24664456478

Committed 20 Apr 2026 11:39AM UTC coverage: 59.905% (-0.3%) from 60.236%

Build # 24664456478

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push

github

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web-flow

Commit Message

Merge pull request #75 from knowledgepixels/fix/timeouts-backoff-breaker

fix/perf/feat: changes 1+7+8 — HTTP timeouts, exponential backoff, circuit breaker

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26.6

src/main/java/com/knowledgepixels/query/JellyNanopubLoader.java

package com.knowledgepixels.query;

import java.io.IOException;
import java.util.concurrent.atomic.AtomicLong;

import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpHead;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.util.EntityUtils;
import org.nanopub.NanopubUtils;
import org.nanopub.jelly.NanopubStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Loads nanopubs from the attached Nanopub Registry via a restartable Jelly stream.
 */
public class JellyNanopubLoader {
    static final String registryUrl;
    private static long lastCommittedCounter = -1;
    private static Long lastKnownSetupId = null;
    // Latest registry metadata fields, updated on each metadata fetch and forwarded to clients
    static volatile String lastCoverageTypes = null;
    static volatile String lastCoverageAgents = null;
    static volatile String lastTestInstance = null;
    static volatile String lastNanopubCount = null;
    private static final CloseableHttpClient metadataClient;
    private static final CloseableHttpClient jellyStreamClient;

    private static final int MAX_RETRIES_METADATA = 10;
    private static final int RETRY_DELAY_METADATA = 3000;
    private static final int RETRY_DELAY_JELLY = 5000;

    /**
     * Circuit-breaker state. Counts consecutive {@code loadUpdates} invocations in
     * which the catch block fired; resets to zero on the next successful batch.
     * Scheduled on the single-threaded executor in {@link MainVerticle}, so a plain
     * {@code int} is enough — no concurrency.
     *
     * <p>When the counter reaches {@link #BREAKER_THRESHOLD}, the next invocation
     * sleeps {@link #BREAKER_PAUSE_MS} before proceeding. Lets the saturated RDF4J
     * drain instead of being hammered every {@link #UPDATES_POLL_INTERVAL} ms.
     *
     * <p>Depends on {@link com.knowledgepixels.query.TripleStore}'s socket timeouts
     * (change 1 of the fix plan) to turn parked commits into propagating exceptions;
     * without them, {@code loadBatch} can park forever, the catch never fires, and
     * this counter stays at zero.
     */
    static volatile int consecutiveBatchFailures = 0;

    static final int BREAKER_THRESHOLD = 3;
    static final long BREAKER_PAUSE_MS = 30_000L;

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

    /**
     * Registry metadata returned by a HEAD request.
     */
    record RegistryMetadata(long loadCounter, Long setupId, String coverageTypes,
                            String coverageAgents, String testInstance, String nanopubCount,
                            String trustStateHash) {}

    /**
     * The interval in milliseconds at which the updates loader should poll for new nanopubs.
     */
    public static final int UPDATES_POLL_INTERVAL = 2000;

    enum LoadingType {
        INITIAL,
        UPDATE,
    }

    static {
        // Initialize registryUrl
        var url = Utils.getEnvString(
                "REGISTRY_FIXED_URL", "https://registry.knowledgepixels.com/"
        );
        if (!url.endsWith("/")) url += "/";
        registryUrl = url;

        metadataClient = HttpClientBuilder.create().setDefaultRequestConfig(Utils.getHttpRequestConfig()).build();
        jellyStreamClient = NanopubUtils.getHttpClient();
    }

    /**
     * Start or continue (after restart) the initial loading procedure. This simply loads all
     * nanopubs from the attached Registry.
     *
     * @param afterCounter which counter to start from (-1 for the beginning)
     */
    public static void loadInitial(long afterCounter) {
        RegistryMetadata metadata = fetchRegistryMetadata();
        updateForwardingMetadata(metadata);
        TrustStateLoader.maybeUpdate(metadata.trustStateHash());
        long targetCounter = metadata.loadCounter();
        log.info("Fetched Registry load counter: {}", targetCounter);
        // Store setupId on initial load
        if (metadata.setupId() != null && lastKnownSetupId == null) {
            lastKnownSetupId = metadata.setupId();
            StatusController.get().setRegistrySetupId(metadata.setupId());
        }
        lastCommittedCounter = afterCounter;
        while (lastCommittedCounter < targetCounter) {
            try {
                loadBatch(lastCommittedCounter, LoadingType.INITIAL);
                log.info("Initial load: loaded batch up to counter {}", lastCommittedCounter);
            } catch (Exception e) {
                log.info("Failed to load batch starting from counter {}", lastCommittedCounter);
                log.info("Failure reason: ", e);
                try {
                    Thread.sleep(RETRY_DELAY_JELLY);
                } catch (InterruptedException e2) {
                    throw new RuntimeException("Interrupted while waiting to retry loading batch.");
                }
            }
        }
        log.info("Initial load complete.");
    }

    /**
     * Check if the Registry has any new nanopubs. If it does, load them.
     * This method should be called periodically, and you should wait for it to finish before
     * calling it again.
     */
    public static void loadUpdates() {
        // Circuit breaker: after BREAKER_THRESHOLD consecutive failed batches, pause
        // before the next attempt so a saturated RDF4J can drain. Check happens before
        // any RDF4J-touching work so the sleep isn't itself under the broken regime.
        if (consecutiveBatchFailures >= BREAKER_THRESHOLD) {
            log.warn("Circuit breaker active after {} consecutive batch failures; pausing {} ms before next attempt",
                    consecutiveBatchFailures, BREAKER_PAUSE_MS);
            try {
                Thread.sleep(BREAKER_PAUSE_MS);
            } catch (InterruptedException e) {
                // Preserve interruption semantics so a graceful shutdown (e.g. via
                // MainVerticle's shutdown hook) isn't blocked by the pause.
                Thread.currentThread().interrupt();
                return;
            }
        }
        try {
            final var status = StatusController.get().getState();
            lastCommittedCounter = status.loadCounter;
            RegistryMetadata metadata = fetchRegistryMetadata();
            updateForwardingMetadata(metadata);
            TrustStateLoader.maybeUpdate(metadata.trustStateHash());
            long targetCounter = metadata.loadCounter();
            Long currentSetupId = metadata.setupId();

            // Detect reset via setupId change
            if (lastKnownSetupId != null && currentSetupId != null
                    && !lastKnownSetupId.equals(currentSetupId)) {
                log.warn("Registry reset detected: setupId {} -> {}", lastKnownSetupId, currentSetupId);
                performResync(currentSetupId);
                return;
            }
            // Detect reset via counter decrease (also covers first run after upgrade
            // where no setupId was persisted yet but the registry has already been reset)
            if (lastCommittedCounter > 0 && targetCounter >= 0
                    && targetCounter < lastCommittedCounter) {
                log.warn("Registry counter decreased {} -> {}, triggering resync",
                        lastCommittedCounter, targetCounter);
                performResync(currentSetupId);
                return;
            }

            // Update lastKnownSetupId on first successful poll
            if (currentSetupId != null && lastKnownSetupId == null) {
                if (lastCommittedCounter > 0) {
                    // Upgrade from a version without setupId tracking. The DB has data but
                    // we can't verify it matches the current registry. Force a resync.
                    log.warn("No stored setupId but DB has data (counter: {}). "
                            + "Forcing resync to ensure data consistency.", lastCommittedCounter);
                    performResync(currentSetupId);
                    return;
                }
                lastKnownSetupId = currentSetupId;
                StatusController.get().setRegistrySetupId(currentSetupId);
            }

            StatusController.get().setLoadingUpdates(status.loadCounter);
            if (lastCommittedCounter >= targetCounter) {
                StatusController.get().setReady();
                return;
            }
            loadBatch(lastCommittedCounter, LoadingType.UPDATE);
            // Batch completed without an exception — reset the breaker counter.
            consecutiveBatchFailures = 0;
            log.info("Loaded {} update(s). Counter: {}, target was: {}",
                    lastCommittedCounter - status.loadCounter, lastCommittedCounter, targetCounter);
            if (lastCommittedCounter < targetCounter) {
                log.info("Warning: expected to load nanopubs up to (inclusive) counter " +
                        targetCounter + " based on the counter reported in Registry's headers, " +
                        "but loaded only up to {}.", lastCommittedCounter);
            }
        } catch (Exception e) {
            consecutiveBatchFailures++;
            log.warn("Failed to load updates. Current counter: {} (consecutive failures: {})",
                    lastCommittedCounter, consecutiveBatchFailures, e);
        } finally {
            try {
                StatusController.get().setReady();
            } catch (Exception e) {
                log.info("Update loader: failed to set status to READY.");
                log.info("Failure Reason: ", e);
            }
        }
    }

    /**
     * Re-stream all nanopubs from the registry after a reset is detected.
     * Existing nanopubs are skipped by NanopubLoader's per-repo dedup.
     *
     * @param newSetupId the new setup ID from the registry, or null if unknown
     */
    private static void performResync(Long newSetupId) {
        log.warn("Starting resync with registry. New setupId: {}", newSetupId);
        StatusController.get().setResetting();
        lastKnownSetupId = newSetupId;
        if (newSetupId != null) {
            StatusController.get().setRegistrySetupId(newSetupId);
        }
        StatusController.get().setLoadingInitial(-1);
        loadInitial(-1);
        StatusController.get().setReady();
        log.warn("Resync complete. Counter: {}", lastCommittedCounter);
    }

    /**
     * Load a batch of nanopubs from the Jelly stream.
     * <p>
     * The method requests the list of all nanopubs from the Registry and reads it for as long
     * as it can. If the stream is interrupted, the method will throw an exception, and you
     * can resume loading from the last known counter.
     *
     * @param afterCounter the last known nanopub counter to have been committed in the DB
     * @param type         the type of loading operation (initial or update)
     */
    static void loadBatch(long afterCounter, LoadingType type) {
        CloseableHttpResponse response;
        try {
            var request = new HttpGet(makeStreamFetchUrl(afterCounter));
            response = jellyStreamClient.execute(request);
        } catch (IOException e) {
            throw new RuntimeException("Failed to fetch Jelly stream from the Registry (I/O error).", e);
        }

        int httpStatus = response.getStatusLine().getStatusCode();
        if (httpStatus < 200 || httpStatus >= 300) {
            EntityUtils.consumeQuietly(response.getEntity());
            throw new RuntimeException("Jelly stream HTTP status is not 2xx: " + httpStatus + ".");
        }

        try (
                var is = response.getEntity().getContent();
                var npStream = NanopubStream.fromByteStream(is).getAsNanopubs()
        ) {
            AtomicLong checkpointTime = new AtomicLong(System.currentTimeMillis());
            AtomicLong checkpointCounter = new AtomicLong(lastCommittedCounter);
            AtomicLong lastSavedCounter = new AtomicLong(lastCommittedCounter);
            AtomicLong loaded = new AtomicLong(0L);

            npStream.forEach(m -> {
                if (!m.isSuccess()) throw new RuntimeException("Failed to load " +
                        "nanopub from Jelly stream. Last known counter: " + lastCommittedCounter,
                        m.getException()
                );
                if (m.getCounter() < lastCommittedCounter) {
                    throw new RuntimeException("Received a nanopub with a counter lower than " +
                            "the last known counter. Last known counter: " + lastCommittedCounter +
                            ", received counter: " + m.getCounter());
                }
                NanopubLoader.load(m.getNanopub(), m.getCounter());
                if (m.getCounter() % 10 == 0) {
                    // Save the committed counter only every 10 nanopubs to reduce DB load
                    saveCommittedCounter(type);
                    lastSavedCounter.set(m.getCounter());
                }
                lastCommittedCounter = m.getCounter();
                loaded.getAndIncrement();

                if (loaded.get() % 50 == 0) {
                    long currTime = System.currentTimeMillis();
                    double speed = 50 / ((currTime - checkpointTime.get()) / 1000.0);
                    log.info("Loading speed: " + String.format("%.2f", speed) +
                            " np/s. Counter: " + lastCommittedCounter);
                    checkpointTime.set(currTime);
                    checkpointCounter.set(lastCommittedCounter);
                }
            });
            // Make sure to save the last committed counter at the end of the batch
            if (lastCommittedCounter >= lastSavedCounter.get()) {
                saveCommittedCounter(type);
            }
        } catch (IOException e) {
            throw new RuntimeException("I/O error while reading the response Jelly stream.", e);
        } finally {
            try {
                response.close();
            } catch (IOException e) {
                log.info("Failed to close the Jelly stream response.");
            }
        }
    }

    /**
     * Save the last committed counter to the DB. Do this every N nanopubs to reduce DB load.
     * Remember to call this method at the end of the batch as well.
     *
     * @param type the type of loading operation (initial or update)
     */
    private static void saveCommittedCounter(LoadingType type) {
        try {
            if (type == LoadingType.INITIAL) {
                StatusController.get().setLoadingInitial(lastCommittedCounter);
            } else {
                StatusController.get().setLoadingUpdates(lastCommittedCounter);
            }
        } catch (Exception e) {
            throw new RuntimeException("Could not update the nanopub counter in DB", e);
        }
    }

    /**
     * Set the last known setup ID. Called from MainVerticle on startup to restore persisted state.
     *
     * @param setupId the setup ID to set, or null if not known
     */
    static void setLastKnownSetupId(Long setupId) {
        lastKnownSetupId = setupId;
    }

    /**
     * Update the cached metadata fields used for forwarding to clients.
     */
    private static void updateForwardingMetadata(RegistryMetadata metadata) {
        lastCoverageTypes = metadata.coverageTypes();
        lastCoverageAgents = metadata.coverageAgents();
        lastTestInstance = metadata.testInstance();
        lastNanopubCount = metadata.nanopubCount();
    }

    /**
     * Run a HEAD request to the Registry to fetch its current metadata (load counter and setup ID).
     *
     * @return the registry metadata
     */
    static RegistryMetadata fetchRegistryMetadata() {
        int tries = 0;
        RegistryMetadata metadata = null;
        while (metadata == null && tries < MAX_RETRIES_METADATA) {
            try {
                metadata = fetchRegistryMetadataInner();
            } catch (Exception e) {
                tries++;
                log.info("Failed to fetch registry metadata, try " + tries +
                        ". Retrying in {}ms...", RETRY_DELAY_METADATA);
                log.info("Failure Reason: ", e);
                try {
                    Thread.sleep(RETRY_DELAY_METADATA);
                } catch (InterruptedException e2) {
                    throw new RuntimeException(
                            "Interrupted while waiting to retry fetching registry metadata.");
                }
            }
        }
        if (metadata == null) {
            throw new RuntimeException("Failed to fetch registry metadata after " +
                    MAX_RETRIES_METADATA + " retries.");
        }
        return metadata;
    }

    /**
     * Inner logic for fetching the registry metadata via HEAD request.
     *
     * @return the registry metadata (load counter and setup ID)
     * @throws IOException if the HTTP request fails
     */
    private static RegistryMetadata fetchRegistryMetadataInner() throws IOException {
        var request = new HttpHead(registryUrl);
        try (var response = metadataClient.execute(request)) {
            int status = response.getStatusLine().getStatusCode();
            EntityUtils.consumeQuietly(response.getEntity());
            if (status < 200 || status >= 300) {
                throw new RuntimeException("Registry metadata HTTP status is not 2xx: " +
                        status + ".");
            }

            // Check if the registry is ready
            var hStatus = response.getHeaders("Nanopub-Registry-Status");
            if (hStatus.length == 0) {
                throw new RuntimeException("Registry did not return a Nanopub-Registry-Status header.");
            }
            if (!"ready".equals(hStatus[0].getValue()) && !"updating".equals(hStatus[0].getValue())) {
                throw new RuntimeException("Registry is not in ready state.");
            }

            // Get the load counter
            var hCounter = response.getHeaders("Nanopub-Registry-Load-Counter");
            if (hCounter.length == 0) {
                throw new RuntimeException("Registry did not return a Nanopub-Registry-Load-Counter header.");
            }
            long loadCounter = Long.parseLong(hCounter[0].getValue());

            // Get the setup ID (optional — older registries may not have it)
            Long setupId = null;
            var hSetupId = response.getHeaders("Nanopub-Registry-Setup-Id");
            if (hSetupId.length > 0) {
                try {
                    setupId = Long.parseLong(hSetupId[0].getValue());
                } catch (NumberFormatException e) {
                    log.info("Could not parse Nanopub-Registry-Setup-Id header: {}", hSetupId[0].getValue());
                }
            }

            // Read metadata headers for forwarding to clients
            String coverageTypes = getHeaderValue(response, "Nanopub-Registry-Coverage-Types");
            String coverageAgents = getHeaderValue(response, "Nanopub-Registry-Coverage-Agents");
            String testInstance = getHeaderValue(response, "Nanopub-Registry-Test-Instance");
            String nanopubCount = getHeaderValue(response, "Nanopub-Registry-Nanopub-Count");
            // Optional — older registries (without trust calculation) won't set this header.
            String trustStateHash = getHeaderValue(response, "Nanopub-Registry-Trust-State-Hash");

            return new RegistryMetadata(loadCounter, setupId, coverageTypes, coverageAgents,
                    testInstance, nanopubCount, trustStateHash);
        }
    }

    private static String getHeaderValue(CloseableHttpResponse response, String name) {
        var headers = response.getHeaders(name);
        return headers.length > 0 ? headers[0].getValue() : null;
    }

    /**
     * Construct the URL for fetching the Jelly stream.
     *
     * @param afterCounter the last known counter to have been committed in the DB
     * @return the URL for fetching the Jelly stream
     */
    private static String makeStreamFetchUrl(long afterCounter) {
        return registryUrl + "nanopubs.jelly?afterCounter=" + afterCounter;
    }
}

1	package com.knowledgepixels.query;
2
3	import java.io.IOException;
4	import java.util.concurrent.atomic.AtomicLong;
5
6	import org.apache.http.client.methods.CloseableHttpResponse;
7	import org.apache.http.client.methods.HttpGet;
8	import org.apache.http.client.methods.HttpHead;
9	import org.apache.http.impl.client.CloseableHttpClient;
10	import org.apache.http.impl.client.HttpClientBuilder;
11	import org.apache.http.util.EntityUtils;
12	import org.nanopub.NanopubUtils;
13	import org.nanopub.jelly.NanopubStream;
14	import org.slf4j.Logger;
15	import org.slf4j.LoggerFactory;
16
17	/**
18	* Loads nanopubs from the attached Nanopub Registry via a restartable Jelly stream.
19	*/
20	public class JellyNanopubLoader {	×
21	static final String registryUrl;
22	private static long lastCommittedCounter = -1;	4✔
23	private static Long lastKnownSetupId = null;	4✔
24	// Latest registry metadata fields, updated on each metadata fetch and forwarded to clients
25	static volatile String lastCoverageTypes = null;	4✔
26	static volatile String lastCoverageAgents = null;	4✔
27	static volatile String lastTestInstance = null;	4✔
28	static volatile String lastNanopubCount = null;	4✔
29	private static final CloseableHttpClient metadataClient;
30	private static final CloseableHttpClient jellyStreamClient;
31
32	private static final int MAX_RETRIES_METADATA = 10;
33	private static final int RETRY_DELAY_METADATA = 3000;
34	private static final int RETRY_DELAY_JELLY = 5000;
35
36	/**
37	* Circuit-breaker state. Counts consecutive {@code loadUpdates} invocations in
38	* which the catch block fired; resets to zero on the next successful batch.
39	* Scheduled on the single-threaded executor in {@link MainVerticle}, so a plain
40	* {@code int} is enough — no concurrency.
41	*
42	* <p>When the counter reaches {@link #BREAKER_THRESHOLD}, the next invocation
43	* sleeps {@link #BREAKER_PAUSE_MS} before proceeding. Lets the saturated RDF4J
44	* drain instead of being hammered every {@link #UPDATES_POLL_INTERVAL} ms.
45	*
46	* <p>Depends on {@link com.knowledgepixels.query.TripleStore}'s socket timeouts
47	* (change 1 of the fix plan) to turn parked commits into propagating exceptions;
48	* without them, {@code loadBatch} can park forever, the catch never fires, and
49	* this counter stays at zero.
50	*/
51	static volatile int consecutiveBatchFailures = 0;	4✔
52
53	static final int BREAKER_THRESHOLD = 3;
54	static final long BREAKER_PAUSE_MS = 30_000L;
55
56	private static final Logger log = LoggerFactory.getLogger(JellyNanopubLoader.class);	6✔
57
58	/**
59	* Registry metadata returned by a HEAD request.
60	*/
61	record RegistryMetadata(long loadCounter, Long setupId, String coverageTypes,	48✔
62	String coverageAgents, String testInstance, String nanopubCount,
63	String trustStateHash) {}
64
65	/**
66	* The interval in milliseconds at which the updates loader should poll for new nanopubs.
67	*/
68	public static final int UPDATES_POLL_INTERVAL = 2000;
69
70	enum LoadingType {	×
71	INITIAL,	×
72	UPDATE,	×
73	}
74
75	static {
76	// Initialize registryUrl
77	var url = Utils.getEnvString(	8✔
78	"REGISTRY_FIXED_URL", "https://registry.knowledgepixels.com/"
79	);
80	if (!url.endsWith("/")) url += "/";	8!
81	registryUrl = url;	4✔
82
83	metadataClient = HttpClientBuilder.create().setDefaultRequestConfig(Utils.getHttpRequestConfig()).build();	10✔
84	jellyStreamClient = NanopubUtils.getHttpClient();	4✔
85	}	2✔
86
87	/**
88	* Start or continue (after restart) the initial loading procedure. This simply loads all
89	* nanopubs from the attached Registry.
90	*
91	* @param afterCounter which counter to start from (-1 for the beginning)
92	*/
93	public static void loadInitial(long afterCounter) {
94	RegistryMetadata metadata = fetchRegistryMetadata();	4✔
95	updateForwardingMetadata(metadata);	4✔
96	TrustStateLoader.maybeUpdate(metadata.trustStateHash());	6✔
97	long targetCounter = metadata.loadCounter();	6✔
98	log.info("Fetched Registry load counter: {}", targetCounter);	10✔
99	// Store setupId on initial load
100	if (metadata.setupId() != null && lastKnownSetupId == null) {	6!
101	lastKnownSetupId = metadata.setupId();	×
102	StatusController.get().setRegistrySetupId(metadata.setupId());	×
103	}
104	lastCommittedCounter = afterCounter;	4✔
105	while (lastCommittedCounter < targetCounter) {	8!
106	try {
107	loadBatch(lastCommittedCounter, LoadingType.INITIAL);	×
108	log.info("Initial load: loaded batch up to counter {}", lastCommittedCounter);	×
109	} catch (Exception e) {	×
110	log.info("Failed to load batch starting from counter {}", lastCommittedCounter);	×
111	log.info("Failure reason: ", e);	×
112	try {
113	Thread.sleep(RETRY_DELAY_JELLY);	×
114	} catch (InterruptedException e2) {	×
115	throw new RuntimeException("Interrupted while waiting to retry loading batch.");	×
116	}	×
117	}	×
118	}
119	log.info("Initial load complete.");	6✔
120	}	2✔
121
122	/**
123	* Check if the Registry has any new nanopubs. If it does, load them.
124	* This method should be called periodically, and you should wait for it to finish before
125	* calling it again.
126	*/
127	public static void loadUpdates() {
128	// Circuit breaker: after BREAKER_THRESHOLD consecutive failed batches, pause
129	// before the next attempt so a saturated RDF4J can drain. Check happens before
130	// any RDF4J-touching work so the sleep isn't itself under the broken regime.
131	if (consecutiveBatchFailures >= BREAKER_THRESHOLD) {	×
132	log.warn("Circuit breaker active after {} consecutive batch failures; pausing {} ms before next attempt",	×
133	consecutiveBatchFailures, BREAKER_PAUSE_MS);	×
134	try {
135	Thread.sleep(BREAKER_PAUSE_MS);	×
136	} catch (InterruptedException e) {	×
137	// Preserve interruption semantics so a graceful shutdown (e.g. via
138	// MainVerticle's shutdown hook) isn't blocked by the pause.
139	Thread.currentThread().interrupt();	×
140	return;	×
141	}	×
142	}
143	try {
144	final var status = StatusController.get().getState();	×
145	lastCommittedCounter = status.loadCounter;	×
146	RegistryMetadata metadata = fetchRegistryMetadata();	×
147	updateForwardingMetadata(metadata);	×
148	TrustStateLoader.maybeUpdate(metadata.trustStateHash());	×
149	long targetCounter = metadata.loadCounter();	×
150	Long currentSetupId = metadata.setupId();	×
151
152	// Detect reset via setupId change
153	if (lastKnownSetupId != null && currentSetupId != null	×
154	&& !lastKnownSetupId.equals(currentSetupId)) {	×
155	log.warn("Registry reset detected: setupId {} -> {}", lastKnownSetupId, currentSetupId);	×
156	performResync(currentSetupId);	×
157	return;	×
158	}
159	// Detect reset via counter decrease (also covers first run after upgrade
160	// where no setupId was persisted yet but the registry has already been reset)
161	if (lastCommittedCounter > 0 && targetCounter >= 0	×
162	&& targetCounter < lastCommittedCounter) {
163	log.warn("Registry counter decreased {} -> {}, triggering resync",	×
164	lastCommittedCounter, targetCounter);	×
165	performResync(currentSetupId);	×
166	return;	×
167	}
168
169	// Update lastKnownSetupId on first successful poll
170	if (currentSetupId != null && lastKnownSetupId == null) {	×
171	if (lastCommittedCounter > 0) {	×
172	// Upgrade from a version without setupId tracking. The DB has data but
173	// we can't verify it matches the current registry. Force a resync.
174	log.warn("No stored setupId but DB has data (counter: {}). "	×
175	+ "Forcing resync to ensure data consistency.", lastCommittedCounter);	×
176	performResync(currentSetupId);	×
177	return;	×
178	}
179	lastKnownSetupId = currentSetupId;	×
180	StatusController.get().setRegistrySetupId(currentSetupId);	×
181	}
182
183	StatusController.get().setLoadingUpdates(status.loadCounter);	×
184	if (lastCommittedCounter >= targetCounter) {	×
185	StatusController.get().setReady();	×
186	return;	×
187	}
188	loadBatch(lastCommittedCounter, LoadingType.UPDATE);	×
189	// Batch completed without an exception — reset the breaker counter.
190	consecutiveBatchFailures = 0;	×
191	log.info("Loaded {} update(s). Counter: {}, target was: {}",	×
192	lastCommittedCounter - status.loadCounter, lastCommittedCounter, targetCounter);	×
193	if (lastCommittedCounter < targetCounter) {	×
194	log.info("Warning: expected to load nanopubs up to (inclusive) counter " +	×
195	targetCounter + " based on the counter reported in Registry's headers, " +
196	"but loaded only up to {}.", lastCommittedCounter);	×
197	}
198	} catch (Exception e) {	×
199	consecutiveBatchFailures++;	×
200	log.warn("Failed to load updates. Current counter: {} (consecutive failures: {})",	×
201	lastCommittedCounter, consecutiveBatchFailures, e);	×
202	} finally {
203	try {
204	StatusController.get().setReady();	×
205	} catch (Exception e) {	×
206	log.info("Update loader: failed to set status to READY.");	×
207	log.info("Failure Reason: ", e);	×
208	}	×
209	}
210	}	×
211
212	/**
213	* Re-stream all nanopubs from the registry after a reset is detected.
214	* Existing nanopubs are skipped by NanopubLoader's per-repo dedup.
215	*
216	* @param newSetupId the new setup ID from the registry, or null if unknown
217	*/
218	private static void performResync(Long newSetupId) {
219	log.warn("Starting resync with registry. New setupId: {}", newSetupId);	×
220	StatusController.get().setResetting();	×
221	lastKnownSetupId = newSetupId;	×
222	if (newSetupId != null) {	×
223	StatusController.get().setRegistrySetupId(newSetupId);	×
224	}
225	StatusController.get().setLoadingInitial(-1);	×
226	loadInitial(-1);	×
227	StatusController.get().setReady();	×
228	log.warn("Resync complete. Counter: {}", lastCommittedCounter);	×
229	}	×
230
231	/**
232	* Load a batch of nanopubs from the Jelly stream.
233	* <p>
234	* The method requests the list of all nanopubs from the Registry and reads it for as long
235	* as it can. If the stream is interrupted, the method will throw an exception, and you
236	* can resume loading from the last known counter.
237	*
238	* @param afterCounter the last known nanopub counter to have been committed in the DB
239	* @param type the type of loading operation (initial or update)
240	*/
241	static void loadBatch(long afterCounter, LoadingType type) {
242	CloseableHttpResponse response;
243	try {
244	var request = new HttpGet(makeStreamFetchUrl(afterCounter));	×
245	response = jellyStreamClient.execute(request);	×
246	} catch (IOException e) {	×
247	throw new RuntimeException("Failed to fetch Jelly stream from the Registry (I/O error).", e);	×
248	}	×
249
250	int httpStatus = response.getStatusLine().getStatusCode();	×
251	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
252	EntityUtils.consumeQuietly(response.getEntity());	×
253	throw new RuntimeException("Jelly stream HTTP status is not 2xx: " + httpStatus + ".");	×
254	}
255
256	try (
257	var is = response.getEntity().getContent();	×
258	var npStream = NanopubStream.fromByteStream(is).getAsNanopubs()	×
259	) {
260	AtomicLong checkpointTime = new AtomicLong(System.currentTimeMillis());	×
261	AtomicLong checkpointCounter = new AtomicLong(lastCommittedCounter);	×
262	AtomicLong lastSavedCounter = new AtomicLong(lastCommittedCounter);	×
263	AtomicLong loaded = new AtomicLong(0L);	×
264
265	npStream.forEach(m -> {	×
266	if (!m.isSuccess()) throw new RuntimeException("Failed to load " +	×
267	"nanopub from Jelly stream. Last known counter: " + lastCommittedCounter,
268	m.getException()	×
269	);
270	if (m.getCounter() < lastCommittedCounter) {	×
271	throw new RuntimeException("Received a nanopub with a counter lower than " +	×
272	"the last known counter. Last known counter: " + lastCommittedCounter +
273	", received counter: " + m.getCounter());	×
274	}
275	NanopubLoader.load(m.getNanopub(), m.getCounter());	×
276	if (m.getCounter() % 10 == 0) {	×
277	// Save the committed counter only every 10 nanopubs to reduce DB load
278	saveCommittedCounter(type);	×
279	lastSavedCounter.set(m.getCounter());	×
280	}
281	lastCommittedCounter = m.getCounter();	×
282	loaded.getAndIncrement();	×
283
284	if (loaded.get() % 50 == 0) {	×
285	long currTime = System.currentTimeMillis();	×
286	double speed = 50 / ((currTime - checkpointTime.get()) / 1000.0);	×
287	log.info("Loading speed: " + String.format("%.2f", speed) +	×
288	" np/s. Counter: " + lastCommittedCounter);
289	checkpointTime.set(currTime);	×
290	checkpointCounter.set(lastCommittedCounter);	×
291	}
292	});	×
293	// Make sure to save the last committed counter at the end of the batch
294	if (lastCommittedCounter >= lastSavedCounter.get()) {	×
295	saveCommittedCounter(type);	×
296	}
297	} catch (IOException e) {	×
298	throw new RuntimeException("I/O error while reading the response Jelly stream.", e);	×
299	} finally {
300	try {
301	response.close();	×
302	} catch (IOException e) {	×
303	log.info("Failed to close the Jelly stream response.");	×
304	}	×
305	}
306	}	×
307
308	/**
309	* Save the last committed counter to the DB. Do this every N nanopubs to reduce DB load.
310	* Remember to call this method at the end of the batch as well.
311	*
312	* @param type the type of loading operation (initial or update)
313	*/
314	private static void saveCommittedCounter(LoadingType type) {
315	try {
316	if (type == LoadingType.INITIAL) {	×
317	StatusController.get().setLoadingInitial(lastCommittedCounter);	×
318	} else {
319	StatusController.get().setLoadingUpdates(lastCommittedCounter);	×
320	}
321	} catch (Exception e) {	×
322	throw new RuntimeException("Could not update the nanopub counter in DB", e);	×
323	}	×
324	}	×
325
326	/**
327	* Set the last known setup ID. Called from MainVerticle on startup to restore persisted state.
328	*
329	* @param setupId the setup ID to set, or null if not known
330	*/
331	static void setLastKnownSetupId(Long setupId) {
332	lastKnownSetupId = setupId;	×
333	}	×
334
335	/**
336	* Update the cached metadata fields used for forwarding to clients.
337	*/
338	private static void updateForwardingMetadata(RegistryMetadata metadata) {
339	lastCoverageTypes = metadata.coverageTypes();	6✔
340	lastCoverageAgents = metadata.coverageAgents();	6✔
341	lastTestInstance = metadata.testInstance();	6✔
342	lastNanopubCount = metadata.nanopubCount();	6✔
343	}	2✔
344
345	/**
346	* Run a HEAD request to the Registry to fetch its current metadata (load counter and setup ID).
347	*
348	* @return the registry metadata
349	*/
350	static RegistryMetadata fetchRegistryMetadata() {
351	int tries = 0;	4✔
352	RegistryMetadata metadata = null;	4✔
353	while (metadata == null && tries < MAX_RETRIES_METADATA) {	10!
354	try {
355	metadata = fetchRegistryMetadataInner();	4✔
356	} catch (Exception e) {	×
357	tries++;	×
358	log.info("Failed to fetch registry metadata, try " + tries +	×
359	". Retrying in {}ms...", RETRY_DELAY_METADATA);	×
360	log.info("Failure Reason: ", e);	×
361	try {
362	Thread.sleep(RETRY_DELAY_METADATA);	×
363	} catch (InterruptedException e2) {	×
364	throw new RuntimeException(	×
365	"Interrupted while waiting to retry fetching registry metadata.");
366	}	×
367	}	2✔
368	}
369	if (metadata == null) {	4!
370	throw new RuntimeException("Failed to fetch registry metadata after " +	×
371	MAX_RETRIES_METADATA + " retries.");
372	}
373	return metadata;	4✔
374	}
375
376	/**
377	* Inner logic for fetching the registry metadata via HEAD request.
378	*
379	* @return the registry metadata (load counter and setup ID)
380	* @throws IOException if the HTTP request fails
381	*/
382	private static RegistryMetadata fetchRegistryMetadataInner() throws IOException {
383	var request = new HttpHead(registryUrl);	10✔
384	try (var response = metadataClient.execute(request)) {	8✔
385	int status = response.getStatusLine().getStatusCode();	8✔
386	EntityUtils.consumeQuietly(response.getEntity());	6✔
387	if (status < 200 \|\| status >= 300) {	12!
388	throw new RuntimeException("Registry metadata HTTP status is not 2xx: " +	×
389	status + ".");
390	}
391
392	// Check if the registry is ready
393	var hStatus = response.getHeaders("Nanopub-Registry-Status");	8✔
394	if (hStatus.length == 0) {	6!
395	throw new RuntimeException("Registry did not return a Nanopub-Registry-Status header.");	×
396	}
397	if (!"ready".equals(hStatus[0].getValue()) && !"updating".equals(hStatus[0].getValue())) {	14!
398	throw new RuntimeException("Registry is not in ready state.");	×
399	}
400
401	// Get the load counter
402	var hCounter = response.getHeaders("Nanopub-Registry-Load-Counter");	8✔
403	if (hCounter.length == 0) {	6!
404	throw new RuntimeException("Registry did not return a Nanopub-Registry-Load-Counter header.");	×
405	}
406	long loadCounter = Long.parseLong(hCounter[0].getValue());	12✔
407
408	// Get the setup ID (optional — older registries may not have it)
409	Long setupId = null;	4✔
410	var hSetupId = response.getHeaders("Nanopub-Registry-Setup-Id");	8✔
411	if (hSetupId.length > 0) {	6!
412	try {
413	setupId = Long.parseLong(hSetupId[0].getValue());	14✔
414	} catch (NumberFormatException e) {	×
415	log.info("Could not parse Nanopub-Registry-Setup-Id header: {}", hSetupId[0].getValue());	×
416	}	2✔
417	}
418
419	// Read metadata headers for forwarding to clients
420	String coverageTypes = getHeaderValue(response, "Nanopub-Registry-Coverage-Types");	8✔
421	String coverageAgents = getHeaderValue(response, "Nanopub-Registry-Coverage-Agents");	8✔
422	String testInstance = getHeaderValue(response, "Nanopub-Registry-Test-Instance");	8✔
423	String nanopubCount = getHeaderValue(response, "Nanopub-Registry-Nanopub-Count");	8✔
424	// Optional — older registries (without trust calculation) won't set this header.
425	String trustStateHash = getHeaderValue(response, "Nanopub-Registry-Trust-State-Hash");	8✔
426
427	return new RegistryMetadata(loadCounter, setupId, coverageTypes, coverageAgents,	26✔
428	testInstance, nanopubCount, trustStateHash);
429	}
430	}
431
432	private static String getHeaderValue(CloseableHttpResponse response, String name) {
433	var headers = response.getHeaders(name);	8✔
434	return headers.length > 0 ? headers[0].getValue() : null;	18!
435	}
436
437	/**
438	* Construct the URL for fetching the Jelly stream.
439	*
440	* @param afterCounter the last known counter to have been committed in the DB
441	* @return the URL for fetching the Jelly stream
442	*/
443	private static String makeStreamFetchUrl(long afterCounter) {
444	return registryUrl + "nanopubs.jelly?afterCounter=" + afterCounter;	×
445	}
446	}

knowledgepixels / nanopub-query / 24664456478

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