24334244342

Committed 13 Apr 2026 08:46AM UTC coverage: 32.151% (-0.2%) from 32.357%

Build # 24334244342

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push

github

Committed by

web-flow

Commit Message

Merge pull request #101 from knowledgepixels/fix/100-sync-nanopubs-from-encountered-pubkey

fix: store and backfill nanopubs from encountered pubkeys

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265 of 924 branches covered (28.68%)

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786 of 2345 relevant lines covered (33.52%)

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8.55

src/main/java/com/knowledgepixels/registry/NanopubLoader.java

package com.knowledgepixels.registry;

import com.mongodb.ErrorCategory;
import com.mongodb.MongoWriteException;
import com.mongodb.client.ClientSession;
import com.mongodb.client.MongoCursor;
import net.trustyuri.TrustyUriUtils;
import net.trustyuri.rdf.RdfModule;
import org.apache.http.Header;
import org.apache.http.HttpResponse;
import org.apache.http.client.HttpClient;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.util.EntityUtils;
import org.bson.Document;
import org.bson.types.Binary;
import org.eclipse.rdf4j.common.exception.RDF4JException;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.nanopub.MalformedNanopubException;
import org.nanopub.Nanopub;
import org.nanopub.NanopubImpl;
import org.nanopub.NanopubUtils;
import org.nanopub.extra.server.GetNanopub;
import org.nanopub.jelly.JellyUtils;
import org.nanopub.jelly.MaybeNanopub;
import org.nanopub.jelly.NanopubStream;
import org.nanopub.trusty.TrustyNanopubUtils;
import org.nanopub.vocabulary.NPX;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicReference;
import java.util.function.Consumer;
import java.util.stream.Stream;

import static com.knowledgepixels.registry.RegistryDB.has;
import static com.knowledgepixels.registry.RegistryDB.insert;

public class NanopubLoader {

    private NanopubLoader() {
    }

    public final static String INTRO_TYPE = NPX.DECLARED_BY.stringValue();
    public final static String INTRO_TYPE_HASH = Utils.getHash(INTRO_TYPE);
    public final static String ENDORSE_TYPE = Utils.APPROVES_OF.stringValue();
    public final static String ENDORSE_TYPE_HASH = Utils.getHash(ENDORSE_TYPE);
    private static final Logger log = LoggerFactory.getLogger(NanopubLoader.class);

    // TODO Distinguish and support these cases:
    //      1. Simple load: load to all core lists if pubkey is "core-loaded", or load to all lists if pubkey is "full-loaded"
    //      2. Core load: load to all core lists (initialize if needed), or load to all lists if pubkey is "full-loaded"
    //      3. Full load: load to all lists (initialize if needed)

    public static void simpleLoad(ClientSession mongoSession, String nanopubId) {
        simpleLoad(mongoSession, nanopubId, true);
    }

    public static void simpleLoad(ClientSession mongoSession, String nanopubId, boolean persistOnRetrieve) {
        if (persistOnRetrieve) {
            simpleLoad(mongoSession, retrieveNanopub(mongoSession, nanopubId));
        } else {
            Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);
            if (np == null) {
                np = getNanopub(nanopubId);
            }
            if (np != null) {
                simpleLoad(mongoSession, np);
            }
        }
    }

    public static void simpleLoad(ClientSession mongoSession, Nanopub np) {
        String pubkey = RegistryDB.getPubkey(np);
        if (pubkey == null) {
            log.info("Ignore (not signed): {}", np.getUri());
            return;
        }
        simpleLoad(mongoSession, np, pubkey);
    }

    /**
     * Loads a nanopub to the appropriate lists, using a pre-verified public key
     * to skip redundant signature verification.
     */
    public static void simpleLoad(ClientSession mongoSession, Nanopub np, String verifiedPubkey) {
        String pubkeyHash = Utils.getHash(verifiedPubkey);
        // TODO Do we need to load anything else here, into the other DB collections?
        if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {
            RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, "$");
        } else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {
            RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, INTRO_TYPE, ENDORSE_TYPE);
        } else {
            // Pubkey not yet loaded (unknown or in transitional "encountered" state): store the
            // nanopub in the nanopubs collection so it is not lost. RUN_OPTIONAL_LOAD will add it
            // to the appropriate lists once the pubkey's intro/endorse have been fetched.
            RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, null);
            if (!has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH))) {
                // Unknown pubkey: create encountered intro list so RUN_OPTIONAL_LOAD picks it up
                try {
                    insert(mongoSession, "lists", new Document("pubkey", pubkeyHash)
                            .append("type", INTRO_TYPE_HASH)
                            .append("status", EntryStatus.encountered.getValue()));
                } catch (MongoWriteException e) {
                    if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;
                }
            }
        }
    }

    private static final int LOAD_PARALLELISM = Integer.parseInt(
            Utils.getEnv("REGISTRY_LOAD_PARALLELISM", String.valueOf(Runtime.getRuntime().availableProcessors())));

    /**
     * Processes a stream of nanopubs in parallel using a thread pool.
     * Each worker thread uses its own MongoDB ClientSession.
     * Backpressure is applied via a semaphore to avoid unbounded memory growth.
     *
     * @param stream    the nanopub stream to process
     * @param processor consumer that processes each nanopub (called with its own ClientSession)
     */
    public static void loadStreamInParallel(Stream<MaybeNanopub> stream, Consumer<Nanopub> processor) {
        if (LOAD_PARALLELISM <= 1) {
            // Fall back to sequential processing
            stream.forEach(m -> {
                if (!m.isSuccess()) throw new AbortingTaskException("Failed to download nanopub; aborting task...");
                processor.accept(m.getNanopub());
            });
            return;
        }

        ExecutorService executor = Executors.newFixedThreadPool(LOAD_PARALLELISM);
        Semaphore semaphore = new Semaphore(LOAD_PARALLELISM * 2);
        AtomicReference<Exception> error = new AtomicReference<>();

        try {
            stream.forEach(m -> {
                if (error.get() != null) return;
                if (!m.isSuccess()) {
                    error.compareAndSet(null, new AbortingTaskException("Failed to download nanopub; aborting task..."));
                    return;
                }
                Nanopub np = m.getNanopub();
                try {
                    semaphore.acquire();
                } catch (InterruptedException e) {
                    Thread.currentThread().interrupt();
                    error.compareAndSet(null, e);
                    return;
                }
                executor.submit(() -> {
                    try {
                        processor.accept(np);
                    } catch (Exception e) {
                        error.compareAndSet(null, e);
                    } finally {
                        semaphore.release();
                    }
                });
            });
        } finally {
            executor.shutdown();
            try {
                executor.awaitTermination(1, TimeUnit.HOURS);
            } catch (InterruptedException e) {
                Thread.currentThread().interrupt();
            }
        }

        if (error.get() != null) {
            if (error.get() instanceof RuntimeException re) throw re;
            throw new RuntimeException("Parallel loading failed", error.get());
        }
    }

    /**
     * Retrieve Nanopubs from the peers of this Nanopub Registry.
     *
     * @param typeHash   The hash of the type of the Nanopub to retrieve.
     * @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
     * @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
     */
    public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash) {
        return retrieveNanopubsFromPeers(typeHash, pubkeyHash, null);
    }

    /**
     * Retrieve Nanopubs from the peers, optionally skipping ahead using checksums.
     *
     * @param typeHash        The hash of the type of the Nanopub to retrieve.
     * @param pubkeyHash      The hash of the pubkey of the Nanopub to retrieve.
     * @param afterChecksums  Comma-separated checksums for skip-ahead (geometric fallback), or null for full fetch.
     * @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
     */
    public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash, String afterChecksums) {
        // TODO Move the code of this method to nanopub-java library.

        List<String> peerUrlsToTry = new ArrayList<>(Utils.getPeerUrls());
        Collections.shuffle(peerUrlsToTry);
        while (!peerUrlsToTry.isEmpty()) {
            String peerUrl = peerUrlsToTry.removeFirst();

            String requestUrl = peerUrl + "list/" + pubkeyHash + "/" + typeHash + ".jelly";
            if (afterChecksums != null) {
                requestUrl += "?afterChecksums=" + afterChecksums;
            }
            log.info("Request: {}", requestUrl);
            try {
                CloseableHttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));
                int httpStatus = resp.getStatusLine().getStatusCode();
                if (httpStatus < 200 || httpStatus >= 300) {
                    log.info("Request failed: {} {}", peerUrl, httpStatus);
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                }
                Header nrStatus = resp.getFirstHeader("Nanopub-Registry-Status");
                if (nrStatus == null) {
                    log.info("Nanopub-Registry-Status header not found at: {}", peerUrl);
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                } else if (!nrStatus.getValue().equals("ready") && !nrStatus.getValue().equals("updating")) {
                    log.info("Peer in non-ready state: {} {}", peerUrl, nrStatus.getValue());
                    EntityUtils.consumeQuietly(resp.getEntity());
                    continue;
                }
                InputStream is = resp.getEntity().getContent();
                return NanopubStream.fromByteStream(is).getAsNanopubs().onClose(() -> {
                    try {
                        resp.close();
                    } catch (IOException e) {
                        log.debug("Error closing HTTP response", e);
                    }
                });
            } catch (UnsupportedOperationException | IOException ex) {
                log.info("Request failed: ", ex);
            }
        }
        return Stream.empty();
    }

    public static Nanopub retrieveNanopub(ClientSession mongoSession, String nanopubId) {
        Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);
        int tryCount = 0;
        while (np == null) {
            if (tryCount > 10) {
                throw new RuntimeException("Could not load nanopub: " + nanopubId);
            } else if (tryCount > 0) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException ex) {
                    log.info("Thread was interrupted", ex);
                }
            }
            log.info("Loading {}", nanopubId);

            // TODO Reach out to other Nanopub Registries here:
            np = getNanopub(nanopubId);
            if (np != null) {
                RegistryDB.loadNanopub(mongoSession, np);
            } else {
                tryCount = tryCount + 1;
            }
        }
        return np;
    }

    public static Nanopub retrieveLocalNanopub(ClientSession mongoSession, String nanopubId) {
        String ac = TrustyUriUtils.getArtifactCode(nanopubId);
        MongoCursor<Document> cursor = RegistryDB.get(mongoSession, Collection.NANOPUBS.toString(), new Document("_id", ac));
        if (!cursor.hasNext()) return null;
        try {
            // Parse from Jelly, not TriG (it's faster)
            return JellyUtils.readFromDB(((Binary) cursor.next().get("jelly")).getData());
        } catch (RDF4JException | MalformedNanopubException ex) {
            log.info("Exception reading Jelly", ex);
            return null;
        }
    }

    // TODO Provide this method in nanopub-java (GetNanopub)
    private static Nanopub getNanopub(String uriOrArtifactCode) {
        List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());
        Collections.shuffle(peerUrls);
        String ac = GetNanopub.getArtifactCode(uriOrArtifactCode);
        if (!ac.startsWith(RdfModule.MODULE_ID)) {
            throw new IllegalArgumentException("Not a trusty URI of type RA");
        }
        while (!peerUrls.isEmpty()) {
            String peerUrl = peerUrls.removeFirst();
            try {
                Nanopub np = get(ac, peerUrl, NanopubUtils.getHttpClient());
                if (np != null) {
                    return np;
                }
            } catch (IOException | RDF4JException | MalformedNanopubException ex) {
                // ignore
            }
        }
        return null;
    }

    // TODO Provide this method in nanopub-java (GetNanopub)
    private static Nanopub get(String artifactCode, String registryUrl, HttpClient httpClient)
            throws IOException, RDF4JException, MalformedNanopubException {
        HttpGet get = null;
        // TODO Get in Jelly format:
        String getUrl = registryUrl + "np/" + artifactCode;
        try {
            get = new HttpGet(getUrl);
        } catch (IllegalArgumentException ex) {
            throw new IOException("invalid URL: " + getUrl);
        }
        get.setHeader("Accept", "application/trig");
        InputStream in = null;
        try {
            HttpResponse resp = httpClient.execute(get);
            if (!wasSuccessful(resp)) {
                EntityUtils.consumeQuietly(resp.getEntity());
                throw new IOException(resp.getStatusLine().toString());
            }
            in = resp.getEntity().getContent();
            Nanopub nanopub = new NanopubImpl(in, RDFFormat.TRIG);
            if (!TrustyNanopubUtils.isValidTrustyNanopub(nanopub)) {
                throw new MalformedNanopubException("Nanopub is not trusty");
            }
            return nanopub;
        } finally {
            if (in != null) in.close();
        }
    }

    private static boolean wasSuccessful(HttpResponse resp) {
        int c = resp.getStatusLine().getStatusCode();
        return c >= 200 && c < 300;
    }

}

1	package com.knowledgepixels.registry;
2
3	import com.mongodb.ErrorCategory;
4	import com.mongodb.MongoWriteException;
5	import com.mongodb.client.ClientSession;
6	import com.mongodb.client.MongoCursor;
7	import net.trustyuri.TrustyUriUtils;
8	import net.trustyuri.rdf.RdfModule;
9	import org.apache.http.Header;
10	import org.apache.http.HttpResponse;
11	import org.apache.http.client.HttpClient;
12	import org.apache.http.client.methods.CloseableHttpResponse;
13	import org.apache.http.client.methods.HttpGet;
14	import org.apache.http.util.EntityUtils;
15	import org.bson.Document;
16	import org.bson.types.Binary;
17	import org.eclipse.rdf4j.common.exception.RDF4JException;
18	import org.eclipse.rdf4j.rio.RDFFormat;
19	import org.nanopub.MalformedNanopubException;
20	import org.nanopub.Nanopub;
21	import org.nanopub.NanopubImpl;
22	import org.nanopub.NanopubUtils;
23	import org.nanopub.extra.server.GetNanopub;
24	import org.nanopub.jelly.JellyUtils;
25	import org.nanopub.jelly.MaybeNanopub;
26	import org.nanopub.jelly.NanopubStream;
27	import org.nanopub.trusty.TrustyNanopubUtils;
28	import org.nanopub.vocabulary.NPX;
29	import org.slf4j.Logger;
30	import org.slf4j.LoggerFactory;
31
32	import java.io.IOException;
33	import java.io.InputStream;
34	import java.util.ArrayList;
35	import java.util.Collections;
36	import java.util.List;
37	import java.util.concurrent.ExecutorService;
38	import java.util.concurrent.Executors;
39	import java.util.concurrent.Semaphore;
40	import java.util.concurrent.TimeUnit;
41	import java.util.concurrent.atomic.AtomicReference;
42	import java.util.function.Consumer;
43	import java.util.stream.Stream;
44
45	import static com.knowledgepixels.registry.RegistryDB.has;
46	import static com.knowledgepixels.registry.RegistryDB.insert;
47
48	public class NanopubLoader {
49
50	private NanopubLoader() {
51	}
52
53	public final static String INTRO_TYPE = NPX.DECLARED_BY.stringValue();	9✔
54	public final static String INTRO_TYPE_HASH = Utils.getHash(INTRO_TYPE);	9✔
55	public final static String ENDORSE_TYPE = Utils.APPROVES_OF.stringValue();	9✔
56	public final static String ENDORSE_TYPE_HASH = Utils.getHash(ENDORSE_TYPE);	9✔
57	private static final Logger log = LoggerFactory.getLogger(NanopubLoader.class);	9✔
58
59	// TODO Distinguish and support these cases:
60	// 1. Simple load: load to all core lists if pubkey is "core-loaded", or load to all lists if pubkey is "full-loaded"
61	// 2. Core load: load to all core lists (initialize if needed), or load to all lists if pubkey is "full-loaded"
62	// 3. Full load: load to all lists (initialize if needed)
63
64	public static void simpleLoad(ClientSession mongoSession, String nanopubId) {
65	simpleLoad(mongoSession, nanopubId, true);	×
66	}	×
67
68	public static void simpleLoad(ClientSession mongoSession, String nanopubId, boolean persistOnRetrieve) {
69	if (persistOnRetrieve) {	×
70	simpleLoad(mongoSession, retrieveNanopub(mongoSession, nanopubId));	×
71	} else {
72	Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);	×
73	if (np == null) {	×
74	np = getNanopub(nanopubId);	×
75	}
76	if (np != null) {	×
77	simpleLoad(mongoSession, np);	×
78	}
79	}
80	}	×
81
82	public static void simpleLoad(ClientSession mongoSession, Nanopub np) {
83	String pubkey = RegistryDB.getPubkey(np);	×
84	if (pubkey == null) {	×
85	log.info("Ignore (not signed): {}", np.getUri());	×
86	return;	×
87	}
88	simpleLoad(mongoSession, np, pubkey);	×
89	}	×
90
91	/**
92	* Loads a nanopub to the appropriate lists, using a pre-verified public key
93	* to skip redundant signature verification.
94	*/
95	public static void simpleLoad(ClientSession mongoSession, Nanopub np, String verifiedPubkey) {
96	String pubkeyHash = Utils.getHash(verifiedPubkey);	9✔
97	// TODO Do we need to load anything else here, into the other DB collections?
98	if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", "$").append("status", "loaded"))) {	45!
99	RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, "$");	×
100	} else if (has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH).append("status", "loaded"))) {	45!
101	RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, pubkeyHash, INTRO_TYPE, ENDORSE_TYPE);	×
102	} else {
103	// Pubkey not yet loaded (unknown or in transitional "encountered" state): store the
104	// nanopub in the nanopubs collection so it is not lost. RUN_OPTIONAL_LOAD will add it
105	// to the appropriate lists once the pubkey's intro/endorse have been fetched.
106	RegistryDB.loadNanopubVerified(mongoSession, np, verifiedPubkey, null);	24✔
107	if (!has(mongoSession, "lists", new Document("pubkey", pubkeyHash).append("type", INTRO_TYPE_HASH))) {	36!
108	// Unknown pubkey: create encountered intro list so RUN_OPTIONAL_LOAD picks it up
109	try {
110	insert(mongoSession, "lists", new Document("pubkey", pubkeyHash)	30✔
111	.append("type", INTRO_TYPE_HASH)	9✔
112	.append("status", EntryStatus.encountered.getValue()));	6✔
113	} catch (MongoWriteException e) {	×
114	if (e.getError().getCategory() != ErrorCategory.DUPLICATE_KEY) throw e;	×
115	}	3✔
116	}
117	}
118	}	3✔
119
120	private static final int LOAD_PARALLELISM = Integer.parseInt(	12✔
121	Utils.getEnv("REGISTRY_LOAD_PARALLELISM", String.valueOf(Runtime.getRuntime().availableProcessors())));	12✔
122
123	/**
124	* Processes a stream of nanopubs in parallel using a thread pool.
125	* Each worker thread uses its own MongoDB ClientSession.
126	* Backpressure is applied via a semaphore to avoid unbounded memory growth.
127	*
128	* @param stream the nanopub stream to process
129	* @param processor consumer that processes each nanopub (called with its own ClientSession)
130	*/
131	public static void loadStreamInParallel(Stream<MaybeNanopub> stream, Consumer<Nanopub> processor) {
132	if (LOAD_PARALLELISM <= 1) {	×
133	// Fall back to sequential processing
134	stream.forEach(m -> {	×
135	if (!m.isSuccess()) throw new AbortingTaskException("Failed to download nanopub; aborting task...");	×
136	processor.accept(m.getNanopub());	×
137	});	×
138	return;	×
139	}
140
141	ExecutorService executor = Executors.newFixedThreadPool(LOAD_PARALLELISM);	×
142	Semaphore semaphore = new Semaphore(LOAD_PARALLELISM * 2);	×
143	AtomicReference<Exception> error = new AtomicReference<>();	×
144
145	try {
146	stream.forEach(m -> {	×
147	if (error.get() != null) return;	×
148	if (!m.isSuccess()) {	×
149	error.compareAndSet(null, new AbortingTaskException("Failed to download nanopub; aborting task..."));	×
150	return;	×
151	}
152	Nanopub np = m.getNanopub();	×
153	try {
154	semaphore.acquire();	×
155	} catch (InterruptedException e) {	×
156	Thread.currentThread().interrupt();	×
157	error.compareAndSet(null, e);	×
158	return;	×
159	}	×
160	executor.submit(() -> {	×
161	try {
162	processor.accept(np);	×
163	} catch (Exception e) {	×
164	error.compareAndSet(null, e);	×
165	} finally {
166	semaphore.release();	×
167	}
168	});	×
169	});	×
170	} finally {
171	executor.shutdown();	×
172	try {
173	executor.awaitTermination(1, TimeUnit.HOURS);	×
174	} catch (InterruptedException e) {	×
175	Thread.currentThread().interrupt();	×
176	}	×
177	}
178
179	if (error.get() != null) {	×
180	if (error.get() instanceof RuntimeException re) throw re;	×
181	throw new RuntimeException("Parallel loading failed", error.get());	×
182	}
183	}	×
184
185	/**
186	* Retrieve Nanopubs from the peers of this Nanopub Registry.
187	*
188	* @param typeHash The hash of the type of the Nanopub to retrieve.
189	* @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
190	* @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
191	*/
192	public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash) {
193	return retrieveNanopubsFromPeers(typeHash, pubkeyHash, null);	×
194	}
195
196	/**
197	* Retrieve Nanopubs from the peers, optionally skipping ahead using checksums.
198	*
199	* @param typeHash The hash of the type of the Nanopub to retrieve.
200	* @param pubkeyHash The hash of the pubkey of the Nanopub to retrieve.
201	* @param afterChecksums Comma-separated checksums for skip-ahead (geometric fallback), or null for full fetch.
202	* @return A stream of MaybeNanopub objects, or an empty stream if no peer is available.
203	*/
204	public static Stream<MaybeNanopub> retrieveNanopubsFromPeers(String typeHash, String pubkeyHash, String afterChecksums) {
205	// TODO Move the code of this method to nanopub-java library.
206
207	List<String> peerUrlsToTry = new ArrayList<>(Utils.getPeerUrls());	×
208	Collections.shuffle(peerUrlsToTry);	×
209	while (!peerUrlsToTry.isEmpty()) {	×
210	String peerUrl = peerUrlsToTry.removeFirst();	×
211
212	String requestUrl = peerUrl + "list/" + pubkeyHash + "/" + typeHash + ".jelly";	×
213	if (afterChecksums != null) {	×
214	requestUrl += "?afterChecksums=" + afterChecksums;	×
215	}
216	log.info("Request: {}", requestUrl);	×
217	try {
218	CloseableHttpResponse resp = NanopubUtils.getHttpClient().execute(new HttpGet(requestUrl));	×
219	int httpStatus = resp.getStatusLine().getStatusCode();	×
220	if (httpStatus < 200 \|\| httpStatus >= 300) {	×
221	log.info("Request failed: {} {}", peerUrl, httpStatus);	×
222	EntityUtils.consumeQuietly(resp.getEntity());	×
223	continue;	×
224	}
225	Header nrStatus = resp.getFirstHeader("Nanopub-Registry-Status");	×
226	if (nrStatus == null) {	×
227	log.info("Nanopub-Registry-Status header not found at: {}", peerUrl);	×
228	EntityUtils.consumeQuietly(resp.getEntity());	×
229	continue;	×
230	} else if (!nrStatus.getValue().equals("ready") && !nrStatus.getValue().equals("updating")) {	×
231	log.info("Peer in non-ready state: {} {}", peerUrl, nrStatus.getValue());	×
232	EntityUtils.consumeQuietly(resp.getEntity());	×
233	continue;	×
234	}
235	InputStream is = resp.getEntity().getContent();	×
236	return NanopubStream.fromByteStream(is).getAsNanopubs().onClose(() -> {	×
237	try {
238	resp.close();	×
239	} catch (IOException e) {	×
240	log.debug("Error closing HTTP response", e);	×
241	}	×
242	});	×
243	} catch (UnsupportedOperationException \| IOException ex) {	×
244	log.info("Request failed: ", ex);	×
245	}
246	}	×
247	return Stream.empty();	×
248	}
249
250	public static Nanopub retrieveNanopub(ClientSession mongoSession, String nanopubId) {
251	Nanopub np = retrieveLocalNanopub(mongoSession, nanopubId);	×
252	int tryCount = 0;	×
253	while (np == null) {	×
254	if (tryCount > 10) {	×
255	throw new RuntimeException("Could not load nanopub: " + nanopubId);	×
256	} else if (tryCount > 0) {	×
257	try {
258	Thread.sleep(100);	×
259	} catch (InterruptedException ex) {	×
260	log.info("Thread was interrupted", ex);	×
261	}	×
262	}
263	log.info("Loading {}", nanopubId);	×
264
265	// TODO Reach out to other Nanopub Registries here:
266	np = getNanopub(nanopubId);	×
267	if (np != null) {	×
268	RegistryDB.loadNanopub(mongoSession, np);	×
269	} else {
270	tryCount = tryCount + 1;	×
271	}
272	}
273	return np;	×
274	}
275
276	public static Nanopub retrieveLocalNanopub(ClientSession mongoSession, String nanopubId) {
277	String ac = TrustyUriUtils.getArtifactCode(nanopubId);	×
278	MongoCursor<Document> cursor = RegistryDB.get(mongoSession, Collection.NANOPUBS.toString(), new Document("_id", ac));	×
279	if (!cursor.hasNext()) return null;	×
280	try {
281	// Parse from Jelly, not TriG (it's faster)
282	return JellyUtils.readFromDB(((Binary) cursor.next().get("jelly")).getData());	×
283	} catch (RDF4JException \| MalformedNanopubException ex) {	×
284	log.info("Exception reading Jelly", ex);	×
285	return null;	×
286	}
287	}
288
289	// TODO Provide this method in nanopub-java (GetNanopub)
290	private static Nanopub getNanopub(String uriOrArtifactCode) {
291	List<String> peerUrls = new ArrayList<>(Utils.getPeerUrls());	×
292	Collections.shuffle(peerUrls);	×
293	String ac = GetNanopub.getArtifactCode(uriOrArtifactCode);	×
294	if (!ac.startsWith(RdfModule.MODULE_ID)) {	×
295	throw new IllegalArgumentException("Not a trusty URI of type RA");	×
296	}
297	while (!peerUrls.isEmpty()) {	×
298	String peerUrl = peerUrls.removeFirst();	×
299	try {
300	Nanopub np = get(ac, peerUrl, NanopubUtils.getHttpClient());	×
301	if (np != null) {	×
302	return np;	×
303	}
304	} catch (IOException \| RDF4JException \| MalformedNanopubException ex) {	×
305	// ignore
306	}	×
307	}	×
308	return null;	×
309	}
310
311	// TODO Provide this method in nanopub-java (GetNanopub)
312	private static Nanopub get(String artifactCode, String registryUrl, HttpClient httpClient)
313	throws IOException, RDF4JException, MalformedNanopubException {
314	HttpGet get = null;	×
315	// TODO Get in Jelly format:
316	String getUrl = registryUrl + "np/" + artifactCode;	×
317	try {
318	get = new HttpGet(getUrl);	×
319	} catch (IllegalArgumentException ex) {	×
320	throw new IOException("invalid URL: " + getUrl);	×
321	}	×
322	get.setHeader("Accept", "application/trig");	×
323	InputStream in = null;	×
324	try {
325	HttpResponse resp = httpClient.execute(get);	×
326	if (!wasSuccessful(resp)) {	×
327	EntityUtils.consumeQuietly(resp.getEntity());	×
328	throw new IOException(resp.getStatusLine().toString());	×
329	}
330	in = resp.getEntity().getContent();	×
331	Nanopub nanopub = new NanopubImpl(in, RDFFormat.TRIG);	×
332	if (!TrustyNanopubUtils.isValidTrustyNanopub(nanopub)) {	×
333	throw new MalformedNanopubException("Nanopub is not trusty");	×
334	}
335	return nanopub;	×
336	} finally {
337	if (in != null) in.close();	×
338	}
339	}
340
341	private static boolean wasSuccessful(HttpResponse resp) {
342	int c = resp.getStatusLine().getStatusCode();	×
343	return c >= 200 && c < 300;	×
344	}
345
346	}

knowledgepixels / nanopub-registry / 24334244342

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