24121799241

Committed 08 Apr 2026 06:42AM UTC coverage: 32.765% (-0.6%) from 33.374%

Build # 24121799241

Build Type

push

github

Committed by

tkuhn

Commit Message

Merge branch 'feat/agent-quota-enforcement'

Coverage Stats

263 of 888 branches covered (29.62%)

Branch coverage included in aggregate %.

793 of 2335 relevant lines covered (33.96%)

5.68 hits per line

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34.9

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");
        // TODO(transition): Remove Load-Counter fallback after all peers upgraded
        Long peerSeqNum = getHeaderLong(resp, "Nanopub-Registry-SeqNum");
        if (peerSeqNum == null) {
            peerSeqNum = getHeaderLong(resp, "Nanopub-Registry-Load-Counter");
        }
        if (peerSetupId == null || peerSeqNum == null) {
            log.info("Peer {} missing setupId or seqNum headers", peerUrl);
            return;
        }

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

    static void syncWithPeer(ClientSession s, String peerUrl, long peerSetupId, long peerSeqNum) {
        Document peerState = getPeerState(s, peerUrl);
        Long lastSetupId = peerState != null ? peerState.getLong("setupId") : null;
        // TODO(transition): Remove loadCounter fallback after all peers upgraded
        Long lastSeqNum = peerState != null ? peerState.getLong("seqNum") : null;
        if (lastSeqNum == null && peerState != null) {
            lastSeqNum = peerState.getLong("loadCounter");
        }

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

        long effectiveSeqNum = lastSeqNum != null ? lastSeqNum : 0;

        if (lastSeqNum != null && lastSeqNum.equals(peerSeqNum)) {
            log.info("Peer {} has no new nanopubs (seqNum unchanged: {})", peerUrl, peerSeqNum);
        } else if (lastSeqNum != null) {
            // Fetch all nanopubs added since our last known position.
            log.info("Peer {} has new nanopubs (seqNum {} -> {}), fetching recent", peerUrl, lastSeqNum, peerSeqNum);
            long lastReceived = loadRecentNanopubs(s, peerUrl, lastSeqNum);
            if (lastReceived > 0) {
                effectiveSeqNum = 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, effectiveSeqNum);
    }

    /**
     * Fetches nanopubs from a peer after the given seqNum.
     * @return the seqNum of the last successfully received nanopub, or -1 if none were received
     */
    private static long loadRecentNanopubs(ClientSession s, String peerUrl, long afterSeqNum) {
        // TODO(transition): Remove afterCounter param after all peers upgraded
        String requestUrl = peerUrl + "nanopubs.jelly?afterSeqNum=" + afterSeqNum + "&afterCounter=" + afterSeqNum;
        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()) {
                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.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 seqNum) {
        collection(Collection.PEER_STATE.toString()).updateOne(s,
                new Document("_id", peerUrl),
                new Document("$set", new Document("_id", peerUrl)
                        .append("setupId", setupId)
                        .append("seqNum", seqNum)
                        // TODO(transition): Remove loadCounter after all peers upgraded
                        .append("loadCounter", seqNum)
                        .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	// TODO(transition): Remove Load-Counter fallback after all peers upgraded
73	Long peerSeqNum = getHeaderLong(resp, "Nanopub-Registry-SeqNum");	×
74	if (peerSeqNum == null) {	×
75	peerSeqNum = getHeaderLong(resp, "Nanopub-Registry-Load-Counter");	×
76	}
77	if (peerSetupId == null \|\| peerSeqNum == null) {	×
78	log.info("Peer {} missing setupId or seqNum headers", peerUrl);	×
79	return;	×
80	}
81
82	syncWithPeer(s, peerUrl, peerSetupId, peerSeqNum);	×
83	}	×
84
85	static void syncWithPeer(ClientSession s, String peerUrl, long peerSetupId, long peerSeqNum) {
86	Document peerState = getPeerState(s, peerUrl);	12✔
87	Long lastSetupId = peerState != null ? peerState.getLong("setupId") : null;	24✔
88	// TODO(transition): Remove loadCounter fallback after all peers upgraded
89	Long lastSeqNum = peerState != null ? peerState.getLong("seqNum") : null;	24✔
90	if (lastSeqNum == null && peerState != null) {	12✔
91	lastSeqNum = peerState.getLong("loadCounter");	12✔
92	}
93
94	if (lastSetupId != null && !lastSetupId.equals(peerSetupId)) {	21✔
95	log.info("Peer {} was reset (setupId changed), resetting tracking", peerUrl);	12✔
96	deletePeerState(s, peerUrl);	9✔
97	lastSeqNum = null;	6✔
98	}
99
100	long effectiveSeqNum = lastSeqNum != null ? lastSeqNum : 0;	21✔
101
102	if (lastSeqNum != null && lastSeqNum.equals(peerSeqNum)) {	21!
103	log.info("Peer {} has no new nanopubs (seqNum unchanged: {})", peerUrl, peerSeqNum);	21✔
104	} else if (lastSeqNum != null) {	6!
105	// Fetch all nanopubs added since our last known position.
106	log.info("Peer {} has new nanopubs (seqNum {} -> {}), fetching recent", peerUrl, lastSeqNum, peerSeqNum);	×
107	long lastReceived = loadRecentNanopubs(s, peerUrl, lastSeqNum);	×
108	if (lastReceived > 0) {	×
109	effectiveSeqNum = lastReceived;	×
110	}
111	// Only discover new pubkeys when the peer has new data
112	discoverPubkeys(s, peerUrl);	×
113	} else {	×
114	log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);	12✔
115	discoverPubkeys(s, peerUrl);	9✔
116	}
117	updatePeerState(s, peerUrl, peerSetupId, effectiveSeqNum);	15✔
118	}	3✔
119
120	/**
121	* Fetches nanopubs from a peer after the given seqNum.
122	* @return the seqNum of the last successfully received nanopub, or -1 if none were received
123	*/
124	private static long loadRecentNanopubs(ClientSession s, String peerUrl, long afterSeqNum) {
125	// TODO(transition): Remove afterCounter param after all peers upgraded
126	String requestUrl = peerUrl + "nanopubs.jelly?afterSeqNum=" + afterSeqNum + "&afterCounter=" + afterSeqNum;	×
127	log.info("Fetching recent nanopubs from: {}", requestUrl);	×
128	AtomicLong lastReceivedCounter = new AtomicLong(-1);	×
129	try {
130	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
131	int httpStatus = resp.getStatusLine().getStatusCode();	×
132	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
133	EntityUtils.consumeQuietly(resp.getEntity());	×
134	log.info("Request failed: {} {}", requestUrl, httpStatus);	×
135	return -1;	×
136	}
137	try (InputStream is = resp.getEntity().getContent()) {	×
138	NanopubLoader.loadStreamInParallel(	×
139	NanopubStream.fromByteStream(is).getAsNanopubs().peek(m -> {	×
140	// Track counter in the main thread as items are consumed from the stream
141	if (m.isSuccess() && m.getCounter() > 0) {	×
142	lastReceivedCounter.set(m.getCounter());	×
143	}
144	}),	×
145	np -> {
146	if (!CoverageFilter.isCovered(np)) return;	×
147	try (ClientSession workerSession = RegistryDB.getClient().startSession()) {	×
148	String pubkey = RegistryDB.getPubkey(np);	×
149	if (pubkey != null) {	×
150	NanopubLoader.simpleLoad(workerSession, np, pubkey);	×
151	}
152	}
153	});	×
154	}
155	} catch (IOException ex) {	×
156	log.info("Failed to fetch recent nanopubs from {}: {}", peerUrl, ex.getMessage());	×
157	}	×
158	log.info("Last received counter from {}: {}", peerUrl, lastReceivedCounter.get());	×
159	return lastReceivedCounter.get();	×
160	}
161
162	static void discoverPubkeys(ClientSession s, String peerUrl) {
163	log.info("Discovering pubkeys from peer: {}", peerUrl);	12✔
164	try {
165	List<String> peerPubkeys = Utils.retrieveListFromJsonUrl(peerUrl + "pubkeys.json");	×
166	int discovered = 0;	×
167	for (String pubkeyHash : peerPubkeys) {	×
168	Document filter = new Document("pubkey", pubkeyHash).append("type", NanopubLoader.INTRO_TYPE_HASH);	×
169	if (!has(s, "lists", filter)) {	×
170	try {
171	insert(s, "lists", new Document("pubkey", pubkeyHash)	×
172	.append("type", NanopubLoader.INTRO_TYPE_HASH)	×
173	.append("status", EntryStatus.encountered.getValue()));	×
174	} catch (MongoWriteException e) {	×
175	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;	×
176	}	×
177	discovered++;	×
178	} else if (!has(s, "lists", new Document(filter).append("status", EntryStatus.loaded.getValue()))) {	×
179	// Set status to encountered if not already loaded (fixes null-status entries from older code)
180	collection("lists").updateMany(s, filter,	×
181	new Document("$set", new Document("status", EntryStatus.encountered.getValue())));	×
182	discovered++;	×
183	}
184	}	×
185	log.info("Discovered {} new pubkeys from peer {}", discovered, peerUrl);	×
186	} catch (Exception ex) {	3✔
187	log.info("Failed to discover pubkeys from {}: {}", peerUrl, ex.getMessage());	18✔
188	}	×
189	}	3✔
190
191	static Document getPeerState(ClientSession s, String peerUrl) {
192	try (MongoCursor<Document> cursor = collection(Collection.PEER_STATE.toString())	27✔
193	.find(s, new Document("_id", peerUrl)).cursor()) {	9✔
194	return cursor.hasNext() ? cursor.next() : null;	33✔
195	}
196	}
197
198	static void updatePeerState(ClientSession s, String peerUrl, long setupId, long seqNum) {
199	collection(Collection.PEER_STATE.toString()).updateOne(s,	63✔
200	new Document("_id", peerUrl),
201	new Document("$set", new Document("_id", peerUrl)
202	.append("setupId", setupId)	12✔
203	.append("seqNum", seqNum)	12✔
204	// TODO(transition): Remove loadCounter after all peers upgraded
205	.append("loadCounter", seqNum)	9✔
206	.append("lastChecked", System.currentTimeMillis())),	24✔
207	new com.mongodb.client.model.UpdateOptions().upsert(true));	3✔
208	}	3✔
209
210	static void deletePeerState(ClientSession s, String peerUrl) {
211	collection(Collection.PEER_STATE.toString()).deleteOne(s, new Document("_id", peerUrl));	33✔
212	}	3✔
213
214	static boolean isTestInstance(HttpResponse resp) {
215	return "true".equals(getHeader(resp, "Nanopub-Registry-Test-Instance"));	18✔
216	}
217
218	static String getHeader(HttpResponse resp, String name) {
219	return resp.getFirstHeader(name) != null ? resp.getFirstHeader(name).getValue() : null;	33✔
220	}
221
222	static Long getHeaderLong(HttpResponse resp, String name) {
223	String value = getHeader(resp, name);	12✔
224	if (value == null \|\| "null".equals(value)) return null;	24✔
225	try {
226	return Long.parseLong(value);	12✔
227	} catch (NumberFormatException ex) {	3✔
228	return null;	6✔
229	}
230	}
231
232	}

knowledgepixels / nanopub-registry / 24121799241

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