Revert "Cool counts"

client-api/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/query/ResultType.java

@@ -94,11 +94,5 @@ public enum ResultType {
 	 * is suitable to time series analysis and/or loading into another 
 	 * instance of HPDS.
 	 */
-	DATAFRAME_TIMESERIES,
-
-	/**
-	 * Count number of patients and number of available concept paths. Useful for federated networks
-	 * where not every concept path in a query is guaranteed to be in a specific portal
-	 */
-	PATIENT_AND_CONCEPT_COUNT
+	DATAFRAME_TIMESERIES
 }

processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/AbstractProcessor.java

@@ -672,7 +672,7 @@ protected PhenoCube getCube(String path) {
 	 * Useful for federated pic-sure's where there are fewer
 	 * guarantees about concept paths.
 	 */
-	public Optional<PhenoCube<?>> nullableGetCube(String path) {
+	protected Optional<PhenoCube<?>> nullableGetCube(String path) {
 		try {
 			return Optional.ofNullable(store.get(path));
 		} catch (InvalidCacheLoadException | ExecutionException e) {

processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/CountProcessor.java

@@ -229,20 +229,4 @@ public Map<String, Object> runVariantCount(Query query) {
 		}
 		return response;
 	}
-
-	public PatientAndConceptCount runPatientAndConceptCount(Query incomingQuery) {
-		log.info("Starting Patient and Concept Count query {}", incomingQuery.getPicSureId());
-		log.info("Calculating available concepts");
-		long concepts = incomingQuery.getFields().stream()
-			.map(abstractProcessor::nullableGetCube)
-			.filter(Optional::isPresent)
-			.count();
-		log.info("Calculating patient counts");
-		int patients = runCounts(incomingQuery);
-		PatientAndConceptCount patientAndConceptCount = new PatientAndConceptCount();
-		patientAndConceptCount.setConceptCount(concepts);
-		patientAndConceptCount.setPatientCount(patients);
-		log.info("Completed Patient and Concept Count query {}", incomingQuery.getPicSureId());
-		return patientAndConceptCount;
-	}
 }

processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/timeseries/TimeseriesProcessor.java → processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/TimeseriesProcessor.java

@@ -1,14 +1,9 @@
-package edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries;
+package edu.harvard.hms.dbmi.avillach.hpds.processing;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.*;
-import java.util.stream.Collectors;
 
-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 edu.harvard.hms.dbmi.avillach.hpds.processing.QueryProcessor;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -41,16 +36,14 @@ public class TimeseriesProcessor implements HpdsProcessor {
 	private Logger log = LoggerFactory.getLogger(QueryProcessor.class);
 
 	private AbstractProcessor abstractProcessor;
-	private final TimeSeriesConversionService conversionService;
 
 	private final String ID_CUBE_NAME;
 	private final int ID_BATCH_SIZE;
 	private final int CACHE_SIZE;
 
 	@Autowired
-	public TimeseriesProcessor(AbstractProcessor abstractProcessor, TimeSeriesConversionService conversionService) {
+	public TimeseriesProcessor(AbstractProcessor abstractProcessor) {
 		this.abstractProcessor = abstractProcessor;
-		this.conversionService = conversionService;
 		// todo: handle these via spring annotations
 		CACHE_SIZE = Integer.parseInt(System.getProperty("CACHE_SIZE", "100"));
 		ID_BATCH_SIZE = Integer.parseInt(System.getProperty("ID_BATCH_SIZE", "0"));
@@ -95,7 +88,6 @@ private void exportTimeData(Query query, AsyncResult result, TreeSet<Integer> id
 		//get a list of all fields mentioned in the query;  export all data associated with any included field
 		List<String> pathList = new LinkedList<String>();
 		pathList.addAll(query.getAnyRecordOf());
-		pathList.addAll(query.getAnyRecordOfMulti().stream().flatMap(Collection::stream).collect(Collectors.toList()));
 		pathList.addAll(query.getFields());
 		pathList.addAll(query.getRequiredFields());
 		pathList.addAll(query.getCategoryFilters().keySet());
@@ -123,24 +115,14 @@ private void addDataForConcepts(Collection<String> pathList, Set<String> exporte
 				if (cube.isStringType()) {
 					KeyAndValue<String> keyAndValue = (KeyAndValue) kvObj;
 					// "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP"
-					String[] entryData = {
-						keyAndValue.getKey().toString(),
-						conceptPath,
-						"",
-						keyAndValue.getValue(),
-						conversionService.toISOString(keyAndValue.getTimestamp())
-					};
+					String[] entryData = { keyAndValue.getKey().toString(), conceptPath, "", keyAndValue.getValue(),
+							keyAndValue.getTimestamp().toString() };
 					dataEntries.add(entryData);
 				} else { // numeric
 					KeyAndValue<Double> keyAndValue = (KeyAndValue) kvObj;
 					// "PATIENT_NUM","CONCEPT_PATH","NVAL_NUM","TVAL_CHAR","TIMESTAMP"
-					String[] entryData = {
-						keyAndValue.getKey().toString(),
-						conceptPath,
-						keyAndValue.getValue().toString(),
-						"",
-						conversionService.toISOString(keyAndValue.getTimestamp())
-					};
+					String[] entryData = { keyAndValue.getKey().toString(), conceptPath,
+							keyAndValue.getValue().toString(), "", keyAndValue.getTimestamp().toString() };
 					dataEntries.add(entryData);
 				}
 				//batch exports so we don't take double memory (valuesForKeys + dataEntries could be a lot of data points)

service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/PicSureService.java

@@ -455,9 +455,6 @@ private Response submitQueryAndWaitForCompletion(QueryRequest resultRequest) thr
 		case COUNT:
 			return queryOkResponse(countProcessor.runCounts(incomingQuery), incomingQuery).build();
 
-		case PATIENT_AND_CONCEPT_COUNT:
-			return queryOkResponse(countProcessor.runPatientAndConceptCount(incomingQuery), incomingQuery).build();
-
 		default:
 			// no valid type
 			return Response.status(Status.BAD_REQUEST).build();

service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java

@@ -7,7 +7,6 @@
 import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
-import edu.harvard.hms.dbmi.avillach.hpds.processing.timeseries.TimeseriesProcessor;
 import edu.harvard.hms.dbmi.avillach.hpds.service.util.QueryDecorator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;