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Commit fe2bdd8f authored by Guillaume Cornut's avatar Guillaume Cornut
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fix: Fix unreliable BrAPI calls using the swagger API instead.

parent e37b3d7e
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backend/src/main/java/fr/inra/urgi/gpds/api/brapi/v1/CallsController.java
View file @ fe2bdd8f
package fr.inra.urgi.gpds.api.brapi.v1;
import com.google.common.collect.Lists;
import com.google.common.reflect.ClassPath;
import com.google.common.collect.ImmutableSet;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiCall;
import fr.inra.urgi.gpds.domain.brapi.v1.response.BrapiListResponse;
import fr.inra.urgi.gpds.domain.criteria.base.PaginationCriteriaImpl;
......@@ -9,15 +8,19 @@ import fr.inra.urgi.gpds.domain.data.CallVO;
import fr.inra.urgi.gpds.domain.response.ApiResponseFactory;
import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import org.springframework.web.bind.annotation.*;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.RestController;
import springfox.documentation.service.ApiDescription;
import springfox.documentation.service.Documentation;
import springfox.documentation.spring.web.DocumentationCache;
import springfox.documentation.spring.web.plugins.Docket;
import javax.validation.Valid;
import java.io.IOException;
import java.lang.reflect.Method;
import java.util.*;
import static org.springframework.web.bind.annotation.RequestMethod.GET;
import static org.springframework.web.bind.annotation.RequestMethod.POST;
import java.util.Comparator;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
/**
* @author gcornut
......@@ -25,132 +28,81 @@ import static org.springframework.web.bind.annotation.RequestMethod.POST;
@Api(tags = {"Breeding API"}, description = "BrAPI endpoint")
@RestController
public class CallsController {
private static final String BRAPI_PATH = "/brapi/v1/";
private static final List<String> DATA_TYPES = Arrays.asList(
public static final Set<String> DEFAULT_DATA_TYPES = ImmutableSet.of(
"json"
);
private static final List<String> BRAPI_VERSIONS = Arrays.asList(
public static final Set<String> DEFAULT_BRAPI_VERSIONS = ImmutableSet.of(
"1.0",
"1.1",
"1.2"
);
private final List<BrapiCall> implementedCalls;
private List<BrapiCall> implementedCalls;
private final DocumentationCache documentationCache;
public CallsController() {
this.implementedCalls = listImplementedCalls();
@Autowired
public CallsController(DocumentationCache documentationCache) {
this.documentationCache = documentationCache;
}
/**
* @link https://github.com/plantbreeding/API/blob/master/Specification/Calls/Calls.md
*/
@ApiOperation("List implemented Breeding API calls")
@GetMapping(value = {"/brapi/v1/calls", "/brapi/v1/"})
@GetMapping("/brapi/v1/calls")
public BrapiListResponse<BrapiCall> calls(@Valid PaginationCriteriaImpl criteria) {
if (implementedCalls == null) {
implementedCalls = swaggerToBrapiCalls();
}
return ApiResponseFactory.createSubListResponse(
criteria.getPageSize(), criteria.getPage(), implementedCalls
);
}
/**
* Generate {@link BrapiCall} by reflectively reading Spring REST
* annotations
* Get swagger API documentation and transform it to list of BrAPI calls
*
* This must be done after swagger has time to generate the API
* documentation and thus can't be done in this class constructor
*/
private List<BrapiCall> listImplementedCalls() {
Map<String, BrapiCall> calls = new HashMap<>();
Class<?> aClass = getClass();
ClassLoader classLoader = aClass.getClassLoader();
ClassPath classPath;
try {
classPath = ClassPath.from(classLoader);
} catch (IOException e) {
throw new RuntimeException(e);
}
String brapiControllerPackage = aClass.getPackage().getName();
Set<ClassPath.ClassInfo> controllerClasses = classPath.getTopLevelClasses(brapiControllerPackage);
for (ClassPath.ClassInfo controllerClassInfo : controllerClasses) {
Class<?> controllerClass = controllerClassInfo.load();
if (controllerClass.getAnnotation(RestController.class) == null) {
// Class is not a RestController
continue;
}
for (Method method : controllerClass.getMethods()) {
ApiOperation apiOperation = method.getAnnotation(ApiOperation.class);
if (apiOperation != null && apiOperation.hidden()) {
// Rest call is hidden = ignore
continue;
}
String[] paths = getCallPath(method);
if (paths == null) {
// No rest path mapping => ignore
continue;
}
for (String path : paths) {
String[] pathSplit = path.split("/brapi/v1/");
if (pathSplit.length != 2) {
continue;
}
path = pathSplit[1];
RequestMethod[] httpMethods = getCallMethods(method);
List<String> httpMethodNames = Lists.newArrayList();
for (RequestMethod httpMethod : httpMethods) {
httpMethodNames.add(httpMethod.name());
}
BrapiCall call = calls.get(path);
if (call == null) {
call = new CallVO(path);
calls.put(path, call);
}
call.getMethods().addAll(httpMethodNames);
call.getDatatypes().addAll(DATA_TYPES);
call.getVersions().addAll(BRAPI_VERSIONS);
}
}
}
ArrayList<BrapiCall> allCalls = new ArrayList<>(calls.values());
// Sort by call name
Collections.sort(allCalls, Comparator.comparing(BrapiCall::getCall));
return allCalls;
}
private String[] getCallPath(Method method) {
RequestMapping annotation = method.getAnnotation(RequestMapping.class);
if (annotation != null) {
return annotation.value();
}
GetMapping getAnnotation = method.getAnnotation(GetMapping.class);
if (getAnnotation != null) {
return getAnnotation.value();
}
PostMapping postAnnotation = method.getAnnotation(PostMapping.class);
if (postAnnotation != null) {
return postAnnotation.value();
}
return null;
}
private RequestMethod[] getCallMethods(Method method) {
RequestMapping annotation = method.getAnnotation(RequestMapping.class);
if (annotation != null) {
return annotation.method();
}
GetMapping getAnnotation = method.getAnnotation(GetMapping.class);
if (getAnnotation != null) {
return new RequestMethod[]{GET};
}
PostMapping postAnnotation = method.getAnnotation(PostMapping.class);
if (postAnnotation != null) {
return new RequestMethod[]{POST};
}
return null;
private List<BrapiCall> swaggerToBrapiCalls() {
Documentation apiDocumentation = this.documentationCache.documentationByGroup(Docket.DEFAULT_GROUP_NAME);
// Get all endpoints
return apiDocumentation.getApiListings().values().stream()
.flatMap(endpointListing -> endpointListing.getApis().stream())
// Only with BrAPI path
.filter(endpointDescription -> endpointDescription.getPath().startsWith(BRAPI_PATH))
// Group by endpoint path (ex: /brapi/v1/phenotype => [GET, POST, ...])
.collect(Collectors.groupingBy(ApiDescription::getPath))
.entrySet().stream()
// Convert to BrAPI call
.map(endpointGroup -> {
String path = endpointGroup.getKey();
List<ApiDescription> endpoints = endpointGroup.getValue();
// BrAPI call path should not include the base BrAPI path
CallVO call = new CallVO(path.replace(BRAPI_PATH, ""));
// List every endpoint for current path
Set<String> methods = endpoints.stream()
// List all operations for each endpoint
.flatMap(endpointDescription -> endpointDescription.getOperations().stream())
// List all methods
.map(operation -> operation.getMethod().toString())
.collect(Collectors.toSet());
call.setMethods(methods);
return call;
})
// Sort by call name
.sorted(Comparator.comparing(CallVO::getCall))
.collect(Collectors.toList());
}
}
backend/src/main/java/fr/inra/urgi/gpds/domain/data/CallVO.java
View file @ fe2bdd8f
......@@ -2,24 +2,23 @@ package fr.inra.urgi.gpds.domain.data;
import fr.inra.urgi.gpds.domain.brapi.v1.data.BrapiCall;
import java.util.HashSet;
import java.util.Set;
import static fr.inra.urgi.gpds.api.brapi.v1.CallsController.DEFAULT_BRAPI_VERSIONS;
import static fr.inra.urgi.gpds.api.brapi.v1.CallsController.DEFAULT_DATA_TYPES;
/**
* @author gcornut
*/
public class CallVO implements BrapiCall {
private String call;
private Set<String> datatypes;
private final String call;
private Set<String> datatypes = DEFAULT_DATA_TYPES;
private Set<String> versions = DEFAULT_BRAPI_VERSIONS;
private Set<String> methods;
private Set<String> versions;
public CallVO(String call) {
this.call = call;
this.datatypes = new HashSet<>();
this.methods = new HashSet<>();
this.versions = new HashSet<>();
}
@Override
......@@ -42,4 +41,15 @@ public class CallVO implements BrapiCall {
return versions;
}
public void setDatatypes(Set<String> datatypes) {
this.datatypes = datatypes;
}
public void setMethods(Set<String> methods) {
this.methods = methods;
}
public void setVersions(Set<String> versions) {
this.versions = versions;
}
}
backend/src/test/java/fr/inra/urgi/gpds/api/brapi/v1/CallsControllerTest.java
View file @ fe2bdd8f
......@@ -3,7 +3,8 @@ package fr.inra.urgi.gpds.api.brapi.v1;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
import org.springframework.boot.test.context.SpringBootTest;
import org.springframework.http.MediaType;
import org.springframework.test.context.junit.jupiter.SpringExtension;
import org.springframework.test.web.servlet.MockMvc;
......@@ -18,7 +19,8 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.
* @author gcornut
*/
@ExtendWith(SpringExtension.class)
@WebMvcTest(controllers = CallsController.class)
@SpringBootTest
@AutoConfigureMockMvc
class CallsControllerTest {
@Autowired
......
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