17120526436

Committed 21 Aug 2025 07:44AM UTC coverage: 49.971% (-0.09%) from 50.058%

Build # 17120526436

Build Type

push

github

Committed by

tkuhn

Commit Message

Define timeouts via environment variables, and some refactoring

Run Details

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Branch coverage included in aggregate %.

629 of 1249 relevant lines covered (50.36%)

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25.15

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;

/**
 * Loads nanopubs from the attached Nanopub Registry via a restartable Jelly stream.
 */
public class JellyNanopubLoader {
    private static final String registryUrl;
    private static long lastCommittedCounter = -1;
    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;

    /**
     * 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) {
        long targetCounter = fetchRegistryLoadCounter();
        System.err.println("Fetched Registry load counter: " + targetCounter);
        lastCommittedCounter = afterCounter;
        while (lastCommittedCounter < targetCounter) {
            try {
                loadBatch(lastCommittedCounter, LoadingType.INITIAL);
                System.err.println("Initial load: loaded batch up to counter " + lastCommittedCounter);
            } catch (Exception e) {
                System.err.println("Failed to load batch starting from counter " + lastCommittedCounter);
                System.err.println(e.getMessage());
                try {
                    Thread.sleep(RETRY_DELAY_JELLY);
                } catch (InterruptedException e2) {
                    throw new RuntimeException("Interrupted while waiting to retry loading batch.");
                }
            }
        }
        System.err.println("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;
            StatusController.get().setLoadingUpdates(status.loadCounter);
            long targetCounter = fetchRegistryLoadCounter();
            if (lastCommittedCounter >= targetCounter) {
                // Keep quiet so as not to spam the log every second
                // System.err.println("No updates to load.");
                StatusController.get().setReady();
                return;
            }
            loadBatch(lastCommittedCounter, LoadingType.UPDATE);
            System.err.println("Loaded " + (lastCommittedCounter - status.loadCounter) +
                    " update(s). Counter: " + lastCommittedCounter + ", target was: " + targetCounter);
            if (lastCommittedCounter < targetCounter) {
                System.err.println("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) {
            System.err.println("Failed to load updates. Current counter: " + lastCommittedCounter);
            System.err.println(e.getMessage());
        } finally {
            try {
                StatusController.get().setReady();
            } catch (Exception e) {
                System.err.println("Update loader: failed to set status to READY.");
                System.err.println(e.getMessage());
            }
        }
    }

    /**
     * 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);
                    System.err.println("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) {
                System.err.println("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);
        }
    }

    /**
     * Run a HEAD request to the Registry to fetch its current load counter.
     *
     * @return the current load counter
     */
    static long fetchRegistryLoadCounter() {
        int tries = 0;
        long counter = -1;
        while (counter == -1 && tries < MAX_RETRIES_METADATA) {
            try {
                counter = fetchRegistryLoadCounterInner();
            } catch (Exception e) {
                tries++;
                System.err.println("Failed to fetch registry load counter, try " + tries +
                        ". Retrying in " + RETRY_DELAY_METADATA + "ms...");
                System.err.println(e.getMessage());
                try {
                    Thread.sleep(RETRY_DELAY_METADATA);
                } catch (InterruptedException e2) {
                    throw new RuntimeException(
                            "Interrupted while waiting to retry fetching registry load counter.");
                }
            }
        }
        if (counter == -1) {
            throw new RuntimeException("Failed to fetch registry load counter after " +
                    MAX_RETRIES_METADATA + " retries.");
        }
        return counter;
    }

    /**
     * Inner logic for fetching the registry load counter.
     *
     * @return the current load counter
     * @throws IOException if the HTTP request fails
     */
    private static long fetchRegistryLoadCounterInner() 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 load counter 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 actual 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.");
            }
            return Long.parseLong(hCounter[0].getValue());
        }
    }

    /**
     * Construct the URL for fetching the Jelly stream.
     *
     * @param afterCounter the last known nanopub 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
15	/**
16	* Loads nanopubs from the attached Nanopub Registry via a restartable Jelly stream.
17	*/
18	public class JellyNanopubLoader {	×
19	private static final String registryUrl;
20	private static long lastCommittedCounter = -1;	2✔
21	private static final CloseableHttpClient metadataClient;
22	private static final CloseableHttpClient jellyStreamClient;
23
24	private static final int MAX_RETRIES_METADATA = 10;
25	private static final int RETRY_DELAY_METADATA = 3000;
26	private static final int RETRY_DELAY_JELLY = 5000;
27
28	/**
29	* The interval in milliseconds at which the updates loader should poll for new nanopubs.
30	*/
31	public static final int UPDATES_POLL_INTERVAL = 2000;
32
33	enum LoadingType {	×
34	INITIAL,	×
35	UPDATE,	×
36	}
37
38	static {
39	// Initialize registryUrl
40	var url = Utils.getEnvString(	4✔
41	"REGISTRY_FIXED_URL", "https://registry.knowledgepixels.com/"
42	);
43	if (!url.endsWith("/")) url += "/";	4!
44	registryUrl = url;	2✔
45
46	metadataClient = HttpClientBuilder.create().setDefaultRequestConfig(Utils.getHttpRequestConfig()).build();	5✔
47	jellyStreamClient = NanopubUtils.getHttpClient();	2✔
48	}	1✔
49
50	/**
51	* Start or continue (after restart) the initial loading procedure. This simply loads all
52	* nanopubs from the attached Registry.
53	*
54	* @param afterCounter which counter to start from (-1 for the beginning)
55	*/
56	public static void loadInitial(long afterCounter) {
57	long targetCounter = fetchRegistryLoadCounter();	2✔
58	System.err.println("Fetched Registry load counter: " + targetCounter);	4✔
59	lastCommittedCounter = afterCounter;	2✔
60	while (lastCommittedCounter < targetCounter) {	4!
61	try {
62	loadBatch(lastCommittedCounter, LoadingType.INITIAL);	×
63	System.err.println("Initial load: loaded batch up to counter " + lastCommittedCounter);	×
64	} catch (Exception e) {	×
65	System.err.println("Failed to load batch starting from counter " + lastCommittedCounter);	×
66	System.err.println(e.getMessage());	×
67	try {
68	Thread.sleep(RETRY_DELAY_JELLY);	×
69	} catch (InterruptedException e2) {	×
70	throw new RuntimeException("Interrupted while waiting to retry loading batch.");	×
71	}	×
72	}	×
73	}
74	System.err.println("Initial load complete.");	3✔
75	}	1✔
76
77	/**
78	* Check if the Registry has any new nanopubs. If it does, load them.
79	* This method should be called periodically, and you should wait for it to finish before
80	* calling it again.
81	*/
82	public static void loadUpdates() {
83	try {
84	final var status = StatusController.get().getState();	×
85	lastCommittedCounter = status.loadCounter;	×
86	StatusController.get().setLoadingUpdates(status.loadCounter);	×
87	long targetCounter = fetchRegistryLoadCounter();	×
88	if (lastCommittedCounter >= targetCounter) {	×
89	// Keep quiet so as not to spam the log every second
90	// System.err.println("No updates to load.");
91	StatusController.get().setReady();	×
92	return;	×
93	}
94	loadBatch(lastCommittedCounter, LoadingType.UPDATE);	×
95	System.err.println("Loaded " + (lastCommittedCounter - status.loadCounter) +	×
96	" update(s). Counter: " + lastCommittedCounter + ", target was: " + targetCounter);
97	if (lastCommittedCounter < targetCounter) {	×
98	System.err.println("Warning: expected to load nanopubs up to (inclusive) counter " +	×
99	targetCounter + " based on the counter reported in Registry's headers, " +
100	"but loaded only up to " + lastCommittedCounter + ".");
101	}
102	} catch (Exception e) {	×
103	System.err.println("Failed to load updates. Current counter: " + lastCommittedCounter);	×
104	System.err.println(e.getMessage());	×
105	} finally {
106	try {
107	StatusController.get().setReady();	×
108	} catch (Exception e) {	×
109	System.err.println("Update loader: failed to set status to READY.");	×
110	System.err.println(e.getMessage());	×
111	}	×
112	}
113	}	×
114
115	/**
116	* Load a batch of nanopubs from the Jelly stream.
117	* <p>
118	* The method requests the list of all nanopubs from the Registry and reads it for as long
119	* as it can. If the stream is interrupted, the method will throw an exception, and you
120	* can resume loading from the last known counter.
121	*
122	* @param afterCounter the last known nanopub counter to have been committed in the DB
123	* @param type the type of loading operation (initial or update)
124	*/
125	static void loadBatch(long afterCounter, LoadingType type) {
126	CloseableHttpResponse response;
127	try {
128	var request = new HttpGet(makeStreamFetchUrl(afterCounter));	×
129	response = jellyStreamClient.execute(request);	×
130	} catch (IOException e) {	×
131	throw new RuntimeException("Failed to fetch Jelly stream from the Registry (I/O error).", e);	×
132	}	×
133
134	int httpStatus = response.getStatusLine().getStatusCode();	×
135	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
136	EntityUtils.consumeQuietly(response.getEntity());	×
137	throw new RuntimeException("Jelly stream HTTP status is not 2xx: " + httpStatus + ".");	×
138	}
139
140	try (
141	var is = response.getEntity().getContent();	×
142	var npStream = NanopubStream.fromByteStream(is).getAsNanopubs()	×
143	) {
144	AtomicLong checkpointTime = new AtomicLong(System.currentTimeMillis());	×
145	AtomicLong checkpointCounter = new AtomicLong(lastCommittedCounter);	×
146	AtomicLong lastSavedCounter = new AtomicLong(lastCommittedCounter);	×
147	AtomicLong loaded = new AtomicLong(0L);	×
148
149	npStream.forEach(m -> {	×
150	if (!m.isSuccess()) throw new RuntimeException("Failed to load " +	×
151	"nanopub from Jelly stream. Last known counter: " + lastCommittedCounter,
152	m.getException()	×
153	);
154	if (m.getCounter() < lastCommittedCounter) {	×
155	throw new RuntimeException("Received a nanopub with a counter lower than " +	×
156	"the last known counter. Last known counter: " + lastCommittedCounter +
157	", received counter: " + m.getCounter());	×
158	}
159	NanopubLoader.load(m.getNanopub(), m.getCounter());	×
160	if (m.getCounter() % 10 == 0) {	×
161	// Save the committed counter only every 10 nanopubs to reduce DB load
162	saveCommittedCounter(type);	×
163	lastSavedCounter.set(m.getCounter());	×
164	}
165	lastCommittedCounter = m.getCounter();	×
166	loaded.getAndIncrement();	×
167
168	if (loaded.get() % 50 == 0) {	×
169	long currTime = System.currentTimeMillis();	×
170	double speed = 50 / ((currTime - checkpointTime.get()) / 1000.0);	×
171	System.err.println("Loading speed: " + String.format("%.2f", speed) +	×
172	" np/s. Counter: " + lastCommittedCounter);
173	checkpointTime.set(currTime);	×
174	checkpointCounter.set(lastCommittedCounter);	×
175	}
176	});	×
177	// Make sure to save the last committed counter at the end of the batch
178	if (lastCommittedCounter >= lastSavedCounter.get()) {	×
179	saveCommittedCounter(type);	×
180	}
181	} catch (IOException e) {	×
182	throw new RuntimeException("I/O error while reading the response Jelly stream.", e);	×
183	} finally {
184	try {
185	response.close();	×
186	} catch (IOException e) {	×
187	System.err.println("Failed to close the Jelly stream response.");	×
188	}	×
189	}
190	}	×
191
192	/**
193	* Save the last committed counter to the DB. Do this every N nanopubs to reduce DB load.
194	* Remember to call this method at the end of the batch as well.
195	*
196	* @param type the type of loading operation (initial or update)
197	*/
198	private static void saveCommittedCounter(LoadingType type) {
199	try {
200	if (type == LoadingType.INITIAL) {	×
201	StatusController.get().setLoadingInitial(lastCommittedCounter);	×
202	} else {
203	StatusController.get().setLoadingUpdates(lastCommittedCounter);	×
204	}
205	} catch (Exception e) {	×
206	throw new RuntimeException("Could not update the nanopub counter in DB", e);	×
207	}	×
208	}	×
209
210	/**
211	* Run a HEAD request to the Registry to fetch its current load counter.
212	*
213	* @return the current load counter
214	*/
215	static long fetchRegistryLoadCounter() {
216	int tries = 0;	2✔
217	long counter = -1;	2✔
218	while (counter == -1 && tries < MAX_RETRIES_METADATA) {	7!
219	try {
220	counter = fetchRegistryLoadCounterInner();	2✔
221	} catch (Exception e) {	×
222	tries++;	×
223	System.err.println("Failed to fetch registry load counter, try " + tries +	×
224	". Retrying in " + RETRY_DELAY_METADATA + "ms...");
225	System.err.println(e.getMessage());	×
226	try {
227	Thread.sleep(RETRY_DELAY_METADATA);	×
228	} catch (InterruptedException e2) {	×
229	throw new RuntimeException(	×
230	"Interrupted while waiting to retry fetching registry load counter.");
231	}	×
232	}	1✔
233	}
234	if (counter == -1) {	4!
235	throw new RuntimeException("Failed to fetch registry load counter after " +	×
236	MAX_RETRIES_METADATA + " retries.");
237	}
238	return counter;	2✔
239	}
240
241	/**
242	* Inner logic for fetching the registry load counter.
243	*
244	* @return the current load counter
245	* @throws IOException if the HTTP request fails
246	*/
247	private static long fetchRegistryLoadCounterInner() throws IOException {
248	var request = new HttpHead(registryUrl);	5✔
249	try (var response = metadataClient.execute(request)) {	4✔
250	int status = response.getStatusLine().getStatusCode();	4✔
251	EntityUtils.consumeQuietly(response.getEntity());	3✔
252	if (status < 200 \|\| status >= 300) {	6!
253	throw new RuntimeException("Registry load counter HTTP status is not 2xx: " +	×
254	status + ".");
255	}
256
257	// Check if the registry is ready
258	var hStatus = response.getHeaders("Nanopub-Registry-Status");	4✔
259	if (hStatus.length == 0) {	3!
260	throw new RuntimeException("Registry did not return a Nanopub-Registry-Status header.");	×
261	}
262	if (!"ready".equals(hStatus[0].getValue()) && !"updating".equals(hStatus[0].getValue())) {	14!
263	throw new RuntimeException("Registry is not in ready state.");	×
264	}
265
266	// Get the actual load counter
267	var hCounter = response.getHeaders("Nanopub-Registry-Load-Counter");	4✔
268	if (hCounter.length == 0) {	3!
269	throw new RuntimeException("Registry did not return a Nanopub-Registry-Load-Counter header.");	×
270	}
271	return Long.parseLong(hCounter[0].getValue());	8✔
272	}
273	}
274
275	/**
276	* Construct the URL for fetching the Jelly stream.
277	*
278	* @param afterCounter the last known nanopub counter to have been committed in the DB
279	* @return the URL for fetching the Jelly stream
280	*/
281	private static String makeStreamFetchUrl(long afterCounter) {
282	return registryUrl + "nanopubs.jelly?afterCounter=" + afterCounter;	×
283	}
284	}

knowledgepixels / nanopub-query / 17120526436

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