24130021648

Committed 08 Apr 2026 10:11AM UTC coverage: 66.468% (-0.5%) from 66.922%

Build # 24130021648

Build Type

push

github

Committed by

tkuhn

Commit Message

feat: align with registry seqNum API and forward registry metadata headers

Migrate from afterCounter to afterSeqNum query parameter (with fallback
for older registries). Prefer Nanopub-Registry-SeqNum header over
Load-Counter for sync cursor. Forward coverage types (defaulting to
"all"), test instance, and nanopub count from registry to clients.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Coverage Stats

233 of 390 branches covered (59.74%)

Branch coverage included in aggregate %.

659 of 952 relevant lines covered (69.22%)

10.24 hits per line

Source File
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29.02

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 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;

    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 testInstance, String nanopubCount) {}

    /**
     * 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);
        long targetCounter = metadata.loadCounter();
        log.info("Fetched Registry seqNum: {}", 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() {
        try {
            final var status = StatusController.get().getState();
            lastCommittedCounter = status.loadCounter;
            RegistryMetadata metadata = fetchRegistryMetadata();
            updateForwardingMetadata(metadata);
            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);
            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) {
            log.info("Failed to load updates. Current counter: {}", lastCommittedCounter);
            log.info("Failure Reason: ", 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();
        lastTestInstance = metadata.testInstance();
        lastNanopubCount = metadata.nanopubCount();
    }

    /**
     * Run a HEAD request to the Registry to fetch its current metadata (seqNum 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 seqNum (preferred) or load counter (fallback for older registries)
            // TODO(transition): Remove Load-Counter fallback after all registries upgraded
            Long seqNum = null;
            var hSeqNum = response.getHeaders("Nanopub-Registry-SeqNum");
            if (hSeqNum.length > 0) {
                seqNum = Long.parseLong(hSeqNum[0].getValue());
            }
            if (seqNum == null) {
                var hCounter = response.getHeaders("Nanopub-Registry-Load-Counter");
                if (hCounter.length > 0) {
                    seqNum = Long.parseLong(hCounter[0].getValue());
                }
            }
            if (seqNum == null) {
                throw new RuntimeException("Registry did not return a Nanopub-Registry-SeqNum or Load-Counter header.");
            }

            // 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 optional metadata headers for forwarding to clients
            String coverageTypes = null;
            var hCovTypes = response.getHeaders("Nanopub-Registry-Coverage-Types");
            if (hCovTypes.length > 0) {
                coverageTypes = hCovTypes[0].getValue();
            }

            String testInstance = null;
            var hTestInstance = response.getHeaders("Nanopub-Registry-Test-Instance");
            if (hTestInstance.length > 0) {
                testInstance = hTestInstance[0].getValue();
            }

            String nanopubCount = null;
            var hNpCount = response.getHeaders("Nanopub-Registry-Nanopub-Count");
            if (hNpCount.length > 0) {
                nanopubCount = hNpCount[0].getValue();
            }

            return new RegistryMetadata(seqNum, setupId, coverageTypes, testInstance, nanopubCount);
        }
    }

    /**
     * Construct the URL for fetching the Jelly stream.
     *
     * @param afterSeqNum the last known seqNum to have been committed in the DB
     * @return the URL for fetching the Jelly stream
     */
    private static String makeStreamFetchUrl(long afterSeqNum) {
        // TODO(transition): Remove afterCounter param after all registries upgraded
        return registryUrl + "nanopubs.jelly?afterSeqNum=" + afterSeqNum + "&afterCounter=" + afterSeqNum;
    }
}

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

knowledgepixels / nanopub-query / 24130021648

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