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hapi-fhir
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Verifying the the recent changes were merged correctly with the refactorings

This commit is contained in:
Adam Carbone 2016-02-05 14:37:30 -05:00
parent 7b5767c514
commit 686d942a90
1 changed files with 90 additions and 83 deletions
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173
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java
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@ -58,7 +58,6 @@ import ca.uhn.fhir.util.ResourceReferenceInfo;
public class ExampleDataUploader extends BaseCommand {
private static final String SPEC_DEFAULT_VERSION = "dstu2";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleDataUploader.class);
@ -77,9 +76,7 @@ public class ExampleDataUploader extends BaseCommand {
Options options = new Options();
Option opt;
opt = new Option("f", "fhirversion", true, "Spec version to upload (default is '" + SPEC_DEFAULT_VERSION + "')");
opt.setRequired(false);
options.addOption(opt);
addFhirVersionOption(options);
opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
opt.setRequired(true);
@ -88,15 +85,15 @@ public class ExampleDataUploader extends BaseCommand {
opt = new Option("l", "limit", true, "Sets a limit to the number of resources the uploader will try to upload");
opt.setRequired(false);
options.addOption(opt);
opt = new Option("d", "data", true, "Local *.zip containing file to use to upload");
opt.setRequired(false);
options.addOption(opt);
opt = new Option("c", "cache", false, "Cache the downloaded examples-json.zip file in the ~/.hapi-fhir-cli/cache directory. Use this file for 12 hours if it exists, instead of fetching it from the internet.");
opt.setRequired(false);
options.addOption(opt);
// opt = new Option("c", "cache", true, "Store a copy of the downloaded example pack on the local disk using a file of the given name. Use this file instead of fetching it from the internet if the file already exists.");
// opt.setRequired(false);
// options.addOption(opt);
@ -106,14 +103,15 @@ public class ExampleDataUploader extends BaseCommand {
@Override
public void run(CommandLine theCommandLine) throws Exception {
String specVersion = theCommandLine.getOptionValue("f", SPEC_DEFAULT_VERSION);
FhirContext ctx = getSpecVersionContext(theCommandLine);
String targetServer = theCommandLine.getOptionValue("t");
if (isBlank(targetServer)) {
throw new ParseException("No target server (-t) specified");
} else if (targetServer.startsWith("http") == false && targetServer.startsWith("file") == false) {
throw new ParseException("Invalid target server specified, must begin with 'http' or 'file'");
}
Integer limit = null;
String limitString = theCommandLine.getOptionValue('l');
if (isNotBlank(limitString)) {
@ -124,65 +122,66 @@ public class ExampleDataUploader extends BaseCommand {
}
}
FhirContext ctx = null;
String specUrl;
if (SPEC_DEFAULT_VERSION.equals(specVersion)) {
ctx = FhirContext.forDstu2();
specUrl = "http://hl7.org/fhir/" + specVersion + "/examples-json.zip";
} else if ("dstu2.1".equals(specVersion)) {
ctx = FhirContext.forDstu2_1();
specUrl = "http://hl7-fhir.github.io/examples-json.zip";
} else {
throw new ParseException("Unknown spec version: " + specVersion);
switch (ctx.getVersion().getVersion()) {
case DSTU2:
specUrl = "http://hl7.org/fhir/dstu2/examples-json.zip";
break;
case DSTU3:
specUrl = "http://hl7-fhir.github.io/examples-json.zip";
break;
default:
throw new ParseException("Invalid spec version for this command: " + ctx.getVersion().getVersion());
}
String filepath = theCommandLine.getOptionValue('d');
boolean cacheFile = theCommandLine.hasOption('c');
String userHomeDir = System.getProperty("user.home");
File applicationDir = new File(userHomeDir + File.separator + "." + "hapi-fhir-cli");
FileUtils.forceMkdir(applicationDir);
if (isNotBlank(filepath)) {
ourLog.info("Loading from local path: {}", filepath);
if (filepath.startsWith("~" + File.separator)) {
filepath = userHomeDir + filepath.substring(1);
}
File suppliedFile = new File(FilenameUtils.normalize(filepath));
File suppliedFile = new File(FilenameUtils.normalize(filepath));
if(suppliedFile.isDirectory()){
Collection<File> inputFiles;
Collection<File> inputFiles;
inputFiles = FileUtils.listFiles(suppliedFile, new String[] {"zip"}, false);
for (File inputFile : inputFiles) {
Bundle bundle = getBundleFromFile(limit, inputFile, ctx);
processBundle(ctx, bundle);
sendBundleToTarget(targetServer, ctx, bundle);
}
} else {
Bundle bundle = getBundleFromFile(limit, suppliedFile, ctx);
processBundle(ctx, bundle);
sendBundleToTarget(targetServer, ctx, bundle);
}
} else {
File cacheDir = new File(applicationDir, "cache" );
FileUtils.forceMkdir(cacheDir);
File inputFile = new File( cacheDir, "examples-json-" + specVersion + ".zip");
Date cacheExpiryDate = DateUtils.addHours(new Date(), -12);
if(!inputFile.exists() | (cacheFile && FileUtils.isFileOlder(inputFile, cacheExpiryDate))){
File exampleFileDownloading = new File( cacheDir, "examples-json-" + specVersion + ".zip.partial");
HttpGet get = new HttpGet(specUrl);
CloseableHttpClient client = HttpClientBuilder.create().build();
CloseableHttpResponse result = client.execute(get);
@ -190,12 +189,12 @@ public class ExampleDataUploader extends BaseCommand {
if (result.getStatusLine().getStatusCode() != 200) {
throw new CommandFailureException("Got HTTP " + result.getStatusLine().getStatusCode() + " response code loading " + specUrl);
}
ourLog.info("Downloading from remote url: {}", specUrl);
downloadFileFromInternet(result, exampleFileDownloading);
FileUtils.moveFile(exampleFileDownloading, inputFile);
if(!cacheFile) {
inputFile.deleteOnExit();
}
@ -203,12 +202,12 @@ public class ExampleDataUploader extends BaseCommand {
ourLog.info("Successfully Loaded example pack ({})", FileUtils.byteCountToDisplaySize( FileUtils.sizeOf(inputFile)));
IOUtils.closeQuietly(result.getEntity().getContent());
}
Bundle bundle = getBundleFromFile(limit, inputFile, ctx);
processBundle(ctx, bundle);
sendBundleToTarget(targetServer, ctx, bundle);
}
}
@ -226,7 +225,6 @@ public class ExampleDataUploader extends BaseCommand {
throw new Exception("File already exists: " + file.getAbsolutePath());
}
FileWriter w = new FileWriter(file, false);
w.append(encoded);
w.close();
} else {
@ -243,14 +241,14 @@ public class ExampleDataUploader extends BaseCommand {
}
}
private void processBundle(FhirContext ctx, Bundle originalBundle) {
private void processBundle(FhirContext ctx, Bundle bundle) {
Map<String, Integer> ids = new HashMap<String, Integer>();
Set<String> fullIds = new HashSet<String>();
for (Iterator<Entry> iterator = originalBundle.getEntry().iterator(); iterator.hasNext();) {
for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext();) {
Entry next = iterator.next();
// DataElement have giant IDs that seem invalid, need to investigate this..
if ("DataElement".equals(next.getResource().getResourceName()) || "OperationOutcome".equals(next.getResource().getResourceName()) || "OperationDefinition".equals(next.getResource().getResourceName())) {
ourLog.info("Skipping " + next.getResource().getResourceName() + " example");
@ -278,7 +276,7 @@ public class ExampleDataUploader extends BaseCommand {
}
Set<String> qualIds = new HashSet<String>();
Map<String, String> renames = new HashMap<String, String>();
for (Iterator<Entry> iterator = originalBundle.getEntry().iterator(); iterator.hasNext();) {
for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext();) {
Entry next = iterator.next();
if (next.getResource().getId().getIdPart() != null) {
String idPart = next.getResource().getId().getIdPart();
@ -299,7 +297,7 @@ public class ExampleDataUploader extends BaseCommand {
}
int goodRefs = 0;
for (Entry next : originalBundle.getEntry()) {
for (Entry next : bundle.getEntry()) {
List<ResourceReferenceInfo> refs = ctx.newTerser().getAllResourceReferences(next.getResource());
for (ResourceReferenceInfo nextRef : refs) {
// if (nextRef.getResourceReference().getReferenceElement().isAbsolute()) {
@ -321,23 +319,32 @@ public class ExampleDataUploader extends BaseCommand {
goodRefs++;
}
}
}
}
// for (Entry next : bundle.getEntry()) {
// if (next.getResource().getId().hasIdPart() &&
// Character.isLetter(next.getResource().getId().getIdPart().charAt(0))) {
// next.getTransaction().setUrl(next.getResource().getResourceName() + '/' +
// next.getResource().getId().getIdPart());
// next.getTransaction().setMethod(HTTPVerbEnum.PUT);
// }
// }
ourLog.info("{} good references", goodRefs);
System.gc();
ourLog.info("Final bundle: {} entries", originalBundle.getEntry().size());
ourLog.info("Final bundle: {} entries", bundle.getEntry().size());
}
private Bundle getBundleFromFile(Integer limit, File inputFile, FhirContext ctx)
throws IOException, UnsupportedEncodingException {
throws IOException, UnsupportedEncodingException {
Bundle bundle = new Bundle();
ZipInputStream zis = new ZipInputStream(FileUtils.openInputStream(inputFile));
byte[] buffer = new byte[2048];
int count = 0;
while (true) {
count++;
@ -349,7 +356,7 @@ public class ExampleDataUploader extends BaseCommand {
if (nextEntry == null) {
break;
}
int len = 0;
ByteArrayOutputStream bos = new ByteArrayOutputStream();
while ((len = zis.read(buffer)) > 0) {
@ -398,39 +405,39 @@ public class ExampleDataUploader extends BaseCommand {
private void downloadFileFromInternet(CloseableHttpResponse result, File localFile ) throws IOException {
FileOutputStream buffer = FileUtils.openOutputStream(localFile);
long maxLength = result.getEntity().getContentLength();
long nextLog = -1;
// ByteArrayOutputStream buffer = new ByteArrayOutputStream();
int nRead;
byte[] data = new byte[16384];
while ((nRead = result.getEntity().getContent().read(data, 0, data.length)) != -1) {
buffer.write(data, 0, nRead);
long fileSize = FileUtils.sizeOf(localFile);
if (fileSize > nextLog) {
System.err.print("\r" + Ansi.ansi().eraseLine());
System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
if (maxLength > 0) {
System.err.print(" [");
int stars = (int)(50.0f * ((float)fileSize / (float)maxLength));
for (int i = 0; i < stars; i++) {
System.err.print("*");
}
for (int i = stars; i < 50; i++) {
System.err.print(" ");
}
System.err.print("]");
}
System.err.flush();
nextLog += 100000;
}
buffer.write(data, 0, nRead);
long fileSize = FileUtils.sizeOf(localFile);
if (fileSize > nextLog) {
System.err.print("\r" + Ansi.ansi().eraseLine());
System.err.print(FileUtils.byteCountToDisplaySize(fileSize));
if (maxLength > 0) {
System.err.print(" [");
int stars = (int)(50.0f * ((float)fileSize / (float)maxLength));
for (int i = 0; i < stars; i++) {
System.err.print("*");
}
for (int i = stars; i < 50; i++) {
System.err.print(" ");
}
System.err.print("]");
}
System.err.flush();
nextLog += 100000;
}
}
buffer.flush();
System.err.println();
System.err.flush();
}
}
private byte[] readStreamFromInternet(CloseableHttpResponse result) throws IOException {
byte[] inputBytes;
{