Add documentation for CLI
This commit is contained in:
jamesagnew
parent
b827823004
commit
0ab8ee386f
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@ -8,7 +8,7 @@
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</encoder>
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</appender>
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<logger name="ca.uhn.fhir.cli" additivity="false" level="info">
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<logger name="ca.uhn.fhir" additivity="false" level="info">
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<appender-ref ref="STDOUT" />
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</logger>
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@ -1,8 +1,8 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the site. I don't know why this works...
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Need to investigate this. -->
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<!-- The parent of this project is the deployable POM. This project isn't deployable, but this keeps it before the root pom in the reactor order when building the
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site. I don't know why this works... Need to investigate this. -->
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-deployable-pom</artifactId>
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@ -321,10 +321,11 @@
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</execution>
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</executions>
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</plugin>
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<!-- <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>cobertura-maven-plugin</artifactId> <version>${maven_cobertura_plugin_version}</version> <configuration> <check> <branchRate>85</branchRate>
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<lineRate>85</lineRate> <haltOnFailure>true</haltOnFailure> <totalBranchRate>85</totalBranchRate> <totalLineRate>85</totalLineRate> <packageLineRate>85</packageLineRate> <packageBranchRate>85</packageBranchRate>
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<regexes> <regex> <pattern>com.example.reallyimportant.*</pattern> <branchRate>90</branchRate> <lineRate>80</lineRate> </regex> <regex> <pattern>com.example.boringcode.*</pattern> <branchRate>40</branchRate>
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<lineRate>30</lineRate> </regex> </regexes> </check> </configuration> <executions> <execution> <goals> <goal>clean</goal> <goal>check</goal> </goals> </execution> </executions> </plugin> -->
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<!-- <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>cobertura-maven-plugin</artifactId> <version>${maven_cobertura_plugin_version}</version> <configuration>
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<check> <branchRate>85</branchRate> <lineRate>85</lineRate> <haltOnFailure>true</haltOnFailure> <totalBranchRate>85</totalBranchRate> <totalLineRate>85</totalLineRate>
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<packageLineRate>85</packageLineRate> <packageBranchRate>85</packageBranchRate> <regexes> <regex> <pattern>com.example.reallyimportant.*</pattern> <branchRate>90</branchRate>
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<lineRate>80</lineRate> </regex> <regex> <pattern>com.example.boringcode.*</pattern> <branchRate>40</branchRate> <lineRate>30</lineRate> </regex> </regexes> </check>
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</configuration> <executions> <execution> <goals> <goal>clean</goal> <goal>check</goal> </goals> </execution> </executions> </plugin> -->
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</plugins>
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<resources>
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</resources>
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@ -109,6 +109,7 @@
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<descriptor>${project.basedir}/src/assembly/hapi-fhir-android-distribution.xml</descriptor>
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<descriptor>${project.basedir}/src/assembly/hapi-fhir-cli.xml</descriptor>
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</descriptors>
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<finalName>hapi-fhir-${project.version}</finalName>
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</configuration>
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</execution>
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</executions>
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@ -25,6 +25,7 @@
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<include>hapi-fhir-cli</include>
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<include>hapi-fhir-cli.cmd</include>
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</includes>
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<fileMode>0555</fileMode>
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</fileSet>
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</fileSets>
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@ -343,8 +343,10 @@
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<targetResourceSpringBeansFile>hapi-fhir-server-resourceproviders-dstu2.xml</targetResourceSpringBeansFile>
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<baseResourceNames></baseResourceNames>
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<excludeResourceNames>
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<!--
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<excludeResourceName>OperationDefinition</excludeResourceName>
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<excludeResourceName>OperationOutcome</excludeResourceName>
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-->
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</excludeResourceNames>
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</configuration>
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</execution>
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@ -1,42 +0,0 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<persistence xmlns="http://java.sun.com/xml/ns/persistence"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
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version="2.0">
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<persistence-unit name="FHIR_UT" transaction-type="RESOURCE_LOCAL">
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<provider>org.hibernate.ejb.HibernatePersistence</provider>
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<class>ca.uhn.fhir.jpa.entity.ForcedId</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTable</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceHistoryTag</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceLink</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceTable</class>
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<class>ca.uhn.fhir.jpa.entity.ResourceTag</class>
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<class>ca.uhn.fhir.jpa.entity.SubscriptionTable</class>
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<class>ca.uhn.fhir.jpa.entity.SubscriptionFlaggedResource</class>
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<class>ca.uhn.fhir.jpa.entity.TagDefinition</class>
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<class>ca.uhn.fhir.jpa.entity.Search</class>
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<class>ca.uhn.fhir.jpa.entity.SearchResult</class>
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<exclude-unlisted-classes>true</exclude-unlisted-classes>
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<properties>
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<property name="hibernate.dialect" value="ca.uhn.fhir.jpa.util.HapiDerbyTenSevenDialect" />
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<property name="hibernate.hbm2ddl.auto" value="update" />
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<property name="hibernate.jdbc.batch_size" value="20" />
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<property name="hibernate.cache.use_minimal_puts" value="true" />
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<property name="hibernate.show_sql" value="false" />
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<property name="hibernate.cache.use_query_cache" value="false" />
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<property name="hibernate.cache.use_second_level_cache" value="false" />
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<property name="hibernate.cache.use_structured_entries" value="false" />
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</properties>
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</persistence-unit>
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</persistence>
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@ -12,7 +12,7 @@
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<context:annotation-config />
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<context:mbean-server />
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<bean depends-on="dbServer" id="myPersistenceDataSource" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">
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<bean depends-on="dbServer" id="myPersistenceDataSourceDstu1" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">
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<!-- ;create=true /opt/glassfish/glassfish4/glassfish/nodes/localhost-domain1/fhirtest/fhirdb -->
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<!-- <property name="url" value="jdbc:hsqldb:hsql://localhost/uhnfhirdb"/>-->
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<!-- <property name="url" value="jdbc:derby:directory:#{systemproperties['fhir.db.location']};create=true" /> -->
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</bean>
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<bean depends-on="dbServer" id="entityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
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<property name="dataSource" ref="myPersistenceDataSource" />
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<property name="dataSource" ref="myPersistenceDataSourceDstu1" />
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<!--
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<property name="persistenceXmlLocation" value="classpath:META-INF/fhirtest_persistence.xml" />
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-->
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<context:annotation-config />
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<context:mbean-server />
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<bean depends-on="dbServer" id="myPersistenceDataSource" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">
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<bean depends-on="dbServer" id="myPersistenceDataSourceDstu2" class="org.apache.commons.dbcp2.BasicDataSource" destroy-method="close">
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<property name="driverClassName" value="org.apache.derby.jdbc.ClientDriver"></property>
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<property name="url" value="jdbc:derby://localhost:1527/#{systemProperties['fhir.db.location.dstu2']};create=true" />
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<property name="username" value="SA" />
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value="sa"/> <property name="testOnBorrow" value="true"/> <property name="validationQuery" value="select 1;"/> </bean> -->
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<bean depends-on="dbServer" id="entityManagerFactory" class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
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<property name="dataSource" ref="myPersistenceDataSource" />
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<property name="dataSource" ref="myPersistenceDataSourceDstu2" />
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<!--
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<property name="persistenceXmlLocation" value="classpath:META-INF/fhirtest_persistence.xml" />
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-->
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<entry key="hibernate.cache.use_structured_entries" value="false" />
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<entry key="hibernate.search.default.directory_provider" value="filesystem" />
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<entry key="hibernate.search.default.indexBase" value="#{systemProperties['fhir.lucene.location.dstu2']};" />
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<entry key="hibernate.search.lucene_version" value="LUCENE_CURRENT" />
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</map>
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</property>
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</bean>
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@ -24,20 +24,6 @@
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<ref bean="myLoggingInterceptor"/>
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</util:list>
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<!--
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<bean class="ca.uhn.fhirtest.HsqldbServer" id="dbServer" init-method="start">
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<constructor-arg>
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<value>
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server.database.0=file:#{systemProperties['fhir.db.location']}/hsql-fhir-db
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server.dbname.0=uhnfhirdb
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server.remote_open=true
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hsqldb.reconfig_logging=false
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hsqldb.default_table_type=cached
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</value>
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</constructor-arg>
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</bean>
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-->
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<!--for mysql-->
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<!--
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<bean id="dbServer" class="ca.uhn.fhirtest.MySqlServer">
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@ -30,8 +30,8 @@ public class UhnFhirTestApp {
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System.setProperty("fhir.db.location", "./target/testdb");
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System.setProperty("fhir.db.location.dstu2", "./target/testdb_dstu2");
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System.setProperty("fhir.lucene.location.dstu2", "./target/testlucene_dstu2");
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System.setProperty("fhir.baseurl.dstu1", base + "Dstu1");
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System.setProperty("fhir.baseurl.dstu2", base + "Dstu1");
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System.setProperty("fhir.baseurl.dstu1", base.replace("Dstu2", "Dstu1"));
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System.setProperty("fhir.baseurl.dstu2", base);
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Server server = new Server(myPort);
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2
pom.xml
2
pom.xml
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<maven.build.timestamp.format>yyyy-MM-dd'T'HH:mm:ss'Z'</maven.build.timestamp.format>
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<!-- This property is used in some of the site documentation where the version is shown, so that we can deploy the site even if the project is on a snapshot version. -->
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<hapi_stable_version>1.1</hapi_stable_version>
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<hapi_stable_version>1.2</hapi_stable_version>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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@ -74,6 +74,7 @@
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<menu name="Using HAPI" inherit="bottom" >
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<item name="Documentation Index" href="./docindex.html"/>
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<item name="Command Line Tool (cli)" href="./doc_cli.html" />
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</menu>
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<menu name="Documentation" inherit="top" >
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<item name="Model API (RI DSTU2)" href="./apidocs-hl7org-dstu2/index.html" />
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<item name="JPA Server API" href="./apidocs-jpaserver/index.html" />
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</item>
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<item name="Command Line Tool (hapi-fhir-cli)" href="./doc_cli.html" />
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<item name="Maven Plugin (hapi-tinder-plugin)" href="./doc_tinder.html" />
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</menu>
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@ -0,0 +1,97 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<document xmlns="http://maven.apache.org/XDOC/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/XDOC/2.0 http://maven.apache.org/xsd/xdoc-2.0.xsd">
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<properties>
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<title>Command Line Tool</title>
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<author email="jamesagnew@users.sourceforge.net">James Agnew</author>
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</properties>
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<body>
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<section name="Command Line Tool for HAPI FHIR">
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<p>
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<b>hapi-fhir-cli</b> is the HAPI FHIR Command Line tool. It features a number of HAPI's
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built-in features as easy to use command line options.
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</p>
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<subsection name="Download and Installation">
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<p>
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You can get the tool by downloading it from our
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<a href="https://github.com/jamesagnew/hapi-fhir/releases">GitHub Releases</a> page
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(look for the archive named <code>hapi-fhir-[version]-cli.tar.bz2</code> or <code>.zip</code> on Windows).
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</p>
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<p>
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When you have downloaded the archive (either ZIP or tar.bz2), expand it into a directory
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where you will keep it, and add this directory to your path.
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</p>
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<p>
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You can now try the tool out by executing the following command: <code>hapi-fhir-cli</code>
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This command should show a help screen, as shown in the screeenshot below.
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</p>
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<img src="./images/hapi-fhir-cli.png" alt="Basic screen shot" style="margin-left: 40px;"/>
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</subsection>
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<subsection name="Troubleshooting">
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<p>
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The tool should work correctly on any system that has Java 6 (or newer) installed. If
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it is not working correctly, first try the following command to test if Java is installed:<br/>
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<code>$ java -version</code>
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</p>
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<p>
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If this command does not produce output similar to the following, you should install/reinstall
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Java.<br/>
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<pre><![CDATA[$ java -version
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java version "1.8.0_60"
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Java(TM) SE Runtime Environment (build 1.8.0_60-b27)
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Java HotSpot(TM) 64-Bit Server VM (build 25.60-b23, mixed mode)]]></pre>
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</p>
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<p>
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If this does not help, please post a question on our
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<a href="https://groups.google.com/d/forum/hapi-fhir">Google Group</a>.
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</p>
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</subsection>
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</section>
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<section name="Server (run-server)">
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<p>
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The CLI tool can be used to start a local, fully functional FHIR server which you can use
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for testing. To start this server, simply issue the command <code>hapi-fhir-cli run-server</code>
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as shown in the example below:
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</p>
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<img src="./images/hapi-fhir-cli-run-server.png" alt="Run Server" style="margin-left: 40px;"/>
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<p>
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Once the server has started, you can access the testing webpage by pointing your
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browser at <a href="http://localhost:8080/">http://localhost:8080/</a>. The FHIR
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server base URL will be <a href="http://localhost:8080/baseDstu2/">http://localhost:8080/baseDstu2/</a>.
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</p>
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<p>
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Note that by default this server will not be populated with any resources at all. You can
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easily populate it with the FHIR example resources by <b>leaving it running</b> and opening
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a second terminal window, then using the <code>hapi-fhir-cli upload-examples</code> command
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(see the section below).
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</p>
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<p>
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The server uses a local Derby database instance for storage. You may want to execute
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this command in an empty directory, which you can clear if you want to reset the server.
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</p>
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</section>
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<section name="Upload Example Resources (upload-examples)">
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<p>
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The <b>upload-examples</b> command downloads the complete set of FHIR example resources from
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the HL7 website, and uploads them to a server of your choice. This can be useful to
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populate a server with test data.
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</p>
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<p>
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To execute this command, uploading test resources to a local CLI server, issue
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the following: <code>hapi-fhir-cli upload-examples -t http://localhost:8080/baseDstu2</code>
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</p>
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<p>
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Note that this command may take a surprisingly long time to complete because of the
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large number of examples.
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</p>
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</section>
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</body>
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</document>
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@ -54,6 +54,8 @@
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<li><a href="./doc_rest_etag.html">ETags</a></li>
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<li><a href="./doc_jpa.html">JPA/Database Server</a></li>
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<li><a href="./doc_tinder.html">Maven Plugin (hapi-tinder-plugin)</a></li>
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<li><a href="./doc_cli.html">Command Line Tool (hapi-fhir-cli)</a></li>
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</ul>
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<h4>JavaDocs</h4>
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