0 +1,14 @@
+package edu.harvard.dbmi.avillach.data.repository;
+
+import edu.harvard.dbmi.avillach.data.entity.NamedDataset;
+import edu.harvard.dbmi.avillach.data.entity.Site;
+
+import javax.enterprise.context.ApplicationScoped;
+import javax.transaction.Transactional;
+import java.util.UUID;
+
+@Transactional
+@ApplicationScoped
+public class SiteRepository extends BaseRepository<Site, UUID>{
+    protected SiteRepository() {super(Site.class);}
+}

pic-sure-api-data/src/main/resources/db/sql/V6__ADD_SITE_TABLE.sql

@@ -0,0 +1,11 @@
+USE `picsure`;
+
+CREATE TABLE `site` (
+    `uuid` binary(16) NOT NULL,
+    `code` varchar(15) COLLATE utf8_bin DEFAULT NULL,
+    `name` varchar(255) COLLATE utf8_bin DEFAULT NULL,
+    `domain` varchar(255) COLLATE utf8_bin DEFAULT NULL,
+    PRIMARY KEY (`uuid`),
+    CONSTRAINT `unique_code` UNIQUE (`code`),
+    CONSTRAINT `unique_domain` UNIQUE (`domain`)
+) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin;

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/PicsureRS.java

@@ -8,12 +8,10 @@
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.HttpHeaders;
 import javax.ws.rs.core.Response;
+import javax.ws.rs.core.SecurityContext;
 
 import edu.harvard.dbmi.avillach.domain.*;
-import edu.harvard.dbmi.avillach.service.FormatService;
-import edu.harvard.dbmi.avillach.service.PicsureInfoService;
-import edu.harvard.dbmi.avillach.service.PicsureQueryService;
-import edu.harvard.dbmi.avillach.service.PicsureSearchService;
+import edu.harvard.dbmi.avillach.service.*;
 import io.swagger.v3.oas.annotations.OpenAPIDefinition;
 import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.info.Info;
@@ -41,6 +39,9 @@ public class PicsureRS {
 	@Inject
 	FormatService formatService;
 
+	@Inject
+	ProxyWebClient proxyWebClient;
+
 	@POST
 	@Path("/info/{resourceId}")
 	@Operation(
@@ -153,11 +154,16 @@ public QueryStatus query(
 
 		@Parameter
 		@QueryParam("isInstitute")
-		Boolean isInstitutionQuery
+		Boolean isInstitutionQuery,
+
+		@Context SecurityContext context
 	) {
-		return isInstitutionQuery == null || !isInstitutionQuery ?
-			queryService.query(dataQueryRequest, headers) :
-			queryService.institutionalQuery(dataQueryRequest, headers);
+		if (isInstitutionQuery == null || !isInstitutionQuery) {
+			return queryService.query(dataQueryRequest, headers);
+		} else {
+			String email = context.getUserPrincipal().getName();
+			return queryService.institutionalQuery((FederatedQueryRequest) dataQueryRequest, headers, email);
+		}
 	}
 
 	@POST
@@ -194,9 +200,11 @@ public QueryStatus queryStatus(
 		@QueryParam("isInstitute")
 		Boolean isInstitutionQuery
 	) {
-		return isInstitutionQuery == null || !isInstitutionQuery ?
-			queryService.queryStatus(queryId, credentialsQueryRequest, headers) :
-			queryService.institutionQueryStatus(queryId, credentialsQueryRequest, headers);
+		if (credentialsQueryRequest instanceof GeneralQueryRequest) {
+			return queryService.queryStatus(queryId, (GeneralQueryRequest) credentialsQueryRequest, headers);
+		} else {
+			return queryService.institutionQueryStatus(queryId, (FederatedQueryRequest) credentialsQueryRequest, headers);
+		}
 	}
 
 	@POST
@@ -271,5 +279,27 @@ public QueryStatus queryMetadata(@PathParam("queryId") UUID queryId, @Context Ht
 	public Response generateContinuousBin(QueryRequest continuousData, @Context HttpHeaders headers) {
 		return formatService.format(continuousData, headers);
 	}
+
+
+	@POST
+	@Path("/proxy/{container}/{request : .+}")
+	@Operation(hidden = true)
+	public Response postProxy(
+		@PathParam("container") String containerId,
+		@PathParam("request") String request,
+		String body
+	) {
+		return proxyWebClient.postProxy(containerId, request, body);
+	}
+
+	@GET
+	@Path("/proxy/{container}/{request : .+}")
+	@Operation(hidden = true)
+	public Response getProxy(
+		@PathParam("container") String containerId,
+		@PathParam("request") String request
+	) {
+		return proxyWebClient.getProxy(containerId, request);
+	}
 
 }

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/security/JWTFilter.java

@@ -8,7 +8,7 @@
 import edu.harvard.dbmi.avillach.data.entity.AuthUser;
 import edu.harvard.dbmi.avillach.data.repository.QueryRepository;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.service.ResourceWebClient;
 import edu.harvard.dbmi.avillach.util.exception.ApplicationException;
 import edu.harvard.dbmi.avillach.util.response.PICSUREResponse;
@@ -204,7 +204,7 @@ private AuthUser callTokenIntroEndpoint(ContainerRequestContext requestContext,
 						edu.harvard.dbmi.avillach.data.entity.Resource resource = resourceRepo.getById(resourceUUID);
 						//logger.info("resource obj: " + resource + "    path: " + resource.getResourceRSPath());
 						if (resource != null && resource.getResourceRSPath() != null){
-							QueryRequest queryRequest = new QueryRequest();
+							GeneralQueryRequest queryRequest = new GeneralQueryRequest();
 							queryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 							queryRequest.setResourceUUID(resourceUUID);
 							queryRequest.setQuery(((Map)queryObject).get("query"));

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureInfoService.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.util.Utilities;
@@ -46,7 +47,7 @@ public ResourceInfo info(UUID resourceId, QueryRequest credentialsQueryRequest,
 			throw new ApplicationException(ApplicationException.MISSING_RESOURCE_PATH);
 		}
 		if (credentialsQueryRequest == null){
-			credentialsQueryRequest = new QueryRequest();
+			credentialsQueryRequest = new GeneralQueryRequest();
 		}
 		if (credentialsQueryRequest.getResourceCredentials() == null){
 			credentialsQueryRequest.setResourceCredentials(new HashMap<String, String>());

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureQueryService.java

@@ -2,10 +2,13 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import edu.harvard.dbmi.avillach.data.entity.DataSharingStatus;
 import edu.harvard.dbmi.avillach.data.entity.Query;
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.QueryRepository;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
+import edu.harvard.dbmi.avillach.domain.FederatedQueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryStatus;
 import edu.harvard.dbmi.avillach.security.JWTFilter;
@@ -47,6 +50,9 @@ public class PicsureQueryService {
 	@Inject
 	ResourceWebClient resourceWebClient;
 
+	@Inject
+	SiteParsingService siteParsingService;
+
 	/**
 	 * Executes a query on a PIC-SURE resource and creates a Query entity in the
 	 * database for the query.
@@ -88,7 +94,7 @@ public QueryStatus query(QueryRequest dataQueryRequest, HttpHeaders headers) {
 	 * @return {@link QueryStatus}
 	 */
 	@Transactional
-	public QueryStatus queryStatus(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
+	public QueryStatus queryStatus(UUID queryId, GeneralQueryRequest credentialsQueryRequest, HttpHeaders headers) {
 		if (queryId == null){
 			throw new ProtocolException(ProtocolException.MISSING_QUERY_ID);
 		}
@@ -277,7 +283,9 @@ public QueryStatus queryMetadata(UUID queryId, HttpHeaders headers){
 	 *                         and resource specific query (could be a string or a json object)
 	 * @return {@link QueryStatus}
 	 */
-	public QueryStatus institutionalQuery(QueryRequest dataQueryRequest, HttpHeaders headers) {
+	public QueryStatus institutionalQuery(FederatedQueryRequest dataQueryRequest, HttpHeaders headers, String email) {
+		String siteCode = siteParsingService.parseSiteOfOrigin(email).orElseThrow(() -> new RuntimeException("Bad email"));
+		dataQueryRequest.setInstitutionOfOrigin(siteCode);
 		Resource resource = verifyQueryRequest(dataQueryRequest, headers);
 		dataQueryRequest.getResourceCredentials().put(ResourceWebClient.BEARER_TOKEN_KEY, resource.getToken());
 
@@ -307,11 +315,14 @@ private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryS
 				throw new ProtocolException(ProtocolException.INCORRECTLY_FORMATTED_REQUEST);
 			}
 		}
-
 		Map<String, Object> metaData = response.getResultMetadata();
 		metaData = metaData == null ? new HashMap<>() : metaData;
-		if (dataQueryRequest.getCommonAreaUUID() != null) {
-			metaData.put("commonAreaUUID", dataQueryRequest.getCommonAreaUUID());
+
+		if (dataQueryRequest instanceof FederatedQueryRequest) {
+			FederatedQueryRequest gicRequest = (FederatedQueryRequest) dataQueryRequest;
+			metaData.put("commonAreaUUID", gicRequest.getCommonAreaUUID());
+			metaData.put("site", gicRequest.getInstitutionOfOrigin());
+			metaData.put("sharingStatus", DataSharingStatus.Unknown);
 		}
 
 		queryEntity.setQuery(queryJson);
@@ -326,7 +337,7 @@ private Query copyQuery(QueryRequest dataQueryRequest, Resource resource, QueryS
 		return queryEntity;
 	}
 
-	public QueryStatus institutionQueryStatus(UUID queryId, QueryRequest credentialsQueryRequest, HttpHeaders headers) {
+	public QueryStatus institutionQueryStatus(UUID queryId, FederatedQueryRequest credentialsQueryRequest, HttpHeaders headers) {
 		if (queryId == null) {
 			throw new ProtocolException(ProtocolException.MISSING_QUERY_ID);
 		}

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/PicsureSearchService.java

@@ -4,6 +4,7 @@
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
 import edu.harvard.dbmi.avillach.domain.PaginatedSearchResult;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.QueryRequest;
 import edu.harvard.dbmi.avillach.domain.SearchResults;
 import edu.harvard.dbmi.avillach.util.Utilities;

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SiteParsingService.java

@@ -0,0 +1,41 @@
+package edu.harvard.dbmi.avillach.service;
+
+import edu.harvard.dbmi.avillach.data.entity.Site;
+import edu.harvard.dbmi.avillach.data.repository.SiteRepository;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.inject.Inject;
+import java.util.List;
+import java.util.Optional;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+public class SiteParsingService {
+
+    private static final Logger LOG = LoggerFactory.getLogger(SiteParsingService.class);
+
+    private static final Pattern emailRegex = Pattern.compile("^([^@]+)(@)(.*)$");
+
+    @Inject
+    SiteRepository repository;
+
+    public Optional<String> parseSiteOfOrigin(String email) {
+        Matcher matcher = emailRegex.matcher(email);
+        if (!matcher.find()) {
+            LOG.warn("Unable to parse domain for email: {}", email);
+            return Optional.empty();
+        }
+
+        List<Site> matchingDomains = repository.getByColumn("domain", matcher.group(3));
+        if (matchingDomains.isEmpty()) {
+            LOG.warn("Unable to match domain for email: {}, looked for domain: {}", email, matcher.group(3));
+            return Optional.empty();
+        }
+        if (matchingDomains.size() > 1) {
+            LOG.warn("Multiple domains match email. This should never happen! Email: {}", email);
+            return Optional.empty();
+        }
+        return Optional.of(matchingDomains.get(0).getCode());
+    }
+}

pic-sure-api-war/src/main/java/edu/harvard/dbmi/avillach/service/SystemService.java

@@ -24,7 +24,7 @@
 import edu.harvard.dbmi.avillach.PicSureWarInit;
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.util.exception.ApplicationException;
 
@@ -126,7 +126,7 @@ private boolean testPSAMAResponds() throws UnsupportedOperationException, IOExce
 
 	private boolean testResourcesRespond(List<Resource> resourcesToTest) {
 		for(Resource resource : resourcesToTest) {
-			ResourceInfo info = new ResourceWebClient().info(resource.getResourceRSPath(), new QueryRequest());
+			ResourceInfo info = new ResourceWebClient().info(resource.getResourceRSPath(), new GeneralQueryRequest());
 			if(info==null) {
 				return false;
 			}

pic-sure-api-war/src/main/resources/META-INF/persistence.xml

@@ -7,6 +7,7 @@
 		<class>edu.harvard.dbmi.avillach.data.entity.Query</class>
 		<class>edu.harvard.dbmi.avillach.data.entity.Resource</class>
 		<class>edu.harvard.dbmi.avillach.data.entity.NamedDataset</class>
+		<class>edu.harvard.dbmi.avillach.data.entity.Site</class>
 
 		<properties>
 			<property name="hibernate.archive.autodetection" value="class" />

pic-sure-api-war/src/test/java/edu/harvard/dbmi/avillach/PicsureInfoServiceTest.java

@@ -2,7 +2,7 @@
 
 import edu.harvard.dbmi.avillach.data.entity.Resource;
 import edu.harvard.dbmi.avillach.data.repository.ResourceRepository;
-import edu.harvard.dbmi.avillach.domain.QueryRequest;
+import edu.harvard.dbmi.avillach.domain.GeneralQueryRequest;
 import edu.harvard.dbmi.avillach.domain.ResourceInfo;
 import edu.harvard.dbmi.avillach.service.PicsureInfoService;
 import edu.harvard.dbmi.avillach.service.ResourceWebClient;
@@ -60,7 +60,7 @@ public void setUp() {
 
     @Test
     public void testInfoEndpoints() {
-        QueryRequest infoRequest = new QueryRequest();
+        GeneralQueryRequest infoRequest = new GeneralQueryRequest();
         Map<String, String> clientCredentials = new HashMap<String, String>();
         infoRequest.setResourceCredentials(clientCredentials);