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add api end point for auto generation of client. #522
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@julie-sullivan
julie-sullivan committed Feb 5, 2020
1 parent f71d1ca commit d3f26d2
Showing 1 changed file with 150 additions and 12 deletions.
162 changes: 150 additions & 12 deletions cellbase-server/src/main/java/org/opencb/cellbase/server/rest/MetaWSServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,8 @@

package org.opencb.cellbase.server.rest;

import io.swagger.annotations.Api;
import io.swagger.annotations.ApiOperation;
import io.swagger.annotations.ApiParam;
import io.swagger.annotations.*;
import org.apache.commons.lang3.StringUtils;
import org.opencb.cellbase.core.api.CellBaseDBAdaptor;
import org.opencb.cellbase.core.common.GitRepositoryState;
import org.opencb.cellbase.core.config.DownloadProperties;
Expand All @@ -28,23 +27,28 @@
import org.opencb.cellbase.core.result.CellBaseDataResult;
import org.opencb.cellbase.server.exception.SpeciesException;
import org.opencb.cellbase.server.exception.VersionException;
import org.opencb.cellbase.server.rest.clinical.ClinicalWSServer;
import org.opencb.cellbase.server.rest.feature.GeneWSServer;
import org.opencb.cellbase.server.rest.feature.IdWSServer;
import org.opencb.cellbase.server.rest.feature.ProteinWSServer;
import org.opencb.cellbase.server.rest.feature.TranscriptWSServer;
import org.opencb.cellbase.server.rest.genomic.ChromosomeWSServer;
import org.opencb.cellbase.server.rest.genomic.RegionWSServer;
import org.opencb.cellbase.server.rest.genomic.VariantWSServer;
import org.opencb.cellbase.server.rest.regulatory.RegulatoryWSServer;
import org.opencb.cellbase.server.rest.regulatory.TfWSServer;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;


import javax.servlet.http.HttpServletRequest;
import javax.ws.rs.GET;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.*;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.UriInfo;
import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
import java.lang.reflect.Method;
import java.lang.reflect.Parameter;
import java.util.*;

/**
* Created by imedina on 04/08/15.
Expand Down Expand Up @@ -194,4 +198,138 @@ public Response status(@PathParam("species")

}

@GET
@Path("/api")
@ApiOperation(value = "API", response = Map.class)
public Response api(@ApiParam(value = "List of categories to get API from") @QueryParam("category") String categoryStr) {
List<LinkedHashMap<String, Object>> api = new ArrayList<>(20);
Map<String, Class> classes = new LinkedHashMap<>();
classes.put("clinical", ClinicalWSServer.class);
classes.put("gene", GeneWSServer.class);
classes.put("genomeSequence", ChromosomeWSServer.class);
classes.put("meta", MetaWSServer.class);
classes.put("protein", ProteinWSServer.class);
classes.put("region", RegionWSServer.class);
classes.put("regulation", RegulatoryWSServer.class);
classes.put("species", SpeciesWSServer.class);
classes.put("tfbs", TfWSServer.class);
classes.put("transcript", TranscriptWSServer.class);
classes.put("variant", VariantWSServer.class);
classes.put("xref", IdWSServer.class);

if (StringUtils.isNotEmpty(categoryStr)) {
for (String category : categoryStr.split(",")) {
api.add(getHelp(classes.get(category)));
}
} else {
// Get API for all categories
for (String category : classes.keySet()) {
api.add(getHelp(classes.get(category)));
}
}
return createOkResponse(new CellBaseDataResult<>(null, 0, Collections.emptyList(), 1,
Collections.singletonList(api), 1));
}

private LinkedHashMap<String, Object> getHelp(Class clazz) {
LinkedHashMap<String, Object> map = new LinkedHashMap<>();

map.put("name", ((Api) clazz.getAnnotation(Api.class)).value());
map.put("path", ((Path) clazz.getAnnotation(Path.class)).value());

List<LinkedHashMap<String, Object>> endpoints = new ArrayList<>(20);
for (Method method : clazz.getMethods()) {
Path pathAnnotation = method.getAnnotation(Path.class);
String httpMethod = "GET";
if (method.getAnnotation(POST.class) != null) {
httpMethod = "POST";
} else {
if (method.getAnnotation(DELETE.class) != null) {
httpMethod = "DELETE";
}
}
ApiOperation apiOperationAnnotation = method.getAnnotation(ApiOperation.class);
if (pathAnnotation != null && apiOperationAnnotation != null && !apiOperationAnnotation.hidden()) {
LinkedHashMap<String, Object> endpoint = new LinkedHashMap<>();
endpoint.put("path", map.get("path") + pathAnnotation.value());
endpoint.put("method", httpMethod);
endpoint.put("response", StringUtils.substringAfterLast(apiOperationAnnotation.response().getName()
.replace("Void", ""), "."));

String responseClass = apiOperationAnnotation.response().getName().replace("Void", "");
endpoint.put("responseClass", responseClass.endsWith(";") ? responseClass : responseClass + ";");
endpoint.put("notes", apiOperationAnnotation.notes());
endpoint.put("description", apiOperationAnnotation.value());

ApiImplicitParams apiImplicitParams = method.getAnnotation(ApiImplicitParams.class);
List<LinkedHashMap<String, Object>> parameters = new ArrayList<>();
if (apiImplicitParams != null) {
for (ApiImplicitParam apiImplicitParam : apiImplicitParams.value()) {
LinkedHashMap<String, Object> parameter = new LinkedHashMap<>();
parameter.put("name", apiImplicitParam.name());
parameter.put("param", apiImplicitParam.paramType());
parameter.put("type", apiImplicitParam.dataType());
parameter.put("typeClass", "java.lang." + StringUtils.capitalize(apiImplicitParam.dataType()));
parameter.put("allowedValues", apiImplicitParam.allowableValues());
parameter.put("required", apiImplicitParam.required());
parameter.put("defaultValue", apiImplicitParam.defaultValue());
parameter.put("description", apiImplicitParam.value());
parameters.add(parameter);
}
}

Parameter[] methodParameters = method.getParameters();
if (methodParameters != null) {
for (Parameter methodParameter : methodParameters) {
ApiParam apiParam = methodParameter.getAnnotation(ApiParam.class);
if (apiParam != null && !apiParam.hidden()) {
LinkedHashMap<String, Object> parameter = new LinkedHashMap<>();
if (methodParameter.getAnnotation(PathParam.class) != null) {
parameter.put("name", methodParameter.getAnnotation(PathParam.class).value());
parameter.put("param", "path");
} else {
if (methodParameter.getAnnotation(QueryParam.class) != null) {
parameter.put("name", methodParameter.getAnnotation(QueryParam.class).value());
parameter.put("param", "query");
} else {
parameter.put("name", "body");
parameter.put("param", "body");
}
}

// Get type in lower case except for 'body' param
String type = methodParameter.getType().getName();
String typeClass = type;
if (typeClass.contains(".")) {
String[] split = typeClass.split("\\.");
type = split[split.length - 1];
if (!parameter.get("param").equals("body")) {
type = type.toLowerCase();

// Complex type different from body are enums
if (type.contains("$")) {
type = "enum";
}
} else {
type = "object";
}
}
parameter.put("type", type);
parameter.put("typeClass", typeClass.endsWith(";") ? typeClass : typeClass + ";");
parameter.put("allowedValues", apiParam.allowableValues());
parameter.put("required", apiParam.required());
parameter.put("defaultValue", apiParam.defaultValue());
parameter.put("description", apiParam.value());
parameters.add(parameter);
}
}
}
endpoint.put("parameters", parameters);
endpoints.add(endpoint);
}
}
map.put("endpoints", endpoints);
return map;
}

}

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