knowledgepixels/nanopub-query | Build 20414263980 | com/knowledgepixels/query/MainVerticle.java | Coveralls

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package com.knowledgepixels.query;

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

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import com.knowledgepixels.query.GrlcSpec.InvalidGrlcSpecException;

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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.Promise;

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import io.vertx.core.buffer.Buffer;

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import io.vertx.core.http.*;

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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.*;

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import io.vertx.micrometer.PrometheusScrapingHandler;

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import io.vertx.micrometer.backends.BackendRegistries;

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import org.eclipse.rdf4j.model.Value;

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import org.slf4j.Logger;

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import org.slf4j.LoggerFactory;

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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.Scanner;

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import java.util.concurrent.Executors;

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import java.util.concurrent.TimeUnit;

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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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    private static final Logger log = LoggerFactory.getLogger(MainVerticle.class);

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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;

234

                if (hashObj == null) {

235

                    label = "";

236

                } else {

237

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

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

240

                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"

256

                         + "</html>");

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});

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

259

            String repos = "";

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

261

            Collections.sort(repoList);

262

            for (String s : repoList) {

263

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

267

                if (hashObj == null) {

268

                    label = "";

269

                } else {

270

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

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

273

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

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            req.response()

276

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

277

                    .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"

289

                         + "</html>");

290

});

291

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

292

            if (css == null) {

293

                css = getResourceAsString("style.css");

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            req.response().end(css);

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});

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        // TODO This is no longer needed and can be removed at some point:

299

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

300

            try {

301

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

302

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

303

            } catch (InvalidGrlcSpecException ex) {

304

                req.response().setStatusCode(400).end(ex.getMessage());

305

            } catch (Exception ex) {

306

                req.response().setStatusCode(500).end("Unexpected error: " + ex.getMessage());

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});

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

311

            try {

312

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

313

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

314

            } catch (InvalidGrlcSpecException ex) {

315

                req.response().setStatusCode(400).end("Invlid grlc API definition: " + ex.getMessage());

316

            } catch (Exception ex) {

317

                req.response().setStatusCode(500).end("Unexpected error: " + ex.getMessage());

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});

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

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        HttpProxy grlcxProxy = HttpProxy.reverseProxy(httpClient);

324

        grlcxProxy.origin(proxyPort, proxy);

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            @Override

329

            @GeneratedFlagForDependentElements

330

            public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {

331

                final ProxyRequest req = context.request();

332

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

333

                if (req.getURI().matches(apiPattern)) {

334

                    try {

335

                        GrlcSpec grlcSpec = new GrlcSpec(req.getURI(), req.proxiedRequest().params());

336

                        req.setMethod(HttpMethod.POST);

337

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                        // Variant 1:

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                        req.putHeader("Content-Type", "application/sparql-query");

340

                        req.setBody(Body.body(Buffer.buffer(grlcSpec.expandQuery())));

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                        // Variant 2:

342

                        //req.putHeader("Content-Type", "application/x-www-form-urlencoded");

343

                        //req.setBody(Body.body(Buffer.buffer("query=" + URLEncoder.encode(grlcSpec.getExpandedQueryContent(), Charsets.UTF_8))));

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                        req.setURI("/rdf4j-server/repositories/" + grlcSpec.getRepoName());

346

                        log.info("Forwarding apix request to /rdf4j-server/repositories/", grlcSpec.getRepoName());

347

                    } catch (InvalidGrlcSpecException ex) {

348

                        return Future.succeededFuture(context.request()

349

                                .response()

350

                                .setStatusCode(400)

351

                                .putHeader("Content-Type", "text/plain")

352

                                .setBody(Body.body(Buffer.buffer("Bad request: " + ex.getMessage()))));

353

                    } catch (Exception ex) {

354

                        return Future.succeededFuture(context.request()

355

                                .response()

356

                                .setStatusCode(500)

357

                                .putHeader("Content-Type", "text/plain")

358

                                .setBody(Body.body(Buffer.buffer("Unexpected error: " + ex.getMessage()))));

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361

                return ProxyInterceptor.super.handleProxyRequest(context);

362

363

364

            @Override

365

            @GeneratedFlagForDependentElements

366

            public Future<Void> handleProxyResponse(ProxyContext context) {

367

                log.info("Receiving api response");

368

                ProxyResponse resp = context.response();

369

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

370

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

371

                resp.putHeader("Content-Disposition", "inline");

372

                return ProxyInterceptor.super.handleProxyResponse(context);

373

374

375

});

376

        proxyRouter.route(HttpMethod.GET, "/api/*").handler(ProxyHandler.create(grlcxProxy));

377

378

        proxyServer.requestHandler(req -> {

379

            applyGlobalHeaders(req.response());

380

            proxyRouter.handle(req);

381

});

382

        proxyServer.listen(9393);

383

384

        // Periodic metrics update

385

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

386

387

388

        new Thread(() -> {

389

            try {

390

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

391

                log.info("Current state: {}, last committed counter: {}", status.state, status.loadCounter);

392

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

393

                    // Do the initial nanopublication loading

394

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

395

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

396

                    if (!LocalNanopubLoader.init()) {

397

                        JellyNanopubLoader.loadInitial(status.loadCounter);

398

                    } else {

399

                        log.info("Local nanopublication loading finished");

400

401

                    StatusController.get().setReady();

402

                } else {

403

                    log.info("Initial load is already done");

404

                    StatusController.get().setReady();

405

406

            } catch (Exception ex) {

407

                log.info("Initial load failed, terminating...", ex);

408

                Runtime.getRuntime().exit(1);

409

410

411

            // Start periodic nanopub loading

412

            log.info("Starting periodic nanopub loading...");

413

            var executor = Executors.newSingleThreadScheduledExecutor();

414

            executor.scheduleWithFixedDelay(

415

                    JellyNanopubLoader::loadUpdates,

416

                    JellyNanopubLoader.UPDATES_POLL_INTERVAL,

417

                    JellyNanopubLoader.UPDATES_POLL_INTERVAL,

418

                    TimeUnit.MILLISECONDS

419

);

420

        }).start();

421

422

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

423

            try {

424

                log.info("Gracefully shutting down...");

425

                TripleStore.get().shutdownRepositories();

426

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

427

                log.info("Graceful shutdown completed");

428

            } catch (Exception ex) {

429

                log.info("Graceful shutdown failed", ex);

430

431

        }));

432

433

434

    private String getResourceAsString(String file) {

435

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

436

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

437

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

438

            return fileContent;

439

440

441

442

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

443

        String queryString = "";

444

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

445

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

446

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

447

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

448

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

449

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

450

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

451

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

452

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

453

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

454

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

455

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

456

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

457

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

458

459

460

461

/**

462

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

463

464

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

465

*/

466

    private static void applyGlobalHeaders(HttpServerResponse response) {

467

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

468

469

knowledgepixels / nanopub-query / 20414263980

Source File
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1	package com.knowledgepixels.query;
2
3	import com.github.jsonldjava.shaded.com.google.common.base.Charsets;
4	import com.knowledgepixels.query.GrlcSpec.InvalidGrlcSpecException;
5	import io.micrometer.prometheus.PrometheusMeterRegistry;
6	import io.vertx.core.AbstractVerticle;
7	import io.vertx.core.Future;
8	import io.vertx.core.Promise;
9	import io.vertx.core.buffer.Buffer;
10	import io.vertx.core.http.*;
11	import io.vertx.ext.web.Router;
12	import io.vertx.ext.web.RoutingContext;
13	import io.vertx.ext.web.handler.CorsHandler;
14	import io.vertx.ext.web.handler.StaticHandler;
15	import io.vertx.ext.web.proxy.handler.ProxyHandler;
16	import io.vertx.httpproxy.*;
17	import io.vertx.micrometer.PrometheusScrapingHandler;
18	import io.vertx.micrometer.backends.BackendRegistries;
19	import org.eclipse.rdf4j.model.Value;
20	import org.slf4j.Logger;
21	import org.slf4j.LoggerFactory;
22
23	import java.io.InputStream;
24	import java.net.URLEncoder;
25	import java.util.ArrayList;
26	import java.util.Collections;
27	import java.util.List;
28	import java.util.Scanner;
29	import java.util.concurrent.Executors;
30	import java.util.concurrent.TimeUnit;
31
32	/**
33	* Main verticle that coordinates the incoming HTTP requests.
34	*/
35	@GeneratedFlagForDependentElements
36	public class MainVerticle extends AbstractVerticle {
37
38	private static String css = null;
39
40	private static final Logger log = LoggerFactory.getLogger(MainVerticle.class);
41
42	/**
43	* Start the main verticle.
44	*
45	* @param startPromise the promise to complete when the verticle is started
46	* @throws Exception if an error occurs during startup
47	*/
48	@Override
49	public void start(Promise<Void> startPromise) throws Exception {
50	HttpClient httpClient = vertx.createHttpClient(
51	new HttpClientOptions()
52	.setConnectTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_CONNECT_TIMEOUT", 1000))
53	.setIdleTimeoutUnit(TimeUnit.SECONDS)
54	.setIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))
55	.setReadIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60))
56	.setWriteIdleTimeout(Utils.getEnvInt("NANOPUB_QUERY_VERTX_IDLE_TIMEOUT", 60)),
57	new PoolOptions().setHttp1MaxSize(200).setHttp2MaxSize(200)
58	);
59
60	HttpServer proxyServer = vertx.createHttpServer();
61	Router proxyRouter = Router.router(vertx);
62	proxyRouter.route().handler(CorsHandler.create().addRelativeOrigin(".*"));
63
64	// Metrics
65	final var metricsHttpServer = vertx.createHttpServer();
66	final var metricsRouter = Router.router(vertx);
67	metricsHttpServer.requestHandler(metricsRouter).listen(9394);
68
69	final var metricsRegistry = (PrometheusMeterRegistry) BackendRegistries.getDefaultNow();
70	final var collector = new MetricsCollector(metricsRegistry);
71	metricsRouter.route("/metrics").handler(PrometheusScrapingHandler.create(metricsRegistry));
72	// ----------
73	// This part is only used if the redirection is not done through Nginx.
74	// See nginx.conf and this bug report: https://github.com/eclipse-rdf4j/rdf4j/discussions/5120
75	HttpProxy rdf4jProxy = HttpProxy.reverseProxy(httpClient);
76	String proxy = Utils.getEnvString("RDF4J_PROXY_HOST", "rdf4j");
77	int proxyPort = Utils.getEnvInt("RDF4J_PROXY_PORT", 8080);
78	rdf4jProxy.origin(proxyPort, proxy);
79
80	rdf4jProxy.addInterceptor(new ProxyInterceptor() {	×
81
82	@Override
83	@GeneratedFlagForDependentElements
84	public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {
85	ProxyRequest request = context.request();
86	request.setURI(request.getURI().replaceAll("/", "_").replaceFirst("^_repo_", "/rdf4j-server/repositories/"));
87	// For later to try to get HTML tables out:
88	// if (request.headers().get("Accept") == null) {
89	// request.putHeader("Accept", "text/html");
90	// }
91	// request.putHeader("Accept", "application/json");
92	return ProxyInterceptor.super.handleProxyRequest(context);
93	}
94
95	@Override
96	@GeneratedFlagForDependentElements
97	public Future<Void> handleProxyResponse(ProxyContext context) {
98	ProxyResponse resp = context.response();
99	resp.putHeader("Access-Control-Allow-Origin", "*");
100	resp.putHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS");
101	// For later to try to get HTML tables out:
102	// String acceptHeader = context.request().headers().get("Accept");
103	// if (acceptHeader != null && acceptHeader.contains("text/html")) {
104	// resp.putHeader("Content-Type", "text/html");
105	// resp.setBody(Body.body(Buffer.buffer("<html><body><strong>test</strong></body></html>")));
106	// }
107	return ProxyInterceptor.super.handleProxyResponse(context);
108	}
109
110	});
111	// ----------
112
113	proxyRouter.route(HttpMethod.GET, "/repo").handler(req -> handleRedirect(req, "/repo"));
114	proxyRouter.route(HttpMethod.GET, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
115	proxyRouter.route(HttpMethod.POST, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
116	proxyRouter.route(HttpMethod.HEAD, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
117	proxyRouter.route(HttpMethod.OPTIONS, "/repo/*").handler(ProxyHandler.create(rdf4jProxy));
118	proxyRouter.route(HttpMethod.GET, "/tools/*").handler(req -> {
119	final String yasguiPattern = "^/tools/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?/yasgui\\.html$";
120	if (req.normalizedPath().matches(yasguiPattern)) {
121	String repo = req.normalizedPath().replaceFirst(yasguiPattern, "$1$2");
122	req.response()
123	.putHeader("content-type", "text/html")
124	.end("<!DOCTYPE html>\n"
125	+ "<html lang=\"en\">\n"
126	+ "<head>\n"
127	+ "<meta charset=\"utf-8\">\n"
128	+ "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"
129	+ "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"
130	+ "<title>Nanopub Query SPARQL Editor for repository: " + repo + "</title>\n"
131	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
132	+ "<link href='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.css' rel='stylesheet' type='text/css'/>\n"
133	+ "<style>.yasgui .endpointText {display:none !important;}</style>\n"
134	+ "<script type=\"text/javascript\">localStorage.clear();</script>\n"
135	+ "</head>\n"
136	+ "<body>\n"
137	+ "<h3>Nanopub Query SPARQL Editor for repository: " + repo + "</h3>\n"
138	+ "<div id='yasgui'></div>\n"
139	+ "<script src='https://cdn.jsdelivr.net/yasgui/2.6.1/yasgui.min.js'></script>\n"
140	+ "<script type=\"text/javascript\">\n"
141	+ "var yasgui = YASGUI(document.getElementById(\"yasgui\"), {\n"
142	+ " yasqe:{sparql:{endpoint:'/repo/" + repo + "'},value:'" + Utils.defaultQuery.replaceAll("\n", "\\\\n") + "'}\n"
143	+ "});\n"
144	+ "</script>\n"
145	+ "</body>\n"
146	+ "</html>");
147	} else {
148	req.response()
149	.putHeader("content-type", "text/plain")
150	.setStatusCode(404)
151	.end("not found");
152	}
153	});
154	proxyRouter.route(HttpMethod.GET, "/page").handler(req -> handleRedirect(req, "/page"));
155	proxyRouter.route(HttpMethod.GET, "/page/*").handler(req -> {
156	final String pagePattern = "^/page/([a-zA-Z0-9-_]+)(/([a-zA-Z0-9-_]+))?$";
157	if (req.normalizedPath().matches(pagePattern)) {
158	String repo = req.normalizedPath().replaceFirst(pagePattern, "$1$2");
159	req.response()
160	.putHeader("content-type", "text/html")
161	.end("<!DOCTYPE html>\n"
162	+ "<html lang=\"en\">\n"
163	+ "<head>\n"
164	+ "<meta charset=\"utf-8\">\n"
165	+ "<meta http-equiv=\"X-UA-Compatible\" content=\"IE=edge\">\n"
166	+ "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1\">\n"
167	+ "<title>Nanopub Query repo: " + repo + "</title>\n"
168	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
169	+ "</head>\n"
170	+ "<body>\n"
171	+ "<h3>Nanopub Query repo: " + repo + "</h3>\n"
172	+ "<p>Endpoint: <a href=\"/repo/" + repo + "\">/repo/" + repo + "</a></p>"
173	+ "<p>YASGUI: <a href=\"/tools/" + repo + "/yasgui.html\">/tools/" + repo + "/yasgui.hml</a></p>"
174	+ "</body>\n"
175	+ "</html>");
176	} else {
177	req.response()
178	.putHeader("content-type", "text/plain")
179	.setStatusCode(404)
180	.end("not found");
181	}
182	});
183	proxyRouter.route(HttpMethod.GET, "/").handler(req -> {
184	String repos = "";
185	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
186	Collections.sort(repoList);
187	for (String s : repoList) {
188	if (s.startsWith("pubkey_") \|\| s.startsWith("type_")) continue;
189	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a></code></li>";
190	}
191	String pinnedApisValue = Utils.getEnvString("NANOPUB_QUERY_PINNED_APIS", "");
192	String[] pinnedApis = pinnedApisValue.split(" ");
193	String pinnedApiLinks = "";
194	if (!pinnedApisValue.isEmpty()) {
195	for (String s : pinnedApis) {
196	pinnedApiLinks = pinnedApiLinks + "<li><a href=\"openapi/?url=spec/" + s + "%3Fapi-version=latest\">" + s.replaceFirst("^.*/", "") + "</a></li>";
197	}
198	pinnedApiLinks = "<p>Pinned APIs:</p>\n" +
199	"<ul>\n" +
200	pinnedApiLinks +
201	"</ul>\n";
202	}
203	req.response()
204	.putHeader("content-type", "text/html")
205	.end("<!DOCTYPE html>\n"
206	+ "<html lang='en'>\n"
207	+ "<head>\n"
208	+ "<title>Nanopub Query</title>\n"
209	+ "<meta charset='utf-8'>\n"
210	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
211	+ "</head>\n"
212	+ "<body>\n"
213	+ "<h1>Nanopub Query</h1>"
214	+ "<p>General repos:</p>"
215	+ "<ul>" + repos + "</ul>"
216	+ "<p>Specific repos:</p>"
217	+ "<ul>"
218	+ "<li><a href=\"/pubkeys\">Pubkey Repos</a></li>"
219	+ "<li><a href=\"/types\">Type Repos</a></li>"
220	+ "</ul>"
221	+ pinnedApiLinks
222	+ "</body>\n"
223	+ "</html>");
224	});
225	proxyRouter.route(HttpMethod.GET, "/pubkeys").handler(req -> {
226	String repos = "";
227	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
228	Collections.sort(repoList);
229	for (String s : repoList) {
230	if (!s.startsWith("pubkey_")) continue;
231	String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");
232	Value hashObj = Utils.getObjectForHash(hash);
233	String label;
234	if (hashObj == null) {
235	label = "";
236	} else {
237	label = " (" + Utils.getShortPubkeyName(hashObj.stringValue()) + ")";
238	}
239	s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");
240	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";
241	}
242	req.response()
243	.putHeader("content-type", "text/html")
244	.end("<!DOCTYPE html>\n"
245	+ "<html lang='en'>\n"
246	+ "<head>\n"
247	+ "<title>Nanopub Query: Pubkey Repos</title>\n"
248	+ "<meta charset='utf-8'>\n"
249	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
250	+ "</head>\n"
251	+ "<body>\n"
252	+ "<h3>Pubkey Repos</h3>"
253	+ "<p>Repos:</p>"
254	+ "<ul>" + repos + "</ul>"
255	+ "</body>\n"
256	+ "</html>");
257	});
258	proxyRouter.route(HttpMethod.GET, "/types").handler(req -> {
259	String repos = "";
260	List<String> repoList = new ArrayList<>(TripleStore.get().getRepositoryNames());
261	Collections.sort(repoList);
262	for (String s : repoList) {
263	if (!s.startsWith("type_")) continue;
264	String hash = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$2");
265	Value hashObj = Utils.getObjectForHash(hash);
266	String label;
267	if (hashObj == null) {
268	label = "";
269	} else {
270	label = " (" + hashObj.stringValue() + ")";
271	}
272	s = s.replaceFirst("^([a-zA-Z0-9-]+)_([a-zA-Z0-9-_]+)$", "$1/$2");
273	repos += "<li><code><a href=\"/page/" + s + "\">" + s + "</a>" + label + "</code></li>";
274	}
275	req.response()
276	.putHeader("content-type", "text/html")
277	.end("<!DOCTYPE html>\n"
278	+ "<html lang='en'>\n"
279	+ "<head>\n"
280	+ "<title>Nanopub Query: Type Repos</title>\n"
281	+ "<meta charset='utf-8'>\n"
282	+ "<link rel=\"stylesheet\" href=\"/style.css\">\n"
283	+ "</head>\n"
284	+ "<body>\n"
285	+ "<h3>Type Repos</h3>"
286	+ "<p>Repos:</p>"
287	+ "<ul>" + repos + "</ul>"
288	+ "</body>\n"
289	+ "</html>");
290	});
291	proxyRouter.route(HttpMethod.GET, "/style.css").handler(req -> {
292	if (css == null) {
293	css = getResourceAsString("style.css");
294	}
295	req.response().end(css);
296	});
297
298	// TODO This is no longer needed and can be removed at some point:
299	proxyRouter.route(HttpMethod.GET, "/grlc-spec/*").handler(req -> {
300	try {
301	GrlcSpec gsp = new GrlcSpec(req.normalizedPath(), req.queryParams());
302	req.response().putHeader("content-type", "text/yaml").end(gsp.getSpec());
303	} catch (InvalidGrlcSpecException ex) {
304	req.response().setStatusCode(400).end(ex.getMessage());
305	} catch (Exception ex) {
306	req.response().setStatusCode(500).end("Unexpected error: " + ex.getMessage());
307	}
308	});
309
310	proxyRouter.route(HttpMethod.GET, "/openapi/spec/*").handler(req -> {
311	try {
312	OpenApiSpecPage osp = new OpenApiSpecPage(req.normalizedPath(), req.queryParams());
313	req.response().putHeader("content-type", "text/yaml").end(osp.getSpec());
314	} catch (InvalidGrlcSpecException ex) {
315	req.response().setStatusCode(400).end("Invlid grlc API definition: " + ex.getMessage());
316	} catch (Exception ex) {
317	req.response().setStatusCode(500).end("Unexpected error: " + ex.getMessage());
318	}
319	});
320
321	proxyRouter.route("/openapi/*").handler(StaticHandler.create("com/knowledgepixels/query/swagger"));
322
323	HttpProxy grlcxProxy = HttpProxy.reverseProxy(httpClient);
324	grlcxProxy.origin(proxyPort, proxy);
325
326	grlcxProxy.addInterceptor(new ProxyInterceptor() {	×
327
328	@Override
329	@GeneratedFlagForDependentElements
330	public Future<ProxyResponse> handleProxyRequest(ProxyContext context) {
331	final ProxyRequest req = context.request();
332	final String apiPattern = "^/api/(RA[a-zA-Z0-9-_]{43})/([a-zA-Z0-9-_]+)([?].*)?$";
333	if (req.getURI().matches(apiPattern)) {
334	try {
335	GrlcSpec grlcSpec = new GrlcSpec(req.getURI(), req.proxiedRequest().params());
336	req.setMethod(HttpMethod.POST);
337
338	// Variant 1:
339	req.putHeader("Content-Type", "application/sparql-query");
340	req.setBody(Body.body(Buffer.buffer(grlcSpec.expandQuery())));
341	// Variant 2:
342	//req.putHeader("Content-Type", "application/x-www-form-urlencoded");
343	//req.setBody(Body.body(Buffer.buffer("query=" + URLEncoder.encode(grlcSpec.getExpandedQueryContent(), Charsets.UTF_8))));
344
345	req.setURI("/rdf4j-server/repositories/" + grlcSpec.getRepoName());
346	log.info("Forwarding apix request to /rdf4j-server/repositories/", grlcSpec.getRepoName());
347	} catch (InvalidGrlcSpecException ex) {
348	return Future.succeededFuture(context.request()
349	.response()
350	.setStatusCode(400)
351	.putHeader("Content-Type", "text/plain")
352	.setBody(Body.body(Buffer.buffer("Bad request: " + ex.getMessage()))));
353	} catch (Exception ex) {
354	return Future.succeededFuture(context.request()
355	.response()
356	.setStatusCode(500)
357	.putHeader("Content-Type", "text/plain")
358	.setBody(Body.body(Buffer.buffer("Unexpected error: " + ex.getMessage()))));
359	}
360	}
361	return ProxyInterceptor.super.handleProxyRequest(context);
362	}
363
364	@Override
365	@GeneratedFlagForDependentElements
366	public Future<Void> handleProxyResponse(ProxyContext context) {
367	log.info("Receiving api response");
368	ProxyResponse resp = context.response();
369	resp.putHeader("Access-Control-Allow-Origin", "*");
370	resp.putHeader("Access-Control-Allow-Methods", "POST, GET, OPTIONS");
371	resp.putHeader("Content-Disposition", "inline");
372	return ProxyInterceptor.super.handleProxyResponse(context);
373	}
374
375	});
376	proxyRouter.route(HttpMethod.GET, "/api/*").handler(ProxyHandler.create(grlcxProxy));
377
378	proxyServer.requestHandler(req -> {
379	applyGlobalHeaders(req.response());
380	proxyRouter.handle(req);
381	});
382	proxyServer.listen(9393);
383
384	// Periodic metrics update
385	vertx.setPeriodic(1000, id -> collector.updateMetrics());
386
387
388	new Thread(() -> {
389	try {
390	var status = StatusController.get().initialize();
391	log.info("Current state: {}, last committed counter: {}", status.state, status.loadCounter);
392	if (status.state == StatusController.State.LAUNCHING \|\| status.state == StatusController.State.LOADING_INITIAL) {
393	// Do the initial nanopublication loading
394	StatusController.get().setLoadingInitial(status.loadCounter);
395	// Fall back to local nanopub loading if the local files are present
396	if (!LocalNanopubLoader.init()) {
397	JellyNanopubLoader.loadInitial(status.loadCounter);
398	} else {
399	log.info("Local nanopublication loading finished");
400	}
401	StatusController.get().setReady();
402	} else {
403	log.info("Initial load is already done");
404	StatusController.get().setReady();
405	}
406	} catch (Exception ex) {
407	log.info("Initial load failed, terminating...", ex);
408	Runtime.getRuntime().exit(1);
409	}
410
411	// Start periodic nanopub loading
412	log.info("Starting periodic nanopub loading...");
413	var executor = Executors.newSingleThreadScheduledExecutor();
414	executor.scheduleWithFixedDelay(
415	JellyNanopubLoader::loadUpdates,
416	JellyNanopubLoader.UPDATES_POLL_INTERVAL,
417	JellyNanopubLoader.UPDATES_POLL_INTERVAL,
418	TimeUnit.MILLISECONDS
419	);
420	}).start();
421
422	Runtime.getRuntime().addShutdownHook(new Thread(() -> {
423	try {
424	log.info("Gracefully shutting down...");
425	TripleStore.get().shutdownRepositories();
426	vertx.close().toCompletionStage().toCompletableFuture().get(5, TimeUnit.SECONDS);
427	log.info("Graceful shutdown completed");
428	} catch (Exception ex) {
429	log.info("Graceful shutdown failed", ex);
430	}
431	}));
432	}
433
434	private String getResourceAsString(String file) {
435	InputStream is = getClass().getClassLoader().getResourceAsStream("com/knowledgepixels/query/" + file);
436	try (Scanner s = new Scanner(is).useDelimiter("\\A")) {
437	String fileContent = s.hasNext() ? s.next() : "";
438	return fileContent;
439	}
440	}
441
442	private static void handleRedirect(RoutingContext req, String path) {
443	String queryString = "";
444	if (!req.queryParam("query").isEmpty())
445	queryString = "?query=" + URLEncoder.encode(req.queryParam("query").getFirst(), Charsets.UTF_8);
446	if (req.queryParam("for-type").size() == 1) {
447	String type = req.queryParam("for-type").getFirst();
448	req.response().putHeader("location", path + "/type/" + Utils.createHash(type) + queryString);
449	req.response().setStatusCode(301).end();
450	} else if (req.queryParam("for-pubkey").size() == 1) {
451	String type = req.queryParam("for-pubkey").getFirst();
452	req.response().putHeader("location", path + "/pubkey/" + Utils.createHash(type) + queryString);
453	req.response().setStatusCode(301).end();
454	} else if (req.queryParam("for-user").size() == 1) {
455	String type = req.queryParam("for-user").getFirst();
456	req.response().putHeader("location", path + "/user/" + Utils.createHash(type) + queryString);
457	req.response().setStatusCode(301).end();
458	}
459	}
460
461	/**
462	* Apply headers to the response that should be present for all requests.
463	*
464	* @param response The response to which the headers should be applied.
465	*/
466	private static void applyGlobalHeaders(HttpServerResponse response) {
467	response.putHeader("Nanopub-Query-Status", StatusController.get().getState().state.toString());
468	}
469	}

knowledgepixels / nanopub-query / 20414263980

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