OpenConceptLab/ocl_issues#339 codesystem validate-code operation and …

…code cleanup
OpenConceptLab · Nov 4, 2020 · 0e69a76 · 0e69a76
1 parent 8a8fb9e
commit 0e69a76
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Showing 14 changed files with 272 additions and 118 deletions.
diff --git a/docker-compose.override.yml b/docker-compose.override.yml
@@ -6,11 +6,12 @@ services:
     restart: "no"
     command: sh -c "/code/startup.sh"
     ports:
-      - ${SERVER_PORT-7000}:${SERVER_PORT-7000}
+      - ${SERVER_PORT-8080}:${SERVER_PORT-8080}
     environment:
       - ENVIRONMENT=${ENVIRONMENT-dev}
       - DATABASE_URL=jdbc:postgresql://host.docker.internal:5432/postgres
       - DATABASE_USERNAME=${DATABASE_USERNAME-postgres}
       - DATABASE_PASSWORD=${DATABASE_PASSWORD-Postgres123}
       - DATABASE_DIALECT=${DATABASE_DIALECT-org.hibernate.dialect.ProgressDialect}
-      - SERVER_PORT=${SERVER_PORT-7000}
+      - SERVER_PORT=${SERVER_PORT-8080}
+      - OCL_SERVLET_BASEURL=${OCL_SERVLET_BASEURL-http://localhost:8080/fhir}
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -6,11 +6,12 @@ services:
     restart: "always"
     command: sh -c "/code/startup.sh"
     ports:
-      - ${SERVER_PORT-7000}:${SERVER_PORT-7000}
+      - ${SERVER_PORT-8080}:${SERVER_PORT-8080}
     environment:
       - ENVIRONMENT=${ENVIRONMENT-dev}
       - DATABASE_URL=${DATABASE_URL-jdbc:postgresql://host.docker.internal:5432/postgres}
       - DATABASE_USERNAME=${DATABASE_USERNAME-postgres}
       - DATABASE_PASSWORD=${DATABASE_PASSWORD-Postgres123}
       - DATABASE_DIALECT=${DATABASE_DIALECT-org.hibernate.dialect.ProgressDialect}
-      - SERVER_PORT=${SERVER_PORT-7000}
+      - SERVER_PORT=${SERVER_PORT-8080}
+      - OCL_SERVLET_BASEURL=${OCL_SERVLET_BASEURL-http://localhost:8080/fhir}
diff --git a/ocl-fhir-ts/pom.xml b/ocl-fhir-ts/pom.xml
@@ -142,6 +142,7 @@
 	</dependencies>
 
 	<build>
+		<finalName>oclfhir</finalName>
 		<plugins>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/OclFhirApplication.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/OclFhirApplication.java
@@ -16,9 +16,13 @@
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.autoconfigure.domain.EntityScan;
 import org.springframework.boot.autoconfigure.web.servlet.error.ErrorMvcAutoConfiguration;
+import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.web.servlet.ServletComponentScan;
+import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.ComponentScan;
+import org.springframework.context.annotation.PropertySource;
+import org.springframework.context.annotation.PropertySources;
 import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 
 import javax.annotation.PostConstruct;
@@ -39,7 +43,12 @@
 })
 @EnableJpaRepositories(basePackageClasses = {ConceptRepository.class})
 @EntityScan(basePackageClasses = {BaseOclEntity.class})
-public class OclFhirApplication {
+public class OclFhirApplication extends SpringBootServletInitializer {
+
+    @Override
+    protected SpringApplicationBuilder configure(SpringApplicationBuilder builder) {
+        return builder.sources(OclFhirApplication.class);
+    }
 
     UserProfile oclUser = null;
 

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/OclFhirRestfulServer.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/OclFhirRestfulServer.java
@@ -14,6 +14,8 @@
 import org.openconceptlab.fhir.provider.ValueSetResourceProvider;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.PropertySource;
+import org.springframework.context.annotation.PropertySources;
 import org.springframework.stereotype.Component;
 
 /**
@@ -24,20 +26,24 @@
 @WebServlet(urlPatterns = "/fhir/*", loadOnStartup = 1)
 public class OclFhirRestfulServer extends RestfulServer {
 
-	@Autowired
 	private CodeSystemResourceProvider codeSystemResourceProvider;
-
-	@Autowired
 	private ValueSetResourceProvider valueSetResourceProvider;
-
-	@Autowired
 	private OclCapabilityStatementProvider oclCapabilityStatementProvider;
+	private OclFhirAuthorizationInterceptor oclFhirAuthorizationInterceptor;
+	private OclFhirLoggingInterceptor oclFhirLoggingInterceptor;
 
 	@Autowired
-	OclFhirAuthorizationInterceptor oclFhirAuthorizationInterceptor;
-
-	@Autowired
-	OclFhirLoggingInterceptor oclFhirLoggingInterceptor;
+	public OclFhirRestfulServer(CodeSystemResourceProvider codeSystemResourceProvider,
+								ValueSetResourceProvider valueSetResourceProvider,
+								OclCapabilityStatementProvider oclCapabilityStatementProvider,
+								OclFhirAuthorizationInterceptor oclFhirAuthorizationInterceptor,
+								OclFhirLoggingInterceptor oclFhirLoggingInterceptor) {
+		this.codeSystemResourceProvider = codeSystemResourceProvider;
+		this.valueSetResourceProvider = valueSetResourceProvider;
+		this.oclCapabilityStatementProvider = oclCapabilityStatementProvider;
+		this.oclFhirAuthorizationInterceptor = oclFhirAuthorizationInterceptor;
+		this.oclFhirLoggingInterceptor = oclFhirLoggingInterceptor;
+	}
 
 	@Value("${ocl.servlet.baseurl}")
 	private String baseUrl;

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/config/Config.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/config/Config.java
@@ -2,9 +2,6 @@
 
 import org.hibernate.boot.model.naming.ImplicitNamingStrategy;
 import org.hibernate.boot.model.naming.ImplicitNamingStrategyLegacyJpaImpl;
-import org.openconceptlab.fhir.model.UserProfile;
-import org.openconceptlab.fhir.repository.UserRepository;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/controller/OclFhirController.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/controller/OclFhirController.java
@@ -65,15 +65,33 @@ public ResponseEntity<String> lookUpCodeSystemsByOrg(@PathVariable String org,
                                          @RequestParam(name = CODE) String code,
                                          @RequestParam(name = VERSION, required = false) String version,
                                          @RequestParam(name = DISP_LANG, required = false) String displayLanguage) {
-        Parameters parameters = generateParameters(system, code, version, displayLanguage, formatOrg(org));
-        return handleLookup(parameters);
+        Parameters parameters = lookupParameters(system, code, version, displayLanguage, formatOrg(org));
+        return handleFhirOperation(parameters, CodeSystem.class, LOOKUP);
     }
 
     @PostMapping(path = {"/orgs/{org}/CodeSystem/$lookup"}, produces = {MediaType.APPLICATION_JSON_VALUE})
     public ResponseEntity<String> lookUpCodeSystemsByOrg(@PathVariable String org, @RequestBody String parameters){
         Parameters params = (Parameters) getResource(parameters);
-        params.addParameter().setName(PROPERTY).setValue(new StringType(formatOrg(org)));
-        return handleLookup(params);
+        params.addParameter().setName(OWNER).setValue(newStringType(formatOrg(org)));
+        return handleFhirOperation(params, CodeSystem.class, LOOKUP);
+    }
+
+    @GetMapping(path = {"/orgs/{org}/CodeSystem/$validate-code"}, produces = {MediaType.APPLICATION_JSON_VALUE})
+    public ResponseEntity<String> validateCodeSystemsByOrg(@PathVariable String org,
+                                                           @RequestParam(name = URL) String url,
+                                                           @RequestParam(name = CODE) String code,
+                                                           @RequestParam(name = VERSION, required = false) String version,
+                                                           @RequestParam(name = DISPLAY, required = false) String display,
+                                                           @RequestParam(name = DISP_LANG, required = false) String displayLanguage) {
+        Parameters parameters = validateCodeParameters(url, code, version, display, displayLanguage, formatOrg(org));
+        return handleFhirOperation(parameters, CodeSystem.class, VALIDATE_CODE);
+    }
+
+    @PostMapping(path = {"/orgs/{org}/CodeSystem/$validate-code"}, produces = {MediaType.APPLICATION_JSON_VALUE})
+    public ResponseEntity<String> validateCodeSystemsByOrg(@PathVariable String org, @RequestBody String parameters){
+        Parameters params = (Parameters) getResource(parameters);
+        params.addParameter().setName(OWNER).setValue(newStringType(formatOrg(org)));
+        return handleFhirOperation(params, CodeSystem.class, VALIDATE_CODE);
     }
 
     @GetMapping(path = {"/orgs/{org}/ValueSet/{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE})
@@ -120,15 +138,33 @@ public ResponseEntity<String> lookUpCodeSystemsByUser(@PathVariable String user,
                                                          @RequestParam(name = CODE) String code,
                                                          @RequestParam(name = VERSION, required = false) String version,
                                                          @RequestParam(name = DISP_LANG, required = false) String displayLanguage) {
-        Parameters parameters = generateParameters(system, code, version, displayLanguage, formatUser(user));
-        return handleLookup(parameters);
+        Parameters parameters = lookupParameters(system, code, version, displayLanguage, formatUser(user));
+        return handleFhirOperation(parameters, CodeSystem.class, LOOKUP);
     }
 
     @PostMapping(path = {"/users/{user}/CodeSystem/$lookup"}, produces = {MediaType.APPLICATION_JSON_VALUE})
     public ResponseEntity<String> lookUpCodeSystemsByUser(@PathVariable String user, @RequestBody String parameters){
         Parameters params = (Parameters) getResource(parameters);
-        params.addParameter().setName(PROPERTY).setValue(new StringType(formatUser(user)));
-        return handleLookup(params);
+        params.addParameter().setName(OWNER).setValue(newStringType(formatUser(user)));
+        return handleFhirOperation(params, CodeSystem.class, LOOKUP);
+    }
+
+    @GetMapping(path = {"/users/{user}/CodeSystem/$validate-code"}, produces = {MediaType.APPLICATION_JSON_VALUE})
+    public ResponseEntity<String> validateCodeSystemsByUser(@PathVariable String user,
+                                                           @RequestParam(name = URL) String url,
+                                                           @RequestParam(name = CODE) String code,
+                                                           @RequestParam(name = VERSION, required = false) String version,
+                                                           @RequestParam(name = DISPLAY, required = false) String display,
+                                                           @RequestParam(name = DISP_LANG, required = false) String displayLanguage) {
+        Parameters parameters = validateCodeParameters(url, code, version, display, displayLanguage, formatUser(user));
+        return handleFhirOperation(parameters, CodeSystem.class, VALIDATE_CODE);
+    }
+
+    @PostMapping(path = {"/users/{user}/CodeSystem/$validate-code"}, produces = {MediaType.APPLICATION_JSON_VALUE})
+    public ResponseEntity<String> validateCodeSystemsByUser(@PathVariable String user, @RequestBody String parameters){
+        Parameters params = (Parameters) getResource(parameters);
+        params.addParameter().setName(OWNER).setValue(newStringType(formatUser(user)));
+        return handleFhirOperation(params, CodeSystem.class, VALIDATE_CODE);
     }
 
     @GetMapping(path = {"/users/{user}/ValueSet/{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE})
@@ -161,9 +197,9 @@ private ResponseEntity<String> handleSearchResource(final Class<? extends Metada
         }
     }
 
-    private ResponseEntity<String> handleLookup(Parameters parameters) {
+    private ResponseEntity<String> handleFhirOperation(Parameters parameters, Class<? extends Resource> type, String operation) {
         try {
-            return ResponseEntity.ok(oclFhirUtil.getResourceAsString(lookUpCodeSystem(parameters)));
+            return ResponseEntity.ok(oclFhirUtil.getResourceAsString(performFhirOperation(parameters, type, operation)));
         } catch (ResourceNotFoundException e) {
             return notFound(e.getStatusCode(), e.getResponseBody());
         } catch (Exception e) {
@@ -186,24 +222,38 @@ private String searchResource(final Class<? extends MetadataResource> resourceCl
         return oclFhirUtil.getResourceAsString(bundle);
     }
 
-    private Parameters lookUpCodeSystem(Parameters parameters) {
+    private Parameters performFhirOperation(Parameters parameters, Class<? extends Resource> type, String operation) {
         return oclFhirUtil.getClient()
                 .operation()
-                .onType(CodeSystem.class)
-                .named(LOOKUP)
+                .onType(type)
+                .named(operation)
                 .withParameters(parameters)
                 .execute();
     }
 
-    private Parameters generateParameters(String system, String code, String version, String displayLanguage, String owner) {
+    private Parameters generateParameters(String code, String version, String displayLanguage, String owner) {
         Parameters parameters = new Parameters();
-        parameters.addParameter().setName(SYSTEM).setValue(new UriType(system));
         parameters.addParameter().setName(CODE).setValue(new CodeType(code));
         if (isValid(version))
-            parameters.addParameter().setName(VERSION).setValue(new StringType(version));
+            parameters.addParameter().setName(VERSION).setValue(newStringType(version));
         if (isValid(displayLanguage))
             parameters.addParameter().setName(DISP_LANG).setValue(new CodeType(displayLanguage));
-        parameters.addParameter().setName(PROPERTY).setValue(new StringType(owner));
+        parameters.addParameter().setName(OWNER).setValue(newStringType(owner));
+        return parameters;
+    }
+
+    private Parameters lookupParameters(String system, String code, String version, String displayLanguage, String owner) {
+        Parameters parameters = generateParameters(code, version, displayLanguage, owner);
+        parameters.addParameter().setName(SYSTEM).setValue(new UriType(system));
+        return parameters;
+    }
+
+    private Parameters validateCodeParameters(String url, String code, String version, String display, String displayLanguage,
+                                              String owner) {
+        Parameters parameters = generateParameters(code, version, displayLanguage, owner);
+        parameters.addParameter().setName(URL).setValue(new UriType(url));
+        if (isValid(display))
+            parameters.addParameter().setName(DISPLAY).setValue(newStringType(display));
         return parameters;
     }