23249943389

Committed 18 Mar 2026 02:32PM UTC coverage: 30.235% (-0.02%) from 30.259%

Build # 23249943389

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #86 from knowledgepixels/fix/peer-sync-transaction-timeout

Fix peer sync stalling due to MongoDB transaction timeout

Run Details

187 of 686 branches covered (27.26%)

Branch coverage included in aggregate %.

623 of 1993 relevant lines covered (31.26%)

5.28 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.Nanopub;
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.info("Error checking peer {}: {}", peerUrl, ex.getMessage());
            }
        }
    }

    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.info("Failed to reach peer {}: {}", 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.info("Peer {} in non-ready state: {}", 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.info("Peer {} missing setupId or loadCounter headers", 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 effectiveLoadCounter = 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.
            // TODO Add per-pubkey afterCounter tracking for more targeted incremental sync
            long delta = peerLoadCounter - lastLoadCounter;
            log.info("Peer {} has {} new nanopubs, fetching recent", peerUrl, delta);
            long lastReceived = loadRecentNanopubs(s, peerUrl, lastLoadCounter);
            if (lastReceived > 0) {
                effectiveLoadCounter = lastReceived;
            }
        } else {
            log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);
        }

        discoverPubkeys(s, peerUrl);
        updatePeerState(s, peerUrl, peerSetupId, effectiveLoadCounter);
    }

    /**
     * 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.info("Request failed: {} {}", requestUrl, httpStatus);
                return -1;
            }
            try (InputStream is = resp.getEntity().getContent()) {
                NanopubStream.fromByteStream(is).getAsNanopubs().forEach(m -> {
                    if (m.isSuccess()) {
                        Nanopub np = null;
                        try {
                            np = m.getNanopub();
                            RegistryDB.loadNanopub(s, np);
                            NanopubLoader.simpleLoad(s, np);
                            if (m.getCounter() > 0) {
                                lastReceivedCounter.set(m.getCounter());
                            }
                        } catch (Exception ex) {
                            log.warn("Skipping nanopub {} during recent fetch: {}",
                                    np != null ? np.getUri() : "unknown", ex.getMessage());
                        }
                    }
                });
            }
        } catch (IOException ex) {
            log.info("Failed to fetch recent nanopubs from {}: {}", peerUrl, ex.getMessage());
        }
        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.info("Failed to discover pubkeys from {}: {}", peerUrl, ex.getMessage());
        }
    }

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

knowledgepixels / nanopub-registry / 23249943389

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