23018791468

Committed 12 Mar 2026 06:56PM UTC coverage: 25.927% (-0.8%) from 26.77%

Build # 23018791468

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #81 from knowledgepixels/feature/load-all-pubkeys

Add REGISTRY_PRIORITIZE_ALL_PUBKEYS and remove full fetch

Run Details

156 of 670 branches covered (23.28%)

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529 of 1972 relevant lines covered (26.83%)

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34.57

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 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;
        }

        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;
        }

        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);
            loadRecentNanopubs(s, peerUrl, lastLoadCounter);
        } else {
            log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);
        }

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

    private static void loadRecentNanopubs(ClientSession s, String peerUrl, long afterCounter) {
        String requestUrl = peerUrl + "nanopubs.jelly?afterCounter=" + afterCounter;
        log.info("Fetching recent nanopubs from: {}", requestUrl);
        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;
            }
            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);
                        } 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());
        }
    }

    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 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
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.info("Error checking peer {}: {}", peerUrl, ex.getMessage());	×
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.info("Failed to reach peer {}: {}", peerUrl, httpStatus);	×
56	return;	×
57	}
58
59	String status = getHeader(resp, "Nanopub-Registry-Status");	×
60	if (!"ready".equals(status) && !"updating".equals(status)) {	×
61	log.info("Peer {} in non-ready state: {}", peerUrl, status);	×
62	return;	×
63	}
64
65	Long peerSetupId = getHeaderLong(resp, "Nanopub-Registry-Setup-Id");	×
66	Long peerLoadCounter = getHeaderLong(resp, "Nanopub-Registry-Load-Counter");	×
67	if (peerSetupId == null \|\| peerLoadCounter == null) {	×
68	log.info("Peer {} missing setupId or loadCounter headers", peerUrl);	×
69	return;	×
70	}
71
72	syncWithPeer(s, peerUrl, peerSetupId, peerLoadCounter);	×
73	}	×
74
75	static void syncWithPeer(ClientSession s, String peerUrl, long peerSetupId, long peerLoadCounter) {
76	Document peerState = getPeerState(s, peerUrl);	12✔
77	Long lastSetupId = peerState != null ? peerState.getLong("setupId") : null;	24✔
78	Long lastLoadCounter = peerState != null ? peerState.getLong("loadCounter") : null;	24✔
79
80	if (lastSetupId != null && !lastSetupId.equals(peerSetupId)) {	21✔
81	log.info("Peer {} was reset (setupId changed), resetting tracking", peerUrl);	12✔
82	deletePeerState(s, peerUrl);	9✔
83	lastLoadCounter = null;	6✔
84	}
85
86	if (lastLoadCounter != null && lastLoadCounter.equals(peerLoadCounter)) {	21!
87	log.info("Peer {} has no new nanopubs (loadCounter unchanged: {})", peerUrl, peerLoadCounter);	21✔
88	} else if (lastLoadCounter != null) {	6!
89	// Fetch all nanopubs added since our last known position.
90	// TODO Add per-pubkey afterCounter tracking for more targeted incremental sync
91	long delta = peerLoadCounter - lastLoadCounter;	×
92	log.info("Peer {} has {} new nanopubs, fetching recent", peerUrl, delta);	×
93	loadRecentNanopubs(s, peerUrl, lastLoadCounter);	×
94	} else {	×
95	log.info("Peer {} is new, pubkey discovery will handle initial sync", peerUrl);	12✔
96	}
97
98	discoverPubkeys(s, peerUrl);	9✔
99	updatePeerState(s, peerUrl, peerSetupId, peerLoadCounter);	15✔
100	}	3✔
101
102	private static void loadRecentNanopubs(ClientSession s, String peerUrl, long afterCounter) {
103	String requestUrl = peerUrl + "nanopubs.jelly?afterCounter=" + afterCounter;	×
104	log.info("Fetching recent nanopubs from: {}", requestUrl);	×
105	try {
106	HttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
107	int httpStatus = resp.getStatusLine().getStatusCode();	×
108	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
109	EntityUtils.consumeQuietly(resp.getEntity());	×
110	log.info("Request failed: {} {}", requestUrl, httpStatus);	×
111	return;	×
112	}
113	try (InputStream is = resp.getEntity().getContent()) {	×
114	NanopubStream.fromByteStream(is).getAsNanopubs().forEach(m -> {	×
115	if (m.isSuccess()) {	×
116	Nanopub np = null;	×
117	try {
118	np = m.getNanopub();	×
119	RegistryDB.loadNanopub(s, np);	×
120	NanopubLoader.simpleLoad(s, np);	×
121	} catch (Exception ex) {	×
122	log.warn("Skipping nanopub {} during recent fetch: {}",	×
123	np != null ? np.getUri() : "unknown", ex.getMessage());	×
124	}	×
125	}
126	});	×
127	}
128	} catch (IOException ex) {	×
129	log.info("Failed to fetch recent nanopubs from {}: {}", peerUrl, ex.getMessage());	×
130	}	×
131	}	×
132
133	static void discoverPubkeys(ClientSession s, String peerUrl) {
134	log.info("Discovering pubkeys from peer: {}", peerUrl);	12✔
135	try {
136	List<String> peerPubkeys = Utils.retrieveListFromJsonUrl(peerUrl + "pubkeys.json");	×
137	int discovered = 0;	×
138	for (String pubkeyHash : peerPubkeys) {	×
139	Document filter = new Document("pubkey", pubkeyHash).append("type", NanopubLoader.INTRO_TYPE_HASH);	×
140	if (!has(s, "lists", filter)) {	×
141	try {
142	insert(s, "lists", new Document("pubkey", pubkeyHash)	×
143	.append("type", NanopubLoader.INTRO_TYPE_HASH)	×
144	.append("status", EntryStatus.encountered.getValue()));	×
145	} catch (MongoWriteException e) {	×
146	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;	×
147	}	×
148	discovered++;	×
149	} else if (!has(s, "lists", new Document(filter).append("status", EntryStatus.loaded.getValue()))) {	×
150	// Set status to encountered if not already loaded (fixes null-status entries from older code)
151	collection("lists").updateMany(s, filter,	×
152	new Document("$set", new Document("status", EntryStatus.encountered.getValue())));	×
153	discovered++;	×
154	}
155	}	×
156	log.info("Discovered {} new pubkeys from peer {}", discovered, peerUrl);	×
157	} catch (Exception ex) {	3✔
158	log.info("Failed to discover pubkeys from {}: {}", peerUrl, ex.getMessage());	18✔
159	}	×
160	}	3✔
161
162	static Document getPeerState(ClientSession s, String peerUrl) {
163	try (MongoCursor<Document> cursor = collection(Collection.PEER_STATE.toString())	27✔
164	.find(s, new Document("_id", peerUrl)).cursor()) {	9✔
165	return cursor.hasNext() ? cursor.next() : null;	33✔
166	}
167	}
168
169	static void updatePeerState(ClientSession s, String peerUrl, long setupId, long loadCounter) {
170	collection(Collection.PEER_STATE.toString()).updateOne(s,	63✔
171	new Document("_id", peerUrl),
172	new Document("$set", new Document("_id", peerUrl)
173	.append("setupId", setupId)	12✔
174	.append("loadCounter", loadCounter)	9✔
175	.append("lastChecked", System.currentTimeMillis())),	24✔
176	new com.mongodb.client.model.UpdateOptions().upsert(true));	3✔
177	}	3✔
178
179	static void deletePeerState(ClientSession s, String peerUrl) {
180	collection(Collection.PEER_STATE.toString()).deleteOne(s, new Document("_id", peerUrl));	33✔
181	}	3✔
182
183	static String getHeader(HttpResponse resp, String name) {
184	return resp.getFirstHeader(name) != null ? resp.getFirstHeader(name).getValue() : null;	33✔
185	}
186
187	static Long getHeaderLong(HttpResponse resp, String name) {
188	String value = getHeader(resp, name);	12✔
189	if (value == null \|\| "null".equals(value)) return null;	24✔
190	try {
191	return Long.parseLong(value);	12✔
192	} catch (NumberFormatException ex) {	3✔
193	return null;	6✔
194	}
195	}
196
197	}

knowledgepixels / nanopub-registry / 23018791468

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