21167271454

Committed 20 Jan 2026 10:01AM UTC coverage: 18.763% (-0.02%) from 18.779%

Build # 21167271454

Build Type

push

github

Committed by

ashleycaselli

Commit Message

refactor(logging): replace System.err with SLF4J logger for improved logging consistency

Run Details

96 of 586 branches covered (16.38%)

Branch coverage included in aggregate %.

350 of 1791 relevant lines covered (19.54%)

3.59 hits per line

Source File
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0.0

src/main/java/com/knowledgepixels/registry/MainVerticle.java

package com.knowledgepixels.registry;

import com.mongodb.client.ClientSession;
import io.micrometer.prometheus.PrometheusMeterRegistry;
import io.vertx.core.AbstractVerticle;
import io.vertx.core.Handler;
import io.vertx.core.Promise;
import io.vertx.core.http.HttpMethod;
import io.vertx.core.http.HttpServer;
import io.vertx.ext.web.Router;
import io.vertx.ext.web.RoutingContext;
import io.vertx.micrometer.PrometheusScrapingHandler;
import io.vertx.micrometer.backends.BackendRegistries;
import net.trustyuri.TrustyUriUtils;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.Rio;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.extra.server.PublishNanopub;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.concurrent.TimeUnit;

import static com.knowledgepixels.registry.RegistryDB.has;
import static com.knowledgepixels.registry.RegistryDB.isSet;

public class MainVerticle extends AbstractVerticle {

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

    @Override
    public void start(Promise<Void> startPromise) {
        HttpServer server = vertx.createHttpServer();
        Router router = Router.router(vertx);
        server.requestHandler(router);
        server.listen(9292);
        router.route(HttpMethod.GET, "/agent*").handler(c -> {
            // /agent/... | /agents | /agentAccounts
            ListPage.show(c);
        });
        router.route(HttpMethod.GET, "/nanopubs*").handler(c -> {
            ListPage.show(c);
        });
        router.route(HttpMethod.GET, "/list*").handler(c -> {
            ListPage.show(c);
        });
        router.route(HttpMethod.GET, "/pubkeys*").handler(c -> {
            ListPage.show(c);
        });
        router.route(HttpMethod.GET, "/np/").handler(c -> {
            c.response().putHeader("Location", "/").setStatusCode(307).end();
        });
        router.route(HttpMethod.GET, "/np/*").handler(c -> {
            NanopubPage.show(c);
        });
        router.route(HttpMethod.GET, "/debug/*").handler(c -> {
            DebugPage.show(c);
        });
        router.route(HttpMethod.GET, "/style.css").handler(c -> {
            ResourcePage.show(c, "style.css", "text/css");
        });

        // Metrics
        final var metricsHttpServer = vertx.createHttpServer();
        final var metricsRouter = Router.router(vertx);
        metricsHttpServer.requestHandler(metricsRouter).listen(9293);

        final var metricsRegistry = (PrometheusMeterRegistry) BackendRegistries.getDefaultNow();
        final var collector = new MetricsCollector(metricsRegistry);
        metricsRouter.route("/metrics").handler(PrometheusScrapingHandler.create(metricsRegistry));

        router.route(HttpMethod.GET, "/*").handler(c -> {
            MainPage.show(c);
        });
        router.route(HttpMethod.HEAD, "/*").handler(c -> {
            MainPage.show(c);
        });

        Handler<RoutingContext> postHandler = c -> {
            c.request().bodyHandler(bh -> {
                try {
                    String contentType = c.request().getHeader("Content-Type");
                    Nanopub np = null;
                    try {
                        np = new NanopubImpl(bh.toString(), Rio.getParserFormatForMIMEType(contentType).orElse(RDFFormat.TRIG));
                    } catch (MalformedNanopubException ex) {
                        ex.printStackTrace();
                    }
                    if (np != null) {
                        try (ClientSession s = RegistryDB.getClient().startSession()) {
                            String ac = TrustyUriUtils.getArtifactCode(np.getUri().toString());
                            if (has(s, Collection.NANOPUBS.toString(), ac)) {
                                logger.info("POST: known nanopub {}", ac);
                            } else {
                                logger.info("POST: new nanopub {}", ac);

                                // TODO Run checks here whether we want to register this nanopub (considering quotas etc.)

                                // Load to nanopub store:
                                boolean success = RegistryDB.loadNanopub(s, np);
                                if (!success)
                                    throw new RuntimeException("Nanopublication not supported: " + np.getUri());
                                // Load to lists, if applicable:
                                NanopubLoader.simpleLoad(s, np);

                                if (!isSet(s, Collection.SERVER_INFO.toString(), "testInstance")) {
                                    // Here we publish it also to the first-generation services, so they know about it too:
                                    // TODO Remove this at some point
                                    try {
                                        new PublishNanopub().publishNanopub(np, "https://np.knowledgepixels.com/");
                                    } catch (Exception ex) {
                                        ex.printStackTrace();
                                    }
                                }
                            }
                        }
                    }
                    c.response().setStatusCode(201);
                } catch (Exception ex) {
                    c.response().setStatusCode(400).setStatusMessage("Error processing nanopub: " + ex.getMessage());
                } finally {
                    c.response().end();
                }
            });
        };
        router.route(HttpMethod.POST, "/").handler(postHandler);
        router.route(HttpMethod.POST, "/np/").handler(postHandler);

        // INIT
        vertx.executeBlocking(() -> {

            RegistryDB.init();

            new Thread(() -> {
                Task.runTasks();
            }).start();

            return null;
        }).onComplete(res -> {
            logger.info("DB initialization finished");
        });

        // Periodic metrics update
        vertx.setPeriodic(1000, id -> collector.updateMetrics());

        // SHUTDOWN
        Runtime.getRuntime().addShutdownHook(new Thread(() -> {
            try {
                logger.info("Gracefully shutting down...");
                RegistryDB.getClient().close();
                vertx.close().toCompletionStage().toCompletableFuture().get(5, TimeUnit.SECONDS);
                logger.info("Graceful shutdown completed");
            } catch (Exception ex) {
                logger.error("Graceful shutdown failed");
                ex.printStackTrace();
            }
        }));

    }

}

1	package com.knowledgepixels.registry;
2
3	import com.mongodb.client.ClientSession;
4	import io.micrometer.prometheus.PrometheusMeterRegistry;
5	import io.vertx.core.AbstractVerticle;
6	import io.vertx.core.Handler;
7	import io.vertx.core.Promise;
8	import io.vertx.core.http.HttpMethod;
9	import io.vertx.core.http.HttpServer;
10	import io.vertx.ext.web.Router;
11	import io.vertx.ext.web.RoutingContext;
12	import io.vertx.micrometer.PrometheusScrapingHandler;
13	import io.vertx.micrometer.backends.BackendRegistries;
14	import net.trustyuri.TrustyUriUtils;
15	import org.eclipse.rdf4j.rio.RDFFormat;
16	import org.eclipse.rdf4j.rio.Rio;
17	import org.nanopub.MalformedNanopubException;
18	import org.nanopub.Nanopub;
19	import org.nanopub.NanopubImpl;
20	import org.nanopub.extra.server.PublishNanopub;
21	import org.slf4j.Logger;
22	import org.slf4j.LoggerFactory;
23
24	import java.util.concurrent.TimeUnit;
25
26	import static com.knowledgepixels.registry.RegistryDB.has;
27	import static com.knowledgepixels.registry.RegistryDB.isSet;
28
29	public class MainVerticle extends AbstractVerticle {	×
30
31	private final Logger logger = LoggerFactory.getLogger(MainVerticle.class);	×
32
33	@Override
34	public void start(Promise<Void> startPromise) {
35	HttpServer server = vertx.createHttpServer();	×
36	Router router = Router.router(vertx);	×
37	server.requestHandler(router);	×
38	server.listen(9292);	×
39	router.route(HttpMethod.GET, "/agent*").handler(c -> {	×
40	// /agent/... \| /agents \| /agentAccounts
41	ListPage.show(c);	×
42	});	×
43	router.route(HttpMethod.GET, "/nanopubs*").handler(c -> {	×
44	ListPage.show(c);	×
45	});	×
46	router.route(HttpMethod.GET, "/list*").handler(c -> {	×
47	ListPage.show(c);	×
48	});	×
49	router.route(HttpMethod.GET, "/pubkeys*").handler(c -> {	×
50	ListPage.show(c);	×
51	});	×
52	router.route(HttpMethod.GET, "/np/").handler(c -> {	×
53	c.response().putHeader("Location", "/").setStatusCode(307).end();	×
54	});	×
55	router.route(HttpMethod.GET, "/np/*").handler(c -> {	×
56	NanopubPage.show(c);	×
57	});	×
58	router.route(HttpMethod.GET, "/debug/*").handler(c -> {	×
59	DebugPage.show(c);	×
60	});	×
61	router.route(HttpMethod.GET, "/style.css").handler(c -> {	×
62	ResourcePage.show(c, "style.css", "text/css");	×
63	});	×
64
65	// Metrics
66	final var metricsHttpServer = vertx.createHttpServer();	×
67	final var metricsRouter = Router.router(vertx);	×
68	metricsHttpServer.requestHandler(metricsRouter).listen(9293);	×
69
70	final var metricsRegistry = (PrometheusMeterRegistry) BackendRegistries.getDefaultNow();	×
71	final var collector = new MetricsCollector(metricsRegistry);	×
72	metricsRouter.route("/metrics").handler(PrometheusScrapingHandler.create(metricsRegistry));	×
73
74	router.route(HttpMethod.GET, "/*").handler(c -> {	×
75	MainPage.show(c);	×
76	});	×
77	router.route(HttpMethod.HEAD, "/*").handler(c -> {	×
78	MainPage.show(c);	×
79	});	×
80
81	Handler<RoutingContext> postHandler = c -> {	×
82	c.request().bodyHandler(bh -> {	×
83	try {
84	String contentType = c.request().getHeader("Content-Type");	×
85	Nanopub np = null;	×
86	try {
87	np = new NanopubImpl(bh.toString(), Rio.getParserFormatForMIMEType(contentType).orElse(RDFFormat.TRIG));	×
88	} catch (MalformedNanopubException ex) {	×
89	ex.printStackTrace();	×
90	}	×
91	if (np != null) {	×
92	try (ClientSession s = RegistryDB.getClient().startSession()) {	×
93	String ac = TrustyUriUtils.getArtifactCode(np.getUri().toString());	×
94	if (has(s, Collection.NANOPUBS.toString(), ac)) {	×
95	logger.info("POST: known nanopub {}", ac);	×
96	} else {
97	logger.info("POST: new nanopub {}", ac);	×
98
99	// TODO Run checks here whether we want to register this nanopub (considering quotas etc.)
100
101	// Load to nanopub store:
102	boolean success = RegistryDB.loadNanopub(s, np);	×
103	if (!success)	×
104	throw new RuntimeException("Nanopublication not supported: " + np.getUri());	×
105	// Load to lists, if applicable:
106	NanopubLoader.simpleLoad(s, np);	×
107
108	if (!isSet(s, Collection.SERVER_INFO.toString(), "testInstance")) {	×
109	// Here we publish it also to the first-generation services, so they know about it too:
110	// TODO Remove this at some point
111	try {
112	new PublishNanopub().publishNanopub(np, "https://np.knowledgepixels.com/");	×
113	} catch (Exception ex) {	×
114	ex.printStackTrace();	×
115	}	×
116	}
117	}
118	}
119	}
120	c.response().setStatusCode(201);	×
121	} catch (Exception ex) {	×
122	c.response().setStatusCode(400).setStatusMessage("Error processing nanopub: " + ex.getMessage());	×
123	} finally {
124	c.response().end();	×
125	}
126	});	×
127	};	×
128	router.route(HttpMethod.POST, "/").handler(postHandler);	×
129	router.route(HttpMethod.POST, "/np/").handler(postHandler);	×
130
131	// INIT
132	vertx.executeBlocking(() -> {	×
133
134	RegistryDB.init();	×
135
136	new Thread(() -> {	×
137	Task.runTasks();	×
138	}).start();	×
139
140	return null;	×
141	}).onComplete(res -> {	×
142	logger.info("DB initialization finished");	×
143	});	×
144
145	// Periodic metrics update
146	vertx.setPeriodic(1000, id -> collector.updateMetrics());	×
147
148	// SHUTDOWN
149	Runtime.getRuntime().addShutdownHook(new Thread(() -> {	×
150	try {
151	logger.info("Gracefully shutting down...");	×
152	RegistryDB.getClient().close();	×
153	vertx.close().toCompletionStage().toCompletableFuture().get(5, TimeUnit.SECONDS);	×
154	logger.info("Graceful shutdown completed");	×
155	} catch (Exception ex) {	×
156	logger.error("Graceful shutdown failed");	×
157	ex.printStackTrace();	×
158	}	×
159	}));	×
160
161	}	×
162
163	}

knowledgepixels / nanopub-registry / 21167271454

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