matchers = Arrays.stream(getSecuredResourcesRoot())
+ .map(AntPathRequestMatcher::new)
+ .toList();
+ return new OrRequestMatcher(matchers.toArray(new AntPathRequestMatcher[0]));
+ }
+
+ public String[] getUnsecuredResources() {
+ return new String[]{
+ "/restapi/**", // Ensure JWT API paths are not secured by the SAML chain
+ "/saml2/web/**",
+ "/swagger-ui/**",
+ "/api-docs/**",
+ "/error-401.html"
+ };
+ }
+
+ public String[] getSecuredResourcesRoot() {
+ // This chain should only handle browser-based SAML flows and the main UI
+ return new String[]{
+ "/login/saml2/sso/**", // SAML Response consumer endpoint
+ "/saml2/**", // SAML metadata and other endpoints
+ "/" // Your application's root/UI entry point
+ };
+ }
+}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/app/SecurityConfiguration.java b/server/catgenome/src/main/java/com/epam/catgenome/app/SecurityConfiguration.java
index 39d68c4a0..487c0188c 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/app/SecurityConfiguration.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/app/SecurityConfiguration.java
@@ -28,7 +28,7 @@
import org.springframework.context.annotation.Import;
@Configuration
-@Import({JWTSecurityConfiguration.class, SAMLSecurityConfiguration.class, NoSecurityConfiguration.class,
+@Import({JWTSecurityConfiguration.class, Saml2SecurityConfiguration.class, NoSecurityConfiguration.class,
AclSecurityConfiguration.class})
public class SecurityConfiguration {
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java b/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java
index aedcd4fd9..f8976bf2a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java
@@ -1,11 +1,11 @@
package com.epam.catgenome.app;
-import org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainerFactory;
+import org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory;
/**
* Enables configuration of Tomcat container, should be used only with embedded container
*/
public interface TomcatConfigurer {
- void configure(TomcatEmbeddedServletContainerFactory tomcat, int cacheSize,
- int tomcatCacheSize);
+ void configure(TomcatServletWebServerFactory tomcat, int cacheSize,
+ int tomcatCacheSize);
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java b/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java
index 72e738426..903e2d96a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java
@@ -1,7 +1,7 @@
package com.epam.catgenome.app;
import org.apache.catalina.webresources.StandardRoot;
-import org.springframework.boot.context.embedded.tomcat.TomcatEmbeddedServletContainerFactory;
+import org.springframework.boot.web.embedded.tomcat.TomcatServletWebServerFactory;
public class TomcatConfigurerImpl implements TomcatConfigurer {
@@ -10,9 +10,9 @@ public TomcatConfigurerImpl() {
}
@Override
- public void configure(TomcatEmbeddedServletContainerFactory tomcat, int cacheSize,
- int tomcatCacheSize) {
- tomcat.addContextCustomizers((context) -> {
+ public void configure(TomcatServletWebServerFactory tomcat, int cacheSize,
+ int tomcatCacheSize) {
+ tomcat.addContextCustomizers(context -> {
StandardRoot standardRoot = new StandardRoot(context);
standardRoot.setCachingAllowed(true);
standardRoot.setCacheMaxSize(cacheSize);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/component/MessageHelper.java b/server/catgenome/src/main/java/com/epam/catgenome/component/MessageHelper.java
index 613dac6ac..5e1e62229 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/component/MessageHelper.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/component/MessageHelper.java
@@ -137,7 +137,7 @@ public static MessageHelper singleton(final MessageSource messageSource) {
synchronized (MessageHelper.class) {
helper = instance;
if (helper == null) {
- Assert.notNull(messageSource);
+ Assert.notNull(messageSource, "");
instance = new MessageHelper(messageSource);
helper = instance;
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/config/SwaggerConfig.java b/server/catgenome/src/main/java/com/epam/catgenome/config/SwaggerConfig.java
deleted file mode 100644
index 6291835f6..000000000
--- a/server/catgenome/src/main/java/com/epam/catgenome/config/SwaggerConfig.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * MIT License
- *
- * Copyright (c) 2016 EPAM Systems
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
- */
-
-package com.epam.catgenome.config;
-
-import javax.servlet.ServletContext;
-
-import com.mangofactory.swagger.configuration.SpringSwaggerConfig;
-import com.mangofactory.swagger.models.dto.ApiInfo;
-import com.mangofactory.swagger.paths.SwaggerPathProvider;
-import com.mangofactory.swagger.plugin.EnableSwagger;
-import com.mangofactory.swagger.plugin.SwaggerSpringMvcPlugin;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.autoconfigure.EnableAutoConfiguration;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Import;
-
-/**
- * Source: SwaggerConfig.java
- * Created: 10/23/15, 5:05 PM
- * Project: CATGenome Browser
- * Make: IntelliJ IDEA 14.1.4, JDK 1.8
- *
- * {@code SwaggerConfig} enables and configures Swagger, used here to generate and provide
- * access to CATGenome REST API documentation through Web App.
- *
- */
-@Configuration
-@EnableSwagger
-@EnableAutoConfiguration
-@Import(SpringSwaggerConfig.class)
-public class SwaggerConfig {
-
- @Autowired
- private ServletContext servletContext;
-
- @Autowired
- private SpringSwaggerConfig springSwaggerConfig;
-
- @SuppressWarnings("unchecked")
- @Bean
- public SwaggerSpringMvcPlugin customImplementation() {
- return new SwaggerSpringMvcPlugin(this.springSwaggerConfig)
- .apiInfo(apiInfo())
- .pathProvider(new SwaggerPathProvider() {
- @Override
- protected String applicationPath() {
- return servletContext.getContextPath();
- }
-
- @Override
- protected String getDocumentationPath() {
- return "/";
- }
- })
- .includePatterns(".*").useDefaultResponseMessages(false);
- }
-
- private ApiInfo apiInfo() {
- return new ApiInfo(
- "CATGenome Browser REST API",
- "CATGenome Browser API description.",
- "API TOS",
- "Denis_Medvedev@epam.com",
- "API License",
- "API License URL"
- );
- }
-
-}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/AbstractRESTController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/AbstractRESTController.java
index bcc1a4ef1..53432727a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/AbstractRESTController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/AbstractRESTController.java
@@ -70,7 +70,7 @@ public abstract class AbstractRESTController {
* is described, using Swagger-compliant annotations. It allows create nice
* documentation automatically.
*/
- protected static final int HTTP_STATUS_OK = 200;
+ protected static final String HTTP_STATUS_OK = "200";
/**
* {@code String} specifies API responses description that explains meaning of different values
@@ -93,7 +93,7 @@ public abstract class AbstractRESTController {
* @throws IOException
*/
protected File transferToTempFile(final MultipartFile multipart) throws IOException {
- Assert.notNull(multipart);
+ Assert.notNull(multipart, "");
final File tmp = File.createTempFile(UUID.randomUUID().toString(), multipart.getOriginalFilename(),
fileManager.getTempDir());
multipart.transferTo(tmp);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/ExceptionHandlerAdvice.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/ExceptionHandlerAdvice.java
index 2954ab147..155875cfc 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/ExceptionHandlerAdvice.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/ExceptionHandlerAdvice.java
@@ -24,9 +24,7 @@
package com.epam.catgenome.controller;
-import java.io.FileNotFoundException;
-import java.sql.SQLException;
-
+import com.epam.catgenome.component.MessageHelper;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -36,14 +34,15 @@
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
import org.springframework.jdbc.BadSqlGrammarException;
-import org.springframework.security.oauth2.common.exceptions.UnauthorizedClientException;
+import org.springframework.security.oauth2.core.OAuth2AuthenticationException;
import org.springframework.web.bind.annotation.ControllerAdvice;
import org.springframework.web.bind.annotation.ExceptionHandler;
import org.springframework.web.bind.annotation.ResponseBody;
import org.springframework.web.context.request.WebRequest;
import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
-import com.epam.catgenome.component.MessageHelper;
+import java.io.FileNotFoundException;
+import java.sql.SQLException;
/**
* Source: ExceptionHandlerAdvice.java
@@ -90,7 +89,7 @@ public final ResponseEntity> handleUncaughtException(final Throwa
} else {
message = MessageHelper.getMessage("error.sql");
}
- } else if (exception instanceof UnauthorizedClientException) {
+ } else if (exception instanceof OAuth2AuthenticationException) {
message = exception.getMessage();
code = HttpStatus.UNAUTHORIZED;
} else {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/Result.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/Result.java
index 43798f5a1..3d02536b6 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/Result.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/Result.java
@@ -24,7 +24,7 @@
package com.epam.catgenome.controller;
-import com.wordnik.swagger.annotations.ApiModelProperty;
+import io.swagger.v3.oas.annotations.media.Schema;
import lombok.NoArgsConstructor;
/**
@@ -73,8 +73,8 @@ public String getMessage() {
return message;
}
- @ApiModelProperty(value = "it defines the status with which an operation may result in",
- allowableValues = "OK, INFO, WARN, ERROR", required = true)
+ @Schema(description = "it defines the status with which an operation may result in",
+ allowableValues = { "OK", "INFO", "WARN", "ERROR" }, required = true)
public ResultStatus getStatus() {
return status;
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/UtilsController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/UtilsController.java
index 2bfadd3cc..24705a3d2 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/UtilsController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/UtilsController.java
@@ -37,6 +37,9 @@
import com.epam.catgenome.manager.UrlShorterManager;
import com.epam.catgenome.util.IndexUtils;
import com.epam.catgenome.entity.UrlWithAliasItem;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.http.MediaType;
@@ -51,9 +54,6 @@
import com.epam.catgenome.manager.BiologicalDataItemManager;
import com.epam.catgenome.manager.FileManager;
import com.fasterxml.jackson.core.JsonProcessingException;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
import static com.epam.catgenome.component.MessageHelper.getMessage;
@@ -90,49 +90,45 @@ public class UtilsController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/version", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns application's version",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns application's version")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadVersion() {
return Result.success(version);
}
@ResponseBody
@RequestMapping(value = "/isRoleModelEnabled", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns application's version",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns application's version")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result isRoleModelEnabled() {
return Result.success(aclSecurityEnabled);
}
@ResponseBody
@RequestMapping(value = "/sessionExpirationBehavior", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns application's version",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns application's version")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result sessionExpirationBehaviour() {
return Result.success(expirationBehavior);
}
@ResponseBody
@RequestMapping(value = "/files", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns directory contents",
- notes = "Returns directory contents, specified by path",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns directory contents",
+ description = "Returns directory contents, specified by path")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadDirectoryContents(@RequestParam(required = false) String path)
throws IOException {
return Result.success(new FilesVO(fileManager.loadDirectoryContents(path), fileManager.getNgsDataRootPath()));
@@ -140,13 +136,12 @@ public Result loadDirectoryContents(@RequestParam(required = false) Str
@ResponseBody
@RequestMapping(value = "/files/allowed", method = RequestMethod.GET)
- @ApiOperation(
- value = "Checks is directory browsing is allowed",
- notes = "Returns true if directory browsing is allowed and false if not",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Checks is directory browsing is allowed",
+ description = "Returns true if directory browsing is allowed and false if not")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result isFilesBrowsingAllowed()
throws IOException {
return Result.success(fileManager.isFilesBrowsingAllowed());
@@ -154,13 +149,12 @@ public Result isFilesBrowsingAllowed()
@ResponseBody
@RequestMapping(value = "/url", method = RequestMethod.POST)
- @ApiOperation(
- value = "Generates URL postfix",
- notes = "Generates URL that displays specified files, optionally on specified interval",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Generates URL postfix",
+ description = "Generates URL that displays specified files, optionally on specified interval")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result generateUrl(
@RequestBody UrlRequestVO request,
@RequestParam(required = false) String chromosomeName,
@@ -173,13 +167,12 @@ public Result generateUrl(
@ResponseBody
@RequestMapping(value = "/urls/allowed", method = RequestMethod.GET)
- @ApiOperation(
- value = "Checks if url file browsing is allowed",
- notes = "Returns true if url file browsing is allowed and false if not",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Checks if url file browsing is allowed",
+ description = "Returns true if url file browsing is allowed and false if not")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result isUrlsBrowsingAllowed()
throws IOException {
return Result.success(fileManager.isUrlsBrowsingAllowed());
@@ -187,12 +180,11 @@ public Result isUrlsBrowsingAllowed()
@ResponseBody
@RequestMapping(value = "/generateShortUrl", method = RequestMethod.POST)
- @ApiOperation(
- value = "Generates short URL postfix",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Generates short URL postfix")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result generateShortUrl(@RequestBody UrlWithAliasItem urlWithAlias) {
String alias = urlWithAlias.getAlias();
String url = urlWithAlias.getUrl();
@@ -210,12 +202,11 @@ public Result generateShortUrl(@RequestBody UrlWithAliasItem urlWithAlia
@ResponseBody
@RequestMapping(value = "/navigate", method = RequestMethod.GET)
- @ApiOperation(
- value = "redirect on a original URL by short URL postfix, or on the 404 if short url doesn't exist",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "redirect on a original URL by short URL postfix, or on the 404 if short url doesn't exist")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void redirectToOriginalUrlByAlias(@RequestParam String alias, HttpServletResponse resp) throws IOException {
Optional maybeOriginalUrl = urlShorterManager.getOriginalUrl(alias);
if (maybeOriginalUrl.isPresent()) {
@@ -230,22 +221,22 @@ public void redirectToOriginalUrlByAlias(@RequestParam String alias, HttpServlet
@ResponseBody
@RequestMapping(value = "/defaultTrackSettings", method = RequestMethod.GET)
- @ApiOperation(
- value = "Return default track settings",
- notes = "Return default track settings, which specified in catgenome.properties file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Return default track settings",
+ description = "Return default track settings, which specified in catgenome.properties file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result>> getDefaultTracksSettings() throws IOException {
return Result.success(fileManager.getDefaultTrackSettings());
}
@ResponseBody
@RequestMapping(value = "/getPathToExistingIndex", method = RequestMethod.GET)
- @ApiOperation(value = "Return path of existing index for file, or null if it don't exist",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)})
+ @Operation(summary = "Return path of existing index for file, or null if it don't exist")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getPathToExistingIndex(@RequestParam String filePath) throws IOException {
return Result.success(IndexUtils.checkExistingIndex(filePath));
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamController.java
index ba28ec617..f88034652 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamController.java
@@ -31,6 +31,10 @@
import com.epam.catgenome.entity.bam.BamFile;
import com.epam.catgenome.entity.bam.Read;
import com.epam.catgenome.manager.bam.BamSecurityService;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
@@ -46,10 +50,6 @@
import com.epam.catgenome.controller.vo.registration.IndexedFileRegistrationRequest;
import com.epam.catgenome.entity.reference.Sequence;
import com.epam.catgenome.entity.track.Track;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
@@ -71,7 +71,7 @@
*
*/
@Controller
-@Api(value = "BAM", description = "BAM Track Management")
+@Tag(name = "BAM", description = "BAM Track Management")
public class BamController extends AbstractRESTController {
private static final String NOTES = "It provides data for a BAM track with the given scale factor between the " +
@@ -98,29 +98,28 @@ public class BamController extends AbstractRESTController {
@ResponseBody
@PostMapping(value = "/bam/register")
- @ApiOperation(
- value = "Registers a BAM file in the system.",
- notes = "Registers a file, stored in a file system (for now). Registration request has the following " +
+ @Operation(
+ summary = "Registers a BAM file in the system.",
+ description = "Registers a file, stored in a file system (for now). Registration request has the following " +
"properties:
" +
"1) referenceId - a reference, for which file is being registered
" +
"2) path - a path to file " +
"3) type - resource type of file: FILE / URL / S3
" +
"4) indexPath - optional a path to an index file (.bai)
" +
"5) name - optional a name for BAM track
" +
- "6) s3BucketId - optional necessarily for cases when type is S3",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "6) s3BucketId - optional necessarily for cases when type is S3")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerBamFile(@RequestBody IndexedFileRegistrationRequest request) throws IOException {
return Result.success(bamSecurityService.registerBam(request));
}
@PostMapping(value = "/bam/track/get")
- @ApiOperation(
- value = "Returns data (chunked) matching the given query to fill in a bam track. Returns all information " +
+ @Operation(
+ summary = "Returns data (chunked) matching the given query to fill in a bam track. Returns all information " +
"about reads.",
- notes = NOTES +
+ description = NOTES +
"
option:
" +
"all the following params are optional, if any of the params is incorrect, " +
"it will be set to default value:
" +
@@ -135,11 +134,10 @@ public Result registerBamFile(@RequestBody IndexedFileRegistrationReque
"6) mode controls BAM display mode: REGIONS - return only regions of possible read " +
"location;
" +
"COVERAGE - return only BAM coverage;
" +
- "FULL - return both reads and coverage",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "FULL - return both reads and coverage")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final ResponseEntity loadTrackStream(
@RequestBody final TrackQuery query,
@RequestParam(required = false) final String fileUrl,
@@ -154,7 +152,7 @@ public final ResponseEntity loadTrackStream(
indexUrl, emitter);
}
HttpHeaders responseHeaders = new HttpHeaders();
- responseHeaders.setContentType(MediaType.APPLICATION_JSON_UTF8);
+ responseHeaders.setContentType(MediaType.APPLICATION_JSON);
return new ResponseEntity<>(emitter, responseHeaders, HttpStatus.OK);
}
@@ -167,9 +165,9 @@ public Result unregisterBamFile(@RequestParam final long bamFileId) thr
@ResponseBody
@PostMapping(value = "/bam/consensus/get")
- @ApiOperation(
- value = "Returns consensus sequence for specified BAM file range.",
- notes = "It provides data about consensus sequence for specified BAM file range " +
+ @Operation(
+ summary = "Returns consensus sequence for specified BAM file range.",
+ description = "It provides data about consensus sequence for specified BAM file range " +
"with the given scale factor between the " +
"beginning position with the first base having position 1 and ending position inclusive in a " +
"target chromosome. All parameters are mandatory and described below:
" +
@@ -180,24 +178,22 @@ public Result unregisterBamFile(@RequestParam final long bamFileId) thr
"4) endIndex is the last base position for a requested window. It is treated " +
"inclusively;
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible " +
- "element on a track (e.g., pixel).",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "element on a track (e.g., pixel).")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Track loadConsensusSequence(@RequestBody final TrackQuery query) throws IOException {
return bamSecurityService.calculateConsensusSequence(convertToTrack(query));
}
@ResponseBody
@PostMapping(value = "/bam/read/load")
- @ApiOperation(
- value = "Returns extended data for a read",
- notes = "Provides extended data about the particular read",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns extended data for a read",
+ description = "Provides extended data about the particular read")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadRead(@RequestBody final ReadQuery query,
@RequestParam(required = false) final String fileUrl,
@RequestParam(required = false) final String indexUrl) throws IOException {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamCoverageController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamCoverageController.java
index ea9f6abcd..34bca844b 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamCoverageController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamCoverageController.java
@@ -31,10 +31,10 @@
import com.epam.catgenome.entity.bam.CoverageQueryParams;
import com.epam.catgenome.manager.bam.BamCoverageSecurityService;
import com.epam.catgenome.util.db.Page;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.apache.lucene.queryparser.classic.ParseException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -64,7 +64,7 @@
*
*/
@Controller
-@Api(value = "bam-coverage", description = "BAM Coverage Management")
+@Tag(name = "bam-coverage", description = "BAM Coverage Management")
public class BamCoverageController extends AbstractRESTController {
@Autowired
@@ -72,26 +72,24 @@ public class BamCoverageController extends AbstractRESTController {
@ResponseBody
@PostMapping(value = "/bam/coverage")
- @ApiOperation(
- value = "Creates coverage with given step for the BAM file",
- notes = "Creates coverage with given step for the BAM file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates coverage with given step for the BAM file",
+ description = "Creates coverage with given step for the BAM file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createCoverage(@RequestBody final BamCoverage coverage) throws IOException {
return Result.success(securityService.createCoverage(coverage));
}
@ResponseBody
@DeleteMapping(value = "/bam/coverage")
- @ApiOperation(
- value = "Deletes BAM coverage by Bam file Id and step",
- notes = "Deletes BAM coverage by Bam file Id and step",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes BAM coverage by Bam file Id and step",
+ description = "Deletes BAM coverage by Bam file Id and step")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteCoverage(@RequestParam final Long bamId,
@RequestParam(required = false) final Integer step)
throws IOException, InterruptedException, ParseException {
@@ -101,13 +99,12 @@ public Result deleteCoverage(@RequestParam final Long bamId,
@ResponseBody
@PostMapping(value = "/bam/coverage/search")
- @ApiOperation(
- value = "Returns coverage intervals for a BAM file",
- notes = "Returns coverage intervals for a BAM file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns coverage intervals for a BAM file",
+ description = "Returns coverage intervals for a BAM file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadCoverage(@RequestBody final CoverageQueryParams params)
throws ParseException, IOException {
return Result.success(securityService.loadCoverage(params));
@@ -115,26 +112,24 @@ public Result> loadCoverage(@RequestBody final CoverageQu
@ResponseBody
@GetMapping(value = "/bam/coverage")
- @ApiOperation(
- value = "Returns all registered coverages for bam files",
- notes = "Returns all registered coverages for bam files",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all registered coverages for bam files",
+ description = "Returns all registered coverages for bam files")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadByBamId(@RequestParam final Set bamIds) throws IOException {
return Result.success(securityService.loadByBamId(bamIds));
}
@ResponseBody
@GetMapping(value = "/bam/coverage/all")
- @ApiOperation(
- value = "Returns all registered coverages",
- notes = "Returns all registered coverages",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all registered coverages",
+ description = "Returns all registered coverages")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadAll() throws IOException {
return Result.success(securityService.loadAll());
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/bed/BedController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/bed/BedController.java
index eaee3e150..abcf960a6 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/bed/BedController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/bed/BedController.java
@@ -31,6 +31,10 @@
import java.nio.file.AccessDeniedException;
import com.epam.catgenome.manager.bed.BedSecurityService;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Controller;
@@ -53,10 +57,6 @@
import com.epam.catgenome.exception.FeatureFileReadingException;
import com.epam.catgenome.exception.HistogramReadingException;
import com.epam.catgenome.exception.FeatureIndexException;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
/**
* Source: BedController
@@ -70,33 +70,34 @@
* calls and manage all operations concerned with Bed data.
*/
@Controller
-@Api(value = "bed", description = "BED Track Management")
+@Tag(name = "bed", description = "BED Track Management")
public class BedController extends AbstractRESTController {
@Autowired
private BedSecurityService bedSecurityService;
@ResponseBody
@RequestMapping(value = "/bed/register", method = RequestMethod.POST)
- @ApiOperation(
- value = "Registers a BED file in the system.",
- notes = "Registers a file, stored in a file system (for now). Registration request has the following " +
+ @Operation(
+ summary = "Registers a BED file in the system.",
+ description = "Registers a file, stored in a file system (for now). Registration request has the following " +
"properties:
" +
"1) referenceId - a reference, for which file is being registered
" +
"2) path - a path to file " +
"3) indexPath - optional a path to an index file
" +
- "4) name - optional a name for gene track",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "4) name - optional a name for gene track")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerBedFile(@RequestBody IndexedFileRegistrationRequest request) {
return Result.success(bedSecurityService.registerBed(request));
}
@ResponseBody
@RequestMapping(value = "/secure/bed/register", method = RequestMethod.DELETE)
- @ApiOperation(value = "Removes a bed file from the system.", notes = "",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(summary = "Removes a bed file from the system.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result unregisterBedFile(@RequestParam final long bedFileId) throws IOException {
BedFile deletedFile = bedSecurityService.unregisterBedFile(bedFileId);
return Result.success(true, getMessage(MessagesConstants.INFO_UNREGISTER, deletedFile.getName()));
@@ -104,9 +105,9 @@ public Result unregisterBedFile(@RequestParam final long bedFileId) thr
@ResponseBody
@RequestMapping(value = "/bed/track/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns data matched the given query to fill in a BED track.",
- notes = "It provides data for a BED track with the given scale factor between the beginning " +
+ @Operation(
+ summary = "Returns data matched the given query to fill in a BED track.",
+ description = "It provides data for a BED track with the given scale factor between the beginning " +
"position with the first base having position 1 and ending position inclusive in a target " +
"chromosome. All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -115,11 +116,10 @@ public Result unregisterBedFile(@RequestParam final long bedFileId) thr
"chromosome always has got position = 1;
" +
"4) endIndex is the last base position for a requested window.
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible element on a" +
- " track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTrack(@RequestBody final TrackQuery trackQuery,
@RequestParam(required = false) final String fileUrl,
@RequestParam(required = false) final String indexUrl)
@@ -134,9 +134,9 @@ public Result> loadTrack(@RequestBody final TrackQuery trackQue
@ResponseBody
@RequestMapping(value = "/bed/track/histogram", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns a histogram of BED records amount on regions of chromosome",
- notes = "It provides histogram for a BEd track with the given scale factor between the " +
+ @Operation(
+ summary = "Returns a histogram of BED records amount on regions of chromosome",
+ description = "It provides histogram for a BEd track with the given scale factor between the " +
"beginning position with the first base having position 1 and ending position inclusive " +
"in a target chromosome. All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -146,11 +146,10 @@ public Result> loadTrack(@RequestBody final TrackQuery trackQue
"4) endIndex is the last base position for a requested window. " +
"It is treated inclusively;
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible element" +
- " on a track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " on a track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadHistogram(@RequestBody final TrackQuery trackQuery)
throws HistogramReadingException {
final Track histogramTrack = convertToTrack(trackQuery);
@@ -159,8 +158,11 @@ public Result> loadHistogram(@RequestBody final TrackQuery trackQuery
@ResponseBody
@RequestMapping(value = "/bed/{bedFileId}/index", method = RequestMethod.GET)
- @ApiOperation(value = "Rebuilds a BED feature index",
- notes = "Rebuilds a BED feature index", produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(summary = "Rebuilds a BED feature index",
+ description = "Rebuilds a BED feature index")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result reindexBed(@PathVariable long bedFileId) throws FeatureIndexException {
BedFile file = bedSecurityService.reindexBedFile(bedFileId);
return Result.success(true, getMessage(MessagesConstants.INFO_FEATURE_INDEX_DONE, file.getId(),
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastController.java
index cfbd243e3..5601bc669 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastController.java
@@ -46,10 +46,10 @@
import com.epam.catgenome.controller.AbstractRESTController;
import com.epam.catgenome.controller.Result;
import com.epam.catgenome.exception.FeatureIndexException;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
@@ -61,44 +61,41 @@
import javax.servlet.http.HttpServletResponse;
@RestController
-@Api(value = "blast", description = "BLAST Task Management")
+@Tag(name = "blast", description = "BLAST Task Management")
@RequiredArgsConstructor
public class BlastController extends AbstractRESTController {
private final BlastTaskSecurityService blastTaskSecurityService;
@GetMapping(value = "/task/{taskId}")
- @ApiOperation(
- value = "Returns a task by given id",
- notes = "Returns a task by given id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a task by given id",
+ description = "Returns a task by given id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadTask(@PathVariable final long taskId) {
return Result.success(blastTaskSecurityService.load(taskId));
}
@GetMapping(value = "/task/{taskId}/result")
- @ApiOperation(
- value = "Returns a task result",
- notes = "Returns a task result",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a task result",
+ description = "Returns a task result")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getResult(@PathVariable final long taskId) throws BlastRequestException {
return Result.success(blastTaskSecurityService.getResult(taskId));
}
@GetMapping(value = "/task/{taskId}/raw")
- @ApiOperation(
- value = "Returns a file with task result",
- notes = "Returns a file with task result",
- produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a file with task result",
+ description = "Returns a file with task result")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void getRawResult(@PathVariable final long taskId, final HttpServletResponse response)
throws BlastRequestException, IOException {
okhttp3.ResponseBody body = blastTaskSecurityService.getRawResult(taskId);
@@ -108,104 +105,96 @@ public void getRawResult(@PathVariable final long taskId, final HttpServletRespo
}
@GetMapping(value = "/task/{taskId}/group")
- @ApiOperation(
- value = "Returns BLAST tasks results grouped by sequence",
- notes = "Returns BLAST tasks results grouped by sequence",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns BLAST tasks results grouped by sequence",
+ description = "Returns BLAST tasks results grouped by sequence")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getGroupedResult(@PathVariable final long taskId)
throws BlastRequestException {
return Result.success(blastTaskSecurityService.getGroupedResult(taskId));
}
@PostMapping(value = "/tasks/count")
- @ApiOperation(
- value = "Returns tasks count",
- notes = "Returns tasks count",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns tasks count",
+ description = "Returns tasks count")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getTasksCount(@RequestBody final List filters) {
return Result.success(blastTaskSecurityService.getTasksCount(filters));
}
@PostMapping(value = "/tasks")
- @ApiOperation(
- value = "Loads all tasks",
- notes = "DB fields mapping: id - task_id, "
+ @Operation(
+ summary = "Loads all tasks",
+ description = "DB fields mapping: id - task_id, "
+ "createdDate - created_date, "
- + "endDate - end_date, statusReason - status_reason",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ + "endDate - end_date, statusReason - status_reason")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadTasks(@RequestBody final QueryParameters queryParameters) {
return Result.success(blastTaskSecurityService.loadAllTasks(queryParameters));
}
@DeleteMapping(value = "/tasks")
- @ApiOperation(
- value = "Delete all not running tasks for current user",
- notes = "Delete all not running tasks for current user",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Delete all not running tasks for current user",
+ description = "Delete all not running tasks for current user")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteTasks() {
blastTaskSecurityService.deleteTasks();
return Result.success(null);
}
@PostMapping(value = "/task")
- @ApiOperation(
- value = "Creates new task or updates existing one",
- notes = "Creates new task or updates existing one",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates new task or updates existing one",
+ description = "Creates new task or updates existing one")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createTask(@RequestBody final TaskVO taskVO)
throws FeatureIndexException, BlastRequestException {
return Result.success(blastTaskSecurityService.create(taskVO));
}
@PostMapping(value = "/createdb")
- @ApiOperation(
- value = "Schedules a task for BLAST database creation",
- notes = "Schedules a task for BLAST database creation",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Schedules a task for BLAST database creation",
+ description = "Schedules a task for BLAST database creation")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createDatabase(@RequestBody final CreateDatabaseRequest request)
throws BlastRequestException {
return Result.success(blastTaskSecurityService.createDatabase(request));
}
@PutMapping(value = "/task/{taskId}/cancel")
- @ApiOperation(
- value = "Cancels a task with given id",
- notes = "Cancels a task with given id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Cancels a task with given id",
+ description = "Cancels a task with given id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result cancelTask(@PathVariable final long taskId) throws BlastRequestException {
blastTaskSecurityService.cancel(taskId);
return Result.success(null);
}
@DeleteMapping(value = "/task/{taskId}")
- @ApiOperation(
- value = "Deletes a task, specified by task ID",
- notes = "Deletes a task, specified by task ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a task, specified by task ID",
+ description = "Deletes a task, specified by task ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteTask(@PathVariable final long taskId) throws IOException {
blastTaskSecurityService.deleteTask(taskId);
return Result.success(null);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastDatabaseController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastDatabaseController.java
index 2d8f309cc..15c4daa6c 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastDatabaseController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastDatabaseController.java
@@ -28,10 +28,10 @@
import com.epam.catgenome.entity.blast.BlastDatabase;
import com.epam.catgenome.entity.blast.BlastDatabaseType;
import com.epam.catgenome.manager.blast.BlastDatabaseSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.DeleteMapping;
@@ -45,58 +45,54 @@
import java.util.List;
@RestController
-@Api(value = "blast-database", description = "BLAST Databases Management")
+@Tag(name = "blast-database", description = "BLAST Databases Management")
@RequiredArgsConstructor
public class BlastDatabaseController extends AbstractRESTController {
private final BlastDatabaseSecurityService blastDatabaseSecurityService;
@PostMapping(value = "/blast/database")
- @ApiOperation(
- value = "Creates new database record or updates existing one",
- notes = "Creates new database record or updates existing one",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates new database record or updates existing one",
+ description = "Creates new database record or updates existing one")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result saveDatabase(@RequestBody final BlastDatabase database) {
blastDatabaseSecurityService.save(database);
return Result.success(null);
}
@GetMapping(value = "/blast/database/{id}")
- @ApiOperation(
- value = "Gets database by Id",
- notes = "Gets database by Id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Gets database by Id",
+ description = "Gets database by Id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadDataBase(@PathVariable final long id) {
return Result.success(blastDatabaseSecurityService.loadById(id));
}
@GetMapping(value = "/blast/databases")
- @ApiOperation(
- value = "Gets databases",
- notes = "Gets databases",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Gets databases",
+ description = "Gets databases")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadDatabases(@RequestParam(required = false) final BlastDatabaseType type,
@RequestParam(required = false) final String path) {
return Result.success(blastDatabaseSecurityService.load(type, path));
}
@DeleteMapping(value = "/blast/database/{id}")
- @ApiOperation(
- value = "Deletes database by Id",
- notes = "Deletes database by Id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes database by Id",
+ description = "Deletes database by Id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteDatabase(@PathVariable final long id) {
blastDatabaseSecurityService.delete(id);
return Result.success(null);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastUtilController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastUtilController.java
index 7ed0c48d9..59e64e0d8 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastUtilController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastUtilController.java
@@ -29,10 +29,10 @@
import com.epam.catgenome.entity.blast.BlastDatabaseType;
import com.epam.catgenome.entity.blast.result.BlastFeatureLocatable;
import com.epam.catgenome.manager.blast.BlastUtilSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.GetMapping;
@@ -40,21 +40,20 @@
import org.springframework.web.bind.annotation.RestController;
@RestController
-@Api(value = "blast-utils", description = "BLAST Utility Controller")
+@Tag(name = "blast-utils", description = "BLAST Utility Controller")
@RequiredArgsConstructor
public class BlastUtilController extends AbstractRESTController {
private final BlastUtilSecurityService blastUtilSecurityService;
@GetMapping(value = "/blast/coordinate")
- @ApiOperation(
- value = "Gets coordinates for feature based on feature accession version",
- notes = "Gets coordinates for feature based on feature accession version " +
- "by requesting information from NCBI DB",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Gets coordinates for feature based on feature accession version",
+ description = "Gets coordinates for feature based on feature accession version " +
+ "by requesting information from NCBI DB")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchCoordinates(@RequestParam final String sequenceId,
@RequestParam final BlastDatabaseType type,
@RequestParam final Long taxId) {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/compound/CompoundController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/compound/CompoundController.java
index 9b546c4d2..01e851b61 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/compound/CompoundController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/compound/CompoundController.java
@@ -29,30 +29,29 @@
import com.epam.catgenome.exception.ExternalDbUnavailableException;
import com.epam.catgenome.manager.externaldb.pug.NCBIPugSecurityService;
import com.fasterxml.jackson.core.JsonProcessingException;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.*;
@RestController
-@Api(value = "compound", description = "Compound Management")
+@Tag(name = "compound", description = "Compound Management")
@RequiredArgsConstructor
public class CompoundController extends AbstractRESTController {
private final NCBIPugSecurityService ncbiPugSecurityService;
@GetMapping(value = "/compound/smiles/{name}")
- @ApiOperation(
- value = "Searches smiles by compound name.",
- notes = "Searches smiles by compound name.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches smiles by compound name.",
+ description = "Searches smiles by compound name.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getProteinPatents(@PathVariable final String name)
throws ExternalDbUnavailableException, JsonProcessingException {
return Result.success(ncbiPugSecurityService.getSmiles(name));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/dataitem/DataItemController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/dataitem/DataItemController.java
index bd9bd2168..e9c4d0479 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/dataitem/DataItemController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/dataitem/DataItemController.java
@@ -43,10 +43,10 @@
import com.epam.catgenome.constant.MessagesConstants;
import com.epam.catgenome.controller.AbstractRESTController;
import com.epam.catgenome.controller.Result;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.*;
import javax.servlet.http.HttpServletResponse;
@@ -61,7 +61,7 @@
*
*/
@Controller
-@Api(value = "DATAITEM", description = "Data Item Management")
+@Tag(name = "DATAITEM", description = "Data Item Management")
public class DataItemController extends AbstractRESTController {
@Autowired
@@ -72,17 +72,16 @@ public class DataItemController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/dataitem/search", method = RequestMethod.GET)
- @ApiOperation(
- value = "Finds all files registered on the server by a specified file name",
- notes = "Finds all files registered on the server by a specified file name" +
+ @Operation(
+ summary = "Finds all files registered on the server by a specified file name",
+ description = "Finds all files registered on the server by a specified file name" +
"Input arguments:" +
"name - search query for the file name," +
"strict - if true a strict, case sensitive search is performed, " +
- "otherwise a substring, case insensitive search is performed.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "otherwise a substring, case insensitive search is performed.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result> findFilesByName(@RequestParam(value = "name") final String name,
@RequestParam(value = "strict", required = false, defaultValue = "true") final boolean strict) {
return Result.success(dataItemSecurityService.findFilesByName(name, strict));
@@ -90,25 +89,23 @@ public final Result> findFilesByName(@RequestParam(valu
@ResponseBody
@RequestMapping(value = "/dataitem/formats", method = RequestMethod.GET)
- @ApiOperation(
- value = "Get all available bed formats.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Get all available bed formats.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getBedFormats() {
return Result.success(dataItemSecurityService.getFormats());
}
@ResponseBody
@RequestMapping(value = "/dataitem/delete", method = RequestMethod.DELETE)
- @ApiOperation(
- value = "Deletes a file, specified by biological item id from the database",
- notes = "Deletes a file, specified by biological item id from the database",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a file, specified by biological item id from the database",
+ description = "Deletes a file, specified by biological item id from the database")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result deleteFileBiBioItemId(@RequestParam(value = "id") final Long id)
throws IOException {
BiologicalDataItem deletedFile = dataItemSecurityService.deleteFileByBioItemId(id);
@@ -117,13 +114,12 @@ public final Result deleteFileBiBioItemId(@RequestParam(value = "id")
@ResponseBody
@RequestMapping(value = "/dataitem/find", method = RequestMethod.GET)
- @ApiOperation(
- value = "Finds a file, specified by biological item id from the database",
- notes = "Finds a file, specified by biological item id from the database",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Finds a file, specified by biological item id from the database",
+ description = "Finds a file, specified by biological item id from the database")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result findFileBiBioItemId(@RequestParam(value = "id") final Long id)
throws IOException {
return Result.success(dataItemSecurityService.findFileByBioItemId(id));
@@ -131,13 +127,12 @@ public final Result findFileBiBioItemId(@RequestParam(value
@ResponseBody
@PutMapping(value = "/dataitem/rename")
- @ApiOperation(
- value = "Updates file name and/or pretty name.",
- notes = "Updates file name and/or pretty name.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates file name and/or pretty name.",
+ description = "Updates file name and/or pretty name.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result rename(
@RequestParam(value = "name") final String name,
@RequestParam(value = "newName", required = false) final String newName,
@@ -147,10 +142,9 @@ public final Result rename(
}
@GetMapping("/dataitem/{id}/download")
- @ApiOperation(
- value = "Downloads a file specified by biological item id",
- notes = "Downloads a file specified by biological item id",
- produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
+ @Operation(
+ summary = "Downloads a file specified by biological item id",
+ description = "Downloads a file specified by biological item id")
public void downloadFileByBiologicalItemId(
@PathVariable(value = "id") final Long id,
@RequestParam(value = "source", defaultValue = "true") final Boolean source,
@@ -163,13 +157,12 @@ public void downloadFileByBiologicalItemId(
@ResponseBody
@GetMapping("/dataitem/{id}/downloadUrl")
- @ApiOperation(
- value = "Generates download url for file specified by biological item id",
- notes = "Generates download url for file specified by biological item id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Generates download url for file specified by biological item id",
+ description = "Generates download url for file specified by biological item id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result generateDownloadUrl(@PathVariable(value = "id") final Long id) {
final BiologicalDataItem biologicalDataItem = dataItemManager.findFileByBioItemId(id);
return Result.success(dataItemSecurityService.generateDownloadUrl(id, biologicalDataItem));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/ExternalDBController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/ExternalDBController.java
index a5423e8d0..09628c8dd 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/ExternalDBController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/ExternalDBController.java
@@ -67,10 +67,10 @@
import com.epam.catgenome.manager.externaldb.UniprotDataManager;
import com.epam.catgenome.manager.externaldb.bindings.uniprot.Entry;
import com.epam.catgenome.manager.externaldb.bindings.uniprot.Uniprot;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -85,7 +85,7 @@
*
* */
@Controller
-@Api(value = "externaldb", description = "External DB Management")
+@Tag(name = "externaldb", description = "External DB Management")
public class ExternalDBController extends AbstractRESTController {
private static final String SUCCESS = "info.database.successful.get";
@@ -130,15 +130,16 @@ public class ExternalDBController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/externaldb/uniprot/{geneId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "UniProt: Retrieves information on protein using geneId.",
- notes = "UniProt database (http://www.uniprot.org/) is being queried for information by gene " +
+ @Operation(summary = "UniProt: Retrieves information on protein using geneId.",
+ description = "UniProt database (http://www.uniprot.org/) is being queried for information by gene " +
"identifier in any database. Protein information in XML form is returned by UniProt, " +
"this information is converted to presentation required by NGGB.
" +
"Examples of id which could be used as a parameter to this service:
" +
"ENSG00000106683 -- Ensembl ID
" +
- "FBgn0000008 -- Fly Base ID
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "FBgn0000008 -- Fly Base ID
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> fetchUniprotData(@PathVariable(value = "geneId") final String geneId)
throws ExternalDbUnavailableException {
@@ -152,15 +153,16 @@ public Result> fetchUniprotData(@PathVariable(value = "gene
@ResponseBody
@RequestMapping(value = "/externaldb/ensembl/{geneId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "Ensembl: Retrieves information on gene using geneId.",
- notes = "Ensembl database (http://rest.ensembl.org/) is being queried for information by gene " +
+ @Operation(summary = "Ensembl: Retrieves information on gene using geneId.",
+ description = "Ensembl database (http://rest.ensembl.org/) is being queried for information by gene " +
"identifier in any database. Gene information in JSON form is returned by Ensembl, " +
"this information is converted to presentation required by NGGB.
" +
"Examples of id which could be used as a parameter to this service:
" +
"ENSG00000106683 -- Ensembl ID
" +
- "FBgn0000008 -- Fly Base ID
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "FBgn0000008 -- Fly Base ID
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchEnsemblData(@PathVariable(value = "geneId") final String geneId)
throws ExternalDbUnavailableException {
@@ -173,14 +175,15 @@ public Result fetchEnsemblData(@PathVariable(value = "geneId") f
@ResponseBody
@RequestMapping(value = "/externaldb/ensembl/variation/variationId={rsId}&species={species}",
method = RequestMethod.GET)
- @ApiOperation(value = "Ensembl: Retrieves information on variation for certain species using variation id(rsId).",
- notes = "Ensembl database (http://rest.ensembl.org/) is being queried by rsId and species " +
+ @Operation(summary = "Ensembl: Retrieves information on variation for certain species using variation id(rsId).",
+ description = "Ensembl database (http://rest.ensembl.org/) is being queried by rsId and species " +
"type. Information of variation for certain species is returned from Ensembl db.
" +
PARAMETERS_NOTE +
RSID_DESCRIPTION_NOTE + "
" +
- "species - species name: human
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "species - species name: human
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchEnsemblVariationData(
@PathVariable(value = VARIATION_ID_NAME) final String rsId,
@PathVariable(value = "species") final String species)
@@ -194,17 +197,18 @@ public Result fetchEnsemblVariationData(
@ResponseBody
@RequestMapping(value = "/externaldb/ensembl/variation/region", method = RequestMethod.POST)
- @ApiOperation(value = "Ensembl: Retrieves information on variations located within certain chromosomal coordiates.",
- notes = "Ensembl database (http://rest.ensembl.org/) is being queried for variations located " +
+ @Operation(summary = "Ensembl: Retrieves information on variations located within certain chromosomal coordiates.",
+ description = "Ensembl database (http://rest.ensembl.org/) is being queried for variations located " +
"in between certain coordinates (start and finish) for certain chromosome " +
"for the given species.
" +
PARAMETERS_NOTE +
"species - species name (e.g. \"human\")
" +
"chromosome - chromosome name (e.g. \"1\")
" +
"start - start coordinate in a given chromosome (e.g. 140424943)
" +
- "finish - end coordinate in a given chromosome (e.g. 140624564)
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "finish - end coordinate in a given chromosome (e.g. 140624564)
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> fetchEnsemblVariationOnRegionData(
@RequestBody final RegionQuery regionQuery)
throws ExternalDbUnavailableException {
@@ -227,8 +231,8 @@ public Result> fetchEnsemblVariationOnRegionData(
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/gene/{geneId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves gene information using gene id.",
- notes = "NCBI database (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/) " +
+ @Operation(summary = "NCBI: Retrieves gene information using gene id.",
+ description = "NCBI database (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/) " +
"is being queried by gene id.
" +
PARAMETERS_NOTE +
"geneId - NCBI gene id or Ensembl gene id (e.g. 3985, ENSG00000106683)
" +
@@ -241,9 +245,10 @@ public Result> fetchEnsemblVariationOnRegionData(
"Summary -- text description of gene
" +
"Related articles in PubMed -- pubmed db articles
" +
"Pathways from BioSystems -- biosystems reference
" +
- "Interactions -- interactions information
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "Interactions -- interactions information
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBIGene(@PathVariable(value = "geneId") final String geneId)
throws ExternalDbUnavailableException {
@@ -255,13 +260,14 @@ public Result fetchNCBIGene(@PathVariable(value = "geneId") final St
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/variation/short/{rsId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves information on short variation using rsId.",
- notes = "NCBI database (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/) is being queried by variation id" +
+ @Operation(summary = "NCBI: Retrieves information on short variation using rsId.",
+ description = "NCBI database (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/) is being queried by variation id" +
"(rsId) for short variation information.
" +
PARAMETERS_NOTE +
- RSID_DESCRIPTION_NOTE,
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ RSID_DESCRIPTION_NOTE)
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBIShortVariation(@PathVariable(value = VARIATION_ID_NAME) final String rsId)
throws ExternalDbUnavailableException {
@@ -273,12 +279,13 @@ public Result fetchNCBIShortVariation(@PathVariable(value = VARI
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/variation/struct/{rsId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves information on structural variation using rsId.",
- notes = "NCBI structural variations db is being queried by rsId.
" +
+ @Operation(summary = "NCBI: Retrieves information on structural variation using rsId.",
+ description = "NCBI structural variations db is being queried by rsId.
" +
PARAMETERS_NOTE +
- RSID_DESCRIPTION_NOTE,
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ RSID_DESCRIPTION_NOTE)
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBIStructVariation(@PathVariable(value = VARIATION_ID_NAME) final String rsId)
throws ExternalDbUnavailableException {
@@ -290,12 +297,13 @@ public Result fetchNCBIStructVariation(@PathVariable(value = VA
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/variation/clin/{rsId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves clinical information on variation using rsId.",
- notes = "NCBI ClinVar is being queried by rsId
" +
+ @Operation(summary = "NCBI: Retrieves clinical information on variation using rsId.",
+ description = "NCBI ClinVar is being queried by rsId
" +
PARAMETERS_NOTE +
- RSID_DESCRIPTION_NOTE,
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ RSID_DESCRIPTION_NOTE)
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBIClinVariation(@PathVariable(value = VARIATION_ID_NAME) final String rsId)
throws ExternalDbUnavailableException {
@@ -308,15 +316,16 @@ public Result fetchNCBIClinVariation(@PathVariable(value = VARIAT
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/taxonomy/{taxId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves information on species from taxonomy database.",
- notes = "NCBI Taxonomy database is being queried by taxId for organism information.
" +
+ @Operation(summary = "NCBI: Retrieves information on species from taxonomy database.",
+ description = "NCBI Taxonomy database is being queried by taxId for organism information.
" +
PARAMETERS_NOTE +
"taxId - id of species in taxonomy database (e.g. 9606)
" +
RETURNS_NOTE +
"commonName - common species name (e.g. \"human\")
" +
- "scientificName - scientific species name (e.g. \"homo sapiens\")
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "scientificName - scientific species name (e.g. \"homo sapiens\")
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBITaxonomyInfo(@PathVariable(value = "taxId") final String taxId)
throws ExternalDbUnavailableException {
@@ -327,10 +336,11 @@ public Result fetchNCBITaxonomyInfo(@PathVariable(value = "taxId
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/taxonomy/{term}", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves list of organisms for search query",
- notes = "NCBI: Retrieves list of organisms for search query",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ @Operation(summary = "NCBI: Retrieves list of organisms for search query",
+ description = "NCBI: Retrieves list of organisms for search query")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getOrganismsByTerm(@PathVariable final String term)
throws ExternalDbUnavailableException, JsonProcessingException {
return Result.success(ncbiAuxiliaryManager.fetchTaxonomyInfosByTermMock(term));
@@ -338,16 +348,18 @@ public Result> getOrganismsByTerm(@PathVariable final Strin
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/variation/{rsId}/get", method = RequestMethod.GET)
- @ApiOperation(value = "NCBI: Retrieves aggregated information on variation using rsId.",
- notes = "Several NCBI databases are being queried by rsId, result information is being aggregated" +
+ @Operation(summary = "NCBI: Retrieves aggregated information on variation using rsId.",
+ description = "Several NCBI databases are being queried by rsId, result information is being aggregated" +
"in a proper way and returned by service.
" +
PARAMETERS_NOTE +
RSID_DESCRIPTION_NOTE +
"Following sequence of queries is peroformed:
" +
"1) Short variation db poll
" +
"2) Clin variation db poll
" +
- "3) Taxonomy db poll
", produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ "3) Taxonomy db poll
")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result fetchNCBIAggregatedVariationInfo(@PathVariable(value = VARIATION_ID_NAME)
final String rsId)
throws ExternalDbUnavailableException {
@@ -362,18 +374,19 @@ public Result fetchNCBIAggregatedVariationInfo(@PathVariable(va
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/variation/region", method = RequestMethod.POST)
- @ApiOperation(
- value = "NCBI: Retrieves information on variations located in given interval",
- notes = "NCBI snp database is being queried for variations in given interval" +
+ @Operation(
+ summary = "NCBI: Retrieves information on variations located in given interval",
+ description = "NCBI snp database is being queried for variations in given interval" +
"in a proper way and returned by service.
" +
PARAMETERS_NOTE +
"species - species name (e.g. \"human\")
" +
"chromosome - chromosome name (e.g. \"1\")
" +
"start - start coordinate in a given chromosome (e.g. 140424943)
" +
"finish - end coordinate in a given chromosome (e.g. 140624564)
" +
- RSID_DESCRIPTION_NOTE,
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(value = { @ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION) })
+ RSID_DESCRIPTION_NOTE)
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> fetchNCBIVariationInfoOnInterval(@RequestBody final RegionQuery regionQuery)
throws ExternalDbUnavailableException {
@@ -388,14 +401,13 @@ public Result> fetchNCBIVariationInfoOnInterval(@RequestBody fin
@ResponseBody
@RequestMapping(value = "/externaldb/blat/search", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns statistics generated by BLAT search.",
- notes = "Provides statistics generated by BLAT search performed on a read sequence. ReferenceId is required "
- + "to search for required species",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns statistics generated by BLAT search.",
+ description = "Provides statistics generated by BLAT search performed on a read sequence. ReferenceId is required "
+ + "to search for required species")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> blatReadSequence(@RequestParam
final Long referenceId,
@RequestBody final ReadSequenceVO readSequence)
@@ -405,13 +417,12 @@ public Result> blatReadSequence(@RequestParam
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/genes/import", method = RequestMethod.PUT)
- @ApiOperation(
- value = "Imports gene ids data from NCBI",
- notes = "Imports gene ids data from NCBI",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Imports gene ids data from NCBI",
+ description = "Imports gene ids data from NCBI")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result importNCBIGeneIdsData(@RequestParam final String path) throws IOException, ParseException {
ncbiEnsemblIdsManager.importData(path);
return Result.success(null);
@@ -419,13 +430,12 @@ public Result importNCBIGeneIdsData(@RequestParam final String path) th
@ResponseBody
@RequestMapping(value = "/externaldb/ncbi/genes/info/import", method = RequestMethod.PUT)
- @ApiOperation(
- value = "Imports genes info data from NCBI",
- notes = "Imports genes info data from NCBI",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Imports genes info data from NCBI",
+ description = "Imports genes info data from NCBI")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result importNCBIGenesInfoData(@RequestParam final String path) throws IOException, ParseException {
ncbiGeneInfoManager.importData(path);
return Result.success(null);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologController.java
index 883e9f114..6a3eeeb54 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologController.java
@@ -30,10 +30,10 @@
import com.epam.catgenome.manager.externaldb.SearchResult;
import com.epam.catgenome.manager.externaldb.homolog.HomologSearchRequest;
import com.epam.catgenome.manager.externaldb.homolog.HomologSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.apache.lucene.queryparser.classic.ParseException;
import org.springframework.http.MediaType;
@@ -44,46 +44,43 @@
import java.util.Map;
@RestController
-@Api(value = "homolog", description = "Homolog Data Management")
+@Tag(name = "homolog", description = "Homolog Data Management")
@RequiredArgsConstructor
public class HomologController extends AbstractRESTController {
private final HomologSecurityService homologSecurityService;
@PostMapping(value = "/homolog/search")
- @ApiOperation(
- value = "Searches homologs by gene ID",
- notes = "Searches homologs by gene ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches homologs by gene ID",
+ description = "Searches homologs by gene ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> search(@RequestBody final HomologSearchRequest searchRequest)
throws IOException, ParseException, ExternalDbUnavailableException {
return Result.success(homologSecurityService.searchHomolog(searchRequest));
}
@GetMapping(value = "/homolog/search")
- @ApiOperation(
- value = "Searches homologs by gene IDs",
- notes = "Searches homologs by gene IDs",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches homologs by gene IDs",
+ description = "Searches homologs by gene IDs")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result>> search(@RequestParam final List geneIds)
throws IOException, ParseException {
return Result.success(homologSecurityService.searchHomolog(geneIds));
}
@PutMapping(value = "/homolog/import")
- @ApiOperation(
- value = "Imports Homolog data",
- notes = "Imports Homolog data",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Imports Homolog data",
+ description = "Imports Homolog data")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result importHomologData(@RequestParam final String databaseName,
@RequestParam final String databasePath)
throws IOException, ParseException {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologeneController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologeneController.java
index a8e5ac073..570338e2a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologeneController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologeneController.java
@@ -29,10 +29,10 @@
import com.epam.catgenome.manager.externaldb.SearchResult;
import com.epam.catgenome.manager.externaldb.homologene.HomologeneSecurityService;
import com.epam.catgenome.manager.externaldb.homologene.HomologeneSearchRequest;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.apache.lucene.queryparser.classic.ParseException;
import org.springframework.http.MediaType;
@@ -43,20 +43,19 @@
import java.util.Map;
@RestController
-@Api(value = "homologene", description = "Homologene Data Management")
+@Tag(name = "homologene", description = "Homologene Data Management")
@RequiredArgsConstructor
public class HomologeneController extends AbstractRESTController {
private final HomologeneSecurityService homologeneSecurityService;
@PostMapping(value = "/homologene/search")
- @ApiOperation(
- value = "Returns list of Homologenes",
- notes = "Returns list of Homologenes",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns list of Homologenes",
+ description = "Returns list of Homologenes")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> search(
@RequestBody final HomologeneSearchRequest query)
throws IOException, ParseException {
@@ -64,26 +63,24 @@ public Result> search(
}
@GetMapping(value = "/homologene/search")
- @ApiOperation(
- value = "Returns list of Homologenes by gene ids",
- notes = "Returns list of Homologenes by gene ids",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns list of Homologenes by gene ids",
+ description = "Returns list of Homologenes by gene ids")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result>> search(@RequestParam final List geneIds)
throws IOException, ParseException {
return Result.success(homologeneSecurityService.searchHomologenes(geneIds));
}
@PutMapping(value = "/homologene/import")
- @ApiOperation(
- value = "Creates Homologene Lucene Index from Homologene file",
- notes = "Creates Homologene Lucene Index from Homologene file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates Homologene Lucene Index from Homologene file",
+ description = "Creates Homologene Lucene Index from Homologene file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result importHomologeneDatabase(@RequestParam final String databasePath)
throws IOException, ParseException {
homologeneSecurityService.importHomologeneDatabase(databasePath);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/TaxonomyController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/TaxonomyController.java
index fb8dddd04..ee28b2fd4 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/TaxonomyController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/TaxonomyController.java
@@ -27,10 +27,10 @@
import com.epam.catgenome.controller.Result;
import com.epam.catgenome.manager.externaldb.taxonomy.TaxonomySecurityService;
import com.epam.catgenome.manager.externaldb.taxonomy.Taxonomy;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.apache.lucene.queryparser.classic.ParseException;
import org.springframework.http.MediaType;
@@ -44,45 +44,42 @@
import java.util.List;
@RestController
-@Api(value = "taxonomy", description = "Taxonomy Data Management")
+@Tag(name = "taxonomy", description = "Taxonomy Data Management")
@RequiredArgsConstructor
public class TaxonomyController extends AbstractRESTController {
private final TaxonomySecurityService taxonomySecurityService;
@GetMapping(value = "/taxonomies/{term}")
- @ApiOperation(
- value = "Returns list of Organisms by term",
- notes = "Returns list of Organisms by term",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns list of Organisms by term",
+ description = "Returns list of Organisms by term")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTaxonomies(@PathVariable final String term)
throws IOException, ParseException {
return Result.success(taxonomySecurityService.searchOrganisms(term));
}
@GetMapping(value = "/taxonomy/{taxId}")
- @ApiOperation(
- value = "Returns Organism by taxId",
- notes = "Returns Organism by taxId",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns Organism by taxId",
+ description = "Returns Organism by taxId")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadTaxonomy(@PathVariable final long taxId) throws IOException, ParseException {
return Result.success(taxonomySecurityService.searchOrganismById(taxId));
}
@PutMapping(value = "/taxonomy/upload")
- @ApiOperation(
- value = "Creates Taxonomy Lucene Index from Taxonomy file",
- notes = "Creates Taxonomy Lucene Index from Taxonomy file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates Taxonomy Lucene Index from Taxonomy file",
+ description = "Creates Taxonomy Lucene Index from Taxonomy file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result uploadTaxonomyDatabase(@RequestParam final String taxonomyFilePath)
throws IOException, ParseException {
taxonomySecurityService.writeLuceneTaxonomyIndex(taxonomyFilePath);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/filter/FilterController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/filter/FilterController.java
index a1adf1965..ea13abaaf 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/filter/FilterController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/filter/FilterController.java
@@ -50,10 +50,10 @@
import com.epam.catgenome.entity.index.VcfIndexEntry;
import com.epam.catgenome.entity.vcf.VcfFilterForm;
import com.epam.catgenome.entity.vcf.VcfFilterInfo;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import javax.servlet.http.HttpServletResponse;
@@ -61,7 +61,7 @@
* A REST controller implementation, responsible for VCF filter services
*/
@RestController
-@Api(value = "Filter", description = "Filtering operations")
+@Tag(name = "Filter", description = "Filtering operations")
public class FilterController extends AbstractRESTController {
@Autowired
private FeatureIndexSecurityService featureIndexSecurityService;
@@ -70,35 +70,33 @@ public class FilterController extends AbstractRESTController {
private VcfSecurityService vcfSecurityService;
@RequestMapping(value = "/filter/searchGenes", method = RequestMethod.POST)
- @ApiOperation(
- value = "Searches for IDs of genes, that are affected by variations",
- notes = "Searches for IDs of genes, that are affected by variations located in VCF files, specified by ids",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for IDs of genes, that are affected by variations",
+ description = "Searches for IDs of genes, that are affected by variations located in VCF files, specified by ids")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> searchGenesInProject(@RequestBody GeneSearchQuery geneQuery) throws IOException {
return Result.success(featureIndexSecurityService.searchGenesInVcfFiles(geneQuery.getSearch(),
geneQuery.getVcfIdsByProject()));
}
@RequestMapping(value = "/filter/info", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns information about VCF filter by file IDs.",
- notes = "Returns information about VCF filter by file IDs, all information taken from file header.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns information about VCF filter by file IDs.",
+ description = "Returns information about VCF filter by file IDs, all information taken from file header.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getFieldInfo(
@RequestBody ItemsByProject vcfFileIdsByProjectId) throws IOException {
return Result.success(vcfSecurityService.getFiltersInfo(vcfFileIdsByProjectId.getValue()));
}
@RequestMapping(value = "/filter", method = RequestMethod.POST)
- @ApiOperation(
- value = "Filters variations for a given VCF file",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Filters variations for a given VCF file",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -149,20 +147,19 @@ public Result getFieldInfo(
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Callable>> filterVcf(@RequestBody final VcfFilterForm filterForm)
throws IOException {
return () -> Result.success(featureIndexSecurityService.filterVariations(filterForm));
}
@RequestMapping(value = "/filter/export", method = RequestMethod.POST)
- @ApiOperation(
- value = "Filters variations for a given VCF file and exports to CSV/TSV",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Filters variations for a given VCF file and exports to CSV/TSV",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -213,9 +210,10 @@ public Callable>> filterVcf(@RequestBody
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
- @ApiResponses(value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)})
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void exportVcf(@RequestBody final VcfExportFilterForm filterForm,
@RequestParam final FileFormat format,
@RequestParam final boolean includeHeader,
@@ -226,9 +224,9 @@ public void exportVcf(@RequestBody final VcfExportFilterForm filterForm,
}
@RequestMapping(value = "/filter/group", method = RequestMethod.POST)
- @ApiOperation(
- value = "Groups variations by given field for a given set of VCF files, according to filter",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Groups variations by given field for a given set of VCF files, according to filter",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -273,11 +271,10 @@ public void exportVcf(@RequestBody final VcfExportFilterForm filterForm,
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Callable>> groupVariations(
@RequestBody final VcfFilterForm filterForm,
@RequestParam String groupBy) {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/gene/GeneController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/gene/GeneController.java
index 5725b6945..71eaf6550 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/gene/GeneController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/gene/GeneController.java
@@ -67,10 +67,10 @@
import com.epam.catgenome.exception.GeneReadingException;
import com.epam.catgenome.exception.HistogramReadingException;
import com.epam.catgenome.util.Utils;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PutMapping;
@@ -91,7 +91,7 @@
* @author Mikhail Miroliubov
*/
@Controller
-@Api(value = "genes", description = "Gene Track Management")
+@Tag(name = "genes", description = "Gene Track Management")
public class GeneController extends AbstractRESTController {
private static final String REFERENCE_ID_FIELD = "referenceId";
@@ -106,18 +106,17 @@ public class GeneController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/gene/register", method = RequestMethod.POST)
- @ApiOperation(
- value = "Registers a gene file in the system.",
- notes = "Registers a file, stored in a file system (for now). Registration request has the following " +
+ @Operation(
+ summary = "Registers a gene file in the system.",
+ description = "Registers a file, stored in a file system (for now). Registration request has the following " +
"properties:
" +
"1) " + REFERENCE_ID_FIELD + " - a reference, for which file is being registered
" +
"2) path - a path to file " +
"3) indexPath - optional a path to an index file
" +
- "4) name - optional a name for gene track",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "4) name - optional a name for gene track")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerGeneFile(@RequestBody
FeatureIndexedFileRegistrationRequest request) {
return Result.success(geneSecurityService.registerGeneFile(request));
@@ -125,8 +124,11 @@ public Result registerGeneFile(@RequestBody
@ResponseBody
@RequestMapping(value = "/secure/gene/register", method = RequestMethod.DELETE)
- @ApiOperation(value = "Unregisters a gene file in the system.",
- notes = "", produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(summary = "Unregisters a gene file in the system.",
+ description = "")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result unregisterGeneFile(@RequestParam final long geneFileId) throws IOException {
GeneFile deletedFile = geneSecurityService.unregisterGeneFile(geneFileId);
return Result.success(true, MessageHelper.getMessage(MessagesConstants.INFO_UNREGISTER, deletedFile.getName()));
@@ -134,11 +136,10 @@ public Result unregisterGeneFile(@RequestParam final long geneFileId) t
@ResponseBody
@RequestMapping(value = "/gene/{geneFileId}/index", method = RequestMethod.GET)
- @ApiOperation(value = "Rebuilds a gene file feature index",
- notes = "Rebuilds a gene file feature index." +
+ @Operation(summary = "Rebuilds a gene file feature index",
+ description = "Rebuilds a gene file feature index." +
"full parameter specifies if full original file should be reindexed, or " +
- "preprocessed large scale and transcript files should be used for indexing.",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ "preprocessed large scale and transcript files should be used for indexing.")
public Result reindexGeneFile(@PathVariable long geneFileId,
@RequestParam(defaultValue = "false") boolean full,
@RequestParam(defaultValue = "false") boolean createTabixIndex) throws IOException {
@@ -149,9 +150,9 @@ public Result reindexGeneFile(@PathVariable long geneFileId,
@ResponseBody
@RequestMapping(value = GENE_URL + REFERENCE_ID_FIELD + "}/track/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns data matched the given query to fill in a gene track.",
- notes = "It provides data for a gene track with the given scale factor between the beginning " +
+ @Operation(
+ summary = "Returns data matched the given query to fill in a gene track.",
+ description = "It provides data for a gene track with the given scale factor between the beginning " +
"position with the first base having position 1 and ending position inclusive in a target " +
"chromosome. All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -160,11 +161,10 @@ public Result reindexGeneFile(@PathVariable long geneFileId,
"chromosome always has got position = 1;
" +
"4) endIndex is the last base position for a requested window.
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible element on a" +
- " track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTrack(@RequestBody final TrackQuery trackQuery,
@PathVariable(value = REFERENCE_ID_FIELD) final Long referenceId,
@RequestParam(required = false) final String fileUrl,
@@ -199,9 +199,9 @@ public Result> loadTrack(@RequestBody final TrackQuery trac
@ResponseBody
@RequestMapping(value = "/gene/transcript/track/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns data matched the given query to fill in a gene track with transcripts.",
- notes = "It provides data for a gene track with the given scale factor between the beginning position " +
+ @Operation(
+ summary = "Returns data matched the given query to fill in a gene track with transcripts.",
+ description = "It provides data for a gene track with the given scale factor between the beginning position " +
"with the first base having position 1 and ending position inclusive in a target chromosome. " +
"All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -210,11 +210,10 @@ public Result> loadTrack(@RequestBody final TrackQuery trac
"chromosome always has got position = 1;
" +
"4) endIndex is the last base position for a requested window.
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible element on a" +
- " track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTrackWithTranscript(@RequestBody final TrackQuery trackQuery,
@RequestParam(required = false) final String fileUrl,
@RequestParam(required = false) final String indexUrl)
@@ -225,13 +224,12 @@ public Result> loadTrackWithTranscript(@RequestBody final
@ResponseBody
@RequestMapping(value = "gene/pbd/{pbdID}/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns a list of entity from PBD",
- notes = "param is PBD ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a list of entity from PBD",
+ description = "param is PBD ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getPBDentity(@PathVariable(value = "pbdID") String pbdID)
throws ExternalDbUnavailableException {
return Result.success(geneSecurityService.getPBDItemsFromBD(pbdID));
@@ -239,9 +237,9 @@ public Result getPBDentity(@PathVariable(value = "pbdID") String p
@ResponseBody
@RequestMapping(value = "/gene/track/histogram", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns a histogram of genes amount on regions of chromosome",
- notes = "It provides histogram for a gene track with the given scale factor between the " +
+ @Operation(
+ summary = "Returns a histogram of genes amount on regions of chromosome",
+ description = "It provides histogram for a gene track with the given scale factor between the " +
"beginning position with the first base having position 1 and ending position inclusive " +
"in a target chromosome. All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -251,11 +249,10 @@ public Result getPBDentity(@PathVariable(value = "pbdID") String p
"4) endIndex is the last base position for a requested window. " +
"It is treated inclusively;
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible element" +
- " on a track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " on a track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadHistogram(@RequestBody final TrackQuery trackQuery) throws HistogramReadingException {
final Track geneTrack = Query2TrackConverter.convertToTrack(trackQuery);
return Result.success(geneSecurityService.loadHistogram(geneTrack));
@@ -263,9 +260,9 @@ public Result> loadHistogram(@RequestBody final TrackQuery trackQuery
@ResponseBody
@RequestMapping(value = GENE_URL + REFERENCE_ID_FIELD + "}/protein/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns reconstructed protein sequence matched to the given query of gene track.",
- notes = "It provides data for a protein sequence with the given scale factor between the beginning " +
+ @Operation(
+ summary = "Returns reconstructed protein sequence matched to the given query of gene track.",
+ description = "It provides data for a protein sequence with the given scale factor between the beginning " +
"position with the first base having position 1 and ending position inclusive in a target " +
"chromosome. All parameters are mandatory and described below:
" +
"1) " + REFERENCE_ID_FIELD + " specifies ID of reference genome;
" +
@@ -276,11 +273,10 @@ public Result> loadHistogram(@RequestBody final TrackQuery trackQuery
"5) endIndex is the last base position for a requested window. " +
"It is treated inclusively;
" +
"6) scaleFactor specifies an inverse value to number of bases per one visible element on a" +
- " track (e.g., pixel) - IS IGNORED FOR NOW",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ " track (e.g., pixel) - IS IGNORED FOR NOW")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadProteinSequence(@RequestBody final TrackQuery trackQuery,
@PathVariable(value = REFERENCE_ID_FIELD) final Long referenceId) throws GeneReadingException {
return Result.success(proteinSecurityService.loadProteinSequence(Query2TrackConverter.convertToTrack(
@@ -289,13 +285,12 @@ public Result> loadProteinSequence(@RequestBody final
@RequestMapping(value = "/gene/aminoacids", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Generate amino acids sequence for the given feature ID, case-insensitive",
- notes = "Generate amino acids sequence for the given feature ID, case-insensitive",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Generate amino acids sequence for the given feature ID, case-insensitive",
+ description = "Generate amino acids sequence for the given feature ID, case-insensitive")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result constructAminoAcidSequence(
@RequestBody ProteinSequenceConstructRequest request) throws IOException {
return Result.success(geneSecurityService.loadProteinSequenceForFeature(request));
@@ -304,10 +299,10 @@ public Result constructAminoAcidSequence(
@ResponseBody
@RequestMapping(value = GENE_URL + REFERENCE_ID_FIELD + "}/variation/protein/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns reconstructed protein sequence matched to the given query of gene track, "
+ @Operation(
+ summary = "Returns reconstructed protein sequence matched to the given query of gene track, "
+ "taking into account variations.",
- notes = "It provides data for a protein sequence with the given scale factor between the beginning " +
+ description = "It provides data for a protein sequence with the given scale factor between the beginning " +
"position with the first base having position 1 and ending position inclusive in a target " +
"chromosome. All parameters are mandatory and described below:
" +
"Body:
" +
@@ -321,8 +316,7 @@ public Result constructAminoAcidSequence(
"5) endIndex is the last base position for a requested window. " +
"It is treated inclusively;
" +
"6) scaleFactor specifies an inverse value to number of bases per one visible element on a" +
- " track (e.g., pixel)",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ " track (e.g., pixel)")
public Result> loadProteinSequenceForVariations(
@RequestBody final ProteinSequenceVariationQuery psVariationQuery, @PathVariable final Long referenceId)
throws GeneReadingException {
@@ -331,14 +325,13 @@ public Result> loadProteinSequenceForVariatio
@RequestMapping(value = "/gene/{trackId}/{chromosomeId}/next", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Returns the next feature for a given track",
- notes = "Returns the next feature for a given track in a given chromosome.
" +
- "Searches from given parameter 'fromPosition' (required)",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns the next feature for a given track",
+ description = "Returns the next feature for a given track in a given chromosome.
" +
+ "Searches from given parameter 'fromPosition' (required)")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result jumpToNextGene(@RequestParam int fromPosition,
@PathVariable(value = "trackId") long geneFileId,
@PathVariable(value = "chromosomeId") long chromosomeId,
@@ -350,15 +343,14 @@ public Result jumpToNextGene(@RequestParam int fromPosition,
@RequestMapping(value = "/gene/{trackId}/{chromosomeId}/prev", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Returns the previous feature for a given track",
- notes = "Returns the previous feature for a given track in a given chromosome.
" +
+ @Operation(
+ summary = "Returns the previous feature for a given track",
+ description = "Returns the previous feature for a given track in a given chromosome.
" +
"Searches from given parameter 'fromPosition' (required), from a given sample (parameter " +
- "'sampleId', optional)",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "'sampleId', optional)")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result jumpToPrevGene(@RequestParam int fromPosition,
@PathVariable(value = "trackId") long geneFileId,
@PathVariable(value = "chromosomeId") long chromosomeId,
@@ -370,17 +362,16 @@ public Result jumpToPrevGene(@RequestParam int fromPosition,
@RequestMapping(value = "/gene/exons/viewport", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Returns exons of the track",
- notes = "Returns all exons of the track on a given interval, specified by:
" +
+ @Operation(
+ summary = "Returns exons of the track",
+ description = "Returns all exons of the track on a given interval, specified by:
" +
"- centerPosition - a position of a view port's center on the reference
" +
"- viewPortSize - a size of a view port in bps
" +
"- intronLength - a value, determine how much of intron region lengths should be shown in bps" +
- "Affects the amount of exons fitted in a view port
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "Affects the amount of exons fitted in a view port")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> fetchExons(@RequestBody ExonViewPortQuery query) throws IOException {
return Result.success(geneSecurityService.loadExonsInViewPort(query.getId(), query.getChromosomeId(),
query.getCenterPosition(), query.getViewPortSize(), query.getIntronLength(), query.getProjectId()));
@@ -388,17 +379,16 @@ public Result> fetchExons(@RequestBody ExonViewPortQuery query) thro
@RequestMapping(value = "/gene/exons/range", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Returns exons of the track",
- notes = "Returns all exons of the track on a given interval, specified by:
" +
+ @Operation(
+ summary = "Returns exons of the track",
+ description = "Returns all exons of the track on a given interval, specified by:
" +
"- startIndex - a start of a range on a chromosome
" +
"- endIndex - an end of a range on a chromosome
" +
"- intronLength - a value, determine how much of intron region lengths should be shown in bps" +
- "Affects the amount of exons fitted in a view port
",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "Affects the amount of exons fitted in a view port")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> fetchExons(@RequestBody ExonRangeQuery query) throws IOException {
return Result.success(geneSecurityService.loadExonsInTrack(query.getId(), query.getChromosomeId(),
query.getStartIndex(), query.getEndIndex(), query.getIntronLength(), query.getProjectId()));
@@ -406,13 +396,12 @@ public Result> fetchExons(@RequestBody ExonRangeQuery query) throws
@GetMapping("/gene/{fileId}/doc")
@ResponseBody
- @ApiOperation(
- value = "Loads specific gene feature content",
- notes = "Loads specific gene feature content",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads specific gene feature content",
+ description = "Loads specific gene feature content")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadGeneFeatureByUid(@PathVariable(value = "fileId") final Long fileId,
@RequestParam(value = "uid") final String uid) {
return Result.success(geneSecurityService.loadGeneFeatureByUid(fileId, uid));
@@ -420,13 +409,12 @@ public Result loadGeneFeatureByUid(@PathVariable(value = "fileId"
@PutMapping("/gene/{fileId}/doc")
@ResponseBody
- @ApiOperation(
- value = "Updates specific gene feature content",
- notes = "Updates specific gene feature content",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates specific gene feature content",
+ description = "Updates specific gene feature content")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateGeneFeatureByUid(@PathVariable(value = "fileId") final Long fileId,
@RequestParam(value = "uid") final String uid,
@RequestBody final GeneHighLevel geneContent) {
@@ -435,13 +423,12 @@ public Result updateGeneFeatureByUid(@PathVariable(value = "fileI
@GetMapping("/gene/{fileId}/activity")
@ResponseBody
- @ApiOperation(
- value = "Returns gene activities by gene file ID and uid",
- notes = "Returns gene activities by gene file ID and uid",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns gene activities by gene file ID and uid",
+ description = "Returns gene activities by gene file ID and uid")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadGeneActivity(@PathVariable(value = "fileId") final Long fileId,
@RequestParam(value = "uid") final String uid) {
return Result.success(geneSecurityService.loadGeneActivity(fileId, uid));
@@ -449,13 +436,12 @@ public Result> loadGeneActivity(@PathVariable(value = "fileId") f
@RequestMapping(value = "/gene/search", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Searches for a given feature ID in all reference gene files, case-insensitive",
- notes = "Searches an index of a gene file for a specified feature ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for a given feature ID in all reference gene files, case-insensitive",
+ description = "Searches an index of a gene file for a specified feature ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> searchFeatures(
@RequestParam final String geneId) throws IOException {
return Result.success(geneSecurityService.searchFeatures(geneId));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/heatmap/HeatmapController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/heatmap/HeatmapController.java
index 17a8863de..b61a3dcf1 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/heatmap/HeatmapController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/heatmap/HeatmapController.java
@@ -31,10 +31,10 @@
import com.epam.catgenome.entity.heatmap.HeatmapAnnotationType;
import com.epam.catgenome.entity.heatmap.HeatmapTree;
import com.epam.catgenome.manager.heatmap.HeatmapSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.DeleteMapping;
@@ -50,45 +50,42 @@
import java.util.List;
@RestController
-@Api(value = "heatmap", description = "Heatmap files Management")
+@Tag(name = "heatmap", description = "Heatmap files Management")
@RequiredArgsConstructor
public class HeatmapController extends AbstractRESTController {
private final HeatmapSecurityService heatmapSecurityService;
@GetMapping(value = "/heatmap/{heatmapId}")
- @ApiOperation(
- value = "Returns a heatmap by given id",
- notes = "Returns a heatmap by given id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a heatmap by given id",
+ description = "Returns a heatmap by given id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadHeatmap(@PathVariable final long heatmapId,
@RequestParam(required = false) final Long projectId) {
return Result.success(heatmapSecurityService.loadHeatmap(heatmapId, projectId));
}
@GetMapping(value = "/heatmaps")
- @ApiOperation(
- value = "Returns all heatmaps",
- notes = "Returns all heatmaps",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all heatmaps",
+ description = "Returns all heatmaps")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadHeatmaps() {
return Result.success(heatmapSecurityService.loadHeatmaps());
}
@GetMapping(value = "/heatmap/{heatmapId}/content")
- @ApiOperation(
- value = "Returns heatmap content",
- notes = "Returns heatmap content",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns heatmap content",
+ description = "Returns heatmap content")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result>>> getContent(@PathVariable final long heatmapId,
@RequestParam(required = false) final Long projectId)
throws IOException {
@@ -96,13 +93,12 @@ public Result>>> getContent(@PathVariable final long heat
}
@PutMapping(value = "/heatmap/{heatmapId}/label/annotation")
- @ApiOperation(
- value = "Updates heatmap annotation for labels",
- notes = "Updates heatmap annotation for labels",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates heatmap annotation for labels",
+ description = "Updates heatmap annotation for labels")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateLabelAnnotation(
@PathVariable final long heatmapId,
@RequestParam(required = false) final String path,
@@ -113,13 +109,12 @@ public Result updateLabelAnnotation(
}
@PutMapping(value = "/heatmap/{heatmapId}/cell/annotation")
- @ApiOperation(
- value = "Updates heatmap annotation for cells",
- notes = "Updates heatmap annotation for cells",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates heatmap annotation for cells",
+ description = "Updates heatmap annotation for cells")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateCellAnnotation(
@PathVariable final long heatmapId,
@RequestParam(required = false) final String path,
@@ -129,26 +124,24 @@ public Result updateCellAnnotation(
}
@GetMapping(value = "/heatmap/{heatmapId}/tree")
- @ApiOperation(
- value = "Returns heatmap tree",
- notes = "Returns heatmap tree",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns heatmap tree",
+ description = "Returns heatmap tree")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getTree(@PathVariable final long heatmapId,
@RequestParam(required = false) final Long projectId) throws IOException {
return Result.success(heatmapSecurityService.getTree(heatmapId, projectId));
}
@PutMapping(value = "/heatmap/{heatmapId}/row/tree")
- @ApiOperation(
- value = "Updates phylogenetic tree for heatmap rows",
- notes = "Updates phylogenetic tree for heatmap rows",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates phylogenetic tree for heatmap rows",
+ description = "Updates phylogenetic tree for heatmap rows")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateRowTree(@PathVariable final long heatmapId,
@RequestParam(required = false) final String path) throws IOException {
heatmapSecurityService.updateRowTree(heatmapId, path);
@@ -156,13 +149,12 @@ public Result updateRowTree(@PathVariable final long heatmapId,
}
@PutMapping(value = "/heatmap/{heatmapId}/column/tree")
- @ApiOperation(
- value = "Updates phylogenetic tree for heatmap columns",
- notes = "Updates phylogenetic tree for heatmap columns",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates phylogenetic tree for heatmap columns",
+ description = "Updates phylogenetic tree for heatmap columns")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateColumnTree(@PathVariable final long heatmapId,
@RequestParam(required = false) final String path) throws IOException {
heatmapSecurityService.updateColumnTree(heatmapId, path);
@@ -170,25 +162,23 @@ public Result updateColumnTree(@PathVariable final long heatmapId,
}
@PostMapping(value = "/heatmap")
- @ApiOperation(
- value = "Registers new heatmap",
- notes = "Registers new heatmap",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Registers new heatmap",
+ description = "Registers new heatmap")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createHeatmap(@RequestBody final HeatmapRegistrationRequest heatmap) throws IOException {
return Result.success(heatmapSecurityService.createHeatmap(heatmap));
}
@DeleteMapping(value = "/heatmap/{heatmapId}")
- @ApiOperation(
- value = "Deletes a heatmap, specified by id",
- notes = "Deletes a heatmap, specified by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a heatmap, specified by id",
+ description = "Deletes a heatmap, specified by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteHeatmap(@PathVariable final long heatmapId) throws IOException {
heatmapSecurityService.deleteHeatmap(heatmapId);
return Result.success(null);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/lineage/LineageTreeController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/lineage/LineageTreeController.java
index a1d841c98..08af92448 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/lineage/LineageTreeController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/lineage/LineageTreeController.java
@@ -29,10 +29,10 @@
import com.epam.catgenome.controller.vo.registration.LineageTreeRegistrationRequest;
import com.epam.catgenome.entity.lineage.LineageTree;
import com.epam.catgenome.manager.lineage.LineageTreeSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.DeleteMapping;
@@ -47,20 +47,19 @@
import java.util.List;
@RestController
-@Api(value = "lineage", description = "Strain Lineage Tree files Management")
+@Tag(name = "lineage", description = "Strain Lineage Tree files Management")
@RequiredArgsConstructor
public class LineageTreeController extends AbstractRESTController {
private final LineageTreeSecurityService lineageTreeSecurityService;
@GetMapping(value = "/lineage/trees/{referenceId}")
- @ApiOperation(
- value = "Returns lineage trees by given parameters",
- notes = "Returns lineage trees by given parameters",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns lineage trees by given parameters",
+ description = "Returns lineage trees by given parameters")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadLineageTrees(@PathVariable final Long referenceId,
@RequestParam(required = false) final Long lineageTreeId,
@RequestParam(required = false) final Long projectId) {
@@ -68,51 +67,47 @@ public Result> loadLineageTrees(@PathVariable final Long refer
}
@GetMapping(value = "/lineage/tree/{lineageTreeId}")
- @ApiOperation(
- value = "Returns a lineage tree by id",
- notes = "Returns a lineage tree by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a lineage tree by id",
+ description = "Returns a lineage tree by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadLineageTree(@PathVariable final Long lineageTreeId,
@RequestParam(required = false) final Long projectId) {
return Result.success(lineageTreeSecurityService.loadLineageTree(lineageTreeId, projectId));
}
@GetMapping(value = "/lineage/trees/all")
- @ApiOperation(
- value = "Returns all lineage trees",
- notes = "Returns all lineage trees",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all lineage trees",
+ description = "Returns all lineage trees")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadAllLineageTrees() {
return Result.success(lineageTreeSecurityService.loadAllLineageTrees());
}
@PostMapping(value = "/lineage/tree")
- @ApiOperation(
- value = "Registers new lineage tree",
- notes = "Registers new lineage tree",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Registers new lineage tree",
+ description = "Registers new lineage tree")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createLineageTree(@RequestBody final LineageTreeRegistrationRequest request)
throws IOException {
return Result.success(lineageTreeSecurityService.createLineageTree(request));
}
@DeleteMapping(value = "/lineage/tree/{lineageTreeId}")
- @ApiOperation(
- value = "Deletes a lineage tree, specified by id",
- notes = "Deletes a lineage tree, specified by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a lineage tree, specified by id",
+ description = "Deletes a lineage tree, specified by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteLineageTree(@PathVariable final long lineageTreeId) throws IOException {
lineageTreeSecurityService.deleteLineageTree(lineageTreeId);
return Result.success(null);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/llm/LLMController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/llm/LLMController.java
index 9a20e48ae..691e29fe1 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/llm/LLMController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/llm/LLMController.java
@@ -29,10 +29,10 @@
import com.epam.catgenome.entity.llm.LLMMessage;
import com.epam.catgenome.entity.llm.LLMProvider;
import com.epam.catgenome.manager.llm.LLMSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.GetMapping;
@@ -44,20 +44,19 @@
import java.util.List;
@RestController
-@Api(value = "LLM", description = "Access to large language models API")
+@Tag(name = "LLM", description = "Access to large language models API")
@RequiredArgsConstructor
public class LLMController extends AbstractRESTController {
private final LLMSecurityService llmSecurityService;
@PostMapping(value = "/llm/summary")
- @ApiOperation(
- value = "Returns summary over specified PubMed articles",
- notes = "Returns summary over specified PubMed articles",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns summary over specified PubMed articles",
+ description = "Returns summary over specified PubMed articles")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getArticleSummary(
@RequestBody final List pubMedIDs,
@RequestParam(required = false, defaultValue = "OPENAI_GPT_35") final LLMProvider provider,
@@ -67,13 +66,12 @@ public Result getArticleSummary(
}
@GetMapping(value = "/llm/patent")
- @ApiOperation(
- value = "Returns summary over google patents",
- notes = "Returns summary over google patents",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns summary over google patents",
+ description = "Returns summary over google patents")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getPatentSummary(
@RequestParam String query,
@RequestParam(required = false, defaultValue = "OPENAI_GPT_35") final LLMProvider provider,
@@ -83,13 +81,12 @@ public Result getPatentSummary(
}
@PostMapping(value = "/llm/chat")
- @ApiOperation(
- value = "Returns LLM model response for chat",
- notes = "Returns LLM model response for chat",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns LLM model response for chat",
+ description = "Returns LLM model response for chat")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getChatResponse(
@RequestBody final List messages,
@RequestParam(required = false, defaultValue = "OPENAI_GPT_35") final LLMProvider provider,
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/metadata/MetadataController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/metadata/MetadataController.java
index 36c40ce73..7225c783a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/metadata/MetadataController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/metadata/MetadataController.java
@@ -28,10 +28,10 @@
import com.epam.catgenome.controller.Result;
import com.epam.catgenome.entity.metadata.MetadataVO;
import com.epam.catgenome.manager.metadata.MetadataSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.GetMapping;
@@ -42,31 +42,29 @@
@RestController
@RequiredArgsConstructor
-@Api(value = "metadata", description = "Metadata Management")
+@Tag(name = "metadata", description = "Metadata Management")
public class MetadataController extends AbstractRESTController {
private final MetadataSecurityService metadataSecurityService;
@PostMapping(value = "/metadata")
- @ApiOperation(
- value = "Creates or updates metadata",
- notes = "Creates or updates metadata",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates or updates metadata",
+ description = "Creates or updates metadata")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result upsertMetadata(@RequestBody final MetadataVO metadataVO) {
return Result.success(metadataSecurityService.upsert(metadataVO));
}
@GetMapping(value = "/metadata")
- @ApiOperation(
- value = "Loads metadata by entity ID and class",
- notes = "Loads metadata by entity ID and class",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads metadata by entity ID and class",
+ description = "Loads metadata by entity ID and class")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getMetadata(@RequestParam final Long id, @RequestParam final String entityClass) {
return Result.success(metadataSecurityService.get(id, entityClass));
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/patents/PatentsController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/patents/PatentsController.java
index 730019462..c307f2558 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/patents/PatentsController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/patents/PatentsController.java
@@ -35,10 +35,10 @@
import com.epam.catgenome.exception.ExternalDbUnavailableException;
import com.epam.catgenome.manager.externaldb.SearchResult;
import com.epam.catgenome.manager.externaldb.patents.PatentsSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.*;
@@ -47,84 +47,78 @@
import java.util.List;
@RestController
-@Api(value = "patents", description = "Patents Management")
+@Tag(name = "patents", description = "Patents Management")
@RequiredArgsConstructor
public class PatentsController extends AbstractRESTController {
private final PatentsSecurityService ncbiPatentsSecurityService;
@PostMapping(value = "/patents/proteins/ncbi")
- @ApiOperation(
- value = "Searches protein patents by name in NCBI database.",
- notes = "Searches protein patents by name in NCBI database.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches protein patents by name in NCBI database.",
+ description = "Searches protein patents by name in NCBI database.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getProteinPatentsNcbi(@RequestBody final PatentsSearchRequest request)
throws ExternalDbUnavailableException {
return Result.success(ncbiPatentsSecurityService.getProteinPatents(request));
}
@PostMapping(value = "/patents/proteins/google")
- @ApiOperation(
- value = "Searches protein patents by name using Google Patents.",
- notes = "Searches protein patents by name using Google Patents.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches protein patents by name using Google Patents.",
+ description = "Searches protein patents by name using Google Patents.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getProteinPatentsGoogle(
@RequestBody final PatentsSearchRequest request) {
return Result.success(ncbiPatentsSecurityService.getProteinPatentsGoogle(request));
}
@PostMapping(value = "/patents/drugs/ncbi")
- @ApiOperation(
- value = "Searches drug patents by name in NCBI database.",
- notes = "Searches drug patents by name in NCBI database.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches drug patents by name in NCBI database.",
+ description = "Searches drug patents by name in NCBI database.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getDrugPatents(@RequestBody final PatentsSearchRequest request)
throws ExternalDbUnavailableException, IOException {
return Result.success(ncbiPatentsSecurityService.getDrugPatents(request));
}
@GetMapping(value = "/patents/drugs/ncbi")
- @ApiOperation(
- value = "Searches drug patents by id in NCBI database.",
- notes = "Searches drug patents by id in NCBI database.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches drug patents by id in NCBI database.",
+ description = "Searches drug patents by id in NCBI database.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getDrugPatents(@RequestParam final String id)
throws ExternalDbUnavailableException, IOException {
return Result.success(ncbiPatentsSecurityService.getDrugPatents(id));
}
@GetMapping(value = "/patents/proteins")
- @ApiOperation(
- value = "Creates BLAST task to search protein patents by sequence.",
- notes = "Creates BLAST task to search protein patents by sequence.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates BLAST task to search protein patents by sequence.",
+ description = "Creates BLAST task to search protein patents by sequence.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getPatents(@RequestParam final String sequence) throws BlastRequestException {
return Result.success(ncbiPatentsSecurityService.getPatents(sequence));
}
@GetMapping(value = "/patents/proteins/{targetId}")
- @ApiOperation(
- value = "Searches protein patents by sequence.",
- notes = "Searches protein patents by sequence.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches protein patents by sequence.",
+ description = "Searches protein patents by sequence.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getPatents(@PathVariable final Long targetId,
@RequestParam final String sequenceId) {
return Result.success(ncbiPatentsSecurityService.getPatents(targetId, sequenceId));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java
index 37f54307b..2db8a9242 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java
@@ -33,10 +33,10 @@
import com.epam.catgenome.entity.pathway.SpeciesDescription;
import com.epam.catgenome.util.db.Page;
import com.epam.catgenome.manager.pathway.PathwaySecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.apache.lucene.queryparser.classic.ParseException;
import org.springframework.http.MediaType;
@@ -53,45 +53,42 @@
import java.util.List;
@RestController
-@Api(value = "pathway", description = "Metabolic Pathways Management")
+@Tag(name = "pathway", description = "Metabolic Pathways Management")
@RequiredArgsConstructor
public class PathwayController extends AbstractRESTController {
private final PathwaySecurityService pathwaySecurityService;
@GetMapping(value = "/pathway/{pathwayId}")
- @ApiOperation(
- value = "Returns a pathway by id",
- notes = "Returns a pathway by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a pathway by id",
+ description = "Returns a pathway by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadPathway(@PathVariable final Long pathwayId,
@RequestParam(required = false) final Long projectId) {
return Result.success(pathwaySecurityService.loadPathway(pathwayId, projectId));
}
@GetMapping(value = "/pathway/all")
- @ApiOperation(
- value = "Returns all registered pathways",
- notes = "Returns all registered pathways",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all registered pathways",
+ description = "Returns all registered pathways")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadPathways(@RequestParam(required = false) final Long projectId) {
return Result.success(pathwaySecurityService.loadPathways(projectId));
}
@GetMapping(value = "/pathway/content/{pathwayId}")
- @ApiOperation(
- value = "Returns a pathway file content by pathway id",
- notes = "Returns a pathway file content by pathway id",
- produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a pathway file content by pathway id",
+ description = "Returns a pathway file content by pathway id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void loadPathwayContent(@PathVariable final Long pathwayId,
@RequestParam(required = false) final Long projectId,
final HttpServletResponse response) throws IOException {
@@ -101,65 +98,60 @@ public void loadPathwayContent(@PathVariable final Long pathwayId,
}
@PostMapping(value = "/pathways")
- @ApiOperation(
- value = "Returns pathways page",
- notes = "Returns pathways page",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns pathways page",
+ description = "Returns pathways page")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadPathways(@RequestBody final PathwayQueryParams params)
throws IOException, ParseException {
return Result.success(pathwaySecurityService.loadPathways(params));
}
@PostMapping(value = "/pathway")
- @ApiOperation(
- value = "Registers new pathway",
- notes = "Registers new pathway",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Registers new pathway",
+ description = "Registers new pathway")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerPathway(@RequestBody final PathwayRegistrationRequest request)
throws IOException {
return Result.success(pathwaySecurityService.registerPathway(request));
}
@PostMapping(value = "/biopax")
- @ApiOperation(
- value = "Registers new BioPAX file",
- notes = "Registers new BioPAX file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Registers new BioPAX file",
+ description = "Registers new BioPAX file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerBioPAX(@RequestBody final BioPAXRegistrationRequest request) throws IOException {
pathwaySecurityService.registerBioPAX(request);
return Result.success(null);
}
@DeleteMapping(value = "/pathway/{pathwayId}")
- @ApiOperation(
- value = "Deletes a pathway, specified by id",
- notes = "Deletes a pathway, specified by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a pathway, specified by id",
+ description = "Deletes a pathway, specified by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deletePathway(@PathVariable final long pathwayId) throws IOException {
pathwaySecurityService.deletePathway(pathwayId);
return Result.success(null);
}
@GetMapping(value = "/pathway/species")
- @ApiOperation(
- value = "Returns list of unique species associated with pathways",
- notes = "Returns list of unique species associated with pathways",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns list of unique species associated with pathways",
+ description = "Returns list of unique species associated with pathways")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadSpecies() {
return Result.success(pathwaySecurityService.loadSpecies());
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/pdb/PdbFileController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/pdb/PdbFileController.java
index 3c91f9c38..a0ab12b19 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/pdb/PdbFileController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/pdb/PdbFileController.java
@@ -30,10 +30,10 @@
import com.epam.catgenome.entity.pdb.PdbFileQueryParams;
import com.epam.catgenome.manager.pdb.PdbFileSecurityService;
import com.epam.catgenome.util.db.Page;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import lombok.RequiredArgsConstructor;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.DeleteMapping;
@@ -50,68 +50,63 @@
import java.util.Map;
@RestController
-@Api(value = "pdb", description = "PDB Files Management")
+@Tag(name = "pdb", description = "PDB Files Management")
@RequiredArgsConstructor
public class PdbFileController extends AbstractRESTController {
private final PdbFileSecurityService service;
@GetMapping(value = "/pdb/{pdbFileId}")
- @ApiOperation(
- value = "Returns a pdb file by given id",
- notes = "Returns a pdb file by given id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a pdb file by given id",
+ description = "Returns a pdb file by given id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result load(@PathVariable final long pdbFileId) {
return Result.success(service.load(pdbFileId));
}
@GetMapping(value = "/pdb")
- @ApiOperation(
- value = "Returns pdb files",
- notes = "Returns pdb files",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns pdb files",
+ description = "Returns pdb files")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> load() {
return Result.success(service.load());
}
@PostMapping(value = "/pdb/filter")
- @ApiOperation(
- value = "Filters pdb files",
- notes = "Filters pdb files. Result can be sorted by gene_id, name(default) and pretty_name fields.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Filters pdb files",
+ description = "Filters pdb files. Result can be sorted by gene_id, name(default) and pretty_name fields.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTarget(@RequestBody final PdbFileQueryParams params) {
return Result.success(service.load(params));
}
@PostMapping(value = "/pdb")
- @ApiOperation(
- value = "Registers new pdb file",
- notes = "Registers new pdb file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Registers new pdb file",
+ description = "Registers new pdb file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result create(@RequestBody final PdbFile pdbFile) throws IOException {
return Result.success(service.create(pdbFile));
}
@PutMapping(value = "/pdb/{pdbFileId}")
- @ApiOperation(
- value = "Updates pdb file metadata",
- notes = "Updates pdb file metadata",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates pdb file metadata",
+ description = "Updates pdb file metadata")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateMetadata(@PathVariable final long pdbFileId,
@RequestBody final Map metadata) {
service.updateMetadata(pdbFileId, metadata);
@@ -119,26 +114,24 @@ public Result updateMetadata(@PathVariable final long pdbFileId,
}
@DeleteMapping(value = "/pdb/{pdbFileId}")
- @ApiOperation(
- value = "Deletes a pdb file, specified by id",
- notes = "Deletes a pdb file, specified by id",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a pdb file, specified by id",
+ description = "Deletes a pdb file, specified by id")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result delete(@PathVariable final long pdbFileId) {
service.delete(pdbFileId);
return Result.success(null);
}
@GetMapping(value = "/pdb/content/{pdbFileId}")
- @ApiOperation(
- value = "Gets pdb file content",
- notes = "Gets pdb file content",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Gets pdb file content",
+ description = "Gets pdb file content")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void load(@PathVariable final long pdbFileId, final HttpServletResponse response) throws IOException {
byte[] bytes = service.loadContent(pdbFileId);
response.getOutputStream().write(bytes);
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/person/RoleController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/person/RoleController.java
index 3f9c3b495..6114758cc 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/person/RoleController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/person/RoleController.java
@@ -32,10 +32,10 @@
import com.epam.catgenome.entity.user.ExtendedRole;
import com.epam.catgenome.entity.user.Role;
import com.epam.catgenome.manager.user.RoleSecurityService;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty;
import org.springframework.http.MediaType;
@@ -54,7 +54,7 @@
*/
@RestController
@ConditionalOnProperty(value = "security.acl.enable", havingValue = "true")
-@Api(value = "Role", description = "Role Management")
+@Tag(name = "Role", description = "Role Management")
public class RoleController extends AbstractRESTController {
@Autowired
@@ -62,14 +62,13 @@ public class RoleController extends AbstractRESTController {
@RequestMapping(value = "/role/loadAll", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Loads all available roles.",
- notes = "Loads all available roles. Parameter loadUsers specifies whether"
- + "list of associated users should be returned with roles.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads all available roles.",
+ description = "Loads all available roles. Parameter loadUsers specifies whether"
+ + "list of associated users should be returned with roles.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadRoles(
@RequestParam(required = false, defaultValue = "false") boolean loadUsers) {
return Result.success(loadUsers ? roleSecurityService.loadRolesWithUsers() : roleSecurityService.loadRoles());
@@ -77,13 +76,12 @@ public Result> loadRoles(
@RequestMapping(value = "/role/{id}/assign", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Assigns a list of users to role.",
- notes = "Assigns a list of users to role",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Assigns a list of users to role.",
+ description = "Assigns a list of users to role")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result assignRole(@PathVariable Long id,
@RequestParam List userIds) {
return Result.success(roleSecurityService.assignRole(id, userIds));
@@ -91,13 +89,12 @@ public Result assignRole(@PathVariable Long id,
@RequestMapping(value = "/role/{id}/remove", method = RequestMethod.DELETE)
@ResponseBody
- @ApiOperation(
- value = "Removes a role from a list of users",
- notes = "Removes a role from a list of users",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Removes a role from a list of users",
+ description = "Removes a role from a list of users")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result removeRole(@PathVariable Long id,
@RequestParam List userIds) {
return Result.success(roleSecurityService.removeRole(id, userIds));
@@ -105,15 +102,14 @@ public Result removeRole(@PathVariable Long id,
@RequestMapping(value = "/role/create", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Creates a new role.",
- notes = "Creates a new role with specified name. Name should not be empty. All roles"
+ @Operation(
+ summary = "Creates a new role.",
+ description = "Creates a new role with specified name. Name should not be empty. All roles"
+ "are supposed to start with 'ROLE_' prefix, if it is not provided, prefix will"
- + "be added automatically.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ + "be added automatically.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createRole(@RequestParam String roleName,
@RequestParam(required = false, defaultValue = "false") boolean userDefault) {
return Result.success(roleSecurityService.createRole(roleName, userDefault));
@@ -121,52 +117,48 @@ public Result createRole(@RequestParam String roleName,
@RequestMapping(value = "/role/{id}", method = RequestMethod.PUT)
@ResponseBody
- @ApiOperation(
- value = "Updates a role specified by ID.",
- notes = "Updates a role specified by ID.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates a role specified by ID.",
+ description = "Updates a role specified by ID.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateRole(@PathVariable Long id, @RequestBody RoleVO roleVO) {
return Result.success(roleSecurityService.updateRole(id, roleVO));
}
@RequestMapping(value = "/role/{id}", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Gets a role specified by ID.",
- notes = "Gets a role specified by ID.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Gets a role specified by ID.",
+ description = "Gets a role specified by ID.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getRole(@PathVariable Long id) {
return Result.success(roleSecurityService.loadRole(id));
}
@RequestMapping(value = "/role/{id}", method = RequestMethod.DELETE)
@ResponseBody
- @ApiOperation(
- value = "Deletes a role specified by ID.",
- notes = "Deletes a role specified by ID along with all permissions set",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a role specified by ID.",
+ description = "Deletes a role specified by ID along with all permissions set")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteRole(@PathVariable Long id) {
return Result.success(roleSecurityService.deleteRole(id));
}
@RequestMapping(value = "/role", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Finds a role specified by name.",
- notes = "Finds a role specified by name.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Finds a role specified by name.",
+ description = "Finds a role specified by name.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadRoleByName(@RequestParam String name) {
return Result.success(roleSecurityService.loadRoleByName(name));
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/person/UserController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/person/UserController.java
index 09b39dae4..fae89e0dd 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/person/UserController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/person/UserController.java
@@ -38,10 +38,10 @@
import com.epam.catgenome.entity.security.NgbUser;
import com.epam.catgenome.manager.user.UserSecurityService;
import com.epam.catgenome.security.UserContext;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
@@ -60,58 +60,54 @@
*/
@RestController
@ConditionalOnProperty(value = "security.acl.enable", havingValue = "true")
-@Api(value = "user", description = "User Management")
+@Tag(name = "user", description = "User Management")
public class UserController extends AbstractRESTController {
@Autowired
private UserSecurityService userSecurityService;
@GetMapping("/user/current")
- @ApiOperation(
- value = "Returns currently logged in user",
- notes = "Returns currently logged in user",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns currently logged in user",
+ description = "Returns currently logged in user")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result currentUser() {
return Result.success(userSecurityService.getUserContext());
}
@GetMapping("/user/token")
- @ApiOperation(
- value = "Creates a JWT token for current user",
- notes = "Creates a JWT token for current user",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates a JWT token for current user",
+ description = "Creates a JWT token for current user")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getToken(@RequestParam(required = false) Long expiration) {
return Result.success(userSecurityService.issueTokenForCurrentUser(expiration));
}
@RequestMapping(value = "/user", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Creates a new user.",
- notes = "Creates a new user with specified username and roles.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates a new user.",
+ description = "Creates a new user with specified username and roles.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result createUser(@RequestBody NgbUserVO userVO) {
return Result.success(userSecurityService.createUser(userVO));
}
@RequestMapping(value = "/user/loadList", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Loads users by names.",
- notes = "Loads users by names.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads users by names.",
+ description = "Loads users by names.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadUsersByNames(@RequestBody IDList userList) {
return Result.success(userSecurityService.loadUsersByNames(userList));
}
@@ -119,39 +115,36 @@ public Result> loadUsersByNames(@RequestBody IDList userList
@RequestMapping(value = "/user/{id}", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Loads a user by a ID.",
- notes = "Loads a user by a ID.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads a user by a ID.",
+ description = "Loads a user by a ID.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadUser(@PathVariable Long id) {
return Result.success(userSecurityService.loadUser(id));
}
@RequestMapping(value = "/user/{id}", method = RequestMethod.PUT)
@ResponseBody
- @ApiOperation(
- value = "Updates a user by a ID.",
- notes = "Updates a user by a ID.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates a user by a ID.",
+ description = "Updates a user by a ID.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateUser(@PathVariable Long id, @RequestBody NgbUserVO userVO) {
return Result.success(userSecurityService.updateUser(id, userVO));
}
@RequestMapping(value = "/user/{id}", method = RequestMethod.DELETE)
@ResponseBody
- @ApiOperation(
- value = "Deletes a user by a ID.",
- notes = "Deletes a user by a ID.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a user by a ID.",
+ description = "Deletes a user by a ID.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteUser(@PathVariable Long id) {
userSecurityService.deleteUser(id);
return Result.success(null);
@@ -159,39 +152,36 @@ public Result deleteUser(@PathVariable Long id) {
@RequestMapping(value = "/users", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Loads all registered users.",
- notes = "Loads all registered users.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads all registered users.",
+ description = "Loads all registered users.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadUsers() {
return Result.success(userSecurityService.loadAllUsers());
}
@RequestMapping(value = "/user", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Loads a user by a name.",
- notes = "Loads a user by a name.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Loads a user by a name.",
+ description = "Loads a user by a name.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadUserByName(@RequestParam String name) {
return Result.success(userSecurityService.loadUserByName(name));
}
@GetMapping(value = "/group/find")
@ResponseBody
- @ApiOperation(
- value = "Finds user group by a prefix (case insensitive).",
- notes = "Finds user group by a prefix (case insensitive).",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Finds user group by a prefix (case insensitive).",
+ description = "Finds user group by a prefix (case insensitive).")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> findGroups(@RequestParam(required = false) String prefix) {
return Result.success(userSecurityService.findGroups(prefix));
}
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java
index 485560caa..f37be73ae 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java
@@ -54,10 +54,10 @@
import com.epam.catgenome.entity.vcf.VcfFilterForm;
import com.epam.catgenome.entity.vcf.VcfFilterInfo;
import com.epam.catgenome.exception.FeatureIndexException;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.DeleteMapping;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
@@ -80,7 +80,7 @@
*
*/
@Controller
-@Api(value = "project", description = "Project Management")
+@Tag(name = "project", description = "Project Management")
public class ProjectController extends AbstractRESTController {
private static final String PROJECT_ID_PARAM = "projectId";
private static final String BIOLOGICAL_ITEM_ID_PARAM = "biologicalItemId";
@@ -93,27 +93,25 @@ public class ProjectController extends AbstractRESTController {
@GetMapping(value = "/project/loadMy")
@ResponseBody
- @ApiOperation(
- value = "Returns all top-level projects",
- notes = "Each summary provides only major metadata per a single project, no files information is provided" +
- " via this service",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all top-level projects",
+ description = "Each summary provides only major metadata per a single project, no files information is provided" +
+ " via this service")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> loadTopLevelProjects() {
return Result.success(ProjectConverter.convertTo(projectSecurityService.loadTopLevelProjects()));
}
@GetMapping(value = "/project/tree")
@ResponseBody
- @ApiOperation(
- value = "Returns all projects in a form of tree hierarchy",
- notes = "Each project contains all it's nested projects and items",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all projects in a form of tree hierarchy",
+ description = "Each project contains all it's nested projects and items")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Callable>> loadProjectsTreeForCurrentUser(
@RequestParam(required = false) Long parentId,
@RequestParam(required = false) String referenceName) {
@@ -123,26 +121,24 @@ public Callable>> loadProjectsTreeForCurrentUser(
@GetMapping(value = "/project/{projectId}/load")
@ResponseBody
- @ApiOperation(
- value = "Returns a project by given ID",
- notes = "Provides extended data, including files in project",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a project by given ID",
+ description = "Provides extended data, including files in project")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadProject(@PathVariable(value = PROJECT_ID_PARAM) final Long projectId) {
return Result.success(ProjectConverter.convertTo(projectSecurityService.load(projectId)));
}
@GetMapping(value = "/project/load")
@ResponseBody
- @ApiOperation(
- value = "Returns a project by given name",
- notes = "Provides extended data, including files in project",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns a project by given name",
+ description = "Provides extended data, including files in project")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result loadProject(@RequestParam final String projectName) {
return Result.success(ProjectConverter.convertTo(
projectSecurityService.load(projectName))
@@ -151,17 +147,16 @@ public Result loadProject(@RequestParam final String projectName) {
@PostMapping(value = "/project/save")
@ResponseBody
- @ApiOperation(
- value = "Creates new project or updates existing one",
- notes = "New project should contain a name field. Updated project should contain id and name fields.
"
+ @Operation(
+ summary = "Creates new project or updates existing one",
+ description = "New project should contain a name field. Updated project should contain id and name fields.
"
+ "Optional parameter parentId stands for creating a new project as a nested project for existing "
+ "one, specified by parentId parameter. Works only for creation of a new project.
"
+ "To move an existing project to another parent project, use /project/{projectId}/move "
- + "service",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ + "service")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result saveProject(@RequestBody ProjectVO project,
@RequestParam(required = false) Long parentId) throws FeatureIndexException {
return Result.success(ProjectConverter.convertTo(projectSecurityService.create(ProjectConverter.convertFrom(
@@ -170,13 +165,12 @@ public Result saveProject(@RequestBody ProjectVO project,
@ResponseBody
@PutMapping(value = "/project/{name}/rename")
- @ApiOperation(
- value = "Updates project name and/or pretty name.",
- notes = "Updates project name and/or pretty name.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Updates project name and/or pretty name.",
+ description = "Updates project name and/or pretty name.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result rename(
@PathVariable(value = "name") final String name,
@RequestParam(value = "newName", required = false) final String newName,
@@ -187,15 +181,14 @@ public final Result rename(
@PutMapping(value = "/project/{projectId}/move")
@ResponseBody
- @ApiOperation(
- value = "Moves a project to a parent project",
- notes = "Moves an existing project, specified by projectId path variable, to a parent project, specified by "
+ @Operation(
+ summary = "Moves a project to a parent project",
+ description = "Moves an existing project, specified by projectId path variable, to a parent project, specified by "
+ "parentID parameter. To move a project to top level, pass no "
- + "parameter",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ + "parameter")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result moveProject(@PathVariable Long projectId, @RequestParam(required = false) Long parentId) {
projectSecurityService.moveProjectToParent(projectId, parentId);
return Result.success(true);
@@ -203,13 +196,12 @@ public Result moveProject(@PathVariable Long projectId, @RequestParam(r
@PutMapping(value = "/project/{projectId}/add/{biologicalItemId}")
@ResponseBody
- @ApiOperation(
- value = "Adds a file to project",
- notes = "Adds a file, specified by its biologicalItemId, to a project, specified by its projectId",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Adds a file to project",
+ description = "Adds a file, specified by its biologicalItemId, to a project, specified by its projectId")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result addProjectItem(@PathVariable(value = PROJECT_ID_PARAM) final Long projectId,
@PathVariable(value = BIOLOGICAL_ITEM_ID_PARAM) final Long biologicalItemId)
throws FeatureIndexException {
@@ -219,13 +211,12 @@ public Result addProjectItem(@PathVariable(value = PROJECT_ID_PARAM)
@DeleteMapping(value = "/project/{projectId}/remove/{biologicalItemId}")
@ResponseBody
- @ApiOperation(
- value = "Removes a file from a project",
- notes = "Removes a file, specified by its biologicalItemId, from a project, specified by its projectId",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Removes a file from a project",
+ description = "Removes a file, specified by its biologicalItemId, from a project, specified by its projectId")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result removeProjectItem(@PathVariable(value = PROJECT_ID_PARAM) final Long projectId,
@PathVariable(value = BIOLOGICAL_ITEM_ID_PARAM) final Long biologicalItemId)
throws FeatureIndexException {
@@ -235,13 +226,12 @@ public Result removeProjectItem(@PathVariable(value = PROJECT_ID_PARA
@PutMapping(value = "/project/{projectId}/hide/{biologicalItemId}")
@ResponseBody
- @ApiOperation(
- value = "Hides a project file",
- notes = "Hides a file, specified by its biologicalItemId, from a project, specified by its projectId",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Hides a project file",
+ description = "Hides a file, specified by its biologicalItemId, from a project, specified by its projectId")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result hideProjectItem(@PathVariable(value = PROJECT_ID_PARAM) final Long projectId,
@PathVariable(value = BIOLOGICAL_ITEM_ID_PARAM) final Long biologicalItemId) {
projectSecurityService.hideProjectItem(projectId, biologicalItemId);
@@ -250,13 +240,12 @@ public Result hideProjectItem(@PathVariable(value = PROJECT_ID_PARAM)
@GetMapping(value = "/project/{projectId}/search")
@ResponseBody
- @ApiOperation(
- value = "Searches for a given feature ID in a given project, case-insensitive",
- notes = "Looks up project files indexes for a given feature ID and returns an index entry",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for a given feature ID in a given project, case-insensitive",
+ description = "Looks up project files indexes for a given feature ID and returns an index entry")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result searchFeatureInProject(
@PathVariable(value = PROJECT_ID_PARAM) final Long projectId, @RequestParam String featureId)
throws IOException {
@@ -265,9 +254,9 @@ public Result searchFeatureInProject(
@PostMapping(value = "/project/{projectId}/filter/vcf")
@ResponseBody
- @ApiOperation(
- value = "Filters variations for a given VCF file in a given project",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Filters variations for a given VCF file in a given project",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -318,11 +307,10 @@ public Result searchFeatureInProject(
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> filterVcf(@RequestBody final VcfFilterForm filterForm,
@PathVariable(value = PROJECT_ID_PARAM) long projectId)
throws IOException {
@@ -331,9 +319,9 @@ public Result> filterVcf(@RequestBody final VcfFilterForm fi
@PostMapping(value = "/project/{projectId}/filter/vcf/new")
@ResponseBody
- @ApiOperation(
- value = "Filters variations for a given VCF file in a given project",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Filters variations for a given VCF file in a given project",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -384,11 +372,10 @@ public Result> filterVcf(@RequestBody final VcfFilterForm fi
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> filterVcfNew(@RequestBody final VcfFilterForm filterForm,
@PathVariable(value = PROJECT_ID_PARAM) long projectId)
throws IOException {
@@ -397,9 +384,9 @@ public Result> filterVcfNew(@RequestBody final
@PostMapping(value = "/project/{projectId}/group/vcf")
@ResponseBody
- @ApiOperation(
- value = "Groups variations by given field for a given project, according to filter",
- notes = "Request should contain the following fields:
" +
+ @Operation(
+ summary = "Groups variations by given field for a given project, according to filter",
+ description = "Request should contain the following fields:
" +
"vcfFileIds: an array of IDs of VCF files to filter
" +
"other fields are optional:
" +
"chromosomeId: an ID of a chromosome to load variations" +
@@ -444,11 +431,10 @@ public Result> filterVcfNew(@RequestBody final
"okay
" +
"impact: an impact of a variation" +
"effect: an effect of a variation" +
- "info: an object, containing requested additional info fields, if they are present",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "info: an object, containing requested additional info fields, if they are present")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> groupVariations(@RequestBody final VcfFilterForm filterForm,
@PathVariable(value = PROJECT_ID_PARAM) long projectId,
@RequestParam String groupBy) throws IOException {
@@ -458,14 +444,13 @@ public Result> groupVariations(@RequestBody final VcfFilterForm filt
@ResponseBody
@PostMapping(value = "/project/{projectId}/filter/vcf/searchGenes")
- @ApiOperation(
- value = "Searches for IDs of genes, that are affected by variations",
- notes = "Searches for IDs of genes, that are affected by variations located in VCF files, specified by " +
- "ids, in a given project, specified by project ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for IDs of genes, that are affected by variations",
+ description = "Searches for IDs of genes, that are affected by variations located in VCF files, specified by " +
+ "ids, in a given project, specified by project ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> searchGenesInProject(@PathVariable(value = PROJECT_ID_PARAM) long projectId,
@RequestBody GeneSearchQuery geneQuery) throws IOException {
return Result.success(
@@ -475,27 +460,25 @@ public Result> searchGenesInProject(@PathVariable(value = PROJECT_ID
@ResponseBody
@GetMapping(value = "/project/{projectId}/filter/vcf/info")
- @ApiOperation(
- value = "Returns information for VCF filter for given project ID",
- notes = "Returns information for VCF filter for given project ID, all information taken from VCF file " +
- "headers.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns information for VCF filter for given project ID",
+ description = "Returns information for VCF filter for given project ID, all information taken from VCF file " +
+ "headers.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result erg(@PathVariable(value = PROJECT_ID_PARAM) final Long projectId) throws IOException {
return Result.success(featureIndexSecurityService.loadVcfFilterInfoForProject(projectId));
}
@DeleteMapping(value = "/project/{projectId}")
@ResponseBody
- @ApiOperation(
- value = "Deletes a project, specified by project ID",
- notes = "Deletes a project with all it's items and bookmarks",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes a project, specified by project ID",
+ description = "Deletes a project with all it's items and bookmarks")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteProject(@PathVariable final long projectId,
@RequestParam(name = "force", required = false, defaultValue = "false")
Boolean force) throws IOException {
@@ -506,13 +489,12 @@ public Result deleteProject(@PathVariable final long projectId,
@PostMapping("/project/{projectId}/description")
@ResponseBody
- @ApiOperation(
- value = "Creates or updates project description",
- notes = "Creates or updates project description",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Creates or updates project description",
+ description = "Creates or updates project description")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result upsertProjectDescription(@PathVariable final Long projectId,
@RequestParam(value = "path", required = false) final String path,
@RequestParam(value = "name", required = false) final String name,
@@ -522,13 +504,12 @@ public Result upsertProjectDescription(@PathVariable final L
@GetMapping("/project/description/{id}")
@ResponseBody
- @ApiOperation(
- value = "Downloads project description file",
- notes = "Downloads project description file",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Downloads project description file",
+ description = "Downloads project description file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void downloadProjectDescription(@PathVariable final Long id, final HttpServletResponse response)
throws IOException {
final InputStream projectDescriptionContent = projectSecurityService.loadProjectDescription(id);
@@ -541,39 +522,36 @@ public void downloadProjectDescription(@PathVariable final Long id, final HttpSe
@GetMapping("/project/{projectId}/description")
@ResponseBody
- @ApiOperation(
- value = "Returns project descriptions info",
- notes = "Returns project descriptions info",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns project descriptions info",
+ description = "Returns project descriptions info")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getProjectDescriptions(@PathVariable final Long projectId) {
return Result.success(projectSecurityService.loadProjectDescriptions(projectId));
}
@DeleteMapping("/project/description/{id}")
@ResponseBody
- @ApiOperation(
- value = "Deletes project description specified by ID",
- notes = "Deletes project description specified by ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes project description specified by ID",
+ description = "Deletes project description specified by ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result deleteProjectDescription(@PathVariable final Long id) {
return Result.success(projectSecurityService.deleteProjectDescription(id));
}
@DeleteMapping("/project/{projectId}/description")
@ResponseBody
- @ApiOperation(
- value = "Deletes project description by project ID",
- notes = "If 'name' parameter was not specified all attached to project descriptions will be removed",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Deletes project description by project ID",
+ description = "If 'name' parameter was not specified all attached to project descriptions will be removed")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> deleteProjectDescriptionByProject(@PathVariable final Long projectId,
@RequestParam(value = "name", required = false) final String name) {
return Result.success(projectSecurityService.deleteProjectDescriptions(projectId, name));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/BookmarkController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/BookmarkController.java
index 65db236b5..06dcde42a 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/BookmarkController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/BookmarkController.java
@@ -27,6 +27,8 @@
import java.io.IOException;
import java.util.List;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.stereotype.Controller;
@@ -41,8 +43,6 @@
import com.epam.catgenome.controller.vo.BookmarkVO;
import com.epam.catgenome.controller.vo.converter.BookmarkConverter;
import com.epam.catgenome.manager.reference.BookmarkManager;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
/**
* {@code BookmarkController} represents implementation of MVC controller which handles
@@ -52,7 +52,7 @@
* calls and manage all operations concerned with bookmarks.
*/
@Controller
-@Api(value = "bookmarks", description = "Bookmarks Management")
+@Tag(name = "bookmarks", description = "Bookmarks Management")
public class BookmarkController extends AbstractRESTController {
@Autowired
@@ -60,20 +60,18 @@ public class BookmarkController extends AbstractRESTController {
@RequestMapping(value = "/bookmarks", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Loads all bookmarks for current user",
- notes = "Bookmarks provide without data on tracks, that vas opened when a bookmark was saved",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(
+ summary = "Loads all bookmarks for current user",
+ description = "Bookmarks provide without data on tracks, that vas opened when a bookmark was saved")
public Result> loadBookmarks() {
return Result.success(BookmarkConverter.convertTo(bookmarkManager.loadAllBookmarks()));
}
@RequestMapping(value = "/bookmark/{bookmarkId}", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Returns bookmark, specified by id",
- notes = "Bookmarks provide data on tracks, that vas opened when a bookmark was saved",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(
+ summary = "Returns bookmark, specified by id",
+ description = "Bookmarks provide data on tracks, that vas opened when a bookmark was saved")
public Result loadBookmark(@PathVariable(value = "bookmarkId") final Long bookmarkId) {
return Result.success(BookmarkConverter.convertTo(bookmarkManager.load(bookmarkId)));
}
@@ -81,10 +79,9 @@ public Result loadBookmark(@PathVariable(value = "bookmarkId") final
@RequestMapping(value = "/bookmark/save", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Saves bookmark for a specific chromosome for a given project",
- notes = "Bookmarks provide data on tracks, that vas opened when a bookmark was saved",
- produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(
+ summary = "Saves bookmark for a specific chromosome for a given project",
+ description = "Bookmarks provide data on tracks, that vas opened when a bookmark was saved")
public Result saveBookmark(@RequestBody final BookmarkVO bookmarkVO) throws IOException {
return Result.success(BookmarkConverter.convertTo(bookmarkManager.create(BookmarkConverter.convertFrom(
bookmarkVO))));
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/CytobandController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/CytobandController.java
index 9b6885ae9..443e6444d 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/CytobandController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/CytobandController.java
@@ -44,10 +44,10 @@
import com.epam.catgenome.entity.reference.cytoband.Cytoband;
import com.epam.catgenome.entity.track.Track;
import com.epam.catgenome.manager.reference.CytobandManager;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
/**
* {@code CytobandController} represents implementation of MVC controller which handles
@@ -57,7 +57,7 @@
* calls and manage all operations concerned with cytobands.
*/
@Controller
-@Api(value = "cytobands", description = "Cytobands Management")
+@Tag(name = "cytobands", description = "Cytobands Management")
public class CytobandController extends AbstractRESTController {
@Autowired
@@ -66,15 +66,14 @@ public class CytobandController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/cytobands/upload", method = RequestMethod.POST,
consumes = MediaType.MULTIPART_FORM_DATA_VALUE)
- @ApiOperation(
- value = "Handles cytobands upload pointing to a corresponded genome that has to be available in the system.",
- notes = "The following cytobands file types are supported: *.txt and *.txt.gz.
" +
+ @Operation(
+ summary = "Handles cytobands upload pointing to a corresponded genome that has to be available in the system.",
+ description = "The following cytobands file types are supported: *.txt and *.txt.gz.
" +
"It results in a payload that provides corresponded genome ID, also a message about succeeded upload " +
- "is sent back.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "is sent back.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result saveCytobands(@RequestParam("referenceId") final Long referenceId,
@RequestParam("saveFile") final MultipartFile multipart)
throws IOException {
@@ -86,20 +85,13 @@ public final Result saveCytobands(@RequestParam("referenceId") final Long
@ResponseBody
@RequestMapping(value = "/cytobands/{chromosomeId}/get", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns data to fill in a cytogenetic ideogram for a particular chromosome.",
- notes = "It provides summary of cytobands for a particular chromosome. In a case when no cytobands can be " +
- "found in the system, this call results in a response with WARN status.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = "It results in a response with HTTP status OK, but " +
- "you should always check $.status, which can take several values:
" +
- "OK means call was done without any problems;
" +
- "ERROR means call was aborted due to errors;
" +
- "WARN means call was done without any problems, but there is no an ideogram that is available for " +
- "a particular chromosome.
" +
- "In both cases - ERROR or WARN - see $.message for additional information.")
- })
+ @Operation(
+ summary = "Returns data to fill in a cytogenetic ideogram for a particular chromosome.",
+ description = "It provides summary of cytobands for a particular chromosome. In a case when no cytobands can be " +
+ "found in the system, this call results in a response with WARN status.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result> loadTrack(@PathVariable final Long chromosomeId) throws IOException {
final Track track = cytobandManager.loadCytobands(chromosomeId);
if (track == null) {
diff --git a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java
index 85d93f091..0baa0ddef 100644
--- a/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java
+++ b/server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java
@@ -64,10 +64,10 @@
import com.epam.catgenome.entity.index.IndexSearchResult;
import com.epam.catgenome.entity.track.Track;
import com.epam.catgenome.exception.ReferenceReadingException;
-import com.wordnik.swagger.annotations.Api;
-import com.wordnik.swagger.annotations.ApiOperation;
-import com.wordnik.swagger.annotations.ApiResponse;
-import com.wordnik.swagger.annotations.ApiResponses;
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.media.Content;
+import io.swagger.v3.oas.annotations.responses.ApiResponse;
+import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.PostMapping;
import org.springframework.web.bind.annotation.RequestBody;
@@ -87,7 +87,7 @@
* calls and manage all operations concerned with a reference.
*/
@Controller
-@Api(value = "reference-genome", description = "Reference Genomes Management")
+@Tag(name = "reference-genome", description = "Reference Genomes Management")
public class ReferenceController extends AbstractRESTController {
@Autowired
@@ -98,15 +98,14 @@ public class ReferenceController extends AbstractRESTController {
@ResponseBody
@RequestMapping(value = "/reference/loadAll", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns all reference genomes that are available in the system at the moment.",
- notes = "Each summary provides only major metadata per a single reference genome, excluding detailed " +
+ @Operation(
+ summary = "Returns all reference genomes that are available in the system at the moment.",
+ description = "Each summary provides only major metadata per a single reference genome, excluding detailed " +
"information about its chromosomes. That means $.payload.chromosomes is always empty or null in " +
- "this case.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "this case.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Callable>> loadAllReferences(
@RequestParam(required = false) String referenceName) throws IOException {
return () -> Result.success(referenceSecurityService.loadAllReferenceGenomes(referenceName));
@@ -114,65 +113,61 @@ public final Callable>> loadAllReferences(
@ResponseBody
@RequestMapping(value = "/reference/{referenceId}/load", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns detailed information about a reference genome associated with the given ID.",
- notes = "It provides major metadata per a single reference genome, including detailed information " +
- "about all its chromosomes.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns detailed information about a reference genome associated with the given ID.",
+ description = "It provides major metadata per a single reference genome, including detailed information " +
+ "about all its chromosomes.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result loadReference(@PathVariable final Long referenceId) throws IOException {
return Result.success(referenceSecurityService.load(referenceId));
}
@ResponseBody
@RequestMapping(value = "/reference/{bioItemID}/loadByBioID", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns meta information about a reference genome associated with the given "
+ @Operation(
+ summary = "Returns meta information about a reference genome associated with the given "
+ "BiologicalDataItem ID.",
- notes = "It provides major metadata per a single reference genome, without information " +
- "about reference chromosomes.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ description = "It provides major metadata per a single reference genome, without information " +
+ "about reference chromosomes.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result loadReferenceBuBioId(@PathVariable final Long bioItemID) throws IOException {
return Result.success(referenceSecurityService.loadReferenceGenomeByBioItemId(bioItemID));
}
@ResponseBody
@RequestMapping(value = "/reference/{referenceId}/loadChromosomes", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns all chromosomes for a reference genome associated with the given ID.",
- notes = "It provides summaries of all chromosomes that are available in the system for the given " +
- "reference genome.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns all chromosomes for a reference genome associated with the given ID.",
+ description = "It provides summaries of all chromosomes that are available in the system for the given " +
+ "reference genome.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result> loadChromosomes(@PathVariable final Long referenceId) throws IOException {
return Result.success(referenceSecurityService.loadChromosomes(referenceId));
}
@ResponseBody
@RequestMapping(value = "/reference/chromosomes/{chromosomeId}/load", method = RequestMethod.GET)
- @ApiOperation(
- value = "Returns detailed information about a single chromosome associated with the given ID.",
- notes = "It provides major metadata per a single chromosome.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns detailed information about a single chromosome associated with the given ID.",
+ description = "It provides major metadata per a single chromosome.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result loadChromosome(@PathVariable final Long chromosomeId) throws IOException {
return Result.success(referenceSecurityService.loadChromosome(chromosomeId));
}
@ResponseBody
@RequestMapping(value = "/reference/track/get", method = RequestMethod.POST)
- @ApiOperation(
- value = "Returns data matched the given query to fill in a reference genome track.",
- notes = "It provides data for a reference genome track with the given scale factor between the " +
+ @Operation(
+ summary = "Returns data matched the given query to fill in a reference genome track.",
+ description = "It provides data for a reference genome track with the given scale factor between the " +
"beginning position with the first base having position 1 and ending position inclusive in a " +
"target chromosome. All parameters are mandatory and described below:
" +
"1) id specifies ID of a track;
" +
@@ -182,11 +177,10 @@ public final Result loadChromosome(@PathVariable final Long chromoso
"4) endIndex is the last base position for a requested window. It is treated " +
"inclusively;
" +
"5) scaleFactor specifies an inverse value to number of bases per one visible " +
- "element on a track (e.g., pixel).",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "element on a track (e.g., pixel).")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public final Result> loadTrack(@RequestBody final TrackQuery query) throws
ReferenceReadingException {
final Track track = referenceSecurityService.getNucleotidesResultFromNib(convertToTrack(query));
@@ -195,13 +189,12 @@ public final Result> loadTrack(@RequestBody final TrackQuery que
@RequestMapping(value = "/reference/{referenceId}/search", method = RequestMethod.GET)
@ResponseBody
- @ApiOperation(
- value = "Searches for a given feature ID in a reference gene file, case-insensitive",
- notes = "Searches an index of a gene file, associated with a given reference's ID for a specified feature ID",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for a given feature ID in a reference gene file, case-insensitive",
+ description = "Searches an index of a gene file, associated with a given reference's ID for a specified feature ID")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> searchFeatureInProject(
@PathVariable(value = "referenceId") final Long referenceId,
@RequestParam final String featureId) throws IOException {
@@ -210,13 +203,12 @@ public Result> searchFeatureInProject(
@RequestMapping(value = "/reference/{referenceId}/filter/gene", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Searches for given filter parameters in a reference gene file, case-insensitive",
- notes = "Searches an index of a gene file, associated with a given reference's ID for filter parameters",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Searches for given filter parameters in a reference gene file, case-insensitive",
+ description = "Searches an index of a gene file, associated with a given reference's ID for filter parameters")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> searchFeatureInProjectWithFilter(
@PathVariable(value = "referenceId") final Long referenceId,
@RequestBody final GeneFilterForm geneFilterForm)
@@ -226,13 +218,14 @@ public Result> searchFeatureInProjectWithFilte
@PostMapping(value = "/reference/{referenceId}/filter/gene/export")
@ResponseBody
- @ApiOperation(
- value = "Searches for given filter parameters in a reference gene file, case-insensitive and exports " +
+ @Operation(
+ summary = "Searches for given filter parameters in a reference gene file, case-insensitive and exports " +
"result to CSV/TSV file",
- notes = "Searches an index of a gene file, associated with a given reference's ID for filter parameters " +
- "and exports result to CSV/TSV file",
- produces = MediaType.APPLICATION_OCTET_STREAM_VALUE)
- @ApiResponses(value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)})
+ description = "Searches an index of a gene file, associated with a given reference's ID for filter parameters " +
+ "and exports result to CSV/TSV file")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public void exportFeatureInProjectWithFilter(@PathVariable final Long referenceId,
@RequestParam final FileFormat format,
@RequestParam final boolean includeHeader,
@@ -247,13 +240,12 @@ public void exportFeatureInProjectWithFilter(@PathVariable final Long referenceI
@RequestMapping(value = "/reference/{referenceId}/filter/gene/info", method = RequestMethod.POST)
@ResponseBody
- @ApiOperation(
- value = "Returns information about possible custom gene table columns",
- notes = "Searches an index of a gene files, associated with a given reference's IDs for filter parameters",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns information about possible custom gene table columns",
+ description = "Searches an index of a gene files, associated with a given reference's IDs for filter parameters")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result getAvailableFieldsToSearch(
@PathVariable(value = "referenceId") final Long referenceId,
@RequestBody(required = false) ItemsByProject fileIdsByProjectId) throws IOException {
@@ -262,13 +254,12 @@ public Result getAvailableFieldsToSearch(
@PostMapping(value = "/reference/{referenceId}/filter/gene/values")
@ResponseBody
- @ApiOperation(
- value = "Returns information about possible custom gene table columns",
- notes = "Searches an index of a gene files, associated with a given reference's IDs for filter parameters",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Returns information about possible custom gene table columns",
+ description = "Searches an index of a gene files, associated with a given reference's IDs for filter parameters")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result> getAvailableFieldValues(
@PathVariable final Long referenceId,
@RequestBody(required = false) final ItemsByProject fileIdsByProjectId,
@@ -279,18 +270,17 @@ public Result> getAvailableFieldValues(
@ResponseBody
@RequestMapping(value = "/secure/reference/register/fasta", method = RequestMethod.POST)
- @ApiOperation(
- value = "Handles FASTA register and parse a new genome in the system.",
- notes = "The following genome file types are supported: *.fasta, *.fasta.gz, *.fa, *.fa.gz, *.fna, " +
+ @Operation(
+ summary = "Handles FASTA register and parse a new genome in the system.",
+ description = "The following genome file types are supported: *.fasta, *.fasta.gz, *.fa, *.fa.gz, *.fna, " +
"*.fna.gz, *.txt, *.txt.gz, *.genbank, *.gbk, *.gb, *.gbf.
" +
"Optionally you can specify a user-friendly name for an uploaded genome through request " +
"parameter name, by default the original file name with omitted extension is used.
" +
"It results in a payload that provides detailed information about a genome, including all " +
- "its chromosomes.",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ "its chromosomes.")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result registerFastaFile(@RequestBody
ReferenceRegistrationRequest request) throws IOException {
return Result.success(referenceSecurityService.registerGenome(request));
@@ -305,13 +295,12 @@ public Result updateReferenceGeneFile(@PathVariable Long referenceId,
@ResponseBody
@RequestMapping(value = "/secure/reference/{referenceId}/updateAnnotation", method = RequestMethod.PUT)
- @ApiOperation(
- value = "Update annotation file to the reference.",
- notes = "Update (add or remove) annotation file for the reference (BED, GTF, GFF).",
- produces = MediaType.APPLICATION_JSON_VALUE)
- @ApiResponses(
- value = {@ApiResponse(code = HTTP_STATUS_OK, message = API_STATUS_DESCRIPTION)
- })
+ @Operation(
+ summary = "Update annotation file to the reference.",
+ description = "Update (add or remove) annotation file for the reference (BED, GTF, GFF).")
+ @ApiResponse(responseCode = HTTP_STATUS_OK,
+ description = API_STATUS_DESCRIPTION,
+ content = @Content(mediaType = MediaType.APPLICATION_JSON_VALUE))
public Result updateReferenceAnnotationFile(@PathVariable Long referenceId,
@RequestParam Long annotationFileId,
@RequestParam(defaultValue = "false") Boolean remove)
@@ -323,8 +312,8 @@ public Result updateReferenceAnnotationFile(@PathVariable Long refere
@ResponseBody
@RequestMapping(value = "/secure/reference/register/fasta", method = RequestMethod.DELETE)
- @ApiOperation(value = "Unregisters a reference file in the system.",
- notes = "Delete all information about this file by id", produces = MediaType.APPLICATION_JSON_VALUE)
+ @Operation(summary = "Unregisters a reference file in the system.",
+ description = "Delete all information about this file by id")
public Result unregisterFastaFile(@RequestParam final long referenceId) throws IOException {
Reference reference = referenceSecurityService.unregisterGenome(referenceId);
return Result.success(true, getMessage(MessagesConstants.INFO_UNREGISTER, reference.getName()));
@@ -332,35 +321,33 @@ public Result