honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Refactor CLI to extract commands

This commit is contained in:
James Agnew 2018-04-30 15:04:35 -04:00
parent d85efbaa5b
commit 392feb7082
36 changed files with 246 additions and 200 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

21
hapi-deployable-pom/pom.xml
View File

@ -115,10 +115,31 @@
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-jcl</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.findbugs</groupId>
<artifactId>annotations</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbynet</artifactId>
</dependency>
<dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derbyclient</artifactId>
</dependency>
</ignoredDependencies>
<ignoredResourcePatterns>
<ignoredResourcePattern>changelog.txt</ignoredResourcePattern>
<ignoredResource>javac.bat</ignoredResource>
<ignoredResource>about.html</ignoredResource>
</ignoredResourcePatterns>
</configuration>
</plugin>

214
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml Normal file
View File

@ -0,0 +1,214 @@
<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">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>3.4.0-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<artifactId>hapi-fhir-cli-api</artifactId>
<packaging>jar</packaging>
<name>HAPI FHIR - Command Line Client - API</name>
<dependencies>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
<version>${project.version}</version>
<type>jar</type>
<classifier>classes</classifier>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.14</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-igpacks</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-commons</artifactId>
</dependency>
<!--
These have been added as explicit dependencies
as JDK9 no longer includes them by default
-->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
<dependency>
<groupId>org.fusesource.jansi</groupId>
<artifactId>jansi</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
</plugins>
</build>
</project>

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/App.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/App.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/BaseApp.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseApp.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/BaseCommand.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BaseCommand.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/CommandFailureException.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/CommandFailureException.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ExampleDataUploader.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/IgPackUploader.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/IgPackUploader.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu2.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu2.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportDstu3.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportR4.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/LoadingValidationSupportR4.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/RunServerCommand.java
View File

21
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/UploadTerminologyCommand.java
View File

@ -37,28 +37,13 @@ public class UploadTerminologyCommand extends BaseCommand {
@Override
public Options getOptions() {
Options options = new Options();
Option opt;
addFhirVersionOption(options);
opt = new Option("t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
opt.setRequired(true);
options.addOption(opt);
opt = new Option("u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
opt.setRequired(false);
options.addOption(opt);
opt = new Option("d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
opt.setRequired(false);
options.addOption(opt);
addRequiredOption(options, "t", "target", true, "Base URL for the target server (e.g. \"http://example.com/fhir\")");
addRequiredOption(options, "u", "url", true, "The code system URL associated with this upload (e.g. " + IHapiTerminologyLoaderSvc.SCT_URI + ")");
addOptionalOption(options, "d", "data", true, "Local file to use to upload (can be a raw file or a ZIP containing the raw file)");
addBasicAuthOption(options);
opt = new Option("v", "verbose", false, "Verbose output");
opt.setRequired(false);
options.addOption(opt);
return options;
}

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidateCommand.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/ValidationDataUploader.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java → hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/WebsocketSubscribeCommand.java
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/resources/logback-cli-off.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-off.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/resources/logback-cli-on.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/main/resources/logback-cli-on.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/script/hapi-fhir-cli → hapi-fhir-cli/hapi-fhir-cli-api/src/main/script/hapi-fhir-cli
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/main/script/hapi-fhir-cli.cmd → hapi-fhir-cli/hapi-fhir-cli-api/src/main/script/hapi-fhir-cli.cmd
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/java/ca/uhn/fhir/cli/InstallIgPackTest.java → hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/InstallIgPackTest.java
View File

4
hapi-fhir-cli/hapi-fhir-cli-app/src/test/java/ca/uhn/fhir/cli/OptionsTest.java → hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/OptionsTest.java
View File

@ -6,6 +6,10 @@ public class OptionsTest {
@Test
public void testOptions() {
UploadTerminologyCommand uploadTerminologyCommand = new UploadTerminologyCommand();
uploadTerminologyCommand.getOptions();
App app = new App();
for (BaseCommand next : app.provideCommands()) {
next.getOptions();

2
hapi-fhir-cli/hapi-fhir-cli-app/src/test/java/ca/uhn/fhir/cli/ValidateTest.java → hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/ValidateTest.java
View File

@ -8,7 +8,7 @@ public class ValidateTest {
@Before
public void before() {
System.setProperty("noexit", "true");
System.setProperty("test", "true");
}
@Test

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-address-official.dstu2.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-address-official.dstu2.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-address.dstu2.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-address.dstu2.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-humanname-familyname-prefix.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-humanname-familyname-prefix.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-humanname-familyname.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-humanname-familyname.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-humanname.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-humanname.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/nl-core-patient.dstu2.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/nl-core-patient.dstu2.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/patient-example-a.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/patient-example-a.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/nl/validate.sh → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/nl/validate.sh
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/patient-uslab-example1.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/patient-uslab-example1.xml
View File

0
hapi-fhir-cli/hapi-fhir-cli-app/src/test/resources/uslab-patient.profile.xml → hapi-fhir-cli/hapi-fhir-cli-api/src/test/resources/uslab-patient.profile.xml
View File

181
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
View File

@ -17,17 +17,6 @@
<dependencies>
<!-- This dependency includes the core HAPI-FHIR classes -->
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-jpaserver-base</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli-jpaserver</artifactId>
@ -48,176 +37,6 @@
<classifier>classes</classifier>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>1.14</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-igpacks</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</dependency>
<dependency>
<groupId>javax.servlet</groupId>
<artifactId>javax.servlet-api</artifactId>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-core</artifactId>
<exclusions>
<exclusion>
<artifactId>commons-logging</artifactId>
<groupId>commons-logging</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-webmvc</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context</artifactId>
<exclusions>
<exclusion>
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-beans</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-tx</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-context-support</artifactId>
</dependency>
<dependency>
<groupId>org.springframework</groupId>
<artifactId>spring-web</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlets</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-server</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-util</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-webapp</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-client</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf</artifactId>
</dependency>
<dependency>
<groupId>org.thymeleaf</groupId>
<artifactId>thymeleaf-spring4</artifactId>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-schematron</artifactId>
<exclusions>
<exclusion>
<artifactId>Saxon-HE</artifactId>
<groupId>net.sf.saxon</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>com.phloc</groupId>
<artifactId>phloc-commons</artifactId>
</dependency>
<!--
These have been added as explicit dependencies
as JDK9 no longer includes them by default
-->
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-core</artifactId>
</dependency>
<dependency>
<groupId>com.sun.xml.bind</groupId>
<artifactId>jaxb-impl</artifactId>
</dependency>
<dependency>
<groupId>org.fusesource.jansi</groupId>
<artifactId>jansi</artifactId>
</dependency>
</dependencies>
<build>

1
hapi-fhir-cli/pom.xml
View File

@ -16,6 +16,7 @@
<modules>
<module>hapi-fhir-cli-jpaserver</module>
<module>hapi-fhir-cli-api</module>
<module>hapi-fhir-cli-app</module>
</modules>

2
pom.xml
View File

@ -40,6 +40,7 @@
</scm>
<repositories>
<!--
<repository>
<snapshots>
<enabled>false</enabled>
@ -52,6 +53,7 @@
<id>jitpack.io</id>
<url>https://jitpack.io</url>
</repository>
-->
</repositories>
<description>