24727603152

Committed 21 Apr 2026 02:18PM UTC coverage: 31.808% (+0.3%) from 31.558%

Build # 24727603152

Build Type

push

github

Committed by

ashleycaselli

Commit Message

chore(logging): enhance info error handling in Nanopub processing

Coverage Stats

280 of 986 branches covered (28.4%)

Branch coverage included in aggregate %.

839 of 2532 relevant lines covered (33.14%)

5.5 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

33.15

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

package com.knowledgepixels.registry;

import com.mongodb.ErrorCategory;
import com.mongodb.MongoWriteException;
import com.mongodb.client.ClientSession;
import com.mongodb.client.MongoCursor;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpHead;
import org.apache.http.util.EntityUtils;
import org.bson.Document;
import org.nanopub.NanopubUtils;
import org.nanopub.jelly.NanopubStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.atomic.AtomicLong;

import static com.knowledgepixels.registry.RegistryDB.*;

/**
 * Checks peer Nanopub Registries for new nanopublications and loads them.
 */
public class RegistryPeerConnector {

    private RegistryPeerConnector() {}

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

    public static void checkPeers(ClientSession s) {
        List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());
        Collections.shuffle(peerUrls);

        for (String peerUrl : peerUrls) {
            try {
                checkPeer(s, peerUrl);
            } catch (Exception ex) {
                log.warn("Failed to check peer {}: {}", peerUrl, ex.getMessage(), ex);
            }
        }
    }

    static void checkPeer(ClientSession s, String peerUrl) throws IOException {
        log.info("Checking peer: {}", peerUrl);

        HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpHead(peerUrl));
        int httpStatus = resp.getStatusLine().getStatusCode();
        EntityUtils.consumeQuietly(resp.getEntity());
        if (httpStatus < 200 || httpStatus >= 300) {
            log.warn("Failed to reach peer {} (HTTP {}); skipping", peerUrl, httpStatus);
            return;
        }

        if (isTestInstance(resp)) {
            log.info("Skipping peer {} because it is a test instance", peerUrl);
            return;
        }

        String status = getHeader(resp, "Nanopub-Registry-Status");
        if (!"ready".equals(status) && !"updating".equals(status)) {
            log.warn("Skipping peer {}: registry status is '{}' (expected 'ready' or 'updating')", peerUrl, status);
            return;
        }

        Long peerSetupId = getHeaderLong(resp, "Nanopub-Registry-Setup-Id");
        Long peerLoadCounter = getHeaderLong(resp, "Nanopub-Registry-Load-Counter");
        if (peerSetupId == null || peerLoadCounter == null) {
            log.warn("Skipping peer {}: missing required headers Nanopub-Registry-Setup-Id or Nanopub-Registry-Load-Counter", peerUrl);
            return;
        }

        syncWithPeer(s, peerUrl, peerSetupId, peerLoadCounter);
    }

    static void syncWithPeer(ClientSession s, String peerUrl, long peerSetupId, long peerLoadCounter) {
        Document peerState = getPeerState(s, peerUrl);
        Long lastSetupId = peerState != null ? peerState.getLong("setupId") : null;
        Long lastLoadCounter = peerState != null ? peerState.getLong("loadCounter") : null;

        if (lastSetupId != null && !lastSetupId.equals(peerSetupId)) {
            log.info("Peer {} was reset (setupId changed), resetting tracking", peerUrl);
            deletePeerState(s, peerUrl);
            lastLoadCounter = null;
        }

        long effectiveCounter = lastLoadCounter != null ? lastLoadCounter : 0;

        if (lastLoadCounter != null && lastLoadCounter.equals(peerLoadCounter)) {
            log.info("Peer {} has no new nanopubs (loadCounter unchanged: {})", peerUrl, peerLoadCounter);
        } else if (lastLoadCounter != null) {
            // Fetch all nanopubs added since our last known position.
            log.info("Peer {} has new nanopubs (loadCounter {} -> {}), fetching recent", peerUrl, lastLoadCounter, peerLoadCounter);
            long lastReceived = loadRecentNanopubs(s, peerUrl, lastLoadCounter);
            if (lastReceived > 0) {
                effectiveCounter = lastReceived;
            }
            // Only discover new pubkeys when the peer has new data
            discoverPubkeys(s, peerUrl);
        } else {
            log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);
            discoverPubkeys(s, peerUrl);
        }
        updatePeerState(s, peerUrl, peerSetupId, effectiveCounter);
    }

    /**
     * Fetches nanopubs from a peer after the given counter.
     *
     * @return the counter of the last successfully received nanopub, or -1 if none were received
     */
    private static long loadRecentNanopubs(ClientSession s, String peerUrl, long afterCounter) {
        String requestUrl = peerUrl + "nanopubs.jelly?afterCounter=" + afterCounter;
        log.info("Fetching recent nanopubs from: {}", requestUrl);
        AtomicLong lastReceivedCounter = new AtomicLong(-1);
        try {
            HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));
            int httpStatus = resp.getStatusLine().getStatusCode();
            if (httpStatus < 200 || httpStatus >= 300) {
                EntityUtils.consumeQuietly(resp.getEntity());
                log.warn("Fetching recent nanopubs from {} failed (HTTP {}); skipping", requestUrl, httpStatus);
                return -1;
            }
            try (InputStream is = resp.getEntity().getContent()) {
                NanopubLoader.loadStreamInParallel(
                        NanopubStream.fromByteStream(is).getAsNanopubs().peek(m -> {
                            // Track counter in the main thread as items are consumed from the stream
                            if (m.isSuccess() && m.getCounter() > 0) {
                                lastReceivedCounter.set(m.getCounter());
                            }
                        }),
                        np -> {
                            if (!CoverageFilter.isCovered(np)) {
                                return;
                            }
                            try (ClientSession workerSession = RegistryDB.getClient().startSession()) {
                                String pubkey = RegistryDB.getPubkey(np);
                                if (pubkey != null) {
                                    NanopubLoader.simpleLoad(workerSession, np, pubkey);
                                }
                            }
                        });
            }
        } catch (IOException ex) {
            log.warn("Failed to fetch recent nanopubs from {}: {}", peerUrl, ex.getMessage(), ex);
        }
        log.info("Last received counter from {}: {}", peerUrl, lastReceivedCounter.get());
        return lastReceivedCounter.get();
    }

    static void discoverPubkeys(ClientSession s, String peerUrl) {
        log.info("Discovering pubkeys from peer: {}", peerUrl);
        try {
            List<String> peerPubkeys = Utils.retrieveListFromJsonUrl(peerUrl + "pubkeys.json");
            int discovered = 0;
            for (String pubkeyHash : peerPubkeys) {
                Document filter = new Document("pubkey", pubkeyHash).append("type", NanopubLoader.INTRO_TYPE_HASH);
                if (!has(s, "lists", filter)) {
                    try {
                        insert(s, "lists", new Document("pubkey", pubkeyHash)
                                .append("type", NanopubLoader.INTRO_TYPE_HASH)
                                .append("status", EntryStatus.encountered.getValue()));
                    } catch (MongoWriteException e) {
                        if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) {
                            throw e;
                        }
                    }
                    discovered++;
                } else if (!has(s, "lists", new Document(filter).append("status", EntryStatus.loaded.getValue()))) {
                    // Set status to encountered if not already loaded (fixes null-status entries from older code)
                    collection("lists").updateMany(s, filter,
                            new Document("$set", new Document("status", EntryStatus.encountered.getValue())));
                    discovered++;
                }
            }
            log.info("Discovered {} new pubkeys from peer {}", discovered, peerUrl);
        } catch (Exception ex) {
            log.warn("Failed to discover pubkeys from {}: {}", peerUrl, ex.getMessage(), ex);
        }
    }

    static Document getPeerState(ClientSession s, String peerUrl) {
        try (MongoCursor<Document> cursor = collection(Collection.PEER_STATE.toString())
                .find(s, new Document("_id", peerUrl)).cursor()) {
            return cursor.hasNext() ? cursor.next() : null;
        }
    }

    static void updatePeerState(ClientSession s, String peerUrl, long setupId, long loadCounter) {
        collection(Collection.PEER_STATE.toString()).updateOne(s,
                new Document("_id", peerUrl),
                new Document("$set", new Document("_id", peerUrl)
                        .append("setupId", setupId)
                        .append("loadCounter", loadCounter)
                        .append("lastChecked", System.currentTimeMillis())),
                new com.mongodb.client.model.UpdateOptions().upsert(true));
    }

    static void deletePeerState(ClientSession s, String peerUrl) {
        collection(Collection.PEER_STATE.toString()).deleteOne(s, new Document("_id", peerUrl));
    }

    static boolean isTestInstance(HttpResponse resp) {
        return "true".equals(getHeader(resp, "Nanopub-Registry-Test-Instance"));
    }

    static String getHeader(HttpResponse resp, String name) {
        return resp.getFirstHeader(name) != null ? resp.getFirstHeader(name).getValue() : null;
    }

    static Long getHeaderLong(HttpResponse resp, String name) {
        String value = getHeader(resp, name);
        if (value == null || "null".equals(value)) {
            return null;
        }
        try {
            return Long.parseLong(value);
        } catch (NumberFormatException ex) {
            return null;
        }
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.mongodb.ErrorCategory;
4	import com.mongodb.MongoWriteException;
5	import com.mongodb.client.ClientSession;
6	import com.mongodb.client.MongoCursor;
7	import org.apache.http.HttpResponse;
8	import org.apache.http.client.methods.HttpGet;
9	import org.apache.http.client.methods.HttpHead;
10	import org.apache.http.util.EntityUtils;
11	import org.bson.Document;
12	import org.nanopub.NanopubUtils;
13	import org.nanopub.jelly.NanopubStream;
14	import org.slf4j.Logger;
15	import org.slf4j.LoggerFactory;
16
17	import java.io.IOException;
18	import java.io.InputStream;
19	import java.util.ArrayList;
20	import java.util.Collections;
21	import java.util.List;
22	import java.util.concurrent.atomic.AtomicLong;
23
24	import static com.knowledgepixels.registry.RegistryDB.*;
25
26	/**
27	* Checks peer Nanopub Registries for new nanopublications and loads them.
28	*/
29	public class RegistryPeerConnector {
30
31	private RegistryPeerConnector() {}
32
33	private static final Logger log = LoggerFactory.getLogger(RegistryPeerConnector.class);	12✔
34
35	public static void checkPeers(ClientSession s) {
36	List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());	×
37	Collections.shuffle(peerUrls);	×
38
39	for (String peerUrl : peerUrls) {	×
40	try {
41	checkPeer(s, peerUrl);	×
42	} catch (Exception ex) {	×
43	log.warn("Failed to check peer {}: {}", peerUrl, ex.getMessage(), ex);	×
44	}	×
45	}	×
46	}	×
47
48	static void checkPeer(ClientSession s, String peerUrl) throws IOException {
49	log.info("Checking peer: {}", peerUrl);	×
50
51	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpHead(peerUrl));	×
52	int httpStatus = resp.getStatusLine().getStatusCode();	×
53	EntityUtils.consumeQuietly(resp.getEntity());	×
54	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
55	log.warn("Failed to reach peer {} (HTTP {}); skipping", peerUrl, httpStatus);	×
56	return;	×
57	}
58
59	if (isTestInstance(resp)) {	×
60	log.info("Skipping peer {} because it is a test instance", peerUrl);	×
61	return;	×
62	}
63
64	String status = getHeader(resp, "Nanopub-Registry-Status");	×
65	if (!"ready".equals(status) && !"updating".equals(status)) {	×
66	log.warn("Skipping peer {}: registry status is '{}' (expected 'ready' or 'updating')", peerUrl, status);	×
67	return;	×
68	}
69
70	Long peerSetupId = getHeaderLong(resp, "Nanopub-Registry-Setup-Id");	×
71	Long peerLoadCounter = getHeaderLong(resp, "Nanopub-Registry-Load-Counter");	×
72	if (peerSetupId == null \|\| peerLoadCounter == null) {	×
73	log.warn("Skipping peer {}: missing required headers Nanopub-Registry-Setup-Id or Nanopub-Registry-Load-Counter", peerUrl);	×
74	return;	×
75	}
76
77	syncWithPeer(s, peerUrl, peerSetupId, peerLoadCounter);	×
78	}	×
79
80	static void syncWithPeer(ClientSession s, String peerUrl, long peerSetupId, long peerLoadCounter) {
81	Document peerState = getPeerState(s, peerUrl);	12✔
82	Long lastSetupId = peerState != null ? peerState.getLong("setupId") : null;	24✔
83	Long lastLoadCounter = peerState != null ? peerState.getLong("loadCounter") : null;	24✔
84
85	if (lastSetupId != null && !lastSetupId.equals(peerSetupId)) {	21✔
86	log.info("Peer {} was reset (setupId changed), resetting tracking", peerUrl);	12✔
87	deletePeerState(s, peerUrl);	9✔
88	lastLoadCounter = null;	6✔
89	}
90
91	long effectiveCounter = lastLoadCounter != null ? lastLoadCounter : 0;	21✔
92
93	if (lastLoadCounter != null && lastLoadCounter.equals(peerLoadCounter)) {	21!
94	log.info("Peer {} has no new nanopubs (loadCounter unchanged: {})", peerUrl, peerLoadCounter);	21✔
95	} else if (lastLoadCounter != null) {	6!
96	// Fetch all nanopubs added since our last known position.
97	log.info("Peer {} has new nanopubs (loadCounter {} -> {}), fetching recent", peerUrl, lastLoadCounter, peerLoadCounter);	×
98	long lastReceived = loadRecentNanopubs(s, peerUrl, lastLoadCounter);	×
99	if (lastReceived > 0) {	×
100	effectiveCounter = lastReceived;	×
101	}
102	// Only discover new pubkeys when the peer has new data
103	discoverPubkeys(s, peerUrl);	×
104	} else {	×
105	log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);	12✔
106	discoverPubkeys(s, peerUrl);	9✔
107	}
108	updatePeerState(s, peerUrl, peerSetupId, effectiveCounter);	15✔
109	}	3✔
110
111	/**
112	* Fetches nanopubs from a peer after the given counter.
113	*
114	* @return the counter of the last successfully received nanopub, or -1 if none were received
115	*/
116	private static long loadRecentNanopubs(ClientSession s, String peerUrl, long afterCounter) {
117	String requestUrl = peerUrl + "nanopubs.jelly?afterCounter=" + afterCounter;	×
118	log.info("Fetching recent nanopubs from: {}", requestUrl);	×
119	AtomicLong lastReceivedCounter = new AtomicLong(-1);	×
120	try {
121	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
122	int httpStatus = resp.getStatusLine().getStatusCode();	×
123	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
124	EntityUtils.consumeQuietly(resp.getEntity());	×
125	log.warn("Fetching recent nanopubs from {} failed (HTTP {}); skipping", requestUrl, httpStatus);	×
126	return -1;	×
127	}
128	try (InputStream is = resp.getEntity().getContent()) {	×
129	NanopubLoader.loadStreamInParallel(	×
130	NanopubStream.fromByteStream(is).getAsNanopubs().peek(m -> {	×
131	// Track counter in the main thread as items are consumed from the stream
132	if (m.isSuccess() && m.getCounter() > 0) {	×
133	lastReceivedCounter.set(m.getCounter());	×
134	}
135	}),	×
136	np -> {
137	if (!CoverageFilter.isCovered(np)) {	×
138	return;	×
139	}
140	try (ClientSession workerSession = RegistryDB.getClient().startSession()) {	×
141	String pubkey = RegistryDB.getPubkey(np);	×
142	if (pubkey != null) {	×
143	NanopubLoader.simpleLoad(workerSession, np, pubkey);	×
144	}
145	}
146	});	×
147	}
148	} catch (IOException ex) {	×
149	log.warn("Failed to fetch recent nanopubs from {}: {}", peerUrl, ex.getMessage(), ex);	×
150	}	×
151	log.info("Last received counter from {}: {}", peerUrl, lastReceivedCounter.get());	×
152	return lastReceivedCounter.get();	×
153	}
154
155	static void discoverPubkeys(ClientSession s, String peerUrl) {
156	log.info("Discovering pubkeys from peer: {}", peerUrl);	12✔
157	try {
158	List<String> peerPubkeys = Utils.retrieveListFromJsonUrl(peerUrl + "pubkeys.json");	×
159	int discovered = 0;	×
160	for (String pubkeyHash : peerPubkeys) {	×
161	Document filter = new Document("pubkey", pubkeyHash).append("type", NanopubLoader.INTRO_TYPE_HASH);	×
162	if (!has(s, "lists", filter)) {	×
163	try {
164	insert(s, "lists", new Document("pubkey", pubkeyHash)	×
165	.append("type", NanopubLoader.INTRO_TYPE_HASH)	×
166	.append("status", EntryStatus.encountered.getValue()));	×
167	} catch (MongoWriteException e) {	×
168	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) {	×
169	throw e;	×
170	}
171	}	×
172	discovered++;	×
173	} else if (!has(s, "lists", new Document(filter).append("status", EntryStatus.loaded.getValue()))) {	×
174	// Set status to encountered if not already loaded (fixes null-status entries from older code)
175	collection("lists").updateMany(s, filter,	×
176	new Document("$set", new Document("status", EntryStatus.encountered.getValue())));	×
177	discovered++;	×
178	}
179	}	×
180	log.info("Discovered {} new pubkeys from peer {}", discovered, peerUrl);	×
181	} catch (Exception ex) {	3✔
182	log.warn("Failed to discover pubkeys from {}: {}", peerUrl, ex.getMessage(), ex);	54✔
183	}	×
184	}	3✔
185
186	static Document getPeerState(ClientSession s, String peerUrl) {
187	try (MongoCursor<Document> cursor = collection(Collection.PEER_STATE.toString())	27✔
188	.find(s, new Document("_id", peerUrl)).cursor()) {	9✔
189	return cursor.hasNext() ? cursor.next() : null;	33✔
190	}
191	}
192
193	static void updatePeerState(ClientSession s, String peerUrl, long setupId, long loadCounter) {
194	collection(Collection.PEER_STATE.toString()).updateOne(s,	63✔
195	new Document("_id", peerUrl),
196	new Document("$set", new Document("_id", peerUrl)
197	.append("setupId", setupId)	12✔
198	.append("loadCounter", loadCounter)	9✔
199	.append("lastChecked", System.currentTimeMillis())),	24✔
200	new com.mongodb.client.model.UpdateOptions().upsert(true));	3✔
201	}	3✔
202
203	static void deletePeerState(ClientSession s, String peerUrl) {
204	collection(Collection.PEER_STATE.toString()).deleteOne(s, new Document("_id", peerUrl));	33✔
205	}	3✔
206
207	static boolean isTestInstance(HttpResponse resp) {
208	return "true".equals(getHeader(resp, "Nanopub-Registry-Test-Instance"));	18✔
209	}
210
211	static String getHeader(HttpResponse resp, String name) {
212	return resp.getFirstHeader(name) != null ? resp.getFirstHeader(name).getValue() : null;	33✔
213	}
214
215	static Long getHeaderLong(HttpResponse resp, String name) {
216	String value = getHeader(resp, name);	12✔
217	if (value == null \|\| "null".equals(value)) {	18✔
218	return null;	6✔
219	}
220	try {
221	return Long.parseLong(value);	12✔
222	} catch (NumberFormatException ex) {	3✔
223	return null;	6✔
224	}
225	}
226
227	}

knowledgepixels / nanopub-registry / 24727603152

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous