Merge pull request #293 from adam-carbone/master
Allow loading from local file/caching
This commit is contained in:
James Agnew
commit
5163d7f1a1
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@ -3,13 +3,21 @@ package ca.uhn.fhir.cli;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.io.BufferedInputStream;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.UnsupportedEncodingException;
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import java.util.Collection;
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import java.util.Date;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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@ -20,7 +28,12 @@ import org.apache.commons.cli.CommandLine;
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import org.apache.commons.cli.Option;
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import org.apache.commons.cli.Options;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.FilenameUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.BooleanUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.time.DateUtils;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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@ -29,8 +42,6 @@ import org.fusesource.jansi.Ansi;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import com.phloc.commons.io.file.FileUtils;
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import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
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import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
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import ca.uhn.fhir.context.FhirContext;
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@ -66,7 +77,7 @@ public class ExampleDataUploader extends BaseCommand {
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Option opt;
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addFhirVersionOption(options);
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opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
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opt.setRequired(true);
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options.addOption(opt);
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@ -75,6 +86,14 @@ public class ExampleDataUploader extends BaseCommand {
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opt.setRequired(false);
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options.addOption(opt);
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opt = new Option("d", "data", true, "Local *.zip containing file to use to upload");
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opt.setRequired(false);
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options.addOption(opt);
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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.");
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opt.setRequired(false);
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options.addOption(opt);
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// 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.");
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// opt.setRequired(false);
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// options.addOption(opt);
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@ -85,13 +104,14 @@ public class ExampleDataUploader extends BaseCommand {
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@Override
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public void run(CommandLine theCommandLine) throws Exception {
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FhirContext ctx = getSpecVersionContext(theCommandLine);
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String targetServer = theCommandLine.getOptionValue("t");
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if (isBlank(targetServer)) {
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throw new ParseException("No target server (-t) specified");
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} else if (targetServer.startsWith("http") == false && targetServer.startsWith("file") == false) {
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throw new ParseException("Invalid target server specified, must begin with 'http' or 'file'");
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}
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Integer limit = null;
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String limitString = theCommandLine.getOptionValue('l');
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if (isNotBlank(limitString)) {
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@ -105,191 +125,97 @@ public class ExampleDataUploader extends BaseCommand {
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String specUrl;
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switch (ctx.getVersion().getVersion()) {
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case DSTU2:
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specUrl = "http://hl7.org/fhir/dstu2/examples-json.zip";
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break;
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case DSTU3:
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specUrl = "http://hl7-fhir.github.io/examples-json.zip";
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break;
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default:
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throw new ParseException("Invalid spec version for this command: " + ctx.getVersion().getVersion());
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case DSTU2:
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specUrl = "http://hl7.org/fhir/dstu2/examples-json.zip";
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break;
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case DSTU3:
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specUrl = "http://hl7-fhir.github.io/examples-json.zip";
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break;
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default:
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throw new ParseException("Invalid spec version for this command: " + ctx.getVersion().getVersion());
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}
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ourLog.info("HTTP fetching: {}", specUrl);
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String filepath = theCommandLine.getOptionValue('d');
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HttpGet get = new HttpGet(specUrl);
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CloseableHttpClient client = HttpClientBuilder.create().build();
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CloseableHttpResponse result = client.execute(get);
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boolean cacheFile = theCommandLine.hasOption('c');
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String userHomeDir = System.getProperty("user.home");
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File applicationDir = new File(userHomeDir + File.separator + "." + "hapi-fhir-cli");
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FileUtils.forceMkdir(applicationDir);
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if (isNotBlank(filepath)) {
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ourLog.info("Loading from local path: {}", filepath);
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if (filepath.startsWith("~" + File.separator)) {
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filepath = userHomeDir + filepath.substring(1);
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}
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File suppliedFile = new File(FilenameUtils.normalize(filepath));
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if(suppliedFile.isDirectory()){
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Collection<File> inputFiles;
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inputFiles = FileUtils.listFiles(suppliedFile, new String[] {"zip"}, false);
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for (File inputFile : inputFiles) {
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Bundle bundle = getBundleFromFile(limit, inputFile, ctx);
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processBundle(ctx, bundle);
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sendBundleToTarget(targetServer, ctx, bundle);
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}
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} else {
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Bundle bundle = getBundleFromFile(limit, suppliedFile, ctx);
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processBundle(ctx, bundle);
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sendBundleToTarget(targetServer, ctx, bundle);
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}
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} else {
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File cacheDir = new File(applicationDir, "cache" );
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FileUtils.forceMkdir(cacheDir);
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File inputFile = new File( cacheDir, "examples-json-" + ctx.getVersion().getVersion() + ".zip");
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Date cacheExpiryDate = DateUtils.addHours(new Date(), -12);
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if(!inputFile.exists() | (cacheFile && FileUtils.isFileOlder(inputFile, cacheExpiryDate))){
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File exampleFileDownloading = new File( cacheDir, "examples-json-" + ctx.getVersion().getVersion() + ".zip.partial");
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HttpGet get = new HttpGet(specUrl);
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CloseableHttpClient client = HttpClientBuilder.create().build();
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CloseableHttpResponse result = client.execute(get);
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if (result.getStatusLine().getStatusCode() != 200) {
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throw new CommandFailureException("Got HTTP " + result.getStatusLine().getStatusCode() + " response code loading " + specUrl);
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}
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ourLog.info("Downloading from remote url: {}", specUrl);
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downloadFileFromInternet(result, exampleFileDownloading);
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FileUtils.moveFile(exampleFileDownloading, inputFile);
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if(!cacheFile) {
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inputFile.deleteOnExit();
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}
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ourLog.info("Successfully Loaded example pack ({})", FileUtils.byteCountToDisplaySize( FileUtils.sizeOf(inputFile)));
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IOUtils.closeQuietly(result.getEntity().getContent());
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}
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Bundle bundle = getBundleFromFile(limit, inputFile, ctx);
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processBundle(ctx, bundle);
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sendBundleToTarget(targetServer, ctx, bundle);
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if (result.getStatusLine().getStatusCode() != 200) {
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throw new CommandFailureException("Got HTTP " + result.getStatusLine().getStatusCode() + " response code loading " + specUrl);
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}
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Bundle bundle = new Bundle();
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{
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byte[] inputBytes = readStreamFromInternet(result);
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IOUtils.closeQuietly(result.getEntity().getContent());
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ourLog.info("Successfully Loaded example pack ({} bytes)", inputBytes.length);
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}
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ZipInputStream zis = new ZipInputStream(new ByteArrayInputStream(inputBytes));
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byte[] buffer = new byte[2048];
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int count = 0;
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while (true) {
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count++;
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if (limit != null && count > limit) {
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break;
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}
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ZipEntry nextEntry = zis.getNextEntry();
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if (nextEntry == null) {
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break;
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}
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int len = 0;
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ByteArrayOutputStream bos = new ByteArrayOutputStream();
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while ((len = zis.read(buffer)) > 0) {
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bos.write(buffer, 0, len);
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}
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byte[] exampleBytes = bos.toByteArray();
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String exampleString = new String(exampleBytes, "UTF-8");
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if (ourLog.isTraceEnabled()) {
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ourLog.trace("Next example: " + exampleString);
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}
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IBaseResource parsed;
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try {
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parsed = ctx.newJsonParser().parseResource(exampleString);
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} catch (DataFormatException e) {
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ourLog.info("FAILED to parse example {}", nextEntry.getName(), e);
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continue;
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}
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ourLog.info("Found example {} - {} - {} chars", nextEntry.getName(), parsed.getClass().getSimpleName(), exampleString.length());
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if (ctx.getResourceDefinition(parsed).getName().equals("Bundle")) {
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BaseRuntimeChildDefinition entryChildDef = ctx.getResourceDefinition(parsed).getChildByName("entry");
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BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
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for (IBase nextEntry1 : entryChildDef.getAccessor().getValues(parsed)) {
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List<IBase> resources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry1);
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if (resources == null) {
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continue;
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}
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for (IBase nextResource : resources) {
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if (!ctx.getResourceDefinition(parsed).getName().equals("Bundle") && ctx.getResourceDefinition(parsed).getName().equals("SearchParameter")) {
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bundle.addEntry().setRequest(new EntryRequest().setMethod(HTTPVerbEnum.POST)).setResource((IResource) nextResource);
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}
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}
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}
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} else {
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if (ctx.getResourceDefinition(parsed).getName().equals("SearchParameter")) {
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continue;
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}
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bundle.addEntry().setRequest(new EntryRequest().setMethod(HTTPVerbEnum.POST)).setResource((IResource) parsed);
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}
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}
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Map<String, Integer> ids = new HashMap<String, Integer>();
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Set<String> fullIds = new HashSet<String>();
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for (int i = 0; i < bundle.getEntry().size(); i++) {
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Entry next = bundle.getEntry().get(i);
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// DataElement have giant IDs that seem invalid, need to investigate this..
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if ("DataElement".equals(next.getResource().getResourceName()) || "OperationOutcome".equals(next.getResource().getResourceName()) || "OperationDefinition".equals(next.getResource().getResourceName())) {
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ourLog.info("Skipping " + next.getResource().getResourceName() + " example");
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bundle.getEntry().remove(i);
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i--;
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} else {
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IdDt resourceId = next.getResource().getId();
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if (!fullIds.add(resourceId.toUnqualifiedVersionless().getValue())) {
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ourLog.info("Discarding duplicate resource: " + resourceId.getValue());
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bundle.getEntry().remove(i);
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i--;
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continue;
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}
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String idPart = resourceId.getIdPart();
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if (idPart != null) {
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if (!ids.containsKey(idPart)) {
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ids.put(idPart, 1);
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} else {
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ids.put(idPart, ids.get(idPart) + 1);
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}
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} else {
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ourLog.info("Discarding resource with not explicit ID");
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bundle.getEntry().remove(i);
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i--;
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}
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}
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}
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Set<String> qualIds = new HashSet<String>();
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Map<String, String> renames = new HashMap<String, String>();
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for (int i = 0; i < bundle.getEntry().size(); i++) {
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Entry next = bundle.getEntry().get(i);
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if (next.getResource().getId().getIdPart() != null) {
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String idPart = next.getResource().getId().getIdPart();
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String originalId = next.getResource().getResourceName() + '/' + idPart;
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if (ids.get(idPart) > 1 || next.getResource().getId().isIdPartValidLong()) {
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idPart = next.getResource().getResourceName() + idPart;
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}
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String nextId = next.getResource().getResourceName() + '/' + idPart;
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if (!qualIds.add(nextId)) {
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ourLog.info("Discarding duplicate resource with ID: " + nextId);
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bundle.getEntry().remove(i);
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i--;
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}
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next.getRequest().setMethod(HTTPVerbEnum.PUT);
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next.getRequest().setUrl(nextId);
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next.getResource().setId("");
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renames.put(originalId, nextId);
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}
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}
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int goodRefs = 0;
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for (Entry next : bundle.getEntry()) {
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List<ResourceReferenceInfo> refs = ctx.newTerser().getAllResourceReferences(next.getResource());
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for (ResourceReferenceInfo nextRef : refs) {
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// if (nextRef.getResourceReference().getReferenceElement().isAbsolute()) {
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// ourLog.info("Discarding absolute reference: {}",
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// nextRef.getResourceReference().getReferenceElement().getValue());
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// nextRef.getResourceReference().getReferenceElement().setValue(null);
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// }
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nextRef.getResourceReference().setResource(null);
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String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
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if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
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if (renames.containsKey(value)) {
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nextRef.getResourceReference().setReference(renames.get(value));
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goodRefs++;
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} else {
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ourLog.info("Discarding unknown reference: {}", value);
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nextRef.getResourceReference().getReferenceElement().setValue(null);
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}
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} else {
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goodRefs++;
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}
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}
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}
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// for (Entry next : bundle.getEntry()) {
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// if (next.getResource().getId().hasIdPart() &&
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// Character.isLetter(next.getResource().getId().getIdPart().charAt(0))) {
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// next.getTransaction().setUrl(next.getResource().getResourceName() + '/' +
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// next.getResource().getId().getIdPart());
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// next.getTransaction().setMethod(HTTPVerbEnum.PUT);
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// }
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// }
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ourLog.info("{} good references", goodRefs);
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System.gc();
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}
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private void sendBundleToTarget(String targetServer, FhirContext ctx, Bundle bundle) throws Exception, IOException {
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String encoded = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(bundle);
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ourLog.info("Final bundle: {} entries", bundle.getEntry().size());
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ourLog.info("Final bundle: {}", FileUtils.getFileSizeDisplay(encoded.length(), 1));
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ourLog.info("Final bundle: {}", FileUtils.byteCountToDisplaySize(encoded.length()));
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if (targetServer.startsWith("file://")) {
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String path = targetServer.substring("file://".length());
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@ -308,7 +234,6 @@ public class ExampleDataUploader extends BaseCommand {
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fhirClient.registerInterceptor(new GZipContentInterceptor());
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long start = System.currentTimeMillis();
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;
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fhirClient.transaction().withBundle(bundle).execute();
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long delay = System.currentTimeMillis() - start;
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@ -316,6 +241,203 @@ public class ExampleDataUploader extends BaseCommand {
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}
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}
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private void processBundle(FhirContext ctx, Bundle bundle) {
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Map<String, Integer> ids = new HashMap<String, Integer>();
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Set<String> fullIds = new HashSet<String>();
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for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext();) {
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Entry next = iterator.next();
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// DataElement have giant IDs that seem invalid, need to investigate this..
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if ("DataElement".equals(next.getResource().getResourceName()) || "OperationOutcome".equals(next.getResource().getResourceName()) || "OperationDefinition".equals(next.getResource().getResourceName())) {
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ourLog.info("Skipping " + next.getResource().getResourceName() + " example");
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iterator.remove();
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} else {
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IdDt resourceId = next.getResource().getId();
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if (!fullIds.add(resourceId.toUnqualifiedVersionless().getValue())) {
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ourLog.info("Discarding duplicate resource: " + resourceId.getValue());
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iterator.remove();
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continue;
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}
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String idPart = resourceId.getIdPart();
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if (idPart != null) {
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if (!ids.containsKey(idPart)) {
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ids.put(idPart, 1);
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} else {
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ids.put(idPart, ids.get(idPart) + 1);
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}
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} else {
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ourLog.info("Discarding resource with not explicit ID");
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iterator.remove();
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}
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}
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}
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Set<String> qualIds = new HashSet<String>();
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Map<String, String> renames = new HashMap<String, String>();
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for (Iterator<Entry> iterator = bundle.getEntry().iterator(); iterator.hasNext();) {
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Entry next = iterator.next();
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if (next.getResource().getId().getIdPart() != null) {
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String idPart = next.getResource().getId().getIdPart();
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String originalId = next.getResource().getResourceName() + '/' + idPart;
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if (ids.get(idPart) > 1 || next.getResource().getId().isIdPartValidLong()) {
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idPart = next.getResource().getResourceName() + idPart;
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}
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String nextId = next.getResource().getResourceName() + '/' + idPart;
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if (!qualIds.add(nextId)) {
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ourLog.info("Discarding duplicate resource with ID: " + nextId);
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iterator.remove();
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}
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next.getRequest().setMethod(HTTPVerbEnum.PUT);
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next.getRequest().setUrl(nextId);
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next.getResource().setId("");
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renames.put(originalId, nextId);
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}
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}
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int goodRefs = 0;
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for (Entry next : bundle.getEntry()) {
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List<ResourceReferenceInfo> refs = ctx.newTerser().getAllResourceReferences(next.getResource());
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for (ResourceReferenceInfo nextRef : refs) {
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// if (nextRef.getResourceReference().getReferenceElement().isAbsolute()) {
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// ourLog.info("Discarding absolute reference: {}",
|
||||
// nextRef.getResourceReference().getReferenceElement().getValue());
|
||||
// nextRef.getResourceReference().getReferenceElement().setValue(null);
|
||||
// }
|
||||
nextRef.getResourceReference().setResource(null);
|
||||
String value = nextRef.getResourceReference().getReferenceElement().toUnqualifiedVersionless().getValue();
|
||||
if (!qualIds.contains(value) && !nextRef.getResourceReference().getReferenceElement().isLocal()) {
|
||||
if (renames.containsKey(value)) {
|
||||
nextRef.getResourceReference().setReference(renames.get(value));
|
||||
goodRefs++;
|
||||
} else {
|
||||
ourLog.info("Discarding unknown reference: {}", value);
|
||||
nextRef.getResourceReference().getReferenceElement().setValue(null);
|
||||
}
|
||||
} else {
|
||||
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", bundle.getEntry().size());
|
||||
|
||||
}
|
||||
|
||||
private Bundle getBundleFromFile(Integer limit, File inputFile, FhirContext ctx)
|
||||
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++;
|
||||
if (limit != null && count > limit) {
|
||||
break;
|
||||
}
|
||||
|
||||
ZipEntry nextEntry = zis.getNextEntry();
|
||||
if (nextEntry == null) {
|
||||
break;
|
||||
}
|
||||
|
||||
int len = 0;
|
||||
ByteArrayOutputStream bos = new ByteArrayOutputStream();
|
||||
while ((len = zis.read(buffer)) > 0) {
|
||||
bos.write(buffer, 0, len);
|
||||
}
|
||||
byte[] exampleBytes = bos.toByteArray();
|
||||
String exampleString = new String(exampleBytes, "UTF-8");
|
||||
|
||||
if (ourLog.isTraceEnabled()) {
|
||||
ourLog.trace("Next example: " + exampleString);
|
||||
}
|
||||
|
||||
IBaseResource parsed;
|
||||
try {
|
||||
parsed = ctx.newJsonParser().parseResource(exampleString);
|
||||
} catch (DataFormatException e) {
|
||||
ourLog.info("FAILED to parse example {}", nextEntry.getName(), e);
|
||||
continue;
|
||||
}
|
||||
ourLog.info("Found example {} - {} - {} chars", nextEntry.getName(), parsed.getClass().getSimpleName(), exampleString.length());
|
||||
|
||||
if (ctx.getResourceDefinition(parsed).getName().equals("Bundle")) {
|
||||
BaseRuntimeChildDefinition entryChildDef = ctx.getResourceDefinition(parsed).getChildByName("entry");
|
||||
BaseRuntimeElementCompositeDefinition<?> entryDef = (BaseRuntimeElementCompositeDefinition<?>) entryChildDef.getChildByName("entry");
|
||||
|
||||
for (IBase nextEntry1 : entryChildDef.getAccessor().getValues(parsed)) {
|
||||
List<IBase> resources = entryDef.getChildByName("resource").getAccessor().getValues(nextEntry1);
|
||||
if (resources == null) {
|
||||
continue;
|
||||
}
|
||||
for (IBase nextResource : resources) {
|
||||
if (!ctx.getResourceDefinition(parsed).getName().equals("Bundle") && ctx.getResourceDefinition(parsed).getName().equals("SearchParameter")) {
|
||||
bundle.addEntry().setRequest(new EntryRequest().setMethod(HTTPVerbEnum.POST)).setResource((IResource) nextResource);
|
||||
}
|
||||
}
|
||||
}
|
||||
} else {
|
||||
if (ctx.getResourceDefinition(parsed).getName().equals("SearchParameter")) {
|
||||
continue;
|
||||
}
|
||||
bundle.addEntry().setRequest(new EntryRequest().setMethod(HTTPVerbEnum.POST)).setResource((IResource) parsed);
|
||||
}
|
||||
}
|
||||
return bundle;
|
||||
}
|
||||
|
||||
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.flush();
|
||||
|
||||
System.err.println();
|
||||
System.err.flush();
|
||||
}
|
||||
|
||||
private byte[] readStreamFromInternet(CloseableHttpResponse result) throws IOException {
|
||||
byte[] inputBytes;
|
||||
{
|
||||
|
|
@ -328,7 +450,7 @@ public class ExampleDataUploader extends BaseCommand {
|
|||
buffer.write(data, 0, nRead);
|
||||
if (buffer.size() > nextLog) {
|
||||
System.err.print("\r" + Ansi.ansi().eraseLine());
|
||||
System.err.print(FileUtils.getFileSizeDisplay(buffer.size(), 1));
|
||||
System.err.print(FileUtils.byteCountToDisplaySize(buffer.size()));
|
||||
if (maxLength > 0) {
|
||||
System.err.print(" [");
|
||||
int stars = (int)(50.0f * ((float)buffer.size() / (float)maxLength));
|
||||
|
|
|
|||
Loading…
Reference in New Issue