knowledgepixels/nanopub-query | Build 17149479353 | com/knowledgepixels/query/MainVerticle.java | Coveralls

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package com.knowledgepixels.query;

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import java.io.InputStream;

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import java.net.URLEncoder;

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import java.util.ArrayList;

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import java.util.Collections;

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import java.util.List;

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import java.util.Map.Entry;

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import java.util.Scanner;

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import java.util.concurrent.Executors;

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import java.util.concurrent.TimeUnit;

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import org.eclipse.rdf4j.model.Value;

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import com.github.jsonldjava.shaded.com.google.common.base.Charsets;

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import io.micrometer.prometheus.PrometheusMeterRegistry;

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import io.vertx.core.AbstractVerticle;

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import io.vertx.core.Future;

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import io.vertx.core.MultiMap;

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import io.vertx.core.Promise;

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import io.vertx.core.http.HttpClient;

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import io.vertx.core.http.HttpClientOptions;

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import io.vertx.core.http.HttpMethod;

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import io.vertx.core.http.HttpServer;

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import io.vertx.core.http.HttpServerResponse;

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import io.vertx.core.http.PoolOptions;

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import io.vertx.ext.web.Router;

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import io.vertx.ext.web.RoutingContext;

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import io.vertx.ext.web.handler.CorsHandler;

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import io.vertx.ext.web.handler.StaticHandler;

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import io.vertx.ext.web.proxy.handler.ProxyHandler;

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import io.vertx.httpproxy.HttpProxy;

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import io.vertx.httpproxy.ProxyContext;

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import io.vertx.httpproxy.ProxyInterceptor;

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import io.vertx.httpproxy.ProxyRequest;

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import io.vertx.httpproxy.ProxyResponse;

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import io.vertx.micrometer.PrometheusScrapingHandler;

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import io.vertx.micrometer.backends.BackendRegistries;

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/**

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 * Main verticle that coordinates the incoming HTTP requests.

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*/

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@GeneratedFlagForDependentElements

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public class MainVerticle extends AbstractVerticle {

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    private static String css = null;

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/**

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     * Start the main verticle.

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     * @param startPromise the promise to complete when the verticle is started

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     * @throws Exception if an error occurs during startup

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*/

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    @Override

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    public void start(Promise<Void> startPromise) throws Exception {

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        HttpClient httpClient = vertx.createHttpClient(

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                new HttpClientOptions()

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                        .setConnectTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_CONNECT_TIMEOUT", 1000))

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                        .setIdleTimeoutUnit(TimeUnit.SECONDS)

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                        .setIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))

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                        .setReadIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))

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                        .setWriteIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60)),

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                new PoolOptions().setHttp1MaxSize(200).setHttp2MaxSize(200)

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);

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        HttpServer proxyServer = vertx.createHttpServer();

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        Router proxyRouter = Router.router(vertx);

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        proxyRouter.route().handler(CorsHandler.create().addRelativeOrigin(".*"));

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        // Metrics

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        final var metricsHttpServer = vertx.createHttpServer();

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        final var metricsRouter = Router.router(vertx);

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        metricsHttpServer.requestHandler(metricsRouter).listen(9394);

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        final var metricsRegistry = (PrometheusMeterRegistry) BackendRegistries.getDefaultNow();

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        final var collector = new MetricsCollector(metricsRegistry);

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        metricsRouter.route("/metrics").handler(PrometheusScrapingHandler.create(metricsRegistry));

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        // ----------

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        // This part is only used if the redirection is not done through Nginx.

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        // See nginx.conf and this bug report: https://github.com/eclipse-rdf4j/rdf4j/discussions/5120

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        HttpProxy rdf4jProxy = HttpProxy.reverseProxy(httpClient);

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        String proxy = Utils.getEnvString("RDF4J_PROXY_HOST", "rdf4j");

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        int proxyPort = Utils.getEnvInt("RDF4J_PROXY_PORT", 8080);

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        rdf4jProxy.origin(proxyPort, proxy);

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            @Override

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            @GeneratedFlagForDependentElements

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            public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {

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                ProxyRequest request = context.request();

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                request.setURI(request.getURI().replaceAll("/", "_").replaceFirst("^_repo_", "/rdf4j-server/repositories/"));

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                // For later to try to get HTML tables out:

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//                                if (request.headers().get("Accept") == null) {

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//                                        request.putHeader("Accept", "text/html");

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//                                }

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//                                request.putHeader("Accept", "application/json");

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                return ProxyInterceptor.super.handleProxyRequest(context);

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            @Override

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            @GeneratedFlagForDependentElements

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            public Future<Void> handleProxyResponse(ProxyContext context) {

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                ProxyResponse resp = context.response();

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                resp.putHeader("Access-Control-Allow-Origin", "*");

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                resp.putHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS");

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                // For later to try to get HTML tables out:

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//                                String acceptHeader = context.request().headers().get("Accept");

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//                                if (acceptHeader != null && acceptHeader.contains("text/html")) {

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//                                        resp.putHeader("Content-Type", "text/html");

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//                                        resp.setBody(Body.body(Buffer.buffer("<html><body><strong>test</strong></body></html>")));

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//                                }

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                return ProxyInterceptor.super.handleProxyResponse(context);

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});

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        // ----------

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        proxyRouter.route(HttpMethod.GET, "/repo").handler(req -> handleRedirect(req, "/repo"));

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        proxyRouter.route(HttpMethod.GET, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));

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        proxyRouter.route(HttpMethod.POST, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));

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        proxyRouter.route(HttpMethod.HEAD, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));

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        proxyRouter.route(HttpMethod.OPTIONS, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));

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        proxyRouter.route(HttpMethod.GET, "/tools/*").handler(req -> {

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            final String yasguiPattern = "^/tools/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?/yasgui\\.html$";

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            if (req.normalizedPath().matches(yasguiPattern)) {

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                String repo = req.normalizedPath().replaceFirst(yasguiPattern, "$1$2");

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                req.response()

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                        .putHeader("content-type", "text/html")

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                        .end("<!DOCTYPE html>\n"

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                                + "<html lang=\"en\">\n"

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                                + "<head>\n"

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                                + "<meta charset=\"utf-8\">\n"

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                                + "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"

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                                + "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"

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                                + "<title>Nanopub Query SPARQL Editor for repository: " + repo + "</title>\n"

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                                + "<link rel=\"stylesheet\" href=\"/style.css\">\n"

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                                + "<link href='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.css' rel='stylesheet' type='text/css'/>\n"

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                                + "<style>.yasgui .endpointText {display:none !important;}</style>\n"

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                                + "<script type=\"text/javascript\">localStorage.clear();</script>\n"

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                                + "</head>\n"

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                                + "<body>\n"

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                                + "<h3>Nanopub Query SPARQL Editor for repository: " + repo + "</h3>\n"

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                                + "<div id='yasgui'></div>\n"

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                                + "<script src='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.js'></script>\n"

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                                + "<script type=\"text/javascript\">\n"

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                                + "var yasgui = YASGUI(document.getElementById(\"yasgui\"), {\n"

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                                + "  yasqe:{sparql:{endpoint:'/repo/" + repo + "'},value:'" + Utils.defaultQuery.replaceAll("\n", "\\\\n") + "'}\n"

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                                + "});\n"

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                                + "</script>\n"

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                                + "</body>\n"

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                                + "</html>");

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            } else {

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                req.response()

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                        .putHeader("content-type", "text/plain")

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                        .setStatusCode(404)

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                        .end("not found");

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});

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        proxyRouter.route(HttpMethod.GET, "/page").handler(req -> handleRedirect(req, "/page"));

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        proxyRouter.route(HttpMethod.GET, "/page/*").handler(req -> {

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            final String pagePattern = "^/page/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?$";

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            if (req.normalizedPath().matches(pagePattern)) {

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                String repo = req.normalizedPath().replaceFirst(pagePattern, "$1$2");

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                req.response()

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                        .putHeader("content-type", "text/html")

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                        .end("<!DOCTYPE html>\n"

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                                + "<html lang=\"en\">\n"

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                                + "<head>\n"

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                                + "<meta charset=\"utf-8\">\n"

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                                + "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"

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                                + "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"

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                                + "<title>Nanopub Query repo: " + repo + "</title>\n"

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                                + "<link rel=\"stylesheet\" href=\"/style.css\">\n"

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                                + "</head>\n"

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                                + "<body>\n"

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                                + "<h3>Nanopub Query repo: " + repo + "</h3>\n"

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                                + "<p>Endpoint: <a href=\"/repo/" + repo + "\">/repo/" + repo + "</a></p>"

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                                + "<p>YASGUI: <a href=\"/tools/" + repo + "/yasgui.html\">/tools/" + repo + "/yasgui.hml</a></p>"

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                                + "</body>\n"

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                                + "</html>");

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            } else {

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                req.response()

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                        .putHeader("content-type", "text/plain")

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                        .setStatusCode(404)

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                        .end("not found");

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});

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        proxyRouter.route(HttpMethod.GET, "/").handler(req -> {

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            String repos = "";

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            List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());

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            Collections.sort(repoList);

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            for (String s : repoList) {

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                if (s.startsWith("pubkey_") || s.startsWith("type_")) continue;

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                repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a></code></li>";

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            String pinnedApisValue = Utils.getEnvString("NANOPUB_QUERY_PINNED_APIS", "");

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            String[] pinnedApis = pinnedApisValue.split(" ");

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            String pinnedApiLinks = "";

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            if (!pinnedApisValue.isEmpty()) {

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                for (String s : pinnedApis) {

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                    pinnedApiLinks = pinnedApiLinks + "<li><a href=\"openapi/?url=spec/" + s + "%3Fapi-version=latest\">" + s.replaceFirst("^.*/", "") + "</a></li>";

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                pinnedApiLinks = "<p>Pinned APIs:</p>\n" +

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                        "<ul>\n" +

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                        pinnedApiLinks +

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                        "</ul>\n";

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            req.response()

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                    .putHeader("content-type", "text/html")

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                    .end("<!DOCTYPE html>\n"

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                            + "<html lang='en'>\n"

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                            + "<head>\n"

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                            + "<title>Nanopub Query</title>\n"

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                            + "<meta charset='utf-8'>\n"

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                            + "<link rel=\"stylesheet\" href=\"/style.css\">\n"

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                            + "</head>\n"

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                            + "<body>\n"

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                            + "<h1>Nanopub Query</h1>"

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                            + "<p>General repos:</p>"

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                            + "<ul>" + repos + "</ul>"

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                            + "<p>Specific repos:</p>"

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                            + "<ul>"

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                            + "<li><a href=\"/pubkeys\">Pubkey Repos</a></li>"

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                            + "<li><a href=\"/types\">Type Repos</a></li>"

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                            + "</ul>"

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                            + pinnedApiLinks

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                            + "</body>\n"

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                            + "</html>");

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});

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        proxyRouter.route(HttpMethod.GET, "/pubkeys").handler(req -> {

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            String repos = "";

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            List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());

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            Collections.sort(repoList);

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            for (String s : repoList) {

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                if (!s.startsWith("pubkey_")) continue;

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                String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");

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                Value hashObj = Utils.getObjectForHash(hash);

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                String label;

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                if (hashObj == null) {

242

                    label = "";

243

                } else {

244

                    label = " (" + Utils.getShortPubkeyName(hashObj.stringValue()) + ")";

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                s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");

247

                repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";

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            req.response()

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                    .putHeader("content-type", "text/html")

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                    .end("<!DOCTYPE html>\n"

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                            + "<html lang='en'>\n"

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                            + "<head>\n"

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                            + "<title>Nanopub Query: Pubkey Repos</title>\n"

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                            + "<meta charset='utf-8'>\n"

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                            + "<link rel=\"stylesheet\" href=\"/style.css\">\n"

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                            + "</head>\n"

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                            + "<body>\n"

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                            + "<h3>Pubkey Repos</h3>"

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                            + "<p>Repos:</p>"

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                            + "<ul>" + repos + "</ul>"

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                            + "</body>\n"

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                            + "</html>");

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});

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        proxyRouter.route(HttpMethod.GET, "/types").handler(req -> {

266

            String repos = "";

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            List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());

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            Collections.sort(repoList);

269

            for (String s : repoList) {

270

                if (!s.startsWith("type_")) continue;

271

                String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");

272

                Value hashObj = Utils.getObjectForHash(hash);

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                String label;

274

                if (hashObj == null) {

275

                    label = "";

276

                } else {

277

                    label = " (" + hashObj.stringValue() + ")";

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279

                s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");

280

                repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";

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282

            req.response()

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                    .putHeader("content-type", "text/html")

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                    .end("<!DOCTYPE html>\n"

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                            + "<html lang='en'>\n"

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                            + "<head>\n"

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                            + "<title>Nanopub Query: Type Repos</title>\n"

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                            + "<meta charset='utf-8'>\n"

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                            + "<link rel=\"stylesheet\" href=\"/style.css\">\n"

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                            + "</head>\n"

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                            + "<body>\n"

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                            + "<h3>Type Repos</h3>"

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                            + "<p>Repos:</p>"

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                            + "<ul>" + repos + "</ul>"

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                            + "</body>\n"

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                            + "</html>");

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});

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        proxyRouter.route(HttpMethod.GET, "/style.css").handler(req -> {

299

            if (css == null) {

300

                css = getResourceAsString("style.css");

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            req.response().end(css);

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});

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        proxyRouter.route(HttpMethod.GET, "/grlc-spec/*").handler(req -> {

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            GrlcSpecPage gsp = new GrlcSpecPage(req.normalizedPath(), req.queryParams());

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            String spec = gsp.getSpec();

308

            if (spec == null) {

309

                req.response().setStatusCode(404).end("query definition not found / not valid");

310

            } else {

311

                req.response().putHeader("content-type", "text/yaml").end(spec);

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});

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        proxyRouter.route(HttpMethod.GET, "/openapi/spec/*").handler(req -> {

316

            OpenApiSpecPage osp = new OpenApiSpecPage(req.normalizedPath(), req.queryParams());

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            String spec = osp.getSpec();

318

            if (spec == null) {

319

                req.response().setStatusCode(404).end("query definition not found / not valid");

320

            } else {

321

                req.response().putHeader("content-type", "text/yaml").end(spec);

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});

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        proxyRouter.route("/openapi/*").handler(StaticHandler.create("com/knowledgepixels/query/swagger"));

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        HttpProxy grlcProxy = HttpProxy.reverseProxy(httpClient);

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        grlcProxy.origin(80, "grlc");

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            @Override

332

            @GeneratedFlagForDependentElements

333

            public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {

334

                final String apiPattern = "^/api/(RA[a-zA-Z0-9-_]{43})/([a-zA-Z0-9-_]+)([?].*)?$";

335

                if (context.request().getURI().matches(apiPattern)) {

336

                    String artifactCode = context.request().getURI().replaceFirst(apiPattern, "$1");

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                    String queryName = context.request().getURI().replaceFirst(apiPattern, "$2");

338

                    String grlcUrlParams = "";

339

                    String grlcSpecUrlParams = "";

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                    MultiMap pm = context.request().proxiedRequest().params();

341

                    for (Entry<String, String> e : pm) {

342

                        if (e.getKey().equals("api-version")) {

343

                            grlcSpecUrlParams += "&" + e.getKey() + "=" + URLEncoder.encode(e.getValue(), Charsets.UTF_8);

344

                        } else {

345

                            grlcUrlParams += "&" + e.getKey() + "=" + URLEncoder.encode(e.getValue(), Charsets.UTF_8);

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                    String url = "/api-url/" + queryName +

349

                            "?specUrl=" + URLEncoder.encode(GrlcSpecPage.nanopubQueryUrl + "grlc-spec/" + artifactCode + "/?" +

350

                            grlcSpecUrlParams, Charsets.UTF_8) + grlcUrlParams;

351

                    context.request().setURI(url);

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353

                return context.sendRequest();

354

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            @Override

357

            @GeneratedFlagForDependentElements

358

            public Future<Void> handleProxyResponse(ProxyContext context) {

359

                // To avoid double entries:

360

                context.response().headers().remove("Access-Control-Allow-Origin");

361

                return context.sendResponse();

362

363

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});

365

366

        proxyServer.requestHandler(req -> {

367

            applyGlobalHeaders(req.response());

368

            proxyRouter.handle(req);

369

});

370

        proxyServer.listen(9393);

371

372

        proxyRouter.route("/api/*").handler(ProxyHandler.create(grlcProxy));

373

        proxyRouter.route("/static/*").handler(ProxyHandler.create(grlcProxy));

374

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        // Periodic metrics update

376

        vertx.setPeriodic(1000, id -> collector.updateMetrics());

377

378

379

        new Thread(() -> {

380

            try {

381

                var status = StatusController.get().initialize();

382

                System.err.println("Current state: " + status.state + ", last committed counter: " + status.loadCounter);

383

                if (status.state == StatusController.State.LAUNCHING || status.state == StatusController.State.LOADING_INITIAL) {

384

                    // Do the initial nanopublication loading

385

                    StatusController.get().setLoadingInitial(status.loadCounter);

386

                    // Fall back to local nanopub loading if the local files are present

387

                    if (!LocalNanopubLoader.init()) {

388

                        JellyNanopubLoader.loadInitial(status.loadCounter);

389

                    } else {

390

                        System.err.println("Local nanopublication loading finished");

391

392

                    StatusController.get().setReady();

393

                } else {

394

                    System.err.println("Initial load is already done");

395

                    StatusController.get().setReady();

396

397

            } catch (Exception ex) {

398

                ex.printStackTrace();

399

                System.err.println("Initial load failed, terminating...");

400

                Runtime.getRuntime().exit(1);

401

402

403

            // Start periodic nanopub loading

404

            System.err.println("Starting periodic nanopub loading...");

405

            var executor = Executors.newSingleThreadScheduledExecutor();

406

            executor.scheduleWithFixedDelay(

407

                    JellyNanopubLoader::loadUpdates,

408

                    JellyNanopubLoader.UPDATES_POLL_INTERVAL,

409

                    JellyNanopubLoader.UPDATES_POLL_INTERVAL,

410

                    TimeUnit.MILLISECONDS

411

);

412

        }).start();

413

414

        Runtime.getRuntime().addShutdownHook(new Thread(() -> {

415

            try {

416

                System.err.println("Gracefully shutting down...");

417

                TripleStore.get().shutdownRepositories();

418

                vertx.close().toCompletionStage().toCompletableFuture().get(5, TimeUnit.SECONDS);

419

                System.err.println("Graceful shutdown completed");

420

            } catch (Exception ex) {

421

                System.err.println("Graceful shutdown failed");

422

                ex.printStackTrace();

423

424

        }));

425

426

427

    private String getResourceAsString(String file) {

428

        InputStream is = getClass().getClassLoader().getResourceAsStream("com/knowledgepixels/query/" + file);

429

        try (Scanner s = new Scanner(is).useDelimiter("\\A")) {

430

            String fileContent = s.hasNext() ? s.next() : "";

431

            return fileContent;

432

433

434

435

    private static void handleRedirect(RoutingContext req, String path) {

436

        String queryString = "";

437

        if (!req.queryParam("query").isEmpty())

438

            queryString = "?query=" + URLEncoder.encode(req.queryParam("query").get(0), Charsets.UTF_8);

439

        if (req.queryParam("for-type").size() == 1) {

440

            String type = req.queryParam("for-type").get(0);

441

            req.response().putHeader("location", path + "/type/" + Utils.createHash(type) + queryString);

442

            req.response().setStatusCode(301).end();

443

        } else if (req.queryParam("for-pubkey").size() == 1) {

444

            String type = req.queryParam("for-pubkey").get(0);

445

            req.response().putHeader("location", path + "/pubkey/" + Utils.createHash(type) + queryString);

446

            req.response().setStatusCode(301).end();

447

        } else if (req.queryParam("for-user").size() == 1) {

448

            String type = req.queryParam("for-user").get(0);

449

            req.response().putHeader("location", path + "/user/" + Utils.createHash(type) + queryString);

450

            req.response().setStatusCode(301).end();

451

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/**

455

     * Apply headers to the response that should be present for all requests.

456

457

     * @param response The response to which the headers should be applied.

458

*/

459

    private static void applyGlobalHeaders(HttpServerResponse response) {

460

        response.putHeader("Nanopub-Query-Status", StatusController.get().getState().state.toString());

461

462

knowledgepixels / nanopub-query / 17149479353

Source File
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1	package com.knowledgepixels.query;
2
3	import java.io.InputStream;
4	import java.net.URLEncoder;
5	import java.util.ArrayList;
6	import java.util.Collections;
7	import java.util.List;
8	import java.util.Map.Entry;
9	import java.util.Scanner;
10	import java.util.concurrent.Executors;
11	import java.util.concurrent.TimeUnit;
12
13	import org.eclipse.rdf4j.model.Value;
14
15	import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
16
17	import io.micrometer.prometheus.PrometheusMeterRegistry;
18	import io.vertx.core.AbstractVerticle;
19	import io.vertx.core.Future;
20	import io.vertx.core.MultiMap;
21	import io.vertx.core.Promise;
22	import io.vertx.core.http.HttpClient;
23	import io.vertx.core.http.HttpClientOptions;
24	import io.vertx.core.http.HttpMethod;
25	import io.vertx.core.http.HttpServer;
26	import io.vertx.core.http.HttpServerResponse;
27	import io.vertx.core.http.PoolOptions;
28	import io.vertx.ext.web.Router;
29	import io.vertx.ext.web.RoutingContext;
30	import io.vertx.ext.web.handler.CorsHandler;
31	import io.vertx.ext.web.handler.StaticHandler;
32	import io.vertx.ext.web.proxy.handler.ProxyHandler;
33	import io.vertx.httpproxy.HttpProxy;
34	import io.vertx.httpproxy.ProxyContext;
35	import io.vertx.httpproxy.ProxyInterceptor;
36	import io.vertx.httpproxy.ProxyRequest;
37	import io.vertx.httpproxy.ProxyResponse;
38	import io.vertx.micrometer.PrometheusScrapingHandler;
39	import io.vertx.micrometer.backends.BackendRegistries;
40
41	/**
42	* Main verticle that coordinates the incoming HTTP requests.
43	*/
44	@GeneratedFlagForDependentElements
45	public class MainVerticle extends AbstractVerticle {
46
47	private static String css = null;
48
49	/**
50	* Start the main verticle.
51	*
52	* @param startPromise the promise to complete when the verticle is started
53	* @throws Exception if an error occurs during startup
54	*/
55	@Override
56	public void start(Promise<Void> startPromise) throws Exception {
57	HttpClient httpClient = vertx.createHttpClient(
58	new HttpClientOptions()
59	.setConnectTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_CONNECT_TIMEOUT", 1000))
60	.setIdleTimeoutUnit(TimeUnit.SECONDS)
61	.setIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))
62	.setReadIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))
63	.setWriteIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60)),
64	new PoolOptions().setHttp1MaxSize(200).setHttp2MaxSize(200)
65	);
66
67	HttpServer proxyServer = vertx.createHttpServer();
68	Router proxyRouter = Router.router(vertx);
69	proxyRouter.route().handler(CorsHandler.create().addRelativeOrigin(".*"));
70
71	// Metrics
72	final var metricsHttpServer = vertx.createHttpServer();
73	final var metricsRouter = Router.router(vertx);
74	metricsHttpServer.requestHandler(metricsRouter).listen(9394);
75
76	final var metricsRegistry = (PrometheusMeterRegistry) BackendRegistries.getDefaultNow();
77	final var collector = new MetricsCollector(metricsRegistry);
78	metricsRouter.route("/metrics").handler(PrometheusScrapingHandler.create(metricsRegistry));
79	// ----------
80	// This part is only used if the redirection is not done through Nginx.
81	// See nginx.conf and this bug report: https://github.com/eclipse-rdf4j/rdf4j/discussions/5120
82	HttpProxy rdf4jProxy = HttpProxy.reverseProxy(httpClient);
83	String proxy = Utils.getEnvString("RDF4J_PROXY_HOST", "rdf4j");
84	int proxyPort = Utils.getEnvInt("RDF4J_PROXY_PORT", 8080);
85	rdf4jProxy.origin(proxyPort, proxy);
86
87	rdf4jProxy.addInterceptor(new ProxyInterceptor() {	×
88
89	@Override
90	@GeneratedFlagForDependentElements
91	public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {
92	ProxyRequest request = context.request();
93	request.setURI(request.getURI().replaceAll("/", "_").replaceFirst("^_repo_", "/rdf4j-server/repositories/"));
94	// For later to try to get HTML tables out:
95	// if (request.headers().get("Accept") == null) {
96	// request.putHeader("Accept", "text/html");
97	// }
98	// request.putHeader("Accept", "application/json");
99	return ProxyInterceptor.super.handleProxyRequest(context);
100	}
101
102	@Override
103	@GeneratedFlagForDependentElements
104	public Future<Void> handleProxyResponse(ProxyContext context) {
105	ProxyResponse resp = context.response();
106	resp.putHeader("Access-Control-Allow-Origin", "*");
107	resp.putHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS");
108	// For later to try to get HTML tables out:
109	// String acceptHeader = context.request().headers().get("Accept");
110	// if (acceptHeader != null && acceptHeader.contains("text/html")) {
111	// resp.putHeader("Content-Type", "text/html");
112	// resp.setBody(Body.body(Buffer.buffer("<html><body><strong>test</strong></body></html>")));
113	// }
114	return ProxyInterceptor.super.handleProxyResponse(context);
115	}
116
117	});
118	// ----------
119
120	proxyRouter.route(HttpMethod.GET, "/repo").handler(req -> handleRedirect(req, "/repo"));
121	proxyRouter.route(HttpMethod.GET, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
122	proxyRouter.route(HttpMethod.POST, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
123	proxyRouter.route(HttpMethod.HEAD, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
124	proxyRouter.route(HttpMethod.OPTIONS, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
125	proxyRouter.route(HttpMethod.GET, "/tools/*").handler(req -> {
126	final String yasguiPattern = "^/tools/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?/yasgui\\.html$";
127	if (req.normalizedPath().matches(yasguiPattern)) {
128	String repo = req.normalizedPath().replaceFirst(yasguiPattern, "$1$2");
129	req.response()
130	.putHeader("content-type", "text/html")
131	.end("<!DOCTYPE html>\n"
132	+ "<html lang=\"en\">\n"
133	+ "<head>\n"
134	+ "<meta charset=\"utf-8\">\n"
135	+ "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"
136	+ "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"
137	+ "<title>Nanopub Query SPARQL Editor for repository: " + repo + "</title>\n"
138	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
139	+ "<link href='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.css' rel='stylesheet' type='text/css'/>\n"
140	+ "<style>.yasgui .endpointText {display:none !important;}</style>\n"
141	+ "<script type=\"text/javascript\">localStorage.clear();</script>\n"
142	+ "</head>\n"
143	+ "<body>\n"
144	+ "<h3>Nanopub Query SPARQL Editor for repository: " + repo + "</h3>\n"
145	+ "<div id='yasgui'></div>\n"
146	+ "<script src='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.js'></script>\n"
147	+ "<script type=\"text/javascript\">\n"
148	+ "var yasgui = YASGUI(document.getElementById(\"yasgui\"), {\n"
149	+ " yasqe:{sparql:{endpoint:'/repo/" + repo + "'},value:'" + Utils.defaultQuery.replaceAll("\n", "\\\\n") + "'}\n"
150	+ "});\n"
151	+ "</script>\n"
152	+ "</body>\n"
153	+ "</html>");
154	} else {
155	req.response()
156	.putHeader("content-type", "text/plain")
157	.setStatusCode(404)
158	.end("not found");
159	}
160	});
161	proxyRouter.route(HttpMethod.GET, "/page").handler(req -> handleRedirect(req, "/page"));
162	proxyRouter.route(HttpMethod.GET, "/page/*").handler(req -> {
163	final String pagePattern = "^/page/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?$";
164	if (req.normalizedPath().matches(pagePattern)) {
165	String repo = req.normalizedPath().replaceFirst(pagePattern, "$1$2");
166	req.response()
167	.putHeader("content-type", "text/html")
168	.end("<!DOCTYPE html>\n"
169	+ "<html lang=\"en\">\n"
170	+ "<head>\n"
171	+ "<meta charset=\"utf-8\">\n"
172	+ "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"
173	+ "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"
174	+ "<title>Nanopub Query repo: " + repo + "</title>\n"
175	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
176	+ "</head>\n"
177	+ "<body>\n"
178	+ "<h3>Nanopub Query repo: " + repo + "</h3>\n"
179	+ "<p>Endpoint: <a href=\"/repo/" + repo + "\">/repo/" + repo + "</a></p>"
180	+ "<p>YASGUI: <a href=\"/tools/" + repo + "/yasgui.html\">/tools/" + repo + "/yasgui.hml</a></p>"
181	+ "</body>\n"
182	+ "</html>");
183	} else {
184	req.response()
185	.putHeader("content-type", "text/plain")
186	.setStatusCode(404)
187	.end("not found");
188	}
189	});
190	proxyRouter.route(HttpMethod.GET, "/").handler(req -> {
191	String repos = "";
192	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
193	Collections.sort(repoList);
194	for (String s : repoList) {
195	if (s.startsWith("pubkey_") \|\| s.startsWith("type_")) continue;
196	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a></code></li>";
197	}
198	String pinnedApisValue = Utils.getEnvString("NANOPUB_QUERY_PINNED_APIS", "");
199	String[] pinnedApis = pinnedApisValue.split(" ");
200	String pinnedApiLinks = "";
201	if (!pinnedApisValue.isEmpty()) {
202	for (String s : pinnedApis) {
203	pinnedApiLinks = pinnedApiLinks + "<li><a href=\"openapi/?url=spec/" + s + "%3Fapi-version=latest\">" + s.replaceFirst("^.*/", "") + "</a></li>";
204	}
205	pinnedApiLinks = "<p>Pinned APIs:</p>\n" +
206	"<ul>\n" +
207	pinnedApiLinks +
208	"</ul>\n";
209	}
210	req.response()
211	.putHeader("content-type", "text/html")
212	.end("<!DOCTYPE html>\n"
213	+ "<html lang='en'>\n"
214	+ "<head>\n"
215	+ "<title>Nanopub Query</title>\n"
216	+ "<meta charset='utf-8'>\n"
217	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
218	+ "</head>\n"
219	+ "<body>\n"
220	+ "<h1>Nanopub Query</h1>"
221	+ "<p>General repos:</p>"
222	+ "<ul>" + repos + "</ul>"
223	+ "<p>Specific repos:</p>"
224	+ "<ul>"
225	+ "<li><a href=\"/pubkeys\">Pubkey Repos</a></li>"
226	+ "<li><a href=\"/types\">Type Repos</a></li>"
227	+ "</ul>"
228	+ pinnedApiLinks
229	+ "</body>\n"
230	+ "</html>");
231	});
232	proxyRouter.route(HttpMethod.GET, "/pubkeys").handler(req -> {
233	String repos = "";
234	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
235	Collections.sort(repoList);
236	for (String s : repoList) {
237	if (!s.startsWith("pubkey_")) continue;
238	String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");
239	Value hashObj = Utils.getObjectForHash(hash);
240	String label;
241	if (hashObj == null) {
242	label = "";
243	} else {
244	label = " (" + Utils.getShortPubkeyName(hashObj.stringValue()) + ")";
245	}
246	s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");
247	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";
248	}
249	req.response()
250	.putHeader("content-type", "text/html")
251	.end("<!DOCTYPE html>\n"
252	+ "<html lang='en'>\n"
253	+ "<head>\n"
254	+ "<title>Nanopub Query: Pubkey Repos</title>\n"
255	+ "<meta charset='utf-8'>\n"
256	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
257	+ "</head>\n"
258	+ "<body>\n"
259	+ "<h3>Pubkey Repos</h3>"
260	+ "<p>Repos:</p>"
261	+ "<ul>" + repos + "</ul>"
262	+ "</body>\n"
263	+ "</html>");
264	});
265	proxyRouter.route(HttpMethod.GET, "/types").handler(req -> {
266	String repos = "";
267	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
268	Collections.sort(repoList);
269	for (String s : repoList) {
270	if (!s.startsWith("type_")) continue;
271	String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");
272	Value hashObj = Utils.getObjectForHash(hash);
273	String label;
274	if (hashObj == null) {
275	label = "";
276	} else {
277	label = " (" + hashObj.stringValue() + ")";
278	}
279	s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");
280	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";
281	}
282	req.response()
283	.putHeader("content-type", "text/html")
284	.end("<!DOCTYPE html>\n"
285	+ "<html lang='en'>\n"
286	+ "<head>\n"
287	+ "<title>Nanopub Query: Type Repos</title>\n"
288	+ "<meta charset='utf-8'>\n"
289	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
290	+ "</head>\n"
291	+ "<body>\n"
292	+ "<h3>Type Repos</h3>"
293	+ "<p>Repos:</p>"
294	+ "<ul>" + repos + "</ul>"
295	+ "</body>\n"
296	+ "</html>");
297	});
298	proxyRouter.route(HttpMethod.GET, "/style.css").handler(req -> {
299	if (css == null) {
300	css = getResourceAsString("style.css");
301	}
302	req.response().end(css);
303	});
304
305	proxyRouter.route(HttpMethod.GET, "/grlc-spec/*").handler(req -> {
306	GrlcSpecPage gsp = new GrlcSpecPage(req.normalizedPath(), req.queryParams());
307	String spec = gsp.getSpec();
308	if (spec == null) {
309	req.response().setStatusCode(404).end("query definition not found / not valid");
310	} else {
311	req.response().putHeader("content-type", "text/yaml").end(spec);
312	}
313	});
314
315	proxyRouter.route(HttpMethod.GET, "/openapi/spec/*").handler(req -> {
316	OpenApiSpecPage osp = new OpenApiSpecPage(req.normalizedPath(), req.queryParams());
317	String spec = osp.getSpec();
318	if (spec == null) {
319	req.response().setStatusCode(404).end("query definition not found / not valid");
320	} else {
321	req.response().putHeader("content-type", "text/yaml").end(spec);
322	}
323	});
324
325	proxyRouter.route("/openapi/*").handler(StaticHandler.create("com/knowledgepixels/query/swagger"));
326
327	HttpProxy grlcProxy = HttpProxy.reverseProxy(httpClient);
328	grlcProxy.origin(80, "grlc");
329	grlcProxy.addInterceptor(new ProxyInterceptor() {	×
330
331	@Override
332	@GeneratedFlagForDependentElements
333	public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {
334	final String apiPattern = "^/api/(RA[a-zA-Z0-9-_]{43})/([a-zA-Z0-9-_]+)([?].*)?$";
335	if (context.request().getURI().matches(apiPattern)) {
336	String artifactCode = context.request().getURI().replaceFirst(apiPattern, "$1");
337	String queryName = context.request().getURI().replaceFirst(apiPattern, "$2");
338	String grlcUrlParams = "";
339	String grlcSpecUrlParams = "";
340	MultiMap pm = context.request().proxiedRequest().params();
341	for (Entry<String, String> e : pm) {
342	if (e.getKey().equals("api-version")) {
343	grlcSpecUrlParams += "&" + e.getKey() + "=" + URLEncoder.encode(e.getValue(), Charsets.UTF_8);
344	} else {
345	grlcUrlParams += "&" + e.getKey() + "=" + URLEncoder.encode(e.getValue(), Charsets.UTF_8);
346	}
347	}
348	String url = "/api-url/" + queryName +
349	"?specUrl=" + URLEncoder.encode(GrlcSpecPage.nanopubQueryUrl + "grlc-spec/" + artifactCode + "/?" +
350	grlcSpecUrlParams, Charsets.UTF_8) + grlcUrlParams;
351	context.request().setURI(url);
352	}
353	return context.sendRequest();
354	}
355
356	@Override
357	@GeneratedFlagForDependentElements
358	public Future<Void> handleProxyResponse(ProxyContext context) {
359	// To avoid double entries:
360	context.response().headers().remove("Access-Control-Allow-Origin");
361	return context.sendResponse();
362	}
363
364	});
365
366	proxyServer.requestHandler(req -> {
367	applyGlobalHeaders(req.response());
368	proxyRouter.handle(req);
369	});
370	proxyServer.listen(9393);
371
372	proxyRouter.route("/api/*").handler(ProxyHandler.create(grlcProxy));
373	proxyRouter.route("/static/*").handler(ProxyHandler.create(grlcProxy));
374
375	// Periodic metrics update
376	vertx.setPeriodic(1000, id -> collector.updateMetrics());
377
378
379	new Thread(() -> {
380	try {
381	var status = StatusController.get().initialize();
382	System.err.println("Current state: " + status.state + ", last committed counter: " + status.loadCounter);
383	if (status.state == StatusController.State.LAUNCHING \|\| status.state == StatusController.State.LOADING_INITIAL) {
384	// Do the initial nanopublication loading
385	StatusController.get().setLoadingInitial(status.loadCounter);
386	// Fall back to local nanopub loading if the local files are present
387	if (!LocalNanopubLoader.init()) {
388	JellyNanopubLoader.loadInitial(status.loadCounter);
389	} else {
390	System.err.println("Local nanopublication loading finished");
391	}
392	StatusController.get().setReady();
393	} else {
394	System.err.println("Initial load is already done");
395	StatusController.get().setReady();
396	}
397	} catch (Exception ex) {
398	ex.printStackTrace();
399	System.err.println("Initial load failed, terminating...");
400	Runtime.getRuntime().exit(1);
401	}
402
403	// Start periodic nanopub loading
404	System.err.println("Starting periodic nanopub loading...");
405	var executor = Executors.newSingleThreadScheduledExecutor();
406	executor.scheduleWithFixedDelay(
407	JellyNanopubLoader::loadUpdates,
408	JellyNanopubLoader.UPDATES_POLL_INTERVAL,
409	JellyNanopubLoader.UPDATES_POLL_INTERVAL,
410	TimeUnit.MILLISECONDS
411	);
412	}).start();
413
414	Runtime.getRuntime().addShutdownHook(new Thread(() -> {
415	try {
416	System.err.println("Gracefully shutting down...");
417	TripleStore.get().shutdownRepositories();
418	vertx.close().toCompletionStage().toCompletableFuture().get(5, TimeUnit.SECONDS);
419	System.err.println("Graceful shutdown completed");
420	} catch (Exception ex) {
421	System.err.println("Graceful shutdown failed");
422	ex.printStackTrace();
423	}
424	}));
425	}
426
427	private String getResourceAsString(String file) {
428	InputStream is = getClass().getClassLoader().getResourceAsStream("com/knowledgepixels/query/" + file);
429	try (Scanner s = new Scanner(is).useDelimiter("\\A")) {
430	String fileContent = s.hasNext() ? s.next() : "";
431	return fileContent;
432	}
433	}
434
435	private static void handleRedirect(RoutingContext req, String path) {
436	String queryString = "";
437	if (!req.queryParam("query").isEmpty())
438	queryString = "?query=" + URLEncoder.encode(req.queryParam("query").get(0), Charsets.UTF_8);
439	if (req.queryParam("for-type").size() == 1) {
440	String type = req.queryParam("for-type").get(0);
441	req.response().putHeader("location", path + "/type/" + Utils.createHash(type) + queryString);
442	req.response().setStatusCode(301).end();
443	} else if (req.queryParam("for-pubkey").size() == 1) {
444	String type = req.queryParam("for-pubkey").get(0);
445	req.response().putHeader("location", path + "/pubkey/" + Utils.createHash(type) + queryString);
446	req.response().setStatusCode(301).end();
447	} else if (req.queryParam("for-user").size() == 1) {
448	String type = req.queryParam("for-user").get(0);
449	req.response().putHeader("location", path + "/user/" + Utils.createHash(type) + queryString);
450	req.response().setStatusCode(301).end();
451	}
452	}
453
454	/**
455	* Apply headers to the response that should be present for all requests.
456	*
457	* @param response The response to which the headers should be applied.
458	*/
459	private static void applyGlobalHeaders(HttpServerResponse response) {
460	response.putHeader("Nanopub-Query-Status", StatusController.get().getState().state.toString());
461	}
462	}

knowledgepixels / nanopub-query / 17149479353

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