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Changes related to GA4GH integration with ega-data-api
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@ashutoshebi
ashutoshebi committed Jan 17, 2021
1 parent 2694a77 commit c04b9db
Showing 1 changed file with 1 addition and 229 deletions.
230 changes: 1 addition & 229 deletions src/main/java/zuulserver/filters/MyZuulFilter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,30 +7,8 @@

import com.netflix.zuul.ZuulFilter;
import com.netflix.zuul.context.RequestContext;
import com.squareup.moshi.JsonAdapter;
import com.squareup.moshi.Moshi;
import com.squareup.moshi.Types;
import okhttp3.*;
import org.apache.commons.lang.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.boot.autoconfigure.security.oauth2.resource.UserInfoTokenServices;
import org.springframework.security.crypto.codec.Base64;
import org.springframework.security.jwt.Jwt;
import org.springframework.security.jwt.JwtHelper;
import org.springframework.security.oauth2.provider.OAuth2Authentication;
import org.springframework.stereotype.Component;
import org.springframework.web.util.UrlPathHelper;
import zuulserver.config.MyServerSettings;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Random;
import org.springframework.security.oauth2.common.exceptions.InvalidTokenException;
import zuulserver.dto.Permission;
import zuulserver.dto.Permissions;

/**
* @author asenf
Expand All @@ -40,18 +18,6 @@ public class MyZuulFilter extends ZuulFilter {

private UrlPathHelper urlPathHelper = new UrlPathHelper();

@Autowired
private MyServerSettings serverSettings;

private static String getBasicEncoded(String user, String password) {
String authString = user + ":" + password;
System.out.println("auth string: " + authString);
byte[] authEncBytes = Base64.encode(authString.getBytes());
String authStringEnc = new String(authEncBytes);
System.out.println("Base64 encoded auth string: " + authStringEnc);
return authStringEnc;
}

@Override
public String filterType() {
return "pre";
Expand All @@ -71,203 +37,9 @@ public boolean shouldFilter() {
public Object run() {
RequestContext ctx = RequestContext.getCurrentContext();
final String requestURI = this.urlPathHelper.getPathWithinApplication(ctx.getRequest());
if (!(requestURI.contains("data") || requestURI.contains("central")|| requestURI.contains("tickets"))) {
if (!(requestURI.contains("data") || requestURI.contains("central") || requestURI.contains("tickets"))) {
throw new NullPointerException();

}

String access_token = "";
try {
access_token = StringUtils.substringAfterLast((String) ctx.getRequest().getHeader("Authorization"), "Bearer ");
} catch (Throwable th) {
}

// Only perform this for ELIXIR tokens - pass EGA tokens straight to the API
boolean isElixirToken = determineTokenOrigin(access_token);
if (isElixirToken) {
String userElixirSub = null;
try {
userElixirSub = getElixirSub(access_token);
} catch (InvalidTokenException ex) {
ctx.setResponseBody(ex.toString());
System.out.println("X: " + ex.toString());
return null;
}

System.out.println("Elixir Sub: " + userElixirSub);
/*
* Old Code
*/
// Contact EGA for Datasets & Elixir User
// List<String> permissions = getElixirPermissions(userElixirSub);
// String permissions_ = "";
// for (int i = 0; i < permissions.size(); i++) { // Neet to test: Is this always 1 String now??
// permissions_ += permissions.get(i);
// if (i < permissions.size() - 1)
// permissions_ += ","; // New - is a Base64 encoded, signed String from EGA
// }
// ctx.addZuulRequestHeader("X-Permissions", permissions_);

/*
* New Code
*/
Permission p = getElixirPermissionsNew(userElixirSub);
ctx.addZuulRequestHeader("X-Permissions", p.getSignatureString());
System.out.println("Signature String: " + p.getSignatureString());

} else {
}

return null;
}
/*
private String getElixirUserEmail(String accessToken) {
String url = serverSettings.getElixirUrl();
UserInfoTokenServices tokenService = new UserInfoTokenServices(url, "");
OAuth2Authentication auth = tokenService.loadAuthentication(accessToken);
LinkedHashMap<String, String> details = (LinkedHashMap<String, String>) auth.getUserAuthentication().getDetails();
String email = details.get("email");
return email;
}
private String getElixirUserId(String accessToken) {
String url = serverSettings.getElixirUrl();
UserInfoTokenServices tokenService = new UserInfoTokenServices(url, "");
OAuth2Authentication auth = tokenService.loadAuthentication(accessToken);
LinkedHashMap<String, String> details = (LinkedHashMap<String, String>) auth.getUserAuthentication().getDetails();
String id = details.get("id");
return id;
}
*/
private String getElixirSub(String accessToken) {
String url = serverSettings.getElixirUrl();
UserInfoTokenServices tokenService = new UserInfoTokenServices(url, serverSettings.getElixirClient());
OAuth2Authentication auth = tokenService.loadAuthentication(accessToken);
LinkedHashMap<String, String> details = (LinkedHashMap<String, String>) auth.getUserAuthentication().getDetails();
String sub = details.get("sub");

return sub;
}

private List<String> getElixirPermissions(String user_id) {
String baseApi = serverSettings.isInternal() ? getInternalUrl() : serverSettings.getElixirUrl(); // MUST BE CHANGED TO "https://ega.ebi.ac.uk/elixir/central/.." IN LOCAL (NON-EBI) INSTALLATIONS
String accessToken = serverSettings.getToken();

OkHttpClient.Builder builder = new OkHttpClient.Builder();
OkHttpClient okHttpClient = builder
.addNetworkInterceptor(new ResponseCacheInterceptor()) // Enable response caching
.cache(new Cache(new File("apiResponses"), 5 * 1024 * 1024)) // Set the cache location and size (5 MB)
.build();

// List all Datasets
Request datasetRequest = new Request.Builder()
.url(baseApi + "/app/elixir/" + user_id + "/datasets")
//.addHeader("Authorization", "Bearer " + accessToken)
.addHeader("Authorization", "Basic " + getBasicEncoded(serverSettings.getBasicUser(), serverSettings.getBasicPass()))
.build();
Moshi MOSHI = new Moshi.Builder().build();
JsonAdapter<List<String>> STRING_JSON_ADAPTER =
MOSHI.adapter(Types.newParameterizedType(List.class, String.class));

List<String> result = new ArrayList<String>(); // Prevent result from bein Null
try {
// Execute the request and retrieve the response.
Response response = null;
int tryCount = 9;
while (tryCount-- > 0 && (response == null || !response.isSuccessful())) {
try {
response = okHttpClient.newCall(datasetRequest).execute();
} catch (Exception ex) {
}
}
ResponseBody body = response.body();
result = STRING_JSON_ADAPTER.fromJson(body.source());
body.close();
System.out.println(result.size() + " Datasets.");

} catch (IOException ex) {
System.out.println("Error getting Datasets: " + ex.toString());
}

return result;
}

private Permission getElixirPermissionsNew(String user_id) {
String baseApi = serverSettings.isInternal() ? getInternalUrl() : serverSettings.getElixirUrl(); // MUST BE CHANGED TO "https://ega.ebi.ac.uk/elixir/central/.." IN LOCAL (NON-EBI) INSTALLATIONS
String accessToken = serverSettings.getToken();

OkHttpClient.Builder builder = new OkHttpClient.Builder();
OkHttpClient okHttpClient = builder
.addNetworkInterceptor(new ResponseCacheInterceptor()) // Enable response caching
.cache(new Cache(new File("apiResponses"), 5 * 1024 * 1024)) // Set the cache location and size (5 MB)
.build();

// List all Datasets
Request datasetRequest = new Request.Builder()
.url(baseApi + "/app/user/" + user_id + "/")
.addHeader("Authorization", "Basic " + getBasicEncoded(serverSettings.getBasicUser(), serverSettings.getBasicPass()))
.build();
Moshi MOSHI = new Moshi.Builder().build();
JsonAdapter<Permissions> STRING_JSON_ADAPTER = MOSHI.adapter(Permissions.class);

Permissions result = null;
try {
// Execute the request and retrieve the response.
Response response = null;
int tryCount = 3;
while (tryCount-- > 0 && (response == null || !response.isSuccessful())) {
try {
System.out.println(" --- " + datasetRequest.toString());
response = okHttpClient.newCall(datasetRequest).execute();
} catch (Exception ex) {
System.out.println("ERROR " + ex.toString());
}
}
if (response.code() != 200) {
throw new IOException(response.toString());
}

ResponseBody body = response.body();
result = STRING_JSON_ADAPTER.fromJson(body.source());
body.close();

} catch (IOException ex) {
System.out.println("Error getting Datasets: " + ex.toString());
}

return result.getPermissions()[0];
}

// Returns 'true' if token originated from ELIXIR
private boolean determineTokenOrigin(String access_token) {
if (access_token == null || access_token.length() == 0)
return false;

Jwt decoded_token = JwtHelper.decode(access_token);
String claims = decoded_token.getClaims();
return (claims.contains(".elixir-czech."));
}

// Returns URL for CENTRAL (Internal Only)
private String getInternalUrl() {
return serverSettings.getUrl();
}

/**
* Interceptor to cache data and maintain it for 10 minutes.
* <p>
* If the same network request is sent within a minute,
* the response is retrieved from cache.
*/
private static class ResponseCacheInterceptor implements Interceptor {
@Override
public okhttp3.Response intercept(Chain chain) throws IOException {
okhttp3.Response originalResponse = chain.proceed(chain.request());
return originalResponse.newBuilder()
.header("Cache-Control", "public, max-age=" + 600)
.build();
}
}
}

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