Add option to upload-terminology for security header

hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java

@@ -3,76 +3,20 @@ package ca.uhn.fhir.cli;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.time.DateUtils;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.fusesource.jansi.Ansi;
-import org.hl7.fhir.dstu3.hapi.validation.DefaultProfileValidationSupport;
-import org.hl7.fhir.dstu3.hapi.validation.FhirInstanceValidator;
-import org.hl7.fhir.dstu3.model.Attachment;
-import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
-import org.hl7.fhir.dstu3.model.Bundle.BundleType;
-import org.hl7.fhir.dstu3.model.Bundle.HTTPVerb;
-import org.hl7.fhir.dstu3.model.IdType;
 import org.hl7.fhir.dstu3.model.Parameters;
-import org.hl7.fhir.dstu3.model.Resource;
 import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.dstu3.model.UriType;
-import org.hl7.fhir.instance.model.api.IBase;
-import org.hl7.fhir.instance.model.api.IBaseBundle;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
-import org.hl7.fhir.instance.model.api.IBaseResource;
-import org.omg.Dynamic.Parameter;
 
-import ca.uhn.fhir.context.BaseRuntimeChildDefinition;
-import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.context.FhirVersionEnum;
 import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
-import ca.uhn.fhir.model.api.IResource;
-import ca.uhn.fhir.model.dstu2.resource.Bundle;
-import ca.uhn.fhir.model.dstu2.resource.Bundle.Entry;
-import ca.uhn.fhir.model.dstu2.resource.Bundle.EntryRequest;
-import ca.uhn.fhir.model.dstu2.valueset.HTTPVerbEnum;
-import ca.uhn.fhir.model.primitive.IdDt;
-import ca.uhn.fhir.model.valueset.BundleTypeEnum;
-import ca.uhn.fhir.parser.DataFormatException;
 import ca.uhn.fhir.rest.client.IGenericClient;
-import ca.uhn.fhir.rest.client.apache.GZipContentInterceptor;
+import ca.uhn.fhir.rest.client.interceptor.BearerTokenAuthInterceptor;
-import ca.uhn.fhir.rest.server.IVersionSpecificBundleFactory;
-import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
-import ca.uhn.fhir.util.BundleUtil;
-import ca.uhn.fhir.util.ResourceReferenceInfo;
-import ca.uhn.fhir.validation.FhirValidator;
-import ca.uhn.fhir.validation.ValidationResult;
 
 public class UploadTerminologyCommand extends BaseCommand {
 
@@ -111,6 +55,10 @@ public class UploadTerminologyCommand extends BaseCommand {
 		opt.setRequired(false);
 		options.addOption(opt);
 
+		opt = new Option("b", "bearer-token", true, "Bearer token to add to the request");
+		opt.setRequired(false);
+		options.addOption(opt);
+
 		return options;
 	}
 
@@ -135,6 +83,9 @@ public class UploadTerminologyCommand extends BaseCommand {
 			throw new ParseException("No data file provided");
 		}
 		
+		String bearerToken = theCommandLine.getOptionValue("b");
+
+		
 		IGenericClient client = super.newClient(ctx, targetServer);
 		IBaseParameters inputParameters;
 		if (ctx.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
@@ -148,6 +99,10 @@ public class UploadTerminologyCommand extends BaseCommand {
 			throw new ParseException("This command does not support FHIR version " + ctx.getVersion().getVersion());
 		}
 
+		if (isNotBlank(bearerToken)) {
+			client.registerInterceptor(new BearerTokenAuthInterceptor(bearerToken));
+		}
+		
 		ourLog.info("Beginning upload - This may take a while...");
 		IBaseParameters response = client
 			.operation()

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java

@@ -65,6 +65,13 @@ public class TermCodeSystemVersion implements Serializable {
 	@Column(name = "RES_VERSION_ID", nullable = false, updatable = false)
 	private Long myResourceVersionId;
 
+	/**
+	 * Constructor
+	 */
+	public TermCodeSystemVersion() {
+		super();
+	}
+
 	public Collection<TermConcept> getConcepts() {
 		if (myConcepts == null) {
 			myConcepts = new ArrayList<TermConcept>();

hapi-fhir-jpaserver-base/src/test/resources/logback-test.xml

@@ -38,7 +38,7 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 	<!-- Set to 'trace' to enable SQL Value logging -->
-	<logger name="org.hibernate.type" additivity="false" level="info">
+	<logger name="org.hibernate.type" additivity="false" level="trace">
 		<appender-ref ref="STDOUT" />
 	</logger>
 

src/changes/changes.xml

@@ -151,6 +151,11 @@
 				populated with the actual target resource instance. Thanks to
 				Neal Acharya for reporting!
 			</action>
+			<action type="add">
+				hapi-fhir-cli upload-terminology command now has an argument
+				"-b FOO" that lets you add an authorization header in the form
+				<![CDATA[<code>Authorization: Bearer FOO</code>]]>
+			</action>
 		</release>
 		<release version="1.6" date="2016-07-07">
 			<action type="fix">

src/site/xdoc/doc_jpa.xml

@@ -241,6 +241,36 @@ public DaoConfig daoConfig() {
 		
 		<!-- 
 		alter table hfj_res_link ALTER COLUMN "TARGET_RESOURCE_ID" NULL;
+		
+		--select sp_index_status, count(*) from hfj_resource group by sp_index_status
+delete from hfj_history_tag where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_res_tag where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_coords where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_number where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_quantity where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_string where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_token where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_spidx_uri where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_search_result where resource_pid in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_res_link where src_resource_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_res_link where target_resource_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_subscription where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_subscription_flag_res where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+
+
+delete from trm_concept_pc_link where pid in (select pid from trm_concept where codesystem_pid in (select pid from trm_codesystem_ver where res_id in (select res_id from hfj_resource where sp_index_status = 2)));
+delete from trm_concept where codesystem_pid in (select pid from trm_codesystem_ver where res_id in (select res_id from hfj_resource where sp_index_status = 2));
+delete from trm_codesystem_ver where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from trm_codesystem where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+
+update hfj_resource set forced_id_pid = null where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+update hfj_res_ver set forced_id_pid = null where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_forced_id where resource_pid in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_resource where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+delete from hfj_res_ver where res_id in (select res_id from hfj_resource where sp_index_status = 2);
+		
+		
+		
 		 -->
 				
 	</body>

src/site/xdoc/hacking_hapi_fhir.xml

@@ -97,6 +97,41 @@
 [INFO] Total time: 20:45 min
 [INFO] Finished at: 2016-02-27T15:05:35+00:00</pre> 
 			</p>
+			
+			<subsection name="Troubleshooting">
+				
+				<p>
+					If the build fails to execute successfully, try the following:
+				</p>
+				<ul>
+					<li>
+						The first thing to try is always a fresh clean build when things aren't working:<br/>
+						<pre>mvn clean install</pre>
+					</li>
+					<li>
+						<b>If you are trying to build a submodule</b> (e.g. <code>hapi-fhir-jpaserver-example</code>), 
+						try building the root project first. Especially when building from the Git <code>master</code>,
+						often times there will be dependencies that require a fresh complete build (note that this is
+						not generally an issue when building from a release version)<br/>
+						<pre><![CDATA[cd [workspace]/hapi-fhir
+mvn install]]></pre>
+					</li>
+					<li>
+						<b>If the build fails with memory issues (or mysteriously dies during unit tests)</b>,
+						your build environment may be running out of memory. By default, the HAPI build executes
+						unit tests in multiple parallel JVMs in order to save time. This can consume a lot of RAM
+						and sometimes causes issues. Try executing with the following command to disable
+						this behaviour:<br/>
+						<pre>mvn -P ALLMODULES,NOPARALLEL install</pre>
+					</li>
+					<li>
+						If you figure something else out, please <b>let us know</b> so that we can add it
+						to this list!
+					</li>
+				</ul>
+			
+			</subsection>
+			
 		</section>
 		
 		<section name="Importing into Eclipse">