Add method to upload SCT to JPA server
This commit is contained in:
jamesagnew
parent
69266dc7d0
commit
cd2af98064
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@ -40,6 +40,7 @@ public class App {
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ourCommands.add(new ValidateCommand());
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ourCommands.add(new ValidationDataUploader());
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ourCommands.add(new WebsocketSubscribeCommand());
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ourCommands.add(new UploadTerminologyCommand());
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Collections.sort(ourCommands);
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}
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@ -0,0 +1,159 @@
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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.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.FileWriter;
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import java.io.IOException;
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import java.io.UnsupportedEncodingException;
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import java.util.ArrayList;
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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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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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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.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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import org.apache.http.impl.client.HttpClientBuilder;
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import org.fusesource.jansi.Ansi;
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import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
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import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
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import org.hl7.fhir.dstu3.model.Attachment;
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import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
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import org.hl7.fhir.dstu3.model.Bundle.BundleType;
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import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
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import org.hl7.fhir.dstu3.model.IdType;
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import org.hl7.fhir.dstu3.model.Parameters;
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import org.hl7.fhir.dstu3.model.Resource;
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import org.hl7.fhir.dstu3.model.StringType;
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import org.hl7.fhir.instance.model.api.IBase;
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import org.hl7.fhir.instance.model.api.IBaseBundle;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.omg.Dynamic.Parameter;
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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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import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
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import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryRequest;
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import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.model.valueset.BundleTypeEnum;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.rest.client.IGenericClient;
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import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
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import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
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import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
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import ca.uhn.fhir.util.BundleUtil;
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import ca.uhn.fhir.util.ResourceReferenceInfo;
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import ca.uhn.fhir.validation.FhirValidator;
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import ca.uhn.fhir.validation.ValidationResult;
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public class UploadTerminologyCommand extends BaseCommand {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(UploadTerminologyCommand.class);
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@Override
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public String getCommandDescription() {
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//@formatter:off
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return "Uploads a terminology package (e.g. a SNOMED CT ZIP file) to a HAPI JPA server. "
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+ "Note that this command uses a custom operation that is only implemented on HAPI "
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+ "JPA servers that have been configured to accept it.";
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//@formatter:on
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}
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@Override
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public String getCommandName() {
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return "upload-terminology";
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}
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@Override
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public Options getOptions() {
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Options options = new Options();
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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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opt = new Option("u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URL + ")");
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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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return options;
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}
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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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String termUrl = theCommandLine.getOptionValue("u");
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if (isBlank(termUrl)) {
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throw new ParseException("No URL provided");
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}
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String datafile = theCommandLine.getOptionValue("d");
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if (isBlank(datafile)) {
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throw new ParseException("No data file provided");
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}
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IGenericClient client = super.newClient(ctx, targetServer);
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IBaseParameters inputParameters;
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if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
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Parameters p = new Parameters();
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p.addParameter().setName("url").setValue(new StringType(termUrl));
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p.addParameter().setName("localfile").setValue(new StringType(datafile));
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inputParameters = p;
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} else {
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throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
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}
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ourLog.info("Beginning upload - This may take a while...");
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IBaseParameters response = client
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.operation()
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.onServer()
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.named("upload-external-code-system")
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.withParameters(inputParameters)
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.execute();
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ourLog.info("Upload complete!");
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}
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}
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@ -210,6 +210,10 @@
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</overlays>
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<webXml>src/main/webapp/WEB-INF/web.xml</webXml>
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<attachClasses>true</attachClasses>
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<excludes>
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WEB-INF/lib/Saxon-HE-*,
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WEB-INF/lib/hapi-*
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</excludes>
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</configuration>
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</plugin>
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@ -1,5 +1,6 @@
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package ca.uhn.fhir.jpa.demo;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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@ -19,6 +20,7 @@ import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu1;
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import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
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import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
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import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
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import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
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import ca.uhn.fhir.model.api.IResource;
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import ca.uhn.fhir.model.dstu2.composite.MetaDt;
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import ca.uhn.fhir.model.dstu2.resource.Bundle;
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@ -74,13 +76,14 @@ public class JpaServerDemo extends RestfulServer {
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* The system provider implements non-resource-type methods, such as
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* transaction, and global history.
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*/
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Object systemProvider;
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List<Object> systemProvider = new ArrayList<Object>();
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if (fhirVersion == FhirVersionEnum.DSTU1) {
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systemProvider = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
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systemProvider.add(myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class));
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} else if (fhirVersion == FhirVersionEnum.DSTU2) {
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systemProvider = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);
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systemProvider.add(myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class));
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} else if (fhirVersion == FhirVersionEnum.DSTU3) {
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systemProvider = myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class);
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systemProvider.add(myAppCtx.getBean("mySystemProviderDstu3", JpaSystemProviderDstu3.class));
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systemProvider.add(myAppCtx.getBean(TerminologyUploaderProviderDstu3.class));
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} else {
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throw new IllegalStateException();
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}
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@ -1,12 +1,20 @@
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package ca.uhn.fhir.jpa.provider.dstu3;
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import static org.apache.commons.lang3.StringUtils.defaultString;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.output.LockableFileWriter;
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import org.hl7.fhir.dstu3.model.Attachment;
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import org.hl7.fhir.dstu3.model.IntegerType;
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import org.hl7.fhir.dstu3.model.Parameters;
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import org.hl7.fhir.dstu3.model.StringType;
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import org.hl7.fhir.dstu3.model.UriType;
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import org.springframework.beans.factory.annotation.Autowired;
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@ -16,9 +24,11 @@ import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc.UploadStatistics;
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import ca.uhn.fhir.rest.annotation.Operation;
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import ca.uhn.fhir.rest.annotation.OperationParam;
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import ca.uhn.fhir.rest.method.RequestDetails;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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public class TerminologyUploaderProviderDstu3 extends BaseJpaProvider {
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private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyUploaderProviderDstu3.class);
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@Autowired
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private IHapiTerminologyLoaderSvc myTerminologyLoaderSvc;
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@ -30,18 +40,28 @@ public class TerminologyUploaderProviderDstu3 extends BaseJpaProvider {
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public Parameters lookup(
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HttpServletRequest theServletRequest,
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@OperationParam(name="url", min=1) UriType theUrl,
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@OperationParam(name="package", min=1) Attachment thePackage,
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@OperationParam(name="package", min=0) Attachment thePackage,
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@OperationParam(name="localfile", min=0) StringType theLocalFile,
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RequestDetails theRequestDetails
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) {
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//@formatter:on
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startRequest(theServletRequest);
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try {
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if (thePackage == null || thePackage.getData() == null || thePackage.getData().length == 0) {
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throw new InvalidRequestException("Missing mandatory 'package' parameter, or package had no data");
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byte[] data;
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if (theLocalFile != null && isNotBlank(theLocalFile.getValue())) {
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ourLog.info("Reading in local file: {}", theLocalFile.getValue());
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try {
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data = IOUtils.toByteArray(new FileInputStream(theLocalFile.getValue()));
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} catch (IOException e) {
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throw new InternalErrorException(e);
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}
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} else if (thePackage == null || thePackage.getData() == null || thePackage.getData().length == 0) {
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throw new InvalidRequestException("No 'localfile' or 'package' parameter, or package had no data");
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} else {
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data = thePackage.getData();
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}
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byte[] data = thePackage.getData();
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String url = theUrl != null ? theUrl.getValueAsString() : null;
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url = defaultString(url);
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@ -1,9 +1,13 @@
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package ca.uhn.fhir.jpa.provider.dstu3;
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import static org.hamcrest.Matchers.greaterThan;
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import static org.junit.Assert.*;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertThat;
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import static org.junit.Assert.fail;
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import java.io.ByteArrayOutputStream;
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import java.io.File;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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@ -12,12 +16,10 @@ import java.util.zip.ZipOutputStream;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.dstu3.model.Attachment;
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import org.hl7.fhir.dstu3.model.BooleanType;
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import org.hl7.fhir.dstu3.model.CodeType;
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import org.hl7.fhir.dstu3.model.IntegerType;
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import org.hl7.fhir.dstu3.model.Parameters;
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import org.hl7.fhir.dstu3.model.StringType;
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import org.hl7.fhir.dstu3.model.UriType;
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import org.hl7.fhir.dstu3.model.ValueSet;
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import org.junit.AfterClass;
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import org.junit.Test;
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@ -56,6 +58,32 @@ public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test
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assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
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}
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@Test
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public void testUploadSctLocalFile() throws Exception {
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byte[] packageBytes = createSctZip();
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File tempFile = File.createTempFile("tmp", ".zip");
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tempFile.deleteOnExit();
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FileOutputStream fos = new FileOutputStream(tempFile);
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fos.write(packageBytes);
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fos.close();
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//@formatter:off
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Parameters respParam = ourClient
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.operation()
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.onServer()
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.named("upload-external-code-system")
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.withParameter(Parameters.class, "url", new UriType(IHapiTerminologyLoaderSvc.SCT_URL))
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.andParameter("localfile", new StringType(tempFile.getAbsolutePath()))
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.execute();
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//@formatter:on
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String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(respParam);
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ourLog.info(resp);
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assertThat(((IntegerType)respParam.getParameter().get(0).getValue()).getValue(), greaterThan(1));
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}
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@Test
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public void testUploadInvalidUrl() throws Exception {
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byte[] packageBytes = createSctZip();
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@ -107,7 +135,7 @@ public class TerminologyProviderDstu3Test extends BaseResourceProviderDstu3Test
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.execute();
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fail();
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} catch (InvalidRequestException e) {
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assertEquals("HTTP 400 Bad Request: Missing mandatory 'package' parameter, or package had no data", e.getMessage());
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assertEquals("HTTP 400 Bad Request: No 'localfile' or 'package' parameter, or package had no data", e.getMessage());
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}
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//@formatter:on
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}
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