mroe

hms-dbmi · Aug 18, 2024 · 4c61647 · 4c61647
1 parent b0ad0a2
commit 4c61647
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Showing 2 changed files with 37 additions and 16 deletions.
diff --git a/...du/harvard/hms/dbmi/avillach/hpds/processing/timeseries/ObservationDistanceProcessor.java b/...du/harvard/hms/dbmi/avillach/hpds/processing/timeseries/ObservationDistanceProcessor.java
@@ -7,11 +7,13 @@
 import edu.harvard.hms.dbmi.avillach.hpds.processing.AbstractProcessor;
 import edu.harvard.hms.dbmi.avillach.hpds.processing.AsyncResult;
 import edu.harvard.hms.dbmi.avillach.hpds.processing.HpdsProcessor;
+import org.apache.commons.io.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;
 import java.nio.file.Files;
@@ -69,22 +71,32 @@ public long distance() {
 
     @Override
     public void runQuery(Query query, AsyncResult asyncResult) {
-        Set<Integer> recordedJourneys = new HashSet<>();
-        for (String concept : query.getAnyRecordOf()) {
-            LOG.info("Creating user journeys for concept {}", concept);
-            Optional<PhenoCube<?>> maybeCube = abstractProcessor.nullableGetCube(concept);
-            if (maybeCube.isEmpty()) {
-                continue;
+
+    }
+
+    public void writeJourney(Query query) {
+        try {
+            String tmpPath = File.createTempFile(System.nanoTime() + "journey", ".tsv").getAbsolutePath();
+            Set<Integer> recordedJourneys = new HashSet<>();
+            for (String concept : query.getAnyRecordOf()) {
+                LOG.info("Creating user journeys for concept {}", concept);
+                Optional<PhenoCube<?>> maybeCube = abstractProcessor.nullableGetCube(concept);
+                if (maybeCube.isEmpty()) {
+                    continue;
+                }
+                maybeCube.get().keyBasedIndex().stream()
+                    .filter(Predicate.not(recordedJourneys::contains))
+                    .map(id -> new PatientJourney(concept, id))
+                    .map(this::updateJourney)
+                    .sorted((a, b) -> -Long.compare(b.distance(), a.distance()))
+                    .peek(j -> recordedJourneys.add(j.patient))
+                    .limit(100)
+                    .forEach(journey -> write(tmpPath, journey));
+                LOG.info("Done creating user journeys for concept {} to {}", concept, tmpPath);
             }
-            maybeCube.get().keyBasedIndex().stream()
-                .filter(Predicate.not(recordedJourneys::contains))
-                .map(id -> new PatientJourney(concept, id))
-                .map(this::updateJourney)
-                .sorted((a, b) -> -Long.compare(b.distance(), a.distance()))
-                .peek(j -> recordedJourneys.add(j.patient))
-                .limit(100)
-                .forEach(journey -> write(asyncResult.getTempFilePath(), journey));
-            LOG.info("Done creating user journeys for concept {} to {}", concept, asyncResult.getTempFilePath());
+        } catch (IOException e) {
+            LOG.error("Can't create temp file", e);
+            return;
         }
     }
 

diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java
@@ -12,6 +12,7 @@
 import javax.ws.rs.core.Response.Status;
 
 import edu.harvard.hms.dbmi.avillach.hpds.data.query.ResultType;
+import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.ObservationDistanceProcessor;
 import edu.harvard.hms.dbmi.avillach.hpds.service.filesharing.FileSharingService;
 import edu.harvard.hms.dbmi.avillach.hpds.service.util.Paginator;
 import edu.harvard.hms.dbmi.avillach.hpds.service.util.QueryDecorator;
@@ -46,7 +47,8 @@ public class PicSureService implements IResourceRS {
 	@Autowired
 	public PicSureService(QueryService queryService, TimelineProcessor timelineProcessor, CountProcessor countProcessor,
 						  VariantListProcessor variantListProcessor, AbstractProcessor abstractProcessor,
-						  Paginator paginator, FileSharingService fileSystemService, QueryDecorator queryDecorator
+						  Paginator paginator, FileSharingService fileSystemService, QueryDecorator queryDecorator,
+						  ObservationDistanceProcessor observationDistanceProcessor
 	) {
 		this.queryService = queryService;
 		this.timelineProcessor = timelineProcessor;
@@ -56,6 +58,7 @@ public PicSureService(QueryService queryService, TimelineProcessor timelineProce
 		this.paginator = paginator;
 		this.fileSystemService = fileSystemService;
 		this.queryDecorator = queryDecorator;
+		this.observationDistanceProcessor = observationDistanceProcessor;
 		Crypto.loadDefaultKey();
 	}
 
@@ -78,6 +81,7 @@ public PicSureService(QueryService queryService, TimelineProcessor timelineProce
 	private final FileSharingService fileSystemService;
 
 	private final QueryDecorator queryDecorator;
+	private final ObservationDistanceProcessor observationDistanceProcessor;
 
 	private static final String QUERY_METADATA_FIELD = "queryMetadata";
 	private static final int RESPONSE_CACHE_SIZE = 50;
@@ -275,6 +279,11 @@ private Optional<String> roundTripUUID(String uuid) {
 	public Response writeQueryResult(
 		@RequestBody() Query query, @PathParam("dataType") String datatype
 	) {
+		log.info("Writing {}", datatype);
+		if ("journey".equals(datatype)) {
+			observationDistanceProcessor.writeJourney(query);
+			return Response.status(400, "good luck!").build();
+		}
 		if (roundTripUUID(query.getPicSureId()).map(id -> !id.equalsIgnoreCase(query.getPicSureId())).orElse(false)) {
 			return Response
 				.status(400, "The query pic-sure ID is not a UUID")