Merge pull request #592 from chuguoxipo/develop

Add exportTimelineForStudy API & Unit Test

src/main/java/org/sagebionetworks/bridge/models/apps/Exporter3Configuration.java

@@ -13,6 +13,7 @@ public final class Exporter3Configuration {
     private String projectId;
     private String rawDataFolderId;
     private Long storageLocationId;
+    private String wikiPageId;
 
     /** Helper method that returns true if all configuration attributes are specified. */
     public boolean isConfigured() {
@@ -112,11 +113,19 @@ public void setStorageLocationId(Long storageLocationId) {
         this.storageLocationId = storageLocationId;
     }
 
+    public String getWikiPageId() {
+        return wikiPageId;
+    }
+
+    public void setWikiPageId(String wikiPageId) {
+        this.wikiPageId = wikiPageId;
+    }
+
     @Override
     public int hashCode() {
         return Objects.hash(createStudyNotificationTopicArn, dataAccessTeamId, exportNotificationTopicArn, participantVersionDemographicsTableId,
                 participantVersionDemographicsViewId, participantVersionTableId, projectId, rawDataFolderId,
-                storageLocationId);
+                storageLocationId, wikiPageId);
     }
 
     @Override
@@ -135,7 +144,8 @@ public boolean equals(Object obj) {
                 && Objects.equals(participantVersionDemographicsViewId, other.participantVersionDemographicsViewId)
                 && Objects.equals(participantVersionTableId, other.participantVersionTableId)
                 && Objects.equals(projectId, other.projectId) && Objects.equals(rawDataFolderId, other.rawDataFolderId)
-                && Objects.equals(storageLocationId, other.storageLocationId);
+                && Objects.equals(storageLocationId, other.storageLocationId)
+                && Objects.equals(wikiPageId, other.wikiPageId);
     }
 
     @Override
@@ -145,6 +155,6 @@ public String toString() {
                 + participantVersionDemographicsTableId + ", participantVersionDemographicsViewId="
                 + participantVersionDemographicsViewId + ", participantVersionTableId=" + participantVersionTableId
                 + ", projectId=" + projectId + ", rawDataFolderId=" + rawDataFolderId + ", storageLocationId="
-                + storageLocationId + "]";
+                + storageLocationId + ", wikiPageId=" + wikiPageId + "]";
     }
 }

src/main/java/org/sagebionetworks/bridge/services/Exporter3Service.java

@@ -1,5 +1,6 @@
 package org.sagebionetworks.bridge.services;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -20,20 +21,31 @@
 import com.amazonaws.services.sqs.AmazonSQS;
 import com.amazonaws.services.sqs.model.SendMessageResult;
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.base.Charsets;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableSet;
+import com.google.common.io.CharSink;
+import com.google.common.io.FileWriteMode;
+import com.google.common.io.Files;
 import org.apache.commons.lang3.StringUtils;
+import org.sagebionetworks.client.SynapseClient;
 import org.sagebionetworks.client.exceptions.SynapseException;
 import org.sagebionetworks.repo.model.Folder;
+import org.sagebionetworks.repo.model.ObjectType;
 import org.sagebionetworks.repo.model.Project;
 import org.sagebionetworks.repo.model.Team;
+import org.sagebionetworks.repo.model.dao.WikiPageKey;
+import org.sagebionetworks.repo.model.dao.WikiPageKeyHelper;
+import org.sagebionetworks.repo.model.file.CloudProviderFileHandleInterface;
 import org.sagebionetworks.repo.model.annotation.v2.AnnotationsValue;
 import org.sagebionetworks.repo.model.annotation.v2.AnnotationsValueType;
 import org.sagebionetworks.repo.model.project.ExternalS3StorageLocationSetting;
 import org.sagebionetworks.repo.model.table.ColumnModel;
 import org.sagebionetworks.repo.model.table.ColumnType;
 import org.sagebionetworks.repo.model.table.EntityView;
+import org.sagebionetworks.repo.model.v2.wiki.V2WikiPage;
 import org.sagebionetworks.repo.model.table.MaterializedView;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -66,6 +78,8 @@
 import org.sagebionetworks.bridge.models.exporter.ExporterSubscriptionRequest;
 import org.sagebionetworks.bridge.models.exporter.ExporterSubscriptionResult;
 import org.sagebionetworks.bridge.models.healthdata.HealthDataRecordEx3;
+import org.sagebionetworks.bridge.models.schedules2.Schedule2;
+import org.sagebionetworks.bridge.models.schedules2.timelines.Timeline;
 import org.sagebionetworks.bridge.models.studies.Study;
 import org.sagebionetworks.bridge.models.upload.Upload;
 import org.sagebionetworks.bridge.models.worker.Exporter3Request;
@@ -265,6 +279,9 @@ public class Exporter3Service {
     private AmazonSQS sqsClient;
     private StudyService studyService;
     private SynapseHelper synapseHelper;
+    private Schedule2Service schedule2Service;
+    private SynapseClient synapseClient;
+    private FileService fileService;
 
     @Autowired
     public final void setConfig(BridgeConfig config) {
@@ -340,11 +357,26 @@ final void setStudyService(StudyService studyService) {
         this.studyService = studyService;
     }
 
+    @Resource(name="exporterSynapseClient")
+    public final void setSynapseClient(SynapseClient synapseClient) {
+        this.synapseClient = synapseClient;
+    }
+
     @Resource(name="exporterSynapseHelper")
     public final void setSynapseHelper(SynapseHelper synapseHelper) {
         this.synapseHelper = synapseHelper;
     }
 
+    @Autowired
+    final void setSchedule2Service(Schedule2Service schedule2Service) {
+        this.schedule2Service = schedule2Service;
+    }
+
+    @Autowired
+    public final void setFileService(FileService fileService) {
+        this.fileService = fileService;
+    }
+
     /**
      * Initializes configs and Synapse resources for Exporter 3.0. Note that if any config already exists, this API
      * will simply ignore them. This allows for two notable scenarios
@@ -438,7 +470,6 @@ public Exporter3Configuration initExporter3ForStudy(String appId, String studyId
                 sendNotification(appId, studyId, "create study", createStudyNotificationTopicArn, notification);
             }
         }
-
         return ex3Config;
     }
 
@@ -934,4 +965,55 @@ private void exportUpload(String appId, String recordId) {
         LOG.info("Sent export request for app " + appId + " record " + recordId + "; received message ID=" +
                 sqsResult.getMessageId());
     }
+
+    // Export timeline  from Bridge to Synapse (Some researchers only have access to Synapse, not Bridge,
+    // so they need access to the Timeline information.).
+    public Exporter3Configuration exportTimelineForStudy(String appId, String studyId) throws BridgeSynapseException,
+            SynapseException, IOException{
+        // Get Timeline to export for the study.
+        Study study = studyService.getStudy(appId, studyId, true);
+        if (study.getScheduleGuid() == null) {
+            throw new EntityNotFoundException(Schedule2.class);
+        }
+        Timeline timeline = schedule2Service.getTimelineForSchedule(appId,
+                study.getScheduleGuid());
+
+        // Check Synapse
+        synapseHelper.checkSynapseWritableOrThrow();
+
+        // If Exporter3 is not enabled for study, initiate Exporter3 for Study;
+        if (!study.isExporter3Enabled()) {
+            initExporter3ForStudy(appId, studyId);
+            study = studyService.getStudy(appId, studyId, true);
+        }
+        Exporter3Configuration exporter3Config = study.getExporter3Configuration();
+
+        // Export the study's Timeline to Synapse as a wiki page in JSON format.
+        // If we have an IOException, the wiki page will almost certainly fail to upload. Instead of catching the exception,
+        // we just let the exception get thrown.
+        JsonNode node = BridgeObjectMapper.get().valueToTree(timeline);
+        File outputFile = File.createTempFile("timelineFor" + studyId, ".txt");
+        CharSink charSink = Files.asCharSink(outputFile, Charsets.UTF_8, FileWriteMode.APPEND);
+        charSink.write(node.toString());
+
+        CloudProviderFileHandleInterface markdown = synapseClient.multipartUpload(outputFile,
+                exporter3Config.getStorageLocationId(), false, false);
+
+        // If first time exporting the timeline for the study, create a new wiki page in Synapse;
+        // If wiki page already exists, update the existing wiki page.
+        if (exporter3Config.getWikiPageId() == null) {
+            V2WikiPage wiki = new V2WikiPage();
+            wiki.setTitle("Exported Timeline for " + studyId);
+            wiki.setMarkdownFileHandleId(markdown.getId());
+            wiki = synapseClient.createV2WikiPage(exporter3Config.getProjectId(), ObjectType.ENTITY, wiki);
+            exporter3Config.setWikiPageId(wiki.getId());
+            studyService.updateStudy(appId, study);
+        } else {
+            WikiPageKey key = WikiPageKeyHelper.createWikiPageKey(exporter3Config.getProjectId(), ObjectType.ENTITY, exporter3Config.getWikiPageId());
+            V2WikiPage getWiki = synapseClient.getV2WikiPage(key);
+            getWiki.setMarkdownFileHandleId(markdown.getId());
+            synapseClient.updateV2WikiPage(exporter3Config.getProjectId(), ObjectType.ENTITY, getWiki);
+        }
+        return exporter3Config;
+    }
 }

src/main/java/org/sagebionetworks/bridge/spring/controllers/Exporter3Controller.java

@@ -96,6 +96,15 @@ public Exporter3Configuration initExporter3ForStudy(@PathVariable String studyId
         return exporter3Service.initExporter3ForStudy(session.getAppId(), studyId);
     }
 
+    @PostMapping("/v5/studies/{studyId}/timeline/export")
+    @ResponseStatus(HttpStatus.CREATED)
+    public Exporter3Configuration exportTimelineForStudy(@PathVariable String studyId)
+            throws BridgeSynapseException, SynapseException, IOException {
+        UserSession session = getAuthenticatedSession(STUDY_DESIGNER, DEVELOPER);
+        CAN_UPDATE_STUDIES.checkAndThrow(STUDY_ID, studyId);
+        return exporter3Service.exportTimelineForStudy(session.getAppId(), studyId);
+    }
+
     /** Subscribe to be notified when health data is exported to the study-specific Synapse project. */
     @PostMapping(path = "/v5/studies/{studyId}/exporter3/notifications/export/subscribe")
     @ResponseStatus(HttpStatus.CREATED)