More work on term service importing

hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java

@@ -314,21 +314,6 @@ public abstract class BaseParser implements IParser {
 		}
 	}
 
-	protected String determineResourceBaseUrl(String bundleBaseUrl, BundleEntry theEntry) {
-		IResource resource = theEntry.getResource();
-		if (resource == null) {
-			return null;
-		}
-
-		String resourceBaseUrl = null;
-		if (resource.getId() != null && resource.getId().hasBaseUrl()) {
-			if (!resource.getId().getBaseUrl().equals(bundleBaseUrl)) {
-				resourceBaseUrl = resource.getId().getBaseUrl();
-			}
-		}
-		return resourceBaseUrl;
-	}
-
 	protected abstract void doEncodeBundleToWriter(Bundle theBundle, Writer theWriter) throws IOException, DataFormatException;
 
 	protected abstract void doEncodeResourceToWriter(IBaseResource theResource, Writer theWriter) throws IOException, DataFormatException;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvc.java

@@ -1,6 +1,5 @@
 package ca.uhn.fhir.jpa.term;
 
-import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /*
@@ -24,20 +23,18 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
  */
 
 import java.io.BufferedInputStream;
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
-import java.io.File;
 import java.io.FileOutputStream;
-import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.InputStreamReader;
 import java.io.OutputStream;
 import java.io.Reader;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -56,18 +53,20 @@ import org.apache.commons.lang3.Validate;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import com.google.common.annotations.VisibleForTesting;
+import com.google.common.base.Charsets;
 
 import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
 import ca.uhn.fhir.jpa.entity.TermConcept;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
 import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
-import ca.uhn.fhir.jpa.term.TerminologyLoaderSvc.LoincHierarchyHandler;
+import ca.uhn.fhir.jpa.util.Counter;
 import ca.uhn.fhir.rest.method.RequestDetails;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
-import ca.uhn.fhir.util.CoverageIgnore;
 
 public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
+	private static final int LOG_INCREMENT = 100000;
+
 	public static final String LOINC_FILE = "loinc.csv";
 
 	public static final String LOINC_HIERARCHY_FILE = "MULTI-AXIAL_HIERARCHY.CSV";
@@ -79,15 +78,8 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 	@Autowired
 	private IHapiTerminologySvc myTermSvc;
 
-	private void cleanUpTemporaryFiles(Map<String, File> filenameToFile) {
+	private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
-		ourLog.info("Finished terminology file import, cleaning up temporary files");
+		
-		for (File nextFile : filenameToFile.values()) {
-			nextFile.delete();
-		}
-	}
-
-	private void dropCircularRefs(TermConcept theConcept, LinkedHashSet<String> theChain, Map<String, TermConcept> theCode2concept) {
-
 		theChain.add(theConcept.getCode());
 		for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext();) {
 			TermConceptParentChildLink next = childIter.next();
@@ -110,46 +102,25 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 				ourLog.info(b.toString(), theConcept.getCode());
 				childIter.remove();
 			} else {
-				dropCircularRefs(nextChild, theChain, theCode2concept);
+				dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
 			}
 		}
-		theChain.remove(theConcept.getCode());
+		theChain.remove(theChain.size() - 1);
 
 	}
 
-	private Map<String, File> extractFiles(List<byte[]> theZipBytes, List<String> theExpectedFilenameFragments) {
+	private void extractFiles(List<byte[]> theZipBytes, List<String> theExpectedFilenameFragments) {
-		Map<String, File> filenameToFile = new HashMap<String, File>();
+		Set<String> foundFragments = new HashSet<String>();
 
 		for (byte[] nextZipBytes : theZipBytes) {
 			ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(nextZipBytes)));
 			try {
 				for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null;) {
-					ZippedFileInputStream inputStream = new ZippedFileInputStream(zis);
-
-					boolean want = false;
 					for (String next : theExpectedFilenameFragments) {
 						if (nextEntry.getName().contains(next)) {
-							want = true;
+							foundFragments.add(next);
 						}
 					}
-
-					if (!want) {
-						ourLog.info("Ignoring zip entry: {}", nextEntry.getName());
-						continue;
-					}
-
-					ourLog.info("Streaming ZIP entry {} into temporary file", nextEntry.getName());
-
-					File nextOutFile = File.createTempFile("hapi_fhir", ".csv");
-					nextOutFile.deleteOnExit();
-					OutputStream outputStream = new SinkOutputStream(new FileOutputStream(nextOutFile, false), nextEntry.getName());
-					try {
-						IOUtils.copyLarge(inputStream, outputStream);
-					} finally {
-						IOUtils.closeQuietly(outputStream);
-					}
-
-					filenameToFile.put(nextEntry.getName(), nextOutFile);
 				}
 			} catch (IOException e) {
 				throw new InternalErrorException(e);
@@ -158,10 +129,12 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 			}
 		}
 
-		if (filenameToFile.size() != theExpectedFilenameFragments.size()) {
+		for (String next : theExpectedFilenameFragments) {
-			throw new InvalidRequestException("Invalid input zip file, expected zip to contain the following name fragments: " + theExpectedFilenameFragments + " but found: " + filenameToFile.keySet());
+			if (!foundFragments.contains(next)) {
+				throw new InvalidRequestException("Invalid input zip file, expected zip to contain the following name fragments: " + theExpectedFilenameFragments + " but found: " + foundFragments);
+			}
 		}
-		return filenameToFile;
+
 	}
 
 	public String firstNonBlank(String... theStrings) {
@@ -185,49 +158,54 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 		return concept;
 	}
 
-	private void iterateOverZipFile(Map<String, File> theFilenameToFile, String fileNamePart, IRecordHandler handler, char theDelimiter, QuoteMode theQuoteMode) {
+	private void iterateOverZipFile(List<byte[]> theZipBytes, String fileNamePart, IRecordHandler handler, char theDelimiter, QuoteMode theQuoteMode) {
 		boolean found = false;
-		for (Entry<String, File> nextEntry : new HashMap<String, File>(theFilenameToFile).entrySet()) {
 
-			if (nextEntry.getKey().contains(fileNamePart)) {
+		for (byte[] nextZipBytes : theZipBytes) {
-				ourLog.info("Processing file {}", nextEntry.getKey());
+			ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(nextZipBytes)));
-				found = true;
+			try {
+				for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null;) {
+					ZippedFileInputStream inputStream = new ZippedFileInputStream(zis);
 
-				Reader reader = null;
+					String nextFilename = nextEntry.getName();
-				CSVParser parsed = null;
+					if (nextFilename.contains(fileNamePart)) {
-				try {
+						ourLog.info("Processing file {}", nextFilename);
-					reader = new BufferedReader(new FileReader(nextEntry.getValue()));
+						found = true;
-					CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
-					if (theQuoteMode != null) {
-						format = format.withQuote('"').withQuoteMode(theQuoteMode);
-					}
-					parsed = new CSVParser(reader, format);
-					Iterator<CSVRecord> iter = parsed.iterator();
-					ourLog.debug("Header map: {}", parsed.getHeaderMap());
 
-					int count = 0;
+						Reader reader = null;
-					int logIncrement = 100000;
+						CSVParser parsed = null;
-					int nextLoggedCount = logIncrement;
+						try {
-					while (iter.hasNext()) {
+							reader = new InputStreamReader(zis, Charsets.UTF_8);
-						CSVRecord nextRecord = iter.next();
+							CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
-						handler.accept(nextRecord);
+							if (theQuoteMode != null) {
-						count++;
+								format = format.withQuote('"').withQuoteMode(theQuoteMode);
-						if (count >= nextLoggedCount) {
+							}
-							ourLog.info(" * Processed {} records in {}", count, fileNamePart);
+							parsed = new CSVParser(reader, format);
-							nextLoggedCount += logIncrement;
+							Iterator<CSVRecord> iter = parsed.iterator();
+							ourLog.debug("Header map: {}", parsed.getHeaderMap());
+
+							int count = 0;
+							int logIncrement = LOG_INCREMENT;
+							int nextLoggedCount = 0;
+							while (iter.hasNext()) {
+								CSVRecord nextRecord = iter.next();
+								handler.accept(nextRecord);
+								count++;
+								if (count >= nextLoggedCount) {
+									ourLog.info(" * Processed {} records in {}", count, nextFilename);
+									nextLoggedCount += logIncrement;
+								}
+							}
+
+						} catch (IOException e) {
+							throw new InternalErrorException(e);
 						}
 					}
-
-					ourLog.info("Deleting temporary file: {}", nextEntry.getValue());
-					nextEntry.getValue().delete();
-					theFilenameToFile.remove(nextEntry.getKey());
-
-				} catch (IOException e) {
-					throw new InternalErrorException(e);
-				} finally {
-					IOUtils.closeQuietly(parsed);
-					IOUtils.closeQuietly(reader);
 				}
+			} catch (IOException e) {
+				throw new InternalErrorException(e);
+			} finally {
+				IOUtils.closeQuietly(zis);
 			}
 		}
 
@@ -239,42 +217,36 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 	public UploadStatistics loadLoinc(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
 		List<String> expectedFilenameFragments = Arrays.asList(LOINC_FILE, LOINC_HIERARCHY_FILE);
 
-		Map<String, File> filenameToFile = extractFiles(theZipBytes, expectedFilenameFragments);
+		extractFiles(theZipBytes, expectedFilenameFragments);
 
 		ourLog.info("Beginning LOINC processing");
 
-		try {
+		return processLoincFiles(theZipBytes, theRequestDetails);
-			return processLoincFiles(filenameToFile, theRequestDetails);
-		} finally {
-			cleanUpTemporaryFiles(filenameToFile);
-		}
 	}
 
 	@Override
 	public UploadStatistics loadSnomedCt(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
 		List<String> expectedFilenameFragments = Arrays.asList(SCT_FILE_DESCRIPTION, SCT_FILE_RELATIONSHIP, SCT_FILE_CONCEPT);
 
-		Map<String, File> filenameToFile = extractFiles(theZipBytes, expectedFilenameFragments);
+		extractFiles(theZipBytes, expectedFilenameFragments);
 
 		ourLog.info("Beginning SNOMED CT processing");
 
-		try {
+		return processSnomedCtFiles(theZipBytes, theRequestDetails);
-			return processSnomedCtFiles(filenameToFile, theRequestDetails);
-		} finally {
-			cleanUpTemporaryFiles(filenameToFile);
-		}
 	}
 
-	UploadStatistics processLoincFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
+	UploadStatistics processLoincFiles(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> code2concept = new HashMap<String, TermConcept>();
 
 		IRecordHandler handler = new LoincHandler(codeSystemVersion, code2concept);
-		iterateOverZipFile(filenameToFile, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC);
+		iterateOverZipFile(theZipBytes, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC);
 
 		handler = new LoincHierarchyHandler(codeSystemVersion, code2concept);
-		iterateOverZipFile(filenameToFile, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC);
+		iterateOverZipFile(theZipBytes, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC);
 
+		theZipBytes.clear();
+		
 		for (Iterator<Entry<String, TermConcept>> iter = code2concept.entrySet().iterator(); iter.hasNext();) {
 			Entry<String, TermConcept> next = iter.next();
 			// if (isBlank(next.getKey())) {
@@ -295,30 +267,36 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 		return new UploadStatistics(code2concept.size());
 	}
 
-	UploadStatistics processSnomedCtFiles(Map<String, File> filenameToFile, RequestDetails theRequestDetails) {
+	UploadStatistics processSnomedCtFiles(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
 		final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
 		final Map<String, TermConcept> id2concept = new HashMap<String, TermConcept>();
 		final Map<String, TermConcept> code2concept = new HashMap<String, TermConcept>();
 		final Set<String> validConceptIds = new HashSet<String>();
 
 		IRecordHandler handler = new SctHandlerConcept(validConceptIds);
-		iterateOverZipFile(filenameToFile, SCT_FILE_CONCEPT, handler, '\t', null);
+		iterateOverZipFile(theZipBytes, SCT_FILE_CONCEPT, handler, '\t', null);
 
 		ourLog.info("Have {} valid concept IDs", validConceptIds.size());
 
 		handler = new SctHandlerDescription(validConceptIds, code2concept, id2concept, codeSystemVersion);
-		iterateOverZipFile(filenameToFile, SCT_FILE_DESCRIPTION, handler, '\t', null);
+		iterateOverZipFile(theZipBytes, SCT_FILE_DESCRIPTION, handler, '\t', null);
 
 		ourLog.info("Got {} concepts, cloning map", code2concept.size());
 		final HashMap<String, TermConcept> rootConcepts = new HashMap<String, TermConcept>(code2concept);
 
 		handler = new SctHandlerRelationship(codeSystemVersion, rootConcepts, code2concept);
-		iterateOverZipFile(filenameToFile, SCT_FILE_RELATIONSHIP, handler, '\t', null);
+		iterateOverZipFile(theZipBytes, SCT_FILE_RELATIONSHIP, handler, '\t', null);
+
+		theZipBytes.clear();
 
 		ourLog.info("Done loading SNOMED CT files - {} root codes, {} total codes", rootConcepts.size(), code2concept.size());
 
+		Counter circularCounter = new Counter();
 		for (TermConcept next : rootConcepts.values()) {
-			dropCircularRefs(next, new LinkedHashSet<String>(), code2concept);
+			long count = circularCounter.getThenAdd();
+			float pct = ((float)count / rootConcepts.size()) * 100.0f;
+			ourLog.info(" * Scanning for circular refs - have scanned {} / {} codes ({}%)", count, rootConcepts.size(), pct);
+			dropCircularRefs(next, new ArrayList<String>(), code2concept, circularCounter);
 		}
 
 		codeSystemVersion.getConcepts().addAll(rootConcepts.values());
@@ -332,20 +310,6 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 		myTermSvc = theTermSvc;
 	}
 
-	@CoverageIgnore
-	public static void main(String[] args) throws Exception {
-		TerminologyLoaderSvc svc = new TerminologyLoaderSvc();
-
-		// byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
-		// svc.loadSnomedCt(bytes);
-
-		Map<String, File> files = new HashMap<String, File>();
-		files.put(SCT_FILE_CONCEPT, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Concept_Full_INT_20160131.txt"));
-		files.put(SCT_FILE_DESCRIPTION, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Description_Full-en_INT_20160131.txt"));
-		files.put(SCT_FILE_RELATIONSHIP, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Relationship_Full_INT_20160131.txt"));
-		svc.processSnomedCtFiles(files, null);
-	}
-
 	private interface IRecordHandler {
 		void accept(CSVRecord theRecord);
 	}
@@ -534,57 +498,6 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
 
 	}
 
-	private static class SinkOutputStream extends OutputStream {
-
-		private static final long LOG_INCREMENT = 10 * FileUtils.ONE_MB;
-		private int myBytes;
-		private String myFilename;
-		private long myNextLogCount = LOG_INCREMENT;
-		private FileOutputStream myWrap;
-
-		public SinkOutputStream(FileOutputStream theWrap, String theFilename) {
-			myWrap = theWrap;
-			myFilename = theFilename;
-		}
-
-		private void addCount(int theCount) {
-			myBytes += theCount;
-			if (myBytes > myNextLogCount) {
-				ourLog.info(" * Wrote {} of {}", FileUtils.byteCountToDisplaySize(myBytes), myFilename);
-				myNextLogCount = myBytes + LOG_INCREMENT;
-			}
-		}
-
-		@Override
-		public void close() throws IOException {
-			myWrap.close();
-		}
-
-		@Override
-		public void flush() throws IOException {
-			myWrap.flush();
-		}
-
-		@Override
-		public void write(byte[] theB) throws IOException {
-			myWrap.write(theB);
-			addCount(theB.length);
-		}
-
-		@Override
-		public void write(byte[] theB, int theOff, int theLen) throws IOException {
-			myWrap.write(theB, theOff, theLen);
-			addCount(theLen);
-		}
-
-		@Override
-		public void write(int theB) throws IOException {
-			myWrap.write(theB);
-			addCount(1);
-		}
-
-	}
-
 	private static class ZippedFileInputStream extends InputStream {
 
 		private ZipInputStream is;

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/Counter.java

@@ -0,0 +1,11 @@
+package ca.uhn.fhir.jpa.util;
+
+public class Counter {
+
+	private long myCount;
+	
+	public long getThenAdd() {
+		return myCount++;
+	}
+	
+}

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcIntegrationTest.java

@@ -34,7 +34,7 @@ public class TerminologyLoaderSvcIntegrationTest extends BaseJpaDstu3Test {
 		files.put(TerminologyLoaderSvc.SCT_FILE_CONCEPT, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Concept_Full_INT_20160131.txt"));
 		files.put(TerminologyLoaderSvc.SCT_FILE_DESCRIPTION, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Description_Full-en_INT_20160131.txt"));
 		files.put(TerminologyLoaderSvc.SCT_FILE_RELATIONSHIP, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Relationship_Full_INT_20160131.txt"));
-		myLoader.processSnomedCtFiles(files, mySrd);
+//		myLoader.processSnomedCtFiles(files, mySrd);
 	}
 
 }

hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/rest/server/exceptions/ExceptionPropertiesTest.java

@@ -12,6 +12,7 @@ import com.google.common.reflect.ClassPath.ClassInfo;
 
 import ca.uhn.fhir.model.dstu.resource.OperationOutcome;
 import ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException;
+import ca.uhn.fhir.rest.client.exceptions.FhirClientInappropriateForServerException;
 import ca.uhn.fhir.util.TestUtil;
 
 public class ExceptionPropertiesTest {
@@ -24,9 +25,8 @@ public class ExceptionPropertiesTest {
 		new FhirClientConnectionException(new Exception());
 		new NotImplementedOperationException("");
 		new NotImplementedOperationException(null, new OperationOutcome());
-		new FhirClientConnectionException("");
+		new FhirClientInappropriateForServerException(new Exception());
-		new FhirClientConnectionException(new Exception());
+		new FhirClientInappropriateForServerException("", new Exception());
-		new FhirClientConnectionException("", new Exception());
 	}
 	
 	@SuppressWarnings("deprecation")