-
Notifications
You must be signed in to change notification settings - Fork 98
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'develop' into TASK-7134
- Loading branch information
Showing
19 changed files
with
939 additions
and
27 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
8 changes: 8 additions & 0 deletions
8
opencga-server/src/main/java/org/opencb/opencga/server/generator/commons/ApiCommons.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| package org.opencb.opencga.server.generator.commons; | ||
|
|
||
| import java.util.List; | ||
|
|
||
| public interface ApiCommons { | ||
|
|
||
| public List<Class<?>> getApiClasses(); | ||
| } |
39 changes: 39 additions & 0 deletions
39
opencga-server/src/main/java/org/opencb/opencga/server/generator/commons/ApiCommonsImpl.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| package org.opencb.opencga.server.generator.commons; | ||
|
|
||
| import org.opencb.opencga.server.rest.*; | ||
| import org.opencb.opencga.server.rest.admin.AdminWSServer; | ||
| import org.opencb.opencga.server.rest.analysis.AlignmentWebService; | ||
| import org.opencb.opencga.server.rest.analysis.ClinicalWebService; | ||
| import org.opencb.opencga.server.rest.analysis.VariantWebService; | ||
| import org.opencb.opencga.server.rest.ga4gh.Ga4ghWSServer; | ||
| import org.opencb.opencga.server.rest.operations.VariantOperationWebService; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| public class ApiCommonsImpl implements ApiCommons { | ||
|
|
||
| public List<Class<?>> getApiClasses(){ | ||
| List<Class<?>> classes = new ArrayList<>(); | ||
| classes.add(OrganizationWSServer.class); | ||
| classes.add(UserWSServer.class); | ||
| classes.add(ProjectWSServer.class); | ||
| classes.add(StudyWSServer.class); | ||
| classes.add(FileWSServer.class); | ||
| classes.add(JobWSServer.class); | ||
| classes.add(SampleWSServer.class); | ||
| classes.add(IndividualWSServer.class); | ||
| classes.add(FamilyWSServer.class); | ||
| classes.add(CohortWSServer.class); | ||
| classes.add(PanelWSServer.class); | ||
| classes.add(AlignmentWebService.class); | ||
| classes.add(VariantWebService.class); | ||
| classes.add(ClinicalWebService.class); | ||
| classes.add(VariantOperationWebService.class); | ||
| classes.add(MetaWSServer.class); | ||
| classes.add(Ga4ghWSServer.class); | ||
| classes.add(AdminWSServer.class); | ||
|
|
||
| return classes; | ||
| } | ||
| } |
209 changes: 209 additions & 0 deletions
209
...erver/src/main/java/org/opencb/opencga/server/generator/openapi/JsonOpenApiGenerator.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,209 @@ | ||
| package org.opencb.opencga.server.generator.openapi; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.glassfish.jersey.media.multipart.FormDataParam; | ||
| import org.opencb.opencga.core.common.GitRepositoryState; | ||
| import org.opencb.opencga.core.tools.annotations.*; | ||
| import org.opencb.opencga.server.generator.commons.ApiCommons; | ||
| import org.opencb.opencga.server.generator.models.RestParameter; | ||
| import org.opencb.opencga.server.generator.openapi.models.*; | ||
| import org.opencb.opencga.server.generator.openapi.common.SwaggerDefinitionGenerator; | ||
|
|
||
| import javax.ws.rs.*; | ||
| import java.util.*; | ||
|
|
||
| public class JsonOpenApiGenerator { | ||
|
|
||
| public Swagger generateJsonOpenApi(ApiCommons apiCommons, String token, String environment) { | ||
| List<Class<?>> classes = apiCommons.getApiClasses(); | ||
| List<Class<?>> beansDefinitions= new ArrayList<>(); | ||
| Swagger swagger = new Swagger(); | ||
| Info info = new Info(); | ||
| info.setTitle("OpenCGA RESTful Web Services"); | ||
| info.setDescription("OpenCGA RESTful Web Services API"); | ||
| info.setVersion(GitRepositoryState.getInstance().getBuildVersion()); | ||
| swagger.setInfo(info); | ||
| swagger.setHost("test.app.zettagenomics.com"); | ||
| swagger.setBasePath(environment + "/opencga/webservices/rest"); | ||
| List<String> schemes = new ArrayList<>(); | ||
| schemes.add("https"); | ||
| swagger.setSchemes(schemes); | ||
| Map<String, Map<String, Method>> paths = new HashMap<>(); | ||
| List<Tag> tags = new ArrayList<>(); | ||
|
|
||
| // Configuración del esquema Bearer | ||
| Map<String, Map<String, Object>> securityDefinitions = new HashMap<>(); | ||
| Map<String, Object> bearerAuth = new HashMap<>(); | ||
| bearerAuth.put("type", "apiKey"); | ||
| bearerAuth.put("name", "Authorization"); | ||
| bearerAuth.put("in", "header"); | ||
| bearerAuth.put("description", "Use 'Bearer <token>' to authenticate"); | ||
| securityDefinitions.put("BearerAuth", bearerAuth); | ||
| swagger.setSecurityDefinitions(securityDefinitions); | ||
| for (Class<?> clazz : classes) { | ||
| Api api = clazz.getAnnotation(Api.class); | ||
| if (api == null) { | ||
| continue; | ||
| } | ||
| tags.add(new Tag(api.value(), api.description())); | ||
|
|
||
| // Obtener ruta base de la clase | ||
| javax.ws.rs.Path classPathAnnotation = clazz.getAnnotation(javax.ws.rs.Path.class); | ||
| String basePath = classPathAnnotation.value(); | ||
| if (classPathAnnotation == null) { | ||
| continue; | ||
| } | ||
|
|
||
| // Procesar métodos | ||
| for (java.lang.reflect.Method wsmethod : clazz.getDeclaredMethods()) { | ||
| ApiOperation apiOperation = wsmethod.getAnnotation(ApiOperation.class); | ||
| if (apiOperation != null) { | ||
| // Crear operación Swagger | ||
| Method method = new Method(); | ||
| method.setSummary(apiOperation.value()); | ||
| method.setDescription(apiOperation.notes()); | ||
| method.setTags(Collections.singletonList(api.value())); | ||
| Map<String,Object> responses=new HashMap<>(); | ||
| responses.put("type", String.valueOf(apiOperation.response())); | ||
| if(apiOperation.response() instanceof Class){ | ||
| beansDefinitions.add((Class) apiOperation.response()); | ||
| } | ||
| method.getResponses().put("200", responses); | ||
|
|
||
| // Obtener el método HTTP | ||
| String httpMethod = extractHttpMethod(wsmethod); | ||
| if (httpMethod == null) continue; | ||
| Consumes consumes = wsmethod.getAnnotation(Consumes.class); | ||
|
|
||
| // Extraer parámetros | ||
| List<Parameter> parameters = extractParameters(wsmethod, token); | ||
| method.setParameters(parameters); | ||
| if (consumes != null){ | ||
| method.getConsumes().addAll(Arrays.asList(consumes.value())); | ||
| } | ||
| method.getProduces().add("application/json"); | ||
|
|
||
| // Ruta completa del endpoint | ||
| javax.ws.rs.Path methodPathAnnotation = wsmethod.getAnnotation(javax.ws.rs.Path.class); | ||
| String fullPath = basePath + (methodPathAnnotation != null ? methodPathAnnotation.value() : ""); | ||
| method.setOperationId(methodPathAnnotation != null ? methodPathAnnotation.value() : ""); | ||
| List tokens = new ArrayList<>(); | ||
| if(!StringUtils.isEmpty(token)){ | ||
| tokens.add("Bearer "+token); | ||
| } | ||
| method.setSecurity(Collections.singletonList(Collections.singletonMap("BearerAuth", tokens))); | ||
|
|
||
| // Crear o actualizar el Path | ||
| paths.put(fullPath, new HashMap<>()); | ||
| paths.get(fullPath).put(httpMethod, method); | ||
| } | ||
| } | ||
| } | ||
| Map<String, Definition> definitions = SwaggerDefinitionGenerator.getDefinitions(beansDefinitions); | ||
| swagger.setTags(tags); | ||
| swagger.setPaths(paths); | ||
| swagger.setDefinitions(definitions); | ||
| return swagger; | ||
| } | ||
|
|
||
| private String extractHttpMethod(java.lang.reflect.Method method) { | ||
| if (method.isAnnotationPresent(GET.class)) { | ||
| return "get"; | ||
| } else if (method.isAnnotationPresent(POST.class)) { | ||
| return "post"; | ||
| } else if (method.isAnnotationPresent(PUT.class)) { | ||
| return "put"; | ||
| } else if (method.isAnnotationPresent(DELETE.class)) { | ||
| return "delete"; | ||
| } | ||
| return null; | ||
| } | ||
|
|
||
| private List<Parameter> extractParameters(java.lang.reflect.Method method, String token) { | ||
| List<Parameter> parameters = new ArrayList<>(); | ||
|
|
||
| // Procesar parámetros definidos con @ApiImplicitParams | ||
| ApiImplicitParams implicitParams = method.getAnnotation(ApiImplicitParams.class); | ||
| if (implicitParams != null) { | ||
| for (ApiImplicitParam implicitParam : implicitParams.value()) { | ||
| Parameter parameter = new Parameter(); | ||
| parameter.setName(implicitParam.name()); | ||
| parameter.setIn(implicitParam.paramType()); | ||
| parameter.setDescription(implicitParam.value()); | ||
| parameter.setRequired(implicitParam.required()); | ||
| parameter.setType(implicitParam.dataType()); | ||
| parameter.setFormat(implicitParam.format()); | ||
| parameter.setDefaultValue(implicitParam.defaultValue()); | ||
| parameters.add(parameter); | ||
| } | ||
| } | ||
|
|
||
| // Procesar parámetros individuales del método | ||
| for (java.lang.reflect.Parameter methodParam : method.getParameters()) { | ||
| // Procesar ApiParam | ||
| // 4.1 Ignore all method parameters without @ApiParam annotations | ||
| Parameter parameter = new Parameter(); | ||
| ApiParam apiParam = methodParam.getAnnotation(ApiParam.class); | ||
| if (apiParam == null || apiParam.hidden()) { | ||
| continue; | ||
| } | ||
|
|
||
| // Procesar PathParam | ||
| PathParam pathParam = methodParam.getAnnotation(PathParam.class); | ||
| if (pathParam != null) { | ||
| parameter.setName(pathParam.value()); | ||
| parameter.setDescription(pathParam.value()); | ||
| parameter.setRequired(true); | ||
| parameter.setType(methodParam.getType().getSimpleName().toLowerCase(Locale.ROOT)); | ||
| } | ||
|
|
||
| // Procesar QueryParam | ||
| QueryParam queryParam = methodParam.getAnnotation(QueryParam.class); | ||
| if (queryParam != null) { | ||
| parameter.setName(queryParam.value()); | ||
| parameter.setDescription(queryParam.value()); | ||
| parameter.setRequired(apiParam.required()); | ||
| parameter.setType(methodParam.getType().getSimpleName().toLowerCase(Locale.ROOT)); | ||
| } | ||
|
|
||
| FormDataParam formDataParam = methodParam.getAnnotation(FormDataParam.class); | ||
| if (formDataParam != null) { | ||
| parameter.setName(formDataParam.value()); | ||
| parameter.setDescription(formDataParam.value()); | ||
| parameter.setRequired(apiParam.required()); | ||
| parameter.setType(methodParam.getType().getSimpleName().toLowerCase(Locale.ROOT)); | ||
|
|
||
| } | ||
| parameter.setIn(getIn(methodParam)); | ||
| parameter.setDefaultValue(apiParam.defaultValue()); | ||
| parameter.setDescription(StringUtils.isEmpty(parameter.getDescription())?apiParam.value():parameter.getDescription()); | ||
| parameters.add(parameter); | ||
| } | ||
|
|
||
| return parameters; | ||
| } | ||
|
|
||
| private String getIn(java.lang.reflect.Parameter methodParameter) { | ||
| if (methodParameter.getAnnotation(PathParam.class) != null) { | ||
| return "path"; | ||
| } else if (methodParameter.getAnnotation(QueryParam.class) != null | ||
| || methodParameter.getAnnotation(FormDataParam.class) != null) { | ||
| return "query"; | ||
| } else { | ||
| return "body"; | ||
| } | ||
| } | ||
|
|
||
| /** | ||
| * Determina la ubicación del parámetro (query, path, etc.). | ||
| */ | ||
| private String determineParameterLocation(java.lang.reflect.Parameter parameter) { | ||
| if (parameter.isAnnotationPresent(PathParam.class)) { | ||
| return "path"; | ||
| } else if (parameter.isAnnotationPresent(QueryParam.class)) { | ||
| return "query"; | ||
| } else if (parameter.isAnnotationPresent(ApiParam.class)) { | ||
| return "query"; // Por defecto si no se especifica | ||
| } | ||
| return "query"; // Predeterminado | ||
| } | ||
| } |
18 changes: 18 additions & 0 deletions
18
...rver/src/main/java/org/opencb/opencga/server/generator/openapi/SwaggerJsonSerializer.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| package org.opencb.opencga.server.generator.openapi; | ||
|
|
||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
| import org.opencb.opencga.server.generator.commons.ApiCommonsImpl; | ||
| import org.opencb.opencga.server.generator.openapi.models.Swagger; | ||
|
|
||
| public class SwaggerJsonSerializer { | ||
| public static void main(String[] args) throws Exception { | ||
| JsonOpenApiGenerator generator = new JsonOpenApiGenerator(); | ||
| Swagger swagger = generator.generateJsonOpenApi(new ApiCommonsImpl(), "El token va aquí", "task-xxxx"); | ||
|
|
||
| ObjectMapper mapper = new ObjectMapper(); | ||
| String swaggerJson = mapper.writerWithDefaultPrettyPrinter().writeValueAsString(swagger); | ||
|
|
||
| System.out.println(swaggerJson); | ||
| } | ||
| } | ||
|
|
Oops, something went wrong.